Sun Aug 4 20:02:26 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_ /Applications/Freesurfer5.3/freesurfer/bin/recon-all -s subjects_name_ -i subjects_name_.img subjid subjects_name_ setenv SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Actual FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer build-stamp.txt: freesurfer-Darwin-lion-stable-pub-v5.3.0 Darwin Pedro-Rosas-MacBook-Pro-2.local 12.4.0 Darwin Kernel Version 12.4.0: Wed May 1 17:57:12 PDT 2013; root:xnu-2050.24.15~1/RELEASE_X86_64 x86_64 cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 256 memorylocked unlimited maxproc 709 PhysMem: 2103M wired, 2737M active, 2142M inactive, 6982M used, 9396M free. ######################################## 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: 2013/08/04-23:02:27-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/04-23:02:27-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@aspasia.local (i686-apple-darwin10.2.0) on 2010-02-26 at 14:19:30 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/04-23:02:27-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/04-23:02:27-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/04-23:02:27-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/04-23:02:27-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/04-23:02:27-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/04-23:02:27-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/04-23:02:27-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/04-23:02:27-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/04-23:02:27-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/04-23:02:27-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/04-23:02:27-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/04-23:02:27-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/04-23:02:27-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/04-23:02:27-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/04-23:02:27-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/04-23:02:27-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/04-23:02:27-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/04-23:02:27-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/04-23:02:27-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/04-23:02:27-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/04-23:02:27-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/04-23:02:27-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/04-23:02:27-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/04-23:02:27-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/04-23:02:27-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/04-23:02:27-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/04-23:02:27-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/04-23:02:27-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/04-23:02:27-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/04-23:02:27-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 $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: 2013/08/04-23:02:27-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 $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: 2013/08/04-23:02:28-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/04-23:02:28-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/04-23:02:28-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/04-23:02:28-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/04-23:02:28-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ####################################### GCADIR /Applications/Freesurfer5.3/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /Applications/Freesurfer5.3/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_ \n mri_convert /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_.img /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/orig/001.mgz \n mri_convert /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_.img /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_.img... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -1, 0) j_ras = (0, 0, 1) k_ras = (1, 0, 0) writing to /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/orig/001.mgz... #------------------------------------------ Started at Sun Aug 4 20:02:26 BRT 2013 Ended at Sun Aug 4 20:02:31 BRT 2013 #@#%# recon-all-run-time-hours 0.001 recon-all -s subjects_name_ finished without error at Sun Aug 4 20:02:31 BRT 2013 \n\n New invocation of recon-all \n\n Tue Aug 6 20:38:31 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_ /Applications/Freesurfer5.3/freesurfer/bin/recon-all -s subjects_name_ -autorecon1 subjid subjects_name_ setenv SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Actual FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer build-stamp.txt: freesurfer-Darwin-lion-stable-pub-v5.3.0 Darwin Pedro-Rosas-MacBook-Pro-2.local 12.4.0 Darwin Kernel Version 12.4.0: Wed May 1 17:57:12 PDT 2013; root:xnu-2050.24.15~1/RELEASE_X86_64 x86_64 cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 256 memorylocked unlimited maxproc 709 PhysMem: 2152M wired, 5004M active, 2606M inactive, 9762M used, 6617M free. ######################################## 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: 2013/08/06-23:38:32-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/06-23:38:32-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@aspasia.local (i686-apple-darwin10.2.0) on 2010-02-26 at 14:19:30 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/06-23:38:32-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/06-23:38:32-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/06-23:38:32-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/06-23:38:32-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/06-23:38:32-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/06-23:38:32-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/06-23:38:32-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/06-23:38:32-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/06-23:38:32-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/06-23:38:32-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/06-23:38:32-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/06-23:38:32-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/06-23:38:32-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/06-23:38:32-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/06-23:38:32-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/06-23:38:32-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/06-23:38:32-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/06-23:38:32-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/06-23:38:32-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/06-23:38:32-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/06-23:38:32-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/06-23:38:32-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/06-23:38:32-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/06-23:38:33-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/06-23:38:33-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/06-23:38:33-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/06-23:38:33-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/06-23:38:33-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/06-23:38:33-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/06-23:38:33-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 $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: 2013/08/06-23:38:33-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 $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: 2013/08/06-23:38:33-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/06-23:38:33-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/06-23:38:33-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/06-23:38:33-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/06-23:38:33-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ####################################### GCADIR /Applications/Freesurfer5.3/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /Applications/Freesurfer5.3/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# MotionCor Tue Aug 6 20:38:33 BRT 2013 Found 1 runs /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/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. \n cp /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/orig/001.mgz /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/rawavg.mgz \n /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_ \n mri_convert /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/rawavg.mgz /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/orig.mgz --conform \n mri_convert /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/rawavg.mgz /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -1, 0) j_ras = (0, 0, 1) k_ras = (1, 0, 0) Original Data has (1.25, 1.25, 1.2) mm size and (192, 192, 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 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/orig.mgz... \n mri_add_xform_to_header -c /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/transforms/talairach.xfm /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/orig.mgz /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/orig.mgz \n INFO: extension is mgz #-------------------------------------------- #@# Talairach Tue Aug 6 20:38:45 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz \n \n talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm \n \n cp transforms/talairach.auto.xfm transforms/talairach.xfm \n #-------------------------------------------- #@# Talairach Failure Detection Tue Aug 6 20:40:24 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6669, pval=0.3663 >= threshold=0.0050) \n awk -f /Applications/Freesurfer5.3/freesurfer/bin/extract_talairach_avi_QA.awk /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/transforms/talairach_avi.log \n \n tal_QC_AZS /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/transforms/talairach_avi.log \n TalAviQA: 0.98211 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Tue Aug 6 20:40:24 BRT 2013 \n mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 \n /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri /Applications/Freesurfer5.3/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 $ Darwin Pedro-Rosas-MacBook-Pro-2.local 12.4.0 Darwin Kernel Version 12.4.0: Wed May 1 17:57:12 PDT 2013; root:xnu-2050.24.15~1/RELEASE_X86_64 x86_64 Tue Aug 6 20:40:24 BRT 2013 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@aspasia.local (i686-apple-darwin10.2.0) on 2010-02-26 at 14:19:30 tmpdir is ./tmp.mri_nu_correct.mni.22345 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.22345/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.22345/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, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.22345/nu0.mnc... -------------------------------------------------------- Iteration 1 Tue Aug 6 20:40:28 BRT 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.22345/nu0.mnc ./tmp.mri_nu_correct.mni.22345/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.22345/0/ [pedrogomesrosa@Pedro-Rosas-MacBook-Pro-2.local:/Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/] [2013-08-06 20:40:28] running: /Applications/Freesurfer5.3/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.22345/0/ ./tmp.mri_nu_correct.mni.22345/nu0.mnc ./tmp.mri_nu_correct.mni.22345/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 20 CV of field change: 0.000938847 [pedrogomesrosa@Pedro-Rosas-MacBook-Pro-2.local:/Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/] [2013-08-06 20:40:40] running: /Applications/Freesurfer5.3/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.22345/nu0.mnc ./tmp.mri_nu_correct.mni.22345/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Tue Aug 6 20:40:43 BRT 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.22345/nu1.mnc ./tmp.mri_nu_correct.mni.22345/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.22345/1/ [pedrogomesrosa@Pedro-Rosas-MacBook-Pro-2.local:/Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/] [2013-08-06 20:40:43] running: /Applications/Freesurfer5.3/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.22345/1/ ./tmp.mri_nu_correct.mni.22345/nu1.mnc ./tmp.mri_nu_correct.mni.22345/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 12 CV of field change: 0.000910631 [pedrogomesrosa@Pedro-Rosas-MacBook-Pro-2.local:/Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/] [2013-08-06 20:40:50] running: /Applications/Freesurfer5.3/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.22345/nu1.mnc ./tmp.mri_nu_correct.mni.22345/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.22345/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.22345/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.22345/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.22345/ones.mgz sysname Darwin hostname Pedro-Rosas-MacBook-Pro-2.local machine x86_64 user pedrogomesrosa input ./tmp.mri_nu_correct.mni.22345/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.22345/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.22345/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.22345/sum.junk --avgwf ./tmp.mri_nu_correct.mni.22345/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.22345/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.22345/sum.junk --avgwf ./tmp.mri_nu_correct.mni.22345/input.mean.dat sysname Darwin hostname Pedro-Rosas-MacBook-Pro-2.local machine x86_64 user pedrogomesrosa UseRobust 0 Loading ./tmp.mri_nu_correct.mni.22345/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.22345/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.22345/ones.mgz --i ./tmp.mri_nu_correct.mni.22345/nu2.mnc --sum ./tmp.mri_nu_correct.mni.22345/sum.junk --avgwf ./tmp.mri_nu_correct.mni.22345/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.22345/ones.mgz --i ./tmp.mri_nu_correct.mni.22345/nu2.mnc --sum ./tmp.mri_nu_correct.mni.22345/sum.junk --avgwf ./tmp.mri_nu_correct.mni.22345/output.mean.dat sysname Darwin hostname Pedro-Rosas-MacBook-Pro-2.local machine x86_64 user pedrogomesrosa UseRobust 0 Loading ./tmp.mri_nu_correct.mni.22345/ones.mgz Loading ./tmp.mri_nu_correct.mni.22345/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.22345/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.22345/nu2.mnc ./tmp.mri_nu_correct.mni.22345/nu2.mnc mul .95706194801120201260 Saving result to './tmp.mri_nu_correct.mni.22345/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.22345/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.22345/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.22345/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 8 seconds. mapping (30, 153) to ( 3, 110) Tue Aug 6 20:41:38 BRT 2013 mri_nu_correct.mni done \n mri_add_xform_to_header -c /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/transforms/talairach.xfm nu.mgz nu.mgz \n INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Tue Aug 6 20:41:40 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri \n mri_normalize -g 1 nu.mgz T1.mgz \n using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.033 0.109 0.042 3.622; -0.120 1.049 0.045 24.743; -0.063 -0.075 1.118 -22.535; 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 = 21 Starting OpenSpline(): npoints = 21 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 109 gm peak at 71 (71), valley at 43 (43) csf peak at 35, setting threshold to 59 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 76 (76), valley at 43 (43) csf peak at 38, setting threshold to 63 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 43 seconds. #-------------------------------------------- #@# Skull Stripping Tue Aug 6 20:44:24 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri \n mri_em_register -skull nu.mgz /Applications/Freesurfer5.3/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta \n aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/Applications/Freesurfer5.3/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=6.0 skull bounding box = (51, 29, 16) --> (203, 255, 209) using (102, 104, 113) as brain centroid... mean wm in atlas = 126, using box (83,76,89) --> (120, 131,136) to find MRI wm before smoothing, mri peak at 107 after smoothing, mri peak at 107, scaling input intensities by 1.178 scaling channel 0 by 1.17757 initial log_p = -4.5 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.468958 @ (0.000, 0.000, 0.000) max log p = -4.350235 @ (-4.545, 4.545, -4.545) max log p = -4.331421 @ (2.273, 2.273, -2.273) max log p = -4.316970 @ (3.409, 3.409, -1.136) max log p = -4.314322 @ (-0.568, 0.568, 1.705) max log p = -4.314322 @ (0.000, 0.000, 0.000) Found translation: (0.6, 10.8, -6.3): log p = -4.314 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.3 (thresh=-4.3) 1.125 0.150 -0.168 -12.872; -0.159 1.226 0.024 10.677; 0.112 0.000 0.997 -19.832; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.125 0.150 -0.168 -12.872; -0.159 1.226 0.024 10.677; 0.112 0.000 0.997 -19.832; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-4.0 (thresh=-4.0) 1.075 0.061 -0.102 -8.272; -0.080 1.276 0.085 -13.284; 0.050 -0.093 1.039 -7.109; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.053 0.061 -0.133 -0.042; -0.080 1.254 0.050 -5.186; 0.084 -0.050 1.057 -19.927; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.055 0.042 -0.152 3.366; -0.063 1.259 0.056 -10.055; 0.102 -0.059 1.053 -20.827; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.054 0.042 -0.152 3.510; -0.063 1.261 0.057 -10.209; 0.102 -0.059 1.054 -20.976; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3481 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.05380 0.04184 -0.15201 3.50984; -0.06282 1.26068 0.05653 -10.20875; 0.10192 -0.05948 1.05420 -20.97564; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.05380 0.04184 -0.15201 3.50984; -0.06282 1.26068 0.05653 -10.20875; 0.10192 -0.05948 1.05420 -20.97564; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.054 0.042 -0.152 3.510; -0.063 1.261 0.057 -10.209; 0.102 -0.059 1.054 -20.976; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.9 (old=-4.5) transform before final EM align: 1.054 0.042 -0.152 3.510; -0.063 1.261 0.057 -10.209; 0.102 -0.059 1.054 -20.976; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 382743 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.05380 0.04184 -0.15201 3.50984; -0.06282 1.26068 0.05653 -10.20875; 0.10192 -0.05948 1.05420 -20.97564; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.05380 0.04184 -0.15201 3.50984; -0.06282 1.26068 0.05653 -10.20875; 0.10192 -0.05948 1.05420 -20.97564; 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) = 4.3 tol 0.000000 final transform: 1.054 0.042 -0.152 3.510; -0.063 1.261 0.057 -10.209; 0.102 -0.059 1.054 -20.976; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 27 minutes and 52 seconds. \n mri_watershed -T1 -brain_atlas /Applications/Freesurfer5.3/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz \n 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=129 y=102 z=116 r=83 first estimation of the main basin volume: 2435844 voxels Looking for seedpoints 2 found in the cerebellum 15 found in the rest of the brain global maximum in x=145, y=87, z=78, Imax=255 CSF=16, 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=2383561411108553 voxels, voxel volume =1.000 = 2383561411108553 mmm3 = 2383561357262.848 cm3 done. PostAnalyze...Basin Prior 13 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=127,y=103, z=108, r=9653 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=31 , nb = 43920 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=22 , nb = 3582 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=14 , nb = 2970 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=28 , nb = 18648 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=29 , nb = 18486 OTHER CSF_MIN=3, CSF_intensity=26, CSF_MAX=40 , nb = 234 Problem with the least square interpolation in GM_MIN calculation. Problem with the least square interpolation in GM_MIN calculation. (2) Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 31, 40, 47, 67 after analyzing : 31, 44, 47, 49 RIGHT_CER before analyzing : 22, 27, 39, 79 after analyzing : 22, 35, 39, 46 LEFT_CER before analyzing : 14, 22, 45, 79 after analyzing : 14, 37, 45, 47 RIGHT_BRAIN before analyzing : 28, 36, 46, 67 after analyzing : 28, 42, 46, 48 LEFT_BRAIN before analyzing : 29, 38, 46, 67 after analyzing : 29, 43, 46, 49 OTHER before analyzing : 40, 5, 0, 2 after analyzing : 5, 18, 25, 19 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...63 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.009 curvature mean = 70.267, std = 7.469 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 3.60, sigma = 5.02 after rotation: sse = 3.60, sigma = 5.02 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 4.14, its var is 5.81 before Erosion-Dilatation 1.45% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...43 iterations mri_strip_skull: done peeling brain Brain Size = 1710101 voxels, voxel volume = 1.000 mm3 = 1710101 mmm3 = 1710.101 cm3 ****************************** Saving brainmask.auto.mgz done \n cp brainmask.auto.mgz brainmask.mgz \n #------------------------------------------ Started at Tue Aug 6 20:38:31 BRT 2013 Ended at Tue Aug 6 21:12:55 BRT 2013 #@#%# recon-all-run-time-hours 0.573 recon-all -s subjects_name_ finished without error at Tue Aug 6 21:12:55 BRT 2013 \n\n New invocation of recon-all \n\n Tue Aug 6 21:12:55 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_ /Applications/Freesurfer5.3/freesurfer/bin/recon-all -s subjects_name_ -autorecon2 subjid subjects_name_ setenv SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Actual FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer build-stamp.txt: freesurfer-Darwin-lion-stable-pub-v5.3.0 Darwin Pedro-Rosas-MacBook-Pro-2.local 12.4.0 Darwin Kernel Version 12.4.0: Wed May 1 17:57:12 PDT 2013; root:xnu-2050.24.15~1/RELEASE_X86_64 x86_64 cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 256 memorylocked unlimited maxproc 709 PhysMem: 2185M wired, 5773M active, 2991M inactive, 11G used, 5427M free. ######################################## 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: 2013/08/07-00:12:56-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-00:12:56-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@aspasia.local (i686-apple-darwin10.2.0) on 2010-02-26 at 14:19:30 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-00:12:56-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-00:12:57-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-00:12:57-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-00:12:57-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-00:12:57-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-00:12:57-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-00:12:57-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-00:12:57-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-00:12:57-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-00:12:57-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-00:12:57-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-00:12:57-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-00:12:57-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-00:12:57-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-00:12:57-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-00:12:57-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-00:12:57-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-00:12:57-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-00:12:57-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-00:12:57-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-00:12:57-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-00:12:57-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-00:12:57-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-00:12:57-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-00:12:57-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-00:12:57-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-00:12:57-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-00:12:57-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-00:12:57-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-00:12:57-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 $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: 2013/08/07-00:12:57-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 $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: 2013/08/07-00:12:57-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-00:12:57-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-00:12:57-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-00:12:57-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-00:12:57-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ####################################### GCADIR /Applications/Freesurfer5.3/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /Applications/Freesurfer5.3/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #------------------------------------- #@# EM Registration Tue Aug 6 21:12:57 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri \n mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /Applications/Freesurfer5.3/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta \n 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 '/Applications/Freesurfer5.3/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=27.0 skull bounding box = (58, 39, 26) --> (195, 162, 201) using (104, 80, 114) as brain centroid... mean wm in atlas = 107, using box (87,65,92) --> (120, 95,135) to find MRI wm before smoothing, mri peak at 107 after smoothing, mri peak at 108, scaling input intensities by 0.991 scaling channel 0 by 0.990741 initial log_p = -4.3 ************************************************ First Search limited to translation only. ************************************************ max log p = -3.942909 @ (-9.091, 9.091, -9.091) max log p = -3.711181 @ (4.545, 4.545, 4.545) max log p = -3.696910 @ (2.273, 2.273, -2.273) max log p = -3.676585 @ (-1.136, 1.136, 3.409) max log p = -3.670083 @ (0.568, -0.568, -0.568) max log p = -3.670083 @ (0.000, 0.000, 0.000) Found translation: (-2.8, 16.5, -4.0): log p = -3.670 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.4, old_max_log_p =-3.7 (thresh=-3.7) 1.066 0.021 -0.139 1.677; 0.000 1.140 0.131 -12.140; 0.131 -0.149 0.983 -3.801; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4) 1.066 0.021 -0.139 1.677; -0.017 1.150 0.001 3.224; 0.129 0.001 0.992 -19.966; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4) 1.066 0.021 -0.139 1.677; -0.017 1.150 0.001 3.224; 0.129 0.001 0.992 -19.966; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.4 (thresh=-3.4) 1.046 0.089 -0.102 -6.856; -0.082 1.146 0.005 9.712; 0.089 0.003 0.996 -17.197; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.2) 1.046 0.089 -0.102 -6.856; -0.082 1.146 0.005 9.712; 0.089 0.003 0.996 -17.197; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.3 (thresh=-3.2) 1.043 0.061 -0.126 -0.315; -0.057 1.144 0.002 7.394; 0.114 0.005 0.990 -20.913; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2) 1.042 0.061 -0.126 -0.166; -0.057 1.146 0.002 7.263; 0.114 0.005 0.990 -20.913; 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 1.04154 0.06091 -0.12561 -0.16595; -0.05662 1.14556 0.00238 7.26309; 0.11388 0.00472 0.98985 -20.91278; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 1.04154 0.06091 -0.12561 -0.16595; -0.05662 1.14556 0.00238 7.26309; 0.11388 0.00472 0.98985 -20.91278; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.042 0.061 -0.126 -0.166; -0.057 1.146 0.002 7.263; 0.114 0.005 0.990 -20.913; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.2 (old=-4.3) transform before final EM align: 1.042 0.061 -0.126 -0.166; -0.057 1.146 0.002 7.263; 0.114 0.005 0.990 -20.913; 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 1.04154 0.06091 -0.12561 -0.16595; -0.05662 1.14556 0.00238 7.26309; 0.11388 0.00472 0.98985 -20.91278; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 1.04154 0.06091 -0.12561 -0.16595; -0.05662 1.14556 0.00238 7.26309; 0.11388 0.00472 0.98985 -20.91278; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 010: -log(p) = 3.7 after pass:transform: ( 1.04, 0.06, -0.13, -0.17) ( -0.06, 1.15, 0.00, 7.26) ( 0.11, 0.00, 0.99, -20.91) dfp_em_step_func: 011: -log(p) = 3.7 after pass:transform: ( 1.04, 0.06, -0.13, -0.17) ( -0.06, 1.15, 0.00, 7.26) ( 0.11, 0.00, 0.99, -20.91) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 013: -log(p) = 3.7 tol 0.000000 final transform: 1.042 0.061 -0.126 -0.166; -0.057 1.146 0.002 7.263; 0.114 0.005 0.990 -20.913; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 27 minutes and 39 seconds. #-------------------------------------- #@# CA Normalize Tue Aug 6 21:40:37 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri \n mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /Applications/Freesurfer5.3/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz \n writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/Applications/Freesurfer5.3/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=27.0 skull bounding box = (58, 39, 26) --> (195, 162, 201) using (104, 80, 114) as brain centroid... mean wm in atlas = 107, using box (87,65,92) --> (120, 95,135) to find MRI wm before smoothing, mri peak at 107 after smoothing, mri peak at 108, scaling input intensities by 0.991 scaling channel 0 by 0.990741 using 244171 sample points... INFO: compute sample coordinates transform 1.042 0.061 -0.126 -0.166; -0.057 1.146 0.002 7.263; 0.114 0.005 0.990 -20.913; 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 (117, 46, 31) --> (190, 150, 200) Left_Cerebral_White_Matter: limiting intensities to 94.0 --> 197.0 1 of 2641 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (65, 44, 35) --> (135, 147, 202) Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 197.0 0 of 2348 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (123, 117, 52) --> (170, 157, 107) Left_Cerebellum_White_Matter: limiting intensities to 91.0 --> 197.0 0 of 30 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (78, 117, 55) --> (125, 154, 111) Right_Cerebellum_White_Matter: limiting intensities to 92.0 --> 197.0 0 of 29 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (111, 113, 88) --> (142, 173, 122) Brain_Stem: limiting intensities to 83.0 --> 197.0 0 of 29 (0.0%) samples deleted using 5077 total control points for intensity normalization... bias field = 1.026 +- 0.052 5 of 5076 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (117, 46, 31) --> (190, 150, 200) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 182.0 3 of 2536 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (65, 44, 35) --> (135, 147, 202) Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 182.0 0 of 2312 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (123, 117, 52) --> (170, 157, 107) Left_Cerebellum_White_Matter: limiting intensities to 85.0 --> 182.0 0 of 52 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (78, 117, 55) --> (125, 154, 111) Right_Cerebellum_White_Matter: limiting intensities to 82.0 --> 182.0 0 of 69 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (111, 113, 88) --> (142, 173, 122) Brain_Stem: limiting intensities to 79.0 --> 182.0 0 of 75 (0.0%) samples deleted using 5044 total control points for intensity normalization... bias field = 1.018 +- 0.036 8 of 5041 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (117, 46, 31) --> (190, 150, 200) Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 178.0 0 of 2511 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (65, 44, 35) --> (135, 147, 202) Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 178.0 0 of 2265 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (123, 117, 52) --> (170, 157, 107) Left_Cerebellum_White_Matter: limiting intensities to 81.0 --> 178.0 0 of 121 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (78, 117, 55) --> (125, 154, 111) Right_Cerebellum_White_Matter: limiting intensities to 81.0 --> 178.0 0 of 98 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (111, 113, 88) --> (142, 173, 122) Brain_Stem: limiting intensities to 74.0 --> 178.0 0 of 161 (0.0%) samples deleted using 5156 total control points for intensity normalization... bias field = 1.014 +- 0.031 5 of 5156 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 58 seconds. #-------------------------------------- #@# CA Reg Tue Aug 6 21:42:35 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri \n mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /Applications/Freesurfer5.3/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.m3z \n not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/Applications/Freesurfer5.3/freesurfer/average/RB_all_2008-03-26.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.20 (predicted orig area = 6.7) 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=0.794, neg=0, invalid=96777 0001: dt=129.472000, rms=0.706 (11.083%), neg=0, invalid=96777 0002: dt=221.952000, rms=0.672 (4.719%), neg=0, invalid=96777 0003: dt=129.472000, rms=0.663 (1.389%), neg=0, invalid=96777 0004: dt=92.480000, rms=0.661 (0.288%), neg=0, invalid=96777 0005: dt=369.920000, rms=0.653 (1.232%), neg=0, invalid=96777 0006: dt=32.368000, rms=0.651 (0.336%), neg=0, invalid=96777 0007: dt=32.368000, rms=0.650 (0.107%), neg=0, invalid=96777 0008: dt=32.368000, rms=0.650 (0.058%), neg=0, invalid=96777 0009: dt=32.368000, rms=0.649 (0.071%), neg=0, invalid=96777 0010: dt=32.368000, rms=0.648 (0.108%), neg=0, invalid=96777 0011: dt=32.368000, rms=0.647 (0.185%), neg=0, invalid=96777 0012: dt=32.368000, rms=0.646 (0.265%), neg=0, invalid=96777 0013: dt=32.368000, rms=0.644 (0.310%), neg=0, invalid=96777 0014: dt=32.368000, rms=0.642 (0.310%), neg=0, invalid=96777 0015: dt=32.368000, rms=0.640 (0.280%), neg=0, invalid=96777 0016: dt=32.368000, rms=0.638 (0.242%), neg=0, invalid=96777 0017: dt=32.368000, rms=0.637 (0.209%), neg=0, invalid=96777 0018: dt=32.368000, rms=0.636 (0.169%), neg=0, invalid=96777 0019: dt=32.368000, rms=0.635 (0.144%), neg=0, invalid=96777 0020: dt=32.368000, rms=0.634 (0.156%), neg=0, invalid=96777 0021: dt=32.368000, rms=0.633 (0.176%), neg=0, invalid=96777 0022: dt=32.368000, rms=0.632 (0.174%), neg=0, invalid=96777 0023: dt=32.368000, rms=0.631 (0.154%), neg=0, invalid=96777 0024: dt=32.368000, rms=0.630 (0.134%), neg=0, invalid=96777 0025: dt=32.368000, rms=0.629 (0.105%), neg=0, invalid=96777 0026: dt=32.368000, rms=0.629 (0.090%), neg=0, invalid=96777 0027: dt=517.888000, rms=0.628 (0.141%), neg=0, invalid=96777 0028: dt=129.472000, rms=0.627 (0.124%), neg=0, invalid=96777 0029: dt=129.472000, rms=0.627 (-0.047%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.627, neg=0, invalid=96777 0030: dt=129.472000, rms=0.627 (0.047%), neg=0, invalid=96777 0031: dt=369.920000, rms=0.625 (0.188%), neg=0, invalid=96777 0032: dt=32.368000, rms=0.625 (0.011%), neg=0, invalid=96777 0033: dt=32.368000, rms=0.625 (0.002%), neg=0, invalid=96777 0034: dt=32.368000, rms=0.625 (-0.020%), neg=0, invalid=96777 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.629, neg=0, invalid=96777 0035: dt=145.152000, rms=0.620 (1.356%), neg=0, invalid=96777 0036: dt=62.208000, rms=0.612 (1.261%), neg=0, invalid=96777 0037: dt=20.736000, rms=0.610 (0.280%), neg=0, invalid=96777 0038: dt=497.664000, rms=0.597 (2.288%), neg=0, invalid=96777 0039: dt=31.104000, rms=0.589 (1.215%), neg=0, invalid=96777 0040: dt=9.072000, rms=0.589 (0.069%), neg=0, invalid=96777 0041: dt=9.072000, rms=0.589 (0.011%), neg=0, invalid=96777 0042: dt=9.072000, rms=0.589 (0.011%), neg=0, invalid=96777 0043: dt=9.072000, rms=0.589 (0.002%), neg=0, invalid=96777 0044: dt=145.152000, rms=0.586 (0.397%), neg=0, invalid=96777 0045: dt=15.552000, rms=0.586 (0.073%), neg=0, invalid=96777 0046: dt=15.552000, rms=0.586 (0.047%), neg=0, invalid=96777 0047: dt=15.552000, rms=0.585 (0.049%), neg=0, invalid=96777 0048: dt=15.552000, rms=0.585 (0.063%), neg=0, invalid=96777 0049: dt=15.552000, rms=0.584 (0.145%), neg=0, invalid=96777 0050: dt=15.552000, rms=0.583 (0.194%), neg=0, invalid=96777 0051: dt=15.552000, rms=0.582 (0.211%), neg=0, invalid=96777 0052: dt=15.552000, rms=0.581 (0.216%), neg=0, invalid=96777 0053: dt=15.552000, rms=0.579 (0.192%), neg=0, invalid=96777 0054: dt=15.552000, rms=0.578 (0.173%), neg=0, invalid=96777 0055: dt=15.552000, rms=0.577 (0.163%), neg=0, invalid=96777 0056: dt=15.552000, rms=0.576 (0.178%), neg=0, invalid=96777 0057: dt=15.552000, rms=0.575 (0.205%), neg=0, invalid=96777 0058: dt=15.552000, rms=0.574 (0.211%), neg=0, invalid=96777 0059: dt=15.552000, rms=0.573 (0.187%), neg=0, invalid=96777 0060: dt=15.552000, rms=0.572 (0.170%), neg=0, invalid=96777 0061: dt=15.552000, rms=0.571 (0.152%), neg=0, invalid=96777 0062: dt=15.552000, rms=0.570 (0.148%), neg=0, invalid=96777 0063: dt=15.552000, rms=0.569 (0.164%), neg=0, invalid=96777 0064: dt=15.552000, rms=0.568 (0.181%), neg=0, invalid=96777 0065: dt=15.552000, rms=0.567 (0.171%), neg=0, invalid=96777 0066: dt=15.552000, rms=0.567 (0.141%), neg=0, invalid=96777 0067: dt=15.552000, rms=0.566 (0.108%), neg=0, invalid=96777 0068: dt=15.552000, rms=0.566 (0.075%), neg=0, invalid=96777 0069: dt=82.944000, rms=0.565 (0.025%), neg=0, invalid=96777 0070: dt=82.944000, rms=0.565 (-0.070%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.565, neg=0, invalid=96777 0071: dt=82.944000, rms=0.564 (0.192%), neg=0, invalid=96777 0072: dt=31.104000, rms=0.564 (0.107%), neg=0, invalid=96777 0073: dt=31.104000, rms=0.563 (0.056%), neg=0, invalid=96777 0074: dt=31.104000, rms=0.563 (0.057%), neg=0, invalid=96777 0075: dt=31.104000, rms=0.563 (0.071%), neg=0, invalid=96777 0076: dt=31.104000, rms=0.562 (0.060%), neg=0, invalid=96777 0077: dt=31.104000, rms=0.562 (0.057%), neg=0, invalid=96777 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.583, neg=0, invalid=96777 0078: dt=8.000000, rms=0.582 (0.106%), neg=0, invalid=96777 0079: dt=2.800000, rms=0.582 (0.021%), neg=0, invalid=96777 0080: dt=2.800000, rms=0.582 (0.005%), neg=0, invalid=96777 0081: dt=2.800000, rms=0.582 (-0.010%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.582, neg=0, invalid=96777 0082: dt=0.000000, rms=0.582 (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=0.636, neg=0, invalid=96777 0083: dt=5.480460, rms=0.624 (1.981%), neg=0, invalid=96777 0084: dt=1.008000, rms=0.624 (0.027%), neg=0, invalid=96777 0085: dt=1.008000, rms=0.624 (0.010%), neg=0, invalid=96777 0086: dt=1.008000, rms=0.624 (-0.023%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.624, neg=0, invalid=96777 0087: dt=0.000000, rms=0.624 (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=0.685, neg=0, invalid=96777 0088: dt=0.895317, rms=0.683 (0.340%), neg=0, invalid=96777 0089: dt=2.090909, rms=0.678 (0.655%), neg=0, invalid=96777 0090: dt=1.166667, rms=0.677 (0.158%), neg=0, invalid=96777 0091: dt=1.166667, rms=0.676 (0.158%), neg=0, invalid=96777 0092: dt=1.166667, rms=0.676 (0.054%), neg=0, invalid=96777 0093: dt=1.166667, rms=0.676 (-0.271%), neg=0, invalid=96777 0094: dt=0.112000, rms=0.676 (0.001%), neg=0, invalid=96777 0095: dt=0.081169, rms=0.676 (0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.676, neg=0, invalid=96777 0096: dt=0.802198, rms=0.675 (0.061%), neg=0, invalid=96777 0097: dt=0.000000, rms=0.675 (-0.000%), 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=0.633, neg=0, invalid=96777 0098: dt=0.448000, rms=0.619 (2.105%), neg=0, invalid=96777 0099: dt=0.000000, rms=0.619 (0.009%), neg=0, invalid=96777 0100: dt=0.050000, rms=0.619 (-0.216%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.619, neg=0, invalid=96777 0101: dt=0.001250, rms=0.619 (0.000%), neg=0, invalid=96777 0102: dt=0.000020, rms=0.619 (-0.001%), neg=0, invalid=96777 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.09974 (11) Left_Lateral_Ventricle (4): linear fit = 0.44 x + 0.0 (1632 voxels, overlap=0.458) Left_Lateral_Ventricle (4): linear fit = 0.44 x + 0.0 (1632 voxels, peak = 10), gca=10.4 gca peak = 0.14022 (22) mri peak = 0.13767 (11) Right_Lateral_Ventricle (43): linear fit = 0.41 x + 0.0 (970 voxels, overlap=0.006) Right_Lateral_Ventricle (43): linear fit = 0.41 x + 0.0 (970 voxels, peak = 9), gca=9.1 gca peak = 0.24234 (100) mri peak = 0.07351 (102) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (473 voxels, overlap=1.004) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (473 voxels, peak = 100), gca=100.5 gca peak = 0.19192 (97) mri peak = 0.06123 (85) Left_Pallidum (13): linear fit = 0.96 x + 0.0 (430 voxels, overlap=0.902) Left_Pallidum (13): linear fit = 0.96 x + 0.0 (430 voxels, peak = 94), gca=93.6 gca peak = 0.24007 (63) mri peak = 0.07992 (69) Right_Hippocampus (53): linear fit = 1.09 x + 0.0 (925 voxels, overlap=0.873) Right_Hippocampus (53): linear fit = 1.09 x + 0.0 (925 voxels, peak = 68), gca=68.4 gca peak = 0.29892 (64) mri peak = 0.07852 (69) Left_Hippocampus (17): linear fit = 1.05 x + 0.0 (915 voxels, overlap=0.998) Left_Hippocampus (17): linear fit = 1.05 x + 0.0 (915 voxels, peak = 68), gca=67.5 gca peak = 0.12541 (104) mri peak = 0.12722 (107) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (79443 voxels, overlap=0.633) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (79443 voxels, peak = 108), gca=107.6 gca peak = 0.13686 (104) mri peak = 0.11533 (107) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (84697 voxels, overlap=0.651) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (84697 voxels, peak = 107), gca=106.6 gca peak = 0.11691 (63) mri peak = 0.03252 (71) Left_Cerebral_Cortex (3): linear fit = 1.05 x + 0.0 (37655 voxels, overlap=0.881) Left_Cerebral_Cortex (3): linear fit = 1.05 x + 0.0 (37655 voxels, peak = 66), gca=66.5 gca peak = 0.13270 (63) mri peak = 0.03335 (63) Right_Cerebral_Cortex (42): linear fit = 1.05 x + 0.0 (38801 voxels, overlap=0.822) Right_Cerebral_Cortex (42): linear fit = 1.05 x + 0.0 (38801 voxels, peak = 66), gca=66.5 gca peak = 0.15182 (70) mri peak = 0.10129 (80) Right_Caudate (50): linear fit = 1.12 x + 0.0 (623 voxels, overlap=0.320) Right_Caudate (50): linear fit = 1.12 x + 0.0 (623 voxels, peak = 79), gca=78.8 gca peak = 0.14251 (76) mri peak = 0.07512 (84) Left_Caudate (11): linear fit = 1.04 x + 0.0 (869 voxels, overlap=0.821) Left_Caudate (11): linear fit = 1.04 x + 0.0 (869 voxels, peak = 79), gca=79.4 gca peak = 0.12116 (60) mri peak = 0.05046 (67) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (32163 voxels, overlap=0.606) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (32163 voxels, peak = 68), gca=67.5 gca peak = 0.12723 (61) mri peak = 0.04863 (68) Right_Cerebellum_Cortex (47): linear fit = 1.15 x + 0.0 (33248 voxels, overlap=0.511) Right_Cerebellum_Cortex (47): linear fit = 1.15 x + 0.0 (33248 voxels, peak = 70), gca=70.5 gca peak = 0.22684 (88) mri peak = 0.09483 (92) Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (10253 voxels, overlap=0.688) Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (10253 voxels, peak = 92), gca=92.0 gca peak = 0.21067 (87) mri peak = 0.09651 (92) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (8841 voxels, overlap=0.731) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (8841 voxels, peak = 92), gca=91.8 gca peak = 0.25455 (62) mri peak = 0.09816 (68) Left_Amygdala (18): linear fit = 1.02 x + 0.0 (403 voxels, overlap=0.973) Left_Amygdala (18): linear fit = 1.02 x + 0.0 (403 voxels, peak = 64), gca=63.5 gca peak = 0.39668 (62) mri peak = 0.09375 (67) Right_Amygdala (54): linear fit = 1.05 x + 0.0 (418 voxels, overlap=0.995) Right_Amygdala (54): linear fit = 1.05 x + 0.0 (418 voxels, peak = 65), gca=65.4 gca peak = 0.10129 (93) mri peak = 0.07487 (101) Left_Thalamus_Proper (10): linear fit = 1.10 x + 0.0 (5770 voxels, overlap=0.412) Left_Thalamus_Proper (10): linear fit = 1.10 x + 0.0 (5770 voxels, peak = 102), gca=101.8 gca peak = 0.12071 (89) mri peak = 0.06402 (99) Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (4677 voxels, overlap=0.629) Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (4677 voxels, peak = 97), gca=97.5 gca peak = 0.13716 (82) mri peak = 0.05788 (91) Left_Putamen (12): linear fit = 1.10 x + 0.0 (2817 voxels, overlap=0.879) Left_Putamen (12): linear fit = 1.10 x + 0.0 (2817 voxels, peak = 90), gca=89.8 gca peak = 0.15214 (84) mri peak = 0.05989 (88) Right_Putamen (51): linear fit = 1.05 x + 0.0 (2578 voxels, overlap=0.857) Right_Putamen (51): linear fit = 1.05 x + 0.0 (2578 voxels, peak = 89), gca=88.6 gca peak = 0.08983 (85) mri peak = 0.07011 (90) Brain_Stem (16): linear fit = 1.09 x + 0.0 (12787 voxels, overlap=0.666) Brain_Stem (16): linear fit = 1.09 x + 0.0 (12787 voxels, peak = 92), gca=92.2 gca peak = 0.11809 (92) mri peak = 0.08816 (104) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (948 voxels, overlap=0.572) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (948 voxels, peak = 99), gca=98.9 gca peak = 0.12914 (94) mri peak = 0.08651 (105) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1288 voxels, overlap=0.681) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1288 voxels, peak = 102), gca=102.0 gca peak = 0.21100 (36) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13542 (27) mri peak = 0.16836 (12) Fourth_Ventricle (15): linear fit = 0.41 x + 0.0 (251 voxels, overlap=0.015) Fourth_Ventricle (15): linear fit = 0.41 x + 0.0 (251 voxels, peak = 11), gca=10.9 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak Third_Ventricle = 0.21100 (36) gca peak Fourth_Ventricle = 0.13542 (27) gca peak CSF = 0.17123 (45) gca peak Left_Accumbens_area = 0.25875 (69) gca peak Left_undetermined = 0.96240 (36) gca peak Left_vessel = 0.33262 (65) gca peak Left_choroid_plexus = 0.09846 (46) gca peak Right_Inf_Lat_Vent = 0.28113 (34) gca peak Right_Accumbens_area = 0.27120 (72) gca peak Right_vessel = 0.61915 (60) gca peak Right_choroid_plexus = 0.12775 (51) gca peak Fifth_Ventricle = 0.45329 (44) gca peak WM_hypointensities = 0.11729 (81) gca peak non_WM_hypointensities = 0.10912 (56) gca peak Optic_Chiasm = 0.33287 (75) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 1.05 x + 0.0 estimating mean wm scale to be 1.03 x + 0.0 estimating mean csf scale to be 0.43 x + 0.0 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=0.634, neg=0, invalid=96777 0103: dt=129.472000, rms=0.620 (2.194%), neg=0, invalid=96777 0104: dt=295.936000, rms=0.615 (0.820%), neg=0, invalid=96777 0105: dt=110.976000, rms=0.612 (0.403%), neg=0, invalid=96777 0106: dt=129.472000, rms=0.611 (0.179%), neg=0, invalid=96777 0107: dt=129.472000, rms=0.609 (0.282%), neg=0, invalid=96777 0108: dt=73.984000, rms=0.609 (0.079%), neg=0, invalid=96777 0109: dt=517.888000, rms=0.606 (0.424%), neg=0, invalid=96777 0110: dt=32.368000, rms=0.605 (0.156%), neg=0, invalid=96777 0111: dt=55.488000, rms=0.605 (0.056%), neg=0, invalid=96777 0112: dt=369.920000, rms=0.604 (0.113%), neg=0, invalid=96777 0113: dt=92.480000, rms=0.603 (0.208%), neg=0, invalid=96777 0114: dt=32.368000, rms=0.603 (0.006%), neg=0, invalid=96777 0115: dt=32.368000, rms=0.603 (0.013%), neg=0, invalid=96777 0116: dt=32.368000, rms=0.603 (0.016%), neg=0, invalid=96777 0117: dt=32.368000, rms=0.603 (0.038%), neg=0, invalid=96777 0118: dt=32.368000, rms=0.602 (0.057%), neg=0, invalid=96777 0119: dt=32.368000, rms=0.602 (0.076%), neg=0, invalid=96777 0120: dt=32.368000, rms=0.601 (0.078%), neg=0, invalid=96777 0121: dt=32.368000, rms=0.601 (0.069%), neg=0, invalid=96777 0122: dt=32.368000, rms=0.601 (0.067%), neg=0, invalid=96777 0123: dt=32.368000, rms=0.600 (0.066%), neg=0, invalid=96777 0124: dt=32.368000, rms=0.600 (0.066%), neg=0, invalid=96777 0125: dt=32.368000, rms=0.599 (0.063%), neg=0, invalid=96777 0126: dt=32.368000, rms=0.599 (0.060%), neg=0, invalid=96777 0127: dt=32.368000, rms=0.599 (0.063%), neg=0, invalid=96777 0128: dt=32.368000, rms=0.598 (0.061%), neg=0, invalid=96777 0129: dt=32.368000, rms=0.598 (0.057%), neg=0, invalid=96777 0130: dt=32.368000, rms=0.598 (0.050%), neg=0, invalid=96777 0131: dt=32.368000, rms=0.597 (0.045%), neg=0, invalid=96777 0132: dt=32.368000, rms=0.597 (0.040%), neg=0, invalid=96777 0133: dt=32.368000, rms=0.597 (0.047%), neg=0, invalid=96777 0134: dt=32.368000, rms=0.597 (0.044%), neg=0, invalid=96777 0135: dt=32.368000, rms=0.596 (0.043%), neg=0, invalid=96777 0136: dt=32.368000, rms=0.596 (0.038%), neg=0, invalid=96777 0137: dt=32.368000, rms=0.596 (0.036%), neg=0, invalid=96777 0138: dt=32.368000, rms=0.596 (0.034%), neg=0, invalid=96777 0139: dt=32.368000, rms=0.595 (0.038%), neg=0, invalid=96777 0140: dt=32.368000, rms=0.595 (0.037%), neg=0, invalid=96777 0141: dt=32.368000, rms=0.595 (0.035%), neg=0, invalid=96777 0142: dt=32.368000, rms=0.595 (0.032%), neg=0, invalid=96777 0143: dt=32.368000, rms=0.595 (0.030%), neg=0, invalid=96777 0144: dt=32.368000, rms=0.594 (0.029%), neg=0, invalid=96777 0145: dt=32.368000, rms=0.594 (0.029%), neg=0, invalid=96777 0146: dt=32.368000, rms=0.594 (0.030%), neg=0, invalid=96777 0147: dt=32.368000, rms=0.594 (0.031%), neg=0, invalid=96777 0148: dt=32.368000, rms=0.594 (0.029%), neg=0, invalid=96777 0149: dt=32.368000, rms=0.594 (0.027%), neg=0, invalid=96777 0150: dt=32.368000, rms=0.593 (0.026%), neg=0, invalid=96777 0151: dt=32.368000, rms=0.593 (0.025%), neg=0, invalid=96777 0152: dt=32.368000, rms=0.593 (0.027%), neg=0, invalid=96777 0153: dt=32.368000, rms=0.593 (0.029%), neg=0, invalid=96777 0154: dt=32.368000, rms=0.593 (0.027%), neg=0, invalid=96777 0155: dt=32.368000, rms=0.593 (0.024%), neg=0, invalid=96777 0156: dt=32.368000, rms=0.593 (0.019%), neg=0, invalid=96777 0157: dt=295.936000, rms=0.593 (0.005%), neg=0, invalid=96777 0158: dt=295.936000, rms=0.592 (0.021%), neg=0, invalid=96777 0159: dt=295.936000, rms=0.592 (-0.118%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.592, neg=0, invalid=96777 0160: dt=110.976000, rms=0.592 (0.080%), neg=0, invalid=96777 0161: dt=129.472000, rms=0.592 (0.067%), neg=0, invalid=96777 0162: dt=92.480000, rms=0.591 (0.015%), neg=0, invalid=96777 0163: dt=92.480000, rms=0.591 (0.034%), neg=0, invalid=96777 0164: dt=92.480000, rms=0.591 (0.039%), neg=0, invalid=96777 0165: dt=92.480000, rms=0.591 (0.039%), neg=0, invalid=96777 0166: dt=92.480000, rms=0.591 (0.046%), neg=0, invalid=96777 0167: dt=92.480000, rms=0.590 (0.051%), neg=0, invalid=96777 0168: dt=92.480000, rms=0.590 (0.039%), neg=0, invalid=96777 0169: dt=92.480000, rms=0.590 (0.027%), neg=0, invalid=96777 0170: dt=92.480000, rms=0.590 (0.028%), neg=0, invalid=96777 0171: dt=92.480000, rms=0.590 (0.021%), neg=0, invalid=96777 0172: dt=92.480000, rms=0.589 (0.028%), neg=0, invalid=96777 0173: dt=92.480000, rms=0.589 (0.034%), neg=0, invalid=96777 0174: dt=92.480000, rms=0.589 (0.042%), neg=0, invalid=96777 0175: dt=92.480000, rms=0.589 (0.030%), neg=0, invalid=96777 0176: dt=92.480000, rms=0.589 (0.037%), neg=0, invalid=96777 0177: dt=92.480000, rms=0.588 (0.040%), neg=0, invalid=96777 0178: dt=92.480000, rms=0.588 (0.032%), neg=0, invalid=96777 0179: dt=92.480000, rms=0.588 (0.030%), neg=0, invalid=96777 0180: dt=92.480000, rms=0.588 (0.034%), neg=0, invalid=96777 0181: dt=92.480000, rms=0.588 (0.040%), neg=0, invalid=96777 0182: dt=92.480000, rms=0.587 (0.045%), neg=0, invalid=96777 0183: dt=92.480000, rms=0.587 (0.046%), neg=0, invalid=96777 0184: dt=92.480000, rms=0.587 (0.040%), neg=0, invalid=96777 0185: dt=92.480000, rms=0.587 (0.033%), neg=0, invalid=96777 0186: dt=92.480000, rms=0.586 (0.026%), neg=0, invalid=96777 0187: dt=92.480000, rms=0.586 (0.033%), neg=0, invalid=96777 0188: dt=92.480000, rms=0.586 (0.035%), neg=0, invalid=96777 0189: dt=92.480000, rms=0.586 (0.034%), neg=0, invalid=96777 0190: dt=92.480000, rms=0.586 (0.030%), neg=0, invalid=96777 0191: dt=92.480000, rms=0.585 (0.037%), neg=0, invalid=96777 0192: dt=92.480000, rms=0.585 (0.035%), neg=0, invalid=96777 0193: dt=92.480000, rms=0.585 (0.026%), neg=0, invalid=96777 0194: dt=92.480000, rms=0.585 (0.024%), neg=0, invalid=96777 0195: dt=92.480000, rms=0.585 (0.026%), neg=0, invalid=96777 0196: dt=92.480000, rms=0.585 (0.034%), neg=0, invalid=96777 0197: dt=92.480000, rms=0.584 (0.021%), neg=0, invalid=96777 0198: dt=92.480000, rms=0.584 (0.021%), neg=0, invalid=96777 0199: dt=369.920000, rms=0.584 (0.014%), neg=0, invalid=96777 0200: dt=369.920000, rms=0.584 (-0.221%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.585, neg=0, invalid=96777 0201: dt=62.208000, rms=0.582 (0.404%), neg=0, invalid=96777 0202: dt=103.680000, rms=0.577 (0.854%), neg=0, invalid=96777 0203: dt=20.736000, rms=0.576 (0.205%), neg=0, invalid=96777 0204: dt=145.152000, rms=0.572 (0.670%), neg=0, invalid=96777 0205: dt=31.104000, rms=0.571 (0.310%), neg=0, invalid=96777 0206: dt=36.288000, rms=0.569 (0.338%), neg=0, invalid=96777 0207: dt=36.288000, rms=0.568 (0.098%), neg=0, invalid=96777 0208: dt=62.208000, rms=0.566 (0.301%), neg=0, invalid=96777 0209: dt=20.736000, rms=0.566 (0.129%), neg=0, invalid=96777 0210: dt=580.608000, rms=0.557 (1.604%), neg=0, invalid=96777 0211: dt=25.920000, rms=0.555 (0.362%), neg=0, invalid=96777 0212: dt=82.944000, rms=0.553 (0.207%), neg=0, invalid=96777 0213: dt=36.288000, rms=0.552 (0.195%), neg=0, invalid=96777 0214: dt=36.288000, rms=0.552 (0.075%), neg=0, invalid=96777 0215: dt=124.416000, rms=0.551 (0.217%), neg=0, invalid=96777 0216: dt=15.552000, rms=0.550 (0.088%), neg=0, invalid=96777 0217: dt=82.944000, rms=0.550 (0.101%), neg=0, invalid=96777 0218: dt=36.288000, rms=0.549 (0.132%), neg=0, invalid=96777 0219: dt=25.920000, rms=0.549 (0.050%), neg=0, invalid=96777 0220: dt=25.920000, rms=0.548 (0.055%), neg=0, invalid=96777 0221: dt=25.920000, rms=0.548 (0.084%), neg=0, invalid=96777 0222: dt=25.920000, rms=0.547 (0.122%), neg=0, invalid=96777 0223: dt=25.920000, rms=0.546 (0.149%), neg=0, invalid=96777 0224: dt=25.920000, rms=0.546 (0.169%), neg=0, invalid=96777 0225: dt=25.920000, rms=0.545 (0.186%), neg=0, invalid=96777 0226: dt=25.920000, rms=0.543 (0.207%), neg=0, invalid=96777 0227: dt=25.920000, rms=0.542 (0.206%), neg=0, invalid=96777 0228: dt=25.920000, rms=0.541 (0.207%), neg=0, invalid=96777 0229: dt=25.920000, rms=0.540 (0.193%), neg=0, invalid=96777 0230: dt=25.920000, rms=0.539 (0.210%), neg=0, invalid=96777 0231: dt=25.920000, rms=0.538 (0.203%), neg=0, invalid=96777 0232: dt=25.920000, rms=0.537 (0.198%), neg=0, invalid=96777 0233: dt=25.920000, rms=0.536 (0.183%), neg=0, invalid=96777 0234: dt=25.920000, rms=0.535 (0.178%), neg=0, invalid=96777 0235: dt=25.920000, rms=0.534 (0.160%), neg=0, invalid=96777 0236: dt=25.920000, rms=0.533 (0.145%), neg=0, invalid=96777 0237: dt=25.920000, rms=0.532 (0.147%), neg=0, invalid=96777 0238: dt=25.920000, rms=0.532 (0.146%), neg=0, invalid=96777 0239: dt=25.920000, rms=0.531 (0.147%), neg=0, invalid=96777 0240: dt=25.920000, rms=0.530 (0.132%), neg=0, invalid=96777 0241: dt=25.920000, rms=0.530 (0.125%), neg=0, invalid=96777 0242: dt=25.920000, rms=0.529 (0.122%), neg=0, invalid=96777 0243: dt=25.920000, rms=0.528 (0.137%), neg=0, invalid=96777 0244: dt=25.920000, rms=0.527 (0.136%), neg=0, invalid=96777 0245: dt=25.920000, rms=0.527 (-0.002%), neg=0, invalid=96777 0246: dt=5.184000, rms=0.527 (0.000%), neg=0, invalid=96777 0247: dt=36.288000, rms=0.527 (0.005%), neg=0, invalid=96777 0248: dt=145.152000, rms=0.527 (0.110%), neg=0, invalid=96777 0249: dt=5.184000, rms=0.527 (-0.004%), neg=0, invalid=96777 0250: dt=5.184000, rms=0.527 (0.002%), neg=0, invalid=96777 0251: dt=5.184000, rms=0.527 (-0.007%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.527, neg=0, invalid=96777 0252: dt=25.920000, rms=0.526 (0.148%), neg=0, invalid=96777 0253: dt=145.152000, rms=0.524 (0.419%), neg=0, invalid=96777 0254: dt=9.072000, rms=0.524 (0.028%), neg=0, invalid=96777 0255: dt=9.072000, rms=0.524 (0.020%), neg=0, invalid=96777 0256: dt=9.072000, rms=0.524 (0.025%), neg=0, invalid=96777 0257: dt=9.072000, rms=0.523 (0.017%), neg=0, invalid=96777 0258: dt=9.072000, rms=0.523 (0.019%), neg=0, invalid=96777 0259: dt=9.072000, rms=0.523 (0.032%), neg=0, invalid=96777 0260: dt=9.072000, rms=0.523 (0.033%), neg=0, invalid=96777 0261: dt=9.072000, rms=0.523 (0.035%), neg=0, invalid=96777 0262: dt=9.072000, rms=0.523 (0.039%), neg=0, invalid=96777 0263: dt=9.072000, rms=0.522 (0.043%), neg=0, invalid=96777 0264: dt=9.072000, rms=0.522 (0.046%), neg=0, invalid=96777 0265: dt=9.072000, rms=0.522 (0.046%), neg=0, invalid=96777 0266: dt=9.072000, rms=0.522 (0.043%), neg=0, invalid=96777 0267: dt=9.072000, rms=0.521 (0.041%), neg=0, invalid=96777 0268: dt=9.072000, rms=0.521 (0.040%), neg=0, invalid=96777 0269: dt=9.072000, rms=0.521 (0.036%), neg=0, invalid=96777 0270: dt=9.072000, rms=0.521 (0.036%), neg=0, invalid=96777 0271: dt=9.072000, rms=0.521 (0.038%), neg=0, invalid=96777 0272: dt=9.072000, rms=0.520 (0.038%), neg=0, invalid=96777 0273: dt=9.072000, rms=0.520 (0.041%), neg=0, invalid=96777 0274: dt=9.072000, rms=0.520 (0.040%), neg=0, invalid=96777 0275: dt=9.072000, rms=0.520 (0.037%), neg=0, invalid=96777 0276: dt=9.072000, rms=0.520 (0.035%), neg=0, invalid=96777 0277: dt=9.072000, rms=0.519 (0.035%), neg=0, invalid=96777 0278: dt=9.072000, rms=0.519 (0.033%), neg=0, invalid=96777 0279: dt=9.072000, rms=0.519 (0.032%), neg=0, invalid=96777 0280: dt=9.072000, rms=0.519 (0.034%), neg=0, invalid=96777 0281: dt=9.072000, rms=0.519 (0.031%), neg=0, invalid=96777 0282: dt=9.072000, rms=0.519 (0.029%), neg=0, invalid=96777 0283: dt=9.072000, rms=0.519 (0.030%), neg=0, invalid=96777 0284: dt=9.072000, rms=0.518 (0.029%), neg=0, invalid=96777 0285: dt=9.072000, rms=0.518 (0.027%), neg=0, invalid=96777 0286: dt=9.072000, rms=0.518 (0.029%), neg=0, invalid=96777 0287: dt=9.072000, rms=0.518 (0.036%), neg=0, invalid=96777 0288: dt=9.072000, rms=0.518 (0.039%), neg=0, invalid=96777 0289: dt=9.072000, rms=0.518 (0.033%), neg=0, invalid=96777 0290: dt=2.268000, rms=0.517 (0.002%), neg=0, invalid=96777 0291: dt=1.134000, rms=0.517 (0.001%), neg=0, invalid=96777 0292: dt=0.486000, rms=0.517 (0.001%), neg=0, invalid=96777 0293: dt=0.030375, rms=0.517 (-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=0.524, neg=0, invalid=96777 0294: dt=0.010937, rms=0.524 (0.000%), neg=0, invalid=96777 0295: dt=0.002734, rms=0.524 (0.000%), neg=0, invalid=96777 0296: dt=0.000684, rms=0.524 (0.000%), neg=0, invalid=96777 0297: dt=0.000171, rms=0.524 (0.000%), neg=0, invalid=96777 0298: dt=0.000011, rms=0.524 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.524, neg=0, invalid=96777 0299: dt=0.000000, rms=0.524 (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=0.545, neg=0, invalid=96777 0300: dt=11.520000, rms=0.523 (4.190%), neg=0, invalid=96777 0301: dt=11.520000, rms=0.515 (1.531%), neg=0, invalid=96777 0302: dt=4.032000, rms=0.512 (0.482%), neg=0, invalid=96777 0303: dt=4.032000, rms=0.510 (0.361%), neg=0, invalid=96777 0304: dt=4.032000, rms=0.509 (0.221%), neg=0, invalid=96777 0305: dt=4.032000, rms=0.508 (0.200%), neg=0, invalid=96777 0306: dt=11.520000, rms=0.506 (0.385%), neg=0, invalid=96777 0307: dt=4.032000, rms=0.506 (0.093%), neg=0, invalid=96777 0308: dt=4.032000, rms=0.505 (0.079%), neg=0, invalid=96777 0309: dt=4.032000, rms=0.505 (0.080%), neg=0, invalid=96777 0310: dt=11.520000, rms=0.504 (0.137%), neg=0, invalid=96777 0311: dt=4.032000, rms=0.504 (0.064%), neg=0, invalid=96777 0312: dt=4.032000, rms=0.504 (0.024%), neg=0, invalid=96777 0313: dt=4.032000, rms=0.504 (0.043%), neg=0, invalid=96777 0314: dt=4.032000, rms=0.503 (0.055%), neg=0, invalid=96777 0315: dt=4.032000, rms=0.503 (0.063%), neg=0, invalid=96777 0316: dt=4.032000, rms=0.503 (0.080%), neg=0, invalid=96777 0317: dt=4.032000, rms=0.502 (0.089%), neg=0, invalid=96777 0318: dt=4.032000, rms=0.502 (0.070%), neg=0, invalid=96777 0319: dt=4.032000, rms=0.502 (0.042%), neg=0, invalid=96777 0320: dt=4.032000, rms=0.501 (0.033%), neg=0, invalid=96777 0321: dt=4.032000, rms=0.501 (0.034%), neg=0, invalid=96777 0322: dt=4.032000, rms=0.501 (0.025%), neg=0, invalid=96777 0323: dt=4.032000, rms=0.501 (0.004%), neg=0, invalid=96777 0324: dt=4.032000, rms=0.501 (0.014%), neg=0, invalid=96777 0325: dt=11.520000, rms=0.501 (0.010%), neg=0, invalid=96777 0326: dt=5.760000, rms=0.501 (0.019%), neg=0, invalid=96777 0327: dt=5.760000, rms=0.501 (0.024%), neg=0, invalid=96777 0328: dt=5.760000, rms=0.501 (0.030%), neg=0, invalid=96777 0329: dt=5.760000, rms=0.500 (0.041%), neg=0, invalid=96777 0330: dt=5.760000, rms=0.500 (0.044%), neg=0, invalid=96777 0331: dt=5.760000, rms=0.500 (0.052%), neg=0, invalid=96777 0332: dt=5.760000, rms=0.500 (0.055%), neg=0, invalid=96777 0333: dt=5.760000, rms=0.499 (0.047%), neg=0, invalid=96777 0334: dt=5.760000, rms=0.499 (0.022%), neg=0, invalid=96777 0335: dt=5.760000, rms=0.499 (0.043%), neg=0, invalid=96777 0336: dt=5.760000, rms=0.499 (0.044%), neg=0, invalid=96777 0337: dt=5.760000, rms=0.499 (0.041%), neg=0, invalid=96777 0338: dt=5.760000, rms=0.498 (0.034%), neg=0, invalid=96777 0339: dt=5.760000, rms=0.498 (0.030%), neg=0, invalid=96777 0340: dt=5.760000, rms=0.498 (0.020%), neg=0, invalid=96777 0341: dt=5.760000, rms=0.498 (0.012%), neg=0, invalid=96777 0342: dt=4.032000, rms=0.498 (0.014%), neg=0, invalid=96777 0343: dt=4.032000, rms=0.498 (0.004%), neg=0, invalid=96777 0344: dt=4.032000, rms=0.498 (0.003%), neg=0, invalid=96777 0345: dt=4.032000, rms=0.498 (0.006%), neg=0, invalid=96777 0346: dt=4.032000, rms=0.498 (0.002%), neg=0, invalid=96777 0347: dt=4.032000, rms=0.498 (0.002%), neg=0, invalid=96777 0348: dt=4.032000, rms=0.498 (0.004%), neg=0, invalid=96777 0349: dt=4.032000, rms=0.498 (0.007%), neg=0, invalid=96777 0350: dt=4.032000, rms=0.498 (0.008%), neg=0, invalid=96777 0351: dt=4.032000, rms=0.498 (0.014%), neg=0, invalid=96777 0352: dt=4.032000, rms=0.498 (0.013%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.498, neg=0, invalid=96777 0353: dt=4.285714, rms=0.497 (0.105%), neg=0, invalid=96777 0354: dt=3.456000, rms=0.497 (0.003%), neg=0, invalid=96777 0355: dt=3.456000, rms=0.497 (-0.002%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.516, neg=0, invalid=96777 0356: dt=0.000000, rms=0.516 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.516, neg=0, invalid=96777 0357: dt=0.000000, rms=0.516 (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=0.485, neg=0, invalid=96777 0358: dt=0.112000, rms=0.481 (0.663%), neg=0, invalid=96777 0359: dt=0.028000, rms=0.481 (0.134%), neg=0, invalid=96777 0360: dt=0.130137, rms=0.478 (0.575%), neg=0, invalid=96777 0361: dt=0.028000, rms=0.477 (0.095%), neg=0, invalid=96777 0362: dt=0.116438, rms=0.476 (0.379%), neg=0, invalid=96777 0363: dt=0.112000, rms=0.474 (0.291%), neg=0, invalid=96777 0364: dt=0.112000, rms=0.473 (0.246%), neg=0, invalid=96777 0365: dt=0.028000, rms=0.473 (0.051%), neg=0, invalid=96777 0366: dt=0.112000, rms=0.472 (0.198%), neg=0, invalid=96777 0367: dt=0.020000, rms=0.472 (0.026%), neg=0, invalid=96777 0368: dt=0.020000, rms=0.472 (0.031%), neg=0, invalid=96777 0369: dt=0.020000, rms=0.472 (0.026%), neg=0, invalid=96777 0370: dt=0.020000, rms=0.471 (0.055%), neg=0, invalid=96777 0371: dt=0.020000, rms=0.471 (0.074%), neg=0, invalid=96777 0372: dt=0.020000, rms=0.471 (0.091%), neg=0, invalid=96777 0373: dt=0.010000, rms=0.470 (0.010%), neg=0, invalid=96777 0374: dt=0.005000, rms=0.470 (0.006%), neg=0, invalid=96777 0375: dt=0.007000, rms=0.470 (0.008%), neg=0, invalid=96777 0376: dt=0.112000, rms=0.470 (0.121%), neg=0, invalid=96777 0377: dt=0.028000, rms=0.470 (0.023%), neg=0, invalid=96777 0378: dt=0.014000, rms=0.470 (0.015%), neg=0, invalid=96777 0379: dt=0.014000, rms=0.470 (0.013%), neg=0, invalid=96777 0380: dt=0.014000, rms=0.469 (0.024%), neg=0, invalid=96777 0381: dt=0.014000, rms=0.469 (0.034%), neg=0, invalid=96777 0382: dt=0.014000, rms=0.469 (0.043%), neg=0, invalid=96777 0383: dt=0.014000, rms=0.469 (0.048%), neg=0, invalid=96777 0384: dt=0.014000, rms=0.469 (0.055%), neg=0, invalid=96777 0385: dt=0.014000, rms=0.468 (0.057%), neg=0, invalid=96777 0386: dt=0.014000, rms=0.468 (0.061%), neg=0, invalid=96777 0387: dt=0.014000, rms=0.468 (0.062%), neg=0, invalid=96777 0388: dt=0.014000, rms=0.468 (0.064%), neg=0, invalid=96777 0389: dt=0.014000, rms=0.467 (0.061%), neg=0, invalid=96777 0390: dt=0.014000, rms=0.467 (0.063%), neg=0, invalid=96777 0391: dt=0.014000, rms=0.467 (0.061%), neg=0, invalid=96777 0392: dt=0.014000, rms=0.466 (0.058%), neg=0, invalid=96777 0393: dt=0.014000, rms=0.466 (0.056%), neg=0, invalid=96777 0394: dt=0.014000, rms=0.466 (0.051%), neg=0, invalid=96777 0395: dt=0.014000, rms=0.466 (0.047%), neg=0, invalid=96777 0396: dt=0.014000, rms=0.465 (0.045%), neg=0, invalid=96777 0397: dt=0.014000, rms=0.465 (0.045%), neg=0, invalid=96777 0398: dt=0.014000, rms=0.465 (0.042%), neg=0, invalid=96777 0399: dt=0.014000, rms=0.465 (0.036%), neg=0, invalid=96777 0400: dt=0.014000, rms=0.465 (0.036%), neg=0, invalid=96777 0401: dt=0.014000, rms=0.465 (0.029%), neg=0, invalid=96777 0402: dt=0.007000, rms=0.465 (0.001%), neg=0, invalid=96777 0403: dt=0.007000, rms=0.465 (0.001%), neg=0, invalid=96777 0404: dt=0.007000, rms=0.465 (0.001%), neg=0, invalid=96777 0405: dt=0.028000, rms=0.465 (0.003%), neg=0, invalid=96777 0406: dt=0.028000, rms=0.465 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.465, neg=0, invalid=96777 0407: dt=0.028000, rms=0.464 (0.054%), neg=0, invalid=96777 0408: dt=0.112000, rms=0.463 (0.198%), neg=0, invalid=96777 0409: dt=0.024000, rms=0.463 (0.035%), neg=0, invalid=96777 0410: dt=0.003000, rms=0.463 (0.002%), neg=0, invalid=96777 0411: dt=0.003000, rms=0.463 (0.004%), neg=0, invalid=96777 0412: dt=0.003000, rms=0.463 (0.007%), neg=0, invalid=96777 0413: dt=0.003000, rms=0.463 (0.010%), neg=0, invalid=96777 0414: dt=0.003000, rms=0.463 (0.013%), neg=0, invalid=96777 0415: dt=0.003000, rms=0.463 (0.017%), neg=0, invalid=96777 0416: dt=0.003000, rms=0.463 (0.018%), neg=0, invalid=96777 0417: dt=0.003000, rms=0.463 (0.021%), neg=0, invalid=96777 0418: dt=0.003000, rms=0.463 (0.019%), neg=0, invalid=96777 0419: dt=0.003000, rms=0.463 (0.021%), neg=0, invalid=96777 0420: dt=0.003000, rms=0.463 (0.022%), neg=0, invalid=96777 0421: dt=0.003000, rms=0.462 (0.022%), neg=0, invalid=96777 0422: dt=0.003000, rms=0.462 (0.024%), neg=0, invalid=96777 0423: dt=0.003000, rms=0.462 (0.023%), neg=0, invalid=96777 0424: dt=0.112000, rms=0.462 (0.092%), neg=0, invalid=96777 0425: dt=0.007000, rms=0.462 (0.003%), neg=0, invalid=96777 0426: dt=0.007000, rms=0.462 (0.006%), neg=0, invalid=96777 0427: dt=0.007000, rms=0.462 (0.005%), neg=0, invalid=96777 0428: dt=0.007000, rms=0.462 (0.008%), neg=0, invalid=96777 0429: dt=0.007000, rms=0.462 (0.013%), neg=0, invalid=96777 0430: dt=0.007000, rms=0.462 (0.015%), neg=0, invalid=96777 0431: dt=0.007000, rms=0.461 (0.018%), neg=0, invalid=96777 0432: dt=0.007000, rms=0.461 (0.017%), neg=0, invalid=96777 0433: dt=0.112000, rms=0.461 (0.057%), neg=0, invalid=96777 0434: dt=0.007000, rms=0.461 (0.002%), neg=0, invalid=96777 0435: dt=0.007000, rms=0.461 (0.001%), neg=0, invalid=96777 0436: dt=0.007000, rms=0.461 (0.005%), neg=0, invalid=96777 0437: dt=0.007000, rms=0.461 (0.004%), neg=0, invalid=96777 0438: dt=0.007000, rms=0.461 (0.006%), neg=0, invalid=96777 0439: dt=0.007000, rms=0.461 (0.005%), neg=0, invalid=96777 0440: dt=0.112000, rms=0.461 (0.043%), neg=0, invalid=96777 0441: dt=0.028000, rms=0.461 (0.007%), 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=0.459, neg=0, invalid=96777 0442: dt=0.000000, rms=0.459 (0.001%), neg=0, invalid=96777 0443: dt=0.000000, rms=0.459 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.459, neg=0, invalid=96777 0444: dt=221.952000, rms=0.458 (0.110%), neg=0, invalid=96777 0445: dt=110.976000, rms=0.458 (0.043%), neg=0, invalid=96777 0446: dt=110.976000, rms=0.458 (0.015%), neg=0, invalid=96777 0447: dt=110.976000, rms=0.458 (0.040%), neg=0, invalid=96777 0448: dt=110.976000, rms=0.458 (0.033%), neg=0, invalid=96777 0449: dt=110.976000, rms=0.458 (0.044%), neg=0, invalid=96777 0450: dt=110.976000, rms=0.458 (0.028%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.458, neg=0, invalid=96777 0451: dt=20.736000, rms=0.457 (0.037%), neg=0, invalid=96777 0452: dt=31.104000, rms=0.457 (0.041%), neg=0, invalid=96777 0453: dt=36.288000, rms=0.457 (0.042%), neg=0, invalid=96777 0454: dt=103.680000, rms=0.457 (0.088%), neg=0, invalid=96777 0455: dt=82.944000, rms=0.456 (0.155%), neg=0, invalid=96777 0456: dt=20.736000, rms=0.456 (0.066%), neg=0, invalid=96777 0457: dt=20.736000, rms=0.455 (0.028%), neg=0, invalid=96777 0458: dt=20.736000, rms=0.455 (0.031%), neg=0, invalid=96777 0459: dt=20.736000, rms=0.455 (0.060%), neg=0, invalid=96777 0460: dt=20.736000, rms=0.455 (0.067%), neg=0, invalid=96777 0461: dt=20.736000, rms=0.454 (0.072%), neg=0, invalid=96777 0462: dt=20.736000, rms=0.454 (0.054%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0463: dt=20.736000, rms=0.454 (0.029%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.454, neg=0, invalid=96777 0464: dt=82.944000, rms=0.452 (0.461%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0465: dt=25.920000, rms=0.451 (0.112%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0466: dt=25.920000, rms=0.451 (0.054%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0467: dt=25.920000, rms=0.451 (0.072%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0468: dt=25.920000, rms=0.450 (0.098%), neg=0, invalid=96777 0469: dt=25.920000, rms=0.450 (0.133%), neg=0, invalid=96777 0470: dt=25.920000, rms=0.449 (0.138%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0471: dt=25.920000, rms=0.449 (0.079%), neg=0, invalid=96777 0472: dt=25.920000, rms=0.449 (0.042%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0473: dt=36.288000, rms=0.448 (0.075%), neg=0, invalid=96777 0474: dt=36.288000, rms=0.448 (0.059%), neg=0, invalid=96777 0475: dt=36.288000, rms=0.448 (-0.001%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.449, neg=0, invalid=96777 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0476: dt=11.200000, rms=0.448 (0.179%), neg=0, invalid=96777 iter 0, gcam->neg = 7 after 7 iterations, nbhd size=1, neg = 0 0477: dt=32.000000, rms=0.446 (0.369%), neg=0, invalid=96777 0478: dt=8.000000, rms=0.446 (0.123%), neg=0, invalid=96777 0479: dt=8.000000, rms=0.445 (0.188%), neg=0, invalid=96777 0480: dt=8.000000, rms=0.444 (0.238%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0481: dt=8.000000, rms=0.442 (0.265%), neg=0, invalid=96777 iter 0, gcam->neg = 9 after 2 iterations, nbhd size=0, neg = 0 0482: dt=8.000000, rms=0.441 (0.226%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 11 iterations, nbhd size=1, neg = 0 0483: dt=8.000000, rms=0.440 (0.222%), neg=0, invalid=96777 iter 0, gcam->neg = 8 after 24 iterations, nbhd size=3, neg = 0 0484: dt=8.000000, rms=0.439 (0.244%), neg=0, invalid=96777 iter 0, gcam->neg = 9 after 15 iterations, nbhd size=2, neg = 0 0485: dt=8.000000, rms=0.439 (0.156%), neg=0, invalid=96777 iter 0, gcam->neg = 17 after 12 iterations, nbhd size=1, neg = 0 0486: dt=8.000000, rms=0.438 (0.123%), neg=0, invalid=96777 iter 0, gcam->neg = 25 after 17 iterations, nbhd size=1, neg = 0 0487: dt=8.000000, rms=0.438 (0.134%), neg=0, invalid=96777 iter 0, gcam->neg = 9 after 1 iterations, nbhd size=0, neg = 0 0488: dt=8.000000, rms=0.437 (0.174%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0489: dt=8.000000, rms=0.436 (0.235%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0490: dt=8.000000, rms=0.435 (0.229%), neg=0, invalid=96777 0491: dt=8.000000, rms=0.434 (0.190%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0492: dt=8.000000, rms=0.433 (0.153%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0493: dt=8.000000, rms=0.433 (0.137%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0494: dt=8.000000, rms=0.432 (0.119%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0495: dt=8.000000, rms=0.432 (0.115%), neg=0, invalid=96777 0496: dt=38.400000, rms=0.431 (0.103%), neg=0, invalid=96777 iter 0, gcam->neg = 47 after 100 iterations, nbhd size=1, neg = 0 0497: dt=38.400000, rms=0.431 (-0.297%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.431, neg=0, invalid=96777 iter 0, gcam->neg = 4 after 27 iterations, nbhd size=4, neg = 0 0498: dt=19.200000, rms=0.429 (0.470%), neg=0, invalid=96777 0499: dt=6.620690, rms=0.429 (0.143%), neg=0, invalid=96777 0500: dt=6.620690, rms=0.428 (0.130%), neg=0, invalid=96777 0501: dt=6.620690, rms=0.427 (0.133%), neg=0, invalid=96777 0502: dt=6.620690, rms=0.427 (0.154%), neg=0, invalid=96777 0503: dt=6.620690, rms=0.426 (0.156%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0504: dt=6.620690, rms=0.426 (0.140%), neg=0, invalid=96777 0505: dt=6.620690, rms=0.425 (0.134%), neg=0, invalid=96777 0506: dt=6.620690, rms=0.425 (0.091%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0507: dt=6.620690, rms=0.424 (0.059%), neg=0, invalid=96777 0508: dt=11.200000, rms=0.424 (0.020%), neg=0, invalid=96777 0509: dt=11.200000, rms=0.424 (0.022%), neg=0, invalid=96777 0510: dt=11.200000, rms=0.424 (0.039%), neg=0, invalid=96777 0511: dt=11.200000, rms=0.424 (0.022%), neg=0, invalid=96777 0512: dt=11.200000, rms=0.424 (0.016%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.430, neg=0, invalid=96777 0513: dt=0.000141, rms=0.430 (0.004%), neg=0, invalid=96777 0514: dt=0.000000, rms=0.430 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.430, neg=0, invalid=96777 0515: dt=4.032000, rms=0.430 (0.075%), neg=0, invalid=96777 0516: dt=4.032000, rms=0.430 (0.043%), neg=0, invalid=96777 0517: dt=4.032000, rms=0.430 (-0.024%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.439, neg=0, invalid=96777 0518: dt=0.320000, rms=0.439 (0.014%), neg=0, invalid=96777 0519: dt=0.384000, rms=0.439 (0.012%), neg=0, invalid=96777 0520: dt=0.384000, rms=0.439 (-0.006%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.439, neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0521: dt=1.792000, rms=0.438 (0.211%), neg=0, invalid=96777 0522: dt=0.028000, rms=0.438 (0.009%), neg=0, invalid=96777 0523: dt=0.028000, rms=0.438 (0.001%), neg=0, invalid=96777 0524: dt=0.028000, rms=0.438 (0.001%), neg=0, invalid=96777 0525: dt=0.028000, rms=0.438 (0.002%), neg=0, invalid=96777 0526: dt=0.028000, rms=0.438 (0.003%), neg=0, invalid=96777 0527: dt=0.028000, rms=0.438 (-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=0.428, neg=0, invalid=96777 iter 0, gcam->neg = 471 after 18 iterations, nbhd size=2, neg = 0 0528: dt=1.509356, rms=0.406 (5.153%), neg=0, invalid=96777 0529: dt=0.000375, rms=0.406 (-0.005%), neg=0, invalid=96777 0530: dt=0.000375, rms=0.406 (0.001%), neg=0, invalid=96777 0531: dt=0.000375, rms=0.406 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.406, neg=0, invalid=96777 0532: dt=0.000438, rms=0.406 (0.000%), neg=0, invalid=96777 0533: dt=0.000000, rms=0.406 (0.001%), neg=0, invalid=96777 0534: dt=0.000000, rms=0.406 (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=0.398, neg=0, invalid=96777 0535: dt=0.000000, rms=0.398 (-0.194%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.398, neg=0, invalid=96777 0536: dt=73.984000, rms=0.398 (0.022%), neg=0, invalid=96777 0537: dt=129.472000, rms=0.398 (0.014%), neg=0, invalid=96777 0538: dt=129.472000, rms=0.398 (-0.006%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.398, neg=0, invalid=96777 0539: dt=0.000000, rms=0.398 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.398, neg=0, invalid=96777 0540: dt=62.208000, rms=0.398 (0.054%), neg=0, invalid=96777 iter 0, gcam->neg = 5 after 1 iterations, nbhd size=0, neg = 0 0541: dt=103.680000, rms=0.398 (0.052%), neg=0, invalid=96777 0542: dt=103.680000, rms=0.398 (0.039%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 12 iterations, nbhd size=2, neg = 0 0543: dt=103.680000, rms=0.398 (-0.023%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.398, neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0544: dt=8.000000, rms=0.398 (0.069%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0545: dt=6.400000, rms=0.398 (0.016%), neg=0, invalid=96777 iter 0, gcam->neg = 8 after 10 iterations, nbhd size=1, neg = 0 0546: dt=6.400000, rms=0.398 (0.000%), neg=0, invalid=96777 iter 0, gcam->neg = 12 after 9 iterations, nbhd size=1, neg = 0 0547: dt=6.400000, rms=0.398 (-0.039%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.398, neg=0, invalid=96777 iter 0, gcam->neg = 26 after 11 iterations, nbhd size=1, neg = 0 0548: dt=25.600000, rms=0.396 (0.438%), neg=0, invalid=96777 iter 0, gcam->neg = 7 after 6 iterations, nbhd size=1, neg = 0 0549: dt=11.200000, rms=0.395 (0.179%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 6 iterations, nbhd size=1, neg = 0 0550: dt=11.200000, rms=0.395 (0.108%), neg=0, invalid=96777 iter 0, gcam->neg = 7 after 1 iterations, nbhd size=0, neg = 0 0551: dt=11.200000, rms=0.394 (0.152%), neg=0, invalid=96777 iter 0, gcam->neg = 9 after 24 iterations, nbhd size=3, neg = 0 0552: dt=11.200000, rms=0.393 (0.222%), neg=0, invalid=96777 iter 0, gcam->neg = 8 after 22 iterations, nbhd size=3, neg = 0 0553: dt=11.200000, rms=0.393 (0.190%), neg=0, invalid=96777 iter 0, gcam->neg = 18 after 31 iterations, nbhd size=1, neg = 0 0554: dt=11.200000, rms=0.392 (0.155%), neg=0, invalid=96777 iter 0, gcam->neg = 14 after 51 iterations, nbhd size=3, neg = 0 0555: dt=11.200000, rms=0.391 (0.164%), neg=0, invalid=96777 iter 0, gcam->neg = 13 after 200 iterations, nbhd size=4, neg = 1 starting rms=0.003, neg=1, removing folds in lattice.... iter 1, dt=0.000188: new neg 0, old_neg 1, delta 1, rms=0.003 (15.782%) 0556: dt=11.200000, rms=0.391 (0.117%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 200 iterations, nbhd size=1, neg = 1 starting rms=0.003, neg=1, removing folds in lattice.... iter 1, dt=0.000156: new neg 0, old_neg 1, delta 1, rms=0.002 (9.405%) 0557: dt=11.200000, rms=0.390 (0.116%), neg=0, invalid=96777 iter 0, gcam->neg = 8 after 16 iterations, nbhd size=2, neg = 0 0558: dt=38.400000, rms=0.390 (0.149%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0559: dt=11.200000, rms=0.390 (0.051%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 7 iterations, nbhd size=1, neg = 0 0560: dt=11.200000, rms=0.389 (0.042%), neg=0, invalid=96777 iter 0, gcam->neg = 10 after 10 iterations, nbhd size=1, neg = 0 0561: dt=11.200000, rms=0.389 (0.040%), neg=0, invalid=96777 iter 0, gcam->neg = 16 after 10 iterations, nbhd size=1, neg = 0 0562: dt=11.200000, rms=0.389 (0.053%), neg=0, invalid=96777 iter 0, gcam->neg = 10 after 200 iterations, nbhd size=4, neg = 1 starting rms=0.003, neg=1, removing folds in lattice.... iter 1, dt=0.000219: new neg 0, old_neg 1, delta 1, rms=0.002 (15.193%) 0563: dt=11.200000, rms=0.389 (-0.069%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.392, neg=0, invalid=96777 iter 0, gcam->neg = 3 after 9 iterations, nbhd size=1, neg = 0 0564: dt=1.008000, rms=0.392 (0.022%), neg=0, invalid=96777 iter 0, gcam->neg = 8 after 16 iterations, nbhd size=2, neg = 0 0565: dt=2.304000, rms=0.391 (0.023%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0566: dt=1.008000, rms=0.391 (0.006%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0567: dt=1.008000, rms=0.391 (0.007%), neg=0, invalid=96777 0568: dt=1.008000, rms=0.391 (0.001%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0569: dt=1.008000, rms=0.391 (-0.018%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.391, neg=0, invalid=96777 iter 0, gcam->neg = 40 after 16 iterations, nbhd size=1, neg = 0 0570: dt=4.500000, rms=0.390 (0.248%), neg=0, invalid=96777 iter 0, gcam->neg = 7 after 10 iterations, nbhd size=1, neg = 0 0571: dt=1.743590, rms=0.390 (0.043%), neg=0, invalid=96777 iter 0, gcam->neg = 7 after 10 iterations, nbhd size=1, neg = 0 0572: dt=1.743590, rms=0.390 (0.057%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 9 iterations, nbhd size=1, neg = 0 0573: dt=1.743590, rms=0.390 (0.088%), neg=0, invalid=96777 iter 0, gcam->neg = 9 after 18 iterations, nbhd size=2, neg = 0 0574: dt=1.743590, rms=0.389 (0.092%), neg=0, invalid=96777 iter 0, gcam->neg = 20 after 18 iterations, nbhd size=2, neg = 0 0575: dt=1.743590, rms=0.389 (0.068%), neg=0, invalid=96777 iter 0, gcam->neg = 16 after 21 iterations, nbhd size=2, neg = 0 0576: dt=1.743590, rms=0.389 (0.069%), neg=0, invalid=96777 iter 0, gcam->neg = 19 after 17 iterations, nbhd size=2, neg = 0 0577: dt=1.743590, rms=0.389 (0.070%), neg=0, invalid=96777 iter 0, gcam->neg = 24 after 14 iterations, nbhd size=1, neg = 0 0578: dt=1.743590, rms=0.388 (0.069%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.393, neg=0, invalid=96777 0579: dt=0.000000, rms=0.393 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.393, neg=0, invalid=96777 0580: dt=0.000000, rms=0.393 (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=0.385, neg=0, invalid=96777 iter 0, gcam->neg = 331 after 31 iterations, nbhd size=3, neg = 0 0581: dt=0.689394, rms=0.377 (2.156%), neg=0, invalid=96777 0582: dt=0.000750, rms=0.377 (0.000%), neg=0, invalid=96777 0583: dt=0.000750, rms=0.377 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.377, neg=0, invalid=96777 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0584: dt=0.001500, rms=0.377 (0.002%), neg=0, invalid=96777 0585: dt=0.001750, rms=0.377 (0.002%), neg=0, invalid=96777 0586: dt=0.001750, rms=0.377 (0.002%), neg=0, invalid=96777 0587: dt=0.001750, rms=0.377 (0.003%), neg=0, invalid=96777 0588: dt=0.001750, rms=0.377 (0.004%), neg=0, invalid=96777 0589: dt=0.001750, rms=0.377 (0.004%), neg=0, invalid=96777 0590: dt=0.001750, rms=0.377 (0.005%), neg=0, invalid=96777 0591: dt=0.001750, rms=0.377 (0.006%), neg=0, invalid=96777 0592: dt=0.001750, rms=0.377 (0.007%), neg=0, invalid=96777 0593: dt=0.001750, rms=0.377 (0.007%), neg=0, invalid=96777 0594: dt=0.001750, rms=0.377 (0.008%), neg=0, invalid=96777 0595: dt=0.001750, rms=0.377 (0.008%), neg=0, invalid=96777 0596: dt=0.001750, rms=0.377 (0.008%), neg=0, invalid=96777 0597: dt=0.001750, rms=0.377 (0.008%), neg=0, invalid=96777 0598: dt=0.001750, rms=0.377 (0.008%), neg=0, invalid=96777 0599: dt=0.001750, rms=0.377 (0.008%), neg=0, invalid=96777 0600: dt=0.001750, rms=0.377 (0.008%), neg=0, invalid=96777 0601: dt=0.001750, rms=0.377 (0.008%), neg=0, invalid=96777 writing output transformation to transforms/talairach.m3z... GCAMwrite registration took 4 hours, 14 minutes and 12 seconds. #-------------------------------------- #@# CA Reg Inv Wed Aug 7 01:56:48 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri \n mri_ca_register -invert-and-save transforms/talairach.m3z \n Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Wed Aug 7 01:58:04 BRT 2013 \n mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /Applications/Freesurfer5.3/freesurfer/average/RB_all_2008-03-26.gca nu_noneck.mgz \n erasing everything more than 25 mm from possible brain reading atlas '/Applications/Freesurfer5.3/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... 11097075 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 1 minutes and 26 seconds. #-------------------------------------- #@# SkullLTA Wed Aug 7 01:59:30 BRT 2013 \n mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /Applications/Freesurfer5.3/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta \n 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 '/Applications/Freesurfer5.3/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=7.0 skull bounding box = (47, 29, 13) --> (205, 200, 214) using (100, 86, 114) as brain centroid... mean wm in atlas = 126, using box (81,65,89) --> (119, 107,138) to find MRI wm before smoothing, mri peak at 107 after smoothing, mri peak at 107, scaling input intensities by 1.178 scaling channel 0 by 1.17757 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.9, old_max_log_p =-4.0 (thresh=-4.0) 1.042 0.061 -0.126 -0.166; -0.065 1.317 0.003 -9.814; 0.122 0.005 1.064 -30.434; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.042 0.061 -0.126 -0.166; -0.065 1.317 0.003 -9.814; 0.122 0.005 1.064 -30.434; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.038 0.021 -0.160 8.389; -0.025 1.269 0.031 -13.047; 0.154 -0.035 1.019 -25.175; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.038 0.021 -0.160 8.389; -0.015 1.264 0.097 -21.341; 0.155 -0.118 1.015 -16.120; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.038 0.039 -0.133 3.011; -0.033 1.267 0.092 -19.113; 0.130 -0.108 1.020 -13.563; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.038 0.039 -0.133 3.011; -0.033 1.267 0.092 -19.113; 0.129 -0.108 1.019 -13.423; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3481 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.03785 0.03893 -0.13322 3.01074; -0.03330 1.26725 0.09163 -19.11323; 0.12943 -0.10764 1.01908 -13.42293; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.03785 0.03893 -0.13322 3.01074; -0.03330 1.26725 0.09163 -19.11323; 0.12943 -0.10764 1.01908 -13.42293; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 007: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.038 0.039 -0.133 3.011; -0.033 1.267 0.092 -19.113; 0.129 -0.108 1.019 -13.423; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.9 (old=-4.0) transform before final EM align: 1.038 0.039 -0.133 3.011; -0.033 1.267 0.092 -19.113; 0.129 -0.108 1.019 -13.423; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 382743 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.03785 0.03893 -0.13322 3.01074; -0.03330 1.26725 0.09163 -19.11323; 0.12943 -0.10764 1.01908 -13.42293; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.03785 0.03893 -0.13322 3.01074; -0.03330 1.26725 0.09163 -19.11323; 0.12943 -0.10764 1.01908 -13.42293; 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: 009: -log(p) = 4.3 tol 0.000000 final transform: 1.038 0.039 -0.133 3.011; -0.033 1.267 0.092 -19.113; 0.129 -0.108 1.019 -13.423; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull_2.lta... registration took 32 minutes and 0 seconds. #-------------------------------------- #@# SubCort Seg Wed Aug 7 02:31:30 BRT 2013 \n mri_ca_label -align norm.mgz transforms/talairach.m3z /Applications/Freesurfer5.3/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz \n sysname Darwin hostname Pedro-Rosas-MacBook-Pro-2.local machine x86_64 setenv SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 cd /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri mri_ca_label -align norm.mgz transforms/talairach.m3z /Applications/Freesurfer5.3/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 /Applications/Freesurfer5.3/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 /Applications/Freesurfer5.3/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 = 0.12037 (11) Left_Lateral_Ventricle (4): linear fit = 0.41 x + 0.0 (103 voxels, overlap=0.765) Left_Lateral_Ventricle (4): linear fit = 0.41 x + 0.0 (103 voxels, peak = 11), gca=11.2 gca peak = 0.14982 (20) mri peak = 0.09493 (11) Right_Lateral_Ventricle (43): linear fit = 0.46 x + 0.0 (127 voxels, overlap=0.059) Right_Lateral_Ventricle (43): linear fit = 0.46 x + 0.0 (127 voxels, peak = 9), gca=9.1 gca peak = 0.28003 (97) mri peak = 0.15134 (100) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (337 voxels, overlap=1.016) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (337 voxels, peak = 99), gca=99.4 gca peak = 0.18160 (96) mri peak = 0.13264 (103) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (275 voxels, overlap=1.013) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (275 voxels, peak = 97), gca=97.4 gca peak = 0.27536 (62) mri peak = 0.09235 (67) Right_Hippocampus (53): linear fit = 1.08 x + 0.0 (1098 voxels, overlap=0.828) Right_Hippocampus (53): linear fit = 1.08 x + 0.0 (1098 voxels, peak = 67), gca=66.7 gca peak = 0.32745 (63) mri peak = 0.08696 (67) Left_Hippocampus (17): linear fit = 1.05 x + 0.0 (936 voxels, overlap=1.010) Left_Hippocampus (17): linear fit = 1.05 x + 0.0 (936 voxels, peak = 66), gca=66.5 gca peak = 0.08597 (105) mri peak = 0.14090 (107) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (48326 voxels, overlap=0.598) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (48326 voxels, peak = 107), gca=106.6 gca peak = 0.09209 (106) mri peak = 0.12300 (108) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (53529 voxels, overlap=0.613) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (53529 voxels, peak = 108), gca=107.6 gca peak = 0.07826 (63) mri peak = 0.03770 (68) Left_Cerebral_Cortex (3): linear fit = 1.08 x + 0.0 (30384 voxels, overlap=0.827) Left_Cerebral_Cortex (3): linear fit = 1.08 x + 0.0 (30384 voxels, peak = 68), gca=67.7 gca peak = 0.08598 (64) mri peak = 0.04000 (67) Right_Cerebral_Cortex (42): linear fit = 1.05 x + 0.0 (29677 voxels, overlap=0.838) Right_Cerebral_Cortex (42): linear fit = 1.05 x + 0.0 (29677 voxels, peak = 68), gca=67.5 gca peak = 0.24164 (71) mri peak = 0.13248 (80) Right_Caudate (50): linear fit = 1.11 x + 0.0 (466 voxels, overlap=0.012) Right_Caudate (50): linear fit = 1.11 x + 0.0 (466 voxels, peak = 78), gca=78.5 gca peak = 0.18227 (75) mri peak = 0.12324 (85) Left_Caudate (11): linear fit = 1.07 x + 0.0 (641 voxels, overlap=0.572) Left_Caudate (11): linear fit = 1.07 x + 0.0 (641 voxels, peak = 80), gca=79.9 gca peak = 0.10629 (62) mri peak = 0.05494 (67) Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (31330 voxels, overlap=0.717) Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (31330 voxels, peak = 70), gca=70.4 gca peak = 0.11668 (59) mri peak = 0.05751 (68) Right_Cerebellum_Cortex (47): linear fit = 1.15 x + 0.0 (28904 voxels, overlap=0.658) Right_Cerebellum_Cortex (47): linear fit = 1.15 x + 0.0 (28904 voxels, peak = 68), gca=68.1 gca peak = 0.17849 (88) mri peak = 0.12909 (92) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (6529 voxels, overlap=0.721) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (6529 voxels, peak = 91), gca=91.1 gca peak = 0.16819 (86) mri peak = 0.12637 (92) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (5919 voxels, overlap=0.724) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (5919 voxels, peak = 91), gca=90.7 gca peak = 0.41688 (64) mri peak = 0.12870 (71) Left_Amygdala (18): linear fit = 1.10 x + 0.0 (282 voxels, overlap=0.945) Left_Amygdala (18): linear fit = 1.10 x + 0.0 (282 voxels, peak = 70), gca=70.1 gca peak = 0.42394 (62) mri peak = 0.11321 (65) Right_Amygdala (54): linear fit = 1.05 x + 0.0 (288 voxels, overlap=1.026) Right_Amygdala (54): linear fit = 1.05 x + 0.0 (288 voxels, peak = 65), gca=65.4 gca peak = 0.10041 (96) mri peak = 0.09056 (99) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (3865 voxels, overlap=0.591) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (3865 voxels, peak = 102), gca=102.2 gca peak = 0.13978 (88) mri peak = 0.08145 (98) Right_Thalamus_Proper (49): linear fit = 1.09 x + 0.0 (3770 voxels, overlap=0.674) Right_Thalamus_Proper (49): linear fit = 1.09 x + 0.0 (3770 voxels, peak = 95), gca=95.5 gca peak = 0.08514 (81) mri peak = 0.06448 (94) Left_Putamen (12): linear fit = 1.09 x + 0.0 (2045 voxels, overlap=0.742) Left_Putamen (12): linear fit = 1.09 x + 0.0 (2045 voxels, peak = 88), gca=87.9 gca peak = 0.09624 (82) mri peak = 0.07909 (88) Right_Putamen (51): linear fit = 1.09 x + 0.0 (1663 voxels, overlap=0.694) Right_Putamen (51): linear fit = 1.09 x + 0.0 (1663 voxels, peak = 89), gca=89.0 gca peak = 0.07543 (88) mri peak = 0.07113 (90) Brain_Stem (16): linear fit = 1.05 x + 0.0 (12015 voxels, overlap=0.687) Brain_Stem (16): linear fit = 1.05 x + 0.0 (12015 voxels, peak = 93), gca=92.8 gca peak = 0.12757 (95) mri peak = 0.09849 (104) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (1159 voxels, overlap=0.520) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (1159 voxels, peak = 102), gca=102.1 gca peak = 0.17004 (92) mri peak = 0.09859 (105) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1320 voxels, overlap=0.699) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1320 voxels, peak = 100), gca=99.8 gca peak = 0.21361 (36) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.26069 (23) mri peak = 0.18824 (12) Fourth_Ventricle (15): linear fit = 0.47 x + 0.0 (85 voxels, overlap=0.018) Fourth_Ventricle (15): linear fit = 0.47 x + 0.0 (85 voxels, peak = 11), gca=10.9 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak Third_Ventricle = 0.21361 (36) gca peak Fourth_Ventricle = 0.26069 (23) gca peak CSF = 0.14367 (38) gca peak Left_Accumbens_area = 0.57033 (70) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65201 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.31129 (32) gca peak Right_Accumbens_area = 0.30219 (72) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.72939 (42) gca peak WM_hypointensities = 0.14821 (82) gca peak non_WM_hypointensities = 0.10354 (53) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.07 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 0.44 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.30620 (11) mri peak = 0.12037 (11) Left_Lateral_Ventricle (4): linear fit = 1.04 x + 0.0 (103 voxels, overlap=0.974) Left_Lateral_Ventricle (4): linear fit = 1.04 x + 0.0 (103 voxels, peak = 11), gca=11.5 gca peak = 0.26211 (10) mri peak = 0.09493 (11) Right_Lateral_Ventricle (43): linear fit = 1.04 x + 0.0 (127 voxels, overlap=0.902) Right_Lateral_Ventricle (43): linear fit = 1.04 x + 0.0 (127 voxels, peak = 10), gca=10.4 gca peak = 0.30362 (100) mri peak = 0.15134 (100) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (337 voxels, overlap=1.006) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (337 voxels, peak = 100), gca=100.5 gca peak = 0.16493 (97) mri peak = 0.13264 (103) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (275 voxels, overlap=1.003) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (275 voxels, peak = 97), gca=97.5 gca peak = 0.27600 (67) mri peak = 0.09235 (67) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1098 voxels, overlap=1.003) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1098 voxels, peak = 67), gca=67.0 gca peak = 0.25221 (66) mri peak = 0.08696 (67) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (936 voxels, overlap=1.008) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (936 voxels, peak = 66), gca=66.0 gca peak = 0.08542 (107) mri peak = 0.14090 (107) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (48326 voxels, overlap=0.631) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (48326 voxels, peak = 108), gca=107.5 gca peak = 0.08742 (107) mri peak = 0.12300 (108) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (53529 voxels, overlap=0.670) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (53529 voxels, peak = 107), gca=107.0 gca peak = 0.07176 (68) mri peak = 0.03770 (68) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (30384 voxels, overlap=0.862) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (30384 voxels, peak = 67), gca=67.0 gca peak = 0.08496 (67) mri peak = 0.04000 (67) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (29677 voxels, overlap=0.906) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (29677 voxels, peak = 66), gca=66.0 gca peak = 0.21521 (78) mri peak = 0.13248 (80) Right_Caudate (50): linear fit = 0.99 x + 0.0 (466 voxels, overlap=1.000) Right_Caudate (50): linear fit = 0.99 x + 0.0 (466 voxels, peak = 77), gca=76.8 gca peak = 0.18179 (80) mri peak = 0.12324 (85) Left_Caudate (11): linear fit = 1.00 x + 0.0 (641 voxels, overlap=0.911) Left_Caudate (11): linear fit = 1.00 x + 0.0 (641 voxels, peak = 80), gca=80.0 gca peak = 0.09356 (69) mri peak = 0.05494 (67) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (31330 voxels, overlap=0.989) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (31330 voxels, peak = 68), gca=68.0 gca peak = 0.10901 (69) mri peak = 0.05751 (68) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (28904 voxels, overlap=0.980) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (28904 voxels, peak = 68), gca=68.0 gca peak = 0.16914 (91) mri peak = 0.12909 (92) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6529 voxels, overlap=0.916) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6529 voxels, peak = 91), gca=90.5 gca peak = 0.16436 (91) mri peak = 0.12637 (92) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5919 voxels, overlap=0.973) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5919 voxels, peak = 91), gca=90.5 gca peak = 0.35476 (70) mri peak = 0.12870 (71) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (282 voxels, overlap=1.018) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (282 voxels, peak = 70), gca=70.0 gca peak = 0.38452 (66) mri peak = 0.11321 (65) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (288 voxels, overlap=1.027) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (288 voxels, peak = 66), gca=66.0 gca peak = 0.11091 (102) mri peak = 0.09056 (99) Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (3865 voxels, overlap=0.895) Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (3865 voxels, peak = 100), gca=100.5 gca peak = 0.11571 (95) mri peak = 0.08145 (98) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (3770 voxels, overlap=0.907) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (3770 voxels, peak = 96), gca=96.4 gca peak = 0.07857 (88) mri peak = 0.06448 (94) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2045 voxels, overlap=0.971) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2045 voxels, peak = 88), gca=87.6 gca peak = 0.10053 (82) mri peak = 0.07909 (88) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1663 voxels, overlap=0.911) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1663 voxels, peak = 81), gca=80.8 gca peak = 0.06919 (93) mri peak = 0.07113 (90) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12015 voxels, overlap=0.801) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12015 voxels, peak = 93), gca=93.0 gca peak = 0.12765 (98) mri peak = 0.09849 (104) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1159 voxels, overlap=0.817) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1159 voxels, peak = 98), gca=98.0 gca peak = 0.16251 (100) mri peak = 0.09859 (105) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1320 voxels, overlap=0.839) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1320 voxels, peak = 100), gca=100.5 gca peak = 0.29232 (16) gca peak = 0.39337 (10) mri peak = 0.18824 (12) Fourth_Ventricle (15): linear fit = 1.14 x + 0.0 (85 voxels, overlap=0.894) Fourth_Ventricle (15): linear fit = 1.14 x + 0.0 (85 voxels, peak = 11), gca=11.4 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.30831 (37) gca peak Third_Ventricle = 0.29232 (16) gca peak CSF = 0.26364 (20) gca peak Left_Accumbens_area = 0.43964 (74) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65148 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.32704 (34) gca peak Right_Accumbens_area = 0.26084 (79) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.46192 (20) gca peak WM_hypointensities = 0.17532 (83) gca peak non_WM_hypointensities = 0.10249 (54) gca peak Optic_Chiasm = 0.34847 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.08 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 25255 gm and wm labels changed (%20 to gray, %80 to white out of all changed labels) 515 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 72618 changed. image ll: -2.154, PF=1.000 pass 2: 11086 changed. image ll: -2.152, PF=1.000 pass 3: 3721 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 25 minutes and 39 seconds. \n mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/transforms/cc_up.lta subjects_name_ \n will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/transforms/cc_up.lta reading aseg from /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/aseg.auto_noCCseg.mgz reading norm from /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/norm.mgz 84524 voxels in left wm, 134386 in right wm, xrange [115, 138] searching rotation angles z=[-10 4], y=[-14 -0] searching scale 1 Z rot -10.0 searching scale 1 Z rot -9.8 searching scale 1 Z rot -9.5 searching scale 1 Z rot -9.3 searching scale 1 Z rot -9.0 searching scale 1 Z rot -8.8 searching scale 1 Z rot -8.5 searching scale 1 Z rot -8.3 searching scale 1 Z rot -8.0 searching scale 1 Z rot -7.8 searching scale 1 Z rot -7.5 searching scale 1 Z rot -7.3 searching scale 1 Z rot -7.0 searching scale 1 Z rot -6.8 searching scale 1 Z rot -6.5 searching scale 1 Z rot -6.3 searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.8 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.3 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.8 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.3 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.8 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.3 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.8 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.3 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.8 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.3 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.8 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.3 searching scale 1 Z rot -0.0 searching scale 1 Z rot 0.2 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.7 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.2 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.7 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.2 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.7 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.2 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.7 global minimum found at slice 128.5, rotations (-7.01, -3.02) final transformation (x=128.5, yr=-7.010, zr=-3.022): 0.991 0.053 -0.122 9.622; -0.052 0.999 0.006 46.127; 0.122 0.000 0.993 1.151; 0.000 0.000 0.000 1.000; updating x range to be [126, 131] in xformed coordinates best xformed slice 129 cc center is found at 129 149 169 eigenvectors: -0.001 -0.003 1.000; 0.032 -0.999 -0.003; 0.999 0.032 0.001; error in mid anterior detected - correcting... error in mid anterior detected - correcting... writing aseg with callosum to /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/aseg.auto.mgz... corpus callosum matter segmentation took 3.0 minutes #-------------------------------------- #@# Merge ASeg Wed Aug 7 03:00:10 BRT 2013 \n cp aseg.auto.mgz aseg.mgz \n #-------------------------------------------- #@# Intensity Normalization2 Wed Aug 7 03:00:11 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri \n mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz \n 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... 2156 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 73 (73), valley at 33 (33) csf peak at 11, setting threshold to 52 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 75 (75), valley at 33 (33) csf peak at 11, setting threshold to 53 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 4 minutes and 35 seconds. #-------------------------------------------- #@# Mask BFS Wed Aug 7 03:04:49 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri \n mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz \n threshold mask volume at 5 DoAbs = 0 Found 1667659 voxels in mask (pct= 9.94) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Wed Aug 7 03:04:52 BRT 2013 \n mri_segment brain.mgz wm.seg.mgz \n doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (103.0): 102.9 +- 6.7 [80.0 --> 125.0] GM (75.0) : 73.7 +- 9.6 [30.0 --> 96.0] setting bottom of white matter range to 83.3 setting top of gray matter range to 93.0 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... 3657 sparsely connected voxels removed... thickening thin strands.... 20 segments, 2988 filled 804 bright non-wm voxels segmented. 1668 diagonally connected voxels added... white matter segmentation took 2.1 minutes writing output to wm.seg.mgz... \n mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz \n preserving editing changes in input volume... auto filling took 0.92 minutes reading wm segmentation from wm.seg.mgz... 283 voxels added to wm to prevent paths from MTL structures to cortex 2296 additional wm voxels added 0 additional wm voxels added SEG EDIT: 27775 voxels turned on, 51630 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.... \n mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz \n Iteration Number : 1 pass 1 (xy+): 26 found - 26 modified | TOTAL: 26 pass 2 (xy+): 0 found - 26 modified | TOTAL: 26 pass 1 (xy-): 27 found - 27 modified | TOTAL: 53 pass 2 (xy-): 0 found - 27 modified | TOTAL: 53 pass 1 (yz+): 14 found - 14 modified | TOTAL: 67 pass 2 (yz+): 0 found - 14 modified | TOTAL: 67 pass 1 (yz-): 25 found - 25 modified | TOTAL: 92 pass 2 (yz-): 0 found - 25 modified | TOTAL: 92 pass 1 (xz+): 23 found - 23 modified | TOTAL: 115 pass 2 (xz+): 0 found - 23 modified | TOTAL: 115 pass 1 (xz-): 14 found - 14 modified | TOTAL: 129 pass 2 (xz-): 0 found - 14 modified | TOTAL: 129 Iteration Number : 1 pass 1 (+++): 14 found - 14 modified | TOTAL: 14 pass 2 (+++): 0 found - 14 modified | TOTAL: 14 pass 1 (+++): 19 found - 19 modified | TOTAL: 33 pass 2 (+++): 0 found - 19 modified | TOTAL: 33 pass 1 (+++): 10 found - 10 modified | TOTAL: 43 pass 2 (+++): 0 found - 10 modified | TOTAL: 43 pass 1 (+++): 13 found - 13 modified | TOTAL: 56 pass 2 (+++): 0 found - 13 modified | TOTAL: 56 Iteration Number : 1 pass 1 (++): 39 found - 39 modified | TOTAL: 39 pass 2 (++): 0 found - 39 modified | TOTAL: 39 pass 1 (+-): 26 found - 26 modified | TOTAL: 65 pass 2 (+-): 0 found - 26 modified | TOTAL: 65 pass 1 (--): 30 found - 30 modified | TOTAL: 95 pass 2 (--): 0 found - 30 modified | TOTAL: 95 pass 1 (-+): 32 found - 32 modified | TOTAL: 127 pass 2 (-+): 0 found - 32 modified | TOTAL: 127 Iteration Number : 2 pass 1 (xy+): 8 found - 8 modified | TOTAL: 8 pass 2 (xy+): 0 found - 8 modified | TOTAL: 8 pass 1 (xy-): 4 found - 4 modified | TOTAL: 12 pass 2 (xy-): 0 found - 4 modified | TOTAL: 12 pass 1 (yz+): 2 found - 2 modified | TOTAL: 14 pass 2 (yz+): 0 found - 2 modified | TOTAL: 14 pass 1 (yz-): 1 found - 1 modified | TOTAL: 15 pass 2 (yz-): 0 found - 1 modified | TOTAL: 15 pass 1 (xz+): 2 found - 2 modified | TOTAL: 17 pass 2 (xz+): 0 found - 2 modified | TOTAL: 17 pass 1 (xz-): 0 found - 0 modified | TOTAL: 17 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 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 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 332 (out of 610175: 0.054411) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Wed Aug 7 03:07:59 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri \n mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz \n 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 1.042 0.061 -0.126 -0.166; -0.057 1.146 0.002 7.263; 0.114 0.005 0.990 -20.913; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.042 0.061 -0.126 -0.166; -0.057 1.146 0.002 7.263; 0.114 0.005 0.990 -20.913; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1279 (min = 350, max = 1400), aspect = 0.52 (min = 0.10, max = 0.75) no need to search using seed (126, 115, 145), TAL = (2.0, 17.0, 13.0) talairach voxel to voxel transform 0.944 -0.051 0.120 3.033; 0.047 0.870 0.004 -6.234; -0.109 0.002 0.996 20.808; 0.000 0.000 0.000 1.000; segmentation indicates cc at (126, 115, 145) --> (2.0, 17.0, 13.0) done. writing output to filled.mgz... filling took 1.0 minutes talairach cc position changed to (2.00, 17.00, 13.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, 17.00, 13.00) SRC: (116.57, 99.49, 153.73) search lh wm seed point around talairach space (-16.00, 17.00, 13.00), SRC: (150.57, 101.18, 149.81) 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 Wed Aug 7 03:09:02 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/scripts \n mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz \n Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 2 found - 2 modified | TOTAL: 3 pass 2 (yz-): 0 found - 2 modified | TOTAL: 3 pass 1 (xz+): 1 found - 1 modified | TOTAL: 4 pass 2 (xz+): 0 found - 1 modified | TOTAL: 4 pass 1 (xz-): 0 found - 0 modified | TOTAL: 4 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 1 found - 1 modified | TOTAL: 2 pass 2 (-+): 0 found - 1 modified | TOTAL: 2 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 6 (out of 296928: 0.002021) Ambiguous edge configurations... mri_pretess done \n mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix \n $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 30: 700 vertices, 797 faces slice 40: 5882 vertices, 6087 faces slice 50: 13851 vertices, 14135 faces slice 60: 22848 vertices, 23166 faces slice 70: 33146 vertices, 33492 faces slice 80: 43737 vertices, 44074 faces slice 90: 54034 vertices, 54408 faces slice 100: 66432 vertices, 66820 faces slice 110: 78729 vertices, 79142 faces slice 120: 90641 vertices, 91085 faces slice 130: 101554 vertices, 101942 faces slice 140: 111288 vertices, 111623 faces slice 150: 119503 vertices, 119802 faces slice 160: 126888 vertices, 127169 faces slice 170: 133232 vertices, 133453 faces slice 180: 138554 vertices, 138742 faces slice 190: 142351 vertices, 142448 faces slice 200: 142876 vertices, 142896 faces slice 210: 142876 vertices, 142896 faces slice 220: 142876 vertices, 142896 faces slice 230: 142876 vertices, 142896 faces slice 240: 142876 vertices, 142896 faces slice 250: 142876 vertices, 142896 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; \n rm -f ../mri/filled-pretess255.mgz \n \n mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix \n counting number of connected components... 142876 voxel in cpt #1: X=-20 [v=142876,e=428688,f=285792] located at (-26.859158, -23.778374, 29.342899) For the whole surface: X=-20 [v=142876,e=428688,f=285792] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Wed Aug 7 03:09:12 BRT 2013 \n mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix \n /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/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 Wed Aug 7 03:09:19 BRT 2013 \n mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix \n /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/scripts avg radius = 47.8 mm, total surface area = 76484 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.5 minutes Not saving sulc step 000: RMS=0.096 (target=0.015) step 005: RMS=0.071 (target=0.015) step 010: RMS=0.052 (target=0.015) step 015: RMS=0.043 (target=0.015) step 020: RMS=0.037 (target=0.015) step 025: RMS=0.034 (target=0.015) step 030: RMS=0.030 (target=0.015) step 035: RMS=0.027 (target=0.015) step 040: RMS=0.026 (target=0.015) step 045: RMS=0.024 (target=0.015) step 050: RMS=0.023 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.023 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Wed Aug 7 03:09:49 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/scripts \n mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix \n 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 0.98 +- 0.55 (0.00-->6.98) (max @ vno 79674 --> 80846) face area 0.02 +- 0.03 (-0.22-->0.64) writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.07 hours scaling brain by 0.299... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.002, avgs=0 005/300: dt: 0.9000, rms radial error=176.748, avgs=0 010/300: dt: 0.9000, rms radial error=176.202, avgs=0 015/300: dt: 0.9000, rms radial error=175.484, avgs=0 020/300: dt: 0.9000, rms radial error=174.664, avgs=0 025/300: dt: 0.9000, rms radial error=173.786, avgs=0 030/300: dt: 0.9000, rms radial error=172.873, avgs=0 035/300: dt: 0.9000, rms radial error=171.940, avgs=0 040/300: dt: 0.9000, rms radial error=170.992, avgs=0 045/300: dt: 0.9000, rms radial error=170.041, avgs=0 050/300: dt: 0.9000, rms radial error=169.091, avgs=0 055/300: dt: 0.9000, rms radial error=168.143, avgs=0 060/300: dt: 0.9000, rms radial error=167.199, avgs=0 065/300: dt: 0.9000, rms radial error=166.260, avgs=0 070/300: dt: 0.9000, rms radial error=165.325, avgs=0 075/300: dt: 0.9000, rms radial error=164.394, avgs=0 080/300: dt: 0.9000, rms radial error=163.469, avgs=0 085/300: dt: 0.9000, rms radial error=162.548, avgs=0 090/300: dt: 0.9000, rms radial error=161.633, avgs=0 095/300: dt: 0.9000, rms radial error=160.722, avgs=0 100/300: dt: 0.9000, rms radial error=159.816, avgs=0 105/300: dt: 0.9000, rms radial error=158.915, avgs=0 110/300: dt: 0.9000, rms radial error=158.019, avgs=0 115/300: dt: 0.9000, rms radial error=157.128, avgs=0 120/300: dt: 0.9000, rms radial error=156.242, avgs=0 125/300: dt: 0.9000, rms radial error=155.361, avgs=0 130/300: dt: 0.9000, rms radial error=154.484, avgs=0 135/300: dt: 0.9000, rms radial error=153.612, avgs=0 140/300: dt: 0.9000, rms radial error=152.745, avgs=0 145/300: dt: 0.9000, rms radial error=151.883, avgs=0 150/300: dt: 0.9000, rms radial error=151.025, avgs=0 155/300: dt: 0.9000, rms radial error=150.173, avgs=0 160/300: dt: 0.9000, rms radial error=149.325, avgs=0 165/300: dt: 0.9000, rms radial error=148.481, avgs=0 170/300: dt: 0.9000, rms radial error=147.643, avgs=0 175/300: dt: 0.9000, rms radial error=146.809, avgs=0 180/300: dt: 0.9000, rms radial error=145.979, avgs=0 185/300: dt: 0.9000, rms radial error=145.154, avgs=0 190/300: dt: 0.9000, rms radial error=144.334, avgs=0 195/300: dt: 0.9000, rms radial error=143.518, avgs=0 200/300: dt: 0.9000, rms radial error=142.707, avgs=0 205/300: dt: 0.9000, rms radial error=141.901, avgs=0 210/300: dt: 0.9000, rms radial error=141.099, avgs=0 215/300: dt: 0.9000, rms radial error=140.301, avgs=0 220/300: dt: 0.9000, rms radial error=139.508, avgs=0 225/300: dt: 0.9000, rms radial error=138.720, avgs=0 230/300: dt: 0.9000, rms radial error=137.936, avgs=0 235/300: dt: 0.9000, rms radial error=137.157, avgs=0 240/300: dt: 0.9000, rms radial error=136.382, avgs=0 245/300: dt: 0.9000, rms radial error=135.611, avgs=0 250/300: dt: 0.9000, rms radial error=134.845, avgs=0 255/300: dt: 0.9000, rms radial error=134.083, avgs=0 260/300: dt: 0.9000, rms radial error=133.325, avgs=0 265/300: dt: 0.9000, rms radial error=132.572, avgs=0 270/300: dt: 0.9000, rms radial error=131.823, avgs=0 275/300: dt: 0.9000, rms radial error=131.078, avgs=0 280/300: dt: 0.9000, rms radial error=130.337, avgs=0 285/300: dt: 0.9000, rms radial error=129.601, avgs=0 290/300: dt: 0.9000, rms radial error=128.868, avgs=0 295/300: dt: 0.9000, rms radial error=128.140, avgs=0 300/300: dt: 0.9000, rms radial error=127.416, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 16866.09 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00013 epoch 2 (K=40.0), pass 1, starting sse = 2850.66 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00001 epoch 3 (K=160.0), pass 1, starting sse = 294.96 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.04/10 = 0.00393 epoch 4 (K=640.0), pass 1, starting sse = 20.85 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.12/12 = 0.01024 final distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Wed Aug 7 03:13:49 BRT 2013 \n cp ../surf/lh.orig.nofix ../surf/lh.orig \n \n cp ../surf/lh.inflated.nofix ../surf/lh.inflated \n /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/scripts \n mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 subjects_name_ lh \n 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=-20 (nv=142876, nf=285792, ne=428688, g=11) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations marking ambiguous vertices... 4459 ambiguous faces found in tessellation segmenting defects... 21 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 6 into 5 20 defects to be corrected 0 vertices coincident reading input surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.0172 (-4.5086) -vertex loglikelihood: -5.8380 (-2.9190) -normal dot loglikelihood: -3.6455 (-3.6455) -quad curv loglikelihood: -6.3155 (-3.1578) Total Loglikelihood : -24.8162 CORRECTING DEFECT 0 (vertices=301, convex hull=205) After retessellation of defect 0, euler #=-18 (140259,419969,279692) : difference with theory (-17) = 1 CORRECTING DEFECT 1 (vertices=179, convex hull=177) After retessellation of defect 1, euler #=-17 (140335,420280,279928) : difference with theory (-16) = 1 CORRECTING DEFECT 2 (vertices=22, convex hull=49) After retessellation of defect 2, euler #=-16 (140347,420331,279968) : difference with theory (-15) = 1 CORRECTING DEFECT 3 (vertices=418, convex hull=331) After retessellation of defect 3, euler #=-15 (140488,420911,280408) : difference with theory (-14) = 1 CORRECTING DEFECT 4 (vertices=15, convex hull=34) After retessellation of defect 4, euler #=-14 (140490,420929,280425) : difference with theory (-13) = 1 CORRECTING DEFECT 5 (vertices=409, convex hull=404) After retessellation of defect 5, euler #=-12 (140644,421591,280935) : difference with theory (-12) = 0 CORRECTING DEFECT 6 (vertices=27, convex hull=27) After retessellation of defect 6, euler #=-11 (140647,421609,280951) : difference with theory (-11) = 0 CORRECTING DEFECT 7 (vertices=6, convex hull=18) After retessellation of defect 7, euler #=-10 (140648,421618,280960) : difference with theory (-10) = 0 CORRECTING DEFECT 8 (vertices=71, convex hull=44) After retessellation of defect 8, euler #=-9 (140659,421668,281000) : difference with theory (-9) = 0 CORRECTING DEFECT 9 (vertices=13, convex hull=19) After retessellation of defect 9, euler #=-8 (140663,421684,281013) : difference with theory (-8) = 0 CORRECTING DEFECT 10 (vertices=7, convex hull=29) After retessellation of defect 10, euler #=-7 (140666,421701,281028) : difference with theory (-7) = 0 CORRECTING DEFECT 11 (vertices=6, convex hull=19) After retessellation of defect 11, euler #=-6 (140666,421706,281034) : difference with theory (-6) = 0 CORRECTING DEFECT 12 (vertices=9, convex hull=26) Warning - incorrect dp selected!!!!(-83.580503 >= -83.580510 ) After retessellation of defect 12, euler #=-5 (140667,421716,281044) : difference with theory (-5) = 0 CORRECTING DEFECT 13 (vertices=931, convex hull=367) After retessellation of defect 13, euler #=-4 (140805,422329,281520) : difference with theory (-4) = 0 CORRECTING DEFECT 14 (vertices=23, convex hull=39) After retessellation of defect 14, euler #=-3 (140813,422368,281552) : difference with theory (-3) = 0 CORRECTING DEFECT 15 (vertices=76, convex hull=27) After retessellation of defect 15, euler #=-2 (140819,422394,281573) : difference with theory (-2) = 0 CORRECTING DEFECT 16 (vertices=21, convex hull=43) After retessellation of defect 16, euler #=-1 (140828,422436,281607) : difference with theory (-1) = 0 CORRECTING DEFECT 17 (vertices=60, convex hull=34) After retessellation of defect 17, euler #=0 (140837,422474,281637) : difference with theory (0) = 0 CORRECTING DEFECT 18 (vertices=28, convex hull=27) After retessellation of defect 18, euler #=1 (140843,422502,281660) : difference with theory (1) = 0 CORRECTING DEFECT 19 (vertices=22, convex hull=59) After retessellation of defect 19, euler #=2 (140852,422550,281700) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.23 (0.07-->10.40) (max @ vno 114345 --> 121315) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.23 (0.07-->10.40) (max @ vno 114345 --> 121315) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 89 mutations (42.6%), 120 crossovers (57.4%), 257 vertices were eliminated building final representation... 2024 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=140852, nf=281700, ne=422550, g=0) writing corrected surface to /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 17.0 minutes 0 defective edges removing intersecting faces 000: 316 intersecting 001: 15 intersecting \n mris_euler_number ../surf/lh.orig \n euler # = v-e+f = 2g-2: 140852 - 422550 + 281700 = 2 --> 0 holes F =2V-4: 281700 = 281704-4 (0) 2E=3F: 845100 = 845100 (0) total defect index = 0 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/scripts \n mris_remove_intersection ../surf/lh.orig ../surf/lh.orig \n intersection removal took 0.00 hours removing intersecting faces 000: 113 intersecting 001: 3 intersecting writing corrected surface to ../surf/lh.orig \n rm ../surf/lh.inflated \n #-------------------------------------------- #@# Make White Surf lh Wed Aug 7 03:30:54 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/scripts \n mris_make_surfaces -noaparc -mgz -T1 brain.finalsurfs subjects_name_ lh \n not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/filled.mgz... reading volume /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/brain.finalsurfs.mgz... reading volume /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/wm.mgz... 10399 bright wm thresholded. 1003 bright non-wm voxels segmented. reading original surface position from /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.orig... computing class statistics... border white: 271713 voxels (1.62%) border gray 292541 voxels (1.74%) WM (96.0): 96.7 +- 6.8 [70.0 --> 110.0] GM (85.0) : 83.2 +- 10.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 62.1 (was 70) setting MAX_BORDER_WHITE to 109.8 (was 105) setting MIN_BORDER_WHITE to 73.0 (was 85) setting MAX_CSF to 51.1 (was 40) setting MAX_GRAY to 96.2 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 67.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 40.2 (was 40) repositioning cortical surface to gray/white boundary reading volume /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->5.44) (max @ vno 84564 --> 140608) face area 0.28 +- 0.13 (0.00-->6.00) mean absolute distance = 0.73 +- 0.90 4712 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=103, GM=73 mean inside = 95.5, mean outside = 80.3 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group mean border=84.2, 70 (70) missing vertices, mean dist 0.3 [0.6 (%37.7)->0.8 (%62.3))] %69 local maxima, %26 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=Pedro, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.26 (0.06-->6.58) (max @ vno 111891 --> 140697) face area 0.28 +- 0.14 (0.00-->4.00) mean absolute distance = 0.42 +- 0.69 4844 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4477561.0, rms=8.91 001: dt: 0.5000, sse=5053161.5, rms=6.357 (0.000%) 002: dt: 0.5000, sse=5313441.0, rms=4.734 (0.000%) 003: dt: 0.5000, sse=5623759.5, rms=3.747 (0.000%) 004: dt: 0.5000, sse=5785901.0, rms=3.132 (0.000%) 005: dt: 0.5000, sse=5966027.5, rms=2.842 (0.000%) 006: dt: 0.5000, sse=6026398.5, rms=2.676 (0.000%) 007: dt: 0.5000, sse=6122480.5, rms=2.620 (0.000%) 008: dt: 0.5000, sse=6106061.5, rms=2.554 (0.000%) rms = 2.55, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=6164936.5, rms=2.547 (0.000%) 010: dt: 0.2500, sse=3507728.8, rms=1.705 (0.000%) 011: dt: 0.2500, sse=3251358.5, rms=1.552 (0.000%) rms = 1.52, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=3164817.8, rms=1.523 (0.000%) rms = 1.50, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=3118263.5, rms=1.504 (0.000%) positioning took 2.0 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=86.5, 36 (13) missing vertices, mean dist -0.2 [0.5 (%65.7)->0.3 (%34.3))] %77 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=Pedro, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.07-->6.58) (max @ vno 111891 --> 140697) face area 0.35 +- 0.17 (0.00-->5.28) mean absolute distance = 0.34 +- 0.48 5721 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3681210.5, rms=4.33 014: dt: 0.5000, sse=3933137.5, rms=2.818 (0.000%) 015: dt: 0.5000, sse=4304677.5, rms=2.346 (0.000%) 016: dt: 0.5000, sse=4574460.0, rms=2.090 (0.000%) rms = 2.12, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=3820280.0, rms=1.656 (0.000%) 018: dt: 0.2500, sse=3530529.2, rms=1.372 (0.000%) 019: dt: 0.2500, sse=3438610.2, rms=1.275 (0.000%) rms = 1.24, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=3405272.0, rms=1.244 (0.000%) rms = 1.22, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=3372727.2, rms=1.225 (0.000%) positioning took 1.3 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group mean border=88.6, 34 (6) missing vertices, mean dist -0.2 [0.4 (%68.5)->0.2 (%31.5))] %84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=Pedro, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.24 (0.05-->6.58) (max @ vno 111891 --> 140697) face area 0.34 +- 0.16 (0.00-->5.28) mean absolute distance = 0.28 +- 0.38 5325 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3575979.5, rms=3.22 022: dt: 0.5000, sse=3830727.0, rms=2.004 (0.000%) 023: dt: 0.5000, sse=4047797.5, rms=1.858 (0.000%) 024: dt: 0.5000, sse=4351299.0, rms=1.792 (0.000%) rms = 2.01, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=3780039.5, rms=1.340 (0.000%) 026: dt: 0.2500, sse=3578155.8, rms=1.161 (0.000%) rms = 1.13, time step reduction 2 of 3 to 0.125... 027: dt: 0.2500, sse=3516013.8, rms=1.130 (0.000%) rms = 1.12, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=3483954.8, rms=1.116 (0.000%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group mean border=89.5, 30 (4) missing vertices, mean dist -0.1 [0.3 (%58.5)->0.2 (%41.5))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=Pedro, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=3507789.8, rms=1.70 029: dt: 0.5000, sse=4229234.0, rms=1.266 (0.000%) rms = 1.50, time step reduction 1 of 3 to 0.250... 030: dt: 0.2500, sse=3897624.0, rms=1.020 (0.000%) 031: dt: 0.2500, sse=3739995.0, rms=0.951 (0.000%) rms = 0.92, time step reduction 2 of 3 to 0.125... 032: dt: 0.2500, sse=3774084.2, rms=0.915 (0.000%) rms = 0.91, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=3773363.8, rms=0.914 (0.000%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group generating cortex label... 26 non-cortical segments detected only using segment with 1835 vertices erasing segment 1 (vno[0] = 65567) erasing segment 2 (vno[0] = 65679) erasing segment 3 (vno[0] = 78792) erasing segment 4 (vno[0] = 84271) erasing segment 5 (vno[0] = 86450) erasing segment 6 (vno[0] = 87627) erasing segment 7 (vno[0] = 87845) erasing segment 8 (vno[0] = 90233) erasing segment 9 (vno[0] = 90253) erasing segment 10 (vno[0] = 92249) erasing segment 11 (vno[0] = 95439) erasing segment 12 (vno[0] = 99713) erasing segment 13 (vno[0] = 101879) erasing segment 14 (vno[0] = 102015) erasing segment 15 (vno[0] = 102900) erasing segment 16 (vno[0] = 103812) erasing segment 17 (vno[0] = 104053) erasing segment 18 (vno[0] = 104740) erasing segment 19 (vno[0] = 105607) erasing segment 20 (vno[0] = 106506) erasing segment 21 (vno[0] = 107485) erasing segment 22 (vno[0] = 110105) erasing segment 23 (vno[0] = 110110) erasing segment 24 (vno[0] = 110135) erasing segment 25 (vno[0] = 113439) writing cortex label to /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/label/lh.cortex.label... writing curvature file /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.curv writing smoothed area to lh.area writing curvature file /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.area vertex spacing 0.88 +- 0.25 (0.07-->6.58) (max @ vno 111891 --> 140697) face area 0.33 +- 0.16 (0.00-->5.06) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... smoothing surface for 5 iterations... mean border=63.4, 56 (56) missing vertices, mean dist 1.6 [0.1 (%0.0)->2.6 (%100.0))] %20 local maxima, %38 large gradients and %38 min vals, 2351 gradients ignored tol=1.0e-04, sigma=2.0, host=Pedro, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=21967492.0, rms=26.88 001: dt: 0.5000, sse=17443170.0, rms=23.575 (0.000%) 002: dt: 0.5000, sse=13914269.0, rms=20.672 (0.000%) 003: dt: 0.5000, sse=11278155.0, rms=18.158 (0.000%) 004: dt: 0.5000, sse=9430512.0, rms=15.979 (0.000%) 005: dt: 0.5000, sse=8170195.0, rms=14.123 (0.000%) 006: dt: 0.5000, sse=7340470.0, rms=12.549 (0.000%) 007: dt: 0.5000, sse=6789355.5, rms=11.139 (0.000%) 008: dt: 0.5000, sse=6364626.5, rms=9.799 (0.000%) 009: dt: 0.5000, sse=6015097.5, rms=8.499 (0.000%) 010: dt: 0.5000, sse=5782992.0, rms=7.225 (0.000%) 011: dt: 0.5000, sse=5625180.5, rms=6.058 (0.000%) 012: dt: 0.5000, sse=5633472.0, rms=5.074 (0.000%) 013: dt: 0.5000, sse=5649196.0, rms=4.361 (0.000%) 014: dt: 0.5000, sse=5737595.0, rms=3.905 (0.000%) 015: dt: 0.5000, sse=5840720.0, rms=3.646 (0.000%) 016: dt: 0.5000, sse=5860938.0, rms=3.499 (0.000%) 017: dt: 0.5000, sse=5903233.5, rms=3.429 (0.000%) 018: dt: 0.5000, sse=5899790.0, rms=3.379 (0.000%) rms = 3.36, time step reduction 1 of 3 to 0.250... 019: dt: 0.5000, sse=5932416.0, rms=3.363 (0.000%) 020: dt: 0.2500, sse=4041107.2, rms=2.695 (0.000%) 021: dt: 0.2500, sse=3897885.2, rms=2.534 (0.000%) rms = 2.51, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=3813403.0, rms=2.509 (0.000%) 023: dt: 0.1250, sse=3634017.8, rms=2.416 (0.000%) rms = 2.40, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=3621975.0, rms=2.404 (0.000%) positioning took 3.5 minutes mean border=61.7, 1333 (14) missing vertices, mean dist 0.1 [0.2 (%47.1)->0.5 (%52.9))] %34 local maxima, %30 large gradients and %31 min vals, 983 gradients ignored tol=1.0e-04, sigma=1.0, host=Pedro, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4110472.8, rms=4.04 025: dt: 0.5000, sse=4345870.5, rms=3.247 (0.000%) rms = 3.26, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=4063587.2, rms=2.779 (0.000%) 027: dt: 0.2500, sse=4104502.0, rms=2.554 (0.000%) 028: dt: 0.2500, sse=4069137.0, rms=2.463 (0.000%) rms = 2.42, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=4098876.5, rms=2.424 (0.000%) 030: dt: 0.1250, sse=3968115.5, rms=2.336 (0.000%) rms = 2.32, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=3974692.5, rms=2.318 (0.000%) positioning took 1.1 minutes mean border=60.8, 1617 (8) missing vertices, mean dist 0.1 [0.2 (%47.3)->0.4 (%52.7))] %43 local maxima, %21 large gradients and %30 min vals, 1078 gradients ignored tol=1.0e-04, sigma=0.5, host=Pedro, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4044743.0, rms=2.74 rms = 2.87, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=3946662.8, rms=2.471 (0.000%) 033: dt: 0.2500, sse=4006584.5, rms=2.318 (0.000%) 034: dt: 0.2500, sse=4107167.8, rms=2.267 (0.000%) rms = 2.24, time step reduction 2 of 3 to 0.125... 035: dt: 0.2500, sse=4150708.8, rms=2.244 (0.000%) 036: dt: 0.1250, sse=4061029.0, rms=2.187 (0.000%) rms = 2.17, time step reduction 3 of 3 to 0.062... 037: dt: 0.1250, sse=4073362.8, rms=2.173 (0.000%) positioning took 1.0 minutes mean border=60.2, 3450 (7) missing vertices, mean dist 0.0 [0.2 (%49.2)->0.3 (%50.8))] %47 local maxima, %17 large gradients and %29 min vals, 1002 gradients ignored tol=1.0e-04, sigma=0.2, host=Pedro, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=4096317.0, rms=2.36 rms = 2.55, time step reduction 1 of 3 to 0.250... 038: dt: 0.2500, sse=4033739.8, rms=2.221 (0.000%) 039: dt: 0.2500, sse=4156457.0, rms=2.148 (0.000%) rms = 2.12, time step reduction 2 of 3 to 0.125... 040: dt: 0.2500, sse=4188242.2, rms=2.119 (0.000%) 041: dt: 0.1250, sse=4114819.5, rms=2.066 (0.000%) rms = 2.06, time step reduction 3 of 3 to 0.062... 042: dt: 0.1250, sse=4136180.0, rms=2.055 (0.000%) positioning took 0.8 minutes writing curvature file /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.area.pial vertex spacing 0.98 +- 0.40 (0.08-->7.31) (max @ vno 95479 --> 94421) face area 0.38 +- 0.28 (0.00-->7.44) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 140852 vertices processed 25000 of 140852 vertices processed 50000 of 140852 vertices processed 75000 of 140852 vertices processed 100000 of 140852 vertices processed 125000 of 140852 vertices processed 0 of 140852 vertices processed 25000 of 140852 vertices processed 50000 of 140852 vertices processed 75000 of 140852 vertices processed 100000 of 140852 vertices processed 125000 of 140852 vertices processed thickness calculation complete, 598:757 truncations. 35300 vertices at 0 distance 98623 vertices at 1 distance 81294 vertices at 2 distance 35505 vertices at 3 distance 12919 vertices at 4 distance 4193 vertices at 5 distance 1350 vertices at 6 distance 456 vertices at 7 distance 186 vertices at 8 distance 81 vertices at 9 distance 52 vertices at 10 distance 33 vertices at 11 distance 27 vertices at 12 distance 15 vertices at 13 distance 5 vertices at 14 distance 4 vertices at 15 distance 4 vertices at 16 distance 6 vertices at 17 distance 5 vertices at 18 distance 5 vertices at 19 distance 3 vertices at 20 distance writing curvature file /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.thickness positioning took 16.4 minutes #-------------------------------------------- #@# Smooth2 lh Wed Aug 7 03:47:16 BRT 2013 \n mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm \n /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 lh Wed Aug 7 03:47:24 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/scripts \n mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated \n avg radius = 47.9 mm, total surface area = 84387 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.109 (target=0.015) step 005: RMS=0.076 (target=0.015) step 010: RMS=0.055 (target=0.015) step 015: RMS=0.045 (target=0.015) step 020: RMS=0.036 (target=0.015) step 025: RMS=0.031 (target=0.015) step 030: RMS=0.026 (target=0.015) step 035: RMS=0.022 (target=0.015) step 040: RMS=0.019 (target=0.015) step 045: RMS=0.016 (target=0.015) step 050: RMS=0.015 (target=0.015) inflation complete. inflation took 0.5 minutes \n mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated \n normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 149 vertices thresholded to be in k1 ~ [-0.26 0.38], k2 ~ [-0.11 0.06] total integrated curvature = 0.599*4pi (7.526) --> 0 handles ICI = 1.7, FI = 10.9, variation=186.061 129 vertices thresholded to be in [-0.01 0.02] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 145 vertices thresholded to be in [-0.15 0.18] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.016, std = 0.024 done. \n#----------------------------------------- #@# Curvature Stats lh Wed Aug 7 03:49:15 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf \n mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm subjects_name_ lh curv sulc \n Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ subjects_name_/lh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 267 ] Gb_filter = 0 WARN: S lookup min: -0.167478 WARN: S explicit min: 0.000000 vertex = 1009 #-------------------------------------------- #@# Tessellate rh Wed Aug 7 03:49:23 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/scripts \n mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz \n Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 2 found - 2 modified | TOTAL: 2 pass 2 (yz+): 0 found - 2 modified | TOTAL: 2 pass 1 (yz-): 2 found - 2 modified | TOTAL: 4 pass 2 (yz-): 0 found - 2 modified | TOTAL: 4 pass 1 (xz+): 0 found - 0 modified | TOTAL: 4 pass 1 (xz-): 1 found - 1 modified | TOTAL: 5 pass 2 (xz-): 0 found - 1 modified | TOTAL: 5 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 5 (out of 291228: 0.001717) Ambiguous edge configurations... mri_pretess done \n mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix \n $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 40: 1466 vertices, 1576 faces slice 50: 5878 vertices, 6047 faces slice 60: 12645 vertices, 12931 faces slice 70: 21241 vertices, 21521 faces slice 80: 30853 vertices, 31216 faces slice 90: 40954 vertices, 41292 faces slice 100: 51846 vertices, 52212 faces slice 110: 64114 vertices, 64528 faces slice 120: 76988 vertices, 77426 faces slice 130: 89297 vertices, 89734 faces slice 140: 101098 vertices, 101511 faces slice 150: 111771 vertices, 112148 faces slice 160: 120568 vertices, 120867 faces slice 170: 128396 vertices, 128650 faces slice 180: 135161 vertices, 135416 faces slice 190: 140744 vertices, 140930 faces slice 200: 142410 vertices, 142432 faces slice 210: 142410 vertices, 142432 faces slice 220: 142410 vertices, 142432 faces slice 230: 142410 vertices, 142432 faces slice 240: 142410 vertices, 142432 faces slice 250: 142410 vertices, 142432 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; \n rm -f ../mri/filled-pretess127.mgz \n \n mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix \n counting number of connected components... 142410 voxel in cpt #1: X=-22 [v=142410,e=427296,f=284864] located at (27.706074, -13.574805, 33.356014) For the whole surface: X=-22 [v=142410,e=427296,f=284864] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Wed Aug 7 03:49:34 BRT 2013 \n mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix \n /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 rh Wed Aug 7 03:49:42 BRT 2013 \n mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix \n /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/scripts avg radius = 46.4 mm, total surface area = 76160 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.5 minutes Not saving sulc step 000: RMS=0.097 (target=0.015) step 005: RMS=0.072 (target=0.015) step 010: RMS=0.053 (target=0.015) step 015: RMS=0.044 (target=0.015) step 020: RMS=0.037 (target=0.015) step 025: RMS=0.032 (target=0.015) step 030: RMS=0.028 (target=0.015) step 035: RMS=0.025 (target=0.015) step 040: RMS=0.023 (target=0.015) step 045: RMS=0.022 (target=0.015) step 050: RMS=0.022 (target=0.015) step 055: RMS=0.021 (target=0.015) step 060: RMS=0.021 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Wed Aug 7 03:50:14 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/scripts \n mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix \n 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 0.98 +- 0.54 (0.00-->7.29) (max @ vno 57577 --> 58801) face area 0.03 +- 0.03 (-0.29-->0.67) writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.08 hours scaling brain by 0.306... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.890, avgs=0 005/300: dt: 0.9000, rms radial error=176.630, avgs=0 010/300: dt: 0.9000, rms radial error=176.073, avgs=0 015/300: dt: 0.9000, rms radial error=175.341, avgs=0 020/300: dt: 0.9000, rms radial error=174.507, avgs=0 025/300: dt: 0.9000, rms radial error=173.615, avgs=0 030/300: dt: 0.9000, rms radial error=172.692, avgs=0 035/300: dt: 0.9000, rms radial error=171.751, avgs=0 040/300: dt: 0.9000, rms radial error=170.804, avgs=0 045/300: dt: 0.9000, rms radial error=169.853, avgs=0 050/300: dt: 0.9000, rms radial error=168.902, avgs=0 055/300: dt: 0.9000, rms radial error=167.954, avgs=0 060/300: dt: 0.9000, rms radial error=167.010, avgs=0 065/300: dt: 0.9000, rms radial error=166.070, avgs=0 070/300: dt: 0.9000, rms radial error=165.135, avgs=0 075/300: dt: 0.9000, rms radial error=164.205, avgs=0 080/300: dt: 0.9000, rms radial error=163.279, avgs=0 085/300: dt: 0.9000, rms radial error=162.360, avgs=0 090/300: dt: 0.9000, rms radial error=161.446, avgs=0 095/300: dt: 0.9000, rms radial error=160.537, avgs=0 100/300: dt: 0.9000, rms radial error=159.633, avgs=0 105/300: dt: 0.9000, rms radial error=158.734, avgs=0 110/300: dt: 0.9000, rms radial error=157.840, avgs=0 115/300: dt: 0.9000, rms radial error=156.950, avgs=0 120/300: dt: 0.9000, rms radial error=156.066, avgs=0 125/300: dt: 0.9000, rms radial error=155.186, avgs=0 130/300: dt: 0.9000, rms radial error=154.311, avgs=0 135/300: dt: 0.9000, rms radial error=153.441, avgs=0 140/300: dt: 0.9000, rms radial error=152.576, avgs=0 145/300: dt: 0.9000, rms radial error=151.715, avgs=0 150/300: dt: 0.9000, rms radial error=150.859, avgs=0 155/300: dt: 0.9000, rms radial error=150.008, avgs=0 160/300: dt: 0.9000, rms radial error=149.162, avgs=0 165/300: dt: 0.9000, rms radial error=148.320, avgs=0 170/300: dt: 0.9000, rms radial error=147.483, avgs=0 175/300: dt: 0.9000, rms radial error=146.651, avgs=0 180/300: dt: 0.9000, rms radial error=145.823, avgs=0 185/300: dt: 0.9000, rms radial error=145.000, avgs=0 190/300: dt: 0.9000, rms radial error=144.182, avgs=0 195/300: dt: 0.9000, rms radial error=143.368, avgs=0 200/300: dt: 0.9000, rms radial error=142.558, avgs=0 205/300: dt: 0.9000, rms radial error=141.753, avgs=0 210/300: dt: 0.9000, rms radial error=140.953, avgs=0 215/300: dt: 0.9000, rms radial error=140.157, avgs=0 220/300: dt: 0.9000, rms radial error=139.365, avgs=0 225/300: dt: 0.9000, rms radial error=138.578, avgs=0 230/300: dt: 0.9000, rms radial error=137.795, avgs=0 235/300: dt: 0.9000, rms radial error=137.017, avgs=0 240/300: dt: 0.9000, rms radial error=136.243, avgs=0 245/300: dt: 0.9000, rms radial error=135.474, avgs=0 250/300: dt: 0.9000, rms radial error=134.708, avgs=0 255/300: dt: 0.9000, rms radial error=133.947, avgs=0 260/300: dt: 0.9000, rms radial error=133.191, avgs=0 265/300: dt: 0.9000, rms radial error=132.438, avgs=0 270/300: dt: 0.9000, rms radial error=131.690, avgs=0 275/300: dt: 0.9000, rms radial error=130.946, avgs=0 280/300: dt: 0.9000, rms radial error=130.206, avgs=0 285/300: dt: 0.9000, rms radial error=129.470, avgs=0 290/300: dt: 0.9000, rms radial error=128.739, avgs=0 295/300: dt: 0.9000, rms radial error=128.011, avgs=0 300/300: dt: 0.9000, rms radial error=127.288, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 16671.09 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00014 epoch 2 (K=40.0), pass 1, starting sse = 2747.14 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00004 epoch 3 (K=160.0), pass 1, starting sse = 267.35 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/11 = 0.00751 epoch 4 (K=640.0), pass 1, starting sse = 14.54 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.12/13 = 0.00935 final distance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Wed Aug 7 03:55:00 BRT 2013 \n cp ../surf/rh.orig.nofix ../surf/rh.orig \n \n cp ../surf/rh.inflated.nofix ../surf/rh.inflated \n /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/scripts \n mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 subjects_name_ rh \n 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=-22 (nv=142410, nf=284864, ne=427296, g=12) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 7 iterations marking ambiguous vertices... 2958 ambiguous faces found in tessellation segmenting defects... 17 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 1 into 0 16 defects to be corrected 0 vertices coincident reading input surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.9225 (-4.4613) -vertex loglikelihood: -5.8445 (-2.9222) -normal dot loglikelihood: -3.6889 (-3.6889) -quad curv loglikelihood: -6.4508 (-3.2254) Total Loglikelihood : -24.9067 CORRECTING DEFECT 0 (vertices=425, convex hull=310) After retessellation of defect 0, euler #=-12 (140680,421516,280824) : difference with theory (-13) = -1 CORRECTING DEFECT 1 (vertices=24, convex hull=54) After retessellation of defect 1, euler #=-11 (140695,421582,280876) : difference with theory (-12) = -1 CORRECTING DEFECT 2 (vertices=516, convex hull=308) After retessellation of defect 2, euler #=-11 (140854,422206,281341) : difference with theory (-11) = 0 CORRECTING DEFECT 3 (vertices=104, convex hull=75) After retessellation of defect 3, euler #=-10 (140880,422316,281426) : difference with theory (-10) = 0 CORRECTING DEFECT 4 (vertices=17, convex hull=21) After retessellation of defect 4, euler #=-9 (140881,422327,281437) : difference with theory (-9) = 0 CORRECTING DEFECT 5 (vertices=6, convex hull=19) After retessellation of defect 5, euler #=-8 (140882,422335,281445) : difference with theory (-8) = 0 CORRECTING DEFECT 6 (vertices=44, convex hull=59) After retessellation of defect 6, euler #=-7 (140902,422418,281509) : difference with theory (-7) = 0 CORRECTING DEFECT 7 (vertices=19, convex hull=63) After retessellation of defect 7, euler #=-6 (140911,422469,281552) : difference with theory (-6) = 0 CORRECTING DEFECT 8 (vertices=39, convex hull=37) After retessellation of defect 8, euler #=-5 (140924,422520,281591) : difference with theory (-5) = 0 CORRECTING DEFECT 9 (vertices=154, convex hull=57) After retessellation of defect 9, euler #=-4 (140935,422580,281641) : difference with theory (-4) = 0 CORRECTING DEFECT 10 (vertices=47, convex hull=78) After retessellation of defect 10, euler #=-3 (140957,422678,281718) : difference with theory (-3) = 0 CORRECTING DEFECT 11 (vertices=88, convex hull=100) After retessellation of defect 11, euler #=-2 (141004,422861,281855) : difference with theory (-2) = 0 CORRECTING DEFECT 12 (vertices=118, convex hull=131) After retessellation of defect 12, euler #=-1 (141070,423123,282052) : difference with theory (-1) = 0 CORRECTING DEFECT 13 (vertices=48, convex hull=77) After retessellation of defect 13, euler #=0 (141087,423206,282119) : difference with theory (0) = 0 CORRECTING DEFECT 14 (vertices=74, convex hull=46) After retessellation of defect 14, euler #=1 (141095,423251,282157) : difference with theory (1) = 0 CORRECTING DEFECT 15 (vertices=74, convex hull=74) After retessellation of defect 15, euler #=2 (141108,423318,282212) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.22 (0.03-->12.68) (max @ vno 47581 --> 54455) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.22 (0.03-->12.68) (max @ vno 47581 --> 54455) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 59 mutations (37.8%), 97 crossovers (62.2%), 99 vertices were eliminated building final representation... 1302 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=141108, nf=282212, ne=423318, g=0) writing corrected surface to /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 13.0 minutes 0 defective edges removing intersecting faces 000: 141 intersecting 001: 22 intersecting \n mris_euler_number ../surf/rh.orig \n euler # = v-e+f = 2g-2: 141108 - 423318 + 282212 = 2 --> 0 holes F =2V-4: 282212 = 282216-4 (0) 2E=3F: 846636 = 846636 (0) total defect index = 0 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/scripts \n mris_remove_intersection ../surf/rh.orig ../surf/rh.orig \n intersection removal took 0.00 hours removing intersecting faces 000: 28 intersecting writing corrected surface to ../surf/rh.orig \n rm ../surf/rh.inflated \n #-------------------------------------------- #@# Make White Surf rh Wed Aug 7 04:08:08 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/scripts \n mris_make_surfaces -noaparc -mgz -T1 brain.finalsurfs subjects_name_ rh \n not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/filled.mgz... reading volume /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/brain.finalsurfs.mgz... reading volume /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/wm.mgz... 9941 bright wm thresholded. 1000 bright non-wm voxels segmented. reading original surface position from /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.orig... computing class statistics... border white: 271713 voxels (1.62%) border gray 292541 voxels (1.74%) WM (96.0): 96.8 +- 6.9 [70.0 --> 110.0] GM (85.0) : 83.3 +- 10.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 63.2 (was 70) setting MAX_BORDER_WHITE to 110.9 (was 105) setting MIN_BORDER_WHITE to 74.0 (was 85) setting MAX_CSF to 52.4 (was 40) setting MAX_GRAY to 97.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 68.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 41.6 (was 40) repositioning cortical surface to gray/white boundary reading volume /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.04-->4.41) (max @ vno 54423 --> 140844) face area 0.28 +- 0.12 (0.00-->4.72) mean absolute distance = 0.71 +- 0.90 3972 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104, GM=74 mean inside = 95.8, mean outside = 80.4 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group mean border=84.8, 17 (17) missing vertices, mean dist 0.3 [0.6 (%38.8)->0.8 (%61.2))] %69 local maxima, %27 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=Pedro, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.25 (0.06-->6.33) (max @ vno 47581 --> 140702) face area 0.28 +- 0.13 (0.00-->5.43) mean absolute distance = 0.40 +- 0.66 3976 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4467280.0, rms=8.73 001: dt: 0.5000, sse=5085096.5, rms=6.107 (0.000%) 002: dt: 0.5000, sse=5392628.0, rms=4.501 (0.000%) 003: dt: 0.5000, sse=5710925.0, rms=3.562 (0.000%) 004: dt: 0.5000, sse=5921119.0, rms=3.007 (0.000%) 005: dt: 0.5000, sse=6057816.0, rms=2.749 (0.000%) 006: dt: 0.5000, sse=6129520.5, rms=2.601 (0.000%) rms = 2.56, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=6193882.0, rms=2.561 (0.000%) 008: dt: 0.2500, sse=3574492.2, rms=1.681 (0.000%) 009: dt: 0.2500, sse=3309745.0, rms=1.515 (0.000%) rms = 1.48, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=3224062.0, rms=1.478 (0.000%) rms = 1.45, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=3176583.2, rms=1.454 (0.000%) positioning took 1.7 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=87.1, 19 (6) missing vertices, mean dist -0.2 [0.5 (%66.9)->0.3 (%33.1))] %76 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=Pedro, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.24 (0.12-->6.71) (max @ vno 47581 --> 140702) face area 0.35 +- 0.16 (0.00-->7.61) mean absolute distance = 0.32 +- 0.48 4598 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3704064.5, rms=4.14 012: dt: 0.5000, sse=4019076.5, rms=2.564 (0.000%) 013: dt: 0.5000, sse=4371413.0, rms=2.211 (0.000%) 014: dt: 0.5000, sse=4668568.0, rms=2.029 (0.000%) rms = 2.17, time step reduction 1 of 3 to 0.250... 015: dt: 0.2500, sse=3902817.5, rms=1.573 (0.000%) 016: dt: 0.2500, sse=3623026.5, rms=1.345 (0.000%) 017: dt: 0.2500, sse=3527025.0, rms=1.278 (0.000%) rms = 1.26, time step reduction 2 of 3 to 0.125... 018: dt: 0.2500, sse=3497131.5, rms=1.259 (0.000%) rms = 1.24, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=3464648.0, rms=1.242 (0.000%) positioning took 1.3 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=89.2, 12 (4) missing vertices, mean dist -0.2 [0.4 (%68.5)->0.2 (%31.5))] %84 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=Pedro, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.24 (0.10-->6.97) (max @ vno 47581 --> 140702) face area 0.34 +- 0.16 (0.00-->7.87) mean absolute distance = 0.27 +- 0.37 4314 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3652499.8, rms=3.08 020: dt: 0.5000, sse=3949293.0, rms=1.950 (0.000%) 021: dt: 0.5000, sse=4151604.5, rms=1.893 (0.000%) rms = 1.85, time step reduction 1 of 3 to 0.250... 022: dt: 0.5000, sse=4492371.5, rms=1.846 (0.000%) 023: dt: 0.2500, sse=3803204.0, rms=1.258 (0.000%) 024: dt: 0.2500, sse=3673217.2, rms=1.159 (0.000%) rms = 1.16, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=3617567.5, rms=1.158 (0.000%) rms = 1.14, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=3594612.0, rms=1.142 (0.000%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=90.1, 14 (3) missing vertices, mean dist -0.1 [0.3 (%58.0)->0.2 (%42.0))] %87 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=Pedro, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=3614299.5, rms=1.63 027: dt: 0.5000, sse=4378090.0, rms=1.290 (0.000%) rms = 1.57, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=4024560.8, rms=1.024 (0.000%) 029: dt: 0.2500, sse=3862594.5, rms=0.955 (0.000%) rms = 0.93, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=3904717.2, rms=0.926 (0.000%) rms = 0.93, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=3904717.2, rms=0.926 (0.000%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group generating cortex label... 9 non-cortical segments detected only using segment with 2380 vertices erasing segment 1 (vno[0] = 92500) erasing segment 2 (vno[0] = 92566) erasing segment 3 (vno[0] = 94859) erasing segment 4 (vno[0] = 96025) erasing segment 5 (vno[0] = 96145) erasing segment 6 (vno[0] = 102813) erasing segment 7 (vno[0] = 103865) erasing segment 8 (vno[0] = 107069) writing cortex label to /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/label/rh.cortex.label... writing curvature file /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.curv writing smoothed area to rh.area writing curvature file /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.area vertex spacing 0.88 +- 0.24 (0.05-->7.06) (max @ vno 47581 --> 140702) face area 0.33 +- 0.16 (0.00-->7.99) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... smoothing surface for 5 iterations... mean border=64.5, 29 (29) missing vertices, mean dist 1.6 [2.5 (%0.0)->2.6 (%100.0))] %19 local maxima, %41 large gradients and %35 min vals, 2575 gradients ignored tol=1.0e-04, sigma=2.0, host=Pedro, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=21207338.0, rms=26.24 001: dt: 0.5000, sse=16739033.0, rms=22.912 (0.000%) 002: dt: 0.5000, sse=13278640.0, rms=19.995 (0.000%) 003: dt: 0.5000, sse=10737233.0, rms=17.478 (0.000%) 004: dt: 0.5000, sse=8977832.0, rms=15.301 (0.000%) 005: dt: 0.5000, sse=7791048.0, rms=13.456 (0.000%) 006: dt: 0.5000, sse=6988955.0, rms=11.919 (0.000%) 007: dt: 0.5000, sse=6496961.0, rms=10.580 (0.000%) 008: dt: 0.5000, sse=6174614.5, rms=9.342 (0.000%) 009: dt: 0.5000, sse=5856215.5, rms=8.134 (0.000%) 010: dt: 0.5000, sse=5678743.0, rms=6.953 (0.000%) 011: dt: 0.5000, sse=5522980.0, rms=5.889 (0.000%) 012: dt: 0.5000, sse=5541120.5, rms=5.007 (0.000%) 013: dt: 0.5000, sse=5598864.0, rms=4.359 (0.000%) 014: dt: 0.5000, sse=5670894.5, rms=3.923 (0.000%) 015: dt: 0.5000, sse=5746322.5, rms=3.667 (0.000%) 016: dt: 0.5000, sse=5779117.5, rms=3.508 (0.000%) 017: dt: 0.5000, sse=5825855.5, rms=3.432 (0.000%) 018: dt: 0.5000, sse=5839677.0, rms=3.375 (0.000%) rms = 3.36, time step reduction 1 of 3 to 0.250... 019: dt: 0.5000, sse=5866300.0, rms=3.359 (0.000%) 020: dt: 0.2500, sse=4058801.2, rms=2.713 (0.000%) 021: dt: 0.2500, sse=3886665.2, rms=2.562 (0.000%) rms = 2.53, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=3799060.0, rms=2.531 (0.000%) 023: dt: 0.1250, sse=3627349.0, rms=2.443 (0.000%) rms = 2.43, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=3609624.5, rms=2.432 (0.000%) positioning took 3.5 minutes mean border=62.7, 1180 (3) missing vertices, mean dist 0.1 [0.2 (%47.4)->0.6 (%52.6))] %34 local maxima, %33 large gradients and %28 min vals, 741 gradients ignored tol=1.0e-04, sigma=1.0, host=Pedro, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4133869.0, rms=4.21 025: dt: 0.5000, sse=4324976.0, rms=3.398 (0.000%) 026: dt: 0.5000, sse=5300565.5, rms=3.270 (0.000%) rms = 3.32, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=4491566.5, rms=2.728 (0.000%) 028: dt: 0.2500, sse=4154958.2, rms=2.491 (0.000%) rms = 2.45, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=4122001.0, rms=2.450 (0.000%) 030: dt: 0.1250, sse=3983902.5, rms=2.361 (0.000%) rms = 2.35, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=3973193.0, rms=2.348 (0.000%) positioning took 1.1 minutes mean border=61.7, 1460 (3) missing vertices, mean dist 0.1 [0.2 (%46.5)->0.4 (%53.5))] %45 local maxima, %22 large gradients and %28 min vals, 864 gradients ignored tol=1.0e-04, sigma=0.5, host=Pedro, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4060926.5, rms=2.86 rms = 2.92, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=3961458.2, rms=2.592 (0.000%) 033: dt: 0.2500, sse=3999970.5, rms=2.422 (0.000%) 034: dt: 0.2500, sse=4093484.5, rms=2.367 (0.000%) rms = 2.34, time step reduction 2 of 3 to 0.125... 035: dt: 0.2500, sse=4136253.8, rms=2.343 (0.000%) 036: dt: 0.1250, sse=4049269.5, rms=2.285 (0.000%) rms = 2.27, time step reduction 3 of 3 to 0.062... 037: dt: 0.1250, sse=4056560.2, rms=2.267 (0.000%) positioning took 1.0 minutes mean border=61.1, 3095 (3) missing vertices, mean dist 0.1 [0.2 (%49.1)->0.3 (%50.9))] %49 local maxima, %18 large gradients and %27 min vals, 845 gradients ignored tol=1.0e-04, sigma=0.2, host=Pedro, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=4076950.2, rms=2.43 rms = 2.56, time step reduction 1 of 3 to 0.250... 038: dt: 0.2500, sse=4023670.5, rms=2.288 (0.000%) 039: dt: 0.2500, sse=4144193.0, rms=2.190 (0.000%) rms = 2.14, time step reduction 2 of 3 to 0.125... 040: dt: 0.2500, sse=4178948.0, rms=2.141 (0.000%) 041: dt: 0.1250, sse=4112835.0, rms=2.080 (0.000%) rms = 2.06, time step reduction 3 of 3 to 0.062... 042: dt: 0.1250, sse=4121978.2, rms=2.056 (0.000%) positioning took 0.8 minutes writing curvature file /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.area.pial vertex spacing 0.98 +- 0.40 (0.06-->8.15) (max @ vno 89089 --> 89063) face area 0.38 +- 0.28 (0.00-->8.77) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 141108 vertices processed 25000 of 141108 vertices processed 50000 of 141108 vertices processed 75000 of 141108 vertices processed 100000 of 141108 vertices processed 125000 of 141108 vertices processed 0 of 141108 vertices processed 25000 of 141108 vertices processed 50000 of 141108 vertices processed 75000 of 141108 vertices processed 100000 of 141108 vertices processed 125000 of 141108 vertices processed thickness calculation complete, 809:888 truncations. 34974 vertices at 0 distance 99316 vertices at 1 distance 81825 vertices at 2 distance 35448 vertices at 3 distance 12961 vertices at 4 distance 4254 vertices at 5 distance 1511 vertices at 6 distance 534 vertices at 7 distance 189 vertices at 8 distance 88 vertices at 9 distance 36 vertices at 10 distance 38 vertices at 11 distance 21 vertices at 12 distance 21 vertices at 13 distance 26 vertices at 14 distance 24 vertices at 15 distance 10 vertices at 16 distance 13 vertices at 17 distance 9 vertices at 18 distance 11 vertices at 19 distance 15 vertices at 20 distance writing curvature file /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.thickness positioning took 16.6 minutes #-------------------------------------------- #@# Smooth2 rh Wed Aug 7 04:24:42 BRT 2013 \n mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm \n /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 rh Wed Aug 7 04:24:49 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/scripts \n mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated \n avg radius = 46.4 mm, total surface area = 84231 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.110 (target=0.015) step 005: RMS=0.077 (target=0.015) step 010: RMS=0.056 (target=0.015) step 015: RMS=0.046 (target=0.015) step 020: RMS=0.037 (target=0.015) step 025: RMS=0.031 (target=0.015) step 030: RMS=0.027 (target=0.015) step 035: RMS=0.022 (target=0.015) step 040: RMS=0.020 (target=0.015) step 045: RMS=0.018 (target=0.015) step 050: RMS=0.017 (target=0.015) step 055: RMS=0.016 (target=0.015) step 060: RMS=0.015 (target=0.015) inflation complete. inflation took 0.5 minutes \n mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated \n normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 165 vertices thresholded to be in k1 ~ [-0.70 0.58], k2 ~ [-0.14 0.15] total integrated curvature = 0.558*4pi (7.017) --> 0 handles ICI = 1.6, FI = 9.1, variation=159.329 129 vertices thresholded to be in [-0.05 0.02] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 129 vertices thresholded to be in [-0.29 0.25] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.016, std = 0.023 done. \n#----------------------------------------- #@# Curvature Stats rh Wed Aug 7 04:26:44 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf \n mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm subjects_name_ rh curv sulc \n Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/rh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ subjects_name_/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 253 ] Gb_filter = 0 WARN: S lookup min: -0.161966 WARN: S explicit min: 0.000000 vertex = 630 #-------------------------------------------- #@# ASeg Stats Wed Aug 7 04:26:52 BRT 2013 \nINFO: mri_segstats will not calculate Supratentorial due to missing ribbon.mgz file /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_ \n mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /Applications/Freesurfer5.3/freesurfer/ASegStatsLUT.txt --subject subjects_name_ \n $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /Applications/Freesurfer5.3/freesurfer/ASegStatsLUT.txt --subject subjects_name_ sysname Darwin hostname Pedro-Rosas-MacBook-Pro-2.local machine x86_64 user pedrogomesrosa UseRobust 0 atlas_icv (eTIV) = 1580638 mm^3 (det: 1.232480 ) mghRead(/Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/ribbon.mgz, -1): could not open file Computing euler number orig.nofix lheno = -20, rheno = -22 orig.nofix lhholes = 11, rhholes = 12 Loading mri/aseg.mgz Getting Brain Volume Statistics Darwin Pedro-Rosas-MacBook-Pro-2.local 12.4.0 Darwin Kernel Version 12.4.0: Wed May 1 17:57:12 PDT 2013; root:xnu-2050.24.15~1/RELEASE_X86_64 x86_64 recon-all -s subjects_name_ exited with ERRORS at Wed Aug 7 04:27:09 BRT 2013 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting \n\n New invocation of recon-all \n\n Wed Aug 7 04:27:09 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_ /Applications/Freesurfer5.3/freesurfer/bin/recon-all -s subjects_name_ -autorecon3 subjid subjects_name_ setenv SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Actual FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer build-stamp.txt: freesurfer-Darwin-lion-stable-pub-v5.3.0 Darwin Pedro-Rosas-MacBook-Pro-2.local 12.4.0 Darwin Kernel Version 12.4.0: Wed May 1 17:57:12 PDT 2013; root:xnu-2050.24.15~1/RELEASE_X86_64 x86_64 cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 256 memorylocked unlimited maxproc 709 PhysMem: 2117M wired, 3839M active, 1901M inactive, 7857M used, 8517M free. ######################################## 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: 2013/08/07-07:27:10-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-07:27:11-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@aspasia.local (i686-apple-darwin10.2.0) on 2010-02-26 at 14:19:30 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-07:27:11-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-07:27:11-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-07:27:11-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-07:27:11-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-07:27:11-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-07:27:11-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-07:27:11-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-07:27:11-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-07:27:11-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-07:27:11-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-07:27:11-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-07:27:11-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-07:27:11-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-07:27:11-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-07:27:11-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-07:27:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-07:27:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-07:27:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-07:27:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-07:27:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-07:27:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-07:27:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-07:27:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-07:27:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-07:27:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-07:27:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-07:27:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-07:27:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-07:27:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-07:27:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 $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: 2013/08/07-07:27:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 $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: 2013/08/07-07:27:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-07:27:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-07:27:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-07:27:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/07-07:27:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: pedrogomesrosa Machine: Pedro-Rosas-MacBook-Pro-2.local Platform: Darwin PlatformVersion: 12.4.0 CompilerName: GCC CompilerVersion: 40200 ####################################### GCADIR /Applications/Freesurfer5.3/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /Applications/Freesurfer5.3/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### \n#----------------------------------------- #@# Curvature Stats lh Wed Aug 7 04:27:13 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf \n mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm subjects_name_ lh curv sulc \n Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ subjects_name_/lh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 267 ] Gb_filter = 0 WARN: S lookup min: -0.167478 WARN: S explicit min: 0.000000 vertex = 1009 #-------------------------------------------- #@# Sphere lh Wed Aug 7 04:27:22 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/scripts \n mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere \n 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... scaling brain by 0.284... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=Pedro, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.86 pass 1: epoch 2 of 3 starting distance error %19.78 unfolding complete - removing small folds... starting distance error %19.68 removing remaining folds... final distance error %19.70 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/lh.sphere spherical transformation took 0.71 hours #-------------------------------------------- #@# Surf Reg lh Wed Aug 7 05:09:42 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/scripts \n mris_register -curv ../surf/lh.sphere /Applications/Freesurfer5.3/freesurfer/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg \n using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /Applications/Freesurfer5.3/freesurfer/average/lh.average.curvature.filled.buckner40.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=Pedro, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 0 randomSeed 0 tol=5.0e-01, sigma=0.0, host=Pedro, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading lh.sulc curvature mean = 0.000, std = 0.583 curvature mean = 0.042, std = 0.938 curvature mean = 0.020, std = 0.848 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, -16.00, 0.00) sse = 372625.4, tmin=1.0650 d=32.00 min @ (-8.00, 8.00, 8.00) sse = 285376.5, tmin=2.1162 d=16.00 min @ (4.00, 0.00, -4.00) sse = 272852.0, tmin=3.2802 d=8.00 min @ (-2.00, 0.00, 2.00) sse = 270344.3, tmin=4.4765 d=4.00 min @ (1.00, 0.00, -1.00) sse = 269438.8, tmin=5.6772 d=2.00 min @ (-0.50, -0.50, -0.50) sse = 268921.8, tmin=6.8807 d=1.00 min @ (0.00, 0.00, 0.25) sse = 268884.6, tmin=8.0223 d=0.50 min @ (0.00, 0.12, 0.00) sse = 268863.7, tmin=9.1760 tol=1.0e+00, sigma=0.5, host=Pedro, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 9.18 min curvature mean = 0.010, std = 0.946 curvature mean = 0.008, std = 0.938 curvature mean = 0.009, std = 0.958 curvature mean = 0.004, std = 0.972 curvature mean = 0.008, std = 0.960 curvature mean = 0.001, std = 0.988 2 Reading smoothwm curvature mean = -0.025, std = 0.259 curvature mean = 0.003, std = 0.067 curvature mean = 0.051, std = 0.394 curvature mean = 0.003, std = 0.079 curvature mean = 0.020, std = 0.604 curvature mean = 0.003, std = 0.086 curvature mean = 0.011, std = 0.745 curvature mean = 0.003, std = 0.088 curvature mean = 0.002, std = 0.848 MRISregister() return, current seed 0 writing registered surface to ../surf/lh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white lh Wed Aug 7 05:36:01 BRT 2013 \n mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white \n reading surface from ../surf/lh.white... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Wed Aug 7 05:36:04 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/scripts \n mrisp_paint -a 5 /Applications/Freesurfer5.3/freesurfer/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv \n averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /Applications/Freesurfer5.3/freesurfer/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Wed Aug 7 05:36:06 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/scripts \n mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 subjects_name_ lh ../surf/lh.sphere.reg /Applications/Freesurfer5.3/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot \n setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /Applications/Freesurfer5.3/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 1.0 using min determinant for regularization = 0.011 0 singular and 384 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1129 labels changed using aseg relabeling using gibbs priors... 000: 3060 changed, 140852 examined... 001: 672 changed, 13130 examined... 002: 148 changed, 3747 examined... 003: 61 changed, 941 examined... 004: 14 changed, 344 examined... 005: 5 changed, 82 examined... 006: 6 changed, 35 examined... 007: 1 changed, 35 examined... 008: 0 changed, 5 examined... 200 labels changed using aseg 000: 104 total segments, 63 labels (176 vertices) changed 001: 41 total segments, 1 labels (2 vertices) changed 002: 40 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 41 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1526 vertices marked for relabeling... 1526 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 55 seconds. #-------------------------------------------- #@# Make Pial Surf lh Wed Aug 7 05:37:01 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/scripts \n mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs subjects_name_ lh \n -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/filled.mgz... reading volume /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/brain.finalsurfs.mgz... reading volume /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/wm.mgz... 10399 bright wm thresholded. 1003 bright non-wm voxels segmented. reading original surface position from /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.orig... computing class statistics... border white: 271713 voxels (1.62%) border gray 292541 voxels (1.74%) WM (96.0): 96.7 +- 6.8 [70.0 --> 110.0] GM (85.0) : 83.2 +- 10.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 62.1 (was 70) setting MAX_BORDER_WHITE to 109.8 (was 105) setting MIN_BORDER_WHITE to 73.0 (was 85) setting MAX_CSF to 51.1 (was 40) setting MAX_GRAY to 96.2 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 67.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 40.2 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=103, GM=73 mean inside = 95.5, mean outside = 80.3 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->5.44) (max @ vno 84564 --> 140608) face area 0.28 +- 0.13 (0.00-->6.00) mean absolute distance = 0.73 +- 0.90 4745 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown deleting segment 2 with 414 points - only 0.00% unknown deleting segment 3 with 22 points - only 0.00% unknown mean border=84.2, 70 (70) missing vertices, mean dist 0.3 [0.6 (%37.7)->0.8 (%62.3))] %69 local maxima, %26 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=Pedro, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.26 (0.06-->6.58) (max @ vno 111891 --> 140697) face area 0.28 +- 0.14 (0.00-->4.00) mean absolute distance = 0.42 +- 0.68 4852 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4485563.5, rms=8.91 001: dt: 0.5000, sse=5064899.0, rms=6.351 (0.000%) 002: dt: 0.5000, sse=5326581.0, rms=4.729 (0.000%) 003: dt: 0.5000, sse=5638107.0, rms=3.743 (0.000%) 004: dt: 0.5000, sse=5802133.5, rms=3.129 (0.000%) 005: dt: 0.5000, sse=5984202.5, rms=2.839 (0.000%) 006: dt: 0.5000, sse=6044717.0, rms=2.674 (0.000%) 007: dt: 0.5000, sse=6142174.5, rms=2.618 (0.000%) 008: dt: 0.5000, sse=6125413.0, rms=2.552 (0.000%) rms = 2.55, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=6186094.5, rms=2.546 (0.000%) 010: dt: 0.2500, sse=3520150.0, rms=1.704 (0.000%) 011: dt: 0.2500, sse=3262859.8, rms=1.552 (0.000%) rms = 1.52, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=3176010.2, rms=1.523 (0.000%) rms = 1.50, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=3129336.5, rms=1.504 (0.000%) positioning took 1.9 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 3 with 349 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 7 with 22 points - only 0.00% unknown deleting segment 9 with 60 points - only 0.00% unknown deleting segment 10 with 5 points - only 0.00% unknown mean border=86.5, 40 (13) missing vertices, mean dist -0.2 [0.5 (%65.8)->0.3 (%34.2))] %77 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=Pedro, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.24 (0.07-->6.74) (max @ vno 111891 --> 140697) face area 0.35 +- 0.17 (0.00-->5.28) mean absolute distance = 0.34 +- 0.48 5741 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3700955.2, rms=4.33 014: dt: 0.5000, sse=3953913.5, rms=2.817 (0.000%) 015: dt: 0.5000, sse=4324836.5, rms=2.346 (0.000%) 016: dt: 0.5000, sse=4594112.5, rms=2.090 (0.000%) rms = 2.12, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=3838066.2, rms=1.657 (0.000%) 018: dt: 0.2500, sse=3548236.5, rms=1.375 (0.000%) 019: dt: 0.2500, sse=3455339.8, rms=1.279 (0.000%) rms = 1.25, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=3421735.0, rms=1.248 (0.000%) rms = 1.23, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=3389263.5, rms=1.228 (0.000%) positioning took 1.3 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown deleting segment 1 with 401 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 2 with 4 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 12 points - only 50.00% unknown deleting segment 5 with 24 points - only 0.00% unknown deleting segment 7 with 72 points - only 0.00% unknown deleting segment 8 with 5 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 9 with 1 points - only 0.00% unknown mean border=88.6, 43 (6) missing vertices, mean dist -0.2 [0.4 (%68.5)->0.2 (%31.5))] %84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=Pedro, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.24 (0.05-->6.86) (max @ vno 111891 --> 140697) face area 0.34 +- 0.16 (0.00-->5.28) mean absolute distance = 0.28 +- 0.38 5357 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3594372.2, rms=3.22 022: dt: 0.5000, sse=3849933.8, rms=2.004 (0.000%) 023: dt: 0.5000, sse=4067993.2, rms=1.859 (0.000%) 024: dt: 0.5000, sse=4370754.0, rms=1.794 (0.000%) rms = 2.01, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=3799445.8, rms=1.343 (0.000%) 026: dt: 0.2500, sse=3596291.2, rms=1.165 (0.000%) rms = 1.13, time step reduction 2 of 3 to 0.125... 027: dt: 0.2500, sse=3534032.0, rms=1.134 (0.000%) rms = 1.12, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=3501080.8, rms=1.119 (0.000%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 445 points - only 0.00% unknown deleting segment 1 with 5 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 2 with 4 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 24 points - only 0.00% unknown deleting segment 5 with 72 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 6 with 1 points - only 0.00% unknown mean border=89.5, 34 (4) missing vertices, mean dist -0.1 [0.3 (%58.4)->0.2 (%41.6))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=Pedro, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=3525774.0, rms=1.70 029: dt: 0.5000, sse=4252497.0, rms=1.268 (0.000%) rms = 1.50, time step reduction 1 of 3 to 0.250... 030: dt: 0.2500, sse=3919016.8, rms=1.023 (0.000%) 031: dt: 0.2500, sse=3762871.5, rms=0.955 (0.000%) rms = 0.92, time step reduction 2 of 3 to 0.125... 032: dt: 0.2500, sse=3795576.5, rms=0.918 (0.000%) rms = 0.92, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=3796450.5, rms=0.917 (0.000%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 2 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group smoothing surface for 5 iterations... mean border=63.4, 53 (53) missing vertices, mean dist 1.6 [0.1 (%0.0)->2.6 (%100.0))] %20 local maxima, %38 large gradients and %38 min vals, 2353 gradients ignored tol=1.0e-04, sigma=2.0, host=Pedro, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=21977946.0, rms=26.88 001: dt: 0.5000, sse=17452128.0, rms=23.578 (0.000%) 002: dt: 0.5000, sse=13921891.0, rms=20.676 (0.000%) 003: dt: 0.5000, sse=11285545.0, rms=18.161 (0.000%) 004: dt: 0.5000, sse=9432256.0, rms=15.981 (0.000%) 005: dt: 0.5000, sse=8169957.0, rms=14.123 (0.000%) 006: dt: 0.5000, sse=7335595.0, rms=12.549 (0.000%) 007: dt: 0.5000, sse=6780724.0, rms=11.135 (0.000%) 008: dt: 0.5000, sse=6350176.5, rms=9.795 (0.000%) 009: dt: 0.5000, sse=5999817.0, rms=8.493 (0.000%) 010: dt: 0.5000, sse=5771654.0, rms=7.221 (0.000%) 011: dt: 0.5000, sse=5603694.5, rms=6.052 (0.000%) 012: dt: 0.5000, sse=5618356.5, rms=5.065 (0.000%) 013: dt: 0.5000, sse=5629188.0, rms=4.349 (0.000%) 014: dt: 0.5000, sse=5719791.0, rms=3.895 (0.000%) 015: dt: 0.5000, sse=5818904.0, rms=3.637 (0.000%) 016: dt: 0.5000, sse=5846451.0, rms=3.491 (0.000%) 017: dt: 0.5000, sse=5877725.5, rms=3.421 (0.000%) 018: dt: 0.5000, sse=5885787.5, rms=3.369 (0.000%) rms = 3.35, time step reduction 1 of 3 to 0.250... 019: dt: 0.5000, sse=5915129.0, rms=3.353 (0.000%) 020: dt: 0.2500, sse=4028112.8, rms=2.683 (0.000%) 021: dt: 0.2500, sse=3887849.8, rms=2.527 (0.000%) rms = 2.50, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=3801764.2, rms=2.501 (0.000%) 023: dt: 0.1250, sse=3626396.8, rms=2.408 (0.000%) rms = 2.40, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=3613098.8, rms=2.398 (0.000%) positioning took 3.7 minutes mean border=61.7, 1336 (14) missing vertices, mean dist 0.1 [0.2 (%47.1)->0.5 (%52.9))] %34 local maxima, %30 large gradients and %31 min vals, 984 gradients ignored tol=1.0e-04, sigma=1.0, host=Pedro, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4101938.0, rms=4.04 025: dt: 0.5000, sse=4335379.0, rms=3.245 (0.000%) rms = 3.26, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=4053081.0, rms=2.778 (0.000%) 027: dt: 0.2500, sse=4089415.5, rms=2.549 (0.000%) 028: dt: 0.2500, sse=4058649.2, rms=2.458 (0.000%) rms = 2.42, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=4084595.2, rms=2.419 (0.000%) 030: dt: 0.1250, sse=3956812.8, rms=2.334 (0.000%) rms = 2.32, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=3959498.2, rms=2.316 (0.000%) positioning took 1.2 minutes mean border=60.8, 1586 (8) missing vertices, mean dist 0.1 [0.2 (%47.3)->0.4 (%52.7))] %43 local maxima, %21 large gradients and %30 min vals, 1093 gradients ignored tol=1.0e-04, sigma=0.5, host=Pedro, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4030069.2, rms=2.74 rms = 2.87, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=3935534.8, rms=2.473 (0.000%) 033: dt: 0.2500, sse=4000804.5, rms=2.321 (0.000%) 034: dt: 0.2500, sse=4102187.2, rms=2.268 (0.000%) rms = 2.25, time step reduction 2 of 3 to 0.125... 035: dt: 0.2500, sse=4146678.5, rms=2.245 (0.000%) 036: dt: 0.1250, sse=4052046.2, rms=2.186 (0.000%) rms = 2.17, time step reduction 3 of 3 to 0.062... 037: dt: 0.1250, sse=4066364.5, rms=2.173 (0.000%) positioning took 1.0 minutes mean border=60.2, 3455 (7) missing vertices, mean dist 0.0 [0.2 (%49.2)->0.3 (%50.8))] %47 local maxima, %17 large gradients and %29 min vals, 999 gradients ignored tol=1.0e-04, sigma=0.2, host=Pedro, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=4090082.5, rms=2.36 rms = 2.55, time step reduction 1 of 3 to 0.250... 038: dt: 0.2500, sse=4028468.2, rms=2.226 (0.000%) 039: dt: 0.2500, sse=4145846.2, rms=2.151 (0.000%) rms = 2.12, time step reduction 2 of 3 to 0.125... 040: dt: 0.2500, sse=4190312.5, rms=2.123 (0.000%) 041: dt: 0.1250, sse=4111257.0, rms=2.072 (0.000%) rms = 2.06, time step reduction 3 of 3 to 0.062... 042: dt: 0.1250, sse=4130477.2, rms=2.059 (0.000%) positioning took 0.8 minutes writing curvature file /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.area.pial vertex spacing 0.98 +- 0.40 (0.07-->7.15) (max @ vno 94405 --> 94421) face area 0.38 +- 0.28 (0.00-->7.47) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 140852 vertices processed 25000 of 140852 vertices processed 50000 of 140852 vertices processed 75000 of 140852 vertices processed 100000 of 140852 vertices processed 125000 of 140852 vertices processed 0 of 140852 vertices processed 25000 of 140852 vertices processed 50000 of 140852 vertices processed 75000 of 140852 vertices processed 100000 of 140852 vertices processed 125000 of 140852 vertices processed thickness calculation complete, 578:740 truncations. 35303 vertices at 0 distance 98671 vertices at 1 distance 81307 vertices at 2 distance 35513 vertices at 3 distance 12887 vertices at 4 distance 4180 vertices at 5 distance 1339 vertices at 6 distance 467 vertices at 7 distance 183 vertices at 8 distance 84 vertices at 9 distance 47 vertices at 10 distance 33 vertices at 11 distance 31 vertices at 12 distance 16 vertices at 13 distance 5 vertices at 14 distance 4 vertices at 15 distance 6 vertices at 16 distance 6 vertices at 17 distance 4 vertices at 18 distance 5 vertices at 19 distance 3 vertices at 20 distance writing curvature file /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.thickness positioning took 15.9 minutes #-------------------------------------------- #@# Surf Volume lh Wed Aug 7 05:52:58 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf \n mris_calc -o lh.area.mid lh.area add lh.area.pial \n Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] \n mris_calc -o lh.area.mid lh.area.mid div 2 \n Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] \n mris_calc -o lh.volume lh.area.mid mul lh.thickness \n Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# WM/GM Contrast lh Wed Aug 7 05:52:58 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/scripts \n pctsurfcon --s subjects_name_ --lh-only \n Log file is /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/scripts/pctsurfcon.log Wed Aug 7 05:52:58 BRT 2013 setenv SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 cd /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/scripts /Applications/Freesurfer5.3/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Darwin Pedro-Rosas-MacBook-Pro-2.local 12.4.0 Darwin Kernel Version 12.4.0: Wed May 1 17:57:12 PDT 2013; root:xnu-2050.24.15~1/RELEASE_X86_64 x86_64 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer mri_vol2surf --mov /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/tmp.pctsurfcon.40516/lh.wm.mgh --regheader subjects_name_ --cortex srcvol = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/orig.mgz as target reference. Loading label /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/label/lh.cortex.label Reading surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 58514 Masking with /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/label/lh.cortex.label Writing to /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/tmp.pctsurfcon.40516/lh.wm.mgh Dim: 140852 1 1 mri_vol2surf --mov /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/tmp.pctsurfcon.40516/lh.gm.mgh --projfrac 0.3 --regheader subjects_name_ --cortex srcvol = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/orig.mgz as target reference. Loading label /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/label/lh.cortex.label Reading surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.white Done reading source surface Reading thickness /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 67882 Masking with /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/label/lh.cortex.label Writing to /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/tmp.pctsurfcon.40516/lh.gm.mgh Dim: 140852 1 1 mri_concat /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/tmp.pctsurfcon.40516/lh.wm.mgh /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/tmp.pctsurfcon.40516/lh.gm.mgh --paired-diff-norm --mul 100 --o /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.w-g.pct.mgh mri_segstats --in /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.w-g.pct.mgh --annot subjects_name_ lh aparc --sum /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/stats/lh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --in /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.w-g.pct.mgh --annot subjects_name_ lh aparc --sum /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/stats/lh.w-g.pct.stats --snr sysname Darwin hostname Pedro-Rosas-MacBook-Pro-2.local machine x86_64 user pedrogomesrosa UseRobust 0 Constructing seg from annotation Reading annotation reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Seg base 1000 Loading /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.w-g.pct.mgh Vertex Area is 0.649958 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 1000 unknown 0 0.000 1 1001 bankssts 1444 986.358 2 1002 caudalanteriorcingulate 968 642.997 3 1003 caudalmiddlefrontal 3297 2123.157 4 1004 corpuscallosum 0 0.000 5 1005 cuneus 2742 1810.921 6 1006 entorhinal 388 278.683 7 1007 fusiform 5784 3886.837 8 1008 inferiorparietal 8287 5467.752 9 1009 inferiortemporal 4857 3189.091 10 1010 isthmuscingulate 1573 990.804 11 1011 lateraloccipital 7662 4858.390 12 1012 lateralorbitofrontal 3909 2645.249 13 1013 lingual 5044 3320.433 14 1014 medialorbitofrontal 2735 1853.294 15 1015 middletemporal 4486 2959.037 16 1016 parahippocampal 1358 887.773 17 1017 paracentral 2259 1363.663 18 1018 parsopercularis 2770 1858.931 19 1019 parsorbitalis 984 645.098 20 1020 parstriangularis 1982 1310.213 21 1021 pericalcarine 2510 1740.166 22 1022 postcentral 7105 4399.843 23 1023 posteriorcingulate 1941 1263.971 24 1024 precentral 7191 4366.501 25 1025 precuneus 5149 3376.010 26 1026 rostralanteriorcingulate 1139 728.105 27 1027 rostralmiddlefrontal 7652 5145.832 28 1028 superiorfrontal 10276 6588.697 29 1029 superiorparietal 9443 5983.725 30 1030 superiortemporal 5927 3845.373 31 1031 supramarginal 6785 4480.977 32 1032 frontalpole 328 217.044 33 1033 temporalpole 671 472.997 34 1034 transversetemporal 875 541.328 35 1035 insula 3295 2134.879 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats lh Wed Aug 7 05:53:06 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/scripts \n mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab subjects_name_ lh white \n computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/wm.mgz... reading input surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.white... reading input pial surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.pial... reading input white surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1444 986 2339 2.417 0.475 0.100 0.025 9 1.4 bankssts 968 643 2140 2.832 0.736 0.162 0.054 19 2.2 caudalanteriorcingulate 3297 2123 5846 2.595 0.578 0.119 0.031 28 4.3 caudalmiddlefrontal 2742 1811 2900 1.572 0.412 0.157 0.053 41 6.3 cuneus 388 279 1330 3.477 0.819 0.133 0.060 6 0.8 entorhinal 5784 3887 12031 2.806 0.623 0.139 0.045 73 10.6 fusiform 8287 5468 14810 2.446 0.717 0.137 0.043 110 13.6 inferiorparietal 4857 3189 10999 3.050 0.683 0.137 0.052 73 11.7 inferiortemporal 1573 991 2864 2.642 0.717 0.159 0.384 2080 43.5 isthmuscingulate 7662 4858 11099 2.115 0.607 0.141 0.050 103 14.8 lateraloccipital 3909 2645 7597 2.730 0.868 0.147 0.053 57 8.3 lateralorbitofrontal 5044 3320 6913 1.964 0.646 0.147 0.056 70 11.4 lingual 2735 1853 4898 2.384 0.804 0.164 0.146 160 15.8 medialorbitofrontal 4486 2959 11116 3.094 0.821 0.136 0.044 63 8.2 middletemporal 1358 888 2442 2.352 0.581 0.095 0.034 10 1.6 parahippocampal 2259 1364 2905 2.024 0.599 0.118 0.038 26 3.9 paracentral 2770 1859 5424 2.642 0.563 0.123 0.034 30 3.9 parsopercularis 984 645 2248 2.585 0.763 0.144 0.042 13 1.8 parsorbitalis 1982 1310 3725 2.421 0.750 0.130 0.043 22 3.4 parstriangularis 2510 1740 2101 1.394 0.414 0.158 0.056 42 6.0 pericalcarine 7105 4400 9332 1.944 0.728 0.118 0.040 83 13.3 postcentral 1941 1264 3474 2.483 0.670 0.146 0.047 55 3.5 posteriorcingulate 7191 4367 11816 2.541 0.737 0.116 0.037 66 11.7 precentral 5149 3376 8020 2.246 0.638 0.130 0.042 79 8.9 precuneus 1139 728 2608 3.187 0.791 0.143 0.050 19 2.3 rostralanteriorcingulate 7652 5146 14058 2.352 0.690 0.148 0.053 129 16.8 rostralmiddlefrontal 10276 6589 20451 2.795 0.633 0.127 0.062 152 29.3 superiorfrontal 9443 5984 13297 2.083 0.615 0.131 0.045 132 18.1 superiorparietal 5927 3845 12265 2.803 0.689 0.112 0.034 55 8.3 superiortemporal 6785 4481 12736 2.532 0.685 0.127 0.035 72 10.0 supramarginal 328 217 790 2.634 0.651 0.195 0.092 9 1.2 frontalpole 671 473 2348 3.459 0.729 0.168 0.061 10 1.9 temporalpole 875 541 1373 2.225 0.558 0.134 0.060 10 2.4 transversetemporal 3295 2135 6861 3.111 0.718 0.123 0.052 39 6.7 insula #----------------------------------------- #@# Cortical Parc 2 lh Wed Aug 7 05:53:29 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/scripts \n mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 subjects_name_ lh ../surf/lh.sphere.reg /Applications/Freesurfer5.3/freesurfer/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot \n setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /Applications/Freesurfer5.3/freesurfer/average/lh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 3.9 0.2 using min determinant for regularization = 0.000 0 singular and 1066 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 91 labels changed using aseg relabeling using gibbs priors... 000: 9428 changed, 140852 examined... 001: 2357 changed, 36199 examined... 002: 725 changed, 12221 examined... 003: 313 changed, 4050 examined... 004: 137 changed, 1760 examined... 005: 86 changed, 824 examined... 006: 60 changed, 471 examined... 007: 34 changed, 323 examined... 008: 15 changed, 189 examined... 009: 3 changed, 91 examined... 010: 1 changed, 20 examined... 011: 0 changed, 5 examined... 46 labels changed using aseg 000: 297 total segments, 215 labels (2299 vertices) changed 001: 96 total segments, 14 labels (47 vertices) changed 002: 82 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 120 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 769 vertices marked for relabeling... 769 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 1 minutes and 13 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Wed Aug 7 05:54:42 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/scripts \n mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab subjects_name_ lh white \n computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/wm.mgz... reading input surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.white... reading input pial surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.pial... reading input white surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1147 794 2198 2.312 0.807 0.157 0.054 18 2.2 G_and_S_frontomargin 1968 1337 3370 2.227 0.598 0.143 0.040 26 3.3 G_and_S_occipital_inf 1586 917 1958 1.887 0.525 0.116 0.041 19 2.8 G_and_S_paracentral 1800 1199 3511 2.521 0.678 0.138 0.046 24 3.4 G_and_S_subcentral 658 423 1617 2.727 0.649 0.174 0.077 13 2.1 G_and_S_transv_frontopol 2422 1605 4861 2.772 0.820 0.139 0.051 35 4.9 G_and_S_cingul-Ant 1244 867 2507 2.859 0.592 0.138 0.040 16 1.9 G_and_S_cingul-Mid-Ant 1450 972 2510 2.423 0.672 0.118 0.039 37 2.0 G_and_S_cingul-Mid-Post 574 370 1383 2.949 0.539 0.200 0.920 2061 40.6 G_cingul-Post-dorsal 484 275 871 2.591 0.758 0.138 0.100 12 2.0 G_cingul-Post-ventral 2495 1670 2607 1.461 0.393 0.159 0.056 45 6.2 G_cuneus 1486 973 3573 2.843 0.516 0.138 0.043 21 2.6 G_front_inf-Opercular 226 145 634 2.903 0.495 0.163 0.047 4 0.5 G_front_inf-Orbital 1316 863 3037 2.691 0.647 0.149 0.055 22 3.1 G_front_inf-Triangul 4285 2746 8965 2.584 0.662 0.152 0.060 85 10.8 G_front_middle 7090 4366 15506 2.912 0.621 0.136 0.072 133 22.3 G_front_sup 510 312 1221 3.304 0.589 0.127 0.050 7 0.9 G_Ins_lg_and_S_cent_ins 807 520 2399 3.622 0.544 0.150 0.081 16 3.0 G_insular_short 2860 1735 5928 2.700 0.664 0.139 0.053 49 5.2 G_occipital_middle 1775 1034 2339 2.141 0.510 0.147 0.069 36 5.1 G_occipital_sup 2728 1796 6282 2.944 0.545 0.152 0.055 46 6.0 G_oc-temp_lat-fusifor 3787 2449 5228 1.882 0.657 0.156 0.062 59 9.4 G_oc-temp_med-Lingual 1252 815 2895 2.725 0.730 0.107 0.048 12 2.1 G_oc-temp_med-Parahip 2421 1613 5912 2.887 0.853 0.161 0.063 49 6.4 G_orbital 3263 2070 7548 2.750 0.794 0.142 0.049 47 6.5 G_pariet_inf-Angular 3285 2169 7424 2.760 0.662 0.134 0.038 42 5.2 G_pariet_inf-Supramar 3836 2317 6791 2.343 0.707 0.128 0.048 61 8.5 G_parietal_sup 2835 1564 3623 1.952 0.675 0.120 0.052 45 7.5 G_postcentral 2771 1429 5471 2.871 0.738 0.107 0.037 26 4.5 G_precentral 2497 1607 4676 2.389 0.612 0.140 0.051 57 5.2 G_precuneus 993 666 2227 2.467 0.598 0.184 0.086 28 3.6 G_rectus 503 336 794 2.446 1.023 0.226 0.513 115 10.3 G_subcallosal 707 423 1214 2.283 0.596 0.135 0.062 9 1.9 G_temp_sup-G_T_transv 2255 1374 6331 3.229 0.699 0.133 0.051 34 4.7 G_temp_sup-Lateral 640 447 1722 3.258 0.509 0.107 0.045 6 0.7 G_temp_sup-Plan_polar 1298 900 2467 2.444 0.624 0.112 0.031 11 1.6 G_temp_sup-Plan_tempo 2301 1466 6359 3.310 0.656 0.150 0.073 48 8.2 G_temporal_inf 2925 1877 8314 3.320 0.737 0.147 0.051 50 6.2 G_temporal_middle 326 216 368 1.758 0.461 0.108 0.026 2 0.3 Lat_Fis-ant-Horizont 391 283 494 2.052 0.736 0.120 0.022 3 0.4 Lat_Fis-ant-Vertical 1151 780 1397 2.212 0.465 0.128 0.037 9 1.8 Lat_Fis-post 2037 1293 2653 1.928 0.516 0.154 0.058 35 4.9 Pole_occipital 1685 1189 5607 3.451 0.687 0.160 0.057 26 4.1 Pole_temporal 2974 2010 3004 1.759 0.707 0.153 0.055 43 7.2 S_calcarine 3085 2103 3360 1.837 0.757 0.116 0.035 23 4.6 S_central 1145 788 1728 2.211 0.551 0.141 0.040 13 2.0 S_cingul-Marginalis 523 353 911 2.695 0.798 0.097 0.025 3 0.5 S_circular_insula_ant 1486 982 2380 2.736 0.683 0.082 0.018 5 1.1 S_circular_insula_inf 1861 1233 2913 2.710 0.523 0.118 0.033 15 2.7 S_circular_insula_sup 677 477 1273 2.986 0.715 0.133 0.035 6 0.9 S_collat_transv_ant 393 266 469 2.183 0.569 0.147 0.046 4 0.7 S_collat_transv_post 2121 1441 2999 2.249 0.514 0.116 0.031 16 2.7 S_front_inf 1459 1002 2002 2.026 0.547 0.121 0.031 12 1.9 S_front_middle 2633 1770 4145 2.445 0.502 0.110 0.048 21 7.2 S_front_sup 509 338 717 2.328 0.513 0.114 0.031 4 0.8 S_interm_prim-Jensen 3436 2353 3986 1.903 0.491 0.125 0.030 32 4.3 S_intrapariet_and_P_trans 1137 773 1188 1.756 0.365 0.151 0.046 13 2.1 S_oc_middle_and_Lunatus 1525 1029 1741 1.992 0.486 0.133 0.035 13 2.3 S_oc_sup_and_transversal 712 475 1017 2.234 0.473 0.140 0.045 8 1.1 S_occipital_ant 1118 728 1685 2.708 0.488 0.114 0.032 8 1.5 S_oc-temp_lat 2385 1658 3592 2.374 0.545 0.101 0.022 12 2.2 S_oc-temp_med_and_Lingual 417 281 647 2.207 0.661 0.156 0.046 5 0.8 S_orbital_lateral 714 551 1116 2.215 0.891 0.127 0.033 8 0.9 S_orbital_med-olfact 1640 1098 2800 2.639 0.824 0.137 0.044 19 2.7 S_orbital-H_Shaped 2043 1321 2296 1.914 0.635 0.124 0.035 19 3.0 S_parieto_occipital 1026 605 1078 2.278 0.800 0.152 0.047 22 1.8 S_pericallosal 3515 2341 4154 1.993 0.536 0.121 0.032 29 4.4 S_postcentral 1391 933 2048 2.522 0.622 0.100 0.022 7 1.3 S_precentral-inf-part 1310 872 1638 2.239 0.558 0.103 0.023 7 1.3 S_precentral-sup-part 577 380 913 2.713 0.894 0.122 0.029 5 0.7 S_suborbital 1075 716 1454 2.093 0.524 0.126 0.036 10 1.5 S_subparietal 1405 977 2090 2.526 0.669 0.117 0.027 10 1.6 S_temporal_inf 5976 3994 8484 2.330 0.529 0.114 0.030 50 6.8 S_temporal_sup 478 313 535 2.039 0.327 0.109 0.027 3 0.5 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Wed Aug 7 05:55:08 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/scripts \n mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 subjects_name_ lh ../surf/lh.sphere.reg /Applications/Freesurfer5.3/freesurfer/average/lh.DKTatlas40.gcs ../label/lh.aparc.DKTatlas40.annot \n setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /Applications/Freesurfer5.3/freesurfer/average/lh.DKTatlas40.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.007 0 singular and 293 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1287 labels changed using aseg relabeling using gibbs priors... 000: 2831 changed, 140852 examined... 001: 689 changed, 12027 examined... 002: 188 changed, 3798 examined... 003: 74 changed, 1155 examined... 004: 41 changed, 447 examined... 005: 19 changed, 212 examined... 006: 11 changed, 110 examined... 007: 6 changed, 76 examined... 008: 6 changed, 42 examined... 009: 1 changed, 33 examined... 010: 1 changed, 9 examined... 011: 1 changed, 5 examined... 012: 0 changed, 11 examined... 174 labels changed using aseg 000: 68 total segments, 35 labels (253 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 45 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 618 vertices marked for relabeling... 618 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas40.annot... classification took 0 minutes and 56 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Wed Aug 7 05:56:04 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/scripts \n mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab subjects_name_ lh white \n computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot. reading volume /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/wm.mgz... reading input surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.white... reading input pial surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.pial... reading input white surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /Applications/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas40.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1500 1001 2996 2.797 0.664 0.145 0.046 23 2.7 caudalanteriorcingulate 3408 2192 6058 2.604 0.580 0.119 0.031 29 4.5 caudalmiddlefrontal 3766 2440 4033 1.634 0.433 0.149 0.050 52 8.1 cuneus 412 289 1309 3.372 0.826 0.126 0.058 5 0.8 entorhinal 5382 3593 10516 2.752 0.597 0.138 0.045 68 9.7 fusiform 7950 5237 14308 2.465 0.723 0.138 0.043 106 13.2 inferiorparietal 4676 3092 11483 3.132 0.702 0.142 0.055 72 12.0 inferiortemporal 1526 954 2773 2.648 0.717 0.158 0.394 2079 43.4 isthmuscingulate 7869 4997 11514 2.116 0.610 0.141 0.049 106 14.8 lateraloccipital 4125 2819 8621 2.793 0.899 0.153 0.056 67 9.1 lateralorbitofrontal 5032 3311 6919 1.967 0.648 0.147 0.056 71 11.4 lingual 2325 1566 4144 2.288 0.691 0.172 0.163 154 15.1 medialorbitofrontal 5976 3965 13419 2.929 0.813 0.130 0.040 75 9.9 middletemporal 1366 890 2460 2.354 0.579 0.094 0.034 10 1.6 parahippocampal 2618 1588 3430 2.052 0.595 0.116 0.036 28 4.3 paracentral 2524 1690 5025 2.674 0.546 0.125 0.035 28 3.7 parsopercularis 1132 734 2287 2.510 0.707 0.132 0.037 12 1.9 parsorbitalis 2391 1611 4347 2.387 0.719 0.134 0.042 27 4.2 parstriangularis 2476 1713 2067 1.396 0.415 0.158 0.056 41 5.9 pericalcarine 7722 4824 10098 1.963 0.719 0.119 0.040 89 14.2 postcentral 2025 1332 3533 2.450 0.673 0.145 0.046 55 3.5 posteriorcingulate 7078 4296 11620 2.546 0.738 0.115 0.037 66 11.4 precentral 5050 3290 8018 2.261 0.645 0.132 0.044 80 9.1 precuneus 1489 967 3198 3.096 0.847 0.144 0.051 25 3.0 rostralanteriorcingulate 5069 3369 9315 2.340 0.706 0.146 0.053 91 11.4 rostralmiddlefrontal 11721 7569 23439 2.729 0.657 0.132 0.063 178 33.3 superiorfrontal 7763 4950 11301 2.116 0.634 0.132 0.046 114 15.4 superiorparietal 7938 5223 16910 2.803 0.704 0.117 0.037 79 11.8 superiortemporal 6667 4403 12316 2.512 0.682 0.127 0.036 71 9.9 supramarginal 857 528 1341 2.218 0.561 0.135 0.061 10 2.4 transversetemporal 2983 1931 6355 3.150 0.721 0.120 0.049 34 6.1 insula \n#----------------------------------------- #@# Curvature Stats rh Wed Aug 7 05:56:25 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf \n mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm subjects_name_ rh curv sulc \n Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/rh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ subjects_name_/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 253 ] Gb_filter = 0 WARN: S lookup min: -0.161966 WARN: S explicit min: 0.000000 vertex = 630 #-------------------------------------------- #@# Sphere rh Wed Aug 7 05:56:34 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/scripts \n mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere \n 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... scaling brain by 0.288... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=Pedro, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %20.35 pass 1: epoch 2 of 3 starting distance error %20.32 unfolding complete - removing small folds... starting distance error %20.25 removing remaining folds... final distance error %20.27 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/rh.sphere spherical transformation took 0.59 hours #-------------------------------------------- #@# Surf Reg rh Wed Aug 7 06:31:59 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/scripts \n mris_register -curv ../surf/rh.sphere /Applications/Freesurfer5.3/freesurfer/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg \n using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /Applications/Freesurfer5.3/freesurfer/average/rh.average.curvature.filled.buckner40.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=Pedro, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 1 randomSeed 0 tol=5.0e-01, sigma=0.0, host=Pedro, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading rh.sulc curvature mean = 0.000, std = 0.602 curvature mean = 0.040, std = 0.931 curvature mean = 0.021, std = 0.857 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, -16.00, 16.00) sse = 387896.3, tmin=1.0251 d=32.00 min @ (0.00, 0.00, -8.00) sse = 346775.0, tmin=2.0334 d=8.00 min @ (-2.00, 0.00, 0.00) sse = 346348.7, tmin=4.1511 d=4.00 min @ (1.00, -1.00, 1.00) sse = 344531.3, tmin=5.2173 d=2.00 min @ (0.00, 0.50, 0.00) sse = 344378.3, tmin=6.2896 d=0.50 min @ (0.00, -0.12, -0.12) sse = 344360.4, tmin=8.5943 tol=1.0e+00, sigma=0.5, host=Pedro, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 8.59 min curvature mean = 0.006, std = 0.947 curvature mean = 0.010, std = 0.936 curvature mean = 0.000, std = 0.953 curvature mean = 0.005, std = 0.970 curvature mean = -0.002, std = 0.953 curvature mean = 0.001, std = 0.986 2 Reading smoothwm curvature mean = -0.028, std = 0.276 curvature mean = 0.005, std = 0.070 curvature mean = 0.057, std = 0.370 curvature mean = 0.005, std = 0.083 curvature mean = 0.023, std = 0.570 curvature mean = 0.005, std = 0.090 curvature mean = 0.013, std = 0.709 curvature mean = 0.006, std = 0.092 curvature mean = 0.005, std = 0.805 MRISregister() return, current seed 0 writing registered surface to ../surf/rh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white rh Wed Aug 7 06:59:37 BRT 2013 \n mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white \n reading surface from ../surf/rh.white... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv rh Wed Aug 7 06:59:39 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/scripts \n mrisp_paint -a 5 /Applications/Freesurfer5.3/freesurfer/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv \n averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /Applications/Freesurfer5.3/freesurfer/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Wed Aug 7 06:59:41 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/scripts \n mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 subjects_name_ rh ../surf/rh.sphere.reg /Applications/Freesurfer5.3/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot \n setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /Applications/Freesurfer5.3/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.006 0 singular and 311 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1128 labels changed using aseg relabeling using gibbs priors... 000: 2985 changed, 141108 examined... 001: 680 changed, 12719 examined... 002: 180 changed, 3871 examined... 003: 61 changed, 1108 examined... 004: 24 changed, 360 examined... 005: 16 changed, 150 examined... 006: 11 changed, 96 examined... 007: 3 changed, 71 examined... 008: 2 changed, 18 examined... 009: 1 changed, 11 examined... 010: 1 changed, 8 examined... 011: 1 changed, 7 examined... 012: 1 changed, 8 examined... 013: 0 changed, 8 examined... 169 labels changed using aseg 000: 97 total segments, 58 labels (333 vertices) changed 001: 40 total segments, 1 labels (3 vertices) changed 002: 39 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 29 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1091 vertices marked for relabeling... 1091 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 54 seconds. #-------------------------------------------- #@# Make Pial Surf rh Wed Aug 7 07:00:36 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/scripts \n mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs subjects_name_ rh \n -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/filled.mgz... reading volume /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/brain.finalsurfs.mgz... reading volume /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/wm.mgz... 9941 bright wm thresholded. 1000 bright non-wm voxels segmented. reading original surface position from /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.orig... computing class statistics... border white: 271713 voxels (1.62%) border gray 292541 voxels (1.74%) WM (96.0): 96.8 +- 6.9 [70.0 --> 110.0] GM (85.0) : 83.3 +- 10.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 63.2 (was 70) setting MAX_BORDER_WHITE to 110.9 (was 105) setting MIN_BORDER_WHITE to 74.0 (was 85) setting MAX_CSF to 52.4 (was 40) setting MAX_GRAY to 97.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 68.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 41.6 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104, GM=74 mean inside = 95.8, mean outside = 80.4 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.04-->4.41) (max @ vno 54423 --> 140844) face area 0.28 +- 0.12 (0.00-->4.72) mean absolute distance = 0.71 +- 0.90 3980 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 3 with 2 points - only 0.00% unknown deleting segment 4 with 25 points - only 0.00% unknown deleting segment 5 with 6 points - only 0.00% unknown deleting segment 6 with 187 points - only 0.00% unknown deleting segment 7 with 6 points - only 0.00% unknown removing 4 vertex label from ripped group mean border=84.8, 17 (17) missing vertices, mean dist 0.3 [0.6 (%38.8)->0.8 (%61.2))] %69 local maxima, %27 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=Pedro, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.25 (0.06-->6.33) (max @ vno 47581 --> 140702) face area 0.28 +- 0.13 (0.00-->5.43) mean absolute distance = 0.40 +- 0.66 3978 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4471232.5, rms=8.73 001: dt: 0.5000, sse=5090976.0, rms=6.104 (0.000%) 002: dt: 0.5000, sse=5398001.0, rms=4.498 (0.000%) 003: dt: 0.5000, sse=5714904.0, rms=3.560 (0.000%) 004: dt: 0.5000, sse=5926428.5, rms=3.005 (0.000%) 005: dt: 0.5000, sse=6063620.0, rms=2.748 (0.000%) 006: dt: 0.5000, sse=6136223.0, rms=2.600 (0.000%) rms = 2.56, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=6201156.5, rms=2.560 (0.000%) 008: dt: 0.2500, sse=3579330.8, rms=1.681 (0.000%) 009: dt: 0.2500, sse=3314880.5, rms=1.515 (0.000%) rms = 1.48, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=3228992.5, rms=1.478 (0.000%) rms = 1.45, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=3181748.5, rms=1.454 (0.000%) positioning took 1.6 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 4 with 4 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown deleting segment 6 with 21 points - only 0.00% unknown deleting segment 7 with 161 points - only 0.00% unknown deleting segment 10 with 9 points - only 0.00% unknown deleting segment 13 with 6 points - only 33.33% unknown mean border=87.1, 19 (6) missing vertices, mean dist -0.2 [0.5 (%66.8)->0.3 (%33.2))] %76 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=Pedro, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.24 (0.12-->6.71) (max @ vno 47581 --> 140702) face area 0.35 +- 0.16 (0.00-->7.61) mean absolute distance = 0.32 +- 0.48 4600 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3710762.5, rms=4.13 012: dt: 0.5000, sse=4027035.5, rms=2.563 (0.000%) 013: dt: 0.5000, sse=4379840.5, rms=2.210 (0.000%) 014: dt: 0.5000, sse=4677615.0, rms=2.028 (0.000%) rms = 2.17, time step reduction 1 of 3 to 0.250... 015: dt: 0.2500, sse=3910700.8, rms=1.573 (0.000%) 016: dt: 0.2500, sse=3630139.8, rms=1.345 (0.000%) 017: dt: 0.2500, sse=3534405.2, rms=1.278 (0.000%) rms = 1.26, time step reduction 2 of 3 to 0.125... 018: dt: 0.2500, sse=3504612.5, rms=1.259 (0.000%) rms = 1.24, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=3472031.2, rms=1.242 (0.000%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 2 with 4 points - only 0.00% unknown deleting segment 3 with 243 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown deleting segment 5 with 9 points - only 0.00% unknown mean border=89.2, 12 (4) missing vertices, mean dist -0.2 [0.4 (%68.4)->0.2 (%31.6))] %84 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=Pedro, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.24 (0.10-->6.97) (max @ vno 47581 --> 140702) face area 0.34 +- 0.16 (0.00-->7.87) mean absolute distance = 0.27 +- 0.38 4327 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3660540.8, rms=3.08 020: dt: 0.5000, sse=3958355.8, rms=1.951 (0.000%) 021: dt: 0.5000, sse=4160975.2, rms=1.892 (0.000%) rms = 1.85, time step reduction 1 of 3 to 0.250... 022: dt: 0.5000, sse=4501801.5, rms=1.845 (0.000%) 023: dt: 0.2500, sse=3811583.2, rms=1.258 (0.000%) 024: dt: 0.2500, sse=3681702.8, rms=1.159 (0.000%) rms = 1.16, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=3626227.5, rms=1.158 (0.000%) rms = 1.14, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=3603224.5, rms=1.142 (0.000%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 3 with 4 points - only 0.00% unknown deleting segment 4 with 257 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown deleting segment 6 with 9 points - only 0.00% unknown deleting segment 7 with 13 points - only 0.00% unknown mean border=90.1, 14 (3) missing vertices, mean dist -0.1 [0.3 (%58.0)->0.2 (%42.0))] %87 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=Pedro, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=3623172.8, rms=1.63 027: dt: 0.5000, sse=4388889.5, rms=1.289 (0.000%) rms = 1.57, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=4035184.0, rms=1.024 (0.000%) 029: dt: 0.2500, sse=3873459.2, rms=0.955 (0.000%) rms = 0.93, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=3915542.8, rms=0.927 (0.000%) rms = 0.93, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=3915542.8, rms=0.927 (0.000%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group smoothing surface for 5 iterations... mean border=64.5, 28 (28) missing vertices, mean dist 1.6 [2.5 (%0.0)->2.6 (%100.0))] %19 local maxima, %41 large gradients and %35 min vals, 2574 gradients ignored tol=1.0e-04, sigma=2.0, host=Pedro, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=21208314.0, rms=26.24 001: dt: 0.5000, sse=16739561.0, rms=22.911 (0.000%) 002: dt: 0.5000, sse=13279148.0, rms=19.993 (0.000%) 003: dt: 0.5000, sse=10737545.0, rms=17.476 (0.000%) 004: dt: 0.5000, sse=8977010.0, rms=15.299 (0.000%) 005: dt: 0.5000, sse=7790572.0, rms=13.453 (0.000%) 006: dt: 0.5000, sse=6986870.0, rms=11.916 (0.000%) 007: dt: 0.5000, sse=6493952.0, rms=10.577 (0.000%) 008: dt: 0.5000, sse=6171833.0, rms=9.338 (0.000%) 009: dt: 0.5000, sse=5855902.0, rms=8.130 (0.000%) 010: dt: 0.5000, sse=5672920.0, rms=6.948 (0.000%) 011: dt: 0.5000, sse=5514767.5, rms=5.881 (0.000%) 012: dt: 0.5000, sse=5537423.0, rms=4.999 (0.000%) 013: dt: 0.5000, sse=5586234.0, rms=4.349 (0.000%) 014: dt: 0.5000, sse=5666699.0, rms=3.914 (0.000%) 015: dt: 0.5000, sse=5736716.0, rms=3.656 (0.000%) 016: dt: 0.5000, sse=5777811.0, rms=3.499 (0.000%) 017: dt: 0.5000, sse=5813325.5, rms=3.425 (0.000%) 018: dt: 0.5000, sse=5838336.0, rms=3.372 (0.000%) rms = 3.36, time step reduction 1 of 3 to 0.250... 019: dt: 0.5000, sse=5860767.0, rms=3.356 (0.000%) 020: dt: 0.2500, sse=4058629.8, rms=2.715 (0.000%) 021: dt: 0.2500, sse=3886524.2, rms=2.569 (0.000%) rms = 2.54, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=3795607.2, rms=2.539 (0.000%) 023: dt: 0.1250, sse=3621732.0, rms=2.452 (0.000%) rms = 2.44, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=3604818.2, rms=2.441 (0.000%) positioning took 3.4 minutes mean border=62.7, 1176 (3) missing vertices, mean dist 0.1 [0.2 (%47.4)->0.6 (%52.6))] %34 local maxima, %33 large gradients and %28 min vals, 753 gradients ignored tol=1.0e-04, sigma=1.0, host=Pedro, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4129520.8, rms=4.21 025: dt: 0.5000, sse=4328247.5, rms=3.403 (0.000%) 026: dt: 0.5000, sse=5294349.5, rms=3.265 (0.000%) rms = 3.32, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=4483471.0, rms=2.723 (0.000%) 028: dt: 0.2500, sse=4147558.5, rms=2.490 (0.000%) rms = 2.45, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=4117690.8, rms=2.454 (0.000%) 030: dt: 0.1250, sse=3974449.2, rms=2.369 (0.000%) rms = 2.36, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=3963135.0, rms=2.358 (0.000%) positioning took 1.1 minutes mean border=61.7, 1463 (3) missing vertices, mean dist 0.1 [0.2 (%46.5)->0.4 (%53.5))] %45 local maxima, %22 large gradients and %28 min vals, 877 gradients ignored tol=1.0e-04, sigma=0.5, host=Pedro, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4049881.8, rms=2.86 rms = 2.92, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=3952097.0, rms=2.593 (0.000%) 033: dt: 0.2500, sse=3998743.0, rms=2.424 (0.000%) 034: dt: 0.2500, sse=4087591.5, rms=2.367 (0.000%) rms = 2.34, time step reduction 2 of 3 to 0.125... 035: dt: 0.2500, sse=4133528.0, rms=2.339 (0.000%) 036: dt: 0.1250, sse=4042405.5, rms=2.279 (0.000%) rms = 2.26, time step reduction 3 of 3 to 0.062... 037: dt: 0.1250, sse=4051590.8, rms=2.260 (0.000%) positioning took 1.0 minutes mean border=61.1, 3113 (3) missing vertices, mean dist 0.1 [0.2 (%49.1)->0.3 (%50.9))] %49 local maxima, %18 large gradients and %27 min vals, 829 gradients ignored tol=1.0e-04, sigma=0.2, host=Pedro, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=4073516.2, rms=2.43 rms = 2.56, time step reduction 1 of 3 to 0.250... 038: dt: 0.2500, sse=4019837.2, rms=2.292 (0.000%) 039: dt: 0.2500, sse=4141519.2, rms=2.192 (0.000%) 040: dt: 0.2500, sse=4175657.0, rms=2.133 (0.000%) rms = 2.08, time step reduction 2 of 3 to 0.125... 041: dt: 0.2500, sse=4225615.5, rms=2.084 (0.000%) 042: dt: 0.1250, sse=4132294.8, rms=2.028 (0.000%) rms = 2.01, time step reduction 3 of 3 to 0.062... 043: dt: 0.1250, sse=4138189.2, rms=2.009 (0.000%) positioning took 1.0 minutes writing curvature file /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.area.pial vertex spacing 0.98 +- 0.40 (0.10-->8.17) (max @ vno 89089 --> 89063) face area 0.38 +- 0.28 (0.00-->8.91) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 141108 vertices processed 25000 of 141108 vertices processed 50000 of 141108 vertices processed 75000 of 141108 vertices processed 100000 of 141108 vertices processed 125000 of 141108 vertices processed 0 of 141108 vertices processed 25000 of 141108 vertices processed 50000 of 141108 vertices processed 75000 of 141108 vertices processed 100000 of 141108 vertices processed 125000 of 141108 vertices processed thickness calculation complete, 840:875 truncations. 34578 vertices at 0 distance 98925 vertices at 1 distance 82125 vertices at 2 distance 35706 vertices at 3 distance 13129 vertices at 4 distance 4345 vertices at 5 distance 1490 vertices at 6 distance 526 vertices at 7 distance 194 vertices at 8 distance 82 vertices at 9 distance 39 vertices at 10 distance 37 vertices at 11 distance 21 vertices at 12 distance 24 vertices at 13 distance 17 vertices at 14 distance 26 vertices at 15 distance 11 vertices at 16 distance 12 vertices at 17 distance 10 vertices at 18 distance 10 vertices at 19 distance 17 vertices at 20 distance writing curvature file /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.thickness positioning took 14.8 minutes #-------------------------------------------- #@# Surf Volume rh Wed Aug 7 07:15:24 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf \n mris_calc -o rh.area.mid rh.area add rh.area.pial \n Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] \n mris_calc -o rh.area.mid rh.area.mid div 2 \n Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] \n mris_calc -o rh.volume rh.area.mid mul rh.thickness \n Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# WM/GM Contrast rh Wed Aug 7 07:15:24 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/scripts \n pctsurfcon --s subjects_name_ --rh-only \n Log file is /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/scripts/pctsurfcon.log Wed Aug 7 07:15:24 BRT 2013 setenv SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 cd /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/scripts /Applications/Freesurfer5.3/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Darwin Pedro-Rosas-MacBook-Pro-2.local 12.4.0 Darwin Kernel Version 12.4.0: Wed May 1 17:57:12 PDT 2013; root:xnu-2050.24.15~1/RELEASE_X86_64 x86_64 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer mri_vol2surf --mov /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/tmp.pctsurfcon.51389/rh.wm.mgh --regheader subjects_name_ --cortex srcvol = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/orig.mgz as target reference. Loading label /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/label/rh.cortex.label Reading surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 58076 Masking with /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/label/rh.cortex.label Writing to /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/tmp.pctsurfcon.51389/rh.wm.mgh Dim: 141108 1 1 mri_vol2surf --mov /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/tmp.pctsurfcon.51389/rh.gm.mgh --projfrac 0.3 --regheader subjects_name_ --cortex srcvol = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/orig.mgz as target reference. Loading label /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/label/rh.cortex.label Reading surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.white Done reading source surface Reading thickness /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 68001 Masking with /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/label/rh.cortex.label Writing to /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/tmp.pctsurfcon.51389/rh.gm.mgh Dim: 141108 1 1 mri_concat /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/tmp.pctsurfcon.51389/rh.wm.mgh /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/tmp.pctsurfcon.51389/rh.gm.mgh --paired-diff-norm --mul 100 --o /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.w-g.pct.mgh mri_segstats --in /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.w-g.pct.mgh --annot subjects_name_ rh aparc --sum /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/stats/rh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --in /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.w-g.pct.mgh --annot subjects_name_ rh aparc --sum /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/stats/rh.w-g.pct.stats --snr sysname Darwin hostname Pedro-Rosas-MacBook-Pro-2.local machine x86_64 user pedrogomesrosa UseRobust 0 Constructing seg from annotation Reading annotation reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Seg base 2000 Loading /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.w-g.pct.mgh Vertex Area is 0.648296 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 2000 unknown 0 0.000 1 2001 bankssts 1343 929.831 2 2002 caudalanteriorcingulate 899 579.431 3 2003 caudalmiddlefrontal 2483 1606.832 4 2004 corpuscallosum 0 0.000 5 2005 cuneus 2494 1643.016 6 2006 entorhinal 395 267.529 7 2007 fusiform 4980 3282.892 8 2008 inferiorparietal 7808 5124.565 9 2009 inferiortemporal 5338 3534.437 10 2010 isthmuscingulate 1120 721.536 11 2011 lateraloccipital 7671 4818.342 12 2012 lateralorbitofrontal 3824 2552.297 13 2013 lingual 4539 2986.229 14 2014 medialorbitofrontal 2734 1898.874 15 2015 middletemporal 5586 3740.712 16 2016 parahippocampal 1067 684.098 17 2017 paracentral 2801 1772.585 18 2018 parsopercularis 2541 1624.124 19 2019 parsorbitalis 1023 678.058 20 2020 parstriangularis 2999 1996.247 21 2021 pericalcarine 2526 1779.709 22 2022 postcentral 7309 4488.448 23 2023 posteriorcingulate 1717 1164.744 24 2024 precentral 7928 4845.023 25 2025 precuneus 5548 3651.652 26 2026 rostralanteriorcingulate 859 568.707 27 2027 rostralmiddlefrontal 8804 5818.964 28 2028 superiorfrontal 10814 6800.798 29 2029 superiorparietal 8527 5403.025 30 2030 superiortemporal 5443 3537.684 31 2031 supramarginal 6711 4405.180 32 2032 frontalpole 488 324.054 33 2033 temporalpole 733 478.129 34 2034 transversetemporal 671 376.104 35 2035 insula 3177 2068.859 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats rh Wed Aug 7 07:15:31 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/scripts \n mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab subjects_name_ rh white \n computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/wm.mgz... reading input surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.white... reading input pial surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.pial... reading input white surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1343 930 2430 2.529 0.554 0.107 0.026 10 1.4 bankssts 899 579 1416 2.484 0.732 0.149 0.035 15 1.3 caudalanteriorcingulate 2483 1607 4340 2.533 0.630 0.119 0.031 22 3.1 caudalmiddlefrontal 2494 1643 2895 1.654 0.565 0.168 0.064 39 6.9 cuneus 395 268 1319 3.882 0.754 0.129 0.037 4 0.6 entorhinal 4980 3283 10098 2.837 0.729 0.134 0.045 67 9.6 fusiform 7808 5125 14822 2.593 0.663 0.139 0.051 108 15.3 inferiorparietal 5338 3534 11459 2.921 0.735 0.150 0.069 143 15.7 inferiortemporal 1120 722 1839 2.333 0.767 0.137 0.056 17 2.6 isthmuscingulate 7671 4818 11772 2.298 0.660 0.145 0.054 112 16.5 lateraloccipital 3824 2552 7480 2.752 0.875 0.149 0.056 59 8.4 lateralorbitofrontal 4539 2986 6048 1.971 0.585 0.155 0.055 67 10.4 lingual 2734 1899 5363 2.376 0.949 0.160 0.075 295 9.5 medialorbitofrontal 5586 3741 14065 3.047 0.685 0.127 0.037 66 8.6 middletemporal 1067 684 2478 3.142 0.839 0.109 0.044 11 1.7 parahippocampal 2801 1773 3982 2.115 0.735 0.129 0.044 33 5.3 paracentral 2541 1624 5054 2.834 0.567 0.127 0.038 29 3.9 parsopercularis 1023 678 2525 2.879 0.761 0.130 0.038 11 1.6 parsorbitalis 2999 1996 5035 2.204 0.622 0.124 0.035 32 4.4 parstriangularis 2526 1780 2072 1.284 0.336 0.143 0.044 29 4.6 pericalcarine 7309 4488 10345 2.041 0.704 0.116 0.035 74 10.7 postcentral 1717 1165 2992 2.385 0.743 0.149 0.049 29 3.2 posteriorcingulate 7928 4845 10951 2.163 0.746 0.118 0.039 86 13.4 precentral 5548 3652 8560 2.214 0.708 0.131 0.038 64 8.8 precuneus 859 569 1682 2.649 0.800 0.146 0.043 15 1.5 rostralanteriorcingulate 8804 5819 15383 2.283 0.697 0.141 0.046 126 16.5 rostralmiddlefrontal 10814 6801 20969 2.681 0.700 0.133 0.046 134 20.8 superiorfrontal 8527 5403 11301 1.954 0.585 0.130 0.040 103 13.9 superiorparietal 5443 3538 11466 2.860 0.591 0.117 0.037 58 7.8 superiortemporal 6711 4405 12416 2.611 0.604 0.138 0.043 91 11.7 supramarginal 488 324 1227 2.656 0.737 0.199 0.095 14 1.9 frontalpole 733 478 2254 3.502 0.946 0.175 0.097 17 3.4 temporalpole 671 376 961 2.225 0.480 0.123 0.040 7 1.1 transversetemporal 3177 2069 6753 3.171 0.800 0.143 0.128 107 21.8 insula #----------------------------------------- #@# Cortical Parc 2 rh Wed Aug 7 07:15:51 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/scripts \n mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 subjects_name_ rh ../surf/rh.sphere.reg /Applications/Freesurfer5.3/freesurfer/average/rh.destrieux.simple.2009-07-29.gcs ../label/rh.aparc.a2009s.annot \n setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /Applications/Freesurfer5.3/freesurfer/average/rh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 1.9 0.2 using min determinant for regularization = 0.000 0 singular and 851 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 6 labels changed using aseg relabeling using gibbs priors... 000: 10291 changed, 141108 examined... 001: 2569 changed, 39121 examined... 002: 815 changed, 12886 examined... 003: 338 changed, 4484 examined... 004: 166 changed, 1910 examined... 005: 77 changed, 899 examined... 006: 49 changed, 442 examined... 007: 24 changed, 273 examined... 008: 10 changed, 155 examined... 009: 7 changed, 67 examined... 010: 5 changed, 38 examined... 011: 2 changed, 24 examined... 012: 2 changed, 9 examined... 013: 1 changed, 10 examined... 014: 0 changed, 6 examined... 8 labels changed using aseg 000: 274 total segments, 194 labels (3233 vertices) changed 001: 104 total segments, 24 labels (124 vertices) changed 002: 82 total segments, 2 labels (3 vertices) changed 003: 80 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 152 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 719 vertices marked for relabeling... 719 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 1 minutes and 10 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Wed Aug 7 07:17:02 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/scripts \n mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab subjects_name_ rh white \n computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/wm.mgz... reading input surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.white... reading input pial surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.pial... reading input white surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1004 687 1849 2.124 0.870 0.170 0.064 23 2.5 G_and_S_frontomargin 1915 1247 3826 2.761 0.699 0.148 0.053 28 3.9 G_and_S_occipital_inf 1216 725 2116 2.473 0.735 0.136 0.055 18 3.0 G_and_S_paracentral 1510 968 2895 2.557 0.625 0.150 0.056 24 3.1 G_and_S_subcentral 1217 823 2600 2.428 0.721 0.176 0.066 26 3.5 G_and_S_transv_frontopol 2996 1988 5409 2.533 0.840 0.142 0.049 43 5.6 G_and_S_cingul-Ant 1741 1163 3205 2.536 0.614 0.138 0.034 21 2.6 G_and_S_cingul-Mid-Ant 2107 1425 3481 2.365 0.708 0.131 0.039 23 3.2 G_and_S_cingul-Mid-Post 373 247 972 2.937 0.578 0.166 0.064 7 1.1 G_cingul-Post-dorsal 204 120 450 2.790 0.700 0.160 0.072 4 0.5 G_cingul-Post-ventral 2314 1594 2621 1.532 0.563 0.163 0.059 34 5.9 G_cuneus 1423 895 3234 2.936 0.592 0.137 0.047 20 2.8 G_front_inf-Opercular 466 319 1124 2.556 0.550 0.126 0.031 5 0.6 G_front_inf-Orbital 1515 966 2964 2.404 0.587 0.143 0.048 23 3.1 G_front_inf-Triangul 3462 2189 7620 2.598 0.729 0.147 0.053 60 7.4 G_front_middle 7161 4359 14505 2.678 0.732 0.137 0.052 101 16.1 G_front_sup 492 318 1289 3.287 0.805 0.138 0.083 8 1.9 G_Ins_lg_and_S_cent_ins 629 403 1979 3.527 0.831 0.167 0.079 15 2.2 G_insular_short 2869 1702 5828 2.750 0.681 0.152 0.063 57 8.4 G_occipital_middle 1755 1120 2212 1.882 0.415 0.140 0.046 23 3.3 G_occipital_sup 1835 1172 3963 2.813 0.719 0.149 0.056 34 4.1 G_oc-temp_lat-fusifor 2860 1851 4076 1.950 0.703 0.168 0.068 51 7.9 G_oc-temp_med-Lingual 1337 872 3910 3.623 0.817 0.153 0.206 77 16.9 G_oc-temp_med-Parahip 2568 1697 6638 3.010 0.792 0.161 0.080 54 7.4 G_orbital 2467 1574 6153 2.938 0.630 0.154 0.072 46 5.4 G_pariet_inf-Angular 3572 2271 7855 2.839 0.613 0.148 0.049 63 7.3 G_pariet_inf-Supramar 2938 1716 4444 2.119 0.684 0.120 0.039 33 4.7 G_parietal_sup 2913 1614 4299 2.100 0.651 0.114 0.037 31 4.6 G_postcentral 3016 1609 4541 2.324 0.862 0.107 0.043 39 5.5 G_precentral 2492 1578 4397 2.247 0.659 0.136 0.047 44 4.7 G_precuneus 738 540 1985 2.883 0.687 0.204 0.133 263 5.0 G_rectus 163 104 373 3.264 0.592 0.108 0.039 2 0.2 G_subcallosal 606 335 979 2.346 0.471 0.121 0.041 6 1.0 G_temp_sup-G_T_transv 2201 1332 5537 3.090 0.582 0.135 0.053 38 4.4 G_temp_sup-Lateral 789 525 1979 3.372 0.661 0.092 0.025 4 0.7 G_temp_sup-Plan_polar 694 479 1427 2.718 0.510 0.100 0.024 4 0.7 G_temp_sup-Plan_tempo 2766 1801 6914 3.107 0.778 0.171 0.096 106 11.5 G_temporal_inf 3434 2265 10110 3.243 0.677 0.142 0.048 64 6.4 G_temporal_middle 482 333 606 1.903 0.515 0.097 0.018 2 0.3 Lat_Fis-ant-Horizont 325 231 509 2.557 0.497 0.117 0.028 3 0.4 Lat_Fis-ant-Vertical 1373 927 1885 2.532 0.631 0.119 0.030 11 1.7 Lat_Fis-post 3669 2355 4405 1.796 0.588 0.158 0.062 58 9.1 Pole_occipital 2056 1361 5658 3.135 0.831 0.158 0.074 38 7.4 Pole_temporal 2492 1660 2599 1.735 0.740 0.132 0.039 27 4.0 S_calcarine 3056 2036 2821 1.531 0.510 0.113 0.031 24 4.0 S_central 1341 907 1967 2.157 0.611 0.131 0.039 15 1.9 S_cingul-Marginalis 732 475 1357 3.158 0.678 0.131 0.037 8 1.0 S_circular_insula_ant 1203 787 1872 2.936 0.651 0.093 0.027 6 1.3 S_circular_insula_inf 1453 975 2180 2.520 0.556 0.124 0.032 12 1.9 S_circular_insula_sup 1175 810 1993 2.727 0.543 0.115 0.031 10 1.6 S_collat_transv_ant 756 515 986 2.233 0.445 0.129 0.039 7 1.1 S_collat_transv_post 2721 1784 3817 2.197 0.546 0.114 0.026 21 3.0 S_front_inf 2096 1402 2938 2.165 0.574 0.130 0.036 20 3.2 S_front_middle 1933 1288 3009 2.289 0.681 0.123 0.035 16 2.7 S_front_sup 600 409 887 2.299 0.393 0.105 0.024 4 0.6 S_interm_prim-Jensen 3320 2272 4333 2.047 0.522 0.132 0.035 32 4.5 S_intrapariet_and_P_trans 1035 698 1265 2.246 0.547 0.138 0.042 11 1.7 S_oc_middle_and_Lunatus 912 602 1165 2.032 0.480 0.121 0.033 7 1.3 S_oc_sup_and_transversal 791 566 1360 2.388 0.524 0.124 0.032 7 1.0 S_occipital_ant 886 595 1213 2.541 0.485 0.117 0.039 7 1.4 S_oc-temp_lat 2132 1423 3285 2.559 0.558 0.101 0.023 13 1.9 S_oc-temp_med_and_Lingual 574 382 557 1.556 0.477 0.132 0.036 6 0.9 S_orbital_lateral 761 536 1022 1.933 1.012 0.108 0.021 5 0.7 S_orbital_med-olfact 1414 949 2376 2.636 0.744 0.136 0.043 15 2.5 S_orbital-H_Shaped 2499 1650 3066 2.006 0.629 0.131 0.040 24 4.2 S_parieto_occipital 1493 939 1588 2.064 0.820 0.137 0.045 27 2.8 S_pericallosal 3376 2238 3907 1.951 0.545 0.119 0.031 29 4.3 S_postcentral 1665 1123 2504 2.598 0.466 0.106 0.024 9 1.7 S_precentral-inf-part 1608 1051 2180 2.207 0.644 0.127 0.036 17 2.6 S_precentral-sup-part 377 260 611 2.198 0.901 0.162 0.068 7 1.1 S_suborbital 1027 686 1572 2.268 0.743 0.136 0.036 10 1.5 S_subparietal 1602 1088 2592 2.732 0.545 0.123 0.030 14 2.1 S_temporal_inf 5915 4053 9496 2.402 0.540 0.114 0.028 47 6.7 S_temporal_sup 292 198 412 2.543 0.489 0.141 0.034 2 0.5 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 rh Wed Aug 7 07:17:24 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/scripts \n mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 subjects_name_ rh ../surf/rh.sphere.reg /Applications/Freesurfer5.3/freesurfer/average/rh.DKTatlas40.gcs ../label/rh.aparc.DKTatlas40.annot \n setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /Applications/Freesurfer5.3/freesurfer/average/rh.DKTatlas40.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.008 0 singular and 237 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1049 labels changed using aseg relabeling using gibbs priors... 000: 2869 changed, 141108 examined... 001: 690 changed, 12004 examined... 002: 212 changed, 3704 examined... 003: 63 changed, 1167 examined... 004: 29 changed, 394 examined... 005: 15 changed, 156 examined... 006: 11 changed, 77 examined... 007: 8 changed, 64 examined... 008: 7 changed, 47 examined... 009: 9 changed, 40 examined... 010: 6 changed, 48 examined... 011: 5 changed, 32 examined... 012: 4 changed, 26 examined... 013: 6 changed, 25 examined... 014: 5 changed, 30 examined... 015: 1 changed, 28 examined... 016: 0 changed, 7 examined... 163 labels changed using aseg 000: 65 total segments, 32 labels (241 vertices) changed 001: 35 total segments, 2 labels (2 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 34 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 592 vertices marked for relabeling... 592 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas40.annot... classification took 0 minutes and 55 seconds. #----------------------------------------- #@# Parcellation Stats 3 rh Wed Aug 7 07:18:19 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/scripts \n mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas40.stats -b -a ../label/rh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab subjects_name_ rh white \n computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot. reading volume /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/wm.mgz... reading input surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.white... reading input pial surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.pial... reading input white surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /Applications/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas40.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 886 571 1395 2.491 0.736 0.148 0.034 15 1.3 caudalanteriorcingulate 2559 1656 4350 2.494 0.634 0.121 0.032 23 3.3 caudalmiddlefrontal 3309 2188 3726 1.667 0.535 0.164 0.059 48 8.5 cuneus 406 283 1354 3.889 0.744 0.132 0.035 4 0.6 entorhinal 4375 2882 8202 2.725 0.653 0.130 0.040 56 7.1 fusiform 7138 4666 13710 2.618 0.674 0.141 0.053 103 14.6 inferiorparietal 5941 3927 13281 2.976 0.774 0.151 0.072 156 18.4 inferiortemporal 1163 750 1892 2.328 0.772 0.134 0.055 17 2.6 isthmuscingulate 7918 4985 12282 2.306 0.666 0.145 0.054 114 16.8 lateraloccipital 4139 2780 8474 2.731 0.893 0.157 0.065 74 10.1 lateralorbitofrontal 4609 3027 6118 1.969 0.589 0.155 0.056 70 10.8 lingual 2042 1423 4591 2.665 0.901 0.173 0.094 290 8.8 medialorbitofrontal 6721 4523 16146 2.957 0.682 0.123 0.034 75 9.7 middletemporal 1065 683 2468 3.136 0.836 0.108 0.042 10 1.6 parahippocampal 2918 1837 4186 2.140 0.749 0.129 0.044 35 5.5 paracentral 2640 1700 5198 2.806 0.575 0.129 0.039 31 4.2 parsopercularis 1391 908 3048 2.750 0.750 0.127 0.037 16 2.1 parsorbitalis 3156 2075 5184 2.217 0.619 0.127 0.036 34 4.8 parstriangularis 2447 1705 1987 1.282 0.329 0.139 0.043 28 4.2 pericalcarine 7880 4863 10965 2.045 0.696 0.118 0.036 80 11.6 postcentral 1822 1236 3108 2.356 0.742 0.148 0.047 29 3.3 posteriorcingulate 7611 4673 10572 2.166 0.752 0.118 0.039 83 12.6 precentral 5546 3658 8681 2.212 0.706 0.130 0.038 63 8.7 precuneus 1082 710 2099 2.605 0.869 0.147 0.043 18 1.9 rostralanteriorcingulate 5566 3651 9816 2.286 0.722 0.136 0.044 76 10.0 rostralmiddlefrontal 14072 8975 26363 2.558 0.723 0.136 0.047 180 27.5 superiorfrontal 7216 4551 9678 1.965 0.592 0.129 0.041 89 11.8 superiorparietal 7172 4689 15598 2.917 0.684 0.127 0.071 145 26.5 superiortemporal 6407 4210 11892 2.594 0.606 0.137 0.042 85 11.1 supramarginal 670 375 960 2.228 0.482 0.123 0.040 7 1.1 transversetemporal 3033 1991 6428 3.141 0.792 0.134 0.054 40 7.0 insula #-------------------------------------------- #@# Cortical ribbon mask Wed Aug 7 07:18:40 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri \n mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon subjects_name_ \n SUBJECTS_DIR is /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 loading input data... computing distance to left white surface computing distance to left pial surface computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 54 writing volume /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/ribbon.mgz writing ribbon files #-------------------------------------------- #@# ASeg Stats Wed Aug 7 07:35:08 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_ \n mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /Applications/Freesurfer5.3/freesurfer/ASegStatsLUT.txt --subject subjects_name_ \n $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /Applications/Freesurfer5.3/freesurfer/ASegStatsLUT.txt --subject subjects_name_ sysname Darwin hostname Pedro-Rosas-MacBook-Pro-2.local machine x86_64 user pedrogomesrosa UseRobust 0 atlas_icv (eTIV) = 1580638 mm^3 (det: 1.232480 ) Computing euler number orig.nofix lheno = -20, rheno = -22 orig.nofix lhholes = 11, rhholes = 12 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 233640.342 233351.000 diff= 289.3 pctdiff= 0.124 rhCtxGM: 232867.605 232440.000 diff= 427.6 pctdiff= 0.184 lhCtxWM: 258429.896 258159.500 diff= 270.4 pctdiff= 0.105 rhCtxWM: 252434.322 253091.500 diff= -657.2 pctdiff=-0.260 SubCortGMVol 61962.000 SupraTentVol 1047981.165 (1046436.000) diff=1545.165 pctdiff=0.147 SupraTentVolNotVent 1040721.165 (1039176.000) diff=1545.165 pctdiff=0.148 BrainSegVol 1202431.000 (1200730.000) diff=1701.000 pctdiff=0.141 BrainSegVolNotVent 1193180.000 (1193273.165) diff=-93.165 pctdiff=-0.008 BrainSegVolNotVent 1193180.000 CerebellumVol 153767.000 VentChorVol 7260.000 3rd4th5thCSF 1991.000 CSFVol 297.000, OptChiasmVol 230.000 MaskVol 1699642.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation 3 4 Left-Lateral-Ventricle 2908 2908.053 4 5 Left-Inf-Lat-Vent 270 270.415 5 7 Left-Cerebellum-White-Matter 17225 17224.953 6 8 Left-Cerebellum-Cortex 61876 61875.883 7 10 Left-Thalamus-Proper 8107 8107.392 8 11 Left-Caudate 3399 3398.750 9 12 Left-Putamen 6161 6161.238 10 13 Left-Pallidum 1534 1533.958 11 14 3rd-Ventricle 714 714.134 12 15 4th-Ventricle 1232 1231.519 13 16 Brain-Stem 23156 23156.197 14 17 Left-Hippocampus 4555 4555.427 15 18 Left-Amygdala 1576 1575.964 16 24 CSF 335 334.897 17 26 Left-Accumbens-area 683 682.878 18 28 Left-VentralDC 4265 4264.563 19 30 Left-vessel 97 96.619 20 31 Left-choroid-plexus 1047 1047.487 23 43 Right-Lateral-Ventricle 2019 2018.592 24 44 Right-Inf-Lat-Vent 122 122.463 25 46 Right-Cerebellum-White-Matter 17024 17024.357 26 47 Right-Cerebellum-Cortex 59923 59923.113 27 49 Right-Thalamus-Proper 7863 7862.901 28 50 Right-Caudate 3432 3431.948 29 51 Right-Putamen 5651 5650.978 30 52 Right-Pallidum 1593 1592.877 31 53 Right-Hippocampus 5060 5060.219 32 54 Right-Amygdala 1541 1541.442 33 58 Right-Accumbens-area 664 663.973 34 60 Right-VentralDC 4336 4336.483 35 62 Right-vessel 93 92.686 36 63 Right-choroid-plexus 1416 1415.571 37 72 5th-Ventricle 0 0.000 38 77 WM-hypointensities 1969 1969.006 39 78 Left-WM-hypointensities 0 0.000 40 79 Right-WM-hypointensities 0 0.000 41 80 non-WM-hypointensities 6 6.439 42 81 Left-non-WM-hypointensities 0 0.000 43 82 Right-non-WM-hypointensities 0 0.000 44 85 Optic-Chiasm 217 217.266 45 251 CC_Posterior 897 896.784 46 252 CC_Mid_Posterior 545 544.793 47 253 CC_Central 519 519.266 48 254 CC_Mid_Anterior 530 529.544 49 255 CC_Anterior 936 935.627 Reporting on 45 segmentations mri_segstats done #----------------------------------------- #@# AParc-to-ASeg Wed Aug 7 07:41:11 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_ \n mri_aparc2aseg --s subjects_name_ --volmask \n SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 subject subjects_name_ outvol /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.white Reading lh pial surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.pial Loading lh annotations from /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Reading rh white surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.white Reading rh pial surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.pial Loading rh annotations from /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 463692 Used brute-force search on 0 voxels Writing output aseg to /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/aparc+aseg.mgz /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_ \n mri_aparc2aseg --s subjects_name_ --volmask --a2009s \n SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 subject subjects_name_ outvol /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.white Reading lh pial surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.pial Loading lh annotations from /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/label/lh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Reading rh white surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.white Reading rh pial surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.pial Loading rh annotations from /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/label/rh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 463692 Used brute-force search on 0 voxels Writing output aseg to /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# WMParc Wed Aug 7 07:47:16 BRT 2013 /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_ \n mri_aparc2aseg --s subjects_name_ --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz \n SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 subject subjects_name_ outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/aparc+aseg.mgz Reading lh white surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.white Reading lh pial surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.pial Loading lh annotations from /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Reading rh white surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.white Reading rh pial surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.pial Loading rh annotations from /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/ribbon.mgz Loading filled from /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/filled.mgz Ripping vertices labeled as unkown Ripped 8036 vertices from left hemi Ripped 8208 vertices from right hemi Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/aseg.mgz Loading Ctx Seg File /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/aparc+aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 973492 Used brute-force search on 777 voxels Fixing Parahip LH WM Found 18 clusters 0 k 1.000000 1 k 1.000000 2 k 2.000000 3 k 1.000000 4 k 1.000000 5 k 2066.000000 6 k 1.000000 7 k 1.000000 8 k 2.000000 9 k 2.000000 10 k 22.000000 11 k 5.000000 12 k 3.000000 13 k 5.000000 14 k 1.000000 15 k 3.000000 16 k 11.000000 17 k 1.000000 Fixing Parahip RH WM Found 12 clusters 0 k 1.000000 1 k 1.000000 2 k 1.000000 3 k 1697.000000 4 k 1.000000 5 k 1.000000 6 k 2.000000 7 k 1.000000 8 k 31.000000 9 k 1.000000 10 k 1.000000 11 k 1.000000 Writing output aseg to mri/wmparc.mgz /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_ \n mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject subjects_name_ --surf-wm-vol --ctab /Applications/Freesurfer5.3/freesurfer/WMParcStatsLUT.txt --etiv \n $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject subjects_name_ --surf-wm-vol --ctab /Applications/Freesurfer5.3/freesurfer/WMParcStatsLUT.txt --etiv sysname Darwin hostname Pedro-Rosas-MacBook-Pro-2.local machine x86_64 user pedrogomesrosa UseRobust 0 atlas_icv (eTIV) = 1580638 mm^3 (det: 1.232480 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 233640.342 233351.000 diff= 289.3 pctdiff= 0.124 rhCtxGM: 232867.605 232440.000 diff= 427.6 pctdiff= 0.184 lhCtxWM: 258429.896 258159.500 diff= 270.4 pctdiff= 0.105 rhCtxWM: 252434.322 253091.500 diff= -657.2 pctdiff=-0.260 SubCortGMVol 61962.000 SupraTentVol 1047981.165 (1046436.000) diff=1545.165 pctdiff=0.147 SupraTentVolNotVent 1040721.165 (1039176.000) diff=1545.165 pctdiff=0.148 BrainSegVol 1202431.000 (1200730.000) diff=1701.000 pctdiff=0.141 BrainSegVolNotVent 1193180.000 (1193273.165) diff=-93.165 pctdiff=-0.008 BrainSegVolNotVent 1193180.000 CerebellumVol 153767.000 VentChorVol 7260.000 3rd4th5thCSF 1991.000 CSFVol 297.000, OptChiasmVol 230.000 MaskVol 1699642.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation 0 3000 wm-lh-unknown 0 0.000 1 3001 wm-lh-bankssts 2773 2773.358 2 3002 wm-lh-caudalanteriorcingulate 2597 2597.441 3 3003 wm-lh-caudalmiddlefrontal 6826 6826.401 4 3004 wm-lh-corpuscallosum 0 0.000 5 3005 wm-lh-cuneus 3394 3394.147 6 3006 wm-lh-entorhinal 504 504.184 7 3007 wm-lh-fusiform 8701 8701.297 8 3008 wm-lh-inferiorparietal 12643 12643.487 9 3009 wm-lh-inferiortemporal 6875 6875.206 10 3010 wm-lh-isthmuscingulate 3574 3573.936 11 3011 wm-lh-lateraloccipital 10938 10938.153 12 3012 wm-lh-lateralorbitofrontal 7256 7256.357 13 3013 wm-lh-lingual 7027 7026.530 14 3014 wm-lh-medialorbitofrontal 3653 3652.697 15 3015 wm-lh-middletemporal 5515 5514.662 16 3016 wm-lh-parahippocampal 2113 2112.795 17 3017 wm-lh-paracentral 3698 3698.479 18 3018 wm-lh-parsopercularis 4607 4606.630 19 3019 wm-lh-parsorbitalis 1104 1104.291 20 3020 wm-lh-parstriangularis 3346 3345.696 21 3021 wm-lh-pericalcarine 4589 4588.764 22 3022 wm-lh-postcentral 9203 9202.782 23 3023 wm-lh-posteriorcingulate 5016 5015.675 24 3024 wm-lh-precentral 13812 13812.390 25 3025 wm-lh-precuneus 9732 9732.098 26 3026 wm-lh-rostralanteriorcingulate 2466 2465.865 27 3027 wm-lh-rostralmiddlefrontal 12185 12185.365 28 3028 wm-lh-superiorfrontal 18141 18141.111 29 3029 wm-lh-superiorparietal 14905 14905.077 30 3030 wm-lh-superiortemporal 8832 8832.133 31 3031 wm-lh-supramarginal 11399 11399.037 32 3032 wm-lh-frontalpole 225 224.826 33 3033 wm-lh-temporalpole 665 665.128 34 3034 wm-lh-transversetemporal 960 959.976 35 3035 wm-lh-insula 8294 8293.773 36 3100 wm-lh-Unknown 0 0.000 37 3101 wm-lh-Corpus_callosum 0 0.000 38 3102 wm-lh-G_and_S_Insula_ONLY_AVERAGE 0 0.000 39 3103 wm-lh-G_cingulate-Isthmus 0 0.000 40 3104 wm-lh-G_cingulate-Main_part 0 0.000 41 3105 wm-lh-G_cuneus 0 0.000 42 3106 wm-lh-G_frontal_inf-Opercular_part 0 0.000 43 3107 wm-lh-G_frontal_inf-Orbital_part 0 0.000 44 3108 wm-lh-G_frontal_inf-Triangular_part 0 0.000 45 3109 wm-lh-G_frontal_middle 0 0.000 46 3110 wm-lh-G_frontal_superior 0 0.000 47 3111 wm-lh-G_frontomarginal 0 0.000 48 3112 wm-lh-G_insular_long 0 0.000 49 3113 wm-lh-G_insular_short 0 0.000 50 3114 wm-lh-G_and_S_occipital_inferior 0 0.000 51 3115 wm-lh-G_occipital_middle 0 0.000 52 3116 wm-lh-G_occipital_superior 0 0.000 53 3117 wm-lh-G_occipit-temp_lat-Or_fusiform 0 0.000 54 3118 wm-lh-G_occipit-temp_med-Lingual_part 0 0.000 55 3119 wm-lh-G_occipit-temp_med-Parahippocampal_part 0 0.000 56 3120 wm-lh-G_orbital 0 0.000 57 3121 wm-lh-G_paracentral 0 0.000 58 3122 wm-lh-G_parietal_inferior-Angular_part 0 0.000 59 3123 wm-lh-G_parietal_inferior-Supramarginal_part 0 0.000 60 3124 wm-lh-G_parietal_superior 0 0.000 61 3125 wm-lh-G_postcentral 0 0.000 62 3126 wm-lh-G_precentral 0 0.000 63 3127 wm-lh-G_precuneus 0 0.000 64 3128 wm-lh-G_rectus 0 0.000 65 3129 wm-lh-G_subcallosal 0 0.000 66 3130 wm-lh-G_subcentral 0 0.000 67 3131 wm-lh-G_temporal_inferior 0 0.000 68 3132 wm-lh-G_temporal_middle 0 0.000 69 3133 wm-lh-G_temp_sup-G_temp_transv_and_interm_S 0 0.000 70 3134 wm-lh-G_temp_sup-Lateral_aspect 0 0.000 71 3135 wm-lh-G_temp_sup-Planum_polare 0 0.000 72 3136 wm-lh-G_temp_sup-Planum_tempolare 0 0.000 73 3137 wm-lh-G_and_S_transverse_frontopolar 0 0.000 74 3138 wm-lh-Lat_Fissure-ant_sgt-ramus_horizontal 0 0.000 75 3139 wm-lh-Lat_Fissure-ant_sgt-ramus_vertical 0 0.000 76 3140 wm-lh-Lat_Fissure-post_sgt 0 0.000 77 3141 wm-lh-Medial_wall 0 0.000 78 3142 wm-lh-Pole_occipital 0 0.000 79 3143 wm-lh-Pole_temporal 0 0.000 80 3144 wm-lh-S_calcarine 0 0.000 81 3145 wm-lh-S_central 0 0.000 82 3146 wm-lh-S_central_insula 0 0.000 83 3147 wm-lh-S_cingulate-Main_part_and_Intracingulate 0 0.000 84 3148 wm-lh-S_cingulate-Marginalis_part 0 0.000 85 3149 wm-lh-S_circular_insula_anterior 0 0.000 86 3150 wm-lh-S_circular_insula_inferior 0 0.000 87 3151 wm-lh-S_circular_insula_superior 0 0.000 88 3152 wm-lh-S_collateral_transverse_ant 0 0.000 89 3153 wm-lh-S_collateral_transverse_post 0 0.000 90 3154 wm-lh-S_frontal_inferior 0 0.000 91 3155 wm-lh-S_frontal_middle 0 0.000 92 3156 wm-lh-S_frontal_superior 0 0.000 93 3157 wm-lh-S_frontomarginal 0 0.000 94 3158 wm-lh-S_intermedius_primus-Jensen 0 0.000 95 3159 wm-lh-S_intraparietal-and_Parietal_transverse 0 0.000 96 3160 wm-lh-S_occipital_anterior 0 0.000 97 3161 wm-lh-S_occipital_middle_and_Lunatus 0 0.000 98 3162 wm-lh-S_occipital_superior_and_transversalis 0 0.000 99 3163 wm-lh-S_occipito-temporal_lateral 0 0.000 100 3164 wm-lh-S_occipito-temporal_medial_and_S_Lingual 0 0.000 101 3165 wm-lh-S_orbital-H_shapped 0 0.000 102 3166 wm-lh-S_orbital_lateral 0 0.000 103 3167 wm-lh-S_orbital_medial-Or_olfactory 0 0.000 104 3168 wm-lh-S_paracentral 0 0.000 105 3169 wm-lh-S_parieto_occipital 0 0.000 106 3170 wm-lh-S_pericallosal 0 0.000 107 3171 wm-lh-S_postcentral 0 0.000 108 3172 wm-lh-S_precentral-Inferior-part 0 0.000 109 3173 wm-lh-S_precentral-Superior-part 0 0.000 110 3174 wm-lh-S_subcentral_ant 0 0.000 111 3175 wm-lh-S_subcentral_post 0 0.000 112 3176 wm-lh-S_suborbital 0 0.000 113 3177 wm-lh-S_subparietal 0 0.000 114 3178 wm-lh-S_supracingulate 0 0.000 115 3179 wm-lh-S_temporal_inferior 0 0.000 116 3180 wm-lh-S_temporal_superior 0 0.000 117 3181 wm-lh-S_temporal_transverse 0 0.000 118 4000 wm-rh-unknown 0 0.000 119 4001 wm-rh-bankssts 2615 2614.956 120 4002 wm-rh-caudalanteriorcingulate 2841 2840.875 121 4003 wm-rh-caudalmiddlefrontal 5427 5426.928 122 4004 wm-rh-corpuscallosum 0 0.000 123 4005 wm-rh-cuneus 2796 2796.208 124 4006 wm-rh-entorhinal 657 657.015 125 4007 wm-rh-fusiform 7450 7449.933 126 4008 wm-rh-inferiorparietal 11927 11926.601 127 4009 wm-rh-inferiortemporal 7044 7043.766 128 4010 wm-rh-isthmuscingulate 2725 2725.168 129 4011 wm-rh-lateraloccipital 10388 10388.322 130 4012 wm-rh-lateralorbitofrontal 7428 7428.120 131 4013 wm-rh-lingual 5996 5995.733 132 4014 wm-rh-medialorbitofrontal 3913 3912.990 133 4015 wm-rh-middletemporal 7319 7318.595 134 4016 wm-rh-parahippocampal 1771 1770.887 135 4017 wm-rh-paracentral 4893 4892.921 136 4018 wm-rh-parsopercularis 3956 3956.488 137 4019 wm-rh-parsorbitalis 1235 1234.589 138 4020 wm-rh-parstriangularis 4644 4644.310 139 4021 wm-rh-pericalcarine 4600 4600.321 140 4022 wm-rh-postcentral 9214 9214.097 141 4023 wm-rh-posteriorcingulate 4800 4800.471 142 4024 wm-rh-precentral 14239 14238.589 143 4025 wm-rh-precuneus 9933 9932.710 144 4026 wm-rh-rostralanteriorcingulate 1921 1921.091 145 4027 wm-rh-rostralmiddlefrontal 13691 13691.180 146 4028 wm-rh-superiorfrontal 18040 18039.980 147 4029 wm-rh-superiorparietal 13907 13907.404 148 4030 wm-rh-superiortemporal 7029 7028.674 149 4031 wm-rh-supramarginal 11037 11036.524 150 4032 wm-rh-frontalpole 363 363.410 151 4033 wm-rh-temporalpole 684 683.659 152 4034 wm-rh-transversetemporal 619 619.361 153 4035 wm-rh-insula 8277 8276.684 154 4100 wm-rh-Unknown 0 0.000 155 4101 wm-rh-Corpus_callosum 0 0.000 156 4102 wm-rh-G_and_S_Insula_ONLY_AVERAGE 0 0.000 157 4103 wm-rh-G_cingulate-Isthmus 0 0.000 158 4104 wm-rh-G_cingulate-Main_part 0 0.000 159 4105 wm-rh-G_cuneus 0 0.000 160 4106 wm-rh-G_frontal_inf-Opercular_part 0 0.000 161 4107 wm-rh-G_frontal_inf-Orbital_part 0 0.000 162 4108 wm-rh-G_frontal_inf-Triangular_part 0 0.000 163 4109 wm-rh-G_frontal_middle 0 0.000 164 4110 wm-rh-G_frontal_superior 0 0.000 165 4111 wm-rh-G_frontomarginal 0 0.000 166 4112 wm-rh-G_insular_long 0 0.000 167 4113 wm-rh-G_insular_short 0 0.000 168 4114 wm-rh-G_and_S_occipital_inferior 0 0.000 169 4115 wm-rh-G_occipital_middle 0 0.000 170 4116 wm-rh-G_occipital_superior 0 0.000 171 4117 wm-rh-G_occipit-temp_lat-Or_fusiform 0 0.000 172 4118 wm-rh-G_occipit-temp_med-Lingual_part 0 0.000 173 4119 wm-rh-G_occipit-temp_med-Parahippocampal_part 0 0.000 174 4120 wm-rh-G_orbital 0 0.000 175 4121 wm-rh-G_paracentral 0 0.000 176 4122 wm-rh-G_parietal_inferior-Angular_part 0 0.000 177 4123 wm-rh-G_parietal_inferior-Supramarginal_part 0 0.000 178 4124 wm-rh-G_parietal_superior 0 0.000 179 4125 wm-rh-G_postcentral 0 0.000 180 4126 wm-rh-G_precentral 0 0.000 181 4127 wm-rh-G_precuneus 0 0.000 182 4128 wm-rh-G_rectus 0 0.000 183 4129 wm-rh-G_subcallosal 0 0.000 184 4130 wm-rh-G_subcentral 0 0.000 185 4131 wm-rh-G_temporal_inferior 0 0.000 186 4132 wm-rh-G_temporal_middle 0 0.000 187 4133 wm-rh-G_temp_sup-G_temp_transv_and_interm_S 0 0.000 188 4134 wm-rh-G_temp_sup-Lateral_aspect 0 0.000 189 4135 wm-rh-G_temp_sup-Planum_polare 0 0.000 190 4136 wm-rh-G_temp_sup-Planum_tempolare 0 0.000 191 4137 wm-rh-G_and_S_transverse_frontopolar 0 0.000 192 4138 wm-rh-Lat_Fissure-ant_sgt-ramus_horizontal 0 0.000 193 4139 wm-rh-Lat_Fissure-ant_sgt-ramus_vertical 0 0.000 194 4140 wm-rh-Lat_Fissure-post_sgt 0 0.000 195 4141 wm-rh-Medial_wall 0 0.000 196 4142 wm-rh-Pole_occipital 0 0.000 197 4143 wm-rh-Pole_temporal 0 0.000 198 4144 wm-rh-S_calcarine 0 0.000 199 4145 wm-rh-S_central 0 0.000 200 4146 wm-rh-S_central_insula 0 0.000 201 4147 wm-rh-S_cingulate-Main_part_and_Intracingulate 0 0.000 202 4148 wm-rh-S_cingulate-Marginalis_part 0 0.000 203 4149 wm-rh-S_circular_insula_anterior 0 0.000 204 4150 wm-rh-S_circular_insula_inferior 0 0.000 205 4151 wm-rh-S_circular_insula_superior 0 0.000 206 4152 wm-rh-S_collateral_transverse_ant 0 0.000 207 4153 wm-rh-S_collateral_transverse_post 0 0.000 208 4154 wm-rh-S_frontal_inferior 0 0.000 209 4155 wm-rh-S_frontal_middle 0 0.000 210 4156 wm-rh-S_frontal_superior 0 0.000 211 4157 wm-rh-S_frontomarginal 0 0.000 212 4158 wm-rh-S_intermedius_primus-Jensen 0 0.000 213 4159 wm-rh-S_intraparietal-and_Parietal_transverse 0 0.000 214 4160 wm-rh-S_occipital_anterior 0 0.000 215 4161 wm-rh-S_occipital_middle_and_Lunatus 0 0.000 216 4162 wm-rh-S_occipital_superior_and_transversalis 0 0.000 217 4163 wm-rh-S_occipito-temporal_lateral 0 0.000 218 4164 wm-rh-S_occipito-temporal_medial_and_S_Lingual 0 0.000 219 4165 wm-rh-S_orbital-H_shapped 0 0.000 220 4166 wm-rh-S_orbital_lateral 0 0.000 221 4167 wm-rh-S_orbital_medial-Or_olfactory 0 0.000 222 4168 wm-rh-S_paracentral 0 0.000 223 4169 wm-rh-S_parieto_occipital 0 0.000 224 4170 wm-rh-S_pericallosal 0 0.000 225 4171 wm-rh-S_postcentral 0 0.000 226 4172 wm-rh-S_precentral-Inferior-part 0 0.000 227 4173 wm-rh-S_precentral-Superior-part 0 0.000 228 4174 wm-rh-S_subcentral_ant 0 0.000 229 4175 wm-rh-S_subcentral_post 0 0.000 230 4176 wm-rh-S_suborbital 0 0.000 231 4177 wm-rh-S_subparietal 0 0.000 232 4178 wm-rh-S_supracingulate 0 0.000 233 4179 wm-rh-S_temporal_inferior 0 0.000 234 4180 wm-rh-S_temporal_superior 0 0.000 235 4181 wm-rh-S_temporal_transverse 0 0.000 236 5001 Left-UnsegmentedWhiteMatter 38064 38064.473 237 5002 Right-UnsegmentedWhiteMatter 37729 37728.793 238 13100 wm_lh_Unknown 0 0.000 239 13101 wm_lh_G_and_S_frontomargin 0 0.000 240 13102 wm_lh_G_and_S_occipital_inf 0 0.000 241 13103 wm_lh_G_and_S_paracentral 0 0.000 242 13104 wm_lh_G_and_S_subcentral 0 0.000 243 13105 wm_lh_G_and_S_transv_frontopol 0 0.000 244 13106 wm_lh_G_and_S_cingul-Ant 0 0.000 245 13107 wm_lh_G_and_S_cingul-Mid-Ant 0 0.000 246 13108 wm_lh_G_and_S_cingul-Mid-Post 0 0.000 247 13109 wm_lh_G_cingul-Post-dorsal 0 0.000 248 13110 wm_lh_G_cingul-Post-ventral 0 0.000 249 13111 wm_lh_G_cuneus 0 0.000 250 13112 wm_lh_G_front_inf-Opercular 0 0.000 251 13113 wm_lh_G_front_inf-Orbital 0 0.000 252 13114 wm_lh_G_front_inf-Triangul 0 0.000 253 13115 wm_lh_G_front_middle 0 0.000 254 13116 wm_lh_G_front_sup 0 0.000 255 13117 wm_lh_G_Ins_lg_and_S_cent_ins 0 0.000 256 13118 wm_lh_G_insular_short 0 0.000 257 13119 wm_lh_G_occipital_middle 0 0.000 258 13120 wm_lh_G_occipital_sup 0 0.000 259 13121 wm_lh_G_oc-temp_lat-fusifor 0 0.000 260 13122 wm_lh_G_oc-temp_med-Lingual 0 0.000 261 13123 wm_lh_G_oc-temp_med-Parahip 0 0.000 262 13124 wm_lh_G_orbital 0 0.000 263 13125 wm_lh_G_pariet_inf-Angular 0 0.000 264 13126 wm_lh_G_pariet_inf-Supramar 0 0.000 265 13127 wm_lh_G_parietal_sup 0 0.000 266 13128 wm_lh_G_postcentral 0 0.000 267 13129 wm_lh_G_precentral 0 0.000 268 13130 wm_lh_G_precuneus 0 0.000 269 13131 wm_lh_G_rectus 0 0.000 270 13132 wm_lh_G_subcallosal 0 0.000 271 13133 wm_lh_G_temp_sup-G_T_transv 0 0.000 272 13134 wm_lh_G_temp_sup-Lateral 0 0.000 273 13135 wm_lh_G_temp_sup-Plan_polar 0 0.000 274 13136 wm_lh_G_temp_sup-Plan_tempo 0 0.000 275 13137 wm_lh_G_temporal_inf 0 0.000 276 13138 wm_lh_G_temporal_middle 0 0.000 277 13139 wm_lh_Lat_Fis-ant-Horizont 0 0.000 278 13140 wm_lh_Lat_Fis-ant-Vertical 0 0.000 279 13141 wm_lh_Lat_Fis-post 0 0.000 280 13142 wm_lh_Medial_wall 0 0.000 281 13143 wm_lh_Pole_occipital 0 0.000 282 13144 wm_lh_Pole_temporal 0 0.000 283 13145 wm_lh_S_calcarine 0 0.000 284 13146 wm_lh_S_central 0 0.000 285 13147 wm_lh_S_cingul-Marginalis 0 0.000 286 13148 wm_lh_S_circular_insula_ant 0 0.000 287 13149 wm_lh_S_circular_insula_inf 0 0.000 288 13150 wm_lh_S_circular_insula_sup 0 0.000 289 13151 wm_lh_S_collat_transv_ant 0 0.000 290 13152 wm_lh_S_collat_transv_post 0 0.000 291 13153 wm_lh_S_front_inf 0 0.000 292 13154 wm_lh_S_front_middle 0 0.000 293 13155 wm_lh_S_front_sup 0 0.000 294 13156 wm_lh_S_interm_prim-Jensen 0 0.000 295 13157 wm_lh_S_intrapariet_and_P_trans 0 0.000 296 13158 wm_lh_S_oc_middle_and_Lunatus 0 0.000 297 13159 wm_lh_S_oc_sup_and_transversal 0 0.000 298 13160 wm_lh_S_occipital_ant 0 0.000 299 13161 wm_lh_S_oc-temp_lat 0 0.000 300 13162 wm_lh_S_oc-temp_med_and_Lingual 0 0.000 301 13163 wm_lh_S_orbital_lateral 0 0.000 302 13164 wm_lh_S_orbital_med-olfact 0 0.000 303 13165 wm_lh_S_orbital-H_Shaped 0 0.000 304 13166 wm_lh_S_parieto_occipital 0 0.000 305 13167 wm_lh_S_pericallosal 0 0.000 306 13168 wm_lh_S_postcentral 0 0.000 307 13169 wm_lh_S_precentral-inf-part 0 0.000 308 13170 wm_lh_S_precentral-sup-part 0 0.000 309 13171 wm_lh_S_suborbital 0 0.000 310 13172 wm_lh_S_subparietal 0 0.000 311 13173 wm_lh_S_temporal_inf 0 0.000 312 13174 wm_lh_S_temporal_sup 0 0.000 313 13175 wm_lh_S_temporal_transverse 0 0.000 314 14100 wm_rh_Unknown 0 0.000 315 14101 wm_rh_G_and_S_frontomargin 0 0.000 316 14102 wm_rh_G_and_S_occipital_inf 0 0.000 317 14103 wm_rh_G_and_S_paracentral 0 0.000 318 14104 wm_rh_G_and_S_subcentral 0 0.000 319 14105 wm_rh_G_and_S_transv_frontopol 0 0.000 320 14106 wm_rh_G_and_S_cingul-Ant 0 0.000 321 14107 wm_rh_G_and_S_cingul-Mid-Ant 0 0.000 322 14108 wm_rh_G_and_S_cingul-Mid-Post 0 0.000 323 14109 wm_rh_G_cingul-Post-dorsal 0 0.000 324 14110 wm_rh_G_cingul-Post-ventral 0 0.000 325 14111 wm_rh_G_cuneus 0 0.000 326 14112 wm_rh_G_front_inf-Opercular 0 0.000 327 14113 wm_rh_G_front_inf-Orbital 0 0.000 328 14114 wm_rh_G_front_inf-Triangul 0 0.000 329 14115 wm_rh_G_front_middle 0 0.000 330 14116 wm_rh_G_front_sup 0 0.000 331 14117 wm_rh_G_Ins_lg_and_S_cent_ins 0 0.000 332 14118 wm_rh_G_insular_short 0 0.000 333 14119 wm_rh_G_occipital_middle 0 0.000 334 14120 wm_rh_G_occipital_sup 0 0.000 335 14121 wm_rh_G_oc-temp_lat-fusifor 0 0.000 336 14122 wm_rh_G_oc-temp_med-Lingual 0 0.000 337 14123 wm_rh_G_oc-temp_med-Parahip 0 0.000 338 14124 wm_rh_G_orbital 0 0.000 339 14125 wm_rh_G_pariet_inf-Angular 0 0.000 340 14126 wm_rh_G_pariet_inf-Supramar 0 0.000 341 14127 wm_rh_G_parietal_sup 0 0.000 342 14128 wm_rh_G_postcentral 0 0.000 343 14129 wm_rh_G_precentral 0 0.000 344 14130 wm_rh_G_precuneus 0 0.000 345 14131 wm_rh_G_rectus 0 0.000 346 14132 wm_rh_G_subcallosal 0 0.000 347 14133 wm_rh_G_temp_sup-G_T_transv 0 0.000 348 14134 wm_rh_G_temp_sup-Lateral 0 0.000 349 14135 wm_rh_G_temp_sup-Plan_polar 0 0.000 350 14136 wm_rh_G_temp_sup-Plan_tempo 0 0.000 351 14137 wm_rh_G_temporal_inf 0 0.000 352 14138 wm_rh_G_temporal_middle 0 0.000 353 14139 wm_rh_Lat_Fis-ant-Horizont 0 0.000 354 14140 wm_rh_Lat_Fis-ant-Vertical 0 0.000 355 14141 wm_rh_Lat_Fis-post 0 0.000 356 14142 wm_rh_Medial_wall 0 0.000 357 14143 wm_rh_Pole_occipital 0 0.000 358 14144 wm_rh_Pole_temporal 0 0.000 359 14145 wm_rh_S_calcarine 0 0.000 360 14146 wm_rh_S_central 0 0.000 361 14147 wm_rh_S_cingul-Marginalis 0 0.000 362 14148 wm_rh_S_circular_insula_ant 0 0.000 363 14149 wm_rh_S_circular_insula_inf 0 0.000 364 14150 wm_rh_S_circular_insula_sup 0 0.000 365 14151 wm_rh_S_collat_transv_ant 0 0.000 366 14152 wm_rh_S_collat_transv_post 0 0.000 367 14153 wm_rh_S_front_inf 0 0.000 368 14154 wm_rh_S_front_middle 0 0.000 369 14155 wm_rh_S_front_sup 0 0.000 370 14156 wm_rh_S_interm_prim-Jensen 0 0.000 371 14157 wm_rh_S_intrapariet_and_P_trans 0 0.000 372 14158 wm_rh_S_oc_middle_and_Lunatus 0 0.000 373 14159 wm_rh_S_oc_sup_and_transversal 0 0.000 374 14160 wm_rh_S_occipital_ant 0 0.000 375 14161 wm_rh_S_oc-temp_lat 0 0.000 376 14162 wm_rh_S_oc-temp_med_and_Lingual 0 0.000 377 14163 wm_rh_S_orbital_lateral 0 0.000 378 14164 wm_rh_S_orbital_med-olfact 0 0.000 379 14165 wm_rh_S_orbital-H_Shaped 0 0.000 380 14166 wm_rh_S_parieto_occipital 0 0.000 381 14167 wm_rh_S_pericallosal 0 0.000 382 14168 wm_rh_S_postcentral 0 0.000 383 14169 wm_rh_S_precentral-inf-part 0 0.000 384 14170 wm_rh_S_precentral-sup-part 0 0.000 385 14171 wm_rh_S_suborbital 0 0.000 386 14172 wm_rh_S_subparietal 0 0.000 387 14173 wm_rh_S_temporal_inf 0 0.000 388 14174 wm_rh_S_temporal_sup 0 0.000 389 14175 wm_rh_S_temporal_transverse 0 0.000 Reporting on 70 segmentations mri_segstats done /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/label #-------------------------------------------- #@# BA Labels lh Wed Aug 7 08:04:15 BRT 2013 \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.BA1.label --trgsubject subjects_name_ --trglabel ./lh.BA1.label --hemi lh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./lh.BA1.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4129 nlabel points Performing mapping from target back to the source label 140852 Number of reverse mapping hits = 497 Checking for and removing duplicates Writing label file ./lh.BA1.label 4626 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.BA2.label --trgsubject subjects_name_ --trglabel ./lh.BA2.label --hemi lh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.BA2.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./lh.BA2.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7909 nlabel points Performing mapping from target back to the source label 140852 Number of reverse mapping hits = 1037 Checking for and removing duplicates Writing label file ./lh.BA2.label 8946 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.BA3a.label --trgsubject subjects_name_ --trglabel ./lh.BA3a.label --hemi lh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.BA3a.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./lh.BA3a.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4077 nlabel points Performing mapping from target back to the source label 140852 Number of reverse mapping hits = 128 Checking for and removing duplicates Writing label file ./lh.BA3a.label 4205 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.BA3b.label --trgsubject subjects_name_ --trglabel ./lh.BA3b.label --hemi lh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.BA3b.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./lh.BA3b.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5983 nlabel points Performing mapping from target back to the source label 140852 Number of reverse mapping hits = 452 Checking for and removing duplicates Writing label file ./lh.BA3b.label 6435 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.BA4a.label --trgsubject subjects_name_ --trglabel ./lh.BA4a.label --hemi lh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.BA4a.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./lh.BA4a.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5784 nlabel points Performing mapping from target back to the source label 140852 Number of reverse mapping hits = 425 Checking for and removing duplicates Writing label file ./lh.BA4a.label 6209 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.BA4p.label --trgsubject subjects_name_ --trglabel ./lh.BA4p.label --hemi lh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.BA4p.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./lh.BA4p.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4070 nlabel points Performing mapping from target back to the source label 140852 Number of reverse mapping hits = 240 Checking for and removing duplicates Writing label file ./lh.BA4p.label 4310 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.BA6.label --trgsubject subjects_name_ --trglabel ./lh.BA6.label --hemi lh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.BA6.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./lh.BA6.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 13589 nlabel points Performing mapping from target back to the source label 140852 Number of reverse mapping hits = 1084 Checking for and removing duplicates Writing label file ./lh.BA6.label 14673 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.BA44.label --trgsubject subjects_name_ --trglabel ./lh.BA44.label --hemi lh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.BA44.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./lh.BA44.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4181 nlabel points Performing mapping from target back to the source label 140852 Number of reverse mapping hits = 517 Checking for and removing duplicates Writing label file ./lh.BA44.label 4698 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.BA45.label --trgsubject subjects_name_ --trglabel ./lh.BA45.label --hemi lh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.BA45.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./lh.BA45.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3422 nlabel points Performing mapping from target back to the source label 140852 Number of reverse mapping hits = 765 Checking for and removing duplicates Writing label file ./lh.BA45.label 4187 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.V1.label --trgsubject subjects_name_ --trglabel ./lh.V1.label --hemi lh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.V1.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./lh.V1.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4641 nlabel points Performing mapping from target back to the source label 140852 Number of reverse mapping hits = 2219 Checking for and removing duplicates Writing label file ./lh.V1.label 6860 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.V2.label --trgsubject subjects_name_ --trglabel ./lh.V2.label --hemi lh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.V2.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./lh.V2.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8114 nlabel points Performing mapping from target back to the source label 140852 Number of reverse mapping hits = 3847 Checking for and removing duplicates Writing label file ./lh.V2.label 11961 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.MT.label --trgsubject subjects_name_ --trglabel ./lh.MT.label --hemi lh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.MT.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./lh.MT.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2018 nlabel points Performing mapping from target back to the source label 140852 Number of reverse mapping hits = 509 Checking for and removing duplicates Writing label file ./lh.MT.label 2527 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.perirhinal.label --trgsubject subjects_name_ --trglabel ./lh.perirhinal.label --hemi lh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.perirhinal.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./lh.perirhinal.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1199 nlabel points Performing mapping from target back to the source label 140852 Number of reverse mapping hits = 140 Checking for and removing duplicates Writing label file ./lh.perirhinal.label 1339 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.BA1.thresh.label --trgsubject subjects_name_ --trglabel ./lh.BA1.thresh.label --hemi lh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.BA1.thresh.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./lh.BA1.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1014 nlabel points Performing mapping from target back to the source label 140852 Number of reverse mapping hits = 100 Checking for and removing duplicates Writing label file ./lh.BA1.thresh.label 1114 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.BA2.thresh.label --trgsubject subjects_name_ --trglabel ./lh.BA2.thresh.label --hemi lh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.BA2.thresh.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./lh.BA2.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2092 nlabel points Performing mapping from target back to the source label 140852 Number of reverse mapping hits = 366 Checking for and removing duplicates Writing label file ./lh.BA2.thresh.label 2458 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.BA3a.thresh.label --trgsubject subjects_name_ --trglabel ./lh.BA3a.thresh.label --hemi lh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.BA3a.thresh.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./lh.BA3a.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1504 nlabel points Performing mapping from target back to the source label 140852 Number of reverse mapping hits = 26 Checking for and removing duplicates Writing label file ./lh.BA3a.thresh.label 1530 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.BA3b.thresh.label --trgsubject subjects_name_ --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.BA3b.thresh.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./lh.BA3b.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1996 nlabel points Performing mapping from target back to the source label 140852 Number of reverse mapping hits = 119 Checking for and removing duplicates Writing label file ./lh.BA3b.thresh.label 2115 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.BA4a.thresh.label --trgsubject subjects_name_ --trglabel ./lh.BA4a.thresh.label --hemi lh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.BA4a.thresh.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./lh.BA4a.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2319 nlabel points Performing mapping from target back to the source label 140852 Number of reverse mapping hits = 182 Checking for and removing duplicates Writing label file ./lh.BA4a.thresh.label 2501 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.BA4p.thresh.label --trgsubject subjects_name_ --trglabel ./lh.BA4p.thresh.label --hemi lh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.BA4p.thresh.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./lh.BA4p.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1549 nlabel points Performing mapping from target back to the source label 140852 Number of reverse mapping hits = 74 Checking for and removing duplicates Writing label file ./lh.BA4p.thresh.label 1623 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.BA6.thresh.label --trgsubject subjects_name_ --trglabel ./lh.BA6.thresh.label --hemi lh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.BA6.thresh.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./lh.BA6.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7035 nlabel points Performing mapping from target back to the source label 140852 Number of reverse mapping hits = 520 Checking for and removing duplicates Writing label file ./lh.BA6.thresh.label 7555 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.BA44.thresh.label --trgsubject subjects_name_ --trglabel ./lh.BA44.thresh.label --hemi lh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.BA44.thresh.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./lh.BA44.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1912 nlabel points Performing mapping from target back to the source label 140852 Number of reverse mapping hits = 246 Checking for and removing duplicates Writing label file ./lh.BA44.thresh.label 2158 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.BA45.thresh.label --trgsubject subjects_name_ --trglabel ./lh.BA45.thresh.label --hemi lh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.BA45.thresh.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./lh.BA45.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1151 nlabel points Performing mapping from target back to the source label 140852 Number of reverse mapping hits = 369 Checking for and removing duplicates Writing label file ./lh.BA45.thresh.label 1520 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.V1.thresh.label --trgsubject subjects_name_ --trglabel ./lh.V1.thresh.label --hemi lh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.V1.thresh.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./lh.V1.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3405 nlabel points Performing mapping from target back to the source label 140852 Number of reverse mapping hits = 1638 Checking for and removing duplicates Writing label file ./lh.V1.thresh.label 5043 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.V2.thresh.label --trgsubject subjects_name_ --trglabel ./lh.V2.thresh.label --hemi lh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.V2.thresh.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./lh.V2.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3334 nlabel points Performing mapping from target back to the source label 140852 Number of reverse mapping hits = 1868 Checking for and removing duplicates Writing label file ./lh.V2.thresh.label 5202 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.MT.thresh.label --trgsubject subjects_name_ --trglabel ./lh.MT.thresh.label --hemi lh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/lh.MT.thresh.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./lh.MT.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 513 nlabel points Performing mapping from target back to the source label 140852 Number of reverse mapping hits = 137 Checking for and removing duplicates Writing label file ./lh.MT.thresh.label 650 mri_label2label: Done \n mris_label2annot --s subjects_name_ --hemi lh --ctab /Applications/Freesurfer5.3/freesurfer/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --l lh.perirhinal.label --a BA --maxstatwinner --noverbose \n Reading ctab /Applications/Freesurfer5.3/freesurfer/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/label cmdline mris_label2annot --s subjects_name_ --hemi lh --ctab /Applications/Freesurfer5.3/freesurfer/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --l lh.perirhinal.label --a BA --maxstatwinner --noverbose sysname Darwin hostname Pedro-Rosas-MacBook-Pro-2.local machine x86_64 user pedrogomesrosa subject subjects_name_ hemi lh SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 ColorTable /Applications/Freesurfer5.3/freesurfer/average/colortable_BA.txt AnnotName BA nlables 13 LabelThresh 0 0.000000 Loading /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.orig 1 1530880 BA1 2 16749699 BA2 3 16711680 BA3a 4 3368703 BA3b 5 1376196 BA4a 6 13382655 BA4p 7 10036737 BA6 8 2490521 BA44 9 39283 BA45 10 3993 V1 11 8508928 V2 12 10027163 MT 13 16422433 perirhinal Mapping unhit to unknown Found 98586 unhit vertices Writing annot to /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/label/lh.BA.annot \n mris_label2annot --s subjects_name_ --hemi lh --ctab /Applications/Freesurfer5.3/freesurfer/average/colortable_BA.txt --l lh.BA1.thresh.label --l lh.BA2.thresh.label --l lh.BA3a.thresh.label --l lh.BA3b.thresh.label --l lh.BA4a.thresh.label --l lh.BA4p.thresh.label --l lh.BA6.thresh.label --l lh.BA44.thresh.label --l lh.BA45.thresh.label --l lh.V1.thresh.label --l lh.V2.thresh.label --l lh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose \n Reading ctab /Applications/Freesurfer5.3/freesurfer/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/label cmdline mris_label2annot --s subjects_name_ --hemi lh --ctab /Applications/Freesurfer5.3/freesurfer/average/colortable_BA.txt --l lh.BA1.thresh.label --l lh.BA2.thresh.label --l lh.BA3a.thresh.label --l lh.BA3b.thresh.label --l lh.BA4a.thresh.label --l lh.BA4p.thresh.label --l lh.BA6.thresh.label --l lh.BA44.thresh.label --l lh.BA45.thresh.label --l lh.V1.thresh.label --l lh.V2.thresh.label --l lh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose sysname Darwin hostname Pedro-Rosas-MacBook-Pro-2.local machine x86_64 user pedrogomesrosa subject subjects_name_ hemi lh SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 ColorTable /Applications/Freesurfer5.3/freesurfer/average/colortable_BA.txt AnnotName BA.thresh nlables 12 LabelThresh 0 0.000000 Loading /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.orig 1 1530880 BA1 2 16749699 BA2 3 16711680 BA3a 4 3368703 BA3b 5 1376196 BA4a 6 13382655 BA4p 7 10036737 BA6 8 2490521 BA44 9 39283 BA45 10 3993 V1 11 8508928 V2 12 10027163 MT Mapping unhit to unknown Found 118634 unhit vertices Writing annot to /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/label/lh.BA.thresh.annot \n mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab subjects_name_ lh white \n computing statistics for each annotation in ./lh.BA.annot. reading volume /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/wm.mgz... reading input surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.white... reading input pial surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.pial... reading input white surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /Applications/Freesurfer5.3/freesurfer/average/colortable_BA.txt) Saving annotation colortable ./BA.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1103 611 1446 1.935 0.598 0.117 0.038 13 1.8 BA1 5000 3156 6782 2.141 0.619 0.123 0.042 62 9.8 BA2 986 650 841 1.702 0.520 0.140 0.040 9 1.8 BA3a 2566 1628 3316 1.795 0.849 0.110 0.030 21 3.3 BA3b 1785 971 2460 2.371 0.720 0.110 0.041 19 3.4 BA4a 1216 850 1794 2.381 0.754 0.128 0.043 11 2.1 BA4p 9010 5368 17154 2.752 0.688 0.114 0.060 124 26.8 BA6 2180 1516 4393 2.728 0.561 0.123 0.033 21 2.8 BA44 2529 1818 5075 2.389 0.680 0.141 0.042 31 3.9 BA45 3903 2770 3928 1.462 0.480 0.159 0.054 56 8.9 V1 9404 5929 11781 1.926 0.577 0.151 0.057 142 21.8 V2 1706 1182 2900 2.287 0.648 0.133 0.035 18 2.3 MT 878 612 2474 3.008 0.862 0.116 0.049 8 1.7 perirhinal \n mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab subjects_name_ lh white \n computing statistics for each annotation in ./lh.BA.thresh.annot. reading volume /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/wm.mgz... reading input surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.white... reading input pial surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.pial... reading input white surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /Applications/Freesurfer5.3/freesurfer/average/colortable_BA.txt) Saving annotation colortable ./BA.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 778 381 860 1.790 0.535 0.134 0.047 11 1.8 BA1 1974 1198 2631 2.074 0.608 0.121 0.053 32 5.5 BA2 765 515 631 1.626 0.465 0.145 0.041 8 1.4 BA3a 1339 906 1141 1.200 0.289 0.093 0.021 7 1.2 BA3b 1600 910 2469 2.503 0.711 0.113 0.040 17 2.8 BA4a 1016 717 1395 2.245 0.678 0.131 0.050 10 2.1 BA4p 5093 2909 9119 2.718 0.668 0.111 0.071 86 17.5 BA6 1600 1075 3138 2.742 0.580 0.128 0.034 18 2.3 BA44 1367 883 2775 2.581 0.607 0.139 0.043 19 2.6 BA45 3076 2341 3501 1.506 0.509 0.164 0.054 46 6.7 V1 3078 2143 3999 1.850 0.553 0.157 0.059 49 6.5 V2 532 353 1065 2.472 0.761 0.134 0.036 7 0.8 MT #-------------------------------------------- #@# BA Labels rh Wed Aug 7 08:08:51 BRT 2013 \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.BA1.label --trgsubject subjects_name_ --trglabel ./rh.BA1.label --hemi rh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.BA1.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./rh.BA1.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3962 nlabel points Performing mapping from target back to the source label 141108 Number of reverse mapping hits = 643 Checking for and removing duplicates Writing label file ./rh.BA1.label 4605 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.BA2.label --trgsubject subjects_name_ --trglabel ./rh.BA2.label --hemi rh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.BA2.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./rh.BA2.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6687 nlabel points Performing mapping from target back to the source label 141108 Number of reverse mapping hits = 976 Checking for and removing duplicates Writing label file ./rh.BA2.label 7663 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.BA3a.label --trgsubject subjects_name_ --trglabel ./rh.BA3a.label --hemi rh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.BA3a.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./rh.BA3a.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3980 nlabel points Performing mapping from target back to the source label 141108 Number of reverse mapping hits = 209 Checking for and removing duplicates Writing label file ./rh.BA3a.label 4189 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.BA3b.label --trgsubject subjects_name_ --trglabel ./rh.BA3b.label --hemi rh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.BA3b.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./rh.BA3b.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4522 nlabel points Performing mapping from target back to the source label 141108 Number of reverse mapping hits = 403 Checking for and removing duplicates Writing label file ./rh.BA3b.label 4925 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.BA4a.label --trgsubject subjects_name_ --trglabel ./rh.BA4a.label --hemi rh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.BA4a.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./rh.BA4a.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5747 nlabel points Performing mapping from target back to the source label 141108 Number of reverse mapping hits = 439 Checking for and removing duplicates Writing label file ./rh.BA4a.label 6186 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.BA4p.label --trgsubject subjects_name_ --trglabel ./rh.BA4p.label --hemi rh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.BA4p.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./rh.BA4p.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4473 nlabel points Performing mapping from target back to the source label 141108 Number of reverse mapping hits = 176 Checking for and removing duplicates Writing label file ./rh.BA4p.label 4649 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.BA6.label --trgsubject subjects_name_ --trglabel ./rh.BA6.label --hemi rh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.BA6.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./rh.BA6.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 12256 nlabel points Performing mapping from target back to the source label 141108 Number of reverse mapping hits = 1728 Checking for and removing duplicates Writing label file ./rh.BA6.label 13984 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.BA44.label --trgsubject subjects_name_ --trglabel ./rh.BA44.label --hemi rh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.BA44.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./rh.BA44.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6912 nlabel points Performing mapping from target back to the source label 141108 Number of reverse mapping hits = 1673 Checking for and removing duplicates Writing label file ./rh.BA44.label 8585 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.BA45.label --trgsubject subjects_name_ --trglabel ./rh.BA45.label --hemi rh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.BA45.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./rh.BA45.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5355 nlabel points Performing mapping from target back to the source label 141108 Number of reverse mapping hits = 1933 Checking for and removing duplicates Writing label file ./rh.BA45.label 7288 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.V1.label --trgsubject subjects_name_ --trglabel ./rh.V1.label --hemi rh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.V1.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./rh.V1.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4727 nlabel points Performing mapping from target back to the source label 141108 Number of reverse mapping hits = 1953 Checking for and removing duplicates Writing label file ./rh.V1.label 6680 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.V2.label --trgsubject subjects_name_ --trglabel ./rh.V2.label --hemi rh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.V2.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./rh.V2.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8016 nlabel points Performing mapping from target back to the source label 141108 Number of reverse mapping hits = 3135 Checking for and removing duplicates Writing label file ./rh.V2.label 11151 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.MT.label --trgsubject subjects_name_ --trglabel ./rh.MT.label --hemi rh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.MT.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./rh.MT.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1932 nlabel points Performing mapping from target back to the source label 141108 Number of reverse mapping hits = 614 Checking for and removing duplicates Writing label file ./rh.MT.label 2546 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.perirhinal.label --trgsubject subjects_name_ --trglabel ./rh.perirhinal.label --hemi rh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.perirhinal.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./rh.perirhinal.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 752 nlabel points Performing mapping from target back to the source label 141108 Number of reverse mapping hits = 65 Checking for and removing duplicates Writing label file ./rh.perirhinal.label 817 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.BA1.thresh.label --trgsubject subjects_name_ --trglabel ./rh.BA1.thresh.label --hemi rh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.BA1.thresh.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./rh.BA1.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 876 nlabel points Performing mapping from target back to the source label 141108 Number of reverse mapping hits = 155 Checking for and removing duplicates Writing label file ./rh.BA1.thresh.label 1031 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.BA2.thresh.label --trgsubject subjects_name_ --trglabel ./rh.BA2.thresh.label --hemi rh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.BA2.thresh.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./rh.BA2.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2688 nlabel points Performing mapping from target back to the source label 141108 Number of reverse mapping hits = 472 Checking for and removing duplicates Writing label file ./rh.BA2.thresh.label 3160 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.BA3a.thresh.label --trgsubject subjects_name_ --trglabel ./rh.BA3a.thresh.label --hemi rh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.BA3a.thresh.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./rh.BA3a.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1698 nlabel points Performing mapping from target back to the source label 141108 Number of reverse mapping hits = 48 Checking for and removing duplicates Writing label file ./rh.BA3a.thresh.label 1746 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.BA3b.thresh.label --trgsubject subjects_name_ --trglabel ./rh.BA3b.thresh.label --hemi rh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.BA3b.thresh.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./rh.BA3b.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2183 nlabel points Performing mapping from target back to the source label 141108 Number of reverse mapping hits = 214 Checking for and removing duplicates Writing label file ./rh.BA3b.thresh.label 2397 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.BA4a.thresh.label --trgsubject subjects_name_ --trglabel ./rh.BA4a.thresh.label --hemi rh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.BA4a.thresh.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./rh.BA4a.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1388 nlabel points Performing mapping from target back to the source label 141108 Number of reverse mapping hits = 65 Checking for and removing duplicates Writing label file ./rh.BA4a.thresh.label 1453 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.BA4p.thresh.label --trgsubject subjects_name_ --trglabel ./rh.BA4p.thresh.label --hemi rh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.BA4p.thresh.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./rh.BA4p.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1489 nlabel points Performing mapping from target back to the source label 141108 Number of reverse mapping hits = 77 Checking for and removing duplicates Writing label file ./rh.BA4p.thresh.label 1566 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.BA6.thresh.label --trgsubject subjects_name_ --trglabel ./rh.BA6.thresh.label --hemi rh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.BA6.thresh.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./rh.BA6.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6959 nlabel points Performing mapping from target back to the source label 141108 Number of reverse mapping hits = 1278 Checking for and removing duplicates Writing label file ./rh.BA6.thresh.label 8237 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.BA44.thresh.label --trgsubject subjects_name_ --trglabel ./rh.BA44.thresh.label --hemi rh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.BA44.thresh.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./rh.BA44.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1012 nlabel points Performing mapping from target back to the source label 141108 Number of reverse mapping hits = 218 Checking for and removing duplicates Writing label file ./rh.BA44.thresh.label 1230 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.BA45.thresh.label --trgsubject subjects_name_ --trglabel ./rh.BA45.thresh.label --hemi rh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.BA45.thresh.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./rh.BA45.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1178 nlabel points Performing mapping from target back to the source label 141108 Number of reverse mapping hits = 518 Checking for and removing duplicates Writing label file ./rh.BA45.thresh.label 1696 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.V1.thresh.label --trgsubject subjects_name_ --trglabel ./rh.V1.thresh.label --hemi rh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.V1.thresh.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./rh.V1.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3232 nlabel points Performing mapping from target back to the source label 141108 Number of reverse mapping hits = 1373 Checking for and removing duplicates Writing label file ./rh.V1.thresh.label 4605 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.V2.thresh.label --trgsubject subjects_name_ --trglabel ./rh.V2.thresh.label --hemi rh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.V2.thresh.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./rh.V2.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3437 nlabel points Performing mapping from target back to the source label 141108 Number of reverse mapping hits = 1494 Checking for and removing duplicates Writing label file ./rh.V2.thresh.label 4931 mri_label2label: Done \n mri_label2label --srcsubject fsaverage --srclabel /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.MT.thresh.label --trgsubject subjects_name_ --trglabel ./rh.MT.thresh.label --hemi rh --regmethod surface \n srclabel = /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/label/rh.MT.thresh.label srcsubject = fsaverage trgsubject = subjects_name_ trglabel = ./rh.MT.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.white Reading target registration /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 268 nlabel points Performing mapping from target back to the source label 141108 Number of reverse mapping hits = 36 Checking for and removing duplicates Writing label file ./rh.MT.thresh.label 304 mri_label2label: Done \n mris_label2annot --s subjects_name_ --hemi rh --ctab /Applications/Freesurfer5.3/freesurfer/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --l rh.perirhinal.label --a BA --maxstatwinner --noverbose \n Reading ctab /Applications/Freesurfer5.3/freesurfer/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/label cmdline mris_label2annot --s subjects_name_ --hemi rh --ctab /Applications/Freesurfer5.3/freesurfer/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --l rh.perirhinal.label --a BA --maxstatwinner --noverbose sysname Darwin hostname Pedro-Rosas-MacBook-Pro-2.local machine x86_64 user pedrogomesrosa subject subjects_name_ hemi rh SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 ColorTable /Applications/Freesurfer5.3/freesurfer/average/colortable_BA.txt AnnotName BA nlables 13 LabelThresh 0 0.000000 Loading /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.orig 1 1530880 BA1 2 16749699 BA2 3 16711680 BA3a 4 3368703 BA3b 5 1376196 BA4a 6 13382655 BA4p 7 10036737 BA6 8 2490521 BA44 9 39283 BA45 10 3993 V1 11 8508928 V2 12 10027163 MT 13 16422433 perirhinal Mapping unhit to unknown Found 95846 unhit vertices Writing annot to /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/label/rh.BA.annot \n mris_label2annot --s subjects_name_ --hemi rh --ctab /Applications/Freesurfer5.3/freesurfer/average/colortable_BA.txt --l rh.BA1.thresh.label --l rh.BA2.thresh.label --l rh.BA3a.thresh.label --l rh.BA3b.thresh.label --l rh.BA4a.thresh.label --l rh.BA4p.thresh.label --l rh.BA6.thresh.label --l rh.BA44.thresh.label --l rh.BA45.thresh.label --l rh.V1.thresh.label --l rh.V2.thresh.label --l rh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose \n Reading ctab /Applications/Freesurfer5.3/freesurfer/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/label cmdline mris_label2annot --s subjects_name_ --hemi rh --ctab /Applications/Freesurfer5.3/freesurfer/average/colortable_BA.txt --l rh.BA1.thresh.label --l rh.BA2.thresh.label --l rh.BA3a.thresh.label --l rh.BA3b.thresh.label --l rh.BA4a.thresh.label --l rh.BA4p.thresh.label --l rh.BA6.thresh.label --l rh.BA44.thresh.label --l rh.BA45.thresh.label --l rh.V1.thresh.label --l rh.V2.thresh.label --l rh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose sysname Darwin hostname Pedro-Rosas-MacBook-Pro-2.local machine x86_64 user pedrogomesrosa subject subjects_name_ hemi rh SUBJECTS_DIR /Users/pedrogomesrosa/Desktop/Estado/Controles/T0 ColorTable /Applications/Freesurfer5.3/freesurfer/average/colortable_BA.txt AnnotName BA.thresh nlables 12 LabelThresh 0 0.000000 Loading /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.orig 1 1530880 BA1 2 16749699 BA2 3 16711680 BA3a 4 3368703 BA3b 5 1376196 BA4a 6 13382655 BA4p 7 10036737 BA6 8 2490521 BA44 9 39283 BA45 10 3993 V1 11 8508928 V2 12 10027163 MT Mapping unhit to unknown Found 117142 unhit vertices Writing annot to /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/label/rh.BA.thresh.annot \n mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab subjects_name_ rh white \n computing statistics for each annotation in ./rh.BA.annot. reading volume /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/wm.mgz... reading input surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.white... reading input pial surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.pial... reading input white surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /Applications/Freesurfer5.3/freesurfer/average/colortable_BA.txt) Saving annotation colortable ./BA.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1275 662 2184 2.472 0.631 0.125 0.049 17 2.5 BA1 4179 2681 5176 1.930 0.579 0.114 0.030 36 5.2 BA2 1044 661 911 1.628 0.541 0.126 0.033 10 1.4 BA3a 1988 1281 2684 1.791 0.722 0.107 0.027 15 2.4 BA3b 1503 920 1988 2.037 0.769 0.122 0.049 19 3.1 BA4a 1203 788 1282 1.741 0.594 0.122 0.039 11 1.9 BA4p 9089 5383 14899 2.493 0.728 0.121 0.044 109 18.0 BA6 4060 2635 7198 2.671 0.580 0.120 0.037 38 5.7 BA44 5691 3683 10071 2.338 0.691 0.129 0.037 66 8.9 BA45 4407 3034 4541 1.455 0.511 0.155 0.053 61 10.1 V1 8437 5329 10575 1.950 0.560 0.154 0.058 127 19.7 V2 1802 1301 3008 2.390 0.549 0.136 0.040 21 2.5 MT 584 396 1859 3.835 0.837 0.126 0.044 6 1.1 perirhinal \n mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab subjects_name_ rh white \n computing statistics for each annotation in ./rh.BA.thresh.annot. reading volume /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/wm.mgz... reading input surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.white... reading input pial surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.pial... reading input white surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /Applications/Freesurfer5.3/freesurfer/average/colortable_BA.txt) Saving annotation colortable ./BA.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 825 406 1247 2.283 0.633 0.127 0.054 13 2.0 BA1 2535 1588 3200 1.922 0.556 0.105 0.027 19 2.8 BA2 942 590 731 1.543 0.460 0.124 0.031 8 1.3 BA3a 1647 1068 1849 1.586 0.602 0.101 0.024 12 1.8 BA3b 839 491 1027 1.919 0.802 0.129 0.051 12 2.0 BA4a 920 634 949 1.600 0.532 0.124 0.040 9 1.5 BA4p 6296 3616 9999 2.515 0.745 0.118 0.041 74 11.3 BA6 1033 672 2284 3.049 0.593 0.130 0.040 13 1.6 BA44 1181 829 2402 2.424 0.627 0.141 0.044 16 2.1 BA45 2936 2245 3400 1.483 0.551 0.160 0.051 40 5.6 V1 4547 2875 5377 1.820 0.549 0.162 0.064 72 11.7 V2 265 198 421 2.100 0.449 0.121 0.027 2 0.3 MT /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label lh Wed Aug 7 08:13:26 BRT 2013 \n mris_spherical_average -erode 1 -orig white -t 0.4 -o subjects_name_ label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label \n painting output onto subject subjects_name_. processing subject lh.EC_average... reading output surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.sphere.reg... eroding label 1 times before writing thresholding label stat at 0.400 before writing only 1 subject - copying statistics... writing label with 914 points to lh.entorhinal_exvivo.label... \n mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label subjects_name_ lh white \n limiting computations to label ./lh.entorhinal_exvivo.label. reading volume /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/wm.mgz... reading input surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.white... reading input pial surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.pial... reading input white surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/lh.white... INFO: assuming MGZ format for volumes. table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 362 228 1086 3.107 0.821 0.173 0.755 49 2.3 ./lh.entorhinal_exvivo.label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label rh Wed Aug 7 08:13:43 BRT 2013 \n mris_spherical_average -erode 1 -orig white -t 0.4 -o subjects_name_ label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label \n painting output onto subject subjects_name_. processing subject rh.EC_average... reading output surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.sphere.reg... eroding label 1 times before writing thresholding label stat at 0.400 before writing only 1 subject - copying statistics... writing label with 731 points to rh.entorhinal_exvivo.label... \n mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label subjects_name_ rh white \n limiting computations to label ./rh.entorhinal_exvivo.label. reading volume /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/mri/wm.mgz... reading input surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.white... reading input pial surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.pial... reading input white surface /Users/pedrogomesrosa/Desktop/Estado/Controles/T0/subjects_name_/surf/rh.white... INFO: assuming MGZ format for volumes. table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 243 157 852 3.417 0.719 0.120 0.059 7 0.9 ./rh.entorhinal_exvivo.label #------------------------------------------ Started at Wed Aug 7 04:27:09 BRT 2013 Ended at Wed Aug 7 08:14:01 BRT 2013 #@#%# recon-all-run-time-hours 3.781 recon-all -s subjects_name_ finished without error at Wed Aug 7 08:14:01 BRT 2013