Thu Aug 8 10:53:42 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005 /opt/freesurfer/5.3.0/bin/recon-all -i /home/data/exppsy/forrest_gump/openfmri.org/sub005/anatomy/highres001.nii.gz -cw256 -all -T2 /home/data/exppsy/forrest_gump/openfmri.org/sub005/anatomy/other/t2w001.nii.gz -T2pial -subjid sub005 -sd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer subjid sub005 setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Actual FREESURFER_HOME /opt/freesurfer/5.3.0 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux snake4 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc unlimited maxlocks unlimited maxsignal 16382 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 99201692 96396048 2805644 0 188520 94505440 -/+ buffers/cache: 1702088 97499604 Swap: 25165780 532 25165248 ######################################## 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: 2013/08/08-08:53:42-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:44-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:44-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:44-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:44-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:44-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:45-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:45-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:45-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:45-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:45-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:45-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:45-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:45-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:45-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/freesurfer/5.3.0/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /opt/freesurfer/5.3.0/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### -cw256 option is now persistent (remove with -clean-cw256) /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub005/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/001.mgz mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub005/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/data/exppsy/forrest_gump/openfmri.org/sub005/anatomy/highres001.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998148, -0.0400878, -0.0457496) j_ras = (-0.0459461, 0.989757, 0.135168) k_ras = (-0.0398624, -0.13702, 0.989766) writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/001.mgz... #-------------------------------------------- #@# T2/FLAIR Input Thu Aug 8 10:54:07 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub005/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/T2raw.mgz mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub005/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/T2raw.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/data/exppsy/forrest_gump/openfmri.org/sub005/anatomy/other/t2w001.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998148, -0.0400878, -0.0457496) j_ras = (-0.0459461, 0.989757, 0.135168) k_ras = (-0.0398624, -0.13702, 0.989766) writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/T2raw.mgz... #-------------------------------------------- #@# MotionCor Thu Aug 8 10:54:24 CEST 2013 Found 1 runs /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/001.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig.mgz --conform --cw256 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig.mgz --conform --cw256 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998148, -0.0400878, -0.0457496) j_ras = (-0.0459461, 0.989757, 0.135168) k_ras = (-0.0398624, -0.13702, 0.989766) Original Data has (0.699913, 0.666667, 0.666667) mm size and (274, 384, 384) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig.mgz... mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/talairach.xfm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Aug 8 10:55:05 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Thu Aug 8 10:58:01 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.5432, pval=0.2115 >= threshold=0.0050) awk -f /opt/freesurfer/5.3.0/bin/extract_talairach_avi_QA.awk /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/talairach_avi.log tal_QC_AZS /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/talairach_avi.log TalAviQA: 0.96657 z-score: -2 #-------------------------------------------- #@# Nu Intensity Correction Thu Aug 8 10:58:01 CEST 2013 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri /opt/freesurfer/5.3.0/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux snake4 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux Thu Aug 8 10:58:01 CEST 2013 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.20260 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.20260/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.20260/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, 4.19095e-09, 3.72529e-09) j_ras = (7.45058e-09, 1.49012e-08, -1) k_ras = (-6.0536e-09, 1, -1.49012e-08) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.20260/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Aug 8 10:58:04 CEST 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.20260/nu0.mnc ./tmp.mri_nu_correct.mni.20260/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.20260/0/ [fkaule@snake4:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/] [2013-08-08 10:58:04] running: /opt/freesurfer/5.3.0/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.20260/0/ ./tmp.mri_nu_correct.mni.20260/nu0.mnc ./tmp.mri_nu_correct.mni.20260/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 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 Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 50 CV of field change: 0.00140342 [fkaule@snake4:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/] [2013-08-08 10:59:11] running: /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.20260/nu0.mnc ./tmp.mri_nu_correct.mni.20260/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Thu Aug 8 10:59:18 CEST 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.20260/nu1.mnc ./tmp.mri_nu_correct.mni.20260/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.20260/1/ [fkaule@snake4:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/] [2013-08-08 10:59:18] running: /opt/freesurfer/5.3.0/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.20260/1/ ./tmp.mri_nu_correct.mni.20260/nu1.mnc ./tmp.mri_nu_correct.mni.20260/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done 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 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: 50 CV of field change: 0.00110121 [fkaule@snake4:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/] [2013-08-08 11:00:10] running: /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.20260/nu1.mnc ./tmp.mri_nu_correct.mni.20260/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.20260/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.20260/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.20260/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.20260/ones.mgz sysname Linux hostname snake4 machine x86_64 user fkaule input ./tmp.mri_nu_correct.mni.20260/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.20260/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.20260/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.20260/sum.junk --avgwf ./tmp.mri_nu_correct.mni.20260/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.20260/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.20260/sum.junk --avgwf ./tmp.mri_nu_correct.mni.20260/input.mean.dat sysname Linux hostname snake4 machine x86_64 user fkaule UseRobust 0 Loading ./tmp.mri_nu_correct.mni.20260/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.20260/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.20260/ones.mgz --i ./tmp.mri_nu_correct.mni.20260/nu2.mnc --sum ./tmp.mri_nu_correct.mni.20260/sum.junk --avgwf ./tmp.mri_nu_correct.mni.20260/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.20260/ones.mgz --i ./tmp.mri_nu_correct.mni.20260/nu2.mnc --sum ./tmp.mri_nu_correct.mni.20260/sum.junk --avgwf ./tmp.mri_nu_correct.mni.20260/output.mean.dat sysname Linux hostname snake4 machine x86_64 user fkaule UseRobust 0 Loading ./tmp.mri_nu_correct.mni.20260/ones.mgz Loading ./tmp.mri_nu_correct.mni.20260/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.20260/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.20260/nu2.mnc ./tmp.mri_nu_correct.mni.20260/nu2.mnc mul .93128273976889651174 Saving result to './tmp.mri_nu_correct.mni.20260/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.20260/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.20260/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.20260/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 4.19095e-09, 3.72529e-09) j_ras = (7.45058e-09, 1.49012e-08, -1) k_ras = (-6.0536e-09, 1, -1.49012e-08) 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 7 seconds. mapping (14, 160) to ( 3, 110) Thu Aug 8 11:00:56 CEST 2013 mri_nu_correct.mni done mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Thu Aug 8 11:00:58 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.191 0.081 0.051 3.985; -0.133 1.061 0.435 -29.785; 0.011 -0.481 1.181 -2.834; 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 = 17 Starting OpenSpline(): npoints = 17 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 108 gm peak at 56 (56), valley at 42 (42) csf peak at 28, setting threshold to 46 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 56 (56), valley at 41 (41) csf peak at 28, setting threshold to 46 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 48 seconds. #-------------------------------------------- #@# Skull Stripping Thu Aug 8 11:03:46 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri mri_em_register -skull nu.mgz /opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta ======= NUMBER OF OPENMP THREADS = 1 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/opt/freesurfer/5.3.0/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=8.0 skull bounding box = (52, 13, 10) --> (201, 255, 209) using (102, 94, 110) as brain centroid... mean wm in atlas = 126, using box (84,64,85) --> (120, 123,134) to find MRI wm before smoothing, mri peak at 108 after smoothing, mri peak at 108, scaling input intensities by 1.167 scaling channel 0 by 1.16667 initial log_p = -4.8 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.553914 @ (-9.091, 27.273, -9.091) max log p = -4.487499 @ (4.545, -4.545, -4.545) max log p = -4.483190 @ (2.273, -6.818, 6.818) max log p = -4.472748 @ (1.136, 1.136, -3.409) max log p = -4.469653 @ (0.568, -0.568, 0.568) max log p = -4.464366 @ (-1.420, 0.284, 2.557) Found translation: (-2.0, 16.8, -7.1): log p = -4.464 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.5 (thresh=-4.5) 1.140 0.057 -0.139 -9.943; 0.000 1.142 0.473 -43.109; 0.161 -0.469 1.132 4.165; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.226 0.062 -0.149 -20.121; 0.000 1.228 0.509 -55.426; 0.149 -0.434 1.047 11.805; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.226 0.062 -0.149 -20.121; 0.000 1.228 0.509 -55.426; 0.149 -0.434 1.047 11.805; 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=-4.0, old_max_log_p =-4.1 (thresh=-4.1) 1.184 0.047 -0.110 -19.960; -0.012 1.242 0.390 -40.153; 0.105 -0.320 1.116 0.548; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.184 0.047 -0.110 -19.960; -0.012 1.242 0.390 -40.153; 0.105 -0.320 1.116 0.548; 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=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.180 0.063 -0.125 -19.391; -0.021 1.243 0.402 -40.394; 0.124 -0.329 1.111 -0.027; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.180 0.063 -0.125 -19.391; -0.021 1.243 0.402 -40.394; 0.124 -0.329 1.111 -0.027; 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 1.18046 0.06254 -0.12483 -19.39090; -0.02094 1.24275 0.40179 -40.39419; 0.12427 -0.32903 1.11130 -0.02731; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.18046 0.06254 -0.12483 -19.39090; -0.02094 1.24275 0.40179 -40.39419; 0.12427 -0.32903 1.11130 -0.02731; 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: 1.180 0.063 -0.125 -19.391; -0.021 1.243 0.402 -40.394; 0.124 -0.329 1.111 -0.027; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -4.0 (old=-4.8) transform before final EM align: 1.180 0.063 -0.125 -19.391; -0.021 1.243 0.402 -40.394; 0.124 -0.329 1.111 -0.027; 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 1.18046 0.06254 -0.12483 -19.39090; -0.02094 1.24275 0.40179 -40.39419; 0.12427 -0.32903 1.11130 -0.02731; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.18046 0.06254 -0.12483 -19.39090; -0.02094 1.24275 0.40179 -40.39419; 0.12427 -0.32903 1.11130 -0.02731; 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: 011: -log(p) = 4.4 tol 0.000000 final transform: 1.180 0.063 -0.125 -19.391; -0.021 1.243 0.402 -40.394; 0.124 -0.329 1.111 -0.027; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 33 minutes and 41 seconds. mri_watershed -T1 -brain_atlas /opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=131 y=83 z=112 r=103 first estimation of the main basin volume: 4591295 voxels Looking for seedpoints 2 found in the cerebellum 14 found in the rest of the brain global maximum in x=157, y=91, z=82, Imax=255 CSF=12, 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=18116230071 voxels, voxel volume =1.000 = 18116230071 mmm3 = 18116229.120 cm3 done. PostAnalyze...Basin Prior 70 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=129,y=94, z=108, r=10265 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 45567 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1032253284 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = 1083673940 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1065167473 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1061764480 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=18 , nb = 1080145814 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 4, 6, 30, 50 after analyzing : 4, 22, 30, 29 RIGHT_CER before analyzing : 4, 4, 24, 64 after analyzing : 4, 18, 25, 29 LEFT_CER before analyzing : 5, 6, 25, 59 after analyzing : 5, 18, 25, 28 RIGHT_BRAIN before analyzing : 4, 6, 30, 50 after analyzing : 4, 22, 30, 29 LEFT_BRAIN before analyzing : 4, 6, 29, 50 after analyzing : 4, 21, 29, 28 OTHER before analyzing : 18, 23, 30, 50 after analyzing : 18, 27, 30, 32 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...66 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.012 curvature mean = 69.916, std = 7.602 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 3.44, sigma = 7.07 after rotation: sse = 3.44, sigma = 7.07 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 4.27, its var is 10.70 before Erosion-Dilatation 2.14% of inacurate vertices after Erosion-Dilatation 2.08% 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...31 iterations mri_strip_skull: done peeling brain Brain Size = 1621646 voxels, voxel volume = 1.000 mm3 = 1621646 mmm3 = 1621.646 cm3 ****************************** Saving brainmask.auto.mgz done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Thu Aug 8 11:37:54 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca transforms/talairach.lta ======= NUMBER OF OPENMP THREADS = 1 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/opt/freesurfer/5.3.0/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=21.0 skull bounding box = (65, 37, 29) --> (193, 173, 196) using (108, 82, 113) as brain centroid... mean wm in atlas = 107, using box (92,65,92) --> (123, 98,133) to find MRI wm before smoothing, mri peak at 107 after smoothing, mri peak at 106, scaling input intensities by 1.009 scaling channel 0 by 1.00943 initial log_p = -4.5 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.085262 @ (-9.091, 27.273, -9.091) max log p = -4.023158 @ (4.545, -4.545, -4.545) max log p = -4.007773 @ (2.273, -2.273, 2.273) max log p = -3.975749 @ (-1.136, 1.136, -1.136) max log p = -3.940902 @ (-0.568, 0.568, 1.705) max log p = -3.933861 @ (-0.284, 2.557, 0.852) Found translation: (-4.3, 24.7, -9.9): log p = -3.934 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.6, old_max_log_p =-3.9 (thresh=-3.9) 1.150 0.000 0.000 -23.922; 0.000 1.111 0.298 -20.026; 0.000 -0.236 0.883 25.853; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.6, old_max_log_p =-3.6 (thresh=-3.6) 1.150 0.000 0.000 -23.922; 0.000 1.111 0.298 -20.026; 0.000 -0.236 0.883 25.853; 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=-3.5, old_max_log_p =-3.6 (thresh=-3.6) 1.101 0.054 -0.075 -14.044; -0.045 1.144 0.243 -11.221; 0.111 -0.172 0.947 -0.263; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.5, old_max_log_p =-3.5 (thresh=-3.5) 1.104 0.046 -0.045 -17.138; -0.038 1.152 0.310 -18.537; 0.079 -0.253 0.949 13.278; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.5, old_max_log_p =-3.5 (thresh=-3.5) 1.101 0.055 -0.075 -14.198; -0.036 1.143 0.341 -21.475; 0.116 -0.289 0.936 13.160; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.5, old_max_log_p =-3.5 (thresh=-3.5) 1.101 0.055 -0.075 -14.198; -0.036 1.143 0.341 -21.475; 0.116 -0.289 0.936 13.160; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.4, old_max_log_p =-3.5 (thresh=-3.5) 1.102 0.041 -0.062 -15.344; -0.028 1.147 0.324 -20.465; 0.098 -0.272 0.946 13.810; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4) 1.098 0.041 -0.062 -14.845; -0.028 1.149 0.325 -20.792; 0.098 -0.272 0.946 13.810; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 8 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4) 1.098 0.041 -0.062 -14.845; -0.028 1.149 0.325 -20.792; 0.098 -0.272 0.946 13.810; 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 1.09796 0.04098 -0.06217 -14.84461; -0.02848 1.14937 0.32503 -20.79175; 0.09809 -0.27194 0.94600 13.81043; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 1.09796 0.04098 -0.06217 -14.84461; -0.02848 1.14937 0.32503 -20.79175; 0.09809 -0.27194 0.94600 13.81043; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.098 0.041 -0.062 -14.845; -0.028 1.149 0.325 -20.792; 0.098 -0.272 0.946 13.810; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.4 (old=-4.5) transform before final EM align: 1.098 0.041 -0.062 -14.845; -0.028 1.149 0.325 -20.792; 0.098 -0.272 0.946 13.810; 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 1.09796 0.04098 -0.06217 -14.84461; -0.02848 1.14937 0.32503 -20.79175; 0.09809 -0.27194 0.94600 13.81043; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 1.09796 0.04098 -0.06217 -14.84461; -0.02848 1.14937 0.32503 -20.79175; 0.09809 -0.27194 0.94600 13.81043; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 012: -log(p) = 4.0 after pass:transform: ( 1.10, 0.04, -0.06, -14.84) ( -0.03, 1.15, 0.33, -20.79) ( 0.10, -0.27, 0.95, 13.81) dfp_em_step_func: 013: -log(p) = 3.9 after pass:transform: ( 1.10, 0.04, -0.06, -14.84) ( -0.03, 1.15, 0.33, -20.79) ( 0.10, -0.27, 0.95, 13.81) dfp_em_step_func: 014: -log(p) = 3.9 after pass:transform: ( 1.10, 0.04, -0.06, -14.84) ( -0.03, 1.15, 0.33, -20.79) ( 0.10, -0.27, 0.95, 13.81) dfp_em_step_func: 015: -log(p) = 3.9 after pass:transform: ( 1.10, 0.04, -0.06, -14.84) ( -0.03, 1.15, 0.33, -20.79) ( 0.10, -0.27, 0.95, 13.81) dfp_em_step_func: 016: -log(p) = 3.9 after pass:transform: ( 1.10, 0.04, -0.06, -14.84) ( -0.03, 1.15, 0.33, -20.79) ( 0.10, -0.27, 0.95, 13.81) dfp_em_step_func: 017: -log(p) = 3.9 after pass:transform: ( 1.10, 0.04, -0.06, -14.84) ( -0.03, 1.15, 0.33, -20.79) ( 0.10, -0.27, 0.95, 13.81) dfp_em_step_func: 018: -log(p) = 3.9 after pass:transform: ( 1.10, 0.04, -0.06, -14.84) ( -0.03, 1.15, 0.33, -20.79) ( 0.10, -0.27, 0.95, 13.81) dfp_em_step_func: 019: -log(p) = 3.9 after pass:transform: ( 1.10, 0.04, -0.06, -14.84) ( -0.03, 1.15, 0.33, -20.79) ( 0.10, -0.27, 0.95, 13.81) dfp_em_step_func: 020: -log(p) = 3.9 after pass:transform: ( 1.10, 0.04, -0.06, -14.84) ( -0.03, 1.15, 0.33, -20.79) ( 0.10, -0.27, 0.95, 13.81) 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= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 022: -log(p) = 3.9 tol 0.000000 final transform: 1.099 0.042 -0.061 -14.845; -0.028 1.149 0.325 -20.792; 0.099 -0.272 0.946 13.810; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 34 minutes and 1 seconds. #-------------------------------------- #@# CA Normalize Thu Aug 8 12:11:54 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/opt/freesurfer/5.3.0/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=21.0 skull bounding box = (65, 37, 29) --> (193, 173, 197) using (108, 82, 113) as brain centroid... mean wm in atlas = 107, using box (92,65,92) --> (123, 98,133) to find MRI wm before smoothing, mri peak at 107 after smoothing, mri peak at 106, scaling input intensities by 1.009 scaling channel 0 by 1.00943 using 244171 sample points... INFO: compute sample coordinates transform 1.099 0.042 -0.061 -14.845; -0.028 1.149 0.325 -20.792; 0.099 -0.272 0.946 13.810; 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 (124, 38, 34) --> (189, 140, 197) Left_Cerebral_White_Matter: limiting intensities to 104.0 --> 153.0 0 of 10 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (71, 36, 35) --> (134, 131, 200) Right_Cerebral_White_Matter: limiting intensities to 103.0 --> 153.0 0 of 14 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (129, 114, 62) --> (173, 154, 115) Left_Cerebellum_White_Matter: limiting intensities to 89.0 --> 153.0 0 of 9 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (86, 114, 62) --> (129, 151, 119) Right_Cerebellum_White_Matter: limiting intensities to 90.0 --> 153.0 0 of 14 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (115, 103, 97) --> (145, 163, 128) Brain_Stem: limiting intensities to 83.0 --> 153.0 3 of 8 (37.5%) samples deleted using 55 total control points for intensity normalization... bias field = 0.932 +- 0.060 0 of 52 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (124, 38, 34) --> (189, 140, 197) Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 144.0 0 of 89 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (71, 36, 35) --> (134, 131, 200) Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 144.0 2 of 88 (2.3%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (129, 114, 62) --> (173, 154, 115) Left_Cerebellum_White_Matter: limiting intensities to 80.0 --> 144.0 0 of 9 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (86, 114, 62) --> (129, 151, 119) Right_Cerebellum_White_Matter: limiting intensities to 84.0 --> 144.0 0 of 9 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (115, 103, 97) --> (145, 163, 128) Brain_Stem: limiting intensities to 88.0 --> 144.0 43 of 50 (86.0%) samples deleted using 245 total control points for intensity normalization... bias field = 0.982 +- 0.048 0 of 200 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (124, 38, 34) --> (189, 140, 197) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 135.0 0 of 213 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (71, 36, 35) --> (134, 131, 200) Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 135.0 0 of 160 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (129, 114, 62) --> (173, 154, 115) Left_Cerebellum_White_Matter: limiting intensities to 95.0 --> 135.0 13 of 16 (81.2%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (86, 114, 62) --> (129, 151, 119) Right_Cerebellum_White_Matter: limiting intensities to 78.0 --> 135.0 0 of 8 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (115, 103, 97) --> (145, 163, 128) Brain_Stem: limiting intensities to 61.0 --> 135.0 1 of 71 (1.4%) samples deleted using 468 total control points for intensity normalization... bias field = 1.028 +- 0.070 1 of 454 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 2 minutes and 3 seconds. #-------------------------------------- #@# CA Reg Thu Aug 8 12:13:57 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log ======= NUMBER OF OPENMP THREADS = 1 ======= reading input volume 'norm.mgz'... reading GCA '/opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.30 (predicted orig area = 6.1) 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=0.901, neg=0, invalid=96777 0001: dt=129.472000, rms=0.801 (11.014%), neg=0, invalid=96777 0002: dt=129.472000, rms=0.774 (3.392%), neg=0, invalid=96777 0003: dt=129.472000, rms=0.764 (1.329%), neg=0, invalid=96777 0004: dt=129.472000, rms=0.757 (0.886%), neg=0, invalid=96777 0005: dt=129.472000, rms=0.752 (0.654%), neg=0, invalid=96777 0006: dt=129.472000, rms=0.748 (0.571%), neg=0, invalid=96777 0007: dt=129.472000, rms=0.745 (0.443%), neg=0, invalid=96777 0008: dt=129.472000, rms=0.741 (0.425%), neg=0, invalid=96777 0009: dt=129.472000, rms=0.739 (0.356%), neg=0, invalid=96777 0010: dt=129.472000, rms=0.736 (0.332%), neg=0, invalid=96777 0011: dt=129.472000, rms=0.734 (0.284%), neg=0, invalid=96777 0012: dt=129.472000, rms=0.732 (0.247%), neg=0, invalid=96777 0013: dt=129.472000, rms=0.731 (0.237%), neg=0, invalid=96777 0014: dt=129.472000, rms=0.728 (0.420%), neg=0, invalid=96777 0015: dt=129.472000, rms=0.724 (0.497%), neg=0, invalid=96777 0016: dt=129.472000, rms=0.720 (0.592%), neg=0, invalid=96777 0017: dt=129.472000, rms=0.716 (0.505%), neg=0, invalid=96777 0018: dt=129.472000, rms=0.714 (0.345%), neg=0, invalid=96777 0019: dt=129.472000, rms=0.712 (0.241%), neg=0, invalid=96777 0020: dt=129.472000, rms=0.710 (0.294%), neg=0, invalid=96777 0021: dt=129.472000, rms=0.708 (0.310%), neg=0, invalid=96777 0022: dt=129.472000, rms=0.705 (0.419%), neg=0, invalid=96777 0023: dt=129.472000, rms=0.702 (0.323%), neg=0, invalid=96777 0024: dt=129.472000, rms=0.700 (0.276%), neg=0, invalid=96777 0025: dt=129.472000, rms=0.699 (0.241%), neg=0, invalid=96777 0026: dt=129.472000, rms=0.697 (0.265%), neg=0, invalid=96777 0027: dt=129.472000, rms=0.695 (0.203%), neg=0, invalid=96777 0028: dt=129.472000, rms=0.694 (0.180%), neg=0, invalid=96777 0029: dt=129.472000, rms=0.693 (0.191%), neg=0, invalid=96777 0030: dt=129.472000, rms=0.691 (0.191%), neg=0, invalid=96777 0031: dt=129.472000, rms=0.690 (0.181%), neg=0, invalid=96777 0032: dt=129.472000, rms=0.689 (0.164%), neg=0, invalid=96777 0033: dt=129.472000, rms=0.688 (0.157%), neg=0, invalid=96777 0034: dt=129.472000, rms=0.687 (0.170%), neg=0, invalid=96777 0035: dt=129.472000, rms=0.686 (0.180%), neg=0, invalid=96777 0036: dt=129.472000, rms=0.684 (0.173%), neg=0, invalid=96777 0037: dt=129.472000, rms=0.683 (0.166%), neg=0, invalid=96777 0038: dt=129.472000, rms=0.682 (0.140%), neg=0, invalid=96777 0039: dt=129.472000, rms=0.682 (0.117%), neg=0, invalid=96777 0040: dt=129.472000, rms=0.681 (0.106%), neg=0, invalid=96777 0041: dt=129.472000, rms=0.681 (0.033%), neg=0, invalid=96777 0042: dt=129.472000, rms=0.681 (-0.002%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.681, neg=0, invalid=96777 0043: dt=92.480000, rms=0.680 (0.038%), neg=0, invalid=96777 0044: dt=369.920000, rms=0.679 (0.171%), neg=0, invalid=96777 0045: dt=32.368000, rms=0.679 (0.020%), neg=0, invalid=96777 0046: dt=32.368000, rms=0.679 (0.014%), neg=0, invalid=96777 0047: dt=32.368000, rms=0.679 (0.016%), neg=0, invalid=96777 0048: dt=32.368000, rms=0.679 (0.018%), neg=0, invalid=96777 0049: dt=32.368000, rms=0.679 (0.031%), neg=0, invalid=96777 0050: dt=32.368000, rms=0.678 (0.042%), neg=0, invalid=96777 0051: dt=32.368000, rms=0.678 (0.046%), neg=0, invalid=96777 0052: dt=32.368000, rms=0.678 (0.038%), neg=0, invalid=96777 0053: dt=32.368000, rms=0.677 (0.028%), neg=0, invalid=96777 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.685, neg=0, invalid=96777 0054: dt=145.152000, rms=0.676 (1.407%), neg=0, invalid=96777 0055: dt=103.680000, rms=0.670 (0.904%), neg=0, invalid=96777 0056: dt=36.288000, rms=0.665 (0.762%), neg=0, invalid=96777 0057: dt=36.288000, rms=0.664 (0.117%), neg=0, invalid=96777 0058: dt=36.288000, rms=0.661 (0.392%), neg=0, invalid=96777 0059: dt=36.288000, rms=0.658 (0.488%), neg=0, invalid=96777 0060: dt=36.288000, rms=0.654 (0.561%), neg=0, invalid=96777 0061: dt=36.288000, rms=0.650 (0.689%), neg=0, invalid=96777 0062: dt=36.288000, rms=0.644 (0.841%), neg=0, invalid=96777 0063: dt=36.288000, rms=0.640 (0.720%), neg=0, invalid=96777 0064: dt=36.288000, rms=0.636 (0.553%), neg=0, invalid=96777 0065: dt=36.288000, rms=0.633 (0.455%), neg=0, invalid=96777 0066: dt=36.288000, rms=0.630 (0.529%), neg=0, invalid=96777 0067: dt=36.288000, rms=0.627 (0.404%), neg=0, invalid=96777 0068: dt=36.288000, rms=0.625 (0.338%), neg=0, invalid=96777 0069: dt=36.288000, rms=0.624 (0.253%), neg=0, invalid=96777 0070: dt=36.288000, rms=0.622 (0.307%), neg=0, invalid=96777 0071: dt=36.288000, rms=0.620 (0.251%), neg=0, invalid=96777 0072: dt=36.288000, rms=0.619 (0.212%), neg=0, invalid=96777 0073: dt=36.288000, rms=0.618 (0.166%), neg=0, invalid=96777 0074: dt=36.288000, rms=0.617 (0.128%), neg=0, invalid=96777 0075: dt=36.288000, rms=0.616 (0.156%), neg=0, invalid=96777 0076: dt=36.288000, rms=0.615 (0.103%), neg=0, invalid=96777 0077: dt=36.288000, rms=0.615 (0.087%), neg=0, invalid=96777 0078: dt=145.152000, rms=0.614 (0.126%), neg=0, invalid=96777 0079: dt=9.072000, rms=0.614 (0.003%), neg=0, invalid=96777 0080: dt=9.072000, rms=0.614 (0.006%), neg=0, invalid=96777 0081: dt=9.072000, rms=0.614 (-0.002%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.614, neg=0, invalid=96777 0082: dt=20.736000, rms=0.614 (0.015%), neg=0, invalid=96777 0083: dt=36.288000, rms=0.614 (0.028%), neg=0, invalid=96777 0084: dt=15.552000, rms=0.614 (0.002%), neg=0, invalid=96777 0085: dt=15.552000, rms=0.614 (0.005%), neg=0, invalid=96777 0086: dt=15.552000, rms=0.614 (0.001%), neg=0, invalid=96777 0087: dt=15.552000, rms=0.614 (-0.010%), neg=0, invalid=96777 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.643, neg=0, invalid=96777 0088: dt=5.423729, rms=0.643 (0.056%), neg=0, invalid=96777 0089: dt=1.600000, rms=0.643 (0.006%), neg=0, invalid=96777 0090: dt=1.600000, rms=0.643 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.643, neg=0, invalid=96777 0091: dt=0.000000, rms=0.643 (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=0.723, neg=0, invalid=96777 0092: dt=5.319372, rms=0.702 (2.891%), neg=0, invalid=96777 0093: dt=3.194030, rms=0.700 (0.187%), neg=0, invalid=96777 0094: dt=3.194030, rms=0.700 (-0.021%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.700, neg=0, invalid=96777 0095: dt=0.000000, rms=0.700 (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=0.779, neg=0, invalid=96777 0096: dt=1.111639, rms=0.775 (0.523%), neg=0, invalid=96777 0097: dt=2.377246, rms=0.767 (0.938%), neg=0, invalid=96777 0098: dt=0.448000, rms=0.767 (0.069%), neg=0, invalid=96777 0099: dt=0.448000, rms=0.767 (0.029%), neg=0, invalid=96777 0100: dt=0.448000, rms=0.766 (0.037%), neg=0, invalid=96777 0101: dt=0.448000, rms=0.766 (0.032%), neg=0, invalid=96777 0102: dt=0.448000, rms=0.766 (0.010%), neg=0, invalid=96777 0103: dt=2.227273, rms=0.765 (0.133%), neg=0, invalid=96777 0104: dt=0.000000, rms=0.765 (0.004%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.765, neg=0, invalid=96777 0105: dt=0.544118, rms=0.764 (0.081%), neg=0, invalid=96777 0106: dt=0.080000, rms=0.764 (-0.002%), 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=0.716, neg=0, invalid=96777 0107: dt=0.154661, rms=0.708 (1.114%), neg=0, invalid=96777 0108: dt=0.000000, rms=0.708 (0.002%), neg=0, invalid=96777 0109: dt=0.050000, rms=0.708 (-0.013%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.708, neg=0, invalid=96777 0110: dt=0.347584, rms=0.704 (0.542%), neg=0, invalid=96777 0111: dt=0.064000, rms=0.703 (0.118%), neg=0, invalid=96777 0112: dt=0.064000, rms=0.703 (-0.007%), neg=0, invalid=96777 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.14301 (55) Left_Lateral_Ventricle (4): linear fit = 2.20 x + 0.0 (1178 voxels, overlap=0.005) Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (1178 voxels, peak = 53), gca=36.0 gca peak = 0.14022 (22) mri peak = 0.10960 ( 7) Right_Lateral_Ventricle (43): linear fit = 0.22 x + 0.0 (604 voxels, overlap=0.005) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (604 voxels, peak = 5), gca=8.8 gca peak = 0.24234 (100) mri peak = 0.12385 (75) Right_Pallidum (52): linear fit = 0.80 x + 0.0 (357 voxels, overlap=0.032) Right_Pallidum (52): linear fit = 0.80 x + 0.0 (357 voxels, peak = 80), gca=79.5 gca peak = 0.19192 (97) mri peak = 0.18787 (75) Left_Pallidum (13): linear fit = 0.77 x + 0.0 (315 voxels, overlap=0.484) Left_Pallidum (13): linear fit = 0.77 x + 0.0 (315 voxels, peak = 75), gca=75.2 gca peak = 0.24007 (63) mri peak = 0.08999 (56) Right_Hippocampus (53): linear fit = 0.85 x + 0.0 (418 voxels, overlap=0.201) Right_Hippocampus (53): linear fit = 0.85 x + 0.0 (418 voxels, peak = 53), gca=53.2 gca peak = 0.29892 (64) mri peak = 0.09388 (58) Left_Hippocampus (17): linear fit = 0.85 x + 0.0 (485 voxels, overlap=0.142) Left_Hippocampus (17): linear fit = 0.85 x + 0.0 (485 voxels, peak = 54), gca=54.1 gca peak = 0.12541 (104) mri peak = 0.06489 (107) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (56578 voxels, overlap=0.897) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (56578 voxels, peak = 107), gca=106.6 gca peak = 0.13686 (104) mri peak = 0.07498 (107) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (57418 voxels, overlap=0.772) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (57418 voxels, peak = 108), gca=107.6 gca peak = 0.11691 (63) mri peak = 0.05213 (50) Left_Cerebral_Cortex (3): linear fit = 0.80 x + 0.0 (14833 voxels, overlap=0.119) Left_Cerebral_Cortex (3): linear fit = 0.80 x + 0.0 (14833 voxels, peak = 50), gca=50.1 gca peak = 0.13270 (63) mri peak = 0.06223 (51) Right_Cerebral_Cortex (42): linear fit = 0.80 x + 0.0 (15455 voxels, overlap=0.110) Right_Cerebral_Cortex (42): linear fit = 0.80 x + 0.0 (15455 voxels, peak = 50), gca=50.1 gca peak = 0.15182 (70) mri peak = 0.10308 (56) Right_Caudate (50): linear fit = 0.79 x + 0.0 (462 voxels, overlap=0.011) Right_Caudate (50): linear fit = 0.79 x + 0.0 (462 voxels, peak = 55), gca=55.0 gca peak = 0.14251 (76) mri peak = 0.11050 (58) Left_Caudate (11): linear fit = 0.75 x + 0.0 (568 voxels, overlap=0.021) Left_Caudate (11): linear fit = 0.75 x + 0.0 (568 voxels, peak = 57), gca=57.4 gca peak = 0.12116 (60) mri peak = 0.05451 (59) Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (9961 voxels, overlap=0.989) Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (9961 voxels, peak = 58), gca=57.9 gca peak = 0.12723 (61) mri peak = 0.05544 (58) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (11865 voxels, overlap=0.991) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (11865 voxels, peak = 60), gca=60.1 gca peak = 0.22684 (88) mri peak = 0.05818 (90) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (5713 voxels, overlap=0.949) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (5713 voxels, peak = 89), gca=89.3 gca peak = 0.21067 (87) mri peak = 0.05650 (87) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5353 voxels, overlap=0.982) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5353 voxels, peak = 87), gca=86.6 gca peak = 0.25455 (62) mri peak = 0.08370 (58) Left_Amygdala (18): linear fit = 0.88 x + 0.0 (258 voxels, overlap=0.694) Left_Amygdala (18): linear fit = 0.88 x + 0.0 (258 voxels, peak = 54), gca=54.2 gca peak = 0.39668 (62) mri peak = 0.12756 (53) Right_Amygdala (54): linear fit = 0.85 x + 0.0 (308 voxels, overlap=0.055) Right_Amygdala (54): linear fit = 0.85 x + 0.0 (308 voxels, peak = 52), gca=52.4 gca peak = 0.10129 (93) mri peak = 0.04906 (85) Left_Thalamus_Proper (10): linear fit = 0.92 x + 0.0 (4675 voxels, overlap=0.919) Left_Thalamus_Proper (10): linear fit = 0.92 x + 0.0 (4675 voxels, peak = 85), gca=85.1 gca peak = 0.12071 (89) mri peak = 0.10826 (77) Right_Thalamus_Proper (49): linear fit = 0.94 x + 0.0 (3726 voxels, overlap=0.445) Right_Thalamus_Proper (49): linear fit = 0.94 x + 0.0 (3726 voxels, peak = 83), gca=83.2 gca peak = 0.13716 (82) mri peak = 0.05377 (75) Left_Putamen (12): linear fit = 0.88 x + 0.0 (1483 voxels, overlap=0.416) Left_Putamen (12): linear fit = 0.88 x + 0.0 (1483 voxels, peak = 73), gca=72.6 gca peak = 0.15214 (84) mri peak = 0.07704 (65) Right_Putamen (51): linear fit = 0.81 x + 0.0 (1907 voxels, overlap=0.013) Right_Putamen (51): linear fit = 0.81 x + 0.0 (1907 voxels, peak = 68), gca=67.6 gca peak = 0.08983 (85) mri peak = 0.10973 (80) Brain_Stem (16): linear fit = 0.99 x + 0.0 (8634 voxels, overlap=0.767) Brain_Stem (16): linear fit = 0.99 x + 0.0 (8634 voxels, peak = 84), gca=83.7 gca peak = 0.11809 (92) mri peak = 0.13966 (83) Right_VentralDC (60): linear fit = 0.90 x + 0.0 (805 voxels, overlap=0.345) Right_VentralDC (60): linear fit = 0.90 x + 0.0 (805 voxels, peak = 83), gca=83.3 gca peak = 0.12914 (94) mri peak = 0.10058 (83) Left_VentralDC (28): linear fit = 0.89 x + 0.0 (928 voxels, overlap=0.419) Left_VentralDC (28): linear fit = 0.89 x + 0.0 (928 voxels, peak = 84), gca=84.1 gca peak = 0.21100 (36) mri peak = 0.12694 (54) Third_Ventricle (14): linear fit = 1.46 x + 0.0 (71 voxels, overlap=0.081) Third_Ventricle (14): linear fit = 1.46 x + 0.0 (71 voxels, peak = 52), gca=52.4 gca peak = 0.13542 (27) mri peak = 0.18125 ( 8) Fourth_Ventricle (15): linear fit = 0.22 x + 0.0 (210 voxels, overlap=0.020) Fourth_Ventricle (15): linear fit = 0.22 x + 0.0 (210 voxels, peak = 6), gca=6.1 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) 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 0.83 x + 0.0 estimating mean wm scale to be 1.03 x + 0.0 estimating mean csf scale to be 1.12 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=0.737, neg=0, invalid=96777 0113: dt=129.472000, rms=0.727 (1.399%), neg=0, invalid=96777 0114: dt=110.976000, rms=0.723 (0.515%), neg=0, invalid=96777 0115: dt=129.472000, rms=0.720 (0.375%), neg=0, invalid=96777 0116: dt=73.984000, rms=0.719 (0.263%), neg=0, invalid=96777 0117: dt=295.936000, rms=0.716 (0.292%), neg=0, invalid=96777 0118: dt=55.488000, rms=0.715 (0.255%), neg=0, invalid=96777 0119: dt=1479.680000, rms=0.709 (0.823%), neg=0, invalid=96777 0120: dt=295.936000, rms=0.707 (0.202%), neg=0, invalid=96777 0121: dt=32.368000, rms=0.707 (0.049%), neg=0, invalid=96777 0122: dt=32.368000, rms=0.707 (0.019%), neg=0, invalid=96777 0123: dt=32.368000, rms=0.707 (0.020%), neg=0, invalid=96777 0124: dt=32.368000, rms=0.707 (0.022%), neg=0, invalid=96777 0125: dt=32.368000, rms=0.706 (0.041%), neg=0, invalid=96777 0126: dt=32.368000, rms=0.706 (0.067%), neg=0, invalid=96777 0127: dt=32.368000, rms=0.705 (0.083%), neg=0, invalid=96777 0128: dt=32.368000, rms=0.705 (0.082%), neg=0, invalid=96777 0129: dt=32.368000, rms=0.704 (0.073%), neg=0, invalid=96777 0130: dt=32.368000, rms=0.704 (0.070%), neg=0, invalid=96777 0131: dt=32.368000, rms=0.703 (0.066%), neg=0, invalid=96777 0132: dt=32.368000, rms=0.703 (0.063%), neg=0, invalid=96777 0133: dt=32.368000, rms=0.702 (0.063%), neg=0, invalid=96777 0134: dt=32.368000, rms=0.702 (0.072%), neg=0, invalid=96777 0135: dt=32.368000, rms=0.701 (0.072%), neg=0, invalid=96777 0136: dt=32.368000, rms=0.701 (0.071%), neg=0, invalid=96777 0137: dt=32.368000, rms=0.700 (0.064%), neg=0, invalid=96777 0138: dt=32.368000, rms=0.700 (0.056%), neg=0, invalid=96777 0139: dt=32.368000, rms=0.700 (0.046%), neg=0, invalid=96777 0140: dt=32.368000, rms=0.699 (0.046%), neg=0, invalid=96777 0141: dt=32.368000, rms=0.699 (0.045%), neg=0, invalid=96777 0142: dt=32.368000, rms=0.699 (0.048%), neg=0, invalid=96777 0143: dt=32.368000, rms=0.698 (0.043%), neg=0, invalid=96777 0144: dt=32.368000, rms=0.698 (0.040%), neg=0, invalid=96777 0145: dt=32.368000, rms=0.698 (0.039%), neg=0, invalid=96777 0146: dt=32.368000, rms=0.698 (0.033%), neg=0, invalid=96777 0147: dt=32.368000, rms=0.697 (0.030%), neg=0, invalid=96777 0148: dt=32.368000, rms=0.697 (0.031%), neg=0, invalid=96777 0149: dt=32.368000, rms=0.697 (0.033%), neg=0, invalid=96777 0150: dt=32.368000, rms=0.697 (0.035%), neg=0, invalid=96777 0151: dt=32.368000, rms=0.696 (0.037%), neg=0, invalid=96777 0152: dt=32.368000, rms=0.696 (0.035%), neg=0, invalid=96777 0153: dt=32.368000, rms=0.696 (0.033%), neg=0, invalid=96777 0154: dt=32.368000, rms=0.696 (0.033%), neg=0, invalid=96777 0155: dt=32.368000, rms=0.695 (0.035%), neg=0, invalid=96777 0156: dt=32.368000, rms=0.695 (0.034%), neg=0, invalid=96777 0157: dt=32.368000, rms=0.695 (0.034%), neg=0, invalid=96777 0158: dt=32.368000, rms=0.695 (0.033%), neg=0, invalid=96777 0159: dt=32.368000, rms=0.695 (0.030%), neg=0, invalid=96777 0160: dt=32.368000, rms=0.694 (0.026%), neg=0, invalid=96777 0161: dt=32.368000, rms=0.694 (0.025%), neg=0, invalid=96777 0162: dt=32.368000, rms=0.694 (0.025%), neg=0, invalid=96777 0163: dt=32.368000, rms=0.694 (0.027%), neg=0, invalid=96777 0164: dt=32.368000, rms=0.694 (0.028%), neg=0, invalid=96777 0165: dt=32.368000, rms=0.693 (0.030%), neg=0, invalid=96777 0166: dt=32.368000, rms=0.693 (0.030%), neg=0, invalid=96777 0167: dt=32.368000, rms=0.693 (0.030%), neg=0, invalid=96777 0168: dt=32.368000, rms=0.693 (0.022%), neg=0, invalid=96777 0169: dt=32.368000, rms=0.693 (0.021%), neg=0, invalid=96777 0170: dt=32.368000, rms=0.693 (0.001%), neg=0, invalid=96777 0171: dt=32.368000, rms=0.693 (0.001%), neg=0, invalid=96777 0172: dt=32.368000, rms=0.693 (0.003%), neg=0, invalid=96777 0173: dt=32.368000, rms=0.693 (0.003%), neg=0, invalid=96777 0174: dt=32.368000, rms=0.693 (0.008%), neg=0, invalid=96777 0175: dt=32.368000, rms=0.693 (0.009%), neg=0, invalid=96777 0176: dt=32.368000, rms=0.692 (0.011%), neg=0, invalid=96777 0177: dt=32.368000, rms=0.692 (0.014%), neg=0, invalid=96777 0178: dt=32.368000, rms=0.692 (0.015%), neg=0, invalid=96777 0179: dt=32.368000, rms=0.692 (0.015%), neg=0, invalid=96777 0180: dt=32.368000, rms=0.692 (0.015%), neg=0, invalid=96777 0181: dt=32.368000, rms=0.692 (0.015%), neg=0, invalid=96777 0182: dt=32.368000, rms=0.692 (0.014%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.692, neg=0, invalid=96777 0183: dt=295.936000, rms=0.690 (0.328%), neg=0, invalid=96777 0184: dt=73.984000, rms=0.689 (0.043%), neg=0, invalid=96777 0185: dt=73.984000, rms=0.689 (0.021%), neg=0, invalid=96777 0186: dt=73.984000, rms=0.689 (0.040%), neg=0, invalid=96777 0187: dt=73.984000, rms=0.689 (0.051%), neg=0, invalid=96777 0188: dt=73.984000, rms=0.688 (0.061%), neg=0, invalid=96777 0189: dt=73.984000, rms=0.688 (0.071%), neg=0, invalid=96777 0190: dt=73.984000, rms=0.687 (0.071%), neg=0, invalid=96777 0191: dt=73.984000, rms=0.687 (0.061%), neg=0, invalid=96777 0192: dt=73.984000, rms=0.686 (0.050%), neg=0, invalid=96777 0193: dt=73.984000, rms=0.686 (0.045%), neg=0, invalid=96777 0194: dt=73.984000, rms=0.686 (0.039%), neg=0, invalid=96777 0195: dt=73.984000, rms=0.686 (0.039%), neg=0, invalid=96777 0196: dt=73.984000, rms=0.685 (0.042%), neg=0, invalid=96777 0197: dt=73.984000, rms=0.685 (0.046%), neg=0, invalid=96777 0198: dt=73.984000, rms=0.685 (0.049%), neg=0, invalid=96777 0199: dt=73.984000, rms=0.684 (0.053%), neg=0, invalid=96777 0200: dt=73.984000, rms=0.684 (0.050%), neg=0, invalid=96777 0201: dt=73.984000, rms=0.684 (0.045%), neg=0, invalid=96777 0202: dt=73.984000, rms=0.683 (0.041%), neg=0, invalid=96777 0203: dt=73.984000, rms=0.683 (0.035%), neg=0, invalid=96777 0204: dt=73.984000, rms=0.683 (0.036%), neg=0, invalid=96777 0205: dt=73.984000, rms=0.683 (0.036%), neg=0, invalid=96777 0206: dt=73.984000, rms=0.682 (0.040%), neg=0, invalid=96777 0207: dt=73.984000, rms=0.682 (0.038%), neg=0, invalid=96777 0208: dt=73.984000, rms=0.682 (0.035%), neg=0, invalid=96777 0209: dt=73.984000, rms=0.682 (0.032%), neg=0, invalid=96777 0210: dt=73.984000, rms=0.681 (0.027%), neg=0, invalid=96777 0211: dt=73.984000, rms=0.681 (0.025%), neg=0, invalid=96777 0212: dt=73.984000, rms=0.681 (0.023%), neg=0, invalid=96777 0213: dt=1479.680000, rms=0.681 (0.059%), neg=0, invalid=96777 0214: dt=73.984000, rms=0.681 (0.027%), neg=0, invalid=96777 0215: dt=73.984000, rms=0.680 (-0.004%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.681, neg=0, invalid=96777 0216: dt=124.416000, rms=0.675 (0.873%), neg=0, invalid=96777 0217: dt=82.944000, rms=0.670 (0.693%), neg=0, invalid=96777 0218: dt=36.288000, rms=0.667 (0.581%), neg=0, invalid=96777 0219: dt=25.920000, rms=0.665 (0.205%), neg=0, invalid=96777 0220: dt=145.152000, rms=0.660 (0.744%), neg=0, invalid=96777 0221: dt=20.736000, rms=0.658 (0.388%), neg=0, invalid=96777 0222: dt=580.608000, rms=0.647 (1.701%), neg=0, invalid=96777 0223: dt=20.025157, rms=0.642 (0.715%), neg=0, invalid=96777 0224: dt=145.152000, rms=0.640 (0.361%), neg=0, invalid=96777 0225: dt=36.288000, rms=0.638 (0.169%), neg=0, invalid=96777 0226: dt=145.152000, rms=0.637 (0.280%), neg=0, invalid=96777 0227: dt=31.104000, rms=0.636 (0.163%), neg=0, invalid=96777 0228: dt=36.288000, rms=0.635 (0.037%), neg=0, invalid=96777 0229: dt=36.288000, rms=0.635 (0.096%), neg=0, invalid=96777 0230: dt=36.288000, rms=0.634 (0.129%), neg=0, invalid=96777 0231: dt=36.288000, rms=0.633 (0.159%), neg=0, invalid=96777 0232: dt=36.288000, rms=0.632 (0.214%), neg=0, invalid=96777 0233: dt=36.288000, rms=0.630 (0.265%), neg=0, invalid=96777 0234: dt=36.288000, rms=0.628 (0.266%), neg=0, invalid=96777 0235: dt=36.288000, rms=0.627 (0.269%), neg=0, invalid=96777 0236: dt=36.288000, rms=0.625 (0.272%), neg=0, invalid=96777 0237: dt=36.288000, rms=0.623 (0.294%), neg=0, invalid=96777 0238: dt=36.288000, rms=0.621 (0.268%), neg=0, invalid=96777 0239: dt=36.288000, rms=0.620 (0.246%), neg=0, invalid=96777 0240: dt=36.288000, rms=0.618 (0.223%), neg=0, invalid=96777 0241: dt=36.288000, rms=0.617 (0.229%), neg=0, invalid=96777 0242: dt=36.288000, rms=0.616 (0.206%), neg=0, invalid=96777 0243: dt=36.288000, rms=0.615 (0.191%), neg=0, invalid=96777 0244: dt=36.288000, rms=0.613 (0.188%), neg=0, invalid=96777 0245: dt=36.288000, rms=0.612 (0.180%), neg=0, invalid=96777 0246: dt=36.288000, rms=0.611 (0.180%), neg=0, invalid=96777 0247: dt=36.288000, rms=0.610 (0.164%), neg=0, invalid=96777 0248: dt=36.288000, rms=0.609 (0.166%), neg=0, invalid=96777 0249: dt=36.288000, rms=0.608 (0.152%), neg=0, invalid=96777 0250: dt=36.288000, rms=0.607 (0.154%), neg=0, invalid=96777 0251: dt=36.288000, rms=0.607 (0.137%), neg=0, invalid=96777 0252: dt=36.288000, rms=0.606 (0.142%), neg=0, invalid=96777 0253: dt=36.288000, rms=0.605 (0.127%), neg=0, invalid=96777 0254: dt=36.288000, rms=0.604 (0.113%), neg=0, invalid=96777 0255: dt=36.288000, rms=0.604 (0.089%), neg=0, invalid=96777 0256: dt=36.288000, rms=0.603 (0.097%), neg=0, invalid=96777 0257: dt=36.288000, rms=0.602 (0.102%), neg=0, invalid=96777 0258: dt=36.288000, rms=0.602 (0.095%), neg=0, invalid=96777 0259: dt=36.288000, rms=0.601 (0.078%), neg=0, invalid=96777 0260: dt=36.288000, rms=0.601 (0.069%), neg=0, invalid=96777 0261: dt=36.288000, rms=0.601 (0.072%), neg=0, invalid=96777 0262: dt=36.288000, rms=0.600 (0.076%), neg=0, invalid=96777 0263: dt=36.288000, rms=0.600 (0.074%), neg=0, invalid=96777 0264: dt=36.288000, rms=0.599 (0.063%), neg=0, invalid=96777 0265: dt=36.288000, rms=0.599 (0.060%), neg=0, invalid=96777 0266: dt=36.288000, rms=0.599 (0.049%), neg=0, invalid=96777 0267: dt=36.288000, rms=0.598 (0.063%), neg=0, invalid=96777 0268: dt=36.288000, rms=0.598 (0.064%), neg=0, invalid=96777 0269: dt=36.288000, rms=0.598 (0.064%), neg=0, invalid=96777 0270: dt=36.288000, rms=0.597 (0.057%), neg=0, invalid=96777 0271: dt=36.288000, rms=0.597 (0.048%), neg=0, invalid=96777 0272: dt=36.288000, rms=0.597 (0.041%), neg=0, invalid=96777 0273: dt=36.288000, rms=0.596 (0.050%), neg=0, invalid=96777 0274: dt=36.288000, rms=0.596 (0.054%), neg=0, invalid=96777 0275: dt=36.288000, rms=0.596 (0.048%), neg=0, invalid=96777 0276: dt=36.288000, rms=0.595 (0.043%), neg=0, invalid=96777 0277: dt=36.288000, rms=0.595 (0.039%), neg=0, invalid=96777 0278: dt=36.288000, rms=0.595 (0.044%), neg=0, invalid=96777 0279: dt=36.288000, rms=0.595 (0.054%), neg=0, invalid=96777 0280: dt=36.288000, rms=0.594 (0.047%), neg=0, invalid=96777 0281: dt=36.288000, rms=0.594 (0.037%), neg=0, invalid=96777 0282: dt=36.288000, rms=0.594 (0.029%), neg=0, invalid=96777 0283: dt=36.288000, rms=0.594 (0.035%), neg=0, invalid=96777 0284: dt=36.288000, rms=0.594 (0.036%), neg=0, invalid=96777 0285: dt=36.288000, rms=0.593 (0.045%), neg=0, invalid=96777 0286: dt=36.288000, rms=0.593 (0.040%), neg=0, invalid=96777 0287: dt=36.288000, rms=0.593 (0.040%), neg=0, invalid=96777 0288: dt=36.288000, rms=0.593 (0.032%), neg=0, invalid=96777 0289: dt=36.288000, rms=0.592 (0.029%), neg=0, invalid=96777 0290: dt=36.288000, rms=0.592 (0.024%), neg=0, invalid=96777 0291: dt=36.288000, rms=0.592 (0.029%), neg=0, invalid=96777 0292: dt=36.288000, rms=0.592 (0.030%), neg=0, invalid=96777 0293: dt=36.288000, rms=0.592 (0.032%), neg=0, invalid=96777 0294: dt=36.288000, rms=0.592 (0.027%), neg=0, invalid=96777 0295: dt=36.288000, rms=0.591 (0.027%), neg=0, invalid=96777 0296: dt=36.288000, rms=0.591 (0.037%), neg=0, invalid=96777 0297: dt=36.288000, rms=0.591 (0.027%), neg=0, invalid=96777 0298: dt=36.288000, rms=0.591 (0.036%), neg=0, invalid=96777 0299: dt=36.288000, rms=0.591 (0.024%), neg=0, invalid=96777 0300: dt=36.288000, rms=0.591 (0.026%), neg=0, invalid=96777 0301: dt=36.288000, rms=0.590 (0.026%), neg=0, invalid=96777 0302: dt=36.288000, rms=0.590 (0.037%), neg=0, invalid=96777 0303: dt=36.288000, rms=0.590 (0.035%), neg=0, invalid=96777 0304: dt=36.288000, rms=0.590 (0.031%), neg=0, invalid=96777 0305: dt=36.288000, rms=0.590 (0.026%), neg=0, invalid=96777 0306: dt=36.288000, rms=0.590 (0.019%), neg=0, invalid=96777 0307: dt=36.288000, rms=0.589 (0.020%), neg=0, invalid=96777 0308: dt=36.288000, rms=0.589 (0.031%), neg=0, invalid=96777 0309: dt=36.288000, rms=0.589 (0.031%), neg=0, invalid=96777 0310: dt=36.288000, rms=0.589 (0.032%), neg=0, invalid=96777 0311: dt=36.288000, rms=0.589 (0.020%), neg=0, invalid=96777 0312: dt=36.288000, rms=0.589 (0.013%), neg=0, invalid=96777 0313: dt=145.152000, rms=0.588 (0.031%), neg=0, invalid=96777 0314: dt=2.268000, rms=0.588 (0.000%), neg=0, invalid=96777 0315: dt=2.268000, rms=0.588 (0.000%), neg=0, invalid=96777 0316: dt=2.268000, rms=0.589 (-0.002%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.589, neg=0, invalid=96777 0317: dt=103.680000, rms=0.587 (0.247%), neg=0, invalid=96777 0318: dt=31.104000, rms=0.586 (0.133%), neg=0, invalid=96777 0319: dt=31.104000, rms=0.586 (0.049%), neg=0, invalid=96777 0320: dt=31.104000, rms=0.586 (0.057%), neg=0, invalid=96777 0321: dt=31.104000, rms=0.585 (0.070%), neg=0, invalid=96777 0322: dt=31.104000, rms=0.585 (0.090%), neg=0, invalid=96777 0323: dt=31.104000, rms=0.584 (0.069%), neg=0, invalid=96777 0324: dt=31.104000, rms=0.584 (0.087%), neg=0, invalid=96777 0325: dt=31.104000, rms=0.583 (0.081%), neg=0, invalid=96777 0326: dt=31.104000, rms=0.583 (0.079%), neg=0, invalid=96777 0327: dt=31.104000, rms=0.582 (0.063%), neg=0, invalid=96777 0328: dt=31.104000, rms=0.582 (0.056%), neg=0, invalid=96777 0329: dt=31.104000, rms=0.582 (0.069%), neg=0, invalid=96777 0330: dt=31.104000, rms=0.581 (0.059%), neg=0, invalid=96777 0331: dt=31.104000, rms=0.581 (0.057%), neg=0, invalid=96777 0332: dt=31.104000, rms=0.581 (0.042%), neg=0, invalid=96777 0333: dt=31.104000, rms=0.581 (0.055%), neg=0, invalid=96777 0334: dt=31.104000, rms=0.580 (0.049%), neg=0, invalid=96777 0335: dt=31.104000, rms=0.580 (0.047%), neg=0, invalid=96777 0336: dt=31.104000, rms=0.580 (0.033%), neg=0, invalid=96777 0337: dt=31.104000, rms=0.580 (0.035%), neg=0, invalid=96777 0338: dt=31.104000, rms=0.579 (0.048%), neg=0, invalid=96777 0339: dt=31.104000, rms=0.579 (0.042%), neg=0, invalid=96777 0340: dt=31.104000, rms=0.579 (0.049%), neg=0, invalid=96777 0341: dt=31.104000, rms=0.579 (0.028%), neg=0, invalid=96777 0342: dt=31.104000, rms=0.578 (0.047%), neg=0, invalid=96777 0343: dt=31.104000, rms=0.578 (0.037%), neg=0, invalid=96777 0344: dt=31.104000, rms=0.578 (0.034%), neg=0, invalid=96777 0345: dt=31.104000, rms=0.578 (0.042%), neg=0, invalid=96777 0346: dt=31.104000, rms=0.577 (0.033%), neg=0, invalid=96777 0347: dt=31.104000, rms=0.577 (0.036%), neg=0, invalid=96777 0348: dt=31.104000, rms=0.577 (0.031%), neg=0, invalid=96777 0349: dt=31.104000, rms=0.577 (0.031%), neg=0, invalid=96777 0350: dt=31.104000, rms=0.577 (0.031%), neg=0, invalid=96777 0351: dt=31.104000, rms=0.577 (0.019%), neg=0, invalid=96777 0352: dt=31.104000, rms=0.576 (0.032%), neg=0, invalid=96777 0353: dt=31.104000, rms=0.576 (0.027%), neg=0, invalid=96777 0354: dt=31.104000, rms=0.576 (0.026%), neg=0, invalid=96777 0355: dt=31.104000, rms=0.576 (0.028%), neg=0, invalid=96777 0356: dt=31.104000, rms=0.576 (0.029%), neg=0, invalid=96777 0357: dt=31.104000, rms=0.576 (0.031%), neg=0, invalid=96777 0358: dt=31.104000, rms=0.575 (0.024%), neg=0, invalid=96777 0359: dt=31.104000, rms=0.575 (0.020%), neg=0, invalid=96777 0360: dt=82.944000, rms=0.575 (0.011%), neg=0, invalid=96777 0361: dt=82.944000, rms=0.575 (-0.046%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.585, neg=0, invalid=96777 0362: dt=25.600000, rms=0.583 (0.206%), neg=0, invalid=96777 0363: dt=25.600000, rms=0.582 (0.207%), neg=0, invalid=96777 0364: dt=8.622222, rms=0.581 (0.138%), neg=0, invalid=96777 0365: dt=32.000000, rms=0.580 (0.214%), neg=0, invalid=96777 0366: dt=8.000000, rms=0.579 (0.173%), neg=0, invalid=96777 0367: dt=38.400000, rms=0.578 (0.202%), neg=0, invalid=96777 0368: dt=7.439252, rms=0.577 (0.233%), neg=0, invalid=96777 0369: dt=128.000000, rms=0.574 (0.510%), neg=0, invalid=96777 0370: dt=9.182266, rms=0.572 (0.315%), neg=0, invalid=96777 0371: dt=11.200000, rms=0.571 (0.166%), neg=0, invalid=96777 0372: dt=19.200000, rms=0.570 (0.168%), neg=0, invalid=96777 0373: dt=10.295652, rms=0.569 (0.201%), neg=0, invalid=96777 0374: dt=11.200000, rms=0.568 (0.170%), neg=0, invalid=96777 0375: dt=11.200000, rms=0.567 (0.094%), neg=0, invalid=96777 0376: dt=11.200000, rms=0.567 (0.100%), neg=0, invalid=96777 0377: dt=25.600000, rms=0.566 (0.090%), neg=0, invalid=96777 0378: dt=9.600000, rms=0.566 (0.130%), neg=0, invalid=96777 0379: dt=11.200000, rms=0.565 (0.069%), neg=0, invalid=96777 0380: dt=19.200000, rms=0.565 (0.102%), neg=0, invalid=96777 0381: dt=8.000000, rms=0.564 (0.076%), neg=0, invalid=96777 0382: dt=44.800000, rms=0.563 (0.142%), neg=0, invalid=96777 0383: dt=6.925373, rms=0.563 (0.137%), neg=0, invalid=96777 0384: dt=153.600000, rms=0.561 (0.251%), neg=0, invalid=96777 0385: dt=8.075829, rms=0.559 (0.406%), neg=0, invalid=96777 0386: dt=9.600000, rms=0.558 (0.162%), neg=0, invalid=96777 0387: dt=11.200000, rms=0.558 (0.063%), neg=0, invalid=96777 0388: dt=32.000000, rms=0.557 (0.070%), neg=0, invalid=96777 0389: dt=8.000000, rms=0.557 (0.070%), neg=0, invalid=96777 0390: dt=19.200000, rms=0.557 (0.048%), neg=0, invalid=96777 0391: dt=19.200000, rms=0.557 (0.004%), neg=0, invalid=96777 0392: dt=19.200000, rms=0.556 (0.132%), neg=0, invalid=96777 0393: dt=19.200000, rms=0.555 (0.224%), neg=0, invalid=96777 0394: dt=19.200000, rms=0.553 (0.195%), neg=0, invalid=96777 0395: dt=19.200000, rms=0.552 (0.210%), neg=0, invalid=96777 0396: dt=19.200000, rms=0.551 (0.259%), neg=0, invalid=96777 0397: dt=19.200000, rms=0.549 (0.320%), neg=0, invalid=96777 0398: dt=19.200000, rms=0.548 (0.234%), neg=0, invalid=96777 0399: dt=19.200000, rms=0.547 (0.227%), neg=0, invalid=96777 0400: dt=19.200000, rms=0.545 (0.294%), neg=0, invalid=96777 0401: dt=19.200000, rms=0.544 (0.233%), neg=0, invalid=96777 0402: dt=19.200000, rms=0.542 (0.237%), neg=0, invalid=96777 0403: dt=19.200000, rms=0.541 (0.204%), neg=0, invalid=96777 0404: dt=19.200000, rms=0.540 (0.171%), neg=0, invalid=96777 0405: dt=19.200000, rms=0.539 (0.210%), neg=0, invalid=96777 0406: dt=19.200000, rms=0.539 (0.125%), neg=0, invalid=96777 0407: dt=19.200000, rms=0.538 (0.154%), neg=0, invalid=96777 0408: dt=19.200000, rms=0.537 (0.173%), neg=0, invalid=96777 0409: dt=19.200000, rms=0.536 (0.109%), neg=0, invalid=96777 0410: dt=19.200000, rms=0.536 (0.116%), neg=0, invalid=96777 0411: dt=19.200000, rms=0.535 (0.116%), neg=0, invalid=96777 0412: dt=19.200000, rms=0.534 (0.118%), neg=0, invalid=96777 0413: dt=19.200000, rms=0.534 (0.107%), neg=0, invalid=96777 0414: dt=19.200000, rms=0.534 (0.028%), neg=0, invalid=96777 0415: dt=19.200000, rms=0.533 (0.109%), neg=0, invalid=96777 0416: dt=19.200000, rms=0.533 (0.086%), neg=0, invalid=96777 0417: dt=19.200000, rms=0.533 (-0.004%), neg=0, invalid=96777 0418: dt=2.800000, rms=0.533 (0.004%), neg=0, invalid=96777 0419: dt=2.800000, rms=0.533 (0.002%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.533, neg=0, invalid=96777 0420: dt=32.000000, rms=0.531 (0.271%), neg=0, invalid=96777 0421: dt=19.200000, rms=0.530 (0.159%), neg=0, invalid=96777 0422: dt=6.400000, rms=0.530 (0.033%), neg=0, invalid=96777 0423: dt=6.400000, rms=0.530 (0.030%), neg=0, invalid=96777 0424: dt=6.400000, rms=0.530 (0.035%), neg=0, invalid=96777 0425: dt=6.400000, rms=0.530 (0.041%), neg=0, invalid=96777 0426: dt=6.400000, rms=0.529 (0.050%), neg=0, invalid=96777 0427: dt=6.400000, rms=0.529 (0.057%), neg=0, invalid=96777 0428: dt=6.400000, rms=0.529 (0.046%), neg=0, invalid=96777 0429: dt=6.400000, rms=0.529 (0.039%), neg=0, invalid=96777 0430: dt=6.400000, rms=0.528 (0.035%), neg=0, invalid=96777 0431: dt=6.400000, rms=0.528 (0.017%), neg=0, invalid=96777 0432: dt=6.400000, rms=0.528 (0.017%), neg=0, invalid=96777 0433: dt=6.400000, rms=0.528 (0.023%), neg=0, invalid=96777 0434: dt=6.400000, rms=0.528 (0.023%), neg=0, invalid=96777 0435: dt=6.400000, rms=0.528 (0.018%), neg=0, invalid=96777 0436: dt=44.800000, rms=0.528 (0.056%), neg=0, invalid=96777 0437: dt=11.200000, rms=0.527 (0.034%), neg=0, invalid=96777 0438: dt=11.200000, rms=0.527 (0.008%), neg=0, invalid=96777 0439: dt=11.200000, rms=0.527 (0.021%), neg=0, invalid=96777 0440: dt=11.200000, rms=0.527 (0.036%), neg=0, invalid=96777 0441: dt=11.200000, rms=0.527 (0.040%), neg=0, invalid=96777 0442: dt=11.200000, rms=0.527 (0.036%), neg=0, invalid=96777 0443: dt=11.200000, rms=0.526 (0.043%), neg=0, invalid=96777 0444: dt=11.200000, rms=0.526 (0.044%), neg=0, invalid=96777 0445: dt=11.200000, rms=0.526 (0.038%), neg=0, invalid=96777 0446: dt=11.200000, rms=0.526 (0.041%), neg=0, invalid=96777 0447: dt=11.200000, rms=0.526 (0.037%), neg=0, invalid=96777 0448: dt=11.200000, rms=0.525 (0.041%), neg=0, invalid=96777 0449: dt=11.200000, rms=0.525 (0.040%), neg=0, invalid=96777 0450: dt=11.200000, rms=0.525 (0.037%), neg=0, invalid=96777 0451: dt=11.200000, rms=0.525 (0.034%), neg=0, invalid=96777 0452: dt=11.200000, rms=0.525 (0.028%), neg=0, invalid=96777 0453: dt=11.200000, rms=0.524 (0.035%), neg=0, invalid=96777 0454: dt=11.200000, rms=0.524 (0.020%), neg=0, invalid=96777 0455: dt=11.200000, rms=0.524 (0.022%), neg=0, invalid=96777 0456: dt=11.200000, rms=0.524 (0.019%), neg=0, invalid=96777 0457: dt=44.800000, rms=0.524 (0.030%), neg=0, invalid=96777 0458: dt=0.000488, rms=0.524 (-0.006%), 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 0459: dt=0.000000, rms=0.545 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.545, neg=0, invalid=96777 0460: dt=0.000000, rms=0.545 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.586, neg=0, invalid=96777 0461: dt=0.448000, rms=0.584 (0.294%), neg=0, invalid=96777 0462: dt=0.520833, rms=0.583 (0.137%), neg=0, invalid=96777 0463: dt=0.080827, rms=0.583 (0.003%), neg=0, invalid=96777 0464: dt=0.080827, rms=0.583 (0.003%), neg=0, invalid=96777 0465: dt=0.080827, rms=0.583 (-0.006%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.583, neg=0, invalid=96777 0466: dt=0.458333, rms=0.583 (0.071%), neg=0, invalid=96777 0467: dt=0.112000, rms=0.583 (0.002%), neg=0, invalid=96777 0468: dt=0.112000, rms=0.583 (0.002%), neg=0, invalid=96777 0469: dt=0.112000, rms=0.583 (-0.011%), 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=0.533, neg=0, invalid=96777 0470: dt=0.112000, rms=0.528 (0.914%), neg=0, invalid=96777 0471: dt=0.112000, rms=0.524 (0.720%), neg=0, invalid=96777 0472: dt=0.007000, rms=0.524 (0.036%), neg=0, invalid=96777 0473: dt=0.007000, rms=0.524 (0.035%), neg=0, invalid=96777 0474: dt=0.007000, rms=0.524 (0.067%), neg=0, invalid=96777 0475: dt=0.007000, rms=0.523 (0.095%), neg=0, invalid=96777 0476: dt=0.007000, rms=0.522 (0.117%), neg=0, invalid=96777 0477: dt=0.007000, rms=0.522 (0.135%), neg=0, invalid=96777 0478: dt=0.007000, rms=0.521 (0.151%), neg=0, invalid=96777 0479: dt=0.007000, rms=0.520 (0.165%), neg=0, invalid=96777 0480: dt=0.007000, rms=0.519 (0.172%), neg=0, invalid=96777 0481: dt=0.007000, rms=0.518 (0.180%), neg=0, invalid=96777 0482: dt=0.007000, rms=0.517 (0.182%), neg=0, invalid=96777 0483: dt=0.007000, rms=0.516 (0.184%), neg=0, invalid=96777 0484: dt=0.007000, rms=0.515 (0.180%), neg=0, invalid=96777 0485: dt=0.007000, rms=0.515 (0.179%), neg=0, invalid=96777 0486: dt=0.007000, rms=0.514 (0.174%), neg=0, invalid=96777 0487: dt=0.007000, rms=0.513 (0.165%), neg=0, invalid=96777 0488: dt=0.007000, rms=0.512 (0.159%), neg=0, invalid=96777 0489: dt=0.007000, rms=0.511 (0.146%), neg=0, invalid=96777 0490: dt=0.007000, rms=0.510 (0.140%), neg=0, invalid=96777 0491: dt=0.007000, rms=0.510 (0.130%), neg=0, invalid=96777 0492: dt=0.007000, rms=0.509 (0.119%), neg=0, invalid=96777 0493: dt=0.007000, rms=0.509 (0.108%), neg=0, invalid=96777 0494: dt=0.007000, rms=0.508 (0.099%), neg=0, invalid=96777 0495: dt=0.007000, rms=0.508 (0.089%), neg=0, invalid=96777 0496: dt=0.007000, rms=0.507 (0.079%), neg=0, invalid=96777 0497: dt=0.007000, rms=0.507 (0.069%), neg=0, invalid=96777 0498: dt=0.007000, rms=0.507 (0.057%), neg=0, invalid=96777 0499: dt=0.007000, rms=0.506 (0.050%), neg=0, invalid=96777 0500: dt=0.007000, rms=0.506 (0.043%), neg=0, invalid=96777 0501: dt=0.007000, rms=0.506 (0.039%), neg=0, invalid=96777 0502: dt=0.007000, rms=0.506 (0.029%), neg=0, invalid=96777 0503: dt=0.007000, rms=0.506 (0.024%), neg=0, invalid=96777 0504: dt=0.007000, rms=0.506 (0.019%), neg=0, invalid=96777 0505: dt=0.000000, rms=0.506 (-0.002%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.506, neg=0, invalid=96777 0506: dt=0.112000, rms=0.504 (0.287%), neg=0, invalid=96777 0507: dt=0.112000, rms=0.503 (0.219%), neg=0, invalid=96777 0508: dt=0.028000, rms=0.503 (0.040%), neg=0, invalid=96777 0509: dt=0.028000, rms=0.503 (0.042%), neg=0, invalid=96777 0510: dt=0.028000, rms=0.502 (0.071%), neg=0, invalid=96777 0511: dt=0.028000, rms=0.502 (0.101%), neg=0, invalid=96777 0512: dt=0.028000, rms=0.501 (0.116%), neg=0, invalid=96777 0513: dt=0.028000, rms=0.501 (0.021%), neg=0, invalid=96777 0514: dt=0.028000, rms=0.501 (0.040%), neg=0, invalid=96777 0515: dt=0.028000, rms=0.501 (0.054%), neg=0, invalid=96777 0516: dt=0.028000, rms=0.500 (0.064%), neg=0, invalid=96777 0517: dt=0.028000, rms=0.500 (0.070%), neg=0, invalid=96777 0518: dt=0.028000, rms=0.500 (0.074%), neg=0, invalid=96777 0519: dt=0.028000, rms=0.499 (0.071%), neg=0, invalid=96777 0520: dt=0.028000, rms=0.499 (0.069%), neg=0, invalid=96777 0521: dt=0.028000, rms=0.499 (0.058%), neg=0, invalid=96777 0522: dt=0.028000, rms=0.498 (0.053%), neg=0, invalid=96777 0523: dt=0.028000, rms=0.498 (0.041%), neg=0, invalid=96777 0524: dt=0.028000, rms=0.498 (0.032%), neg=0, invalid=96777 0525: dt=0.028000, rms=0.498 (0.026%), neg=0, invalid=96777 0526: dt=0.028000, rms=0.498 (0.016%), neg=0, invalid=96777 0527: dt=0.028000, rms=0.498 (0.005%), neg=0, invalid=96777 0528: dt=0.000000, rms=0.498 (0.002%), neg=0, invalid=96777 0529: dt=0.050000, rms=0.498 (-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=0.496, neg=0, invalid=96777 0530: dt=0.000000, rms=0.496 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.496, neg=0, invalid=96777 0531: dt=129.472000, rms=0.496 (0.034%), neg=0, invalid=96777 0532: dt=129.472000, rms=0.496 (0.018%), neg=0, invalid=96777 0533: dt=129.472000, rms=0.495 (0.015%), neg=0, invalid=96777 0534: dt=129.472000, rms=0.495 (0.014%), neg=0, invalid=96777 0535: dt=129.472000, rms=0.495 (0.032%), neg=0, invalid=96777 0536: dt=129.472000, rms=0.495 (0.032%), neg=0, invalid=96777 0537: dt=129.472000, rms=0.495 (-0.003%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.495, neg=0, invalid=96777 0538: dt=25.920000, rms=0.495 (0.045%), neg=0, invalid=96777 0539: dt=7.776000, rms=0.495 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.495, neg=0, invalid=96777 0540: dt=103.680000, rms=0.494 (0.232%), neg=0, invalid=96777 0541: dt=36.288000, rms=0.493 (0.157%), neg=0, invalid=96777 0542: dt=36.288000, rms=0.493 (0.022%), neg=0, invalid=96777 0543: dt=36.288000, rms=0.492 (0.112%), neg=0, invalid=96777 0544: dt=36.288000, rms=0.492 (0.128%), neg=0, invalid=96777 0545: dt=36.288000, rms=0.491 (0.114%), neg=0, invalid=96777 0546: dt=36.288000, rms=0.491 (0.037%), neg=0, invalid=96777 0547: dt=31.104000, rms=0.491 (0.076%), neg=0, invalid=96777 0548: dt=9.072000, rms=0.491 (0.002%), neg=0, invalid=96777 0549: dt=9.072000, rms=0.491 (0.003%), neg=0, invalid=96777 0550: dt=9.072000, rms=0.491 (0.002%), neg=0, invalid=96777 0551: dt=9.072000, rms=0.490 (0.013%), neg=0, invalid=96777 0552: dt=9.072000, rms=0.490 (0.017%), neg=0, invalid=96777 0553: dt=9.072000, rms=0.490 (0.017%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.490, neg=0, invalid=96777 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0554: dt=32.000000, rms=0.488 (0.495%), neg=0, invalid=96777 iter 0, gcam->neg = 51 after 31 iterations, nbhd size=3, neg = 0 0555: dt=32.000000, rms=0.487 (0.282%), neg=0, invalid=96777 0556: dt=8.000000, rms=0.486 (0.111%), neg=0, invalid=96777 0557: dt=8.000000, rms=0.486 (0.081%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 13 iterations, nbhd size=2, neg = 0 0558: dt=8.000000, rms=0.485 (0.109%), neg=0, invalid=96777 0559: dt=8.000000, rms=0.484 (0.150%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0560: dt=8.000000, rms=0.484 (0.134%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0561: dt=8.000000, rms=0.483 (0.130%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0562: dt=8.000000, rms=0.483 (0.114%), neg=0, invalid=96777 0563: dt=8.000000, rms=0.482 (0.099%), neg=0, invalid=96777 0564: dt=11.200000, rms=0.482 (0.053%), neg=0, invalid=96777 0565: dt=11.200000, rms=0.482 (0.041%), neg=0, invalid=96777 0566: dt=11.200000, rms=0.481 (0.090%), neg=0, invalid=96777 0567: dt=11.200000, rms=0.481 (0.100%), neg=0, invalid=96777 0568: dt=11.200000, rms=0.480 (0.105%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0569: dt=11.200000, rms=0.480 (0.111%), neg=0, invalid=96777 0570: dt=11.200000, rms=0.479 (0.082%), neg=0, invalid=96777 iter 0, gcam->neg = 7 after 19 iterations, nbhd size=3, neg = 0 0571: dt=11.200000, rms=0.479 (0.081%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.479, neg=0, invalid=96777 iter 0, gcam->neg = 7 after 21 iterations, nbhd size=2, neg = 0 0572: dt=38.400000, rms=0.475 (0.740%), neg=0, invalid=96777 0573: dt=8.000000, rms=0.474 (0.222%), neg=0, invalid=96777 0574: dt=8.000000, rms=0.474 (0.136%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 5 iterations, nbhd size=1, neg = 0 0575: dt=8.000000, rms=0.473 (0.140%), neg=0, invalid=96777 0576: dt=8.000000, rms=0.472 (0.228%), neg=0, invalid=96777 0577: dt=8.000000, rms=0.471 (0.177%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0578: dt=8.000000, rms=0.470 (0.181%), neg=0, invalid=96777 0579: dt=8.000000, rms=0.470 (0.155%), neg=0, invalid=96777 0580: dt=8.000000, rms=0.469 (0.120%), neg=0, invalid=96777 0581: dt=8.000000, rms=0.468 (0.122%), neg=0, invalid=96777 0582: dt=8.000000, rms=0.468 (0.089%), neg=0, invalid=96777 0583: dt=9.600000, rms=0.468 (0.024%), neg=0, invalid=96777 0584: dt=9.600000, rms=0.468 (0.054%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0585: dt=9.600000, rms=0.467 (0.041%), neg=0, invalid=96777 0586: dt=9.600000, rms=0.467 (0.038%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.471, neg=0, invalid=96777 iter 0, gcam->neg = 18 after 17 iterations, nbhd size=1, neg = 0 0587: dt=2.333333, rms=0.471 (0.046%), neg=0, invalid=96777 0588: dt=1.008000, rms=0.471 (0.011%), neg=0, invalid=96777 0589: dt=1.008000, rms=0.471 (0.024%), neg=0, invalid=96777 0590: dt=1.008000, rms=0.470 (0.035%), neg=0, invalid=96777 iter 0, gcam->neg = 8 after 9 iterations, nbhd size=1, neg = 0 0591: dt=1.008000, rms=0.470 (0.022%), neg=0, invalid=96777 iter 0, gcam->neg = 7 after 7 iterations, nbhd size=1, neg = 0 0592: dt=1.008000, rms=0.470 (-0.018%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.470, neg=0, invalid=96777 iter 0, gcam->neg = 19 after 11 iterations, nbhd size=1, neg = 0 0593: dt=4.258065, rms=0.470 (0.149%), neg=0, invalid=96777 iter 0, gcam->neg = 44 after 16 iterations, nbhd size=1, neg = 0 0594: dt=7.111111, rms=0.468 (0.246%), neg=0, invalid=96777 0595: dt=0.015750, rms=0.468 (0.003%), neg=0, invalid=96777 0596: dt=0.015750, rms=0.468 (0.000%), neg=0, invalid=96777 0597: dt=0.015750, rms=0.468 (0.000%), neg=0, invalid=96777 0598: dt=0.015750, rms=0.468 (0.000%), neg=0, invalid=96777 0599: dt=0.015750, rms=0.468 (0.001%), neg=0, invalid=96777 0600: dt=0.015750, rms=0.468 (0.001%), neg=0, invalid=96777 0601: dt=0.015750, rms=0.468 (0.001%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.474, neg=0, invalid=96777 0602: dt=0.000000, rms=0.474 (-0.002%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.474, neg=0, invalid=96777 0603: dt=0.000000, rms=0.474 (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=0.465, neg=0, invalid=96777 iter 0, gcam->neg = 802 after 29 iterations, nbhd size=2, neg = 0 0604: dt=1.832792, rms=0.423 (8.972%), neg=0, invalid=96777 0605: dt=0.000109, rms=0.423 (-0.003%), neg=0, invalid=96777 0606: dt=0.000109, rms=0.423 (0.001%), neg=0, invalid=96777 0607: dt=0.000109, rms=0.423 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.423, neg=0, invalid=96777 0608: dt=0.000313, rms=0.423 (0.000%), neg=0, invalid=96777 0609: dt=0.000000, rms=0.423 (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=0.408, neg=0, invalid=96777 0610: dt=0.000000, rms=0.409 (-0.320%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.409, neg=0, invalid=96777 0611: dt=8.092000, rms=0.409 (0.001%), neg=0, invalid=96777 0612: dt=8.092000, rms=0.409 (0.000%), neg=0, invalid=96777 0613: dt=8.092000, rms=0.409 (-0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.409, neg=0, invalid=96777 0614: dt=0.000000, rms=0.409 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.409, neg=0, invalid=96777 0615: dt=15.552000, rms=0.409 (0.012%), neg=0, invalid=96777 0616: dt=9.072000, rms=0.409 (0.002%), neg=0, invalid=96777 0617: dt=9.072000, rms=0.409 (0.000%), neg=0, invalid=96777 0618: dt=9.072000, rms=0.409 (-0.003%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.410, neg=0, invalid=96777 0619: dt=2.800000, rms=0.410 (0.010%), neg=0, invalid=96777 0620: dt=1.600000, rms=0.410 (0.001%), neg=0, invalid=96777 0621: dt=1.600000, rms=0.410 (0.002%), neg=0, invalid=96777 0622: dt=1.600000, rms=0.410 (-0.004%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.410, neg=0, invalid=96777 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0623: dt=32.000000, rms=0.409 (0.182%), neg=0, invalid=96777 iter 0, gcam->neg = 16 after 16 iterations, nbhd size=2, neg = 0 0624: dt=25.600000, rms=0.409 (0.131%), neg=0, invalid=96777 iter 0, gcam->neg = 17 after 45 iterations, nbhd size=1, neg = 0 0625: dt=25.600000, rms=0.409 (-0.628%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.411, neg=0, invalid=96777 0626: dt=0.009000, rms=0.411 (0.000%), neg=0, invalid=96777 iter 0, gcam->neg = 8 after 29 iterations, nbhd size=3, neg = 0 0627: dt=1.142857, rms=0.411 (0.016%), neg=0, invalid=96777 0628: dt=0.063000, rms=0.411 (0.001%), neg=0, invalid=96777 0629: dt=0.063000, rms=0.411 (0.003%), neg=0, invalid=96777 0630: dt=0.063000, rms=0.411 (0.007%), neg=0, invalid=96777 0631: dt=0.063000, rms=0.411 (0.010%), neg=0, invalid=96777 0632: dt=0.063000, rms=0.411 (0.013%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0633: dt=0.063000, rms=0.411 (0.015%), neg=0, invalid=96777 0634: dt=0.063000, rms=0.411 (0.013%), neg=0, invalid=96777 0635: dt=0.063000, rms=0.410 (0.014%), neg=0, invalid=96777 0636: dt=0.063000, rms=0.410 (0.016%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0637: dt=0.063000, rms=0.410 (0.017%), neg=0, invalid=96777 0638: dt=0.063000, rms=0.410 (0.018%), neg=0, invalid=96777 0639: dt=0.063000, rms=0.410 (0.019%), neg=0, invalid=96777 0640: dt=0.063000, rms=0.410 (0.019%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0641: dt=0.063000, rms=0.410 (0.026%), neg=0, invalid=96777 0642: dt=0.063000, rms=0.410 (0.019%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.410, neg=0, invalid=96777 iter 0, gcam->neg = 43 after 51 iterations, nbhd size=4, neg = 0 0643: dt=7.161905, rms=0.408 (0.428%), neg=0, invalid=96777 0644: dt=0.003938, rms=0.408 (0.000%), neg=0, invalid=96777 0645: dt=0.003938, rms=0.408 (0.000%), neg=0, invalid=96777 0646: dt=0.003938, rms=0.408 (0.000%), neg=0, invalid=96777 0647: dt=0.003938, rms=0.408 (0.000%), neg=0, invalid=96777 0648: dt=0.003938, rms=0.408 (0.001%), neg=0, invalid=96777 0649: dt=0.003938, rms=0.408 (0.001%), neg=0, invalid=96777 0650: dt=0.003938, rms=0.408 (0.001%), neg=0, invalid=96777 0651: dt=0.003938, rms=0.408 (0.001%), neg=0, invalid=96777 0652: dt=0.003938, rms=0.408 (0.001%), neg=0, invalid=96777 0653: dt=0.003938, rms=0.408 (0.001%), neg=0, invalid=96777 0654: dt=0.003938, rms=0.408 (0.001%), neg=0, invalid=96777 0655: dt=0.003938, rms=0.408 (0.001%), neg=0, invalid=96777 0656: dt=0.003938, rms=0.408 (0.001%), neg=0, invalid=96777 0657: dt=0.003938, rms=0.408 (0.001%), neg=0, invalid=96777 0658: dt=0.003938, rms=0.408 (0.001%), neg=0, invalid=96777 0659: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777 0660: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777 0661: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777 0662: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777 0663: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777 0664: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777 0665: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777 0666: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777 0667: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777 0668: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777 0669: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777 0670: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777 0671: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777 0672: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777 0673: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777 0674: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777 0675: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777 0676: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777 0677: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777 0678: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777 0679: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777 0680: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777 0681: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777 0682: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777 0683: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777 0684: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777 0685: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777 iter 0, gcam->neg = 132 after 56 iterations, nbhd size=4, neg = 0 0686: dt=13.824000, rms=0.406 (0.376%), neg=0, invalid=96777 0687: dt=0.000984, rms=0.406 (0.000%), neg=0, invalid=96777 0688: dt=0.000984, rms=0.406 (0.000%), neg=0, invalid=96777 0689: dt=0.000984, rms=0.406 (-0.000%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.412, neg=0, invalid=96777 0690: dt=0.000160, rms=0.412 (0.000%), neg=0, invalid=96777 0691: dt=0.000000, rms=0.412 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.412, neg=0, invalid=96777 0692: dt=0.000078, rms=0.412 (0.000%), neg=0, invalid=96777 0693: dt=0.000078, rms=0.412 (-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=0.403, neg=0, invalid=96777 iter 0, gcam->neg = 224 after 35 iterations, nbhd size=3, neg = 0 0694: dt=0.448000, rms=0.394 (2.045%), neg=0, invalid=96777 0695: dt=0.000015, rms=0.394 (0.001%), neg=0, invalid=96777 0696: dt=0.000015, rms=0.394 (0.000%), neg=0, invalid=96777 0697: dt=0.000015, rms=0.394 (0.000%), neg=0, invalid=96777 0698: dt=0.000015, rms=0.394 (0.000%), neg=0, invalid=96777 0699: dt=0.000015, rms=0.394 (0.000%), neg=0, invalid=96777 0700: dt=0.000750, rms=0.394 (0.000%), neg=0, invalid=96777 iter 0, gcam->neg = 6 after 6 iterations, nbhd size=1, neg = 0 0701: dt=0.024000, rms=0.394 (0.010%), neg=0, invalid=96777 0702: dt=0.000004, rms=0.394 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.394, neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0703: dt=0.000250, rms=0.394 (0.001%), neg=0, invalid=96777 0704: dt=0.000027, rms=0.394 (0.000%), neg=0, invalid=96777 0705: dt=0.000027, rms=0.394 (0.000%), neg=0, invalid=96777 0706: dt=0.000027, rms=0.394 (0.000%), neg=0, invalid=96777 0707: dt=0.000027, rms=0.394 (0.000%), neg=0, invalid=96777 0708: dt=0.000027, rms=0.394 (0.000%), neg=0, invalid=96777 0709: dt=0.000027, rms=0.394 (0.000%), neg=0, invalid=96777 0710: dt=0.000027, rms=0.394 (0.000%), neg=0, invalid=96777 0711: dt=0.000027, rms=0.394 (0.000%), neg=0, invalid=96777 0712: dt=0.000027, rms=0.394 (0.000%), neg=0, invalid=96777 0713: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777 0714: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777 0715: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777 0716: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777 0717: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777 0718: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777 0719: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777 0720: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777 0721: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777 0722: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777 0723: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777 0724: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777 0725: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777 0726: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777 0727: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777 0728: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777 0729: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777 0730: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777 0731: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777 0732: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777 0733: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777 0734: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777 0735: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777 0736: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777 0737: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777 0738: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777 0739: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777 0740: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777 0741: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777 0742: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777 0743: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777 0744: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777 0745: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777 0746: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777 0747: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777 writing output transformation to transforms/talairach.m3z... GCAMwrite registration took 4 hours, 18 minutes and 0 seconds. #-------------------------------------- #@# CA Reg Inv Thu Aug 8 16:31:57 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Thu Aug 8 16:33:31 CEST 2013 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/opt/freesurfer/5.3.0/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... 11389683 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 1 minutes and 34 seconds. #-------------------------------------- #@# SkullLTA Thu Aug 8 16:35:04 CEST 2013 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta ======= NUMBER OF OPENMP THREADS = 1 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 5 using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach_with_skull_2.log reading '/opt/freesurfer/5.3.0/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=9.0 skull bounding box = (54, 13, 0) --> (212, 197, 196) using (107, 74, 98) as brain centroid... mean wm in atlas = 126, using box (88,51,74) --> (126, 96,122) to find MRI wm before smoothing, mri peak at 108 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=-4.1, old_max_log_p =-4.2 (thresh=-4.2) 1.264 0.048 -0.071 -35.935; -0.018 1.270 0.513 -54.525; 0.125 -0.518 1.107 15.895; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.264 0.048 -0.071 -35.935; -0.018 1.270 0.513 -54.525; 0.125 -0.518 1.107 15.895; 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=-4.0, old_max_log_p =-4.1 (thresh=-4.1) 1.239 0.047 -0.069 -30.915; -0.022 1.310 0.483 -52.599; 0.125 -0.478 1.123 12.280; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.239 0.047 -0.069 -30.915; -0.022 1.285 0.474 -49.342; 0.122 -0.469 1.102 14.038; 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=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.236 0.047 -0.069 -30.548; -0.021 1.283 0.484 -50.756; 0.123 -0.480 1.098 14.970; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.236 0.047 -0.069 -30.548; -0.021 1.283 0.484 -50.756; 0.123 -0.480 1.098 14.970; 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 1.23617 0.04681 -0.06911 -30.54774; -0.02084 1.28282 0.48392 -50.75591; 0.12254 -0.47982 1.09813 14.96986; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.23617 0.04681 -0.06911 -30.54774; -0.02084 1.28282 0.48392 -50.75591; 0.12254 -0.47982 1.09813 14.96986; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 4 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 007: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.236 0.047 -0.069 -30.548; -0.021 1.283 0.484 -50.756; 0.123 -0.480 1.098 14.970; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -4.0 (old=-4.2) transform before final EM align: 1.236 0.047 -0.069 -30.548; -0.021 1.283 0.484 -50.756; 0.123 -0.480 1.098 14.970; 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 1.23617 0.04681 -0.06911 -30.54774; -0.02084 1.28282 0.48392 -50.75591; 0.12254 -0.47982 1.09813 14.96986; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.23617 0.04681 -0.06911 -30.54774; -0.02084 1.28282 0.48392 -50.75591; 0.12254 -0.47982 1.09813 14.96986; 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) = 4.4 tol 0.000000 final transform: 1.236 0.047 -0.069 -30.548; -0.021 1.283 0.484 -50.756; 0.123 -0.480 1.098 14.970; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull_2.lta... registration took 31 minutes and 47 seconds. #-------------------------------------- #@# SubCort Seg Thu Aug 8 17:06:52 CEST 2013 mri_ca_label -align norm.mgz transforms/talairach.m3z /opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz sysname Linux hostname snake4 machine x86_64 setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri mri_ca_label -align norm.mgz transforms/talairach.m3z /opt/freesurfer/5.3.0/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 /opt/freesurfer/5.3.0/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 /opt/freesurfer/5.3.0/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 = 0.10814 ( 4) Left_Lateral_Ventricle (4): linear fit = 0.12 x + 0.0 (311 voxels, overlap=0.085) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (311 voxels, peak = 3), gca=10.8 gca peak = 0.14982 (20) mri peak = 0.14647 ( 5) Right_Lateral_Ventricle (43): linear fit = 0.19 x + 0.0 (179 voxels, overlap=0.007) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (179 voxels, peak = 4), gca=8.0 gca peak = 0.28003 (97) mri peak = 0.12552 (83) Right_Pallidum (52): linear fit = 0.82 x + 0.0 (321 voxels, overlap=0.039) Right_Pallidum (52): linear fit = 0.82 x + 0.0 (321 voxels, peak = 80), gca=80.0 gca peak = 0.18160 (96) mri peak = 0.12184 (78) Left_Pallidum (13): linear fit = 0.79 x + 0.0 (271 voxels, overlap=0.047) Left_Pallidum (13): linear fit = 0.79 x + 0.0 (271 voxels, peak = 75), gca=75.4 gca peak = 0.27536 (62) mri peak = 0.10294 (53) Right_Hippocampus (53): linear fit = 0.83 x + 0.0 (530 voxels, overlap=0.031) Right_Hippocampus (53): linear fit = 0.83 x + 0.0 (530 voxels, peak = 52), gca=51.8 gca peak = 0.32745 (63) mri peak = 0.09040 (58) Left_Hippocampus (17): linear fit = 0.85 x + 0.0 (600 voxels, overlap=0.060) Left_Hippocampus (17): linear fit = 0.85 x + 0.0 (600 voxels, peak = 53), gca=53.2 gca peak = 0.08597 (105) mri peak = 0.06879 (108) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (31675 voxels, overlap=0.786) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (31675 voxels, peak = 107), gca=106.6 gca peak = 0.09209 (106) mri peak = 0.07904 (108) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (30610 voxels, overlap=0.709) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (30610 voxels, peak = 109), gca=108.6 gca peak = 0.07826 (63) mri peak = 0.05015 (50) Left_Cerebral_Cortex (3): linear fit = 0.80 x + 0.0 (15235 voxels, overlap=0.375) Left_Cerebral_Cortex (3): linear fit = 0.80 x + 0.0 (15235 voxels, peak = 50), gca=50.1 gca peak = 0.08598 (64) mri peak = 0.05696 (51) Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (14577 voxels, overlap=0.266) Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (14577 voxels, peak = 53), gca=52.8 gca peak = 0.24164 (71) mri peak = 0.12107 (58) Right_Caudate (50): linear fit = 0.79 x + 0.0 (638 voxels, overlap=0.024) Right_Caudate (50): linear fit = 0.79 x + 0.0 (638 voxels, peak = 56), gca=55.7 gca peak = 0.18227 (75) mri peak = 0.10473 (58) Left_Caudate (11): linear fit = 0.77 x + 0.0 (590 voxels, overlap=0.026) Left_Caudate (11): linear fit = 0.77 x + 0.0 (590 voxels, peak = 58), gca=58.1 gca peak = 0.10629 (62) mri peak = 0.06110 (59) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (10502 voxels, overlap=0.995) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (10502 voxels, peak = 61), gca=61.1 gca peak = 0.11668 (59) mri peak = 0.05820 (61) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (9892 voxels, overlap=0.999) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (9892 voxels, peak = 60), gca=60.5 gca peak = 0.17849 (88) mri peak = 0.08017 (90) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (3946 voxels, overlap=0.991) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (3946 voxels, peak = 88), gca=87.6 gca peak = 0.16819 (86) mri peak = 0.06108 (89) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (3732 voxels, overlap=0.997) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (3732 voxels, peak = 87), gca=87.3 gca peak = 0.41688 (64) mri peak = 0.10381 (55) Left_Amygdala (18): linear fit = 0.85 x + 0.0 (337 voxels, overlap=0.763) Left_Amygdala (18): linear fit = 0.85 x + 0.0 (337 voxels, peak = 54), gca=54.1 gca peak = 0.42394 (62) mri peak = 0.15749 (54) Right_Amygdala (54): linear fit = 0.86 x + 0.0 (156 voxels, overlap=0.052) Right_Amygdala (54): linear fit = 0.86 x + 0.0 (156 voxels, peak = 53), gca=53.0 gca peak = 0.10041 (96) mri peak = 0.07050 (80) Left_Thalamus_Proper (10): linear fit = 0.88 x + 0.0 (2851 voxels, overlap=0.291) Left_Thalamus_Proper (10): linear fit = 0.88 x + 0.0 (2851 voxels, peak = 84), gca=84.0 gca peak = 0.13978 (88) mri peak = 0.10651 (77) Right_Thalamus_Proper (49): linear fit = 0.89 x + 0.0 (3096 voxels, overlap=0.419) Right_Thalamus_Proper (49): linear fit = 0.89 x + 0.0 (3096 voxels, peak = 79), gca=78.8 gca peak = 0.08514 (81) mri peak = 0.07602 (68) Left_Putamen (12): linear fit = 0.81 x + 0.0 (1997 voxels, overlap=0.127) Left_Putamen (12): linear fit = 0.81 x + 0.0 (1997 voxels, peak = 65), gca=65.2 gca peak = 0.09624 (82) mri peak = 0.09486 (66) Right_Putamen (51): linear fit = 0.79 x + 0.0 (1835 voxels, overlap=0.013) Right_Putamen (51): linear fit = 0.79 x + 0.0 (1835 voxels, peak = 64), gca=64.4 gca peak = 0.07543 (88) mri peak = 0.10827 (83) Brain_Stem (16): linear fit = 0.96 x + 0.0 (7866 voxels, overlap=0.698) Brain_Stem (16): linear fit = 0.96 x + 0.0 (7866 voxels, peak = 85), gca=84.9 gca peak = 0.12757 (95) mri peak = 0.12170 (85) Right_VentralDC (60): linear fit = 0.90 x + 0.0 (818 voxels, overlap=0.213) Right_VentralDC (60): linear fit = 0.90 x + 0.0 (818 voxels, peak = 86), gca=86.0 gca peak = 0.17004 (92) mri peak = 0.10560 (83) Left_VentralDC (28): linear fit = 0.89 x + 0.0 (884 voxels, overlap=0.452) Left_VentralDC (28): linear fit = 0.89 x + 0.0 (884 voxels, peak = 82), gca=82.3 gca peak = 0.21361 (36) mri peak = 0.15680 (54) gca peak = 0.26069 (23) mri peak = 0.17261 ( 8) Fourth_Ventricle (15): linear fit = 0.26 x + 0.0 (233 voxels, overlap=0.024) Fourth_Ventricle (15): linear fit = 0.26 x + 0.0 (233 voxels, peak = 6), gca=6.1 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak Third_Ventricle = 0.21361 (36) gca peak Fourth_Ventricle = 0.26069 (23) gca peak CSF = 0.14367 (38) gca peak Left_Accumbens_area = 0.57033 (70) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65201 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.31129 (32) gca peak Right_Accumbens_area = 0.30219 (72) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.72939 (42) gca peak WM_hypointensities = 0.14821 (82) gca peak non_WM_hypointensities = 0.10354 (53) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means estimating mean gm scale to be 0.83 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 0.40 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.31600 (11) mri peak = 0.10814 ( 4) Left_Lateral_Ventricle (4): linear fit = 0.28 x + 0.0 (311 voxels, overlap=0.465) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (311 voxels, peak = 3), gca=4.4 gca peak = 0.29325 ( 9) mri peak = 0.14647 ( 5) Right_Lateral_Ventricle (43): linear fit = 0.44 x + 0.0 (179 voxels, overlap=0.716) Right_Lateral_Ventricle (43): linear fit = 0.44 x + 0.0 (179 voxels, peak = 4), gca=4.0 gca peak = 0.26612 (81) mri peak = 0.12552 (83) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (321 voxels, overlap=0.995) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (321 voxels, peak = 81), gca=81.0 gca peak = 0.23030 (75) mri peak = 0.12184 (78) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (271 voxels, overlap=1.006) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (271 voxels, peak = 75), gca=75.0 gca peak = 0.32075 (52) mri peak = 0.10294 (53) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (530 voxels, overlap=1.005) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (530 voxels, peak = 52), gca=52.0 gca peak = 0.29771 (53) mri peak = 0.09040 (58) Left_Hippocampus (17): linear fit = 1.01 x + 0.0 (600 voxels, overlap=1.004) Left_Hippocampus (17): linear fit = 1.01 x + 0.0 (600 voxels, peak = 54), gca=53.8 gca peak = 0.08541 (107) mri peak = 0.06879 (108) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (31675 voxels, overlap=0.834) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (31675 voxels, peak = 108), gca=107.5 gca peak = 0.08551 (108) mri peak = 0.07904 (108) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (30610 voxels, overlap=0.783) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (30610 voxels, peak = 108), gca=108.0 gca peak = 0.09720 (50) mri peak = 0.05015 (50) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (15235 voxels, overlap=0.993) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (15235 voxels, peak = 50), gca=50.0 gca peak = 0.10545 (53) mri peak = 0.05696 (51) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (14577 voxels, overlap=0.985) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (14577 voxels, peak = 52), gca=52.2 gca peak = 0.26700 (58) mri peak = 0.12107 (58) Right_Caudate (50): linear fit = 1.04 x + 0.0 (638 voxels, overlap=0.999) Right_Caudate (50): linear fit = 1.04 x + 0.0 (638 voxels, peak = 61), gca=60.6 gca peak = 0.19395 (58) mri peak = 0.10473 (58) Left_Caudate (11): linear fit = 1.00 x + 0.0 (590 voxels, overlap=0.986) Left_Caudate (11): linear fit = 1.00 x + 0.0 (590 voxels, peak = 58), gca=58.0 gca peak = 0.11171 (61) mri peak = 0.06110 (59) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (10502 voxels, overlap=0.991) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (10502 voxels, peak = 63), gca=62.5 gca peak = 0.12569 (61) mri peak = 0.05820 (61) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (9892 voxels, overlap=0.992) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (9892 voxels, peak = 59), gca=58.9 gca peak = 0.18438 (87) mri peak = 0.08017 (90) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (3946 voxels, overlap=0.987) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (3946 voxels, peak = 88), gca=88.3 gca peak = 0.16063 (88) mri peak = 0.06108 (89) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (3732 voxels, overlap=1.000) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (3732 voxels, peak = 88), gca=87.6 gca peak = 0.57967 (54) mri peak = 0.10381 (55) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (337 voxels, overlap=1.023) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (337 voxels, peak = 54), gca=54.0 gca peak = 0.49427 (53) mri peak = 0.15749 (54) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (156 voxels, overlap=1.014) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (156 voxels, peak = 53), gca=53.0 gca peak = 0.10699 (84) mri peak = 0.07050 (80) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (2851 voxels, overlap=0.969) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (2851 voxels, peak = 84), gca=83.6 gca peak = 0.10983 (79) mri peak = 0.10651 (77) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3096 voxels, overlap=0.894) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3096 voxels, peak = 79), gca=78.6 gca peak = 0.10378 (65) mri peak = 0.07602 (68) Left_Putamen (12): linear fit = 1.02 x + 0.0 (1997 voxels, overlap=0.991) Left_Putamen (12): linear fit = 1.02 x + 0.0 (1997 voxels, peak = 67), gca=66.6 gca peak = 0.12788 (60) mri peak = 0.09486 (66) Right_Putamen (51): linear fit = 1.02 x + 0.0 (1835 voxels, overlap=0.990) Right_Putamen (51): linear fit = 1.02 x + 0.0 (1835 voxels, peak = 62), gca=61.5 gca peak = 0.08675 (85) mri peak = 0.10827 (83) Brain_Stem (16): linear fit = 1.02 x + 0.0 (7866 voxels, overlap=0.662) Brain_Stem (16): linear fit = 1.02 x + 0.0 (7866 voxels, peak = 87), gca=87.1 gca peak = 0.12656 (86) mri peak = 0.12170 (85) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (818 voxels, overlap=0.780) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (818 voxels, peak = 86), gca=86.0 gca peak = 0.15972 (83) mri peak = 0.10560 (83) Left_VentralDC (28): linear fit = 1.01 x + 0.0 (884 voxels, overlap=0.856) Left_VentralDC (28): linear fit = 1.01 x + 0.0 (884 voxels, peak = 84), gca=84.2 gca peak = 0.35640 (14) mri peak = 0.15680 (54) gca peak = 0.33827 ( 9) mri peak = 0.17261 ( 8) Fourth_Ventricle (15): linear fit = 0.68 x + 0.0 (233 voxels, overlap=0.798) Fourth_Ventricle (15): linear fit = 0.68 x + 0.0 (233 voxels, peak = 6), gca=6.1 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.27462 (30) gca peak Third_Ventricle = 0.35640 (14) gca peak CSF = 0.30128 (18) gca peak Left_Accumbens_area = 0.58351 (54) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.43797 (61) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.30433 (27) gca peak Right_Accumbens_area = 0.41720 (58) gca peak Right_vessel = 0.57787 (60) gca peak Right_choroid_plexus = 0.10381 (48) gca peak Fifth_Ventricle = 0.45329 (19) gca peak WM_hypointensities = 0.17688 (83) gca peak non_WM_hypointensities = 0.11865 (54) gca peak Optic_Chiasm = 0.34833 (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 0.51 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 11423 gm and wm labels changed (%12 to gray, %88 to white out of all changed labels) 289 hippocampal voxels changed. 2 amygdala voxels changed. pass 1: 88309 changed. image ll: -2.193, PF=1.000 pass 2: 15767 changed. image ll: -2.190, PF=1.000 pass 3: 5631 changed. pass 4: 2444 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 20 minutes and 45 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/cc_up.lta sub005 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/cc_up.lta reading aseg from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/aseg.auto_noCCseg.mgz reading norm from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/norm.mgz 37418 voxels in left wm, 96637 in right wm, xrange [119, 135] searching rotation angles z=[-11 3], y=[-11 3] searching scale 1 Z rot -10.7 searching scale 1 Z rot -10.4 searching scale 1 Z rot -10.2 searching scale 1 Z rot -9.9 searching scale 1 Z rot -9.7 searching scale 1 Z rot -9.4 searching scale 1 Z rot -9.2 searching scale 1 Z rot -8.9 searching scale 1 Z rot -8.7 searching scale 1 Z rot -8.4 searching scale 1 Z rot -8.2 searching scale 1 Z rot -7.9 searching scale 1 Z rot -7.7 searching scale 1 Z rot -7.4 searching scale 1 Z rot -7.2 searching scale 1 Z rot -6.9 searching scale 1 Z rot -6.7 searching scale 1 Z rot -6.4 searching scale 1 Z rot -6.2 searching scale 1 Z rot -5.9 searching scale 1 Z rot -5.7 searching scale 1 Z rot -5.4 searching scale 1 Z rot -5.2 searching scale 1 Z rot -4.9 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.4 searching scale 1 Z rot -4.2 searching scale 1 Z rot -3.9 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.4 searching scale 1 Z rot -3.2 searching scale 1 Z rot -2.9 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.4 searching scale 1 Z rot -2.2 searching scale 1 Z rot -1.9 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.4 searching scale 1 Z rot -1.2 searching scale 1 Z rot -0.9 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.4 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.1 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.6 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.1 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.6 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.1 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.6 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.1 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.6 searching scale 1 Z rot 3.8 global minimum found at slice 129.0, rotations (-4.50, -3.17) final transformation (x=129.0, yr=-4.495, zr=-3.173): 0.995 0.055 -0.078 2.066; -0.055 0.998 0.004 50.852; 0.078 -0.000 0.997 27.169; 0.000 0.000 0.000 1.000; updating x range to be [126, 130] in xformed coordinates best xformed slice 128 cc center is found at 128 143 135 eigenvectors: -0.001 -0.003 1.000; -0.190 -0.982 -0.003; 0.982 -0.190 0.001; error in mid anterior detected - correcting... writing aseg with callosum to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/aseg.auto.mgz... corpus callosum matter segmentation took 1.7 minutes #-------------------------------------- #@# Merge ASeg Thu Aug 8 17:29:22 CEST 2013 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Thu Aug 8 17:29:22 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 2381 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 109 gm peak at 56 (56), valley at 20 (20) csf peak at 28, setting threshold to 46 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 56 (56), valley at 19 (19) csf peak at 28, setting threshold to 46 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 4 minutes and 18 seconds. #-------------------------------------------- #@# Mask BFS Thu Aug 8 17:33:42 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1476227 voxels in mask (pct= 8.80) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Thu Aug 8 17:33:44 CEST 2013 mri_segment brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (107.0): 107.1 +- 4.9 [80.0 --> 125.0] GM (67.0) : 66.0 +- 9.4 [30.0 --> 96.0] setting bottom of white matter range to 75.4 setting top of gray matter range to 84.7 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 8711 sparsely connected voxels removed... thickening thin strands.... 20 segments, 6051 filled 785 bright non-wm voxels segmented. 4744 diagonally connected voxels added... white matter segmentation took 1.8 minutes writing output to wm.seg.mgz... mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.62 minutes reading wm segmentation from wm.seg.mgz... 92 voxels added to wm to prevent paths from MTL structures to cortex 791 additional wm voxels added 0 additional wm voxels added SEG EDIT: 38026 voxels turned on, 36556 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 0 new 0 115,126,128 old 0 new 0 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 17 found - 17 modified | TOTAL: 17 pass 2 (xy+): 0 found - 17 modified | TOTAL: 17 pass 1 (xy-): 22 found - 22 modified | TOTAL: 39 pass 2 (xy-): 0 found - 22 modified | TOTAL: 39 pass 1 (yz+): 34 found - 34 modified | TOTAL: 73 pass 2 (yz+): 0 found - 34 modified | TOTAL: 73 pass 1 (yz-): 30 found - 30 modified | TOTAL: 103 pass 2 (yz-): 0 found - 30 modified | TOTAL: 103 pass 1 (xz+): 20 found - 20 modified | TOTAL: 123 pass 2 (xz+): 0 found - 20 modified | TOTAL: 123 pass 1 (xz-): 23 found - 23 modified | TOTAL: 146 pass 2 (xz-): 0 found - 23 modified | TOTAL: 146 Iteration Number : 1 pass 1 (+++): 10 found - 10 modified | TOTAL: 10 pass 2 (+++): 0 found - 10 modified | TOTAL: 10 pass 1 (+++): 12 found - 12 modified | TOTAL: 22 pass 2 (+++): 0 found - 12 modified | TOTAL: 22 pass 1 (+++): 12 found - 12 modified | TOTAL: 34 pass 2 (+++): 0 found - 12 modified | TOTAL: 34 pass 1 (+++): 11 found - 11 modified | TOTAL: 45 pass 2 (+++): 0 found - 11 modified | TOTAL: 45 Iteration Number : 1 pass 1 (++): 290 found - 290 modified | TOTAL: 290 pass 2 (++): 0 found - 290 modified | TOTAL: 290 pass 1 (+-): 235 found - 235 modified | TOTAL: 525 pass 2 (+-): 1 found - 236 modified | TOTAL: 526 pass 3 (+-): 0 found - 236 modified | TOTAL: 526 pass 1 (--): 257 found - 257 modified | TOTAL: 783 pass 2 (--): 0 found - 257 modified | TOTAL: 783 pass 1 (-+): 240 found - 240 modified | TOTAL: 1023 pass 2 (-+): 0 found - 240 modified | TOTAL: 1023 Iteration Number : 2 pass 1 (xy+): 5 found - 5 modified | TOTAL: 5 pass 2 (xy+): 0 found - 5 modified | TOTAL: 5 pass 1 (xy-): 7 found - 7 modified | TOTAL: 12 pass 2 (xy-): 0 found - 7 modified | TOTAL: 12 pass 1 (yz+): 3 found - 3 modified | TOTAL: 15 pass 2 (yz+): 0 found - 3 modified | TOTAL: 15 pass 1 (yz-): 4 found - 4 modified | TOTAL: 19 pass 2 (yz-): 0 found - 4 modified | TOTAL: 19 pass 1 (xz+): 5 found - 5 modified | TOTAL: 24 pass 2 (xz+): 0 found - 5 modified | TOTAL: 24 pass 1 (xz-): 2 found - 2 modified | TOTAL: 26 pass 2 (xz-): 0 found - 2 modified | TOTAL: 26 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 4 Iteration Number : 2 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 1 found - 1 modified | TOTAL: 2 pass 2 (--): 0 found - 1 modified | TOTAL: 2 pass 1 (-+): 1 found - 1 modified | TOTAL: 3 pass 2 (-+): 0 found - 1 modified | TOTAL: 3 Iteration Number : 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-): 1 found - 1 modified | TOTAL: 1 pass 2 (xz-): 0 found - 1 modified | TOTAL: 1 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 1248 (out of 502039: 0.248586) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Thu Aug 8 17:36:13 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.099 0.042 -0.061 -14.845; -0.028 1.149 0.325 -20.792; 0.099 -0.272 0.946 13.810; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.099 0.042 -0.061 -14.845; -0.028 1.149 0.325 -20.792; 0.099 -0.272 0.946 13.810; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 2587 (min = 350, max = 1400), aspect = 1.43 (min = 0.10, max = 0.75) need search nearby using seed (126, 116, 146), TAL = (2.0, 18.0, 12.0) talairach voxel to voxel transform 0.904 -0.017 0.065 12.161; 0.045 0.804 -0.273 21.157; -0.081 0.233 0.972 -9.785; 0.000 0.000 0.000 1.000; segmentation indicates cc at (126, 116, 146) --> (2.0, 18.0, 12.0) done. writing output to filled.mgz... filling took 0.9 minutes talairach cc position changed to (2.00, 18.00, 12.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, 18.00, 12.00) SRC: (117.19, 79.40, 150.28) search lh wm seed point around talairach space (-16.00, 18.00, 12.00), SRC: (149.73, 81.03, 147.36) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Thu Aug 8 17:37:08 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 1 found - 1 modified | TOTAL: 3 pass 2 (xy-): 0 found - 1 modified | TOTAL: 3 pass 1 (yz+): 0 found - 0 modified | TOTAL: 3 pass 1 (yz-): 1 found - 1 modified | TOTAL: 4 pass 2 (yz-): 0 found - 1 modified | TOTAL: 4 pass 1 (xz+): 1 found - 1 modified | TOTAL: 5 pass 2 (xz+): 0 found - 1 modified | TOTAL: 5 pass 1 (xz-): 3 found - 3 modified | TOTAL: 8 pass 2 (xz-): 0 found - 3 modified | TOTAL: 8 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 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 1 found - 1 modified | TOTAL: 2 pass 2 (+-): 0 found - 1 modified | TOTAL: 2 pass 1 (--): 0 found - 0 modified | TOTAL: 2 pass 1 (-+): 1 found - 1 modified | TOTAL: 3 pass 2 (-+): 0 found - 1 modified | TOTAL: 3 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 11 (out of 243070: 0.004525) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 30: 275 vertices, 334 faces slice 40: 5225 vertices, 5463 faces slice 50: 14011 vertices, 14356 faces slice 60: 25378 vertices, 25806 faces slice 70: 37928 vertices, 38377 faces slice 80: 49484 vertices, 49874 faces slice 90: 60012 vertices, 60374 faces slice 100: 71070 vertices, 71447 faces slice 110: 81719 vertices, 82133 faces slice 120: 92216 vertices, 92635 faces slice 130: 102284 vertices, 102683 faces slice 140: 112784 vertices, 113151 faces slice 150: 121893 vertices, 122235 faces slice 160: 129983 vertices, 130269 faces slice 170: 135798 vertices, 136026 faces slice 180: 140298 vertices, 140506 faces slice 190: 143125 vertices, 143245 faces slice 200: 143522 vertices, 143568 faces slice 210: 143522 vertices, 143568 faces slice 220: 143522 vertices, 143568 faces slice 230: 143522 vertices, 143568 faces slice 240: 143522 vertices, 143568 faces slice 250: 143522 vertices, 143568 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 143522 voxel in cpt #1: X=-46 [v=143522,e=430704,f=287136] located at (-27.371929, -26.230808, 38.191643) For the whole surface: X=-46 [v=143522,e=430704,f=287136] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Thu Aug 8 17:37:15 CEST 2013 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Thu Aug 8 17:37:20 CEST 2013 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts avg radius = 47.8 mm, total surface area = 74380 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.6 minutes Not saving sulc step 000: RMS=0.104 (target=0.015) step 005: RMS=0.076 (target=0.015) step 010: RMS=0.056 (target=0.015) step 015: RMS=0.047 (target=0.015) step 020: RMS=0.040 (target=0.015) step 025: RMS=0.036 (target=0.015) step 030: RMS=0.032 (target=0.015) step 035: RMS=0.029 (target=0.015) step 040: RMS=0.028 (target=0.015) step 045: RMS=0.026 (target=0.015) step 050: RMS=0.025 (target=0.015) step 055: RMS=0.025 (target=0.015) step 060: RMS=0.025 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Thu Aug 8 17:37:54 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.96 +- 0.59 (0.00-->7.70) (max @ vno 59673 --> 60711) face area 0.02 +- 0.03 (-0.22-->0.80) scaling brain by 0.302... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.621, avgs=0 005/300: dt: 0.9000, rms radial error=176.366, avgs=0 010/300: dt: 0.9000, rms radial error=175.818, avgs=0 015/300: dt: 0.9000, rms radial error=175.096, avgs=0 020/300: dt: 0.9000, rms radial error=174.271, avgs=0 025/300: dt: 0.9000, rms radial error=173.388, avgs=0 030/300: dt: 0.9000, rms radial error=172.468, avgs=0 035/300: dt: 0.9000, rms radial error=171.533, avgs=0 040/300: dt: 0.9000, rms radial error=170.590, avgs=0 045/300: dt: 0.9000, rms radial error=169.645, avgs=0 050/300: dt: 0.9000, rms radial error=168.701, avgs=0 055/300: dt: 0.9000, rms radial error=167.760, avgs=0 060/300: dt: 0.9000, rms radial error=166.822, avgs=0 065/300: dt: 0.9000, rms radial error=165.889, avgs=0 070/300: dt: 0.9000, rms radial error=164.960, avgs=0 075/300: dt: 0.9000, rms radial error=164.035, avgs=0 080/300: dt: 0.9000, rms radial error=163.116, avgs=0 085/300: dt: 0.9000, rms radial error=162.202, avgs=0 090/300: dt: 0.9000, rms radial error=161.292, avgs=0 095/300: dt: 0.9000, rms radial error=160.387, avgs=0 100/300: dt: 0.9000, rms radial error=159.487, avgs=0 105/300: dt: 0.9000, rms radial error=158.592, avgs=0 110/300: dt: 0.9000, rms radial error=157.702, avgs=0 115/300: dt: 0.9000, rms radial error=156.816, avgs=0 120/300: dt: 0.9000, rms radial error=155.935, avgs=0 125/300: dt: 0.9000, rms radial error=155.059, avgs=0 130/300: dt: 0.9000, rms radial error=154.187, avgs=0 135/300: dt: 0.9000, rms radial error=153.320, avgs=0 140/300: dt: 0.9000, rms radial error=152.458, avgs=0 145/300: dt: 0.9000, rms radial error=151.600, avgs=0 150/300: dt: 0.9000, rms radial error=150.747, avgs=0 155/300: dt: 0.9000, rms radial error=149.898, avgs=0 160/300: dt: 0.9000, rms radial error=149.055, avgs=0 165/300: dt: 0.9000, rms radial error=148.216, avgs=0 170/300: dt: 0.9000, rms radial error=147.382, avgs=0 175/300: dt: 0.9000, rms radial error=146.552, avgs=0 180/300: dt: 0.9000, rms radial error=145.727, avgs=0 185/300: dt: 0.9000, rms radial error=144.906, avgs=0 190/300: dt: 0.9000, rms radial error=144.090, avgs=0 195/300: dt: 0.9000, rms radial error=143.279, avgs=0 200/300: dt: 0.9000, rms radial error=142.471, avgs=0 205/300: dt: 0.9000, rms radial error=141.669, avgs=0 210/300: dt: 0.9000, rms radial error=140.870, avgs=0 215/300: dt: 0.9000, rms radial error=140.077, avgs=0 220/300: dt: 0.9000, rms radial error=139.287, avgs=0 225/300: dt: 0.9000, rms radial error=138.502, avgs=0 230/300: dt: 0.9000, rms radial error=137.721, avgs=0 235/300: dt: 0.9000, rms radial error=136.945, avgs=0 240/300: dt: 0.9000, rms radial error=136.172, avgs=0 245/300: dt: 0.9000, rms radial error=135.405, avgs=0 250/300: dt: 0.9000, rms radial error=134.641, avgs=0 255/300: dt: 0.9000, rms radial error=133.882, avgs=0 260/300: dt: 0.9000, rms radial error=133.127, avgs=0 265/300: dt: 0.9000, rms radial error=132.376, avgs=0 270/300: dt: 0.9000, rms radial error=131.629, avgs=0 275/300: dt: 0.9000, rms radial error=130.886, avgs=0 280/300: dt: 0.9000, rms radial error=130.148, avgs=0 285/300: dt: 0.9000, rms radial error=129.414, avgs=0 290/300: dt: 0.9000, rms radial error=128.683, avgs=0 295/300: dt: 0.9000, rms radial error=127.957, avgs=0 300/300: dt: 0.9000, rms radial error=127.235, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 17016.37 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 = 2959.58 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00002 epoch 3 (K=160.0), pass 1, starting sse = 342.52 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/11 = 0.00504 epoch 4 (K=640.0), pass 1, starting sse = 26.16 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.12/13 = 0.00932 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.08 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Thu Aug 8 17:42:53 CEST 2013 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub005 lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-46 (nv=143522, nf=287136, ne=430704, g=24) 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 13 iterations marking ambiguous vertices... 3404 ambiguous faces found in tessellation segmenting defects... 32 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 5 into 4 31 defects to be corrected 0 vertices coincident reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.8018 (-4.9009) -vertex loglikelihood: -6.6801 (-3.3400) -normal dot loglikelihood: -3.6316 (-3.6316) -quad curv loglikelihood: -6.5082 (-3.2541) Total Loglikelihood : -26.6216 CORRECTING DEFECT 0 (vertices=36, convex hull=80) After retessellation of defect 0, euler #=-28 (141428,423391,281935) : difference with theory (-28) = 0 CORRECTING DEFECT 1 (vertices=33, convex hull=67) After retessellation of defect 1, euler #=-27 (141442,423458,281989) : difference with theory (-27) = 0 CORRECTING DEFECT 2 (vertices=26, convex hull=40) After retessellation of defect 2, euler #=-26 (141444,423480,282010) : difference with theory (-26) = 0 CORRECTING DEFECT 3 (vertices=7, convex hull=30) After retessellation of defect 3, euler #=-25 (141447,423499,282027) : difference with theory (-25) = 0 CORRECTING DEFECT 4 (vertices=213, convex hull=130) After retessellation of defect 4, euler #=-23 (141496,423706,282187) : difference with theory (-24) = -1 CORRECTING DEFECT 5 (vertices=54, convex hull=64) After retessellation of defect 5, euler #=-22 (141520,423802,282260) : difference with theory (-23) = -1 CORRECTING DEFECT 6 (vertices=43, convex hull=89) After retessellation of defect 6, euler #=-21 (141536,423888,282331) : difference with theory (-22) = -1 CORRECTING DEFECT 7 (vertices=44, convex hull=76) After retessellation of defect 7, euler #=-20 (141565,424007,282422) : difference with theory (-21) = -1 CORRECTING DEFECT 8 (vertices=26, convex hull=62) After retessellation of defect 8, euler #=-19 (141582,424082,282481) : difference with theory (-20) = -1 CORRECTING DEFECT 9 (vertices=24, convex hull=68) After retessellation of defect 9, euler #=-18 (141596,424151,282537) : difference with theory (-19) = -1 CORRECTING DEFECT 10 (vertices=358, convex hull=225) After retessellation of defect 10, euler #=-17 (141611,424305,282677) : difference with theory (-18) = -1 CORRECTING DEFECT 11 (vertices=28, convex hull=57) After retessellation of defect 11, euler #=-16 (141631,424387,282740) : difference with theory (-17) = -1 CORRECTING DEFECT 12 (vertices=11, convex hull=25) After retessellation of defect 12, euler #=-15 (141634,424403,282754) : difference with theory (-16) = -1 CORRECTING DEFECT 13 (vertices=11, convex hull=30) After retessellation of defect 13, euler #=-14 (141637,424422,282771) : difference with theory (-15) = -1 CORRECTING DEFECT 14 (vertices=49, convex hull=21) After retessellation of defect 14, euler #=-13 (141638,424431,282780) : difference with theory (-14) = -1 CORRECTING DEFECT 15 (vertices=170, convex hull=93) After retessellation of defect 15, euler #=-13 (141666,424567,282888) : difference with theory (-13) = 0 CORRECTING DEFECT 16 (vertices=23, convex hull=18) After retessellation of defect 16, euler #=-12 (141672,424590,282906) : difference with theory (-12) = 0 CORRECTING DEFECT 17 (vertices=197, convex hull=176) After retessellation of defect 17, euler #=-11 (141715,424800,283074) : difference with theory (-11) = 0 CORRECTING DEFECT 18 (vertices=72, convex hull=82) After retessellation of defect 18, euler #=-10 (141744,424925,283171) : difference with theory (-10) = 0 CORRECTING DEFECT 19 (vertices=5, convex hull=19) After retessellation of defect 19, euler #=-9 (141744,424931,283178) : difference with theory (-9) = 0 CORRECTING DEFECT 20 (vertices=57, convex hull=81) After retessellation of defect 20, euler #=-8 (141770,425043,283265) : difference with theory (-8) = 0 CORRECTING DEFECT 21 (vertices=8, convex hull=9) After retessellation of defect 21, euler #=-7 (141770,425045,283268) : difference with theory (-7) = 0 CORRECTING DEFECT 22 (vertices=25, convex hull=63) After retessellation of defect 22, euler #=-6 (141787,425123,283330) : difference with theory (-6) = 0 CORRECTING DEFECT 23 (vertices=240, convex hull=50) After retessellation of defect 23, euler #=-5 (141798,425178,283375) : difference with theory (-5) = 0 CORRECTING DEFECT 24 (vertices=88, convex hull=55) After retessellation of defect 24, euler #=-4 (141813,425246,283429) : difference with theory (-4) = 0 CORRECTING DEFECT 25 (vertices=83, convex hull=104) After retessellation of defect 25, euler #=-3 (141858,425428,283567) : difference with theory (-3) = 0 CORRECTING DEFECT 26 (vertices=89, convex hull=105) After retessellation of defect 26, euler #=-2 (141884,425552,283666) : difference with theory (-2) = 0 CORRECTING DEFECT 27 (vertices=10, convex hull=34) After retessellation of defect 27, euler #=-1 (141886,425569,283682) : difference with theory (-1) = 0 CORRECTING DEFECT 28 (vertices=32, convex hull=70) After retessellation of defect 28, euler #=0 (141900,425638,283738) : difference with theory (0) = 0 CORRECTING DEFECT 29 (vertices=29, convex hull=68) After retessellation of defect 29, euler #=1 (141909,425693,283785) : difference with theory (1) = 0 CORRECTING DEFECT 30 (vertices=19, convex hull=68) After retessellation of defect 30, euler #=2 (141918,425748,283832) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.23 (0.06-->9.14) (max @ vno 60346 --> 65969) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.23 (0.06-->9.14) (max @ vno 60346 --> 65969) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 93 mutations (33.5%), 185 crossovers (66.5%), 223 vertices were eliminated building final representation... 1604 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=141918, nf=283832, ne=425748, g=0) writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 26.5 minutes 0 defective edges removing intersecting faces 000: 220 intersecting 001: 15 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 141918 - 425748 + 283832 = 2 --> 0 holes F =2V-4: 283832 = 283836-4 (0) 2E=3F: 851496 = 851496 (0) total defect index = 0 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 18 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Thu Aug 8 18:09:28 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub005 lh only generating white matter surface not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz... 16905 bright wm thresholded. 908 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.orig... computing class statistics... border white: 254363 voxels (1.52%) border gray 296177 voxels (1.77%) WM (91.0): 92.4 +- 10.3 [70.0 --> 110.0] GM (74.0) : 72.6 +- 12.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 46.3 (was 70) setting MAX_BORDER_WHITE to 114.3 (was 105) setting MIN_BORDER_WHITE to 59.0 (was 85) setting MAX_CSF to 33.6 (was 40) setting MAX_GRAY to 93.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 52.7 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 20.9 (was 40) repositioning cortical surface to gray/white boundary reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.22 (0.01-->3.88) (max @ vno 67884 --> 71912) face area 0.28 +- 0.12 (0.00-->6.13) mean absolute distance = 0.64 +- 0.75 4354 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=59 mean inside = 92.3, mean outside = 67.9 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=72.7, 45 (45) missing vertices, mean dist 0.3 [0.5 (%33.5)->0.7 (%66.5))] %74 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=snake, 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 +- 0.27 (0.04-->5.98) (max @ vno 60346 --> 65969) face area 0.28 +- 0.13 (0.00-->4.83) mean absolute distance = 0.29 +- 0.45 2871 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=7465551.0, rms=13.21 001: dt: 0.5000, sse=7823105.0, rms=9.481 (0.000%) 002: dt: 0.5000, sse=8288571.5, rms=7.465 (0.000%) 003: dt: 0.5000, sse=8446310.0, rms=6.251 (0.000%) 004: dt: 0.5000, sse=8744839.0, rms=5.521 (0.000%) 005: dt: 0.5000, sse=8775113.0, rms=5.122 (0.000%) 006: dt: 0.5000, sse=8937678.0, rms=4.871 (0.000%) 007: dt: 0.5000, sse=8850499.0, rms=4.747 (0.000%) 008: dt: 0.5000, sse=8937956.0, rms=4.631 (0.000%) rms = 4.59, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=8824802.0, rms=4.586 (0.000%) 010: dt: 0.2500, sse=5836391.5, rms=3.250 (0.000%) 011: dt: 0.2500, sse=5373295.5, rms=2.813 (0.000%) 012: dt: 0.2500, sse=5091939.5, rms=2.713 (0.000%) 013: dt: 0.2500, sse=5008144.0, rms=2.627 (0.000%) rms = 2.60, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=4908885.0, rms=2.600 (0.000%) 015: dt: 0.1250, sse=4619963.5, rms=2.301 (0.000%) rms = 2.26, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=4568109.0, rms=2.259 (0.000%) positioning took 2.1 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group mean border=76.9, 33 (3) missing vertices, mean dist -0.2 [0.3 (%77.2)->0.2 (%22.8))] %83 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.26 (0.06-->6.25) (max @ vno 60346 --> 65969) face area 0.35 +- 0.17 (0.00-->6.29) mean absolute distance = 0.21 +- 0.30 3014 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5456520.0, rms=5.76 017: dt: 0.5000, sse=5856689.5, rms=4.107 (0.000%) rms = 4.62, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=5323868.5, rms=2.954 (0.000%) 019: dt: 0.2500, sse=5138993.5, rms=2.467 (0.000%) 020: dt: 0.2500, sse=5071286.5, rms=2.113 (0.000%) rms = 2.09, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=5062744.5, rms=2.086 (0.000%) 022: dt: 0.1250, sse=4871787.0, rms=1.829 (0.000%) rms = 1.79, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=4819964.5, rms=1.785 (0.000%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=80.0, 24 (1) missing vertices, mean dist -0.1 [0.2 (%74.6)->0.2 (%25.4))] %89 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.25 (0.12-->6.37) (max @ vno 60346 --> 65969) face area 0.34 +- 0.17 (0.00-->6.20) mean absolute distance = 0.16 +- 0.25 2371 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5157340.0, rms=4.08 rms = 4.12, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=4968705.0, rms=2.871 (0.000%) 025: dt: 0.2500, sse=4855665.0, rms=1.873 (0.000%) 026: dt: 0.2500, sse=4894005.0, rms=1.737 (0.000%) 027: dt: 0.2500, sse=4925580.5, rms=1.673 (0.000%) rms = 1.73, time step reduction 2 of 3 to 0.125... 028: dt: 0.1250, sse=4866839.0, rms=1.601 (0.000%) 029: dt: 0.1250, sse=4781871.5, rms=1.520 (0.000%) rms = 1.52, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=4781871.5, rms=1.520 (0.002%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=81.0, 36 (1) missing vertices, mean dist -0.0 [0.2 (%57.8)->0.2 (%42.2))] %91 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=snake, 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=4805187.0, rms=1.86 rms = 2.87, time step reduction 1 of 3 to 0.250... 031: dt: 0.2500, sse=4889560.5, rms=1.247 (0.000%) 032: dt: 0.2500, sse=5074887.5, rms=1.124 (0.000%) rms = 1.13, time step reduction 2 of 3 to 0.125... rms = 1.11, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=5078172.0, rms=1.111 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 9 non-cortical segments detected only using segment with 1837 vertices erasing segment 1 (vno[0] = 86517) erasing segment 2 (vno[0] = 93790) erasing segment 3 (vno[0] = 100688) erasing segment 4 (vno[0] = 102748) erasing segment 5 (vno[0] = 107796) erasing segment 6 (vno[0] = 107856) erasing segment 7 (vno[0] = 108814) erasing segment 8 (vno[0] = 109084) writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/lh.cortex.label... writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.curv writing smoothed area to lh.area writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.area vertex spacing 0.90 +- 0.26 (0.06-->6.37) (max @ vno 60346 --> 65969) face area 0.34 +- 0.16 (0.00-->6.17) refinement took 6.9 minutes #-------------------------------------------- #@# Smooth2 lh Thu Aug 8 18:16:24 CEST 2013 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 lh Thu Aug 8 18:16:28 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 48.1 mm, total surface area = 86492 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.121 (target=0.015) step 005: RMS=0.082 (target=0.015) step 010: RMS=0.060 (target=0.015) step 015: RMS=0.049 (target=0.015) step 020: RMS=0.040 (target=0.015) step 025: RMS=0.034 (target=0.015) step 030: RMS=0.028 (target=0.015) step 035: RMS=0.023 (target=0.015) step 040: RMS=0.020 (target=0.015) step 045: RMS=0.018 (target=0.015) step 050: RMS=0.016 (target=0.015) step 055: RMS=0.015 (target=0.015) inflation complete. inflation took 0.5 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 156 vertices thresholded to be in k1 ~ [-0.22 1.31], k2 ~ [-0.11 0.05] total integrated curvature = 0.539*4pi (6.769) --> 0 handles ICI = 1.6, FI = 11.3, variation=188.525 116 vertices thresholded to be in [-0.04 0.01] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 106 vertices thresholded to be in [-0.14 0.28] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.017, std = 0.023 done. #----------------------------------------- #@# Curvature Stats lh Thu Aug 8 18:18:49 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub005 lh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ sub005/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 [ 252 ] Gb_filter = 0 WARN: S lookup min: -0.208057 WARN: S explicit min: 0.000000 vertex = 345 #-------------------------------------------- #@# Sphere lh Thu Aug 8 18:18:54 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 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 0.279... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=snake, 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 %21.03 pass 1: epoch 2 of 3 starting distance error %20.99 unfolding complete - removing small folds... starting distance error %20.92 removing remaining folds... final distance error %20.94 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/lh.sphere spherical transformation took 0.93 hours #-------------------------------------------- #@# Surf Reg lh Thu Aug 8 19:14:36 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts mris_register -curv ../surf/lh.sphere /opt/freesurfer/5.3.0/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /opt/freesurfer/5.3.0/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=snake, 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=snake, 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 = 0.565 curvature mean = 0.044, std = 0.936 curvature mean = 0.024, std = 0.846 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 0.00) sse = 346648.8, tmin=1.1476 d=32.00 min @ (8.00, 0.00, -8.00) sse = 268100.4, tmin=2.2979 d=16.00 min @ (0.00, 4.00, 0.00) sse = 239922.3, tmin=3.4634 d=4.00 min @ (-1.00, -1.00, 0.00) sse = 237072.4, tmin=5.8038 d=2.00 min @ (0.00, 0.50, -0.50) sse = 236492.4, tmin=6.9803 d=1.00 min @ (0.00, -0.25, 0.00) sse = 236457.6, tmin=8.1529 d=0.50 min @ (-0.12, 0.00, 0.12) sse = 236426.1, tmin=9.3353 tol=1.0e+00, sigma=0.5, host=snake, 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 9.34 min curvature mean = 0.008, std = 0.945 curvature mean = 0.012, std = 0.931 curvature mean = 0.005, std = 0.957 curvature mean = 0.006, std = 0.967 curvature mean = 0.003, std = 0.958 curvature mean = 0.002, std = 0.984 2 Reading smoothwm curvature mean = -0.023, std = 0.319 curvature mean = 0.003, std = 0.067 curvature mean = 0.075, std = 0.300 curvature mean = 0.003, std = 0.079 curvature mean = 0.035, std = 0.481 curvature mean = 0.004, std = 0.084 curvature mean = 0.018, std = 0.625 curvature mean = 0.004, std = 0.087 curvature mean = 0.007, std = 0.740 MRISregister() return, current seed 0 writing registered surface to ../surf/lh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white lh Thu Aug 8 19:42:54 CEST 2013 mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Thu Aug 8 19:42:56 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts mrisp_paint -a 5 /opt/freesurfer/5.3.0/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /opt/freesurfer/5.3.0/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Thu Aug 8 19:42:58 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub005 lh ../surf/lh.sphere.reg /opt/freesurfer/5.3.0/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /opt/freesurfer/5.3.0/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... 1217 labels changed using aseg relabeling using gibbs priors... 000: 3352 changed, 141918 examined... 001: 780 changed, 14134 examined... 002: 182 changed, 4320 examined... 003: 74 changed, 1125 examined... 004: 25 changed, 423 examined... 005: 12 changed, 157 examined... 006: 2 changed, 74 examined... 007: 3 changed, 14 examined... 008: 3 changed, 14 examined... 009: 0 changed, 17 examined... 217 labels changed using aseg 000: 129 total segments, 79 labels (294 vertices) changed 001: 51 total segments, 3 labels (8 vertices) changed 002: 48 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 53 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1496 vertices marked for relabeling... 1496 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 1 minutes and 3 seconds. #-------------------------------------------- #@# Make Pial Surf lh Thu Aug 8 19:44:01 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub005 lh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz... 16905 bright wm thresholded. 908 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.orig... computing class statistics... border white: 254363 voxels (1.52%) border gray 296177 voxels (1.77%) WM (91.0): 92.4 +- 10.3 [70.0 --> 110.0] GM (74.0) : 72.6 +- 12.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 46.3 (was 70) setting MAX_BORDER_WHITE to 114.3 (was 105) setting MIN_BORDER_WHITE to 59.0 (was 85) setting MAX_CSF to 33.6 (was 40) setting MAX_GRAY to 93.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 52.7 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 20.9 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104, GM=59 mean inside = 92.3, mean outside = 67.9 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.22 (0.01-->3.88) (max @ vno 67884 --> 71912) face area 0.28 +- 0.12 (0.00-->6.13) mean absolute distance = 0.64 +- 0.75 4354 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 5 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown deleting segment 4 with 7 points - only 0.00% unknown deleting segment 5 with 10 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown deleting segment 7 with 12 points - only 0.00% unknown deleting segment 8 with 11 points - only 0.00% unknown mean border=72.7, 45 (45) missing vertices, mean dist 0.3 [0.5 (%33.5)->0.7 (%66.5))] %74 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=snake, 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 +- 0.27 (0.04-->5.98) (max @ vno 60346 --> 65969) face area 0.28 +- 0.13 (0.00-->4.83) mean absolute distance = 0.29 +- 0.45 2898 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=7467556.5, rms=13.21 001: dt: 0.5000, sse=7823144.0, rms=9.481 (0.000%) 002: dt: 0.5000, sse=8288121.5, rms=7.465 (0.000%) 003: dt: 0.5000, sse=8444273.0, rms=6.250 (0.000%) 004: dt: 0.5000, sse=8744771.0, rms=5.521 (0.000%) 005: dt: 0.5000, sse=8774059.0, rms=5.121 (0.000%) 006: dt: 0.5000, sse=8938711.0, rms=4.871 (0.000%) 007: dt: 0.5000, sse=8848783.0, rms=4.747 (0.000%) 008: dt: 0.5000, sse=8938806.0, rms=4.631 (0.000%) rms = 4.59, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=8824362.0, rms=4.586 (0.000%) 010: dt: 0.2500, sse=5834917.0, rms=3.249 (0.000%) 011: dt: 0.2500, sse=5370926.5, rms=2.813 (0.000%) 012: dt: 0.2500, sse=5090155.0, rms=2.713 (0.000%) 013: dt: 0.2500, sse=5006923.0, rms=2.627 (0.000%) rms = 2.60, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=4908233.0, rms=2.600 (0.000%) 015: dt: 0.1250, sse=4618744.5, rms=2.301 (0.000%) rms = 2.26, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=4566825.0, rms=2.259 (0.000%) positioning took 2.0 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 5 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 3 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 6 with 1 points - only 0.00% unknown deleting segment 8 with 7 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 12 with 5 points - only 0.00% unknown deleting segment 16 with 10 points - only 0.00% unknown deleting segment 17 with 26 points - only 0.00% unknown deleting segment 18 with 13 points - only 0.00% unknown mean border=76.9, 33 (3) missing vertices, mean dist -0.2 [0.3 (%77.2)->0.2 (%22.8))] %83 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.26 (0.06-->6.25) (max @ vno 60346 --> 65969) face area 0.35 +- 0.17 (0.00-->6.29) mean absolute distance = 0.21 +- 0.31 3043 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5461817.5, rms=5.76 017: dt: 0.5000, sse=5862041.5, rms=4.109 (0.000%) rms = 4.62, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=5328916.0, rms=2.957 (0.000%) 019: dt: 0.2500, sse=5143362.5, rms=2.471 (0.000%) 020: dt: 0.2500, sse=5076333.5, rms=2.117 (0.000%) rms = 2.09, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=5067423.0, rms=2.090 (0.000%) 022: dt: 0.1250, sse=4876173.5, rms=1.833 (0.000%) rms = 1.79, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=4825049.0, rms=1.789 (0.000%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 5 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown deleting segment 6 with 12 points - only 0.00% unknown deleting segment 7 with 6 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 9 points - only 0.00% unknown deleting segment 11 with 10 points - only 0.00% unknown deleting segment 12 with 10 points - only 0.00% unknown deleting segment 13 with 23 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 14 with 2 points - only 0.00% unknown deleting segment 15 with 13 points - only 0.00% unknown mean border=80.0, 26 (1) missing vertices, mean dist -0.1 [0.2 (%74.6)->0.2 (%25.4))] %89 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.25 (0.12-->6.37) (max @ vno 60346 --> 65969) face area 0.34 +- 0.17 (0.00-->6.20) mean absolute distance = 0.16 +- 0.25 2374 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5162456.5, rms=4.07 rms = 4.12, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=4973562.0, rms=2.871 (0.000%) 025: dt: 0.2500, sse=4860126.5, rms=1.874 (0.000%) 026: dt: 0.2500, sse=4898094.5, rms=1.739 (0.000%) 027: dt: 0.2500, sse=4930149.0, rms=1.674 (0.000%) rms = 1.74, time step reduction 2 of 3 to 0.125... 028: dt: 0.1250, sse=4871542.5, rms=1.603 (0.000%) 029: dt: 0.1250, sse=4786188.0, rms=1.522 (0.000%) rms = 1.52, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=4786188.0, rms=1.522 (0.002%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 7 points - only 0.00% unknown deleting segment 1 with 5 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 1 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 12 points - only 0.00% unknown deleting segment 6 with 8 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 9 points - only 0.00% unknown deleting segment 9 with 10 points - only 0.00% unknown deleting segment 10 with 26 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 11 with 2 points - only 0.00% unknown deleting segment 12 with 13 points - only 0.00% unknown mean border=81.0, 37 (1) missing vertices, mean dist -0.0 [0.2 (%57.8)->0.2 (%42.2))] %91 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=snake, 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=4809803.0, rms=1.86 rms = 2.87, time step reduction 1 of 3 to 0.250... 031: dt: 0.2500, sse=4895558.5, rms=1.248 (0.000%) 032: dt: 0.2500, sse=5083564.5, rms=1.125 (0.000%) rms = 1.13, time step reduction 2 of 3 to 0.125... rms = 1.11, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=5086603.5, rms=1.112 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... smoothing surface for 5 iterations... mean border=48.8, 50 (50) missing vertices, mean dist 1.7 [0.1 (%0.0)->2.4 (%100.0))] %14 local maxima, %53 large gradients and %29 min vals, 2134 gradients ignored tol=1.0e-04, sigma=2.0, host=snake, 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=30289990.0, rms=31.59 001: dt: 0.5000, sse=21800954.0, rms=26.170 (0.000%) 002: dt: 0.5000, sse=15971152.0, rms=21.701 (0.000%) 003: dt: 0.5000, sse=12148614.0, rms=18.115 (0.000%) 004: dt: 0.5000, sse=9780426.0, rms=15.278 (0.000%) 005: dt: 0.5000, sse=8437585.0, rms=13.078 (0.000%) 006: dt: 0.5000, sse=7662182.0, rms=11.387 (0.000%) 007: dt: 0.5000, sse=7225883.0, rms=9.970 (0.000%) 008: dt: 0.5000, sse=6913676.0, rms=8.697 (0.000%) 009: dt: 0.5000, sse=6786730.5, rms=7.576 (0.000%) 010: dt: 0.5000, sse=6749302.0, rms=6.605 (0.000%) 011: dt: 0.5000, sse=6830642.0, rms=5.824 (0.000%) 012: dt: 0.5000, sse=6971648.0, rms=5.217 (0.000%) 013: dt: 0.5000, sse=7091683.0, rms=4.818 (0.000%) 014: dt: 0.5000, sse=7275634.5, rms=4.533 (0.000%) 015: dt: 0.5000, sse=7341044.0, rms=4.376 (0.000%) 016: dt: 0.5000, sse=7434937.0, rms=4.253 (0.000%) 017: dt: 0.5000, sse=7446205.5, rms=4.195 (0.000%) 018: dt: 0.5000, sse=7537203.0, rms=4.118 (0.000%) rms = 4.08, time step reduction 1 of 3 to 0.250... 019: dt: 0.5000, sse=7507748.0, rms=4.084 (0.000%) 020: dt: 0.2500, sse=5595185.5, rms=3.491 (0.000%) 021: dt: 0.2500, sse=5435547.5, rms=3.331 (0.000%) rms = 3.31, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=5313698.0, rms=3.315 (0.000%) 023: dt: 0.1250, sse=5111725.5, rms=3.205 (0.000%) rms = 3.19, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=5080553.5, rms=3.191 (0.000%) positioning took 3.0 minutes mean border=46.7, 968 (6) missing vertices, mean dist 0.2 [0.2 (%49.6)->0.7 (%50.4))] %31 local maxima, %41 large gradients and %24 min vals, 755 gradients ignored tol=1.0e-04, sigma=1.0, host=snake, 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=5729900.0, rms=4.94 025: dt: 0.5000, sse=6068042.5, rms=4.384 (0.000%) 026: dt: 0.5000, sse=7701572.0, rms=4.262 (0.000%) rms = 4.25, time step reduction 1 of 3 to 0.250... 027: dt: 0.5000, sse=7383714.0, rms=4.246 (0.000%) 028: dt: 0.2500, sse=6186324.5, rms=3.485 (0.000%) 029: dt: 0.2500, sse=6044504.0, rms=3.247 (0.000%) rms = 3.22, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=5939641.0, rms=3.225 (0.000%) 031: dt: 0.1250, sse=5726174.5, rms=3.064 (0.000%) rms = 3.04, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=5701814.5, rms=3.035 (0.000%) positioning took 1.0 minutes mean border=44.5, 1143 (6) missing vertices, mean dist 0.1 [0.2 (%38.5)->0.4 (%61.5))] %50 local maxima, %21 large gradients and %24 min vals, 972 gradients ignored tol=1.0e-04, sigma=0.5, host=snake, 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=5982376.5, rms=4.27 033: dt: 0.5000, sse=6237107.0, rms=4.116 (0.000%) rms = 4.08, time step reduction 1 of 3 to 0.250... 034: dt: 0.5000, sse=8157539.0, rms=4.081 (0.000%) 035: dt: 0.2500, sse=6246182.0, rms=3.293 (0.000%) 036: dt: 0.2500, sse=6389504.5, rms=3.050 (0.000%) rms = 3.06, time step reduction 2 of 3 to 0.125... 037: dt: 0.1250, sse=6265465.5, rms=2.968 (0.000%) 038: dt: 0.1250, sse=6056920.0, rms=2.853 (0.000%) rms = 2.83, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=6003770.5, rms=2.835 (0.000%) positioning took 1.0 minutes mean border=43.4, 2406 (4) missing vertices, mean dist 0.1 [0.2 (%44.6)->0.3 (%55.4))] %54 local maxima, %17 large gradients and %24 min vals, 744 gradients ignored tol=1.0e-04, sigma=0.2, host=snake, 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=6071459.0, rms=3.22 rms = 3.84, time step reduction 1 of 3 to 0.250... 040: dt: 0.2500, sse=5918450.0, rms=2.969 (0.000%) 041: dt: 0.2500, sse=6100094.5, rms=2.889 (0.000%) rms = 2.87, time step reduction 2 of 3 to 0.125... 042: dt: 0.2500, sse=6193060.5, rms=2.868 (0.000%) 043: dt: 0.1250, sse=6082456.0, rms=2.754 (0.000%) rms = 2.73, time step reduction 3 of 3 to 0.062... 044: dt: 0.1250, sse=6088207.0, rms=2.734 (0.000%) positioning took 0.7 minutes writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.area.pial vertex spacing 1.03 +- 0.44 (0.06-->9.25) (max @ vno 100866 --> 99891) face area 0.42 +- 0.32 (0.00-->11.30) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 141918 vertices processed 25000 of 141918 vertices processed 50000 of 141918 vertices processed 75000 of 141918 vertices processed 100000 of 141918 vertices processed 125000 of 141918 vertices processed 0 of 141918 vertices processed 25000 of 141918 vertices processed 50000 of 141918 vertices processed 75000 of 141918 vertices processed 100000 of 141918 vertices processed 125000 of 141918 vertices processed thickness calculation complete, 398:1170 truncations. 26237 vertices at 0 distance 88713 vertices at 1 distance 94532 vertices at 2 distance 43911 vertices at 3 distance 13606 vertices at 4 distance 3907 vertices at 5 distance 1120 vertices at 6 distance 387 vertices at 7 distance 191 vertices at 8 distance 98 vertices at 9 distance 53 vertices at 10 distance 43 vertices at 11 distance 26 vertices at 12 distance 28 vertices at 13 distance 16 vertices at 14 distance 19 vertices at 15 distance 27 vertices at 16 distance 17 vertices at 17 distance 6 vertices at 18 distance 9 vertices at 19 distance 14 vertices at 20 distance writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.thickness positioning took 13.8 minutes #-------------------------------------------- #@# Surf Volume lh Thu Aug 8 19:57:51 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.volume lh.area.mid mul lh.thickness Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# WM/GM Contrast lh Thu Aug 8 19:57:51 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts pctsurfcon --s sub005 --lh-only Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts/pctsurfcon.log Thu Aug 8 19:57:51 CEST 2013 setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts /opt/freesurfer/5.3.0/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux snake4 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux FREESURFER_HOME /opt/freesurfer/5.3.0 mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/tmp.pctsurfcon.32269/lh.wm.mgh --regheader sub005 --cortex srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig.mgz as target reference. Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/lh.cortex.label Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 = 109466 Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/lh.cortex.label Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/tmp.pctsurfcon.32269/lh.wm.mgh Dim: 141918 1 1 mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/tmp.pctsurfcon.32269/lh.gm.mgh --projfrac 0.3 --regheader sub005 --cortex srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig.mgz as target reference. Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/lh.cortex.label Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white Done reading source surface Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 = 126137 Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/lh.cortex.label Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/tmp.pctsurfcon.32269/lh.gm.mgh Dim: 141918 1 1 mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/tmp.pctsurfcon.32269/lh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/tmp.pctsurfcon.32269/lh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.w-g.pct.mgh mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.w-g.pct.mgh --annot sub005 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.w-g.pct.mgh --annot sub005 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/stats/lh.w-g.pct.stats --snr sysname Linux hostname snake4 machine x86_64 user fkaule 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.w-g.pct.mgh Vertex Area is 0.670531 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 1000 unknown 0 0.000 1 1001 bankssts 1722 1207.068 2 1002 caudalanteriorcingulate 877 616.236 3 1003 caudalmiddlefrontal 3619 2446.539 4 1004 corpuscallosum 0 0.000 5 1005 cuneus 2565 1689.801 6 1006 entorhinal 606 428.386 7 1007 fusiform 4512 3134.628 8 1008 inferiorparietal 6034 3977.454 9 1009 inferiortemporal 5113 3484.146 10 1010 isthmuscingulate 1632 1065.528 11 1011 lateraloccipital 9016 5810.531 12 1012 lateralorbitofrontal 4111 2725.845 13 1013 lingual 5608 3867.486 14 1014 medialorbitofrontal 2772 1890.563 15 1015 middletemporal 4814 3256.627 16 1016 parahippocampal 926 622.722 17 1017 paracentral 1973 1270.574 18 1018 parsopercularis 2922 1995.094 19 1019 parsorbitalis 1048 686.831 20 1020 parstriangularis 2076 1369.012 21 1021 pericalcarine 2558 1771.464 22 1022 postcentral 7081 4667.076 23 1023 posteriorcingulate 1867 1243.578 24 1024 precentral 6904 4575.087 25 1025 precuneus 5653 3799.979 26 1026 rostralanteriorcingulate 1532 1033.005 27 1027 rostralmiddlefrontal 8995 6119.219 28 1028 superiorfrontal 11617 7997.352 29 1029 superiorparietal 8754 5766.701 30 1030 superiortemporal 6406 4413.473 31 1031 supramarginal 5764 3893.233 32 1032 frontalpole 418 251.037 33 1033 temporalpole 837 553.961 34 1034 transversetemporal 822 507.131 35 1035 insula 3345 2193.028 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats lh Thu Aug 8 19:58:04 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab sub005 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 1722 1207 2999 2.567 0.457 0.135 0.038 20 2.6 bankssts 877 616 1558 2.320 0.599 0.145 0.045 16 1.5 caudalanteriorcingulate 3619 2447 6845 2.489 0.417 0.140 0.042 51 6.3 caudalmiddlefrontal 2565 1690 4212 2.219 0.475 0.166 0.064 57 7.2 cuneus 606 428 2268 3.682 0.648 0.171 0.072 11 1.9 entorhinal 4512 3135 9751 2.761 0.589 0.161 0.060 88 10.9 fusiform 6034 3977 11629 2.586 0.463 0.147 0.059 122 12.9 inferiorparietal 5113 3484 11423 2.753 0.658 0.160 0.089 143 15.3 inferiortemporal 1632 1066 3029 2.570 0.730 0.165 0.074 38 4.5 isthmuscingulate 9016 5811 14639 2.251 0.483 0.160 0.071 215 24.2 lateraloccipital 4111 2726 8158 2.581 0.671 0.158 0.070 97 10.8 lateralorbitofrontal 5608 3867 9904 2.311 0.556 0.175 0.077 134 17.1 lingual 2772 1891 5268 2.243 0.856 0.190 0.115 142 10.7 medialorbitofrontal 4814 3257 11042 2.672 0.611 0.156 0.070 117 12.8 middletemporal 926 623 2362 3.298 0.667 0.155 0.062 20 2.2 parahippocampal 1973 1271 3634 2.482 0.539 0.128 0.041 26 3.2 paracentral 2922 1995 6104 2.625 0.434 0.151 0.056 54 6.6 parsopercularis 1048 687 2215 2.421 0.659 0.171 0.076 29 2.8 parsorbitalis 2076 1369 3814 2.470 0.558 0.148 0.056 38 4.5 parstriangularis 2558 1771 3523 2.023 0.528 0.164 0.076 45 7.3 pericalcarine 7081 4667 12024 2.211 0.588 0.146 0.053 132 14.9 postcentral 1867 1244 3475 2.633 0.551 0.169 0.124 149 5.1 posteriorcingulate 6904 4575 13529 2.642 0.519 0.128 0.056 105 16.4 precentral 5653 3800 10487 2.603 0.500 0.153 0.062 113 13.2 precuneus 1532 1033 3300 2.736 0.720 0.153 0.061 33 3.9 rostralanteriorcingulate 8995 6119 16203 2.242 0.560 0.179 0.095 275 32.4 rostralmiddlefrontal 11617 7997 23675 2.528 0.561 0.148 0.053 215 24.3 superiorfrontal 8754 5767 14762 2.282 0.417 0.139 0.064 296 28.4 superiorparietal 6406 4413 14656 2.846 0.591 0.150 0.051 126 13.8 superiortemporal 5764 3893 11519 2.656 0.490 0.152 0.064 113 14.9 supramarginal 418 251 782 2.194 0.751 0.219 0.132 26 2.2 frontalpole 837 554 2851 3.583 0.651 0.154 0.072 15 2.6 temporalpole 822 507 1644 2.808 0.362 0.145 0.049 13 1.6 transversetemporal 3345 2193 7111 3.161 0.837 0.124 0.068 55 7.9 insula #----------------------------------------- #@# Cortical Parc 2 lh Thu Aug 8 19:58:23 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub005 lh ../surf/lh.sphere.reg /opt/freesurfer/5.3.0/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /opt/freesurfer/5.3.0/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... 52 labels changed using aseg relabeling using gibbs priors... 000: 9826 changed, 141918 examined... 001: 2460 changed, 37405 examined... 002: 781 changed, 12468 examined... 003: 300 changed, 4185 examined... 004: 116 changed, 1682 examined... 005: 71 changed, 654 examined... 006: 42 changed, 404 examined... 007: 21 changed, 221 examined... 008: 19 changed, 124 examined... 009: 14 changed, 92 examined... 010: 5 changed, 61 examined... 011: 0 changed, 25 examined... 14 labels changed using aseg 000: 310 total segments, 227 labels (2923 vertices) changed 001: 105 total segments, 22 labels (72 vertices) changed 002: 83 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 154 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 849 vertices marked for relabeling... 849 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 1 minutes and 12 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Thu Aug 8 19:59:34 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab sub005 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 1378 920 2400 2.108 0.663 0.191 0.113 51 5.6 G_and_S_frontomargin 2137 1388 4192 2.534 0.497 0.172 0.075 48 5.4 G_and_S_occipital_inf 1433 892 2756 2.463 0.533 0.143 0.113 38 6.4 G_and_S_paracentral 1687 1137 3728 2.800 0.498 0.158 0.057 34 4.1 G_and_S_subcentral 855 564 1523 2.088 0.539 0.203 0.151 37 4.2 G_and_S_transv_frontopol 2884 1986 5490 2.523 0.718 0.150 0.053 53 6.2 G_and_S_cingul-Ant 1436 1023 2855 2.592 0.537 0.137 0.060 35 3.0 G_and_S_cingul-Mid-Ant 1437 979 2702 2.627 0.433 0.134 0.045 20 2.4 G_and_S_cingul-Mid-Post 555 371 1371 2.977 0.492 0.198 0.098 20 2.4 G_cingul-Post-dorsal 419 269 860 2.553 0.872 0.173 0.087 12 1.2 G_cingul-Post-ventral 2319 1544 3782 2.101 0.476 0.179 0.077 60 7.8 G_cuneus 1839 1236 4307 2.751 0.443 0.163 0.065 43 4.6 G_front_inf-Opercular 308 188 818 2.873 0.439 0.169 0.063 8 0.8 G_front_inf-Orbital 1298 865 3033 2.748 0.476 0.179 0.087 38 4.4 G_front_inf-Triangul 4376 2983 9909 2.551 0.482 0.185 0.093 148 16.4 G_front_middle 7586 5135 17357 2.653 0.542 0.158 0.062 165 18.4 G_front_sup 411 247 1034 3.697 0.833 0.128 0.069 7 1.1 G_Ins_lg_and_S_cent_ins 828 506 2535 3.749 0.786 0.155 0.139 31 3.8 G_insular_short 2469 1549 5012 2.536 0.418 0.169 0.073 82 7.4 G_occipital_middle 2099 1345 3730 2.273 0.505 0.156 0.146 193 17.5 G_occipital_sup 1349 941 3454 2.830 0.453 0.187 0.076 39 4.3 G_oc-temp_lat-fusifor 3839 2584 7020 2.335 0.577 0.194 0.094 113 14.3 G_oc-temp_med-Lingual 1312 897 3979 3.324 0.692 0.165 0.067 27 3.5 G_oc-temp_med-Parahip 2634 1745 6352 2.661 0.726 0.185 0.099 93 9.7 G_orbital 2305 1493 5492 2.809 0.400 0.165 0.077 71 6.6 G_pariet_inf-Angular 2786 1914 6816 2.834 0.494 0.168 0.076 73 8.7 G_pariet_inf-Supramar 2945 1960 5603 2.359 0.396 0.152 0.054 64 6.3 G_parietal_sup 2788 1803 5312 2.286 0.517 0.158 0.062 70 6.5 G_postcentral 2489 1608 6267 2.854 0.473 0.136 0.055 45 5.8 G_precentral 2128 1440 5062 2.863 0.443 0.178 0.079 62 5.9 G_precuneus 971 642 2029 2.161 0.743 0.225 0.136 84 4.3 G_rectus 386 280 996 3.136 0.819 0.243 0.230 31 2.8 G_subcallosal 735 447 1700 2.922 0.329 0.159 0.055 14 1.6 G_temp_sup-G_T_transv 2548 1741 7321 3.120 0.549 0.182 0.076 81 7.6 G_temp_sup-Lateral 809 613 2338 3.316 0.753 0.145 0.048 11 1.7 G_temp_sup-Plan_polar 1099 752 2287 2.648 0.476 0.123 0.046 15 1.8 G_temp_sup-Plan_tempo 2622 1759 6914 2.844 0.720 0.181 0.122 105 10.3 G_temporal_inf 3152 2141 8157 2.712 0.602 0.168 0.078 90 8.9 G_temporal_middle 334 216 424 2.220 0.372 0.102 0.028 2 0.3 Lat_Fis-ant-Horizont 313 216 569 2.707 0.398 0.136 0.039 3 0.6 Lat_Fis-ant-Vertical 1254 838 1702 2.478 0.385 0.130 0.039 13 2.1 Lat_Fis-post 2689 1680 3876 2.019 0.502 0.168 0.094 82 9.5 Pole_occipital 2203 1485 7022 3.451 0.652 0.174 0.087 58 7.3 Pole_temporal 3185 2225 4539 2.107 0.553 0.147 0.063 49 7.5 S_calcarine 3244 2207 4057 1.992 0.570 0.120 0.032 25 4.5 S_central 1047 695 1580 2.329 0.491 0.158 0.064 22 2.4 S_cingul-Marginalis 517 342 915 2.774 0.424 0.099 0.024 2 0.6 S_circular_insula_ant 1382 936 2162 2.717 0.609 0.098 0.022 7 1.3 S_circular_insula_inf 1891 1288 2962 2.584 0.481 0.113 0.035 14 2.6 S_circular_insula_sup 1249 895 2023 2.493 0.408 0.110 0.022 9 1.2 S_collat_transv_ant 641 434 732 2.152 0.335 0.154 0.049 9 1.3 S_collat_transv_post 2379 1609 3381 2.168 0.452 0.139 0.041 32 4.1 S_front_inf 1677 1160 2496 2.029 0.499 0.158 0.078 34 5.0 S_front_middle 3655 2520 5939 2.264 0.444 0.140 0.040 55 6.0 S_front_sup 283 196 376 2.214 0.280 0.120 0.024 2 0.4 S_interm_prim-Jensen 2513 1694 3835 2.315 0.343 0.135 0.040 33 3.9 S_intrapariet_and_P_trans 1281 890 1710 2.027 0.401 0.140 0.039 14 2.1 S_oc_middle_and_Lunatus 1579 1040 2518 2.320 0.388 0.145 0.048 24 3.1 S_oc_sup_and_transversal 1113 759 1706 2.322 0.394 0.128 0.040 12 1.6 S_occipital_ant 815 566 1243 2.458 0.445 0.143 0.051 11 1.5 S_oc-temp_lat 2022 1442 3743 2.711 0.603 0.141 0.044 29 3.5 S_oc-temp_med_and_Lingual 349 244 476 1.709 0.481 0.160 0.054 7 0.7 S_orbital_lateral 869 577 1213 2.181 0.985 0.114 0.031 7 1.0 S_orbital_med-olfact 1647 1094 2575 2.338 0.505 0.148 0.058 25 3.4 S_orbital-H_Shaped 2922 1941 4366 2.454 0.442 0.127 0.036 30 4.4 S_parieto_occipital 1242 762 1435 2.260 0.699 0.150 0.130 119 2.8 S_pericallosal 3378 2213 4710 2.252 0.418 0.122 0.038 33 5.3 S_postcentral 1443 960 2116 2.453 0.379 0.110 0.025 11 1.6 S_precentral-inf-part 1417 987 2064 2.378 0.371 0.114 0.033 13 2.1 S_precentral-sup-part 727 499 1459 2.366 0.805 0.193 0.111 25 3.0 S_suborbital 908 626 1673 2.536 0.422 0.148 0.061 14 2.4 S_subparietal 1618 1090 2551 2.494 0.570 0.140 0.044 20 3.1 S_temporal_inf 5634 3826 9162 2.498 0.446 0.129 0.046 71 10.2 S_temporal_sup 428 292 591 2.311 0.348 0.129 0.038 4 0.7 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Thu Aug 8 19:59:53 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub005 lh ../surf/lh.sphere.reg /opt/freesurfer/5.3.0/average/lh.DKTatlas40.gcs ../label/lh.aparc.DKTatlas40.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /opt/freesurfer/5.3.0/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... 885 labels changed using aseg relabeling using gibbs priors... 000: 2945 changed, 141918 examined... 001: 688 changed, 12520 examined... 002: 204 changed, 3815 examined... 003: 64 changed, 1156 examined... 004: 29 changed, 370 examined... 005: 19 changed, 181 examined... 006: 6 changed, 103 examined... 007: 5 changed, 33 examined... 008: 6 changed, 29 examined... 009: 4 changed, 32 examined... 010: 2 changed, 24 examined... 011: 2 changed, 13 examined... 012: 0 changed, 9 examined... 120 labels changed using aseg 000: 76 total segments, 43 labels (294 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 50 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 548 vertices marked for relabeling... 548 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas40.annot... classification took 1 minutes and 3 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Thu Aug 8 20:00:57 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts 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 sub005 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 1671 1153 3163 2.490 0.601 0.142 0.052 38 2.9 caudalanteriorcingulate 3626 2449 6864 2.490 0.417 0.139 0.042 51 6.3 caudalmiddlefrontal 3762 2482 6201 2.243 0.484 0.158 0.060 76 9.5 cuneus 573 410 2117 3.651 0.657 0.175 0.072 11 1.7 entorhinal 3815 2663 7446 2.660 0.490 0.157 0.055 70 8.5 fusiform 5685 3744 10981 2.586 0.459 0.147 0.059 117 12.1 inferiorparietal 5444 3708 13060 2.824 0.711 0.162 0.090 152 16.7 inferiortemporal 1575 1036 2928 2.568 0.738 0.167 0.075 37 4.5 isthmuscingulate 9358 6044 15353 2.247 0.493 0.159 0.071 223 24.8 lateraloccipital 4491 2954 8915 2.535 0.742 0.168 0.086 129 13.8 lateralorbitofrontal 5567 3840 9821 2.313 0.551 0.175 0.077 132 16.9 lingual 2370 1617 4625 2.223 0.858 0.199 0.125 137 10.1 medialorbitofrontal 6389 4331 13618 2.615 0.587 0.151 0.062 136 15.6 middletemporal 950 640 2411 3.280 0.675 0.156 0.061 21 2.3 parahippocampal 2314 1496 4189 2.477 0.514 0.126 0.041 29 3.8 paracentral 2616 1773 5364 2.620 0.442 0.151 0.058 51 6.0 parsopercularis 1199 780 2457 2.532 0.517 0.141 0.050 21 2.4 parsorbitalis 2606 1746 4857 2.452 0.549 0.150 0.055 47 5.9 parstriangularis 2555 1773 3550 2.032 0.526 0.161 0.073 44 7.0 pericalcarine 7867 5196 13271 2.227 0.579 0.147 0.053 144 16.6 postcentral 1950 1311 3572 2.629 0.520 0.165 0.111 139 5.0 posteriorcingulate 6928 4596 13547 2.643 0.516 0.127 0.055 104 16.4 precentral 5405 3636 10347 2.613 0.499 0.154 0.063 110 13.0 precuneus 1926 1309 4152 2.719 0.746 0.156 0.062 42 4.8 rostralanteriorcingulate 5870 3989 10343 2.256 0.562 0.176 0.088 170 20.5 rostralmiddlefrontal 13343 9154 26756 2.445 0.580 0.157 0.066 300 33.3 superiorfrontal 6797 4449 11473 2.299 0.410 0.140 0.069 268 24.9 superiorparietal 8836 6083 20519 2.901 0.635 0.150 0.054 166 19.6 superiortemporal 5438 3668 10765 2.660 0.490 0.151 0.064 107 14.1 supramarginal 775 478 1556 2.808 0.357 0.144 0.049 12 1.4 transversetemporal 2798 1822 6173 3.228 0.806 0.120 0.069 46 6.8 insula #-------------------------------------------- #@# Tessellate rh Thu Aug 8 20:01:16 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 1 found - 1 modified | TOTAL: 4 pass 2 (xy-): 0 found - 1 modified | TOTAL: 4 pass 1 (yz+): 0 found - 0 modified | TOTAL: 4 pass 1 (yz-): 6 found - 6 modified | TOTAL: 10 pass 2 (yz-): 0 found - 6 modified | TOTAL: 10 pass 1 (xz+): 0 found - 0 modified | TOTAL: 10 pass 1 (xz-): 1 found - 1 modified | TOTAL: 11 pass 2 (xz-): 0 found - 1 modified | TOTAL: 11 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 3 found - 3 modified | TOTAL: 3 pass 2 (--): 0 found - 3 modified | TOTAL: 3 pass 1 (-+): 1 found - 1 modified | TOTAL: 4 pass 2 (-+): 0 found - 1 modified | TOTAL: 4 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 = 15 (out of 240260: 0.006243) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 40: 1452 vertices, 1594 faces slice 50: 7719 vertices, 8000 faces slice 60: 16737 vertices, 17128 faces slice 70: 28710 vertices, 29125 faces slice 80: 40003 vertices, 40388 faces slice 90: 51408 vertices, 51787 faces slice 100: 62316 vertices, 62685 faces slice 110: 72926 vertices, 73310 faces slice 120: 83757 vertices, 84160 faces slice 130: 94781 vertices, 95175 faces slice 140: 106061 vertices, 106508 faces slice 150: 117008 vertices, 117377 faces slice 160: 126598 vertices, 126940 faces slice 170: 133174 vertices, 133404 faces slice 180: 138488 vertices, 138680 faces slice 190: 142387 vertices, 142536 faces slice 200: 143688 vertices, 143714 faces slice 210: 143688 vertices, 143714 faces slice 220: 143688 vertices, 143714 faces slice 230: 143688 vertices, 143714 faces slice 240: 143688 vertices, 143714 faces slice 250: 143688 vertices, 143714 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 143688 voxel in cpt #1: X=-26 [v=143688,e=431142,f=287428] located at (24.793489, -19.142183, 42.190880) For the whole surface: X=-26 [v=143688,e=431142,f=287428] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Thu Aug 8 20:01:23 CEST 2013 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 rh Thu Aug 8 20:01:28 CEST 2013 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts avg radius = 46.7 mm, total surface area = 74244 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.7 minutes Not saving sulc step 000: RMS=0.103 (target=0.015) step 005: RMS=0.075 (target=0.015) step 010: RMS=0.054 (target=0.015) step 015: RMS=0.045 (target=0.015) step 020: RMS=0.039 (target=0.015) step 025: RMS=0.034 (target=0.015) step 030: RMS=0.030 (target=0.015) step 035: RMS=0.028 (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=0.022 (target=0.015) step 060: RMS=0.022 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Thu Aug 8 20:02:08 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.97 +- 0.58 (0.00-->6.28) (max @ vno 59778 --> 60967) face area 0.02 +- 0.03 (-0.07-->0.60) scaling brain by 0.306... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.619, avgs=0 005/300: dt: 0.9000, rms radial error=176.360, avgs=0 010/300: dt: 0.9000, rms radial error=175.805, avgs=0 015/300: dt: 0.9000, rms radial error=175.076, avgs=0 020/300: dt: 0.9000, rms radial error=174.245, avgs=0 025/300: dt: 0.9000, rms radial error=173.354, avgs=0 030/300: dt: 0.9000, rms radial error=172.432, avgs=0 035/300: dt: 0.9000, rms radial error=171.492, avgs=0 040/300: dt: 0.9000, rms radial error=170.546, avgs=0 045/300: dt: 0.9000, rms radial error=169.603, avgs=0 050/300: dt: 0.9000, rms radial error=168.661, avgs=0 055/300: dt: 0.9000, rms radial error=167.721, avgs=0 060/300: dt: 0.9000, rms radial error=166.784, avgs=0 065/300: dt: 0.9000, rms radial error=165.852, avgs=0 070/300: dt: 0.9000, rms radial error=164.924, avgs=0 075/300: dt: 0.9000, rms radial error=164.000, avgs=0 080/300: dt: 0.9000, rms radial error=163.082, avgs=0 085/300: dt: 0.9000, rms radial error=162.168, avgs=0 090/300: dt: 0.9000, rms radial error=161.259, avgs=0 095/300: dt: 0.9000, rms radial error=160.355, avgs=0 100/300: dt: 0.9000, rms radial error=159.456, avgs=0 105/300: dt: 0.9000, rms radial error=158.562, avgs=0 110/300: dt: 0.9000, rms radial error=157.673, avgs=0 115/300: dt: 0.9000, rms radial error=156.788, avgs=0 120/300: dt: 0.9000, rms radial error=155.909, avgs=0 125/300: dt: 0.9000, rms radial error=155.034, avgs=0 130/300: dt: 0.9000, rms radial error=154.163, avgs=0 135/300: dt: 0.9000, rms radial error=153.298, avgs=0 140/300: dt: 0.9000, rms radial error=152.437, avgs=0 145/300: dt: 0.9000, rms radial error=151.581, avgs=0 150/300: dt: 0.9000, rms radial error=150.730, avgs=0 155/300: dt: 0.9000, rms radial error=149.883, avgs=0 160/300: dt: 0.9000, rms radial error=149.040, avgs=0 165/300: dt: 0.9000, rms radial error=148.203, avgs=0 170/300: dt: 0.9000, rms radial error=147.370, avgs=0 175/300: dt: 0.9000, rms radial error=146.541, avgs=0 180/300: dt: 0.9000, rms radial error=145.717, avgs=0 185/300: dt: 0.9000, rms radial error=144.898, avgs=0 190/300: dt: 0.9000, rms radial error=144.083, avgs=0 195/300: dt: 0.9000, rms radial error=143.273, avgs=0 200/300: dt: 0.9000, rms radial error=142.467, avgs=0 205/300: dt: 0.9000, rms radial error=141.665, avgs=0 210/300: dt: 0.9000, rms radial error=140.868, avgs=0 215/300: dt: 0.9000, rms radial error=140.075, avgs=0 220/300: dt: 0.9000, rms radial error=139.286, avgs=0 225/300: dt: 0.9000, rms radial error=138.502, avgs=0 230/300: dt: 0.9000, rms radial error=137.722, avgs=0 235/300: dt: 0.9000, rms radial error=136.947, avgs=0 240/300: dt: 0.9000, rms radial error=136.175, avgs=0 245/300: dt: 0.9000, rms radial error=135.409, avgs=0 250/300: dt: 0.9000, rms radial error=134.646, avgs=0 255/300: dt: 0.9000, rms radial error=133.888, avgs=0 260/300: dt: 0.9000, rms radial error=133.133, avgs=0 265/300: dt: 0.9000, rms radial error=132.384, avgs=0 270/300: dt: 0.9000, rms radial error=131.638, avgs=0 275/300: dt: 0.9000, rms radial error=130.897, avgs=0 280/300: dt: 0.9000, rms radial error=130.159, avgs=0 285/300: dt: 0.9000, rms radial error=129.426, avgs=0 290/300: dt: 0.9000, rms radial error=128.697, avgs=0 295/300: dt: 0.9000, rms radial error=127.972, avgs=0 300/300: dt: 0.9000, rms radial error=127.251, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 16961.32 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00011 epoch 2 (K=40.0), pass 1, starting sse = 2903.24 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00010 epoch 3 (K=160.0), pass 1, starting sse = 313.09 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.09/11 = 0.00783 epoch 4 (K=640.0), pass 1, starting sse = 17.73 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/13 = 0.00827 final writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.08 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Thu Aug 8 20:06:51 CEST 2013 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub005 rh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-26 (nv=143688, nf=287428, ne=431142, g=14) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 12 iterations marking ambiguous vertices... 2055 ambiguous faces found in tessellation segmenting defects... 27 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 27 defects to be corrected 0 vertices coincident reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.8290 (-4.9145) -vertex loglikelihood: -6.6454 (-3.3227) -normal dot loglikelihood: -3.5952 (-3.5952) -quad curv loglikelihood: -6.5467 (-3.2734) Total Loglikelihood : -26.6163 CORRECTING DEFECT 0 (vertices=19, convex hull=60) After retessellation of defect 0, euler #=-24 (142408,426667,284235) : difference with theory (-24) = 0 CORRECTING DEFECT 1 (vertices=33, convex hull=49) After retessellation of defect 1, euler #=-23 (142413,426700,284264) : difference with theory (-23) = 0 CORRECTING DEFECT 2 (vertices=85, convex hull=62) After retessellation of defect 2, euler #=-22 (142430,426773,284321) : difference with theory (-22) = 0 CORRECTING DEFECT 3 (vertices=91, convex hull=93) After retessellation of defect 3, euler #=-21 (142440,426843,284382) : difference with theory (-21) = 0 CORRECTING DEFECT 4 (vertices=25, convex hull=67) After retessellation of defect 4, euler #=-20 (142450,426900,284430) : difference with theory (-20) = 0 CORRECTING DEFECT 5 (vertices=18, convex hull=25) After retessellation of defect 5, euler #=-19 (142453,426917,284445) : difference with theory (-19) = 0 CORRECTING DEFECT 6 (vertices=35, convex hull=59) After retessellation of defect 6, euler #=-18 (142462,426970,284490) : difference with theory (-18) = 0 CORRECTING DEFECT 7 (vertices=48, convex hull=67) After retessellation of defect 7, euler #=-17 (142491,427087,284579) : difference with theory (-17) = 0 CORRECTING DEFECT 8 (vertices=15, convex hull=32) After retessellation of defect 8, euler #=-16 (142496,427112,284600) : difference with theory (-16) = 0 CORRECTING DEFECT 9 (vertices=136, convex hull=30) After retessellation of defect 9, euler #=-15 (142504,427145,284626) : difference with theory (-15) = 0 CORRECTING DEFECT 10 (vertices=6, convex hull=13) After retessellation of defect 10, euler #=-14 (142504,427148,284630) : difference with theory (-14) = 0 CORRECTING DEFECT 11 (vertices=88, convex hull=27) After retessellation of defect 11, euler #=-13 (142512,427179,284654) : difference with theory (-13) = 0 CORRECTING DEFECT 12 (vertices=18, convex hull=23) After retessellation of defect 12, euler #=-12 (142515,427195,284668) : difference with theory (-12) = 0 CORRECTING DEFECT 13 (vertices=39, convex hull=56) After retessellation of defect 13, euler #=-11 (142535,427275,284729) : difference with theory (-11) = 0 CORRECTING DEFECT 14 (vertices=56, convex hull=53) After retessellation of defect 14, euler #=-10 (142553,427353,284790) : difference with theory (-10) = 0 CORRECTING DEFECT 15 (vertices=10, convex hull=14) After retessellation of defect 15, euler #=-9 (142555,427364,284800) : difference with theory (-9) = 0 CORRECTING DEFECT 16 (vertices=84, convex hull=79) After retessellation of defect 16, euler #=-8 (142574,427456,284874) : difference with theory (-8) = 0 CORRECTING DEFECT 17 (vertices=32, convex hull=61) After retessellation of defect 17, euler #=-7 (142594,427544,284943) : difference with theory (-7) = 0 CORRECTING DEFECT 18 (vertices=20, convex hull=50) After retessellation of defect 18, euler #=-6 (142606,427599,284987) : difference with theory (-6) = 0 CORRECTING DEFECT 19 (vertices=128, convex hull=53) After retessellation of defect 19, euler #=-5 (142614,427645,285026) : difference with theory (-5) = 0 CORRECTING DEFECT 20 (vertices=45, convex hull=90) After retessellation of defect 20, euler #=-4 (142639,427755,285112) : difference with theory (-4) = 0 CORRECTING DEFECT 21 (vertices=69, convex hull=84) After retessellation of defect 21, euler #=-3 (142657,427841,285181) : difference with theory (-3) = 0 CORRECTING DEFECT 22 (vertices=47, convex hull=66) After retessellation of defect 22, euler #=-2 (142685,427954,285267) : difference with theory (-2) = 0 CORRECTING DEFECT 23 (vertices=86, convex hull=95) After retessellation of defect 23, euler #=-1 (142711,428075,285363) : difference with theory (-1) = 0 CORRECTING DEFECT 24 (vertices=11, convex hull=19) After retessellation of defect 24, euler #=0 (142712,428082,285370) : difference with theory (0) = 0 CORRECTING DEFECT 25 (vertices=24, convex hull=53) After retessellation of defect 25, euler #=1 (142722,428134,285413) : difference with theory (1) = 0 CORRECTING DEFECT 26 (vertices=23, convex hull=66) After retessellation of defect 26, euler #=2 (142731,428187,285458) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.08-->9.58) (max @ vno 16176 --> 26838) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.22 (0.08-->9.58) (max @ vno 16176 --> 26838) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 103 mutations (36.1%), 182 crossovers (63.9%), 53 vertices were eliminated building final representation... 957 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=142731, nf=285458, ne=428187, g=0) writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 16.0 minutes 0 defective edges removing intersecting faces 000: 77 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 142731 - 428187 + 285458 = 2 --> 0 holes F =2V-4: 285458 = 285462-4 (0) 2E=3F: 856374 = 856374 (0) total defect index = 0 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 16 intersecting 001: 6 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Thu Aug 8 20:22:58 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub005 rh only generating white matter surface not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz... 17487 bright wm thresholded. 908 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.orig... computing class statistics... border white: 254363 voxels (1.52%) border gray 296177 voxels (1.77%) WM (91.0): 92.5 +- 10.3 [70.0 --> 110.0] GM (74.0) : 72.5 +- 12.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 44.2 (was 70) setting MAX_BORDER_WHITE to 115.3 (was 105) setting MIN_BORDER_WHITE to 57.0 (was 85) setting MAX_CSF to 31.3 (was 40) setting MAX_GRAY to 94.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 50.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 18.5 (was 40) repositioning cortical surface to gray/white boundary reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.22 (0.01-->3.89) (max @ vno 16176 --> 26838) face area 0.27 +- 0.12 (0.00-->1.52) mean absolute distance = 0.64 +- 0.71 5092 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=105, GM=57 mean inside = 92.4, mean outside = 67.6 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group mean border=71.6, 17 (17) missing vertices, mean dist 0.4 [0.4 (%30.8)->0.7 (%69.2))] %78 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=snake, 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 +- 0.27 (0.08-->3.85) (max @ vno 100129 --> 101238) face area 0.27 +- 0.13 (0.00-->1.99) mean absolute distance = 0.29 +- 0.43 3359 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=7953829.5, rms=13.82 001: dt: 0.5000, sse=8023892.0, rms=9.975 (0.000%) 002: dt: 0.5000, sse=8355369.0, rms=7.823 (0.000%) 003: dt: 0.5000, sse=8480620.0, rms=6.470 (0.000%) 004: dt: 0.5000, sse=8764958.0, rms=5.656 (0.000%) 005: dt: 0.5000, sse=8813126.0, rms=5.178 (0.000%) 006: dt: 0.5000, sse=8973657.0, rms=4.904 (0.000%) 007: dt: 0.5000, sse=8960889.0, rms=4.754 (0.000%) 008: dt: 0.5000, sse=9043888.0, rms=4.639 (0.000%) 009: dt: 0.5000, sse=8924771.0, rms=4.582 (0.000%) 010: dt: 0.5000, sse=8987706.0, rms=4.514 (0.000%) rms = 4.49, time step reduction 1 of 3 to 0.250... 011: dt: 0.5000, sse=8876608.0, rms=4.495 (0.000%) 012: dt: 0.2500, sse=5798995.0, rms=3.158 (0.000%) 013: dt: 0.2500, sse=5317273.0, rms=2.702 (0.000%) 014: dt: 0.2500, sse=5017348.5, rms=2.594 (0.000%) 015: dt: 0.2500, sse=4933934.5, rms=2.504 (0.000%) rms = 2.47, time step reduction 2 of 3 to 0.125... 016: dt: 0.2500, sse=4830886.0, rms=2.471 (0.000%) 017: dt: 0.1250, sse=4575423.5, rms=2.219 (0.000%) rms = 2.18, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=4526973.0, rms=2.184 (0.000%) positioning took 2.3 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=76.1, 30 (0) missing vertices, mean dist -0.2 [0.3 (%78.7)->0.2 (%21.3))] %86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.26 (0.03-->3.41) (max @ vno 16176 --> 26838) face area 0.35 +- 0.17 (0.00-->2.12) mean absolute distance = 0.21 +- 0.29 2676 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5551025.0, rms=6.07 019: dt: 0.5000, sse=5772346.5, rms=4.079 (0.000%) rms = 4.63, time step reduction 1 of 3 to 0.250... 020: dt: 0.2500, sse=5267387.5, rms=2.914 (0.000%) 021: dt: 0.2500, sse=5100009.5, rms=2.430 (0.000%) 022: dt: 0.2500, sse=5021002.0, rms=2.053 (0.000%) rms = 2.02, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=5002119.0, rms=2.023 (0.000%) 024: dt: 0.1250, sse=4814917.5, rms=1.773 (0.000%) rms = 1.74, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=4759359.5, rms=1.740 (0.000%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=79.4, 26 (0) missing vertices, mean dist -0.1 [0.2 (%76.4)->0.2 (%23.6))] %92 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.25 (0.05-->3.40) (max @ vno 16176 --> 26838) face area 0.34 +- 0.16 (0.00-->1.90) mean absolute distance = 0.16 +- 0.23 2959 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5157159.5, rms=4.29 026: dt: 0.5000, sse=5526874.5, rms=4.197 (0.000%) rms = 4.46, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=5029497.0, rms=2.643 (0.000%) 028: dt: 0.2500, sse=4918106.5, rms=2.197 (0.000%) 029: dt: 0.2500, sse=4975793.0, rms=1.864 (0.000%) rms = 1.92, time step reduction 2 of 3 to 0.125... 030: dt: 0.1250, sse=4901236.0, rms=1.721 (0.000%) 031: dt: 0.1250, sse=4798075.0, rms=1.525 (0.000%) rms = 1.51, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=4759845.5, rms=1.507 (0.000%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=80.5, 27 (0) missing vertices, mean dist -0.0 [0.2 (%58.4)->0.2 (%41.6))] %93 local maxima, % 2 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=snake, 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=4783962.0, rms=1.86 rms = 2.90, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=4886889.0, rms=1.227 (0.000%) 034: dt: 0.2500, sse=5051746.0, rms=1.116 (0.000%) rms = 1.11, time step reduction 2 of 3 to 0.125... 035: dt: 0.2500, sse=5147129.5, rms=1.115 (0.000%) rms = 1.09, time step reduction 3 of 3 to 0.062... 036: dt: 0.1250, sse=5181376.0, rms=1.094 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group generating cortex label... 10 non-cortical segments detected only using segment with 1811 vertices erasing segment 1 (vno[0] = 64919) erasing segment 2 (vno[0] = 65987) erasing segment 3 (vno[0] = 87960) erasing segment 4 (vno[0] = 90268) erasing segment 5 (vno[0] = 95842) erasing segment 6 (vno[0] = 101342) erasing segment 7 (vno[0] = 101668) erasing segment 8 (vno[0] = 107056) erasing segment 9 (vno[0] = 113300) writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/rh.cortex.label... writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.curv writing smoothed area to rh.area writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.area vertex spacing 0.90 +- 0.25 (0.04-->3.45) (max @ vno 16176 --> 26838) face area 0.34 +- 0.16 (0.00-->1.92) refinement took 7.0 minutes #-------------------------------------------- #@# Smooth2 rh Thu Aug 8 20:30:00 CEST 2013 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 rh Thu Aug 8 20:30:05 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 46.9 mm, total surface area = 86834 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.120 (target=0.015) step 005: RMS=0.082 (target=0.015) step 010: RMS=0.058 (target=0.015) step 015: RMS=0.048 (target=0.015) step 020: RMS=0.039 (target=0.015) step 025: RMS=0.033 (target=0.015) step 030: RMS=0.027 (target=0.015) step 035: RMS=0.022 (target=0.015) step 040: RMS=0.019 (target=0.015) step 045: RMS=0.018 (target=0.015) step 050: RMS=0.016 (target=0.015) step 055: RMS=0.015 (target=0.015) inflation complete. inflation took 0.6 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 151 vertices thresholded to be in k1 ~ [-0.20 1.09], k2 ~ [-0.08 0.07] total integrated curvature = 0.660*4pi (8.297) --> 0 handles ICI = 1.7, FI = 10.8, variation=182.011 123 vertices thresholded to be in [-0.03 0.01] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 118 vertices thresholded to be in [-0.11 0.24] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.016, std = 0.023 done. #----------------------------------------- #@# Curvature Stats rh Thu Aug 8 20:32:31 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub005 rh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/rh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ sub005/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 [ 270 ] Gb_filter = 0 WARN: S lookup min: -0.130205 WARN: S explicit min: 0.000000 vertex = 162 #-------------------------------------------- #@# Sphere rh Thu Aug 8 20:32:36 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 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 0.282... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=snake, 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 %21.20 pass 1: epoch 2 of 3 starting distance error %21.15 unfolding complete - removing small folds... starting distance error %21.07 removing remaining folds... final distance error %21.09 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/rh.sphere spherical transformation took 1.12 hours #-------------------------------------------- #@# Surf Reg rh Thu Aug 8 21:40:02 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts mris_register -curv ../surf/rh.sphere /opt/freesurfer/5.3.0/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /opt/freesurfer/5.3.0/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=snake, 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=snake, 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 = 0.576 curvature mean = 0.032, std = 0.936 curvature mean = 0.024, std = 0.848 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 0.00) sse = 379358.7, tmin=1.1240 d=32.00 min @ (0.00, -8.00, 0.00) sse = 276429.3, tmin=2.2516 d=16.00 min @ (-4.00, 0.00, 0.00) sse = 261174.7, tmin=3.3972 d=8.00 min @ (2.00, 0.00, 0.00) sse = 259918.8, tmin=4.5631 d=4.00 min @ (-1.00, 0.00, 0.00) sse = 258530.6, tmin=5.7408 d=2.00 min @ (0.00, -0.50, -0.50) sse = 257876.9, tmin=6.9290 d=1.00 min @ (0.00, 0.00, 0.25) sse = 257809.8, tmin=8.1105 d=0.50 min @ (0.00, 0.00, -0.12) sse = 257800.2, tmin=9.2995 tol=1.0e+00, sigma=0.5, host=snake, 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 9.30 min curvature mean = 0.003, std = 0.940 curvature mean = 0.012, std = 0.934 curvature mean = -0.003, std = 0.946 curvature mean = 0.006, std = 0.969 curvature mean = -0.004, std = 0.946 curvature mean = 0.001, std = 0.987 2 Reading smoothwm curvature mean = -0.026, std = 0.339 curvature mean = 0.005, std = 0.070 curvature mean = 0.066, std = 0.291 curvature mean = 0.006, std = 0.083 curvature mean = 0.033, std = 0.463 curvature mean = 0.006, std = 0.089 curvature mean = 0.018, std = 0.596 curvature mean = 0.007, std = 0.090 curvature mean = 0.006, std = 0.707 MRISregister() return, current seed 0 writing registered surface to ../surf/rh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white rh Thu Aug 8 22:09:57 CEST 2013 mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv rh Thu Aug 8 22:09:59 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts mrisp_paint -a 5 /opt/freesurfer/5.3.0/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /opt/freesurfer/5.3.0/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Thu Aug 8 22:10:01 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub005 rh ../surf/rh.sphere.reg /opt/freesurfer/5.3.0/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /opt/freesurfer/5.3.0/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... 1263 labels changed using aseg relabeling using gibbs priors... 000: 3060 changed, 142731 examined... 001: 693 changed, 13043 examined... 002: 182 changed, 3884 examined... 003: 63 changed, 1039 examined... 004: 33 changed, 395 examined... 005: 15 changed, 211 examined... 006: 7 changed, 82 examined... 007: 3 changed, 46 examined... 008: 3 changed, 17 examined... 009: 2 changed, 16 examined... 010: 1 changed, 12 examined... 011: 0 changed, 10 examined... 179 labels changed using aseg 000: 106 total segments, 69 labels (430 vertices) changed 001: 41 total segments, 4 labels (9 vertices) changed 002: 37 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... 1537 vertices marked for relabeling... 1537 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 1 minutes and 4 seconds. #-------------------------------------------- #@# Make Pial Surf rh Thu Aug 8 22:11:05 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub005 rh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz... 17487 bright wm thresholded. 908 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.orig... computing class statistics... border white: 254363 voxels (1.52%) border gray 296177 voxels (1.77%) WM (91.0): 92.5 +- 10.3 [70.0 --> 110.0] GM (74.0) : 72.5 +- 12.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 44.2 (was 70) setting MAX_BORDER_WHITE to 115.3 (was 105) setting MIN_BORDER_WHITE to 57.0 (was 85) setting MAX_CSF to 31.3 (was 40) setting MAX_GRAY to 94.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 50.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 18.5 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=57 mean inside = 92.4, mean outside = 67.6 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.22 (0.01-->3.89) (max @ vno 16176 --> 26838) face area 0.27 +- 0.12 (0.00-->1.52) mean absolute distance = 0.64 +- 0.71 4497 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 21 points - only 0.00% unknown deleting segment 3 with 407 points - only 0.00% unknown deleting segment 4 with 6 points - only 0.00% unknown deleting segment 5 with 15 points - only 0.00% unknown deleting segment 6 with 35 points - only 0.00% unknown deleting segment 8 with 131 points - only 0.00% unknown removing 2 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 10 with 1 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 11 with 3 points - only 0.00% unknown mean border=71.5, 17 (17) missing vertices, mean dist 0.4 [0.4 (%30.8)->0.7 (%69.2))] %78 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=snake, 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 +- 0.27 (0.08-->3.85) (max @ vno 100129 --> 101238) face area 0.27 +- 0.13 (0.00-->1.99) mean absolute distance = 0.29 +- 0.43 2898 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=7974956.0, rms=13.81 001: dt: 0.5000, sse=8051567.5, rms=9.964 (0.000%) 002: dt: 0.5000, sse=8390382.0, rms=7.816 (0.000%) 003: dt: 0.5000, sse=8513470.0, rms=6.464 (0.000%) 004: dt: 0.5000, sse=8805081.0, rms=5.650 (0.000%) 005: dt: 0.5000, sse=8847354.0, rms=5.173 (0.000%) 006: dt: 0.5000, sse=9017397.0, rms=4.899 (0.000%) 007: dt: 0.5000, sse=8997915.0, rms=4.750 (0.000%) 008: dt: 0.5000, sse=9087754.0, rms=4.635 (0.000%) 009: dt: 0.5000, sse=8963565.0, rms=4.578 (0.000%) 010: dt: 0.5000, sse=9031501.0, rms=4.510 (0.000%) rms = 4.49, time step reduction 1 of 3 to 0.250... 011: dt: 0.5000, sse=8915012.0, rms=4.491 (0.000%) 012: dt: 0.2500, sse=5827361.5, rms=3.157 (0.000%) 013: dt: 0.2500, sse=5342220.0, rms=2.702 (0.000%) 014: dt: 0.2500, sse=5041012.5, rms=2.594 (0.000%) 015: dt: 0.2500, sse=4959373.0, rms=2.504 (0.000%) rms = 2.47, time step reduction 2 of 3 to 0.125... 016: dt: 0.2500, sse=4856800.0, rms=2.472 (0.000%) 017: dt: 0.1250, sse=4602698.0, rms=2.221 (0.000%) rms = 2.19, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=4552583.0, rms=2.186 (0.000%) positioning took 2.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 24 points - only 0.00% unknown deleting segment 2 with 337 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 14 points - only 0.00% unknown deleting segment 5 with 21 points - only 0.00% unknown deleting segment 6 with 82 points - only 0.00% unknown removing 2 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 10 with 1 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 11 with 2 points - only 0.00% unknown mean border=76.1, 36 (0) missing vertices, mean dist -0.2 [0.3 (%78.7)->0.2 (%21.3))] %87 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.26 (0.03-->3.41) (max @ vno 16176 --> 26838) face area 0.35 +- 0.16 (0.00-->2.12) mean absolute distance = 0.21 +- 0.29 2731 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5578387.0, rms=6.06 019: dt: 0.5000, sse=5803824.0, rms=4.075 (0.000%) rms = 4.63, time step reduction 1 of 3 to 0.250... 020: dt: 0.2500, sse=5297082.0, rms=2.913 (0.000%) 021: dt: 0.2500, sse=5130555.0, rms=2.431 (0.000%) 022: dt: 0.2500, sse=5050317.0, rms=2.056 (0.000%) rms = 2.03, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=5033606.5, rms=2.025 (0.000%) 024: dt: 0.1250, sse=4846455.0, rms=1.777 (0.000%) rms = 1.74, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=4789915.5, rms=1.745 (0.000%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 26 points - only 0.00% unknown deleting segment 1 with 347 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 3 with 14 points - only 0.00% unknown deleting segment 4 with 35 points - only 0.00% unknown deleting segment 5 with 96 points - only 0.00% unknown removing 2 vertex label from ripped group removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown mean border=79.4, 36 (0) missing vertices, mean dist -0.1 [0.2 (%76.3)->0.2 (%23.7))] %92 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.25 (0.05-->3.40) (max @ vno 16176 --> 26838) face area 0.34 +- 0.16 (0.00-->1.90) mean absolute distance = 0.16 +- 0.24 3015 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5188923.0, rms=4.29 026: dt: 0.5000, sse=5556812.0, rms=4.194 (0.000%) rms = 4.45, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=5059351.0, rms=2.643 (0.000%) 028: dt: 0.2500, sse=4949751.0, rms=2.198 (0.000%) 029: dt: 0.2500, sse=5007317.0, rms=1.866 (0.000%) rms = 1.93, time step reduction 2 of 3 to 0.125... 030: dt: 0.1250, sse=4932588.0, rms=1.724 (0.000%) 031: dt: 0.1250, sse=4830113.5, rms=1.528 (0.000%) rms = 1.51, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=4792010.5, rms=1.511 (0.000%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 27 points - only 0.00% unknown deleting segment 1 with 357 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 3 with 14 points - only 0.00% unknown deleting segment 4 with 38 points - only 0.00% unknown deleting segment 5 with 97 points - only 0.00% unknown removing 2 vertex label from ripped group removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 8 with 3 points - only 0.00% unknown mean border=80.4, 44 (0) missing vertices, mean dist -0.0 [0.2 (%58.3)->0.2 (%41.7))] %94 local maxima, % 2 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=snake, 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=4816013.0, rms=1.86 rms = 2.89, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=4921099.0, rms=1.229 (0.000%) 034: dt: 0.2500, sse=5086477.0, rms=1.120 (0.000%) rms = 1.12, time step reduction 2 of 3 to 0.125... 035: dt: 0.2500, sse=5182359.5, rms=1.118 (0.000%) rms = 1.10, time step reduction 3 of 3 to 0.062... 036: dt: 0.1250, sse=5216694.0, rms=1.098 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group smoothing surface for 5 iterations... mean border=47.0, 17 (17) missing vertices, mean dist 1.6 [0.1 (%0.0)->2.5 (%100.0))] %13 local maxima, %49 large gradients and %34 min vals, 1981 gradients ignored tol=1.0e-04, sigma=2.0, host=snake, 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=32687258.0, rms=32.87 001: dt: 0.5000, sse=23541896.0, rms=27.294 (0.000%) 002: dt: 0.5000, sse=17181850.0, rms=22.662 (0.000%) 003: dt: 0.5000, sse=12882107.0, rms=18.921 (0.000%) 004: dt: 0.5000, sse=10166871.0, rms=15.962 (0.000%) 005: dt: 0.5000, sse=8560958.0, rms=13.686 (0.000%) 006: dt: 0.5000, sse=7721739.0, rms=11.966 (0.000%) 007: dt: 0.5000, sse=7264538.5, rms=10.538 (0.000%) 008: dt: 0.5000, sse=6987229.0, rms=9.271 (0.000%) 009: dt: 0.5000, sse=6821755.0, rms=8.116 (0.000%) 010: dt: 0.5000, sse=6813513.0, rms=7.128 (0.000%) 011: dt: 0.5000, sse=6887935.5, rms=6.267 (0.000%) 012: dt: 0.5000, sse=7026273.0, rms=5.592 (0.000%) 013: dt: 0.5000, sse=7175993.5, rms=5.107 (0.000%) 014: dt: 0.5000, sse=7383276.0, rms=4.783 (0.000%) 015: dt: 0.5000, sse=7477753.5, rms=4.552 (0.000%) 016: dt: 0.5000, sse=7615588.5, rms=4.414 (0.000%) 017: dt: 0.5000, sse=7696858.0, rms=4.308 (0.000%) 018: dt: 0.5000, sse=7721887.0, rms=4.250 (0.000%) 019: dt: 0.5000, sse=7753909.5, rms=4.193 (0.000%) rms = 4.16, time step reduction 1 of 3 to 0.250... 020: dt: 0.5000, sse=7737565.0, rms=4.163 (0.000%) 021: dt: 0.2500, sse=5664220.0, rms=3.557 (0.000%) 022: dt: 0.2500, sse=5510557.0, rms=3.383 (0.000%) rms = 3.37, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=5390627.0, rms=3.371 (0.000%) 024: dt: 0.1250, sse=5130935.0, rms=3.255 (0.000%) rms = 3.24, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=5100158.5, rms=3.240 (0.000%) positioning took 3.2 minutes mean border=45.2, 1262 (1) missing vertices, mean dist 0.1 [0.2 (%51.6)->0.6 (%48.4))] %27 local maxima, %40 large gradients and %29 min vals, 627 gradients ignored tol=1.0e-04, sigma=1.0, host=snake, 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=5669908.5, rms=4.67 026: dt: 0.5000, sse=6032153.5, rms=4.185 (0.000%) rms = 4.18, time step reduction 1 of 3 to 0.250... 027: dt: 0.5000, sse=7871497.5, rms=4.175 (0.000%) 028: dt: 0.2500, sse=5947648.0, rms=3.437 (0.000%) 029: dt: 0.2500, sse=6007609.0, rms=3.230 (0.000%) rms = 3.21, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=5869163.0, rms=3.211 (0.000%) 031: dt: 0.1250, sse=5675499.5, rms=3.045 (0.000%) rms = 3.02, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=5653774.5, rms=3.019 (0.000%) positioning took 0.9 minutes mean border=43.2, 1446 (0) missing vertices, mean dist 0.1 [0.2 (%40.2)->0.4 (%59.8))] %46 local maxima, %20 large gradients and %29 min vals, 845 gradients ignored tol=1.0e-04, sigma=0.5, host=snake, 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=5880118.5, rms=4.05 rms = 4.11, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=5654855.5, rms=3.538 (0.000%) 034: dt: 0.2500, sse=5666655.5, rms=3.227 (0.000%) 035: dt: 0.2500, sse=5916288.0, rms=3.131 (0.000%) rms = 3.11, time step reduction 2 of 3 to 0.125... 036: dt: 0.2500, sse=6017766.0, rms=3.107 (0.000%) 037: dt: 0.1250, sse=5807498.5, rms=2.969 (0.000%) rms = 2.94, time step reduction 3 of 3 to 0.062... 038: dt: 0.1250, sse=5821897.5, rms=2.941 (0.000%) positioning took 0.9 minutes mean border=42.2, 3039 (0) missing vertices, mean dist 0.0 [0.2 (%46.3)->0.3 (%53.7))] %49 local maxima, %17 large gradients and %28 min vals, 714 gradients ignored tol=1.0e-04, sigma=0.2, host=snake, 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=5880054.5, rms=3.27 rms = 3.94, time step reduction 1 of 3 to 0.250... 039: dt: 0.2500, sse=5762743.0, rms=3.028 (0.000%) 040: dt: 0.2500, sse=6033981.0, rms=2.963 (0.000%) rms = 2.94, time step reduction 2 of 3 to 0.125... 041: dt: 0.2500, sse=6114455.5, rms=2.939 (0.000%) 042: dt: 0.1250, sse=5996697.0, rms=2.822 (0.000%) rms = 2.80, time step reduction 3 of 3 to 0.062... 043: dt: 0.1250, sse=6027581.5, rms=2.799 (0.000%) positioning took 0.8 minutes writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.area.pial vertex spacing 1.02 +- 0.44 (0.08-->10.36) (max @ vno 100313 --> 100290) face area 0.41 +- 0.31 (0.00-->8.44) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 142731 vertices processed 25000 of 142731 vertices processed 50000 of 142731 vertices processed 75000 of 142731 vertices processed 100000 of 142731 vertices processed 125000 of 142731 vertices processed 0 of 142731 vertices processed 25000 of 142731 vertices processed 50000 of 142731 vertices processed 75000 of 142731 vertices processed 100000 of 142731 vertices processed 125000 of 142731 vertices processed thickness calculation complete, 509:894 truncations. 26532 vertices at 0 distance 86068 vertices at 1 distance 94051 vertices at 2 distance 45703 vertices at 3 distance 15020 vertices at 4 distance 4402 vertices at 5 distance 1461 vertices at 6 distance 497 vertices at 7 distance 208 vertices at 8 distance 99 vertices at 9 distance 69 vertices at 10 distance 54 vertices at 11 distance 42 vertices at 12 distance 31 vertices at 13 distance 41 vertices at 14 distance 27 vertices at 15 distance 22 vertices at 16 distance 30 vertices at 17 distance 15 vertices at 18 distance 26 vertices at 19 distance 30 vertices at 20 distance writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.thickness positioning took 14.0 minutes #-------------------------------------------- #@# Surf Volume rh Thu Aug 8 22:25:08 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.volume rh.area.mid mul rh.thickness Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# WM/GM Contrast rh Thu Aug 8 22:25:08 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts pctsurfcon --s sub005 --rh-only Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts/pctsurfcon.log Thu Aug 8 22:25:08 CEST 2013 setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts /opt/freesurfer/5.3.0/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux snake4 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux FREESURFER_HOME /opt/freesurfer/5.3.0 mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/tmp.pctsurfcon.3128/rh.wm.mgh --regheader sub005 --cortex srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig.mgz as target reference. Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/rh.cortex.label Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 = 109659 Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/rh.cortex.label Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/tmp.pctsurfcon.3128/rh.wm.mgh Dim: 142731 1 1 mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/tmp.pctsurfcon.3128/rh.gm.mgh --projfrac 0.3 --regheader sub005 --cortex srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig.mgz as target reference. Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/rh.cortex.label Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white Done reading source surface Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 = 126459 Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/rh.cortex.label Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/tmp.pctsurfcon.3128/rh.gm.mgh Dim: 142731 1 1 mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/tmp.pctsurfcon.3128/rh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/tmp.pctsurfcon.3128/rh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.w-g.pct.mgh mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.w-g.pct.mgh --annot sub005 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.w-g.pct.mgh --annot sub005 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/stats/rh.w-g.pct.stats --snr sysname Linux hostname snake4 machine x86_64 user fkaule 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.w-g.pct.mgh Vertex Area is 0.668906 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 2000 unknown 0 0.000 1 2001 bankssts 1466 1011.292 2 2002 caudalanteriorcingulate 1392 963.256 3 2003 caudalmiddlefrontal 2933 1968.508 4 2004 corpuscallosum 0 0.000 5 2005 cuneus 2742 1828.445 6 2006 entorhinal 409 296.847 7 2007 fusiform 4234 2918.080 8 2008 inferiorparietal 7531 5073.565 9 2009 inferiortemporal 4962 3371.515 10 2010 isthmuscingulate 1391 913.005 11 2011 lateraloccipital 8721 5637.396 12 2012 lateralorbitofrontal 3882 2586.580 13 2013 lingual 5061 3518.732 14 2014 medialorbitofrontal 2758 1879.153 15 2015 middletemporal 5832 3893.341 16 2016 parahippocampal 1017 695.444 17 2017 paracentral 2053 1357.055 18 2018 parsopercularis 2225 1508.707 19 2019 parsorbitalis 1283 864.903 20 2020 parstriangularis 2251 1520.839 21 2021 pericalcarine 2693 1885.410 22 2022 postcentral 7051 4680.771 23 2023 posteriorcingulate 2072 1355.862 24 2024 precentral 7509 4989.827 25 2025 precuneus 6367 4323.134 26 2026 rostralanteriorcingulate 1172 801.977 27 2027 rostralmiddlefrontal 9311 6297.768 28 2028 superiorfrontal 11943 8113.219 29 2029 superiorparietal 8560 5645.194 30 2030 superiortemporal 6303 4164.996 31 2031 supramarginal 5440 3636.528 32 2032 frontalpole 440 298.384 33 2033 temporalpole 609 439.274 34 2034 transversetemporal 586 359.799 35 2035 insula 3048 1982.912 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats rh Thu Aug 8 22:25:22 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab sub005 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 1466 1011 2843 2.862 0.444 0.123 0.031 12 2.0 bankssts 1392 963 2920 2.794 0.861 0.162 0.047 32 2.6 caudalanteriorcingulate 2933 1969 5442 2.524 0.420 0.135 0.045 41 4.9 caudalmiddlefrontal 2742 1828 4417 2.135 0.463 0.186 0.068 63 8.2 cuneus 409 297 1418 3.459 0.640 0.181 0.065 8 1.1 entorhinal 4234 2918 8870 2.747 0.626 0.162 0.066 93 10.4 fusiform 7531 5074 14195 2.456 0.488 0.152 0.059 161 17.2 inferiorparietal 4962 3372 10567 2.743 0.649 0.166 0.081 127 15.5 inferiortemporal 1391 913 2984 2.722 0.737 0.168 0.073 33 3.7 isthmuscingulate 8721 5637 14933 2.342 0.487 0.159 0.063 184 21.4 lateraloccipital 3882 2587 7910 2.706 0.679 0.153 0.072 75 11.5 lateralorbitofrontal 5061 3519 8685 2.272 0.570 0.179 0.076 121 15.5 lingual 2758 1879 5533 2.555 0.737 0.170 0.094 87 10.8 medialorbitofrontal 5832 3893 14311 3.017 0.593 0.155 0.061 126 14.2 middletemporal 1017 695 2693 3.388 0.725 0.164 0.082 19 2.7 parahippocampal 2053 1357 3598 2.404 0.521 0.128 0.040 25 3.7 paracentral 2225 1509 4406 2.626 0.412 0.151 0.054 41 5.0 parsopercularis 1283 865 2929 2.632 0.624 0.169 0.074 35 3.7 parsorbitalis 2251 1521 4403 2.572 0.544 0.151 0.076 48 5.0 parstriangularis 2693 1885 3347 1.868 0.385 0.154 0.060 41 6.6 pericalcarine 7051 4681 12337 2.291 0.666 0.146 0.052 123 15.2 postcentral 2072 1356 3583 2.553 0.782 0.152 0.053 37 4.3 posteriorcingulate 7509 4990 14781 2.617 0.529 0.131 0.040 100 12.6 precentral 6367 4323 11532 2.516 0.534 0.160 0.104 181 16.1 precuneus 1172 802 2983 3.140 0.563 0.186 0.074 36 3.3 rostralanteriorcingulate 9311 6298 18017 2.411 0.516 0.174 0.083 262 27.8 rostralmiddlefrontal 11943 8113 24982 2.643 0.527 0.148 0.049 204 24.7 superiorfrontal 8560 5645 13489 2.166 0.385 0.134 0.046 150 15.9 superiorparietal 6303 4165 14776 3.025 0.565 0.131 0.044 83 10.8 superiortemporal 5440 3637 10297 2.539 0.506 0.147 0.050 101 11.1 supramarginal 440 298 1089 2.682 0.473 0.235 0.149 24 2.0 frontalpole 609 439 2191 3.708 0.776 0.194 0.112 18 2.7 temporalpole 586 360 1196 2.869 0.399 0.140 0.043 8 1.1 transversetemporal 3048 1983 6248 3.030 0.721 0.146 0.132 122 9.1 insula #----------------------------------------- #@# Cortical Parc 2 rh Thu Aug 8 22:25:40 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub005 rh ../surf/rh.sphere.reg /opt/freesurfer/5.3.0/average/rh.destrieux.simple.2009-07-29.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /opt/freesurfer/5.3.0/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... 1 labels changed using aseg relabeling using gibbs priors... 000: 10303 changed, 142731 examined... 001: 2418 changed, 39284 examined... 002: 725 changed, 12393 examined... 003: 309 changed, 4022 examined... 004: 137 changed, 1713 examined... 005: 71 changed, 771 examined... 006: 32 changed, 398 examined... 007: 14 changed, 171 examined... 008: 6 changed, 73 examined... 009: 1 changed, 33 examined... 010: 0 changed, 7 examined... 1 labels changed using aseg 000: 280 total segments, 198 labels (2806 vertices) changed 001: 91 total segments, 10 labels (85 vertices) changed 002: 81 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 170 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1015 vertices marked for relabeling... 1015 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 1 minutes and 12 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Thu Aug 8 22:26:52 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab sub005 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 1108 756 2276 2.516 0.659 0.190 0.096 35 3.8 G_and_S_frontomargin 1549 1024 3239 2.627 0.567 0.172 0.063 32 4.0 G_and_S_occipital_inf 1222 811 2579 2.497 0.536 0.144 0.052 22 2.7 G_and_S_paracentral 1584 1077 3694 2.983 0.569 0.178 0.068 40 4.2 G_and_S_subcentral 1041 722 2191 2.400 0.478 0.209 0.114 45 4.3 G_and_S_transv_frontopol 3083 2124 6447 2.783 0.627 0.150 0.051 60 6.4 G_and_S_cingul-Ant 1743 1230 3628 2.861 0.606 0.143 0.044 28 3.0 G_and_S_cingul-Mid-Ant 1618 1066 3101 2.762 0.553 0.140 0.045 23 2.9 G_and_S_cingul-Mid-Post 583 391 1516 3.170 0.616 0.182 0.075 13 1.8 G_cingul-Post-dorsal 308 216 907 3.088 0.494 0.180 0.083 8 0.9 G_cingul-Post-ventral 2424 1653 3889 2.027 0.462 0.186 0.068 58 7.1 G_cuneus 1253 880 3286 2.796 0.384 0.175 0.068 37 3.5 G_front_inf-Opercular 453 281 1074 2.807 0.388 0.157 0.067 13 1.2 G_front_inf-Orbital 1146 767 2911 2.875 0.525 0.182 0.120 40 3.4 G_front_inf-Triangul 4282 2878 9989 2.613 0.466 0.186 0.096 135 13.7 G_front_middle 7812 5249 17851 2.690 0.535 0.162 0.062 167 19.9 G_front_sup 390 231 858 3.242 0.844 0.142 0.131 27 1.8 G_Ins_lg_and_S_cent_ins 492 334 1657 3.445 0.769 0.205 0.130 20 2.2 G_insular_short 2484 1587 5560 2.651 0.431 0.181 0.079 73 7.6 G_occipital_middle 2166 1376 3595 2.218 0.372 0.138 0.048 42 4.2 G_occipital_sup 1465 977 3183 2.673 0.588 0.179 0.086 42 4.3 G_oc-temp_lat-fusifor 3441 2387 6426 2.338 0.597 0.202 0.096 104 12.9 G_oc-temp_med-Lingual 1347 922 3927 3.392 0.615 0.198 0.225 87 5.2 G_oc-temp_med-Parahip 2825 1869 6987 2.844 0.761 0.173 0.090 81 9.6 G_orbital 2767 1853 6243 2.630 0.483 0.175 0.084 89 8.5 G_pariet_inf-Angular 2999 1989 6905 2.695 0.507 0.159 0.058 74 7.4 G_pariet_inf-Supramar 2514 1656 4383 2.177 0.417 0.137 0.055 56 5.2 G_parietal_sup 2687 1736 5477 2.442 0.541 0.162 0.062 63 7.2 G_postcentral 2735 1754 6735 2.862 0.465 0.139 0.046 45 5.4 G_precentral 2549 1693 5430 2.552 0.442 0.184 0.185 129 8.6 G_precuneus 685 458 1499 2.414 0.604 0.208 0.129 36 3.5 G_rectus 374 237 946 3.492 0.658 0.086 0.032 2 0.4 G_subcallosal 524 318 1175 3.038 0.408 0.143 0.045 8 1.0 G_temp_sup-G_T_transv 2216 1451 6790 3.273 0.525 0.156 0.066 48 5.3 G_temp_sup-Lateral 803 540 2236 3.614 0.548 0.148 0.056 11 1.6 G_temp_sup-Plan_polar 653 444 1390 2.803 0.463 0.123 0.035 9 0.9 G_temp_sup-Plan_tempo 2620 1772 6373 2.819 0.664 0.190 0.112 98 10.8 G_temporal_inf 3481 2316 10197 3.233 0.555 0.178 0.077 104 10.9 G_temporal_middle 433 291 554 2.153 0.328 0.103 0.024 2 0.5 Lat_Fis-ant-Horizont 158 113 278 2.516 0.396 0.111 0.027 1 0.1 Lat_Fis-ant-Vertical 1337 878 1965 2.681 0.452 0.139 0.046 14 2.6 Lat_Fis-post 3497 2251 5303 2.118 0.487 0.172 0.074 90 10.2 Pole_occipital 1904 1290 5707 3.275 0.754 0.177 0.094 48 7.0 Pole_temporal 3123 2185 4083 1.994 0.518 0.153 0.060 51 7.8 S_calcarine 3113 2117 3790 1.947 0.568 0.117 0.033 25 4.4 S_central 1331 897 2062 2.218 0.436 0.130 0.044 17 2.4 S_cingul-Marginalis 431 296 765 2.350 0.543 0.102 0.027 2 0.5 S_circular_insula_ant 1472 972 2444 2.834 0.576 0.104 0.027 9 1.8 S_circular_insula_inf 1536 1030 2456 2.611 0.424 0.110 0.031 11 2.1 S_circular_insula_sup 961 688 1533 2.438 0.422 0.120 0.030 9 1.3 S_collat_transv_ant 799 548 1074 2.381 0.488 0.160 0.056 12 1.7 S_collat_transv_post 2330 1591 3634 2.315 0.407 0.159 0.056 46 5.5 S_front_inf 2032 1370 3355 2.210 0.451 0.139 0.054 46 4.2 S_front_middle 2901 1990 4381 2.289 0.397 0.122 0.033 27 4.1 S_front_sup 422 273 513 2.178 0.362 0.128 0.034 4 0.6 S_interm_prim-Jensen 3092 2104 4297 2.096 0.341 0.125 0.035 36 4.8 S_intrapariet_and_P_trans 1401 949 1795 2.019 0.388 0.136 0.041 14 2.3 S_oc_middle_and_Lunatus 1895 1251 2820 2.315 0.386 0.123 0.032 20 2.5 S_oc_sup_and_transversal 885 598 1491 2.553 0.382 0.132 0.038 11 1.4 S_occipital_ant 797 561 1483 2.375 0.461 0.145 0.044 13 1.3 S_oc-temp_lat 1772 1259 3190 2.769 0.570 0.127 0.034 15 2.6 S_oc-temp_med_and_Lingual 450 314 821 2.505 0.712 0.184 0.077 10 1.5 S_orbital_lateral 753 542 1293 2.471 0.675 0.113 0.030 6 0.8 S_orbital_med-olfact 1514 1011 2576 2.517 0.533 0.159 0.075 27 5.2 S_orbital-H_Shaped 3033 2023 4590 2.512 0.573 0.141 0.048 39 5.8 S_parieto_occipital 1733 1106 2170 2.203 0.868 0.150 0.051 33 3.1 S_pericallosal 2790 1867 3906 2.182 0.423 0.124 0.039 30 4.4 S_postcentral 2078 1365 3190 2.500 0.359 0.133 0.044 25 3.6 S_precentral-inf-part 1550 1044 2302 2.351 0.395 0.110 0.024 10 1.7 S_precentral-sup-part 546 387 1188 2.761 0.685 0.199 0.128 19 3.4 S_suborbital 1409 949 2539 2.483 0.419 0.152 0.054 27 3.1 S_subparietal 1527 1037 2351 2.573 0.517 0.127 0.032 13 2.2 S_temporal_inf 6414 4323 10724 2.609 0.502 0.120 0.032 56 8.4 S_temporal_sup 402 288 735 2.728 0.391 0.101 0.017 2 0.3 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 rh Thu Aug 8 22:27:12 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub005 rh ../surf/rh.sphere.reg /opt/freesurfer/5.3.0/average/rh.DKTatlas40.gcs ../label/rh.aparc.DKTatlas40.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /opt/freesurfer/5.3.0/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... 868 labels changed using aseg relabeling using gibbs priors... 000: 2762 changed, 142731 examined... 001: 620 changed, 11882 examined... 002: 150 changed, 3350 examined... 003: 56 changed, 873 examined... 004: 29 changed, 336 examined... 005: 21 changed, 188 examined... 006: 11 changed, 112 examined... 007: 6 changed, 56 examined... 008: 2 changed, 28 examined... 009: 2 changed, 12 examined... 010: 3 changed, 14 examined... 011: 1 changed, 10 examined... 012: 2 changed, 8 examined... 013: 4 changed, 9 examined... 014: 2 changed, 17 examined... 015: 4 changed, 16 examined... 016: 5 changed, 22 examined... 017: 3 changed, 25 examined... 018: 2 changed, 17 examined... 019: 2 changed, 10 examined... 020: 4 changed, 15 examined... 021: 4 changed, 20 examined... 022: 6 changed, 19 examined... 023: 2 changed, 24 examined... 024: 0 changed, 14 examined... 123 labels changed using aseg 000: 60 total segments, 27 labels (142 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 38 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 882 vertices marked for relabeling... 882 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas40.annot... classification took 1 minutes and 3 seconds. #----------------------------------------- #@# Parcellation Stats 3 rh Thu Aug 8 22:28:15 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts 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 sub005 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 1481 1023 3113 2.785 0.879 0.164 0.048 34 2.8 caudalanteriorcingulate 3008 2012 5518 2.522 0.418 0.136 0.045 42 5.0 caudalmiddlefrontal 3414 2266 5375 2.168 0.474 0.179 0.062 75 9.3 cuneus 476 348 1547 3.386 0.667 0.177 0.063 9 1.3 entorhinal 3620 2523 7105 2.663 0.563 0.158 0.062 77 8.1 fusiform 7071 4757 13141 2.429 0.488 0.150 0.058 149 15.8 inferiorparietal 5470 3706 12225 2.807 0.682 0.168 0.083 141 17.7 inferiortemporal 1456 951 3021 2.667 0.747 0.159 0.067 30 3.5 isthmuscingulate 9060 5834 15587 2.343 0.492 0.160 0.063 195 22.6 lateraloccipital 4314 2878 9192 2.727 0.706 0.163 0.079 98 13.4 lateralorbitofrontal 5028 3488 8609 2.273 0.571 0.177 0.075 119 15.2 lingual 2228 1510 4623 2.599 0.779 0.170 0.093 72 9.0 medialorbitofrontal 6930 4654 16399 2.990 0.569 0.151 0.057 137 15.9 middletemporal 1013 692 2666 3.367 0.724 0.164 0.082 19 2.7 parahippocampal 2206 1456 3926 2.411 0.514 0.128 0.042 28 4.0 paracentral 2296 1547 4447 2.602 0.406 0.151 0.056 43 5.2 parsopercularis 1376 923 2876 2.597 0.564 0.150 0.059 28 3.2 parsorbitalis 2428 1648 4962 2.613 0.550 0.168 0.086 68 6.8 parstriangularis 2731 1925 3440 1.870 0.384 0.157 0.064 43 7.1 pericalcarine 7512 5021 13182 2.294 0.654 0.146 0.053 138 16.2 postcentral 2084 1363 3682 2.633 0.759 0.154 0.054 38 4.4 posteriorcingulate 7216 4802 14396 2.640 0.530 0.132 0.040 97 12.1 precentral 6437 4368 11732 2.493 0.534 0.158 0.103 185 16.3 precuneus 1289 882 3250 3.113 0.561 0.183 0.071 37 3.5 rostralanteriorcingulate 6222 4217 11979 2.401 0.498 0.171 0.082 169 18.0 rostralmiddlefrontal 15115 10273 30789 2.575 0.537 0.153 0.058 297 35.1 superiorfrontal 7177 4734 11399 2.172 0.390 0.134 0.045 120 13.3 superiorparietal 8069 5373 19040 3.048 0.613 0.139 0.071 164 16.1 superiortemporal 5127 3422 9698 2.542 0.504 0.148 0.050 95 10.4 supramarginal 567 346 1170 2.872 0.397 0.139 0.043 8 1.1 transversetemporal 2826 1840 5815 2.961 0.706 0.134 0.068 64 7.2 insula #-------------------------------------------- #@# Refine Pial Surfs w/ T2/FLAIR Thu Aug 8 22:28:33 CEST 2013 bbregister --s sub005 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.lta --init-fsl --T2 Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.dat.log Thu Aug 8 22:28:33 CEST 2013 setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts /opt/freesurfer/5.3.0/bin/bbregister --s sub005 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.lta --init-fsl --T2 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ Linux snake4 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux FREESURFER_HOME /opt/freesurfer/5.3.0 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/T2raw.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998148, -0.0400878, -0.0457496) j_ras = (-0.0459461, 0.989757, 0.135168) k_ras = (-0.0398624, -0.13702, 0.989766) writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii... fslregister --s sub005 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister --dof 6 --fsvol brainmask.mgz Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/reg.init.dat.fslregister.log Thu Aug 8 22:28:38 CEST 2013 --s sub005 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister --dof 6 --fsvol brainmask.mgz $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ snake4 Linux snake4 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux nIters 1 -------------------------------------- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister/refvol.fslregister.nii mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister/refvol.fslregister.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/brainmask.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 4.19095e-09, 3.72529e-09) j_ras = (7.45058e-09, 1.49012e-08, -1) k_ras = (-6.0536e-09, 1, -1.49012e-08) writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister/refvol.fslregister.nii... -------------------------------------- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister/movvol.fslregister.nii --frame 0 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998148, -0.0400878, -0.0457496) j_ras = (-0.0459461, 0.989757, 0.135168) k_ras = (-0.0398624, -0.13702, 0.989766) keeping frame 0 writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister/movvol.fslregister.nii... Mov determinant is -0.311072 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister/movvol.fslregister.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister/reg0.3412.dat --regheader --fslregout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/reg.init.dat.fsl.mat0 --s sub005 --noedit tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister/movvol.fslregister.nii reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister/reg0.3412.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig.mgz Ttarg: -------------------- -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; INFO: loading movable /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister/movvol.fslregister.nii Tmov: -------------------- -0.700 0.000 0.000 95.888; 0.000 0.000 0.667 -128.000; 0.000 -0.667 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 0.998 0.040 0.046 0.000; -0.040 -0.137 0.990 0.000; 0.046 -0.990 -0.135 -0.000; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 0.998 0.040 0.046 0.000; -0.040 -0.137 0.990 0.000; 0.046 -0.990 -0.135 -0.000; 0.000 0.000 0.000 1.000; Determinant 1 subject = sub005 RegMat --------------------------- 0.998 0.040 0.046 0.000; -0.040 -0.137 0.990 0.000; 0.046 -0.990 -0.135 -0.000; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -0.311072, ref det = -1 Thu Aug 8 22:28:45 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/reg.init.dat.fsl.mat0 Thu Aug 8 22:33:07 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/reg.init.dat.fsl.mat -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister/fslmat0.trans.mat -schedule /opt/freesurfer/5.3.0/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s sub005 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/reg.init.dat --fslreg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/reg.init.dat.fsl.mat --noedit tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl ---- FSL registration matrix -------- 0.998 0.047 0.039 21.016; 0.045 -0.142 -0.989 269.550; -0.041 0.989 -0.144 23.522; 0.000 0.000 0.000 1.000; --------------------------------------- INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/reg.init.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig.mgz Ttarg: -------------------- -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; INFO: loading movable /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii Tmov: -------------------- -0.700 0.000 0.000 95.888; 0.000 0.000 0.667 -128.000; 0.000 -0.667 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 FSLOUTPUTTYPE NIFTI fsl2TkReg: mov det = -0.311072, ref det = -1 ---- Input registration matrix (computed) -------- 0.998 0.041 0.045 -0.245; -0.039 -0.144 0.989 1.084; 0.047 -0.989 -0.142 -0.427; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 0.998 0.041 0.045 -0.245; -0.039 -0.144 0.989 1.084; 0.047 -0.989 -0.142 -0.427; 0.000 0.000 0.000 1.000; Determinant 1 subject = sub005 RegMat --------------------------- 0.998 0.041 0.045 -0.245; -0.039 -0.144 0.989 1.084; 0.047 -0.989 -0.142 -0.427; 0.000 0.000 0.000 1.000; Started at Thu Aug 8 22:28:38 CEST 2013 Ended at Thu Aug 8 22:39:14 CEST 2013 fslregister Done To check results, run: tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/reg.init.dat --surf orig mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $ setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Linux hostname snake4 machine x86_64 user fkaule movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/reg.init.dat subject sub005 dof 6 outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1376880629 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.998 0.041 0.045 -0.245; -0.039 -0.144 0.989 1.084; 0.047 -0.989 -0.142 -0.427; 0.000 0.000 0.000 1.000; Loading mov Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 1.023099 1 -25.0 -25.0 25.0 0.979907 2 -25.0 25.0 -25.0 1.030559 3 -25.0 25.0 25.0 0.988352 4 25.0 -25.0 -25.0 1.019131 5 25.0 -25.0 25.0 1.007005 6 25.0 25.0 -25.0 0.997025 7 25.0 25.0 25.0 0.996223 REL: 8 0.289642 8.041302 1.005163 rel = 0.288155 Initial costs ---------------- Number of surface hits 2708 WM Intensity 62.0586 +/- 9.7971 Ctx Intensity 75.0981 +/- 11.8063 Pct Contrast 18.8287 +/- 18.3670 Cost 0.2896 RelCost 0.2882 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9907 0.9907 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.9867 0.9867 0.0 6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.9472 0.9472 0.0 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.8797 0.8797 0.0 21 -4.0000 -4.0000 -4.0000 4.0000 0.0000 -4.0000 0.8635 0.8635 0.0 39 -4.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.8061 0.8061 0.0 102 -4.0000 0.0000 -4.0000 4.0000 0.0000 -4.0000 0.7972 0.7972 0.0 120 -4.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.6820 0.6820 0.0 346 0.0000 0.0000 -4.0000 4.0000 0.0000 0.0000 0.6487 0.6487 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.2896 0.2896 0.0 Brute Force -------------------------- Min cost was 0.289642 Number of iterations 729 Search time 2.071000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 6 0.382 0.000 0.000 0.000 0.000 0.000 0.2875510287 7 0.222 0.000 0.000 0.000 0.000 0.000 0.2849389020 9 0.242 0.000 0.000 0.000 0.000 0.000 0.2847667733 10 0.295 0.000 0.000 0.000 0.000 0.000 0.2843241020 13 0.302 0.000 0.000 0.000 0.000 0.000 0.2842948424 15 0.304 0.000 0.000 0.000 0.000 0.000 0.2842915679 16 0.305 0.000 0.000 0.000 0.000 0.000 0.2842905660 20 0.305 -1.618 0.000 0.000 0.000 0.000 0.2495972257 21 0.305 -0.949 0.000 0.000 0.000 0.000 0.2002943882 26 0.305 -0.927 0.000 0.000 0.000 0.000 0.2002444441 27 0.305 -0.926 0.000 0.000 0.000 0.000 0.2002406533 28 0.305 -0.907 0.000 0.000 0.000 0.000 0.2001984559 30 0.305 -0.911 0.000 0.000 0.000 0.000 0.2001899098 32 0.305 -0.912 0.000 0.000 0.000 0.000 0.2001892511 33 0.305 -0.913 0.000 0.000 0.000 0.000 0.2001891441 36 0.305 -0.913 1.000 0.000 0.000 0.000 0.1381889852 40 0.305 -0.913 0.618 0.000 0.000 0.000 0.1324581935 41 0.305 -0.913 0.723 0.000 0.000 0.000 0.1297224871 52 0.305 -0.913 0.723 0.186 0.000 0.000 0.1236983204 55 0.305 -0.913 0.723 0.205 0.000 0.000 0.1236259223 56 0.305 -0.913 0.723 0.201 0.000 0.000 0.1236165933 58 0.305 -0.913 0.723 0.202 0.000 0.000 0.1236164808 66 0.305 -0.913 0.723 0.202 -0.055 0.000 0.1236023184 67 0.305 -0.913 0.723 0.202 -0.028 0.000 0.1233162785 69 0.305 -0.913 0.723 0.202 -0.031 0.000 0.1233137649 71 0.305 -0.913 0.723 0.202 -0.030 0.000 0.1233131600 78 0.305 -0.913 0.723 0.202 -0.030 0.014 0.1232478044 80 0.305 -0.913 0.723 0.202 -0.030 0.013 0.1232431079 82 0.305 -0.913 0.723 0.202 -0.030 0.011 0.1232418379 91 0.131 -0.913 0.723 0.202 -0.030 0.011 0.1215356273 92 0.169 -0.913 0.723 0.202 -0.030 0.011 0.1212382536 93 0.180 -0.913 0.723 0.202 -0.030 0.011 0.1209722775 95 0.201 -0.913 0.723 0.202 -0.030 0.011 0.1207660962 96 0.202 -0.913 0.723 0.202 -0.030 0.011 0.1207640196 98 0.203 -0.913 0.723 0.202 -0.030 0.011 0.1207634108 104 0.203 -0.531 0.723 0.202 -0.030 0.011 0.1199165303 105 0.203 -0.712 0.723 0.202 -0.030 0.011 0.1172291128 106 0.203 -0.709 0.723 0.202 -0.030 0.011 0.1171359149 107 0.203 -0.648 0.723 0.202 -0.030 0.011 0.1149859175 109 0.203 -0.646 0.723 0.202 -0.030 0.011 0.1149601028 110 0.203 -0.638 0.723 0.202 -0.030 0.011 0.1149341249 112 0.203 -0.641 0.723 0.202 -0.030 0.011 0.1149093135 114 0.203 -0.640 0.723 0.202 -0.030 0.011 0.1149081895 122 0.203 -0.640 0.618 0.202 -0.030 0.011 0.1137925047 123 0.203 -0.640 0.637 0.202 -0.030 0.011 0.1133155955 124 0.203 -0.640 0.658 0.202 -0.030 0.011 0.1131624220 126 0.203 -0.640 0.659 0.202 -0.030 0.011 0.1131607241 138 0.203 -0.640 0.659 0.239 -0.030 0.011 0.1117690752 139 0.203 -0.640 0.659 0.249 -0.030 0.011 0.1116990746 148 0.203 -0.640 0.659 0.249 0.002 0.011 0.1110058374 150 0.203 -0.640 0.659 0.249 0.009 0.011 0.1109928885 152 0.203 -0.640 0.659 0.249 0.012 0.011 0.1109923277 155 0.203 -0.640 0.659 0.249 0.011 0.011 0.1109918560 165 0.203 -0.640 0.659 0.249 0.011 0.023 0.1108774772 166 0.203 -0.640 0.659 0.249 0.011 0.025 0.1108740055 176 0.185 -0.640 0.659 0.249 0.011 0.025 0.1104775027 178 0.148 -0.640 0.659 0.249 0.011 0.025 0.1101365746 179 0.147 -0.640 0.659 0.249 0.011 0.025 0.1101230889 181 0.141 -0.640 0.659 0.249 0.011 0.025 0.1101047797 182 0.142 -0.640 0.659 0.249 0.011 0.025 0.1101038582 193 0.142 -0.637 0.659 0.249 0.011 0.025 0.1100936795 194 0.142 -0.636 0.659 0.249 0.011 0.025 0.1100920155 203 0.142 -0.636 0.624 0.249 0.011 0.025 0.1099191270 204 0.142 -0.636 0.626 0.249 0.011 0.025 0.1099004090 205 0.142 -0.636 0.635 0.249 0.011 0.025 0.1098696713 206 0.142 -0.636 0.634 0.249 0.011 0.025 0.1098682124 207 0.142 -0.636 0.633 0.249 0.011 0.025 0.1098679143 218 0.142 -0.636 0.633 0.275 0.011 0.025 0.1095496118 219 0.142 -0.636 0.633 0.272 0.011 0.025 0.1095292521 220 0.142 -0.636 0.633 0.269 0.011 0.025 0.1095254362 222 0.142 -0.636 0.633 0.268 0.011 0.025 0.1095240561 225 0.142 -0.636 0.633 0.267 0.011 0.025 0.1095237670 236 0.142 -0.636 0.633 0.267 0.008 0.025 0.1095152913 246 0.142 -0.636 0.633 0.267 0.008 0.016 0.1094430861 248 0.142 -0.636 0.633 0.267 0.008 0.013 0.1094347720 251 0.081 -0.631 0.608 0.285 0.005 0.001 0.1092368770 258 0.070 -0.630 0.604 0.289 0.004 -0.001 0.1091834610 259 0.064 -0.630 0.601 0.290 0.004 -0.002 0.1091705622 261 0.063 -0.630 0.601 0.291 0.004 -0.002 0.1091695847 262 0.063 -0.630 0.601 0.291 0.004 -0.002 0.1091694202 276 0.063 -0.630 0.601 0.291 0.004 -0.018 0.1090683424 278 0.063 -0.630 0.601 0.291 0.004 -0.016 0.1090664895 287 0.063 -0.697 0.601 0.291 0.004 -0.016 0.1088188134 288 0.063 -0.675 0.601 0.291 0.004 -0.016 0.1087908274 289 0.063 -0.680 0.601 0.291 0.004 -0.016 0.1087791364 290 0.063 -0.683 0.601 0.291 0.004 -0.016 0.1087740261 292 0.063 -0.685 0.601 0.291 0.004 -0.016 0.1087714766 300 0.063 -0.685 0.527 0.291 0.004 -0.016 0.1086968602 301 0.063 -0.685 0.561 0.291 0.004 -0.016 0.1084013625 304 0.063 -0.685 0.559 0.291 0.004 -0.016 0.1083982760 312 0.063 -0.685 0.559 0.374 0.004 -0.016 0.1074879688 313 0.063 -0.685 0.559 0.359 0.004 -0.016 0.1073068643 314 0.063 -0.685 0.559 0.348 0.004 -0.016 0.1072600868 316 0.063 -0.685 0.559 0.350 0.004 -0.016 0.1072584777 319 0.063 -0.685 0.559 0.349 0.004 -0.016 0.1072583324 329 0.063 -0.685 0.559 0.349 -0.007 -0.016 0.1072306562 330 0.063 -0.685 0.559 0.349 -0.005 -0.016 0.1072226564 331 0.063 -0.685 0.559 0.349 -0.003 -0.016 0.1072206461 338 0.040 -0.683 0.549 0.356 -0.004 -0.020 0.1069850578 340 0.037 -0.683 0.548 0.357 -0.005 -0.021 0.1069819009 344 0.037 -0.683 0.548 0.357 -0.005 -0.021 0.1069818886 345 0.037 -0.683 0.548 0.357 -0.005 -0.021 0.1069818819 346 0.037 -0.683 0.548 0.357 -0.005 -0.021 0.1069814242 357 0.037 -0.683 0.548 0.357 -0.005 -0.033 0.1069710359 358 0.037 -0.683 0.548 0.357 -0.005 -0.029 0.1069617699 359 0.037 -0.683 0.548 0.357 -0.005 -0.028 0.1069584656 360 0.037 -0.683 0.548 0.357 -0.005 -0.025 0.1069570477 362 0.037 -0.683 0.548 0.357 -0.005 -0.026 0.1069561095 369 0.037 -0.684 0.548 0.357 -0.005 -0.026 0.1069349676 372 0.037 -0.704 0.548 0.357 -0.005 -0.026 0.1066906814 374 0.037 -0.706 0.548 0.357 -0.005 -0.026 0.1066889689 383 0.037 -0.706 0.521 0.357 -0.005 -0.026 0.1063755448 385 0.037 -0.706 0.520 0.357 -0.005 -0.026 0.1063749633 395 0.037 -0.706 0.520 0.366 -0.005 -0.026 0.1063218328 396 0.037 -0.706 0.520 0.365 -0.005 -0.026 0.1063215903 407 0.037 -0.706 0.520 0.365 0.001 -0.026 0.1062978189 408 0.037 -0.706 0.520 0.365 0.003 -0.026 0.1062949581 435 0.037 -0.706 0.520 0.365 0.003 -0.030 0.1062665141 436 0.037 -0.706 0.520 0.365 0.003 -0.037 0.1062642181 438 0.037 -0.706 0.520 0.365 0.003 -0.034 0.1062610066 449 0.037 -0.702 0.520 0.365 0.003 -0.034 0.1062574819 450 0.037 -0.703 0.520 0.365 0.003 -0.034 0.1062574307 451 0.037 -0.704 0.520 0.365 0.003 -0.034 0.1062573129 459 0.037 -0.704 0.514 0.365 0.003 -0.034 0.1062290992 461 0.037 -0.704 0.512 0.365 0.003 -0.034 0.1062276281 463 0.037 -0.704 0.513 0.365 0.003 -0.034 0.1062273500 472 0.037 -0.704 0.513 0.368 0.003 -0.034 0.1062175192 484 0.037 -0.704 0.513 0.368 0.004 -0.034 0.1062170679 492 0.036 -0.704 0.513 0.368 0.004 -0.034 0.1062162706 493 0.035 -0.704 0.512 0.368 0.004 -0.034 0.1062161029 494 0.036 -0.704 0.512 0.368 0.004 -0.034 0.1062159616 495 0.036 -0.704 0.513 0.368 0.004 -0.034 0.1062158085 497 0.036 -0.704 0.513 0.368 0.004 -0.034 0.1062158018 509 0.036 -0.704 0.513 0.368 0.004 -0.033 0.1062156146 519 0.036 -0.699 0.513 0.368 0.004 -0.033 0.1062084337 520 0.036 -0.700 0.513 0.368 0.004 -0.033 0.1062080971 529 0.036 -0.700 0.511 0.368 0.004 -0.033 0.1062052817 531 0.036 -0.700 0.510 0.368 0.004 -0.033 0.1062044378 541 0.036 -0.700 0.510 0.371 0.004 -0.033 0.1061932443 553 0.036 -0.700 0.510 0.371 0.005 -0.033 0.1061928190 568 0.036 -0.696 0.507 0.374 0.006 -0.032 0.1061794847 571 0.036 -0.691 0.502 0.378 0.008 -0.030 0.1061737460 572 0.036 -0.692 0.503 0.378 0.008 -0.031 0.1061729740 590 0.036 -0.692 0.503 0.378 0.008 -0.029 0.1061704114 601 0.036 -0.694 0.503 0.378 0.008 -0.029 0.1061696215 611 0.036 -0.694 0.502 0.378 0.008 -0.029 0.1061683423 620 0.037 -0.694 0.502 0.377 0.008 -0.029 0.1061682512 621 0.036 -0.694 0.502 0.377 0.008 -0.029 0.1061681329 634 0.036 -0.694 0.502 0.377 0.006 -0.029 0.1061662794 637 0.036 -0.690 0.499 0.380 0.008 -0.028 0.1061635550 642 0.036 -0.689 0.499 0.381 0.008 -0.028 0.1061633157 643 0.036 -0.689 0.498 0.381 0.008 -0.028 0.1061632022 649 0.036 -0.689 0.498 0.381 0.008 -0.028 0.1061630480 651 0.036 -0.689 0.498 0.381 0.008 -0.028 0.1061627578 Powell done niters = 7 Computing relative cost 0 -25.0 -25.0 -25.0 1.019498 1 -25.0 -25.0 25.0 0.985191 2 -25.0 25.0 -25.0 1.045901 3 -25.0 25.0 25.0 0.969446 4 25.0 -25.0 -25.0 1.019311 5 25.0 -25.0 25.0 1.015777 6 25.0 25.0 -25.0 1.017980 7 25.0 25.0 25.0 0.995817 REL: 8 0.106163 8.068922 1.008615 rel = 0.105256 Number of iterations 7 Min cost was 0.106163 Number of FunctionCalls 653 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 1.758000 sec Parameters at optimum (transmm) 0.03647 -0.68907 0.49831 Parameters at optimum (rotdeg) 0.38096 0.00784 -0.02772 Final costs ---------------- Number of surface hits 2708 WM Intensity 61.6351 +/- 8.8930 Ctx Intensity 74.6180 +/- 8.4127 Pct Contrast 19.3022 +/- 12.5299 Cost 0.1062 RelCost 0.2882 Reg at min cost was 0.998 0.040 0.046 -0.208; -0.040 -0.138 0.990 0.397; 0.046 -0.990 -0.136 0.078; 0.000 0.000 0.000 1.000; Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/bbr.pass1.dat, type = 14 Original Reg 0.998 0.041 0.045 -0.245; -0.039 -0.144 0.989 1.084; 0.047 -0.989 -0.142 -0.427; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg 0.000 0.000 -0.000 -0.037; 0.001 -0.007 -0.001 0.686; 0.000 0.001 -0.007 -0.506; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 1.154599 Computing change in rh position Surface RMS Diff (mm) 1.150041 1.538647 mri_segreg done mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $ setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname snake4 machine x86_64 user fkaule movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/bbr.pass1.dat subject sub005 dof 6 outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1375996544 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.998 0.040 0.046 -0.208; -0.040 -0.138 0.990 0.397; 0.046 -0.990 -0.136 0.078; 0.000 0.000 0.000 1.000; Loading mov Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 1.005462 1 -25.0 -25.0 25.0 0.992291 2 -25.0 25.0 -25.0 0.996881 3 -25.0 25.0 25.0 1.003206 4 25.0 -25.0 -25.0 1.011859 5 25.0 -25.0 25.0 1.013799 6 25.0 25.0 -25.0 1.010146 7 25.0 25.0 25.0 1.017436 REL: 8 0.128535 8.051080 1.006385 rel = 0.127719 Initial costs ---------------- Number of surface hits 269746 WM Intensity 61.6292 +/- 8.6363 Ctx Intensity 74.3609 +/- 8.5585 Pct Contrast 18.9094 +/- 12.8492 Cost 0.1285 RelCost 0.1277 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1173 0.1173 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.1115 0.1115 0.0 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.1090 0.1090 0.0 30 -0.1000 -0.1000 0.0000 -0.1000 0.0000 -0.1000 0.1083 0.1083 0.0 39 -0.1000 -0.1000 0.0000 0.0000 0.0000 -0.1000 0.1074 0.1074 0.0 174 -0.1000 0.1000 -0.1000 0.0000 0.0000 -0.1000 0.1074 0.1074 0.0 177 -0.1000 0.1000 -0.1000 0.0000 0.1000 -0.1000 0.1069 0.1069 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1062 0.1062 0.0 Brute Force -------------------------- Min cost was 0.106163 Number of iterations 729 Search time 1.975000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 7 0.095 0.000 0.000 0.000 0.000 0.000 0.1276986789 8 0.086 0.000 0.000 0.000 0.000 0.000 0.1276851776 17 0.086 -0.033 0.000 0.000 0.000 0.000 0.1276021483 18 0.086 -0.026 0.000 0.000 0.000 0.000 0.1275904397 19 0.086 -0.024 0.000 0.000 0.000 0.000 0.1275888059 20 0.086 -0.023 0.000 0.000 0.000 0.000 0.1275887083 29 0.086 -0.023 -0.025 0.000 0.000 0.000 0.1275488480 31 0.086 -0.023 -0.018 0.000 0.000 0.000 0.1275401496 40 0.086 -0.023 -0.018 0.057 0.000 0.000 0.1273557294 41 0.086 -0.023 -0.018 0.037 0.000 0.000 0.1272652095 42 0.086 -0.023 -0.018 0.036 0.000 0.000 0.1272638958 43 0.086 -0.023 -0.018 0.032 0.000 0.000 0.1272637054 45 0.086 -0.023 -0.018 0.034 0.000 0.000 0.1272628172 53 0.086 -0.023 -0.018 0.034 0.073 0.000 0.1262796992 54 0.086 -0.023 -0.018 0.034 0.082 0.000 0.1262495215 55 0.086 -0.023 -0.018 0.034 0.091 0.000 0.1262414946 56 0.086 -0.023 -0.018 0.034 0.090 0.000 0.1262411198 64 0.086 -0.023 -0.018 0.034 0.090 -0.061 0.1259444663 65 0.086 -0.023 -0.018 0.034 0.090 -0.047 0.1259245357 66 0.086 -0.023 -0.018 0.034 0.090 -0.049 0.1259242525 75 0.028 -0.023 -0.018 0.034 0.090 -0.049 0.1253291140 76 0.011 -0.023 -0.018 0.034 0.090 -0.049 0.1253221404 77 0.018 -0.023 -0.018 0.034 0.090 -0.049 0.1253176300 86 0.018 -0.020 -0.018 0.034 0.090 -0.049 0.1253106241 87 0.018 -0.012 -0.018 0.034 0.090 -0.049 0.1253004838 89 0.018 -0.013 -0.018 0.034 0.090 -0.049 0.1253004170 98 0.018 -0.013 -0.029 0.034 0.090 -0.049 0.1252166108 99 0.018 -0.013 -0.060 0.034 0.090 -0.049 0.1251544413 101 0.018 -0.013 -0.052 0.034 0.090 -0.049 0.1251455374 111 0.018 -0.013 -0.052 0.055 0.090 -0.049 0.1250470272 113 0.018 -0.013 -0.052 0.054 0.090 -0.049 0.1250469694 123 0.018 -0.013 -0.052 0.054 0.104 -0.049 0.1250054866 134 0.018 -0.013 -0.052 0.054 0.105 -0.101 0.1247433447 135 0.018 -0.013 -0.052 0.054 0.105 -0.092 0.1247348076 136 0.018 -0.013 -0.052 0.054 0.105 -0.093 0.1247346904 138 -0.051 -0.002 -0.085 0.073 0.121 -0.138 0.1241889945 145 -0.064 -0.000 -0.092 0.077 0.124 -0.147 0.1241772385 146 -0.063 -0.001 -0.091 0.077 0.124 -0.146 0.1241769550 147 -0.062 -0.001 -0.091 0.076 0.123 -0.146 0.1241769070 148 -0.062 -0.001 -0.091 0.077 0.123 -0.146 0.1241768290 150 -0.062 -0.001 -0.091 0.077 0.123 -0.146 0.1241768221 159 -0.062 -0.001 -0.091 0.077 0.124 -0.142 0.1241742429 161 -0.062 -0.001 -0.091 0.077 0.124 -0.140 0.1241741537 163 -0.062 -0.001 -0.091 0.077 0.124 -0.141 0.1241740603 170 -0.062 -0.008 -0.091 0.077 0.124 -0.141 0.1241513131 171 -0.062 -0.018 -0.091 0.077 0.124 -0.141 0.1241390012 172 -0.062 -0.017 -0.091 0.077 0.124 -0.141 0.1241385887 181 -0.062 -0.017 -0.100 0.077 0.124 -0.141 0.1241307105 191 -0.062 -0.017 -0.100 0.078 0.124 -0.141 0.1241300920 192 -0.062 -0.017 -0.100 0.079 0.124 -0.141 0.1241300738 202 -0.062 -0.017 -0.100 0.079 0.121 -0.141 0.1241295335 229 -0.062 -0.017 -0.100 0.079 0.121 -0.144 0.1241288897 240 -0.062 -0.016 -0.100 0.079 0.121 -0.144 0.1241288124 249 -0.062 -0.016 -0.101 0.079 0.121 -0.144 0.1241284920 268 -0.062 -0.016 -0.101 0.079 0.122 -0.144 0.1241283505 283 -0.061 -0.016 -0.101 0.078 0.122 -0.143 0.1241282091 284 -0.061 -0.016 -0.101 0.078 0.122 -0.143 0.1241281650 Powell done niters = 4 Computing relative cost 0 -25.0 -25.0 -25.0 1.005757 1 -25.0 -25.0 25.0 0.993111 2 -25.0 25.0 -25.0 0.997448 3 -25.0 25.0 25.0 1.004378 4 25.0 -25.0 -25.0 1.012542 5 25.0 -25.0 25.0 1.014481 6 25.0 25.0 -25.0 1.010670 7 25.0 25.0 25.0 1.015250 REL: 8 0.124128 8.053638 1.006705 rel = 0.123301 Number of iterations 4 Min cost was 0.124128 Number of FunctionCalls 347 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 37.643000 sec Parameters at optimum (transmm) -0.06133 -0.01618 -0.10078 Parameters at optimum (rotdeg) 0.07825 0.12163 -0.14307 Final costs ---------------- Number of surface hits 269746 WM Intensity 61.6231 +/- 8.6135 Ctx Intensity 74.3282 +/- 8.5477 Pct Contrast 18.8727 +/- 12.8167 Cost 0.1241 RelCost 0.1277 Reg at min cost was 0.998 0.038 0.048 -0.268; -0.042 -0.136 0.990 0.382; 0.044 -0.990 -0.134 -0.021; 0.000 0.000 0.000 1.000; Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.dat, type = 14 Original Reg 0.998 0.040 0.046 -0.208; -0.040 -0.138 0.990 0.397; 0.046 -0.990 -0.136 0.078; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg 0.000 0.002 -0.002 0.060; 0.003 -0.001 -0.000 0.016; 0.002 0.000 -0.001 0.100; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.148487 Computing change in rh position Surface RMS Diff (mm) 0.171396 0.321705 mri_segreg done tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.dat --noedit --ltaout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.lta tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/T2raw.mgz reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- 0.998 0.038 0.048 -0.268; -0.042 -0.136 0.990 0.382; 0.044 -0.990 -0.134 -0.021; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- INFO: loading target /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig.mgz Ttarg: -------------------- -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; INFO: loading movable /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/T2raw.mgz Tmov: -------------------- -0.700 0.000 0.000 95.888; 0.000 0.000 0.667 -128.000; 0.000 -0.667 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 0.998 0.038 0.048 -0.268; -0.042 -0.136 0.990 0.382; 0.044 -0.990 -0.134 -0.021; 0.000 0.000 0.000 1.000; Determinant 1 subject = sub005 RegMat --------------------------- 0.998 0.038 0.048 -0.268; -0.042 -0.136 0.990 0.382; 0.044 -0.990 -0.134 -0.021; 0.000 0.000 0.000 1.000; transformed matrix: 1.000 0.002 -0.002 0.180; -0.002 1.000 0.001 0.052; 0.002 -0.001 1.000 -0.349; 0.000 0.000 0.000 1.000; transformed matrix: 0.699 0.029 0.028 20.940; 0.034 -0.090 -0.660 267.665; -0.027 0.660 -0.091 22.410; 0.000 0.000 0.000 1.000; Cleaning up Started at Thu Aug 8 22:28:33 CEST 2013 Ended at Thu Aug 8 22:40:43 CEST 2013 BBR-Run-Time-Sec 730 bbregister Done To check results, run: tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.dat --surf mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/T2.mgz mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/T2.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/T2raw.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998148, -0.0400878, -0.0457496) j_ras = (-0.0459461, 0.989757, 0.135168) k_ras = (-0.0398624, -0.13702, 0.989766) INFO: Reading transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.lta... Reading transform with LTAreadEx() reading extra input line subject sub005 reading extra input line fscale 0.150000 reading template info from volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig.mgz... INFO: Applying transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 1.000 0.002 -0.002 0.180; -0.002 1.000 0.001 0.052; 0.002 -0.001 1.000 -0.349; 0.000 0.000 0.000 1.000; --------------------------------- Applying LTAtransformInterp (resample_type 1) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/T2.mgz... mri_normalize -aseg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/aseg.mgz -sigma 4 -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white identity.nofile -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white identity.nofile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/T2.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/T2.mgz using segmentation for initial intensity normalization using Gaussian smoothing of bias field, sigma=4.000 reading from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/T2.mgz... computing distance transform computing distance transform computing nonmaximum suppression 8547 non wm control points removed building Voronoi diagram... performing soap bubble smoothing, sigma = 0... smoothing bias field writing normalized volume to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/T2.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.woT2.pial `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.woT2.pial' mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub005 lh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... refining pial surfaces placement using T2 volume ../mri/T2 using white starting white location... using woT2.pial starting pial locations... 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz... 16905 bright wm thresholded. 908 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.orig... computing class statistics... border white: 254363 voxels (1.52%) border gray 296177 voxels (1.77%) WM (91.0): 92.4 +- 10.3 [70.0 --> 110.0] GM (74.0) : 72.6 +- 12.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 46.3 (was 70) setting MAX_BORDER_WHITE to 114.3 (was 105) setting MIN_BORDER_WHITE to 59.0 (was 85) setting MAX_CSF to 33.6 (was 40) setting MAX_GRAY to 93.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 52.7 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 20.9 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104, GM=59 mean inside = 92.3, mean outside = 67.9 smoothing surface for 5 iterations... reading initial white vertex positions from white... 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.90 +- 0.26 (0.02-->6.37) (max @ vno 60346 --> 65969) face area 0.34 +- 0.16 (0.00-->6.14) averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 5 points - only 0.00% unknown deleting segment 1 with 5 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 3 points - only 0.00% unknown deleting segment 5 with 7 points - only 0.00% unknown deleting segment 7 with 7 points - only 0.00% unknown deleting segment 8 with 10 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 10 with 7 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 11 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 12 with 1 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 13 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 14 with 2 points - only 0.00% unknown deleting segment 15 with 11 points - only 0.00% unknown tol=1.0e-04, sigma=2.0, host=snake, 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 0.90 +- 0.25 (0.07-->6.37) (max @ vno 60346 --> 65969) face area 0.34 +- 0.16 (0.00-->6.14) averaging target values for 5 iterations... 000: dt: 0.0000, sse=5050607.0, rms=0.00 rms = 2.57, time step reduction 1 of 3 to 0.250... rms = 0.65, time step reduction 2 of 3 to 0.125... rms = 0.08, time step reduction 3 of 3 to 0.062... 001: dt: 0.1250, sse=5050607.0, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 5 points - only 0.00% unknown deleting segment 1 with 5 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown deleting segment 3 with 7 points - only 0.00% unknown deleting segment 4 with 7 points - only 0.00% unknown deleting segment 5 with 10 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 7 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 8 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 9 with 1 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 10 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 11 with 2 points - only 0.00% unknown deleting segment 12 with 11 points - only 0.00% unknown tol=1.0e-04, sigma=1.0, host=snake, 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-->6.37) (max @ vno 60346 --> 65969) face area 0.34 +- 0.16 (0.00-->6.14) averaging target values for 5 iterations... 000: dt: 0.0000, sse=5050607.0, rms=0.00 rms = 2.58, time step reduction 1 of 3 to 0.250... rms = 0.66, time step reduction 2 of 3 to 0.125... rms = 0.08, time step reduction 3 of 3 to 0.062... 002: dt: 0.1250, sse=5050607.0, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 5 points - only 0.00% unknown deleting segment 1 with 5 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown deleting segment 3 with 7 points - only 0.00% unknown deleting segment 4 with 7 points - only 0.00% unknown deleting segment 5 with 10 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 7 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 8 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 9 with 1 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 10 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 11 with 2 points - only 0.00% unknown deleting segment 12 with 11 points - only 0.00% unknown tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.25 (0.07-->6.37) (max @ vno 60346 --> 65969) face area 0.34 +- 0.16 (0.00-->6.14) averaging target values for 5 iterations... 000: dt: 0.0000, sse=5050607.0, rms=0.00 rms = 2.57, time step reduction 1 of 3 to 0.250... rms = 0.65, time step reduction 2 of 3 to 0.125... rms = 0.08, time step reduction 3 of 3 to 0.062... 003: dt: 0.1250, sse=5050607.0, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 5 points - only 0.00% unknown deleting segment 1 with 5 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown deleting segment 3 with 7 points - only 0.00% unknown deleting segment 4 with 7 points - only 0.00% unknown deleting segment 5 with 10 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 7 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 8 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 9 with 1 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 10 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 11 with 2 points - only 0.00% unknown deleting segment 12 with 11 points - only 0.00% unknown tol=1.0e-04, sigma=0.2, host=snake, 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=5050607.0, rms=0.00 rms = 2.58, time step reduction 1 of 3 to 0.250... rms = 0.66, time step reduction 2 of 3 to 0.125... rms = 0.08, time step reduction 3 of 3 to 0.062... 004: dt: 0.1250, sse=5050607.0, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group smoothing surface for 5 iterations... reading initial pial vertex positions from woT2.pial... repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [93.00 201.00], gm=147.00+-18.00, and vertices in regions > 138.0 39902 surface locations found to contain inconsistent values (4917 in, 34985 out) tol=1.0e-04, sigma=2.0, host=snake, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.100, l_nspring=0.050, l_location=1.000, l_curv=0.100 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=600642.1, rms=0.23 001: dt: 0.5000, sse=558236.2, rms=0.225 (0.000%) 002: dt: 0.5000, sse=533914.7, rms=0.213 (0.000%) 003: dt: 0.5000, sse=515651.6, rms=0.204 (0.000%) 004: dt: 0.5000, sse=502599.2, rms=0.196 (0.000%) 005: dt: 0.5000, sse=492409.3, rms=0.188 (0.000%) 006: dt: 0.5000, sse=483755.8, rms=0.182 (0.000%) 007: dt: 0.5000, sse=476508.9, rms=0.177 (0.000%) 008: dt: 0.5000, sse=470561.8, rms=0.173 (0.000%) 009: dt: 0.5000, sse=466122.2, rms=0.169 (0.000%) 010: dt: 0.5000, sse=461843.5, rms=0.166 (0.000%) 011: dt: 0.5000, sse=458462.7, rms=0.163 (0.000%) 012: dt: 0.5000, sse=454836.3, rms=0.161 (0.000%) 013: dt: 0.5000, sse=451619.2, rms=0.159 (0.000%) 014: dt: 0.5000, sse=448957.2, rms=0.157 (0.000%) 015: dt: 0.5000, sse=446102.2, rms=0.156 (0.000%) 016: dt: 0.5000, sse=443480.9, rms=0.155 (0.000%) 017: dt: 0.5000, sse=441197.8, rms=0.154 (0.000%) 018: dt: 0.5000, sse=439113.6, rms=0.153 (0.000%) 019: dt: 0.5000, sse=437142.9, rms=0.152 (0.000%) 020: dt: 0.5000, sse=435140.2, rms=0.152 (0.000%) 021: dt: 0.5000, sse=433160.8, rms=0.152 (0.000%) 022: dt: 0.5000, sse=431352.5, rms=0.151 (0.000%) 023: dt: 0.5000, sse=429420.1, rms=0.151 (0.000%) 024: dt: 0.5000, sse=427848.3, rms=0.151 (0.000%) 025: dt: 0.5000, sse=426204.8, rms=0.152 (0.000%) 026: dt: 0.5000, sse=424777.1, rms=0.152 (0.000%) 027: dt: 0.5000, sse=423328.6, rms=0.152 (0.000%) 028: dt: 0.5000, sse=421760.3, rms=0.152 (0.000%) 029: dt: 0.5000, sse=420302.5, rms=0.153 (0.000%) 030: dt: 0.5000, sse=418962.1, rms=0.153 (0.000%) positioning took 3.9 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [95.00 203.00], gm=149.00+-18.00, and vertices in regions > 140.0 33374 surface locations found to contain inconsistent values (2355 in, 31019 out) tol=1.0e-04, sigma=1.0, host=snake, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.010, l_nspring=0.005, l_location=1.000, l_curv=0.010 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=43511.0, rms=0.13 031: dt: 0.5000, sse=43237.3, rms=0.124 (0.000%) 032: dt: 0.5000, sse=44110.6, rms=0.114 (0.000%) 033: dt: 0.5000, sse=45179.7, rms=0.106 (0.000%) 034: dt: 0.5000, sse=46053.3, rms=0.101 (0.000%) 035: dt: 0.5000, sse=46756.7, rms=0.096 (0.000%) 036: dt: 0.5000, sse=47483.6, rms=0.091 (0.000%) 037: dt: 0.5000, sse=48150.4, rms=0.087 (0.000%) 038: dt: 0.5000, sse=48806.6, rms=0.083 (0.000%) 039: dt: 0.5000, sse=49470.3, rms=0.079 (0.000%) 040: dt: 0.5000, sse=50079.9, rms=0.076 (0.000%) 041: dt: 0.5000, sse=50691.2, rms=0.072 (0.000%) 042: dt: 0.5000, sse=51227.9, rms=0.070 (0.000%) 043: dt: 0.5000, sse=51750.8, rms=0.067 (0.000%) 044: dt: 0.5000, sse=52241.1, rms=0.064 (0.000%) 045: dt: 0.5000, sse=52685.6, rms=0.062 (0.000%) 046: dt: 0.5000, sse=53108.8, rms=0.060 (0.000%) 047: dt: 0.5000, sse=53478.3, rms=0.058 (0.000%) 048: dt: 0.5000, sse=53860.7, rms=0.056 (0.000%) 049: dt: 0.5000, sse=54227.8, rms=0.055 (0.000%) 050: dt: 0.5000, sse=54557.1, rms=0.053 (0.000%) 051: dt: 0.5000, sse=54863.1, rms=0.051 (0.000%) 052: dt: 0.5000, sse=55143.0, rms=0.050 (0.000%) 053: dt: 0.5000, sse=55400.5, rms=0.049 (0.000%) 054: dt: 0.5000, sse=55647.8, rms=0.048 (0.000%) 055: dt: 0.5000, sse=55892.6, rms=0.047 (0.000%) 056: dt: 0.5000, sse=56113.1, rms=0.045 (0.000%) 057: dt: 0.5000, sse=56309.4, rms=0.044 (0.000%) 058: dt: 0.5000, sse=56514.7, rms=0.044 (0.000%) 059: dt: 0.5000, sse=56702.4, rms=0.043 (0.000%) 060: dt: 0.5000, sse=56866.8, rms=0.042 (0.000%) positioning took 3.8 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [86.70 207.30], gm=147.00+-20.10, and vertices in regions > 136.9 31361 surface locations found to contain inconsistent values (145 in, 31216 out) tol=1.0e-04, sigma=0.5, host=snake, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.001, l_nspring=0.000, l_location=1.000, l_curv=0.001 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=6152.8, rms=0.06 061: dt: 0.5000, sse=6117.8, rms=0.056 (0.000%) 062: dt: 0.5000, sse=6198.5, rms=0.049 (0.000%) 063: dt: 0.5000, sse=6289.8, rms=0.045 (0.000%) 064: dt: 0.5000, sse=6363.1, rms=0.042 (0.000%) 065: dt: 0.5000, sse=6414.4, rms=0.040 (0.000%) 066: dt: 0.5000, sse=6444.6, rms=0.038 (0.000%) 067: dt: 0.5000, sse=6463.7, rms=0.037 (0.000%) 068: dt: 0.5000, sse=6477.9, rms=0.035 (0.000%) 069: dt: 0.5000, sse=6494.1, rms=0.034 (0.000%) 070: dt: 0.5000, sse=6508.1, rms=0.033 (0.000%) 071: dt: 0.5000, sse=6521.8, rms=0.032 (0.000%) 072: dt: 0.5000, sse=6535.8, rms=0.031 (0.000%) 073: dt: 0.5000, sse=6546.9, rms=0.030 (0.000%) 074: dt: 0.5000, sse=6556.2, rms=0.030 (0.000%) 075: dt: 0.5000, sse=6563.5, rms=0.029 (0.000%) 076: dt: 0.5000, sse=6570.3, rms=0.028 (0.000%) 077: dt: 0.5000, sse=6577.6, rms=0.028 (0.000%) 078: dt: 0.5000, sse=6583.6, rms=0.027 (0.000%) 079: dt: 0.5000, sse=6590.4, rms=0.027 (0.000%) 080: dt: 0.5000, sse=6594.0, rms=0.026 (0.000%) 081: dt: 0.5000, sse=6597.6, rms=0.026 (0.000%) 082: dt: 0.5000, sse=6603.0, rms=0.026 (0.000%) 083: dt: 0.5000, sse=6605.6, rms=0.025 (0.000%) 084: dt: 0.5000, sse=6609.8, rms=0.025 (0.000%) 085: dt: 0.5000, sse=6612.6, rms=0.025 (0.000%) 086: dt: 0.5000, sse=6617.1, rms=0.025 (0.000%) 087: dt: 0.5000, sse=6619.4, rms=0.025 (0.000%) 088: dt: 0.5000, sse=6621.2, rms=0.024 (0.000%) 089: dt: 0.5000, sse=6622.7, rms=0.024 (0.000%) 090: dt: 0.5000, sse=6622.9, rms=0.024 (0.000%) positioning took 3.8 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [94.50 205.50], gm=150.00+-18.50, and vertices in regions > 140.7 30232 surface locations found to contain inconsistent values (315 in, 29917 out) tol=1.0e-04, sigma=0.2, host=snake, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.000, l_nspring=0.000, l_location=1.000, l_curv=0.000 mom=0.00, dt=0.50 writing pial surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=788.6, rms=0.03 091: dt: 0.5000, sse=787.5, rms=0.031 (0.000%) 092: dt: 0.5000, sse=777.6, rms=0.030 (0.000%) 093: dt: 0.5000, sse=770.0, rms=0.029 (0.000%) 094: dt: 0.5000, sse=763.9, rms=0.028 (0.000%) 095: dt: 0.5000, sse=758.1, rms=0.027 (0.000%) 096: dt: 0.5000, sse=754.1, rms=0.026 (0.000%) 097: dt: 0.5000, sse=751.2, rms=0.026 (0.000%) 098: dt: 0.5000, sse=748.6, rms=0.026 (0.000%) 099: dt: 0.5000, sse=746.1, rms=0.025 (0.000%) 100: dt: 0.5000, sse=743.8, rms=0.025 (0.000%) 101: dt: 0.5000, sse=741.2, rms=0.025 (0.000%) 102: dt: 0.5000, sse=739.0, rms=0.024 (0.000%) 103: dt: 0.5000, sse=736.9, rms=0.024 (0.000%) 104: dt: 0.5000, sse=735.0, rms=0.023 (0.000%) 105: dt: 0.5000, sse=733.7, rms=0.023 (0.000%) 106: dt: 0.5000, sse=732.3, rms=0.023 (0.000%) 107: dt: 0.5000, sse=730.8, rms=0.023 (0.000%) 108: dt: 0.5000, sse=729.8, rms=0.023 (0.000%) 109: dt: 0.5000, sse=728.8, rms=0.022 (0.000%) 110: dt: 0.5000, sse=727.3, rms=0.022 (0.000%) 111: dt: 0.5000, sse=726.6, rms=0.022 (0.000%) 112: dt: 0.5000, sse=725.8, rms=0.022 (0.000%) 113: dt: 0.5000, sse=725.5, rms=0.022 (0.000%) 114: dt: 0.5000, sse=724.7, rms=0.022 (0.000%) 115: dt: 0.5000, sse=724.0, rms=0.022 (0.000%) 116: dt: 0.5000, sse=723.7, rms=0.021 (0.000%) 117: dt: 0.5000, sse=723.5, rms=0.021 (0.000%) 118: dt: 0.5000, sse=723.0, rms=0.021 (0.000%) 119: dt: 0.5000, sse=722.6, rms=0.021 (0.000%) 120: dt: 0.5000, sse=722.6, rms=0.021 (0.000%) positioning took 3.8 minutes writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.area.pial vertex spacing 1.03 +- 0.45 (0.07-->9.27) (max @ vno 100866 --> 99891) face area 0.42 +- 0.33 (0.00-->7.39) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 141918 vertices processed 25000 of 141918 vertices processed 50000 of 141918 vertices processed 75000 of 141918 vertices processed 100000 of 141918 vertices processed 125000 of 141918 vertices processed 0 of 141918 vertices processed 25000 of 141918 vertices processed 50000 of 141918 vertices processed 75000 of 141918 vertices processed 100000 of 141918 vertices processed 125000 of 141918 vertices processed thickness calculation complete, 408:1172 truncations. 26003 vertices at 0 distance 88664 vertices at 1 distance 93876 vertices at 2 distance 44360 vertices at 3 distance 13906 vertices at 4 distance 3987 vertices at 5 distance 1213 vertices at 6 distance 454 vertices at 7 distance 208 vertices at 8 distance 105 vertices at 9 distance 62 vertices at 10 distance 50 vertices at 11 distance 21 vertices at 12 distance 28 vertices at 13 distance 13 vertices at 14 distance 16 vertices at 15 distance 13 vertices at 16 distance 14 vertices at 17 distance 8 vertices at 18 distance 6 vertices at 19 distance 9 vertices at 20 distance writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.thickness positioning took 18.7 minutes /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.woT2.pial `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.woT2.pial' mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub005 rh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... refining pial surfaces placement using T2 volume ../mri/T2 using white starting white location... using woT2.pial starting pial locations... 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz... 17487 bright wm thresholded. 908 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.orig... computing class statistics... border white: 254363 voxels (1.52%) border gray 296177 voxels (1.77%) WM (91.0): 92.5 +- 10.3 [70.0 --> 110.0] GM (74.0) : 72.5 +- 12.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 44.2 (was 70) setting MAX_BORDER_WHITE to 115.3 (was 105) setting MIN_BORDER_WHITE to 57.0 (was 85) setting MAX_CSF to 31.3 (was 40) setting MAX_GRAY to 94.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 50.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 18.5 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=57 mean inside = 92.4, mean outside = 67.6 smoothing surface for 5 iterations... reading initial white vertex positions from white... 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.90 +- 0.25 (0.01-->3.85) (max @ vno 100129 --> 101238) face area 0.33 +- 0.16 (0.00-->1.91) averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 23 points - only 0.00% unknown deleting segment 3 with 417 points - only 0.00% unknown deleting segment 4 with 6 points - only 0.00% unknown deleting segment 5 with 15 points - only 0.00% unknown deleting segment 6 with 35 points - only 0.00% unknown deleting segment 8 with 123 points - only 0.00% unknown removing 2 vertex label from ripped group removing 2 vertex label from ripped group deleting segment 10 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 11 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 12 with 2 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 13 with 1 points - only 0.00% unknown tol=1.0e-04, sigma=2.0, host=snake, 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 0.90 +- 0.25 (0.04-->3.45) (max @ vno 16176 --> 26838) face area 0.33 +- 0.16 (0.00-->1.91) averaging target values for 5 iterations... 000: dt: 0.0000, sse=5162962.0, rms=0.00 rms = 1.14, time step reduction 1 of 3 to 0.250... rms = 0.29, time step reduction 2 of 3 to 0.125... rms = 0.04, time step reduction 3 of 3 to 0.062... 001: dt: 0.1250, sse=5162962.0, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 23 points - only 0.00% unknown deleting segment 1 with 417 points - only 0.00% unknown deleting segment 2 with 6 points - only 0.00% unknown deleting segment 3 with 15 points - only 0.00% unknown deleting segment 4 with 35 points - only 0.00% unknown deleting segment 5 with 123 points - only 0.00% unknown removing 2 vertex label from ripped group removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 8 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 10 with 1 points - only 0.00% unknown tol=1.0e-04, sigma=1.0, host=snake, 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 (0.04-->3.45) (max @ vno 16176 --> 26838) face area 0.33 +- 0.16 (0.00-->1.91) averaging target values for 5 iterations... 000: dt: 0.0000, sse=5162962.0, rms=0.00 rms = 1.14, time step reduction 1 of 3 to 0.250... rms = 0.29, time step reduction 2 of 3 to 0.125... rms = 0.04, time step reduction 3 of 3 to 0.062... 002: dt: 0.1250, sse=5162962.0, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 23 points - only 0.00% unknown deleting segment 1 with 417 points - only 0.00% unknown deleting segment 2 with 6 points - only 0.00% unknown deleting segment 3 with 15 points - only 0.00% unknown deleting segment 4 with 35 points - only 0.00% unknown deleting segment 5 with 123 points - only 0.00% unknown removing 2 vertex label from ripped group removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 8 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 10 with 1 points - only 0.00% unknown tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.25 (0.04-->3.45) (max @ vno 16176 --> 26838) face area 0.33 +- 0.16 (0.00-->1.91) averaging target values for 5 iterations... 000: dt: 0.0000, sse=5162962.0, rms=0.00 rms = 1.14, time step reduction 1 of 3 to 0.250... rms = 0.29, time step reduction 2 of 3 to 0.125... rms = 0.04, time step reduction 3 of 3 to 0.062... 003: dt: 0.1250, sse=5162962.0, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 23 points - only 0.00% unknown deleting segment 1 with 417 points - only 0.00% unknown deleting segment 2 with 6 points - only 0.00% unknown deleting segment 3 with 15 points - only 0.00% unknown deleting segment 4 with 35 points - only 0.00% unknown deleting segment 5 with 123 points - only 0.00% unknown removing 2 vertex label from ripped group removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 8 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 10 with 1 points - only 0.00% unknown tol=1.0e-04, sigma=0.2, host=snake, 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=5162962.0, rms=0.00 rms = 1.14, time step reduction 1 of 3 to 0.250... rms = 0.29, time step reduction 2 of 3 to 0.125... rms = 0.04, time step reduction 3 of 3 to 0.062... 004: dt: 0.1250, sse=5162962.0, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group smoothing surface for 5 iterations... reading initial pial vertex positions from woT2.pial... repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [109.60 186.40], gm=148.00+-12.80, and vertices in regions > 141.6 47738 surface locations found to contain inconsistent values (14669 in, 33069 out) tol=1.0e-04, sigma=2.0, host=snake, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.100, l_nspring=0.050, l_location=1.000, l_curv=0.100 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=595744.5, rms=0.30 001: dt: 0.5000, sse=553502.8, rms=0.293 (0.000%) 002: dt: 0.5000, sse=526265.1, rms=0.278 (0.000%) 003: dt: 0.5000, sse=507833.2, rms=0.267 (0.000%) 004: dt: 0.5000, sse=493413.0, rms=0.256 (0.000%) 005: dt: 0.5000, sse=482884.1, rms=0.247 (0.000%) 006: dt: 0.5000, sse=475175.9, rms=0.238 (0.000%) 007: dt: 0.5000, sse=468719.2, rms=0.231 (0.000%) 008: dt: 0.5000, sse=464184.7, rms=0.224 (0.000%) 009: dt: 0.5000, sse=460380.4, rms=0.218 (0.000%) 010: dt: 0.5000, sse=456370.3, rms=0.213 (0.000%) 011: dt: 0.5000, sse=452858.3, rms=0.208 (0.000%) 012: dt: 0.5000, sse=449262.8, rms=0.204 (0.000%) 013: dt: 0.5000, sse=447372.7, rms=0.200 (0.000%) 014: dt: 0.5000, sse=445664.4, rms=0.196 (0.000%) 015: dt: 0.5000, sse=442769.7, rms=0.193 (0.000%) 016: dt: 0.5000, sse=440411.4, rms=0.190 (0.000%) 017: dt: 0.5000, sse=438380.6, rms=0.188 (0.000%) 018: dt: 0.5000, sse=436463.2, rms=0.186 (0.000%) 019: dt: 0.5000, sse=434983.2, rms=0.184 (0.000%) 020: dt: 0.5000, sse=433417.6, rms=0.182 (0.000%) 021: dt: 0.5000, sse=431715.5, rms=0.181 (0.000%) 022: dt: 0.5000, sse=430139.5, rms=0.180 (0.000%) 023: dt: 0.5000, sse=428766.2, rms=0.179 (0.000%) 024: dt: 0.5000, sse=427525.1, rms=0.178 (0.000%) 025: dt: 0.5000, sse=426358.1, rms=0.177 (0.000%) 026: dt: 0.5000, sse=425162.5, rms=0.176 (0.000%) 027: dt: 0.5000, sse=423851.8, rms=0.175 (0.000%) 028: dt: 0.5000, sse=422741.6, rms=0.175 (0.000%) 029: dt: 0.5000, sse=421578.2, rms=0.175 (0.000%) 030: dt: 0.5000, sse=420429.8, rms=0.174 (0.000%) positioning took 4.0 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [92.50 203.50], gm=148.00+-18.50, and vertices in regions > 138.7 33313 surface locations found to contain inconsistent values (596 in, 32717 out) tol=1.0e-04, sigma=1.0, host=snake, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.010, l_nspring=0.005, l_location=1.000, l_curv=0.010 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=44169.9, rms=0.15 031: dt: 0.5000, sse=43709.6, rms=0.140 (0.000%) 032: dt: 0.5000, sse=43635.3, rms=0.126 (0.000%) 033: dt: 0.5000, sse=44064.6, rms=0.116 (0.000%) 034: dt: 0.5000, sse=44681.9, rms=0.109 (0.000%) 035: dt: 0.5000, sse=45409.6, rms=0.102 (0.000%) 036: dt: 0.5000, sse=46091.4, rms=0.096 (0.000%) 037: dt: 0.5000, sse=46703.8, rms=0.092 (0.000%) 038: dt: 0.5000, sse=47346.7, rms=0.087 (0.000%) 039: dt: 0.5000, sse=48021.3, rms=0.083 (0.000%) 040: dt: 0.5000, sse=48703.4, rms=0.080 (0.000%) 041: dt: 0.5000, sse=49356.8, rms=0.076 (0.000%) 042: dt: 0.5000, sse=49973.1, rms=0.073 (0.000%) 043: dt: 0.5000, sse=50597.7, rms=0.070 (0.000%) 044: dt: 0.5000, sse=51164.7, rms=0.068 (0.000%) 045: dt: 0.5000, sse=51701.1, rms=0.065 (0.000%) 046: dt: 0.5000, sse=52197.3, rms=0.063 (0.000%) 047: dt: 0.5000, sse=52662.8, rms=0.061 (0.000%) 048: dt: 0.5000, sse=53139.7, rms=0.059 (0.000%) 049: dt: 0.5000, sse=53547.9, rms=0.057 (0.000%) 050: dt: 0.5000, sse=53955.6, rms=0.056 (0.000%) 051: dt: 0.5000, sse=54322.5, rms=0.054 (0.000%) 052: dt: 0.5000, sse=54684.1, rms=0.053 (0.000%) 053: dt: 0.5000, sse=55005.9, rms=0.052 (0.000%) 054: dt: 0.5000, sse=55301.5, rms=0.050 (0.000%) 055: dt: 0.5000, sse=55574.7, rms=0.049 (0.000%) 056: dt: 0.5000, sse=55856.3, rms=0.048 (0.000%) 057: dt: 0.5000, sse=56084.7, rms=0.047 (0.000%) 058: dt: 0.5000, sse=56310.9, rms=0.046 (0.000%) 059: dt: 0.5000, sse=56538.4, rms=0.045 (0.000%) 060: dt: 0.5000, sse=56739.1, rms=0.045 (0.000%) positioning took 3.9 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [91.00 205.00], gm=148.00+-19.00, and vertices in regions > 138.5 32297 surface locations found to contain inconsistent values (167 in, 32130 out) tol=1.0e-04, sigma=0.5, host=snake, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.001, l_nspring=0.000, l_location=1.000, l_curv=0.001 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=6056.2, rms=0.05 061: dt: 0.5000, sse=6037.1, rms=0.052 (0.000%) 062: dt: 0.5000, sse=6115.4, rms=0.046 (0.000%) 063: dt: 0.5000, sse=6191.6, rms=0.042 (0.000%) 064: dt: 0.5000, sse=6254.1, rms=0.040 (0.000%) 065: dt: 0.5000, sse=6296.4, rms=0.038 (0.000%) 066: dt: 0.5000, sse=6318.2, rms=0.037 (0.000%) 067: dt: 0.5000, sse=6332.2, rms=0.035 (0.000%) 068: dt: 0.5000, sse=6344.6, rms=0.034 (0.000%) 069: dt: 0.5000, sse=6354.9, rms=0.033 (0.000%) 070: dt: 0.5000, sse=6366.8, rms=0.033 (0.000%) 071: dt: 0.5000, sse=6376.0, rms=0.032 (0.000%) 072: dt: 0.5000, sse=6388.8, rms=0.031 (0.000%) 073: dt: 0.5000, sse=6396.9, rms=0.030 (0.000%) 074: dt: 0.5000, sse=6404.4, rms=0.030 (0.000%) 075: dt: 0.5000, sse=6411.4, rms=0.029 (0.000%) 076: dt: 0.5000, sse=6418.0, rms=0.029 (0.000%) 077: dt: 0.5000, sse=6423.0, rms=0.028 (0.000%) 078: dt: 0.5000, sse=6428.2, rms=0.028 (0.000%) 079: dt: 0.5000, sse=6431.9, rms=0.028 (0.000%) 080: dt: 0.5000, sse=6435.7, rms=0.027 (0.000%) 081: dt: 0.5000, sse=6438.2, rms=0.027 (0.000%) 082: dt: 0.5000, sse=6443.0, rms=0.027 (0.000%) 083: dt: 0.5000, sse=6445.1, rms=0.026 (0.000%) 084: dt: 0.5000, sse=6448.3, rms=0.026 (0.000%) 085: dt: 0.5000, sse=6451.8, rms=0.026 (0.000%) 086: dt: 0.5000, sse=6454.8, rms=0.026 (0.000%) 087: dt: 0.5000, sse=6456.1, rms=0.026 (0.000%) 088: dt: 0.5000, sse=6458.5, rms=0.026 (0.000%) 089: dt: 0.5000, sse=6458.8, rms=0.026 (0.000%) 090: dt: 0.5000, sse=6460.6, rms=0.025 (0.000%) positioning took 3.8 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [90.10 205.90], gm=148.00+-19.30, and vertices in regions > 138.3 32407 surface locations found to contain inconsistent values (38 in, 32369 out) tol=1.0e-04, sigma=0.2, host=snake, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.000, l_nspring=0.000, l_location=1.000, l_curv=0.000 mom=0.00, dt=0.50 writing pial surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=790.5, rms=0.03 091: dt: 0.5000, sse=783.6, rms=0.033 (0.000%) 092: dt: 0.5000, sse=761.9, rms=0.029 (0.000%) 093: dt: 0.5000, sse=755.3, rms=0.028 (0.000%) 094: dt: 0.5000, sse=752.2, rms=0.027 (0.000%) 095: dt: 0.5000, sse=749.1, rms=0.026 (0.000%) 096: dt: 0.5000, sse=746.9, rms=0.026 (0.000%) 097: dt: 0.5000, sse=745.1, rms=0.026 (0.000%) 098: dt: 0.5000, sse=743.6, rms=0.026 (0.000%) 099: dt: 0.5000, sse=741.8, rms=0.025 (0.000%) 100: dt: 0.5000, sse=740.3, rms=0.025 (0.000%) 101: dt: 0.5000, sse=739.0, rms=0.025 (0.000%) 102: dt: 0.5000, sse=737.9, rms=0.025 (0.000%) 103: dt: 0.5000, sse=736.8, rms=0.024 (0.000%) 104: dt: 0.5000, sse=735.8, rms=0.024 (0.000%) 105: dt: 0.5000, sse=735.2, rms=0.024 (0.000%) 106: dt: 0.5000, sse=734.3, rms=0.024 (0.000%) 107: dt: 0.5000, sse=733.7, rms=0.024 (0.000%) 108: dt: 0.5000, sse=733.1, rms=0.024 (0.000%) 109: dt: 0.5000, sse=732.4, rms=0.024 (0.000%) 110: dt: 0.5000, sse=732.1, rms=0.024 (0.000%) 111: dt: 0.5000, sse=731.6, rms=0.024 (0.000%) 112: dt: 0.5000, sse=731.3, rms=0.023 (0.000%) 113: dt: 0.5000, sse=731.4, rms=0.023 (0.000%) 114: dt: 0.5000, sse=731.1, rms=0.023 (0.000%) 115: dt: 0.5000, sse=730.8, rms=0.023 (0.000%) 116: dt: 0.5000, sse=730.6, rms=0.023 (0.000%) 117: dt: 0.5000, sse=730.5, rms=0.023 (0.000%) 118: dt: 0.5000, sse=730.4, rms=0.023 (0.000%) 119: dt: 0.5000, sse=730.3, rms=0.023 (0.000%) 120: dt: 0.5000, sse=730.0, rms=0.023 (0.000%) positioning took 3.8 minutes writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.area.pial vertex spacing 1.03 +- 0.45 (0.06-->9.77) (max @ vno 101427 --> 100291) face area 0.41 +- 0.32 (0.00-->8.28) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 142731 vertices processed 25000 of 142731 vertices processed 50000 of 142731 vertices processed 75000 of 142731 vertices processed 100000 of 142731 vertices processed 125000 of 142731 vertices processed 0 of 142731 vertices processed 25000 of 142731 vertices processed 50000 of 142731 vertices processed 75000 of 142731 vertices processed 100000 of 142731 vertices processed 125000 of 142731 vertices processed thickness calculation complete, 479:847 truncations. 26619 vertices at 0 distance 86850 vertices at 1 distance 93570 vertices at 2 distance 45217 vertices at 3 distance 14907 vertices at 4 distance 4679 vertices at 5 distance 1443 vertices at 6 distance 510 vertices at 7 distance 201 vertices at 8 distance 105 vertices at 9 distance 67 vertices at 10 distance 46 vertices at 11 distance 39 vertices at 12 distance 35 vertices at 13 distance 32 vertices at 14 distance 22 vertices at 15 distance 23 vertices at 16 distance 28 vertices at 17 distance 14 vertices at 18 distance 27 vertices at 19 distance 32 vertices at 20 distance writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.thickness positioning took 19.2 minutes #-------------------------------------------- #@# Surf Volume lh Thu Aug 8 23:20:13 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.volume lh.area.mid mul lh.thickness Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ] #-------------------------------------------- #@# Surf Volume rh Thu Aug 8 23:20:13 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.volume rh.area.mid mul rh.thickness Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ] #-------------------------------------------- #@# Cortical ribbon mask Thu Aug 8 23:20:14 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon sub005 SUBJECTS_DIR is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer loading input data... computing distance to left white surface computing distance to left pial surface computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 11 writing volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/ribbon.mgz writing ribbon files #-------------------------------------------- #@# ASeg Stats Thu Aug 8 23:37:33 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005 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 /opt/freesurfer/5.3.0/ASegStatsLUT.txt --subject sub005 $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 /opt/freesurfer/5.3.0/ASegStatsLUT.txt --subject sub005 sysname Linux hostname snake4 machine x86_64 user fkaule UseRobust 0 atlas_icv (eTIV) = 1108117 mm^3 (det: 1.758032 ) Computing euler number orig.nofix lheno = -46, rheno = -26 orig.nofix lhholes = 24, rhholes = 14 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 265530.343 264563.000 diff= 967.3 pctdiff= 0.364 rhCtxGM: 265717.542 264874.000 diff= 843.5 pctdiff= 0.317 lhCtxWM: 210790.046 210779.500 diff= 10.5 pctdiff= 0.005 rhCtxWM: 210686.930 210543.500 diff= 143.4 pctdiff= 0.068 SubCortGMVol 62575.000 SupraTentVol 1025743.861 (1023088.000) diff=2655.861 pctdiff=0.259 SupraTentVolNotVent 1016210.861 (1013555.000) diff=2655.861 pctdiff=0.261 BrainSegVol 1150498.000 (1149006.000) diff=1492.000 pctdiff=0.130 BrainSegVolNotVent 1139009.000 (1140759.861) diff=-1750.861 pctdiff=-0.154 BrainSegVolNotVent 1139009.000 CerebellumVol 125240.000 VentChorVol 9533.000 3rd4th5thCSF 1956.000 CSFVol 477.000, OptChiasmVol 201.000 MaskVol 1526731.000 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 3278 3277.959 4 5 Left-Inf-Lat-Vent 580 579.936 5 7 Left-Cerebellum-White-Matter 12975 12975.378 6 8 Left-Cerebellum-Cortex 49757 49756.992 7 10 Left-Thalamus-Proper 7832 7832.081 8 11 Left-Caudate 3508 3508.107 9 12 Left-Putamen 6400 6400.005 10 13 Left-Pallidum 1978 1978.220 11 14 3rd-Ventricle 341 341.234 12 15 4th-Ventricle 1298 1297.907 13 16 Brain-Stem 20989 20988.875 14 17 Left-Hippocampus 3854 3853.685 15 18 Left-Amygdala 1671 1670.966 16 24 CSF 491 491.288 17 26 Left-Accumbens-area 577 577.471 18 28 Left-VentralDC 4012 4012.331 19 30 Left-vessel 127 127.376 20 31 Left-choroid-plexus 1356 1356.293 23 43 Right-Lateral-Ventricle 2569 2569.490 24 44 Right-Inf-Lat-Vent 409 409.412 25 46 Right-Cerebellum-White-Matter 14142 14142.228 26 47 Right-Cerebellum-Cortex 50562 50562.211 27 49 Right-Thalamus-Proper 7753 7752.948 28 50 Right-Caudate 3833 3832.621 29 51 Right-Putamen 6146 6145.553 30 52 Right-Pallidum 2178 2178.489 31 53 Right-Hippocampus 4059 4058.912 32 54 Right-Amygdala 1391 1391.412 33 58 Right-Accumbens-area 632 631.959 34 60 Right-VentralDC 4180 4180.111 35 62 Right-vessel 65 65.004 36 63 Right-choroid-plexus 1217 1216.556 37 72 5th-Ventricle 0 0.000 38 77 WM-hypointensities 1410 1410.145 39 78 Left-WM-hypointensities 0 0.000 40 79 Right-WM-hypointensities 0 0.000 41 80 non-WM-hypointensities 9 9.365 42 81 Left-non-WM-hypointensities 0 0.000 43 82 Right-non-WM-hypointensities 0 0.000 44 85 Optic-Chiasm 220 220.139 45 251 CC_Posterior 700 700.031 46 252 CC_Mid_Posterior 332 332.204 47 253 CC_Central 354 353.958 48 254 CC_Mid_Anterior 393 392.745 49 255 CC_Anterior 742 742.297 Reporting on 45 segmentations mri_segstats done #----------------------------------------- #@# AParc-to-ASeg Thu Aug 8 23:40:22 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005 mri_aparc2aseg --s sub005 --volmask SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer subject sub005 outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white Reading lh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.pial Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white Reading rh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.pial Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 = 527907 Used brute-force search on 0 voxels Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/aparc+aseg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005 mri_aparc2aseg --s sub005 --volmask --a2009s SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer subject sub005 outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white Reading lh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.pial Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white Reading rh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.pial Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 = 527907 Used brute-force search on 0 voxels Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# WMParc Thu Aug 8 23:45:15 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005 mri_aparc2aseg --s sub005 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer subject sub005 outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/aparc+aseg.mgz Reading lh white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white Reading lh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.pial Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white Reading rh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.pial Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/ribbon.mgz Loading filled from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/filled.mgz Ripping vertices labeled as unkown Ripped 7419 vertices from left hemi Ripped 7484 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/aseg.mgz Loading Ctx Seg File /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 = 948174 Used brute-force search on 3 voxels Fixing Parahip LH WM Found 11 clusters 0 k 1.000000 1 k 1.000000 2 k 1.000000 3 k 4.000000 4 k 6.000000 5 k 1.000000 6 k 1.000000 7 k 3.000000 8 k 2.000000 9 k 1266.000000 10 k 5.000000 Fixing Parahip RH WM Found 1 clusters 0 k 1504.000000 Writing output aseg to mri/wmparc.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005 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 sub005 --surf-wm-vol --ctab /opt/freesurfer/5.3.0/WMParcStatsLUT.txt --etiv $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 sub005 --surf-wm-vol --ctab /opt/freesurfer/5.3.0/WMParcStatsLUT.txt --etiv sysname Linux hostname snake4 machine x86_64 user fkaule UseRobust 0 atlas_icv (eTIV) = 1108117 mm^3 (det: 1.758032 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 265530.343 264563.000 diff= 967.3 pctdiff= 0.364 rhCtxGM: 265717.542 264874.000 diff= 843.5 pctdiff= 0.317 lhCtxWM: 210790.046 210779.500 diff= 10.5 pctdiff= 0.005 rhCtxWM: 210686.930 210543.500 diff= 143.4 pctdiff= 0.068 SubCortGMVol 62575.000 SupraTentVol 1025743.861 (1023088.000) diff=2655.861 pctdiff=0.259 SupraTentVolNotVent 1016210.861 (1013555.000) diff=2655.861 pctdiff=0.261 BrainSegVol 1150498.000 (1149006.000) diff=1492.000 pctdiff=0.130 BrainSegVolNotVent 1139009.000 (1140759.861) diff=-1750.861 pctdiff=-0.154 BrainSegVolNotVent 1139009.000 CerebellumVol 125240.000 VentChorVol 9533.000 3rd4th5thCSF 1956.000 CSFVol 477.000, OptChiasmVol 201.000 MaskVol 1526731.000 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 3450 3450.128 2 3002 wm-lh-caudalanteriorcingulate 3079 3079.494 3 3003 wm-lh-caudalmiddlefrontal 5858 5858.020 4 3004 wm-lh-corpuscallosum 0 0.000 5 3005 wm-lh-cuneus 2317 2316.710 6 3006 wm-lh-entorhinal 737 737.111 7 3007 wm-lh-fusiform 6795 6795.264 8 3008 wm-lh-inferiorparietal 8042 8041.741 9 3009 wm-lh-inferiortemporal 5693 5693.238 10 3010 wm-lh-isthmuscingulate 3544 3544.322 11 3011 wm-lh-lateraloccipital 9210 9210.244 12 3012 wm-lh-lateralorbitofrontal 6234 6234.106 13 3013 wm-lh-lingual 5646 5646.042 14 3014 wm-lh-medialorbitofrontal 2965 2965.262 15 3015 wm-lh-middletemporal 4819 4819.383 16 3016 wm-lh-parahippocampal 1324 1324.135 17 3017 wm-lh-paracentral 2937 2937.116 18 3018 wm-lh-parsopercularis 3904 3903.856 19 3019 wm-lh-parsorbitalis 887 887.268 20 3020 wm-lh-parstriangularis 3079 3079.248 21 3021 wm-lh-pericalcarine 3652 3652.237 22 3022 wm-lh-postcentral 7938 7937.846 23 3023 wm-lh-posteriorcingulate 4597 4596.842 24 3024 wm-lh-precentral 11645 11645.031 25 3025 wm-lh-precuneus 8653 8652.616 26 3026 wm-lh-rostralanteriorcingulate 3059 3058.752 27 3027 wm-lh-rostralmiddlefrontal 12814 12814.424 28 3028 wm-lh-superiorfrontal 17570 17569.916 29 3029 wm-lh-superiorparietal 9900 9900.281 30 3030 wm-lh-superiortemporal 8486 8486.334 31 3031 wm-lh-supramarginal 8145 8145.244 32 3032 wm-lh-frontalpole 244 244.129 33 3033 wm-lh-temporalpole 612 612.238 34 3034 wm-lh-transversetemporal 894 894.139 35 3035 wm-lh-insula 8582 8582.195 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 3220 3219.576 120 4002 wm-rh-caudalanteriorcingulate 3311 3310.707 121 4003 wm-rh-caudalmiddlefrontal 4912 4912.257 122 4004 wm-rh-corpuscallosum 0 0.000 123 4005 wm-rh-cuneus 2049 2048.841 124 4006 wm-rh-entorhinal 470 469.973 125 4007 wm-rh-fusiform 5955 5954.564 126 4008 wm-rh-inferiorparietal 9604 9604.001 127 4009 wm-rh-inferiortemporal 5882 5882.254 128 4010 wm-rh-isthmuscingulate 2583 2582.677 129 4011 wm-rh-lateraloccipital 9286 9286.469 130 4012 wm-rh-lateralorbitofrontal 6155 6154.931 131 4013 wm-rh-lingual 5510 5509.599 132 4014 wm-rh-medialorbitofrontal 3455 3455.048 133 4015 wm-rh-middletemporal 6159 6158.569 134 4016 wm-rh-parahippocampal 1559 1558.510 135 4017 wm-rh-paracentral 3884 3884.006 136 4018 wm-rh-parsopercularis 3478 3478.004 137 4019 wm-rh-parsorbitalis 1207 1207.092 138 4020 wm-rh-parstriangularis 3691 3690.768 139 4021 wm-rh-pericalcarine 3452 3452.041 140 4022 wm-rh-postcentral 7737 7737.457 141 4023 wm-rh-posteriorcingulate 5053 5053.350 142 4024 wm-rh-precentral 12575 12574.738 143 4025 wm-rh-precuneus 9707 9706.634 144 4026 wm-rh-rostralanteriorcingulate 2264 2264.011 145 4027 wm-rh-rostralmiddlefrontal 12224 12223.950 146 4028 wm-rh-superiorfrontal 17833 17832.582 147 4029 wm-rh-superiorparietal 9683 9682.954 148 4030 wm-rh-superiortemporal 7574 7574.444 149 4031 wm-rh-supramarginal 7712 7712.035 150 4032 wm-rh-frontalpole 276 275.609 151 4033 wm-rh-temporalpole 623 622.763 152 4034 wm-rh-transversetemporal 632 632.412 153 4035 wm-rh-insula 7648 7648.365 154 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 24132 24131.932 237 5002 Right-UnsegmentedWhiteMatter 24033 24033.498 238 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label #-------------------------------------------- #@# BA Labels lh Thu Aug 8 23:56:39 CEST 2013 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.label --trgsubject sub005 --trglabel ./lh.BA1.label --hemi lh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918 Number of reverse mapping hits = 365 Checking for and removing duplicates Writing label file ./lh.BA1.label 4494 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.label --trgsubject sub005 --trglabel ./lh.BA2.label --hemi lh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918 Number of reverse mapping hits = 907 Checking for and removing duplicates Writing label file ./lh.BA2.label 8816 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.label --trgsubject sub005 --trglabel ./lh.BA3a.label --hemi lh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918 Number of reverse mapping hits = 198 Checking for and removing duplicates Writing label file ./lh.BA3a.label 4275 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.label --trgsubject sub005 --trglabel ./lh.BA3b.label --hemi lh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918 Number of reverse mapping hits = 428 Checking for and removing duplicates Writing label file ./lh.BA3b.label 6411 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.label --trgsubject sub005 --trglabel ./lh.BA4a.label --hemi lh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918 Number of reverse mapping hits = 261 Checking for and removing duplicates Writing label file ./lh.BA4a.label 6045 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.label --trgsubject sub005 --trglabel ./lh.BA4p.label --hemi lh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918 Number of reverse mapping hits = 239 Checking for and removing duplicates Writing label file ./lh.BA4p.label 4309 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.label --trgsubject sub005 --trglabel ./lh.BA6.label --hemi lh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918 Number of reverse mapping hits = 1562 Checking for and removing duplicates Writing label file ./lh.BA6.label 15151 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.label --trgsubject sub005 --trglabel ./lh.BA44.label --hemi lh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918 Number of reverse mapping hits = 621 Checking for and removing duplicates Writing label file ./lh.BA44.label 4802 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.label --trgsubject sub005 --trglabel ./lh.BA45.label --hemi lh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918 Number of reverse mapping hits = 994 Checking for and removing duplicates Writing label file ./lh.BA45.label 4416 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.label --trgsubject sub005 --trglabel ./lh.V1.label --hemi lh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918 Number of reverse mapping hits = 2066 Checking for and removing duplicates Writing label file ./lh.V1.label 6707 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.label --trgsubject sub005 --trglabel ./lh.V2.label --hemi lh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918 Number of reverse mapping hits = 4214 Checking for and removing duplicates Writing label file ./lh.V2.label 12328 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.label --trgsubject sub005 --trglabel ./lh.MT.label --hemi lh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918 Number of reverse mapping hits = 844 Checking for and removing duplicates Writing label file ./lh.MT.label 2862 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.perirhinal.label --trgsubject sub005 --trglabel ./lh.perirhinal.label --hemi lh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.perirhinal.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918 Number of reverse mapping hits = 171 Checking for and removing duplicates Writing label file ./lh.perirhinal.label 1370 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.thresh.label --trgsubject sub005 --trglabel ./lh.BA1.thresh.label --hemi lh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.thresh.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918 Number of reverse mapping hits = 53 Checking for and removing duplicates Writing label file ./lh.BA1.thresh.label 1067 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.thresh.label --trgsubject sub005 --trglabel ./lh.BA2.thresh.label --hemi lh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.thresh.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918 Number of reverse mapping hits = 421 Checking for and removing duplicates Writing label file ./lh.BA2.thresh.label 2513 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.thresh.label --trgsubject sub005 --trglabel ./lh.BA3a.thresh.label --hemi lh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.thresh.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918 Number of reverse mapping hits = 35 Checking for and removing duplicates Writing label file ./lh.BA3a.thresh.label 1539 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.thresh.label --trgsubject sub005 --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.thresh.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918 Number of reverse mapping hits = 160 Checking for and removing duplicates Writing label file ./lh.BA3b.thresh.label 2156 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.thresh.label --trgsubject sub005 --trglabel ./lh.BA4a.thresh.label --hemi lh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.thresh.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918 Number of reverse mapping hits = 108 Checking for and removing duplicates Writing label file ./lh.BA4a.thresh.label 2427 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.thresh.label --trgsubject sub005 --trglabel ./lh.BA4p.thresh.label --hemi lh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.thresh.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918 Number of reverse mapping hits = 119 Checking for and removing duplicates Writing label file ./lh.BA4p.thresh.label 1668 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.thresh.label --trgsubject sub005 --trglabel ./lh.BA6.thresh.label --hemi lh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.thresh.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918 Number of reverse mapping hits = 682 Checking for and removing duplicates Writing label file ./lh.BA6.thresh.label 7717 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.thresh.label --trgsubject sub005 --trglabel ./lh.BA44.thresh.label --hemi lh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.thresh.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918 Number of reverse mapping hits = 285 Checking for and removing duplicates Writing label file ./lh.BA44.thresh.label 2197 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.thresh.label --trgsubject sub005 --trglabel ./lh.BA45.thresh.label --hemi lh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.thresh.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918 Number of reverse mapping hits = 531 Checking for and removing duplicates Writing label file ./lh.BA45.thresh.label 1682 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.thresh.label --trgsubject sub005 --trglabel ./lh.V1.thresh.label --hemi lh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.thresh.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918 Number of reverse mapping hits = 1544 Checking for and removing duplicates Writing label file ./lh.V1.thresh.label 4949 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.thresh.label --trgsubject sub005 --trglabel ./lh.V2.thresh.label --hemi lh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.thresh.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918 Number of reverse mapping hits = 1787 Checking for and removing duplicates Writing label file ./lh.V2.thresh.label 5121 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.thresh.label --trgsubject sub005 --trglabel ./lh.MT.thresh.label --hemi lh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.thresh.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918 Number of reverse mapping hits = 248 Checking for and removing duplicates Writing label file ./lh.MT.thresh.label 761 mri_label2label: Done mris_label2annot --s sub005 --hemi lh --ctab /opt/freesurfer/5.3.0/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 Reading ctab /opt/freesurfer/5.3.0/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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label cmdline mris_label2annot --s sub005 --hemi lh --ctab /opt/freesurfer/5.3.0/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 Linux hostname snake4 machine x86_64 user fkaule subject sub005 hemi lh SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer ColorTable /opt/freesurfer/5.3.0/average/colortable_BA.txt AnnotName BA nlables 13 LabelThresh 0 0.000000 Loading /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 95912 unhit vertices Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/lh.BA.annot mris_label2annot --s sub005 --hemi lh --ctab /opt/freesurfer/5.3.0/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 Reading ctab /opt/freesurfer/5.3.0/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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label cmdline mris_label2annot --s sub005 --hemi lh --ctab /opt/freesurfer/5.3.0/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 Linux hostname snake4 machine x86_64 user fkaule subject sub005 hemi lh SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer ColorTable /opt/freesurfer/5.3.0/average/colortable_BA.txt AnnotName BA.thresh nlables 12 LabelThresh 0 0.000000 Loading /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 115470 unhit vertices Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/lh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab sub005 lh white computing statistics for each annotation in ./lh.BA.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /opt/freesurfer/5.3.0/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 1026 622 2411 2.723 0.400 0.177 0.069 27 2.7 BA1 4750 3166 8222 2.418 0.459 0.134 0.044 64 8.5 BA2 981 660 1032 2.009 0.416 0.131 0.073 10 1.6 BA3a 2545 1704 4262 2.134 0.609 0.142 0.056 55 5.5 BA3b 1426 887 3348 2.907 0.563 0.122 0.057 23 3.4 BA4a 1346 911 2520 2.663 0.446 0.118 0.074 23 5.7 BA4p 10036 6823 23603 2.795 0.545 0.135 0.043 150 18.1 BA6 2472 1671 5347 2.737 0.459 0.148 0.050 44 4.8 BA44 3412 2305 6933 2.529 0.607 0.155 0.063 69 8.4 BA45 4350 3000 6105 1.972 0.520 0.166 0.079 87 12.6 V1 9950 6520 15611 2.236 0.515 0.173 0.084 254 31.5 V2 2611 1725 4760 2.450 0.433 0.156 0.064 59 6.7 MT 1101 746 3309 3.365 0.725 0.175 0.102 29 4.1 perirhinal mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab sub005 lh white computing statistics for each annotation in ./lh.BA.thresh.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /opt/freesurfer/5.3.0/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 630 380 1469 2.704 0.443 0.183 0.077 17 1.7 BA1 2031 1338 3733 2.372 0.437 0.144 0.055 35 4.4 BA2 815 554 815 1.971 0.412 0.139 0.040 7 1.3 BA3a 1591 1079 2219 1.844 0.441 0.121 0.033 16 2.3 BA3b 1353 861 3359 2.992 0.504 0.119 0.057 21 3.3 BA4a 1134 759 1989 2.619 0.429 0.110 0.030 8 1.4 BA4p 5447 3689 12997 2.825 0.542 0.137 0.043 78 9.9 BA6 1718 1154 3620 2.670 0.455 0.142 0.044 27 3.1 BA44 1585 1060 3854 2.844 0.441 0.182 0.085 45 5.4 BA45 4634 3169 6415 1.960 0.513 0.166 0.079 92 13.8 V1 4772 3149 7474 2.177 0.540 0.187 0.100 143 17.3 V2 738 500 1210 2.380 0.431 0.136 0.041 8 1.2 MT #-------------------------------------------- #@# BA Labels rh Fri Aug 9 00:01:11 CEST 2013 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.label --trgsubject sub005 --trglabel ./rh.BA1.label --hemi rh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731 Number of reverse mapping hits = 464 Checking for and removing duplicates Writing label file ./rh.BA1.label 4426 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.label --trgsubject sub005 --trglabel ./rh.BA2.label --hemi rh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731 Number of reverse mapping hits = 750 Checking for and removing duplicates Writing label file ./rh.BA2.label 7437 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.label --trgsubject sub005 --trglabel ./rh.BA3a.label --hemi rh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731 Number of reverse mapping hits = 223 Checking for and removing duplicates Writing label file ./rh.BA3a.label 4203 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.label --trgsubject sub005 --trglabel ./rh.BA3b.label --hemi rh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731 Number of reverse mapping hits = 370 Checking for and removing duplicates Writing label file ./rh.BA3b.label 4892 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.label --trgsubject sub005 --trglabel ./rh.BA4a.label --hemi rh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731 Number of reverse mapping hits = 244 Checking for and removing duplicates Writing label file ./rh.BA4a.label 5991 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.label --trgsubject sub005 --trglabel ./rh.BA4p.label --hemi rh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731 Number of reverse mapping hits = 184 Checking for and removing duplicates Writing label file ./rh.BA4p.label 4657 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.label --trgsubject sub005 --trglabel ./rh.BA6.label --hemi rh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731 Number of reverse mapping hits = 1182 Checking for and removing duplicates Writing label file ./rh.BA6.label 13438 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.label --trgsubject sub005 --trglabel ./rh.BA44.label --hemi rh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731 Number of reverse mapping hits = 1300 Checking for and removing duplicates Writing label file ./rh.BA44.label 8212 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.label --trgsubject sub005 --trglabel ./rh.BA45.label --hemi rh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731 Number of reverse mapping hits = 1267 Checking for and removing duplicates Writing label file ./rh.BA45.label 6622 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.label --trgsubject sub005 --trglabel ./rh.V1.label --hemi rh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731 Number of reverse mapping hits = 2180 Checking for and removing duplicates Writing label file ./rh.V1.label 6907 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.label --trgsubject sub005 --trglabel ./rh.V2.label --hemi rh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731 Number of reverse mapping hits = 4090 Checking for and removing duplicates Writing label file ./rh.V2.label 12106 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.label --trgsubject sub005 --trglabel ./rh.MT.label --hemi rh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731 Number of reverse mapping hits = 678 Checking for and removing duplicates Writing label file ./rh.MT.label 2610 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.perirhinal.label --trgsubject sub005 --trglabel ./rh.perirhinal.label --hemi rh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.perirhinal.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731 Number of reverse mapping hits = 67 Checking for and removing duplicates Writing label file ./rh.perirhinal.label 819 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.thresh.label --trgsubject sub005 --trglabel ./rh.BA1.thresh.label --hemi rh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.thresh.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731 Number of reverse mapping hits = 85 Checking for and removing duplicates Writing label file ./rh.BA1.thresh.label 961 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.thresh.label --trgsubject sub005 --trglabel ./rh.BA2.thresh.label --hemi rh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.thresh.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731 Number of reverse mapping hits = 400 Checking for and removing duplicates Writing label file ./rh.BA2.thresh.label 3088 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.thresh.label --trgsubject sub005 --trglabel ./rh.BA3a.thresh.label --hemi rh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.thresh.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731 Number of reverse mapping hits = 51 Checking for and removing duplicates Writing label file ./rh.BA3a.thresh.label 1749 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.thresh.label --trgsubject sub005 --trglabel ./rh.BA3b.thresh.label --hemi rh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.thresh.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731 Number of reverse mapping hits = 253 Checking for and removing duplicates Writing label file ./rh.BA3b.thresh.label 2436 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.thresh.label --trgsubject sub005 --trglabel ./rh.BA4a.thresh.label --hemi rh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.thresh.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731 Number of reverse mapping hits = 52 Checking for and removing duplicates Writing label file ./rh.BA4a.thresh.label 1440 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.thresh.label --trgsubject sub005 --trglabel ./rh.BA4p.thresh.label --hemi rh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.thresh.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731 Number of reverse mapping hits = 84 Checking for and removing duplicates Writing label file ./rh.BA4p.thresh.label 1573 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.thresh.label --trgsubject sub005 --trglabel ./rh.BA6.thresh.label --hemi rh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.thresh.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731 Number of reverse mapping hits = 634 Checking for and removing duplicates Writing label file ./rh.BA6.thresh.label 7593 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.thresh.label --trgsubject sub005 --trglabel ./rh.BA44.thresh.label --hemi rh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.thresh.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731 Number of reverse mapping hits = 294 Checking for and removing duplicates Writing label file ./rh.BA44.thresh.label 1306 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.thresh.label --trgsubject sub005 --trglabel ./rh.BA45.thresh.label --hemi rh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.thresh.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731 Number of reverse mapping hits = 210 Checking for and removing duplicates Writing label file ./rh.BA45.thresh.label 1388 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.thresh.label --trgsubject sub005 --trglabel ./rh.V1.thresh.label --hemi rh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.thresh.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731 Number of reverse mapping hits = 1478 Checking for and removing duplicates Writing label file ./rh.V1.thresh.label 4710 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.thresh.label --trgsubject sub005 --trglabel ./rh.V2.thresh.label --hemi rh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.thresh.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731 Number of reverse mapping hits = 1846 Checking for and removing duplicates Writing label file ./rh.V2.thresh.label 5283 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.thresh.label --trgsubject sub005 --trglabel ./rh.MT.thresh.label --hemi rh --regmethod surface srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.thresh.label srcsubject = fsaverage trgsubject = sub005 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731 Number of reverse mapping hits = 104 Checking for and removing duplicates Writing label file ./rh.MT.thresh.label 372 mri_label2label: Done mris_label2annot --s sub005 --hemi rh --ctab /opt/freesurfer/5.3.0/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 Reading ctab /opt/freesurfer/5.3.0/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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label cmdline mris_label2annot --s sub005 --hemi rh --ctab /opt/freesurfer/5.3.0/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 Linux hostname snake4 machine x86_64 user fkaule subject sub005 hemi rh SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer ColorTable /opt/freesurfer/5.3.0/average/colortable_BA.txt AnnotName BA nlables 13 LabelThresh 0 0.000000 Loading /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 97144 unhit vertices Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/rh.BA.annot mris_label2annot --s sub005 --hemi rh --ctab /opt/freesurfer/5.3.0/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 Reading ctab /opt/freesurfer/5.3.0/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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label cmdline mris_label2annot --s sub005 --hemi rh --ctab /opt/freesurfer/5.3.0/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 Linux hostname snake4 machine x86_64 user fkaule subject sub005 hemi rh SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer ColorTable /opt/freesurfer/5.3.0/average/colortable_BA.txt AnnotName BA.thresh nlables 12 LabelThresh 0 0.000000 Loading /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 117875 unhit vertices Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/rh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab sub005 rh white computing statistics for each annotation in ./rh.BA.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /opt/freesurfer/5.3.0/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 975 595 2203 2.639 0.530 0.171 0.065 25 2.4 BA1 3840 2574 6869 2.407 0.495 0.136 0.047 59 7.9 BA2 1071 723 1151 1.991 0.455 0.139 0.040 11 2.0 BA3a 2158 1451 3589 2.086 0.615 0.137 0.043 32 3.8 BA3b 1379 886 3306 2.871 0.451 0.115 0.035 12 2.1 BA4a 1210 820 2193 2.588 0.464 0.111 0.033 10 1.6 BA4p 8459 5637 20058 2.858 0.530 0.138 0.045 124 16.2 BA6 4455 3008 8970 2.721 0.412 0.147 0.049 78 9.3 BA44 4707 3204 10460 2.699 0.493 0.171 0.081 127 13.1 BA45 4620 3252 6567 1.959 0.449 0.171 0.075 105 13.7 V1 9723 6398 14910 2.208 0.498 0.173 0.075 268 27.2 V2 2416 1636 4124 2.457 0.483 0.137 0.043 34 4.3 MT 574 404 1552 3.250 0.612 0.181 0.076 11 1.9 perirhinal mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab sub005 rh white computing statistics for each annotation in ./rh.BA.thresh.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /opt/freesurfer/5.3.0/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 657 378 1476 2.700 0.521 0.167 0.062 17 1.6 BA1 2341 1576 4341 2.410 0.509 0.137 0.045 36 4.0 BA2 896 602 889 1.983 0.436 0.140 0.040 8 1.5 BA3a 1801 1240 2555 1.856 0.456 0.123 0.035 19 2.8 BA3b 787 493 1834 2.889 0.432 0.120 0.039 9 1.3 BA4a 1029 701 1835 2.580 0.468 0.110 0.032 8 1.4 BA4p 5314 3504 12341 2.823 0.558 0.133 0.043 74 9.7 BA6 1147 777 2509 2.793 0.368 0.152 0.056 23 2.7 BA44 1152 784 3010 2.942 0.412 0.186 0.119 42 3.4 BA45 4420 3110 6220 1.954 0.446 0.166 0.073 96 12.7 V1 4971 3333 7490 2.104 0.529 0.188 0.093 178 15.6 V2 341 227 697 2.638 0.407 0.158 0.064 8 0.9 MT /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label lh Fri Aug 9 00:05:43 CEST 2013 mris_spherical_average -erode 1 -orig white -t 0.4 -o sub005 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject sub005. processing subject lh.EC_average... reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 1036 points to lh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label sub005 lh white limiting computations to label ./lh.entorhinal_exvivo.label. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 348 238 1115 3.022 0.738 0.148 0.061 6 1.1 ./lh.entorhinal_exvivo.label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label rh Fri Aug 9 00:05:58 CEST 2013 mris_spherical_average -erode 1 -orig white -t 0.4 -o sub005 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label painting output onto subject sub005. processing subject rh.EC_average... reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 680 points to rh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label sub005 rh white limiting computations to label ./rh.entorhinal_exvivo.label. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 186 126 548 2.946 0.441 0.175 0.047 4 0.4 ./rh.entorhinal_exvivo.label #------------------------------------------ Started at Thu Aug 8 10:53:42 CEST 2013 Ended at Fri Aug 9 00:06:13 CEST 2013 #@#%# recon-all-run-time-hours 13.209 recon-all -s sub005 finished without error at Fri Aug 9 00:06:14 CEST 2013