Thu Aug 8 10:54:16 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009 /opt/freesurfer/5.3.0/bin/recon-all -i /home/data/exppsy/forrest_gump/openfmri.org/sub009/anatomy/highres001.nii.gz -cw256 -all -T2 /home/data/exppsy/forrest_gump/openfmri.org/sub009/anatomy/other/t2w001.nii.gz -T2pial -subjid sub009 -sd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer subjid sub009 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 snake6 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 96979476 2222216 0 118440 94733872 -/+ buffers/cache: 2127164 97074528 Swap: 25165780 2780 25163000 ######################################## 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: 2013/08/08-08:54:16-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: snake6 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: 2013/08/08-08:54:17-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: snake6 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: 2013/08/08-08:54:17-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: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:17-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: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:17-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: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:17-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: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:17-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: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:17-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: snake6 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: 2013/08/08-08:54:18-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: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-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: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-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: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-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: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-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: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-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: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-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: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-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: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-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: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-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: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-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: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-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: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-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: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-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: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-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: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-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: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-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: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-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: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-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: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-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: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-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: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-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: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-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: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-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: snake6 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: 2013/08/08-08:54:20-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: snake6 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: 2013/08/08-08:54:20-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: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-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: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-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: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-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: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-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: snake6 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/sub009 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub009/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/orig/001.mgz mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub009/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/anatomy/highres001.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.995894, -0.015333, -0.0892185) j_ras = (-0.0248655, 0.993977, 0.106735) k_ras = (-0.0870445, -0.108515, 0.990277) writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/orig/001.mgz... #-------------------------------------------- #@# T2/FLAIR Input Thu Aug 8 10:54:37 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub009/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/orig/T2raw.mgz mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub009/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/anatomy/other/t2w001.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.995894, -0.015333, -0.0892185) j_ras = (-0.0248655, 0.993977, 0.106735) k_ras = (-0.0870445, -0.108515, 0.990277) writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/orig/T2raw.mgz... #-------------------------------------------- #@# MotionCor Thu Aug 8 10:54:53 CEST 2013 Found 1 runs /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/mri/orig/001.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/orig.mgz --conform --cw256 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.995894, -0.015333, -0.0892185) j_ras = (-0.0248655, 0.993977, 0.106735) k_ras = (-0.0870445, -0.108515, 0.990277) Original Data has (0.699944, 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/sub009/mri/orig.mgz... mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/talairach.xfm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Aug 8 10:55:33 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 10:58:05 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6607, pval=0.3663 >= threshold=0.0050) awk -f /opt/freesurfer/5.3.0/bin/extract_talairach_avi_QA.awk /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/talairach_avi.log tal_QC_AZS /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/talairach_avi.log TalAviQA: 0.96174 z-score: -3 #-------------------------------------------- #@# Nu Intensity Correction Thu Aug 8 10:58:05 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/sub009/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 snake6 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux Thu Aug 8 10:58:05 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.24221 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.24221/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.24221/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, -1.86265e-09, 0) j_ras = (-7.45058e-09, 0, -1) k_ras = (-4.65661e-09, 1, 7.45058e-09) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.24221/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Aug 8 10:58:09 CEST 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.24221/nu0.mnc ./tmp.mri_nu_correct.mni.24221/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.24221/0/ [fkaule@snake6:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/] [2013-08-08 10:58:09] 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.24221/0/ ./tmp.mri_nu_correct.mni.24221/nu0.mnc ./tmp.mri_nu_correct.mni.24221/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 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Processing:.................................................................Done Number of iterations: 25 CV of field change: 0.000985702 [fkaule@snake6:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/] [2013-08-08 10:58:42] running: /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.24221/nu0.mnc ./tmp.mri_nu_correct.mni.24221/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Thu Aug 8 10:58:49 CEST 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.24221/nu1.mnc ./tmp.mri_nu_correct.mni.24221/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.24221/1/ [fkaule@snake6:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/] [2013-08-08 10:58:49] 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.24221/1/ ./tmp.mri_nu_correct.mni.24221/nu1.mnc ./tmp.mri_nu_correct.mni.24221/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 Number of iterations: 17 CV of field change: 0.000992556 [fkaule@snake6:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/] [2013-08-08 10:59:12] running: /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.24221/nu1.mnc ./tmp.mri_nu_correct.mni.24221/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.24221/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.24221/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/sub009/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.24221/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.24221/ones.mgz sysname Linux hostname snake6 machine x86_64 user fkaule input ./tmp.mri_nu_correct.mni.24221/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.24221/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.24221/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.24221/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24221/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.24221/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.24221/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24221/input.mean.dat sysname Linux hostname snake6 machine x86_64 user fkaule UseRobust 0 Loading ./tmp.mri_nu_correct.mni.24221/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.24221/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.24221/ones.mgz --i ./tmp.mri_nu_correct.mni.24221/nu2.mnc --sum ./tmp.mri_nu_correct.mni.24221/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24221/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.24221/ones.mgz --i ./tmp.mri_nu_correct.mni.24221/nu2.mnc --sum ./tmp.mri_nu_correct.mni.24221/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24221/output.mean.dat sysname Linux hostname snake6 machine x86_64 user fkaule UseRobust 0 Loading ./tmp.mri_nu_correct.mni.24221/ones.mgz Loading ./tmp.mri_nu_correct.mni.24221/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.24221/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.24221/nu2.mnc ./tmp.mri_nu_correct.mni.24221/nu2.mnc mul .98260516135876169345 Saving result to './tmp.mri_nu_correct.mni.24221/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.24221/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.24221/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.24221/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.86265e-09, 0) j_ras = (-7.45058e-09, 0, -1) k_ras = (-4.65661e-09, 1, 7.45058e-09) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 9 seconds. mapping ( 7, 158) to ( 3, 110) Thu Aug 8 11:00:00 CEST 2013 mri_nu_correct.mni done mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Thu Aug 8 11:00:01 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.178 0.038 0.046 4.031; -0.025 1.063 0.346 -41.083; 0.001 -0.446 1.152 -9.389; 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 75 (75), valley at 17 (17) csf peak at 14, setting threshold to 54 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 48 (48), valley at 36 (36) csf peak at 10, setting threshold to 35 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 53 seconds. #-------------------------------------------- #@# Skull Stripping Thu Aug 8 11:02:54 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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=10.0 skull bounding box = (56, 20, 17) --> (201, 255, 204) using (104, 98, 111) as brain centroid... mean wm in atlas = 126, using box (86,69,88) --> (121, 127,134) to find MRI wm before smoothing, mri peak at 109 after smoothing, mri peak at 109, scaling input intensities by 1.156 scaling channel 0 by 1.15596 initial log_p = -4.8 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.547387 @ (-9.091, 9.091, -9.091) max log p = -4.444653 @ (4.545, 13.636, -4.545) max log p = -4.395447 @ (2.273, -2.273, 2.273) max log p = -4.376290 @ (-1.136, -1.136, 1.136) max log p = -4.358931 @ (0.568, -0.568, -0.568) max log p = -4.358931 @ (0.000, 0.000, 0.000) Found translation: (-2.8, 18.7, -10.8): log p = -4.359 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.4 (thresh=-4.4) 1.064 0.000 0.000 -11.039; 0.000 1.148 0.453 -41.755; 0.000 -0.432 0.988 42.330; 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) 1.144 0.000 0.000 -21.299; 0.000 1.105 0.296 -20.559; 0.000 -0.278 1.038 21.616; 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) 1.144 0.000 0.000 -21.299; 0.000 1.105 0.296 -20.559; 0.000 -0.278 1.038 21.616; 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) 1.121 0.036 0.008 -24.844; -0.038 1.133 0.268 -17.144; 0.000 -0.232 1.009 18.195; 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) 1.121 0.036 0.008 -24.844; -0.038 1.133 0.268 -17.144; 0.000 -0.232 1.009 18.195; 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) 1.123 0.036 0.008 -25.021; -0.038 1.133 0.268 -17.144; 0.000 -0.232 1.010 18.092; 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 1.12280 0.03577 0.00846 -25.02088; -0.03812 1.13299 0.26790 -17.14352; 0.00000 -0.23178 1.00976 18.09197; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.12280 0.03577 0.00846 -25.02088; -0.03812 1.13299 0.26790 -17.14352; 0.00000 -0.23178 1.00976 18.09197; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.123 0.036 0.008 -25.021; -0.038 1.133 0.268 -17.144; 0.000 -0.232 1.010 18.092; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -4.0 (old=-4.8) transform before final EM align: 1.123 0.036 0.008 -25.021; -0.038 1.133 0.268 -17.144; 0.000 -0.232 1.010 18.092; 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 1.12280 0.03577 0.00846 -25.02088; -0.03812 1.13299 0.26790 -17.14352; 0.00000 -0.23178 1.00976 18.09197; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.12280 0.03577 0.00846 -25.02088; -0.03812 1.13299 0.26790 -17.14352; 0.00000 -0.23178 1.00976 18.09197; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 009: -log(p) = 4.4 after pass:transform: ( 1.12, 0.04, 0.01, -25.02) ( -0.04, 1.13, 0.27, -17.14) ( -0.00, -0.23, 1.01, 18.09) 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: 011: -log(p) = 4.4 tol 0.000000 final transform: 1.123 0.036 0.008 -25.021; -0.038 1.133 0.268 -17.144; -0.000 -0.232 1.010 18.092; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 29 minutes and 25 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=88 z=112 r=93 first estimation of the main basin volume: 3459359 voxels Looking for seedpoints 2 found in the cerebellum 16 found in the rest of the brain global maximum in x=150, y=87, z=72, 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=20174662590 voxels, voxel volume =1.000 = 20174662590 mmm3 = 20174661.632 cm3 done. PostAnalyze...Basin Prior 98 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=130,y=100, z=110, r=10562 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=9 , nb = 45587 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=15 , nb = -1032719808 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=12 , nb = 1099334728 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=9 , nb = -1061402847 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=8 , nb = 1082764002 OTHER CSF_MIN=2, CSF_intensity=10, CSF_MAX=24 , nb = 1070255838 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 9, 11, 24, 56 after analyzing : 9, 20, 25, 29 RIGHT_CER before analyzing : 15, 16, 20, 61 after analyzing : 15, 22, 25, 31 LEFT_CER before analyzing : 12, 16, 30, 59 after analyzing : 12, 25, 30, 33 RIGHT_BRAIN before analyzing : 9, 12, 26, 54 after analyzing : 9, 21, 26, 29 LEFT_BRAIN before analyzing : 8, 10, 22, 54 after analyzing : 8, 20, 25, 28 OTHER before analyzing : 24, 58, 83, 93 after analyzing : 24, 74, 83, 78 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...71 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.013 curvature mean = 70.185, std = 8.838 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 2.78, sigma = 4.84 after rotation: sse = 2.78, sigma = 4.84 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 3.23, its var is 5.52 before Erosion-Dilatation 1.18% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...41 iterations mri_strip_skull: done peeling brain Brain Size = 1742949 voxels, voxel volume = 1.000 mm3 = 1742949 mmm3 = 1742.949 cm3 ****************************** Saving brainmask.auto.mgz done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Thu Aug 8 11:32:47 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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=23.0 skull bounding box = (66, 40, 34) --> (191, 179, 197) using (108, 86, 116) as brain centroid... mean wm in atlas = 107, using box (93,69,96) --> (123, 103,136) to find MRI wm before smoothing, mri peak at 109 after smoothing, mri peak at 109, scaling input intensities by 0.982 scaling channel 0 by 0.981651 initial log_p = -4.4 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.030836 @ (-9.091, 27.273, -9.091) max log p = -3.875740 @ (4.545, -13.636, -4.545) max log p = -3.829614 @ (-2.273, 2.273, 2.273) max log p = -3.783844 @ (3.409, 1.136, -1.136) max log p = -3.783844 @ (0.000, 0.000, 0.000) max log p = -3.783844 @ (0.000, 0.000, 0.000) Found translation: (-3.4, 17.0, -12.5): log p = -3.784 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.6, old_max_log_p =-3.8 (thresh=-3.8) 1.140 0.140 0.053 -42.102; -0.150 1.063 0.399 -9.357; 0.000 -0.390 0.833 54.385; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p =-3.6 (thresh=-3.6) 1.143 0.025 -0.099 -14.797; 0.000 1.118 0.276 -21.293; 0.139 -0.245 0.943 2.459; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p =-3.5 (thresh=-3.5) 1.057 0.024 -0.092 -4.177; 0.018 1.077 0.397 -33.521; 0.138 -0.389 0.899 29.133; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p =-3.5 (thresh=-3.5) 1.057 0.024 -0.092 -4.177; 0.018 1.077 0.397 -33.521; 0.138 -0.389 0.899 29.133; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.4, old_max_log_p =-3.5 (thresh=-3.5) 1.083 0.038 -0.021 -18.504; -0.027 1.099 0.338 -23.505; 0.069 -0.318 0.927 26.206; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.4 (thresh=-3.4) 1.083 0.038 -0.021 -18.504; -0.025 1.108 0.375 -28.734; 0.070 -0.354 0.916 32.782; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3) 1.083 0.038 -0.021 -18.504; -0.025 1.108 0.375 -28.734; 0.070 -0.354 0.916 32.782; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3) 1.084 0.047 -0.018 -19.865; -0.035 1.110 0.359 -25.815; 0.070 -0.337 0.925 29.655; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 8 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3) 1.086 0.047 -0.018 -20.209; -0.035 1.106 0.358 -25.307; 0.070 -0.337 0.925 29.655; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 9 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3) 1.086 0.047 -0.018 -20.209; -0.035 1.106 0.358 -25.307; 0.070 -0.337 0.925 29.655; 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 1.08629 0.04736 -0.01826 -20.20926; -0.03464 1.10598 0.35761 -25.30689; 0.07002 -0.33722 0.92503 29.65523; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 1.08629 0.04736 -0.01826 -20.20926; -0.03464 1.10598 0.35761 -25.30689; 0.07002 -0.33722 0.92503 29.65523; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 012: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.086 0.047 -0.018 -20.209; -0.035 1.106 0.358 -25.307; 0.070 -0.337 0.925 29.655; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.3 (old=-4.4) transform before final EM align: 1.086 0.047 -0.018 -20.209; -0.035 1.106 0.358 -25.307; 0.070 -0.337 0.925 29.655; 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 1.08629 0.04736 -0.01826 -20.20926; -0.03464 1.10598 0.35761 -25.30689; 0.07002 -0.33722 0.92503 29.65523; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 1.08629 0.04736 -0.01826 -20.20926; -0.03464 1.10598 0.35761 -25.30689; 0.07002 -0.33722 0.92503 29.65523; 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: 014: -log(p) = 3.9 tol 0.000000 final transform: 1.086 0.047 -0.018 -20.209; -0.035 1.106 0.358 -25.307; 0.070 -0.337 0.925 29.655; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 37 minutes and 38 seconds. #-------------------------------------- #@# CA Normalize Thu Aug 8 12:10:25 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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=23.0 skull bounding box = (66, 40, 34) --> (191, 179, 197) using (108, 86, 116) as brain centroid... mean wm in atlas = 107, using box (93,69,96) --> (123, 103,136) to find MRI wm before smoothing, mri peak at 109 after smoothing, mri peak at 109, scaling input intensities by 0.982 scaling channel 0 by 0.981651 using 244171 sample points... INFO: compute sample coordinates transform 1.086 0.047 -0.018 -20.209; -0.035 1.106 0.358 -25.307; 0.070 -0.337 0.925 29.655; 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 (127, 43, 32) --> (192, 149, 197) Left_Cerebral_White_Matter: limiting intensities to 100.0 --> 166.0 0 of 19 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (72, 41, 33) --> (134, 139, 199) Right_Cerebral_White_Matter: limiting intensities to 100.0 --> 166.0 0 of 10 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (131, 122, 63) --> (176, 162, 117) Left_Cerebellum_White_Matter: limiting intensities to 91.0 --> 166.0 0 of 10 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (87, 122, 63) --> (131, 159, 120) Right_Cerebellum_White_Matter: limiting intensities to 95.0 --> 166.0 0 of 7 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (116, 109, 97) --> (146, 170, 128) Brain_Stem: limiting intensities to 83.0 --> 166.0 0 of 14 (0.0%) samples deleted using 60 total control points for intensity normalization... bias field = 0.937 +- 0.079 0 of 60 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (127, 43, 32) --> (192, 149, 197) Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 154.0 0 of 92 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (72, 41, 33) --> (134, 139, 199) Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 154.0 0 of 97 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (131, 122, 63) --> (176, 162, 117) Left_Cerebellum_White_Matter: limiting intensities to 81.0 --> 154.0 0 of 33 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (87, 122, 63) --> (131, 159, 120) Right_Cerebellum_White_Matter: limiting intensities to 79.0 --> 154.0 0 of 53 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (116, 109, 97) --> (146, 170, 128) Brain_Stem: limiting intensities to 72.0 --> 154.0 0 of 56 (0.0%) samples deleted using 331 total control points for intensity normalization... bias field = 1.002 +- 0.051 0 of 331 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (127, 43, 32) --> (192, 149, 197) Left_Cerebral_White_Matter: limiting intensities to 93.0 --> 152.0 0 of 189 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (72, 41, 33) --> (134, 139, 199) Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 152.0 0 of 203 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (131, 122, 63) --> (176, 162, 117) Left_Cerebellum_White_Matter: limiting intensities to 80.0 --> 152.0 0 of 63 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (87, 122, 63) --> (131, 159, 120) Right_Cerebellum_White_Matter: limiting intensities to 79.0 --> 152.0 0 of 36 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (116, 109, 97) --> (146, 170, 128) Brain_Stem: limiting intensities to 72.0 --> 152.0 0 of 64 (0.0%) samples deleted using 555 total control points for intensity normalization... bias field = 1.010 +- 0.042 0 of 555 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 2 minutes and 4 seconds. #-------------------------------------- #@# CA Reg Thu Aug 8 12:12:30 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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) = 1.25 (predicted orig area = 6.4) 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=0.943, neg=0, invalid=96777 0001: dt=129.472000, rms=0.856 (9.248%), neg=0, invalid=96777 0002: dt=129.472000, rms=0.841 (1.783%), neg=0, invalid=96777 0003: dt=295.936000, rms=0.823 (2.113%), neg=0, invalid=96777 0004: dt=73.984000, rms=0.818 (0.612%), neg=0, invalid=96777 0005: dt=443.904000, rms=0.809 (1.128%), neg=0, invalid=96777 0006: dt=55.488000, rms=0.804 (0.535%), neg=0, invalid=96777 0007: dt=443.904000, rms=0.800 (0.614%), neg=0, invalid=96777 0008: dt=92.480000, rms=0.795 (0.586%), neg=0, invalid=96777 0009: dt=110.976000, rms=0.794 (0.132%), neg=0, invalid=96777 0010: dt=110.976000, rms=0.792 (0.229%), neg=0, invalid=96777 0011: dt=110.976000, rms=0.789 (0.325%), neg=0, invalid=96777 0012: dt=110.976000, rms=0.786 (0.403%), neg=0, invalid=96777 0013: dt=110.976000, rms=0.783 (0.462%), neg=0, invalid=96777 0014: dt=110.976000, rms=0.778 (0.563%), neg=0, invalid=96777 0015: dt=110.976000, rms=0.774 (0.526%), neg=0, invalid=96777 0016: dt=110.976000, rms=0.770 (0.464%), neg=0, invalid=96777 0017: dt=110.976000, rms=0.767 (0.399%), neg=0, invalid=96777 0018: dt=110.976000, rms=0.764 (0.455%), neg=0, invalid=96777 0019: dt=110.976000, rms=0.760 (0.446%), neg=0, invalid=96777 0020: dt=110.976000, rms=0.758 (0.379%), neg=0, invalid=96777 0021: dt=110.976000, rms=0.755 (0.304%), neg=0, invalid=96777 0022: dt=110.976000, rms=0.753 (0.310%), neg=0, invalid=96777 0023: dt=110.976000, rms=0.750 (0.393%), neg=0, invalid=96777 0024: dt=110.976000, rms=0.747 (0.358%), neg=0, invalid=96777 0025: dt=110.976000, rms=0.745 (0.303%), neg=0, invalid=96777 0026: dt=110.976000, rms=0.743 (0.283%), neg=0, invalid=96777 0027: dt=110.976000, rms=0.740 (0.329%), neg=0, invalid=96777 0028: dt=110.976000, rms=0.738 (0.332%), neg=0, invalid=96777 0029: dt=110.976000, rms=0.736 (0.272%), neg=0, invalid=96777 0030: dt=110.976000, rms=0.734 (0.233%), neg=0, invalid=96777 0031: dt=110.976000, rms=0.733 (0.221%), neg=0, invalid=96777 0032: dt=110.976000, rms=0.731 (0.209%), neg=0, invalid=96777 0033: dt=110.976000, rms=0.730 (0.183%), neg=0, invalid=96777 0034: dt=110.976000, rms=0.729 (0.147%), neg=0, invalid=96777 0035: dt=110.976000, rms=0.728 (0.140%), neg=0, invalid=96777 0036: dt=110.976000, rms=0.726 (0.174%), neg=0, invalid=96777 0037: dt=110.976000, rms=0.725 (0.152%), neg=0, invalid=96777 0038: dt=110.976000, rms=0.725 (0.111%), neg=0, invalid=96777 0039: dt=110.976000, rms=0.724 (0.094%), neg=0, invalid=96777 0040: dt=443.904000, rms=0.723 (0.122%), neg=0, invalid=96777 0041: dt=8.092000, rms=0.723 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.723, neg=0, invalid=96777 0042: dt=27.744000, rms=0.723 (0.015%), neg=0, invalid=96777 0043: dt=32.368000, rms=0.723 (0.008%), neg=0, invalid=96777 0044: dt=32.368000, rms=0.723 (0.009%), neg=0, invalid=96777 0045: dt=32.368000, rms=0.723 (0.014%), neg=0, invalid=96777 0046: dt=32.368000, rms=0.723 (0.009%), neg=0, invalid=96777 0047: dt=32.368000, rms=0.723 (0.010%), neg=0, invalid=96777 0048: dt=32.368000, rms=0.722 (0.031%), neg=0, invalid=96777 0049: dt=32.368000, rms=0.722 (0.037%), neg=0, invalid=96777 0050: dt=32.368000, rms=0.722 (0.038%), neg=0, invalid=96777 0051: dt=32.368000, rms=0.722 (0.015%), neg=0, invalid=96777 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.731, neg=0, invalid=96777 0052: dt=145.152000, rms=0.719 (1.570%), neg=0, invalid=96777 0053: dt=62.208000, rms=0.713 (0.887%), neg=0, invalid=96777 0054: dt=20.736000, rms=0.711 (0.304%), neg=0, invalid=96777 0055: dt=145.152000, rms=0.704 (1.012%), neg=0, invalid=96777 0056: dt=25.920000, rms=0.700 (0.482%), neg=0, invalid=96777 0057: dt=103.680000, rms=0.697 (0.437%), neg=0, invalid=96777 0058: dt=20.736000, rms=0.695 (0.304%), neg=0, invalid=96777 0059: dt=103.680000, rms=0.691 (0.523%), neg=0, invalid=96777 0060: dt=9.072000, rms=0.691 (0.113%), neg=0, invalid=96777 0061: dt=9.072000, rms=0.690 (0.077%), neg=0, invalid=96777 0062: dt=9.072000, rms=0.690 (0.077%), neg=0, invalid=96777 0063: dt=9.072000, rms=0.689 (0.088%), neg=0, invalid=96777 0064: dt=9.072000, rms=0.688 (0.109%), neg=0, invalid=96777 0065: dt=9.072000, rms=0.687 (0.153%), neg=0, invalid=96777 0066: dt=9.072000, rms=0.686 (0.212%), neg=0, invalid=96777 0067: dt=9.072000, rms=0.684 (0.237%), neg=0, invalid=96777 0068: dt=9.072000, rms=0.682 (0.233%), neg=0, invalid=96777 0069: dt=9.072000, rms=0.681 (0.224%), neg=0, invalid=96777 0070: dt=9.072000, rms=0.680 (0.209%), neg=0, invalid=96777 0071: dt=9.072000, rms=0.678 (0.200%), neg=0, invalid=96777 0072: dt=9.072000, rms=0.677 (0.199%), neg=0, invalid=96777 0073: dt=9.072000, rms=0.675 (0.208%), neg=0, invalid=96777 0074: dt=9.072000, rms=0.674 (0.220%), neg=0, invalid=96777 0075: dt=9.072000, rms=0.672 (0.213%), neg=0, invalid=96777 0076: dt=9.072000, rms=0.671 (0.196%), neg=0, invalid=96777 0077: dt=9.072000, rms=0.670 (0.181%), neg=0, invalid=96777 0078: dt=9.072000, rms=0.669 (0.170%), neg=0, invalid=96777 0079: dt=9.072000, rms=0.668 (0.168%), neg=0, invalid=96777 0080: dt=9.072000, rms=0.667 (0.165%), neg=0, invalid=96777 0081: dt=9.072000, rms=0.666 (0.152%), neg=0, invalid=96777 0082: dt=9.072000, rms=0.665 (0.138%), neg=0, invalid=96777 0083: dt=9.072000, rms=0.664 (0.136%), neg=0, invalid=96777 0084: dt=9.072000, rms=0.663 (0.140%), neg=0, invalid=96777 0085: dt=9.072000, rms=0.662 (0.139%), neg=0, invalid=96777 0086: dt=9.072000, rms=0.661 (0.133%), neg=0, invalid=96777 0087: dt=9.072000, rms=0.660 (0.123%), neg=0, invalid=96777 0088: dt=9.072000, rms=0.659 (0.112%), neg=0, invalid=96777 0089: dt=82.944000, rms=0.659 (0.029%), neg=0, invalid=96777 0090: dt=82.944000, rms=0.659 (0.070%), neg=0, invalid=96777 0091: dt=82.944000, rms=0.659 (-0.684%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.659, neg=0, invalid=96777 0092: dt=9.072000, rms=0.659 (0.042%), neg=0, invalid=96777 0093: dt=15.552000, rms=0.658 (0.033%), neg=0, invalid=96777 0094: dt=15.552000, rms=0.658 (-0.001%), neg=0, invalid=96777 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.687, neg=0, invalid=96777 0095: dt=7.245283, rms=0.686 (0.088%), neg=0, invalid=96777 0096: dt=4.800000, rms=0.686 (0.035%), neg=0, invalid=96777 0097: dt=4.800000, rms=0.686 (0.008%), neg=0, invalid=96777 0098: dt=4.800000, rms=0.686 (-0.040%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.686, neg=0, invalid=96777 0099: dt=0.000000, rms=0.686 (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=0.758, neg=0, invalid=96777 0100: dt=4.958678, rms=0.746 (1.494%), neg=0, invalid=96777 0101: dt=3.090909, rms=0.746 (0.108%), neg=0, invalid=96777 0102: dt=3.090909, rms=0.746 (-0.008%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.746, neg=0, invalid=96777 0103: dt=0.000000, rms=0.746 (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=0.831, neg=0, invalid=96777 0104: dt=0.640625, rms=0.830 (0.200%), neg=0, invalid=96777 0105: dt=1.792000, rms=0.826 (0.441%), neg=0, invalid=96777 0106: dt=3.634146, rms=0.818 (1.034%), neg=0, invalid=96777 0107: dt=0.250000, rms=0.817 (0.021%), neg=0, invalid=96777 0108: dt=0.250000, rms=0.817 (-0.005%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.817, neg=0, invalid=96777 0109: dt=0.500000, rms=0.817 (0.081%), neg=0, invalid=96777 0110: dt=0.448000, rms=0.817 (0.019%), neg=0, invalid=96777 0111: dt=0.448000, rms=0.816 (0.019%), neg=0, invalid=96777 0112: dt=0.448000, rms=0.816 (0.023%), neg=0, invalid=96777 0113: dt=0.448000, rms=0.816 (0.020%), neg=0, invalid=96777 0114: dt=0.448000, rms=0.816 (-0.011%), 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=0.759, neg=0, invalid=96777 0115: dt=0.448000, rms=0.735 (3.238%), neg=0, invalid=96777 0116: dt=0.000000, rms=0.735 (0.005%), neg=0, invalid=96777 0117: dt=0.050000, rms=0.735 (-0.555%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.735, neg=0, invalid=96777 0118: dt=0.000000, rms=0.735 (0.000%), neg=0, invalid=96777 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.12602 ( 7) Left_Lateral_Ventricle (4): linear fit = 0.25 x + 0.0 (1403 voxels, overlap=0.006) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (1403 voxels, peak = 6), gca=9.6 gca peak = 0.14022 (22) mri peak = 0.14839 ( 9) Right_Lateral_Ventricle (43): linear fit = 0.28 x + 0.0 (1135 voxels, overlap=0.007) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (1135 voxels, peak = 6), gca=8.8 gca peak = 0.24234 (100) mri peak = 0.06586 (90) Right_Pallidum (52): linear fit = 0.89 x + 0.0 (411 voxels, overlap=0.889) Right_Pallidum (52): linear fit = 0.89 x + 0.0 (411 voxels, peak = 90), gca=89.5 gca peak = 0.19192 (97) mri peak = 0.06932 (98) Left_Pallidum (13): linear fit = 0.96 x + 0.0 (316 voxels, overlap=0.899) Left_Pallidum (13): linear fit = 0.96 x + 0.0 (316 voxels, peak = 94), gca=93.6 gca peak = 0.24007 (63) mri peak = 0.06304 (54) Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (480 voxels, overlap=0.729) Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (480 voxels, peak = 55), gca=55.1 gca peak = 0.29892 (64) mri peak = 0.09093 (58) Left_Hippocampus (17): linear fit = 0.89 x + 0.0 (448 voxels, overlap=0.692) Left_Hippocampus (17): linear fit = 0.89 x + 0.0 (448 voxels, peak = 57), gca=57.3 gca peak = 0.12541 (104) mri peak = 0.07831 (106) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (54261 voxels, overlap=0.812) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (54261 voxels, peak = 106), gca=105.6 gca peak = 0.13686 (104) mri peak = 0.08418 (107) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (55024 voxels, overlap=0.713) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (55024 voxels, peak = 108), gca=107.6 gca peak = 0.11691 (63) mri peak = 0.05989 (51) Left_Cerebral_Cortex (3): linear fit = 0.82 x + 0.0 (14984 voxels, overlap=0.186) Left_Cerebral_Cortex (3): linear fit = 0.82 x + 0.0 (14984 voxels, peak = 52), gca=52.0 gca peak = 0.13270 (63) mri peak = 0.06439 (51) Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (14237 voxels, overlap=0.058) Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (14237 voxels, peak = 52), gca=52.0 gca peak = 0.15182 (70) mri peak = 0.08129 (99) Right_Caudate (50): linear fit = 0.75 x + 0.0 (348 voxels, overlap=0.015) Right_Caudate (50): linear fit = 0.75 x + 0.0 (348 voxels, peak = 52), gca=52.2 gca peak = 0.14251 (76) mri peak = 0.06402 (68) Left_Caudate (11): linear fit = 0.89 x + 0.0 (413 voxels, overlap=0.515) Left_Caudate (11): linear fit = 0.89 x + 0.0 (413 voxels, peak = 68), gca=68.0 gca peak = 0.12116 (60) mri peak = 0.03405 (56) Left_Cerebellum_Cortex (8): linear fit = 0.92 x + 0.0 (7629 voxels, overlap=0.839) Left_Cerebellum_Cortex (8): linear fit = 0.92 x + 0.0 (7629 voxels, peak = 55), gca=54.9 gca peak = 0.12723 (61) mri peak = 0.03984 (56) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (9635 voxels, overlap=0.972) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (9635 voxels, peak = 59), gca=58.9 gca peak = 0.22684 (88) mri peak = 0.08304 (94) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (6490 voxels, overlap=0.843) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (6490 voxels, peak = 93), gca=92.8 gca peak = 0.21067 (87) mri peak = 0.06685 (93) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (5978 voxels, overlap=0.923) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (5978 voxels, peak = 92), gca=91.8 gca peak = 0.25455 (62) mri peak = 0.08174 (61) Left_Amygdala (18): linear fit = 0.93 x + 0.0 (326 voxels, overlap=0.595) Left_Amygdala (18): linear fit = 0.93 x + 0.0 (326 voxels, peak = 57), gca=57.4 gca peak = 0.39668 (62) mri peak = 0.10628 (55) Right_Amygdala (54): linear fit = 0.88 x + 0.0 (239 voxels, overlap=0.239) Right_Amygdala (54): linear fit = 0.88 x + 0.0 (239 voxels, peak = 54), gca=54.2 gca peak = 0.10129 (93) mri peak = 0.04774 (90) Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (4655 voxels, overlap=0.988) Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (4655 voxels, peak = 91), gca=90.7 gca peak = 0.12071 (89) mri peak = 0.06468 (76) Right_Thalamus_Proper (49): linear fit = 0.94 x + 0.0 (2818 voxels, overlap=0.796) Right_Thalamus_Proper (49): linear fit = 0.94 x + 0.0 (2818 voxels, peak = 84), gca=84.1 gca peak = 0.13716 (82) mri peak = 0.05848 (80) Left_Putamen (12): linear fit = 0.96 x + 0.0 (1773 voxels, overlap=0.949) Left_Putamen (12): linear fit = 0.96 x + 0.0 (1773 voxels, peak = 79), gca=79.1 gca peak = 0.15214 (84) mri peak = 0.03921 (92) Right_Putamen (51): linear fit = 1.12 x + 0.0 (2027 voxels, overlap=0.239) Right_Putamen (51): linear fit = 1.12 x + 0.0 (2027 voxels, peak = 94), gca=94.5 gca peak = 0.08983 (85) mri peak = 0.06970 (88) Brain_Stem (16): linear fit = 1.07 x + 0.0 (9927 voxels, overlap=0.778) Brain_Stem (16): linear fit = 1.07 x + 0.0 (9927 voxels, peak = 91), gca=90.5 gca peak = 0.11809 (92) mri peak = 0.05692 (95) Right_VentralDC (60): linear fit = 1.03 x + 0.0 (773 voxels, overlap=0.751) Right_VentralDC (60): linear fit = 1.03 x + 0.0 (773 voxels, peak = 95), gca=95.2 gca peak = 0.12914 (94) mri peak = 0.06803 (96) Left_VentralDC (28): linear fit = 1.03 x + 0.0 (978 voxels, overlap=0.836) Left_VentralDC (28): linear fit = 1.03 x + 0.0 (978 voxels, peak = 97), gca=97.3 gca peak = 0.21100 (36) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13542 (27) mri peak = 0.19355 ( 8) Fourth_Ventricle (15): linear fit = 0.28 x + 0.0 (313 voxels, overlap=0.024) Fourth_Ventricle (15): linear fit = 0.28 x + 0.0 (313 voxels, peak = 7), gca=7.4 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak Third_Ventricle = 0.21100 (36) gca peak Fourth_Ventricle = 0.13542 (27) gca peak CSF = 0.17123 (45) gca peak Left_Accumbens_area = 0.25875 (69) gca peak Left_undetermined = 0.96240 (36) gca peak Left_vessel = 0.33262 (65) gca peak Left_choroid_plexus = 0.09846 (46) gca peak Right_Inf_Lat_Vent = 0.28113 (34) gca peak Right_Accumbens_area = 0.27120 (72) gca peak Right_vessel = 0.61915 (60) gca peak Right_choroid_plexus = 0.12775 (51) gca peak Fifth_Ventricle = 0.45329 (44) gca peak WM_hypointensities = 0.11729 (81) gca peak non_WM_hypointensities = 0.10912 (56) gca peak Optic_Chiasm = 0.33287 (75) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 0.87 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 0.40 x + 0.0 saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.752, neg=0, invalid=96777 0119: dt=129.472000, rms=0.746 (0.816%), neg=0, invalid=96777 0120: dt=129.472000, rms=0.744 (0.259%), neg=0, invalid=96777 0121: dt=129.472000, rms=0.743 (0.197%), neg=0, invalid=96777 0122: dt=92.480000, rms=0.742 (0.084%), neg=0, invalid=96777 0123: dt=129.472000, rms=0.741 (0.128%), neg=0, invalid=96777 0124: dt=92.480000, rms=0.741 (0.058%), neg=0, invalid=96777 0125: dt=129.472000, rms=0.740 (0.100%), neg=0, invalid=96777 0126: dt=92.480000, rms=0.740 (0.040%), neg=0, invalid=96777 0127: dt=92.480000, rms=0.739 (0.065%), neg=0, invalid=96777 0128: dt=92.480000, rms=0.738 (0.096%), neg=0, invalid=96777 0129: dt=92.480000, rms=0.737 (0.113%), neg=0, invalid=96777 0130: dt=92.480000, rms=0.737 (0.110%), neg=0, invalid=96777 0131: dt=92.480000, rms=0.736 (0.142%), neg=0, invalid=96777 0132: dt=92.480000, rms=0.735 (0.151%), neg=0, invalid=96777 0133: dt=92.480000, rms=0.733 (0.144%), neg=0, invalid=96777 0134: dt=92.480000, rms=0.732 (0.138%), neg=0, invalid=96777 0135: dt=92.480000, rms=0.731 (0.146%), neg=0, invalid=96777 0136: dt=92.480000, rms=0.730 (0.157%), neg=0, invalid=96777 0137: dt=92.480000, rms=0.729 (0.144%), neg=0, invalid=96777 0138: dt=92.480000, rms=0.728 (0.134%), neg=0, invalid=96777 0139: dt=92.480000, rms=0.727 (0.135%), neg=0, invalid=96777 0140: dt=92.480000, rms=0.726 (0.128%), neg=0, invalid=96777 0141: dt=92.480000, rms=0.725 (0.124%), neg=0, invalid=96777 0142: dt=92.480000, rms=0.725 (0.121%), neg=0, invalid=96777 0143: dt=92.480000, rms=0.724 (0.112%), neg=0, invalid=96777 0144: dt=92.480000, rms=0.723 (0.108%), neg=0, invalid=96777 0145: dt=92.480000, rms=0.722 (0.124%), neg=0, invalid=96777 0146: dt=92.480000, rms=0.721 (0.113%), neg=0, invalid=96777 0147: dt=92.480000, rms=0.720 (0.104%), neg=0, invalid=96777 0148: dt=92.480000, rms=0.720 (0.131%), neg=0, invalid=96777 0149: dt=92.480000, rms=0.719 (0.112%), neg=0, invalid=96777 0150: dt=92.480000, rms=0.718 (0.093%), neg=0, invalid=96777 0151: dt=92.480000, rms=0.717 (0.132%), neg=0, invalid=96777 0152: dt=92.480000, rms=0.716 (0.122%), neg=0, invalid=96777 0153: dt=92.480000, rms=0.716 (0.067%), neg=0, invalid=96777 0154: dt=92.480000, rms=0.715 (0.067%), neg=0, invalid=96777 0155: dt=92.480000, rms=0.715 (0.094%), neg=0, invalid=96777 0156: dt=92.480000, rms=0.714 (0.091%), neg=0, invalid=96777 0157: dt=92.480000, rms=0.713 (0.077%), neg=0, invalid=96777 0158: dt=92.480000, rms=0.713 (0.065%), neg=0, invalid=96777 0159: dt=92.480000, rms=0.712 (0.071%), neg=0, invalid=96777 0160: dt=92.480000, rms=0.712 (0.090%), neg=0, invalid=96777 0161: dt=92.480000, rms=0.711 (0.077%), neg=0, invalid=96777 0162: dt=92.480000, rms=0.711 (0.060%), neg=0, invalid=96777 0163: dt=92.480000, rms=0.710 (0.049%), neg=0, invalid=96777 0164: dt=92.480000, rms=0.710 (0.060%), neg=0, invalid=96777 0165: dt=92.480000, rms=0.710 (0.069%), neg=0, invalid=96777 0166: dt=92.480000, rms=0.709 (0.060%), neg=0, invalid=96777 0167: dt=92.480000, rms=0.709 (0.046%), neg=0, invalid=96777 0168: dt=92.480000, rms=0.708 (0.039%), neg=0, invalid=96777 0169: dt=92.480000, rms=0.708 (0.053%), neg=0, invalid=96777 0170: dt=92.480000, rms=0.708 (0.055%), neg=0, invalid=96777 0171: dt=92.480000, rms=0.707 (0.050%), neg=0, invalid=96777 0172: dt=92.480000, rms=0.707 (0.038%), neg=0, invalid=96777 0173: dt=92.480000, rms=0.707 (0.057%), neg=0, invalid=96777 0174: dt=92.480000, rms=0.706 (0.048%), neg=0, invalid=96777 0175: dt=92.480000, rms=0.706 (0.024%), neg=0, invalid=96777 0176: dt=92.480000, rms=0.706 (0.039%), neg=0, invalid=96777 0177: dt=92.480000, rms=0.705 (0.060%), neg=0, invalid=96777 0178: dt=92.480000, rms=0.705 (0.015%), neg=0, invalid=96777 0179: dt=92.480000, rms=0.705 (0.011%), neg=0, invalid=96777 0180: dt=129.472000, rms=0.705 (0.053%), neg=0, invalid=96777 0181: dt=0.000000, rms=0.705 (0.001%), neg=0, invalid=96777 0182: dt=0.850000, rms=0.705 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.705, neg=0, invalid=96777 0183: dt=92.480000, rms=0.705 (0.045%), neg=0, invalid=96777 0184: dt=129.472000, rms=0.704 (0.135%), neg=0, invalid=96777 0185: dt=27.744000, rms=0.704 (0.007%), neg=0, invalid=96777 0186: dt=27.744000, rms=0.704 (0.002%), neg=0, invalid=96777 0187: dt=27.744000, rms=0.704 (0.002%), neg=0, invalid=96777 0188: dt=27.744000, rms=0.704 (0.005%), neg=0, invalid=96777 0189: dt=27.744000, rms=0.703 (0.033%), neg=0, invalid=96777 0190: dt=27.744000, rms=0.703 (0.042%), neg=0, invalid=96777 0191: dt=27.744000, rms=0.703 (0.037%), neg=0, invalid=96777 0192: dt=27.744000, rms=0.703 (0.027%), neg=0, invalid=96777 0193: dt=27.744000, rms=0.702 (0.012%), neg=0, invalid=96777 0194: dt=27.744000, rms=0.702 (0.003%), neg=0, invalid=96777 0195: dt=369.920000, rms=0.702 (0.063%), neg=0, invalid=96777 0196: dt=18.496000, rms=0.702 (0.005%), neg=0, invalid=96777 0197: dt=18.496000, rms=0.702 (0.000%), neg=0, invalid=96777 0198: dt=18.496000, rms=0.702 (-0.009%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.703, neg=0, invalid=96777 0199: dt=124.416000, rms=0.699 (0.601%), neg=0, invalid=96777 0200: dt=31.104000, rms=0.694 (0.701%), neg=0, invalid=96777 0201: dt=25.920000, rms=0.692 (0.215%), neg=0, invalid=96777 0202: dt=124.416000, rms=0.688 (0.587%), neg=0, invalid=96777 0203: dt=25.920000, rms=0.685 (0.423%), neg=0, invalid=96777 0204: dt=103.680000, rms=0.683 (0.379%), neg=0, invalid=96777 0205: dt=20.736000, rms=0.680 (0.417%), neg=0, invalid=96777 0206: dt=82.944000, rms=0.678 (0.248%), neg=0, invalid=96777 0207: dt=25.920000, rms=0.676 (0.294%), neg=0, invalid=96777 0208: dt=25.920000, rms=0.676 (0.104%), neg=0, invalid=96777 0209: dt=103.680000, rms=0.674 (0.287%), neg=0, invalid=96777 0210: dt=20.736000, rms=0.672 (0.237%), neg=0, invalid=96777 0211: dt=497.664000, rms=0.662 (1.531%), neg=0, invalid=96777 0212: dt=36.288000, rms=0.659 (0.377%), neg=0, invalid=96777 0213: dt=9.072000, rms=0.659 (0.047%), neg=0, invalid=96777 0214: dt=9.072000, rms=0.659 (0.025%), neg=0, invalid=96777 0215: dt=9.072000, rms=0.659 (0.025%), neg=0, invalid=96777 0216: dt=9.072000, rms=0.658 (0.035%), neg=0, invalid=96777 0217: dt=9.072000, rms=0.658 (0.060%), neg=0, invalid=96777 0218: dt=9.072000, rms=0.658 (0.081%), neg=0, invalid=96777 0219: dt=9.072000, rms=0.657 (0.097%), neg=0, invalid=96777 0220: dt=9.072000, rms=0.656 (0.100%), neg=0, invalid=96777 0221: dt=9.072000, rms=0.656 (0.027%), neg=0, invalid=96777 0222: dt=9.072000, rms=0.656 (0.026%), neg=0, invalid=96777 0223: dt=0.567000, rms=0.656 (0.002%), neg=0, invalid=96777 0224: dt=0.017719, rms=0.656 (0.000%), neg=0, invalid=96777 0225: dt=0.002215, rms=0.656 (0.000%), neg=0, invalid=96777 0226: dt=0.002215, rms=0.656 (0.000%), neg=0, invalid=96777 0227: dt=0.001107, rms=0.656 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.656, neg=0, invalid=96777 0228: dt=145.152000, rms=0.651 (0.710%), neg=0, invalid=96777 0229: dt=36.288000, rms=0.650 (0.150%), neg=0, invalid=96777 0230: dt=145.152000, rms=0.648 (0.362%), neg=0, invalid=96777 0231: dt=9.072000, rms=0.648 (0.019%), neg=0, invalid=96777 0232: dt=9.072000, rms=0.648 (0.018%), neg=0, invalid=96777 0233: dt=9.072000, rms=0.648 (0.023%), neg=0, invalid=96777 0234: dt=9.072000, rms=0.647 (0.036%), neg=0, invalid=96777 0235: dt=9.072000, rms=0.647 (0.058%), neg=0, invalid=96777 0236: dt=9.072000, rms=0.646 (0.083%), neg=0, invalid=96777 0237: dt=9.072000, rms=0.646 (0.101%), neg=0, invalid=96777 0238: dt=9.072000, rms=0.645 (0.105%), neg=0, invalid=96777 0239: dt=9.072000, rms=0.644 (0.105%), neg=0, invalid=96777 0240: dt=9.072000, rms=0.644 (0.102%), neg=0, invalid=96777 0241: dt=9.072000, rms=0.643 (0.100%), neg=0, invalid=96777 0242: dt=9.072000, rms=0.642 (0.094%), neg=0, invalid=96777 0243: dt=9.072000, rms=0.642 (0.096%), neg=0, invalid=96777 0244: dt=9.072000, rms=0.641 (0.097%), neg=0, invalid=96777 0245: dt=9.072000, rms=0.640 (0.119%), neg=0, invalid=96777 0246: dt=9.072000, rms=0.640 (0.123%), neg=0, invalid=96777 0247: dt=9.072000, rms=0.639 (0.124%), neg=0, invalid=96777 0248: dt=9.072000, rms=0.638 (0.121%), neg=0, invalid=96777 0249: dt=9.072000, rms=0.637 (0.118%), neg=0, invalid=96777 0250: dt=9.072000, rms=0.637 (0.112%), neg=0, invalid=96777 0251: dt=9.072000, rms=0.636 (0.098%), neg=0, invalid=96777 0252: dt=9.072000, rms=0.635 (0.103%), neg=0, invalid=96777 0253: dt=9.072000, rms=0.635 (0.098%), neg=0, invalid=96777 0254: dt=9.072000, rms=0.634 (0.099%), neg=0, invalid=96777 0255: dt=9.072000, rms=0.633 (0.104%), neg=0, invalid=96777 0256: dt=9.072000, rms=0.633 (0.101%), neg=0, invalid=96777 0257: dt=9.072000, rms=0.632 (0.096%), neg=0, invalid=96777 0258: dt=9.072000, rms=0.632 (0.096%), neg=0, invalid=96777 0259: dt=9.072000, rms=0.631 (0.093%), neg=0, invalid=96777 0260: dt=9.072000, rms=0.630 (0.089%), neg=0, invalid=96777 0261: dt=9.072000, rms=0.630 (0.086%), neg=0, invalid=96777 0262: dt=9.072000, rms=0.629 (0.087%), neg=0, invalid=96777 0263: dt=9.072000, rms=0.629 (0.083%), neg=0, invalid=96777 0264: dt=9.072000, rms=0.628 (0.078%), neg=0, invalid=96777 0265: dt=9.072000, rms=0.628 (0.079%), neg=0, invalid=96777 0266: dt=9.072000, rms=0.627 (0.074%), neg=0, invalid=96777 0267: dt=9.072000, rms=0.627 (0.071%), neg=0, invalid=96777 0268: dt=9.072000, rms=0.627 (0.006%), neg=0, invalid=96777 0269: dt=9.072000, rms=0.627 (0.015%), neg=0, invalid=96777 0270: dt=9.072000, rms=0.627 (0.017%), neg=0, invalid=96777 0271: dt=9.072000, rms=0.627 (0.021%), neg=0, invalid=96777 0272: dt=9.072000, rms=0.626 (0.027%), neg=0, invalid=96777 0273: dt=9.072000, rms=0.626 (0.031%), neg=0, invalid=96777 0274: dt=9.072000, rms=0.626 (0.033%), neg=0, invalid=96777 0275: dt=9.072000, rms=0.626 (0.034%), neg=0, invalid=96777 0276: dt=9.072000, rms=0.626 (0.035%), neg=0, invalid=96777 0277: dt=9.072000, rms=0.625 (0.037%), neg=0, invalid=96777 0278: dt=9.072000, rms=0.625 (0.040%), neg=0, invalid=96777 0279: dt=9.072000, rms=0.625 (0.041%), neg=0, invalid=96777 0280: dt=9.072000, rms=0.625 (0.043%), neg=0, invalid=96777 0281: dt=9.072000, rms=0.624 (0.046%), neg=0, invalid=96777 0282: dt=9.072000, rms=0.624 (0.044%), neg=0, invalid=96777 0283: dt=9.072000, rms=0.624 (0.046%), neg=0, invalid=96777 0284: dt=9.072000, rms=0.623 (0.043%), neg=0, invalid=96777 0285: dt=9.072000, rms=0.623 (0.042%), neg=0, invalid=96777 0286: dt=9.072000, rms=0.623 (0.045%), neg=0, invalid=96777 0287: dt=9.072000, rms=0.623 (0.044%), neg=0, invalid=96777 0288: dt=9.072000, rms=0.622 (0.049%), neg=0, invalid=96777 0289: dt=9.072000, rms=0.622 (0.047%), neg=0, invalid=96777 0290: dt=9.072000, rms=0.622 (0.049%), neg=0, invalid=96777 0291: dt=9.072000, rms=0.621 (0.046%), neg=0, invalid=96777 0292: dt=9.072000, rms=0.621 (0.049%), neg=0, invalid=96777 0293: dt=9.072000, rms=0.621 (0.043%), neg=0, invalid=96777 0294: dt=9.072000, rms=0.621 (0.044%), neg=0, invalid=96777 0295: dt=9.072000, rms=0.620 (0.043%), neg=0, invalid=96777 0296: dt=9.072000, rms=0.620 (0.041%), neg=0, invalid=96777 0297: dt=9.072000, rms=0.620 (0.043%), neg=0, invalid=96777 0298: dt=9.072000, rms=0.620 (0.042%), neg=0, invalid=96777 0299: dt=9.072000, rms=0.619 (0.042%), neg=0, invalid=96777 0300: dt=9.072000, rms=0.619 (0.043%), neg=0, invalid=96777 0301: dt=9.072000, rms=0.619 (0.041%), neg=0, invalid=96777 0302: dt=9.072000, rms=0.619 (0.041%), neg=0, invalid=96777 0303: dt=9.072000, rms=0.618 (0.041%), neg=0, invalid=96777 0304: dt=9.072000, rms=0.618 (0.041%), neg=0, invalid=96777 0305: dt=9.072000, rms=0.618 (0.042%), neg=0, invalid=96777 0306: dt=9.072000, rms=0.617 (0.040%), neg=0, invalid=96777 0307: dt=9.072000, rms=0.617 (0.041%), neg=0, invalid=96777 0308: dt=9.072000, rms=0.617 (0.038%), neg=0, invalid=96777 0309: dt=9.072000, rms=0.617 (0.039%), neg=0, invalid=96777 0310: dt=9.072000, rms=0.617 (0.040%), neg=0, invalid=96777 0311: dt=9.072000, rms=0.616 (0.038%), neg=0, invalid=96777 0312: dt=9.072000, rms=0.616 (0.038%), neg=0, invalid=96777 0313: dt=9.072000, rms=0.616 (0.036%), neg=0, invalid=96777 0314: dt=9.072000, rms=0.616 (0.035%), neg=0, invalid=96777 0315: dt=9.072000, rms=0.615 (0.037%), neg=0, invalid=96777 0316: dt=9.072000, rms=0.615 (0.035%), neg=0, invalid=96777 0317: dt=9.072000, rms=0.615 (0.037%), neg=0, invalid=96777 0318: dt=9.072000, rms=0.615 (0.037%), neg=0, invalid=96777 0319: dt=9.072000, rms=0.614 (0.036%), neg=0, invalid=96777 0320: dt=9.072000, rms=0.614 (0.035%), neg=0, invalid=96777 0321: dt=9.072000, rms=0.614 (0.036%), neg=0, invalid=96777 0322: dt=9.072000, rms=0.614 (0.033%), neg=0, invalid=96777 0323: dt=9.072000, rms=0.614 (0.031%), neg=0, invalid=96777 0324: dt=9.072000, rms=0.613 (0.033%), neg=0, invalid=96777 0325: dt=9.072000, rms=0.613 (0.032%), neg=0, invalid=96777 0326: dt=9.072000, rms=0.613 (0.029%), neg=0, invalid=96777 0327: dt=9.072000, rms=0.613 (0.030%), neg=0, invalid=96777 0328: dt=9.072000, rms=0.613 (0.031%), neg=0, invalid=96777 0329: dt=9.072000, rms=0.613 (0.029%), neg=0, invalid=96777 0330: dt=9.072000, rms=0.612 (0.030%), neg=0, invalid=96777 0331: dt=9.072000, rms=0.612 (0.029%), neg=0, invalid=96777 0332: dt=9.072000, rms=0.612 (0.030%), neg=0, invalid=96777 0333: dt=9.072000, rms=0.612 (0.030%), neg=0, invalid=96777 0334: dt=9.072000, rms=0.612 (0.028%), neg=0, invalid=96777 0335: dt=9.072000, rms=0.611 (0.027%), neg=0, invalid=96777 0336: dt=9.072000, rms=0.611 (0.026%), neg=0, invalid=96777 0337: dt=9.072000, rms=0.611 (0.024%), neg=0, invalid=96777 0338: dt=9.072000, rms=0.611 (0.026%), neg=0, invalid=96777 0339: dt=9.072000, rms=0.611 (0.028%), neg=0, invalid=96777 0340: dt=9.072000, rms=0.611 (0.028%), neg=0, invalid=96777 0341: dt=9.072000, rms=0.610 (0.029%), neg=0, invalid=96777 0342: dt=9.072000, rms=0.610 (0.028%), neg=0, invalid=96777 0343: dt=9.072000, rms=0.610 (0.026%), neg=0, invalid=96777 0344: dt=9.072000, rms=0.610 (0.024%), neg=0, invalid=96777 0345: dt=9.072000, rms=0.610 (0.022%), neg=0, invalid=96777 0346: dt=580.608000, rms=0.609 (0.106%), neg=0, invalid=96777 0347: dt=20.736000, rms=0.609 (0.045%), neg=0, invalid=96777 0348: dt=20.736000, rms=0.609 (0.011%), neg=0, invalid=96777 0349: dt=20.736000, rms=0.609 (0.014%), neg=0, invalid=96777 0350: dt=20.736000, rms=0.609 (0.015%), neg=0, invalid=96777 0351: dt=20.736000, rms=0.609 (0.018%), neg=0, invalid=96777 0352: dt=20.736000, rms=0.608 (0.027%), neg=0, invalid=96777 0353: dt=20.736000, rms=0.608 (0.020%), neg=0, invalid=96777 0354: dt=20.736000, rms=0.608 (0.022%), neg=0, invalid=96777 0355: dt=20.736000, rms=0.608 (0.023%), neg=0, invalid=96777 0356: dt=20.736000, rms=0.608 (0.026%), neg=0, invalid=96777 0357: dt=20.736000, rms=0.608 (0.036%), neg=0, invalid=96777 0358: dt=20.736000, rms=0.607 (0.038%), neg=0, invalid=96777 0359: dt=20.736000, rms=0.607 (0.035%), neg=0, invalid=96777 0360: dt=20.736000, rms=0.607 (0.028%), neg=0, invalid=96777 0361: dt=20.736000, rms=0.607 (0.038%), neg=0, invalid=96777 0362: dt=20.736000, rms=0.607 (0.041%), neg=0, invalid=96777 0363: dt=20.736000, rms=0.606 (0.042%), neg=0, invalid=96777 0364: dt=20.736000, rms=0.606 (0.042%), neg=0, invalid=96777 0365: dt=20.736000, rms=0.606 (0.041%), neg=0, invalid=96777 0366: dt=20.736000, rms=0.606 (0.036%), neg=0, invalid=96777 0367: dt=20.736000, rms=0.605 (0.035%), neg=0, invalid=96777 0368: dt=20.736000, rms=0.605 (0.033%), neg=0, invalid=96777 0369: dt=20.736000, rms=0.605 (0.034%), neg=0, invalid=96777 0370: dt=20.736000, rms=0.605 (0.041%), neg=0, invalid=96777 0371: dt=20.736000, rms=0.605 (0.037%), neg=0, invalid=96777 0372: dt=20.736000, rms=0.604 (0.037%), neg=0, invalid=96777 0373: dt=20.736000, rms=0.604 (0.034%), neg=0, invalid=96777 0374: dt=20.736000, rms=0.604 (0.040%), neg=0, invalid=96777 0375: dt=20.736000, rms=0.604 (0.040%), neg=0, invalid=96777 0376: dt=20.736000, rms=0.603 (0.034%), neg=0, invalid=96777 0377: dt=20.736000, rms=0.603 (0.034%), neg=0, invalid=96777 0378: dt=20.736000, rms=0.603 (0.032%), neg=0, invalid=96777 0379: dt=20.736000, rms=0.603 (0.036%), neg=0, invalid=96777 0380: dt=20.736000, rms=0.603 (0.036%), neg=0, invalid=96777 0381: dt=20.736000, rms=0.602 (0.037%), neg=0, invalid=96777 0382: dt=20.736000, rms=0.602 (0.031%), neg=0, invalid=96777 0383: dt=20.736000, rms=0.602 (0.035%), neg=0, invalid=96777 0384: dt=20.736000, rms=0.602 (0.036%), neg=0, invalid=96777 0385: dt=20.736000, rms=0.602 (0.033%), neg=0, invalid=96777 0386: dt=20.736000, rms=0.601 (0.031%), neg=0, invalid=96777 0387: dt=20.736000, rms=0.601 (0.032%), neg=0, invalid=96777 0388: dt=20.736000, rms=0.601 (0.035%), neg=0, invalid=96777 0389: dt=20.736000, rms=0.601 (0.034%), neg=0, invalid=96777 0390: dt=20.736000, rms=0.601 (0.030%), neg=0, invalid=96777 0391: dt=20.736000, rms=0.600 (0.029%), neg=0, invalid=96777 0392: dt=20.736000, rms=0.600 (0.034%), neg=0, invalid=96777 0393: dt=20.736000, rms=0.600 (0.032%), neg=0, invalid=96777 0394: dt=20.736000, rms=0.600 (0.027%), neg=0, invalid=96777 0395: dt=20.736000, rms=0.600 (0.028%), neg=0, invalid=96777 0396: dt=20.736000, rms=0.599 (0.028%), neg=0, invalid=96777 0397: dt=20.736000, rms=0.599 (0.032%), neg=0, invalid=96777 0398: dt=20.736000, rms=0.599 (0.033%), neg=0, invalid=96777 0399: dt=20.736000, rms=0.599 (0.029%), neg=0, invalid=96777 0400: dt=20.736000, rms=0.599 (0.024%), neg=0, invalid=96777 0401: dt=20.736000, rms=0.599 (0.028%), neg=0, invalid=96777 0402: dt=20.736000, rms=0.598 (0.028%), neg=0, invalid=96777 0403: dt=20.736000, rms=0.598 (0.026%), neg=0, invalid=96777 0404: dt=20.736000, rms=0.598 (0.030%), neg=0, invalid=96777 0405: dt=20.736000, rms=0.598 (0.028%), neg=0, invalid=96777 0406: dt=20.736000, rms=0.598 (0.025%), neg=0, invalid=96777 0407: dt=20.736000, rms=0.598 (0.025%), neg=0, invalid=96777 0408: dt=20.736000, rms=0.597 (0.024%), neg=0, invalid=96777 0409: dt=20.736000, rms=0.597 (0.024%), neg=0, invalid=96777 0410: dt=6.480000, rms=0.597 (0.004%), neg=0, invalid=96777 0411: dt=6.480000, rms=0.597 (-0.001%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.605, neg=0, invalid=96777 0412: dt=38.400000, rms=0.602 (0.539%), neg=0, invalid=96777 0413: dt=38.400000, rms=0.597 (0.816%), neg=0, invalid=96777 0414: dt=9.600000, rms=0.596 (0.163%), neg=0, invalid=96777 0415: dt=11.200000, rms=0.594 (0.197%), neg=0, invalid=96777 0416: dt=19.200000, rms=0.593 (0.191%), neg=0, invalid=96777 0417: dt=7.734807, rms=0.592 (0.225%), neg=0, invalid=96777 0418: dt=11.200000, rms=0.591 (0.155%), neg=0, invalid=96777 0419: dt=19.200000, rms=0.590 (0.260%), neg=0, invalid=96777 0420: dt=7.218045, rms=0.589 (0.156%), neg=0, invalid=96777 0421: dt=44.800000, rms=0.585 (0.531%), neg=0, invalid=96777 0422: dt=7.366906, rms=0.585 (0.134%), neg=0, invalid=96777 0423: dt=44.800000, rms=0.582 (0.502%), neg=0, invalid=96777 0424: dt=11.200000, rms=0.581 (0.096%), neg=0, invalid=96777 0425: dt=44.800000, rms=0.580 (0.236%), neg=0, invalid=96777 0426: dt=6.400000, rms=0.579 (0.127%), neg=0, invalid=96777 0427: dt=11.200000, rms=0.578 (0.180%), neg=0, invalid=96777 0428: dt=11.200000, rms=0.577 (0.107%), neg=0, invalid=96777 0429: dt=19.200000, rms=0.577 (0.106%), neg=0, invalid=96777 0430: dt=6.400000, rms=0.576 (0.072%), neg=0, invalid=96777 0431: dt=19.200000, rms=0.576 (0.104%), neg=0, invalid=96777 0432: dt=9.600000, rms=0.575 (0.108%), neg=0, invalid=96777 0433: dt=9.600000, rms=0.575 (0.069%), neg=0, invalid=96777 0434: dt=25.600000, rms=0.574 (0.154%), neg=0, invalid=96777 0435: dt=6.521739, rms=0.573 (0.077%), neg=0, invalid=96777 0436: dt=44.800000, rms=0.572 (0.285%), neg=0, invalid=96777 0437: dt=11.200000, rms=0.572 (0.051%), neg=0, invalid=96777 0438: dt=32.000000, rms=0.571 (0.125%), neg=0, invalid=96777 0439: dt=6.776471, rms=0.570 (0.089%), neg=0, invalid=96777 0440: dt=44.800000, rms=0.569 (0.202%), neg=0, invalid=96777 0441: dt=6.400000, rms=0.569 (0.063%), neg=0, invalid=96777 0442: dt=19.200000, rms=0.568 (0.074%), neg=0, invalid=96777 0443: dt=6.400000, rms=0.568 (0.045%), neg=0, invalid=96777 0444: dt=6.400000, rms=0.568 (0.040%), neg=0, invalid=96777 0445: dt=6.400000, rms=0.568 (0.063%), neg=0, invalid=96777 0446: dt=6.400000, rms=0.567 (0.083%), neg=0, invalid=96777 0447: dt=6.400000, rms=0.566 (0.105%), neg=0, invalid=96777 0448: dt=6.400000, rms=0.566 (0.115%), neg=0, invalid=96777 0449: dt=6.400000, rms=0.565 (0.125%), neg=0, invalid=96777 0450: dt=6.400000, rms=0.564 (0.139%), neg=0, invalid=96777 0451: dt=6.400000, rms=0.564 (0.148%), neg=0, invalid=96777 0452: dt=6.400000, rms=0.563 (0.147%), neg=0, invalid=96777 0453: dt=6.400000, rms=0.562 (0.150%), neg=0, invalid=96777 0454: dt=6.400000, rms=0.561 (0.157%), neg=0, invalid=96777 0455: dt=6.400000, rms=0.560 (0.165%), neg=0, invalid=96777 0456: dt=6.400000, rms=0.559 (0.166%), neg=0, invalid=96777 0457: dt=6.400000, rms=0.558 (0.154%), neg=0, invalid=96777 0458: dt=6.400000, rms=0.557 (0.145%), neg=0, invalid=96777 0459: dt=6.400000, rms=0.557 (0.132%), neg=0, invalid=96777 0460: dt=6.400000, rms=0.556 (0.129%), neg=0, invalid=96777 0461: dt=6.400000, rms=0.555 (0.125%), neg=0, invalid=96777 0462: dt=6.400000, rms=0.555 (0.130%), neg=0, invalid=96777 0463: dt=6.400000, rms=0.554 (0.020%), neg=0, invalid=96777 0464: dt=6.400000, rms=0.554 (0.029%), neg=0, invalid=96777 0465: dt=6.400000, rms=0.554 (0.030%), neg=0, invalid=96777 0466: dt=6.400000, rms=0.554 (0.035%), neg=0, invalid=96777 0467: dt=6.400000, rms=0.554 (0.029%), neg=0, invalid=96777 0468: dt=6.400000, rms=0.554 (0.030%), neg=0, invalid=96777 0469: dt=6.400000, rms=0.553 (0.041%), neg=0, invalid=96777 0470: dt=6.400000, rms=0.553 (0.041%), neg=0, invalid=96777 0471: dt=6.400000, rms=0.553 (0.043%), neg=0, invalid=96777 0472: dt=6.400000, rms=0.553 (0.055%), neg=0, invalid=96777 0473: dt=6.400000, rms=0.552 (0.059%), neg=0, invalid=96777 0474: dt=6.400000, rms=0.552 (0.064%), neg=0, invalid=96777 0475: dt=6.400000, rms=0.552 (0.065%), neg=0, invalid=96777 0476: dt=6.400000, rms=0.551 (0.065%), neg=0, invalid=96777 0477: dt=6.400000, rms=0.551 (0.070%), neg=0, invalid=96777 0478: dt=6.400000, rms=0.550 (0.067%), neg=0, invalid=96777 0479: dt=6.400000, rms=0.550 (0.064%), neg=0, invalid=96777 0480: dt=6.400000, rms=0.550 (0.058%), neg=0, invalid=96777 0481: dt=6.400000, rms=0.549 (0.064%), neg=0, invalid=96777 0482: dt=6.400000, rms=0.549 (0.061%), neg=0, invalid=96777 0483: dt=6.400000, rms=0.549 (0.062%), neg=0, invalid=96777 0484: dt=6.400000, rms=0.548 (0.057%), neg=0, invalid=96777 0485: dt=6.400000, rms=0.548 (0.058%), neg=0, invalid=96777 0486: dt=6.400000, rms=0.548 (0.056%), neg=0, invalid=96777 0487: dt=6.400000, rms=0.547 (0.059%), neg=0, invalid=96777 0488: dt=6.400000, rms=0.547 (0.060%), neg=0, invalid=96777 0489: dt=6.400000, rms=0.547 (0.060%), neg=0, invalid=96777 0490: dt=6.400000, rms=0.547 (0.058%), neg=0, invalid=96777 0491: dt=6.400000, rms=0.546 (0.052%), neg=0, invalid=96777 0492: dt=6.400000, rms=0.546 (0.049%), neg=0, invalid=96777 0493: dt=6.400000, rms=0.546 (0.046%), neg=0, invalid=96777 0494: dt=6.400000, rms=0.545 (0.048%), neg=0, invalid=96777 0495: dt=6.400000, rms=0.545 (0.045%), neg=0, invalid=96777 0496: dt=6.400000, rms=0.545 (0.044%), neg=0, invalid=96777 0497: dt=6.400000, rms=0.545 (0.045%), neg=0, invalid=96777 0498: dt=6.400000, rms=0.544 (0.043%), neg=0, invalid=96777 0499: dt=6.400000, rms=0.544 (0.040%), neg=0, invalid=96777 0500: dt=6.400000, rms=0.544 (0.039%), neg=0, invalid=96777 0501: dt=6.400000, rms=0.544 (0.036%), neg=0, invalid=96777 0502: dt=6.400000, rms=0.544 (0.034%), neg=0, invalid=96777 0503: dt=6.400000, rms=0.544 (0.033%), neg=0, invalid=96777 0504: dt=6.400000, rms=0.543 (0.035%), neg=0, invalid=96777 0505: dt=6.400000, rms=0.543 (0.038%), neg=0, invalid=96777 0506: dt=6.400000, rms=0.543 (0.045%), neg=0, invalid=96777 0507: dt=6.400000, rms=0.543 (0.039%), neg=0, invalid=96777 0508: dt=6.400000, rms=0.542 (0.033%), neg=0, invalid=96777 0509: dt=6.400000, rms=0.542 (0.029%), neg=0, invalid=96777 0510: dt=6.400000, rms=0.542 (0.032%), neg=0, invalid=96777 0511: dt=6.400000, rms=0.542 (0.024%), neg=0, invalid=96777 0512: dt=6.400000, rms=0.542 (0.027%), neg=0, invalid=96777 0513: dt=6.400000, rms=0.542 (0.023%), neg=0, invalid=96777 0514: dt=6.400000, rms=0.542 (0.029%), neg=0, invalid=96777 0515: dt=6.400000, rms=0.541 (0.028%), neg=0, invalid=96777 0516: dt=6.400000, rms=0.541 (0.022%), neg=0, invalid=96777 0517: dt=6.400000, rms=0.541 (0.024%), neg=0, invalid=96777 0518: dt=6.400000, rms=0.541 (0.022%), neg=0, invalid=96777 0519: dt=1.600000, rms=0.541 (0.001%), neg=0, invalid=96777 0520: dt=1.600000, rms=0.541 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.541, neg=0, invalid=96777 0521: dt=38.400000, rms=0.539 (0.327%), neg=0, invalid=96777 0522: dt=19.200000, rms=0.539 (0.102%), neg=0, invalid=96777 0523: dt=2.800000, rms=0.539 (0.004%), neg=0, invalid=96777 0524: dt=2.800000, rms=0.539 (0.012%), neg=0, invalid=96777 0525: dt=2.800000, rms=0.539 (0.017%), neg=0, invalid=96777 0526: dt=2.800000, rms=0.539 (0.011%), neg=0, invalid=96777 0527: dt=2.800000, rms=0.538 (0.016%), neg=0, invalid=96777 0528: dt=2.800000, rms=0.538 (0.016%), neg=0, invalid=96777 0529: dt=2.800000, rms=0.538 (0.016%), neg=0, invalid=96777 0530: dt=32.000000, rms=0.538 (0.035%), neg=0, invalid=96777 0531: dt=8.000000, rms=0.538 (0.009%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.564, neg=0, invalid=96777 0532: dt=0.000000, rms=0.564 (0.003%), neg=0, invalid=96777 0533: dt=0.000000, rms=0.564 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.564, neg=0, invalid=96777 0534: dt=0.000000, rms=0.564 (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=0.615, neg=0, invalid=96777 0535: dt=1.122762, rms=0.611 (0.633%), neg=0, invalid=96777 0536: dt=0.275000, rms=0.611 (0.021%), neg=0, invalid=96777 0537: dt=0.275000, rms=0.611 (-0.009%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.611, neg=0, invalid=96777 0538: dt=0.541667, rms=0.610 (0.109%), neg=0, invalid=96777 0539: dt=0.384000, rms=0.610 (0.023%), neg=0, invalid=96777 0540: dt=0.384000, rms=0.610 (-0.012%), 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=0.554, neg=0, invalid=96777 0541: dt=0.384000, rms=0.536 (3.354%), neg=0, invalid=96777 0542: dt=0.005000, rms=0.536 (0.012%), neg=0, invalid=96777 0543: dt=0.005000, rms=0.536 (0.012%), neg=0, invalid=96777 0544: dt=0.005000, rms=0.535 (0.025%), neg=0, invalid=96777 0545: dt=0.005000, rms=0.535 (0.013%), neg=0, invalid=96777 0546: dt=0.005000, rms=0.535 (0.024%), neg=0, invalid=96777 0547: dt=0.005000, rms=0.535 (0.034%), neg=0, invalid=96777 0548: dt=0.005000, rms=0.535 (0.044%), neg=0, invalid=96777 0549: dt=0.005000, rms=0.535 (0.052%), neg=0, invalid=96777 0550: dt=0.005000, rms=0.534 (0.057%), neg=0, invalid=96777 0551: dt=0.005000, rms=0.534 (0.063%), neg=0, invalid=96777 0552: dt=0.005000, rms=0.534 (0.068%), neg=0, invalid=96777 0553: dt=0.005000, rms=0.533 (0.071%), neg=0, invalid=96777 0554: dt=0.005000, rms=0.533 (0.074%), neg=0, invalid=96777 0555: dt=0.005000, rms=0.532 (0.076%), neg=0, invalid=96777 0556: dt=0.005000, rms=0.532 (0.077%), neg=0, invalid=96777 0557: dt=0.005000, rms=0.532 (0.078%), neg=0, invalid=96777 0558: dt=0.005000, rms=0.531 (0.079%), neg=0, invalid=96777 0559: dt=0.005000, rms=0.531 (0.078%), neg=0, invalid=96777 0560: dt=0.005000, rms=0.530 (0.078%), neg=0, invalid=96777 0561: dt=0.005000, rms=0.530 (0.075%), neg=0, invalid=96777 0562: dt=0.005000, rms=0.529 (0.074%), neg=0, invalid=96777 0563: dt=0.005000, rms=0.529 (0.073%), neg=0, invalid=96777 0564: dt=0.005000, rms=0.529 (0.070%), neg=0, invalid=96777 0565: dt=0.005000, rms=0.528 (0.071%), neg=0, invalid=96777 0566: dt=0.005000, rms=0.528 (0.068%), neg=0, invalid=96777 0567: dt=0.005000, rms=0.528 (0.065%), neg=0, invalid=96777 0568: dt=0.005000, rms=0.527 (0.060%), neg=0, invalid=96777 0569: dt=0.005000, rms=0.527 (0.060%), neg=0, invalid=96777 0570: dt=0.005000, rms=0.527 (0.060%), neg=0, invalid=96777 0571: dt=0.005000, rms=0.526 (0.054%), neg=0, invalid=96777 0572: dt=0.005000, rms=0.526 (0.053%), neg=0, invalid=96777 0573: dt=0.005000, rms=0.526 (0.050%), neg=0, invalid=96777 0574: dt=0.005000, rms=0.526 (0.047%), neg=0, invalid=96777 0575: dt=0.005000, rms=0.525 (0.045%), neg=0, invalid=96777 0576: dt=0.005000, rms=0.525 (0.043%), neg=0, invalid=96777 0577: dt=0.005000, rms=0.525 (0.040%), neg=0, invalid=96777 0578: dt=0.005000, rms=0.525 (0.041%), neg=0, invalid=96777 0579: dt=0.005000, rms=0.525 (0.033%), neg=0, invalid=96777 0580: dt=0.005000, rms=0.524 (0.034%), neg=0, invalid=96777 0581: dt=0.005000, rms=0.524 (0.029%), neg=0, invalid=96777 0582: dt=0.005000, rms=0.524 (0.031%), neg=0, invalid=96777 0583: dt=0.005000, rms=0.524 (0.028%), neg=0, invalid=96777 0584: dt=0.005000, rms=0.524 (0.028%), neg=0, invalid=96777 0585: dt=0.005000, rms=0.524 (0.023%), neg=0, invalid=96777 0586: dt=0.005000, rms=0.524 (0.023%), neg=0, invalid=96777 0587: dt=0.112000, rms=0.523 (0.022%), neg=0, invalid=96777 0588: dt=0.003500, rms=0.523 (0.003%), neg=0, invalid=96777 0589: dt=0.003500, rms=0.523 (0.001%), neg=0, invalid=96777 0590: dt=0.001750, rms=0.523 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.523, neg=0, invalid=96777 0591: dt=0.007000, rms=0.523 (0.021%), neg=0, invalid=96777 0592: dt=0.007000, rms=0.523 (0.022%), neg=0, invalid=96777 0593: dt=0.114062, rms=0.521 (0.359%), neg=0, invalid=96777 0594: dt=0.112000, rms=0.520 (0.265%), neg=0, invalid=96777 0595: dt=0.007000, rms=0.520 (0.015%), neg=0, invalid=96777 0596: dt=0.007000, rms=0.520 (0.013%), neg=0, invalid=96777 0597: dt=0.007000, rms=0.520 (0.023%), neg=0, invalid=96777 0598: dt=0.007000, rms=0.519 (0.033%), neg=0, invalid=96777 0599: dt=0.007000, rms=0.519 (0.043%), neg=0, invalid=96777 0600: dt=0.007000, rms=0.519 (0.049%), neg=0, invalid=96777 0601: dt=0.007000, rms=0.519 (0.054%), neg=0, invalid=96777 0602: dt=0.007000, rms=0.518 (0.060%), neg=0, invalid=96777 0603: dt=0.007000, rms=0.518 (0.059%), neg=0, invalid=96777 0604: dt=0.007000, rms=0.518 (0.062%), neg=0, invalid=96777 0605: dt=0.007000, rms=0.517 (0.061%), neg=0, invalid=96777 0606: dt=0.007000, rms=0.517 (0.064%), neg=0, invalid=96777 0607: dt=0.007000, rms=0.517 (0.063%), neg=0, invalid=96777 0608: dt=0.007000, rms=0.516 (0.063%), neg=0, invalid=96777 0609: dt=0.007000, rms=0.516 (0.059%), neg=0, invalid=96777 0610: dt=0.007000, rms=0.516 (0.055%), neg=0, invalid=96777 0611: dt=0.007000, rms=0.516 (0.053%), neg=0, invalid=96777 0612: dt=0.007000, rms=0.515 (0.048%), neg=0, invalid=96777 0613: dt=0.007000, rms=0.515 (0.045%), neg=0, invalid=96777 0614: dt=0.007000, rms=0.515 (0.039%), neg=0, invalid=96777 0615: dt=0.007000, rms=0.515 (0.036%), neg=0, invalid=96777 0616: dt=0.007000, rms=0.515 (0.033%), neg=0, invalid=96777 0617: dt=0.007000, rms=0.514 (0.030%), neg=0, invalid=96777 0618: dt=0.007000, rms=0.514 (0.021%), neg=0, invalid=96777 0619: dt=0.007000, rms=0.514 (0.023%), neg=0, invalid=96777 0620: dt=0.007000, rms=0.514 (0.018%), neg=0, invalid=96777 0621: dt=0.000000, rms=0.514 (-0.003%), 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=0.512, neg=0, invalid=96777 0622: dt=32.368000, rms=0.512 (0.006%), neg=0, invalid=96777 0623: dt=18.496000, rms=0.512 (0.001%), neg=0, invalid=96777 0624: dt=18.496000, rms=0.512 (-0.003%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.512, neg=0, invalid=96777 0625: dt=129.472000, rms=0.512 (0.047%), neg=0, invalid=96777 0626: dt=92.480000, rms=0.512 (0.022%), neg=0, invalid=96777 0627: dt=92.480000, rms=0.512 (0.017%), neg=0, invalid=96777 0628: dt=92.480000, rms=0.511 (0.040%), neg=0, invalid=96777 0629: dt=92.480000, rms=0.511 (0.011%), neg=0, invalid=96777 0630: dt=92.480000, rms=0.511 (0.053%), neg=0, invalid=96777 0631: dt=92.480000, rms=0.511 (0.017%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.511, neg=0, invalid=96777 0632: dt=36.288000, rms=0.510 (0.186%), neg=0, invalid=96777 0633: dt=36.288000, rms=0.509 (0.109%), neg=0, invalid=96777 0634: dt=36.288000, rms=0.509 (0.034%), neg=0, invalid=96777 0635: dt=36.288000, rms=0.509 (0.016%), neg=0, invalid=96777 0636: dt=36.288000, rms=0.509 (-0.038%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.509, neg=0, invalid=96777 0637: dt=82.944000, rms=0.507 (0.431%), neg=0, invalid=96777 0638: dt=9.072000, rms=0.507 (0.072%), neg=0, invalid=96777 0639: dt=9.072000, rms=0.506 (0.041%), neg=0, invalid=96777 0640: dt=9.072000, rms=0.506 (0.047%), neg=0, invalid=96777 0641: dt=9.072000, rms=0.506 (0.054%), neg=0, invalid=96777 0642: dt=9.072000, rms=0.506 (0.052%), neg=0, invalid=96777 0643: dt=9.072000, rms=0.505 (0.068%), neg=0, invalid=96777 0644: dt=9.072000, rms=0.505 (0.074%), neg=0, invalid=96777 0645: dt=9.072000, rms=0.504 (0.079%), neg=0, invalid=96777 0646: dt=9.072000, rms=0.504 (0.072%), neg=0, invalid=96777 0647: dt=103.680000, rms=0.504 (0.072%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.504, neg=0, invalid=96777 iter 0, gcam->neg = 80 after 10 iterations, nbhd size=1, neg = 0 0648: dt=38.400000, rms=0.499 (0.902%), neg=0, invalid=96777 0649: dt=5.468927, rms=0.498 (0.206%), neg=0, invalid=96777 0650: dt=5.468927, rms=0.498 (0.160%), neg=0, invalid=96777 0651: dt=5.468927, rms=0.497 (0.213%), neg=0, invalid=96777 0652: dt=5.468927, rms=0.495 (0.243%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0653: dt=5.468927, rms=0.494 (0.220%), neg=0, invalid=96777 0654: dt=5.468927, rms=0.493 (0.202%), neg=0, invalid=96777 0655: dt=5.468927, rms=0.492 (0.198%), neg=0, invalid=96777 0656: dt=5.468927, rms=0.491 (0.175%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0657: dt=5.468927, rms=0.491 (0.136%), neg=0, invalid=96777 0658: dt=5.468927, rms=0.490 (0.120%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0659: dt=5.468927, rms=0.490 (0.105%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 7 iterations, nbhd size=1, neg = 0 0660: dt=44.800000, rms=0.488 (0.259%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 7 iterations, nbhd size=1, neg = 0 0661: dt=6.400000, rms=0.488 (0.044%), neg=0, invalid=96777 0662: dt=6.400000, rms=0.488 (0.046%), neg=0, invalid=96777 0663: dt=6.400000, rms=0.488 (0.059%), neg=0, invalid=96777 0664: dt=6.400000, rms=0.487 (0.068%), neg=0, invalid=96777 0665: dt=6.400000, rms=0.487 (0.066%), neg=0, invalid=96777 0666: dt=6.400000, rms=0.487 (0.085%), neg=0, invalid=96777 0667: dt=6.400000, rms=0.486 (0.098%), neg=0, invalid=96777 0668: dt=6.400000, rms=0.486 (0.099%), neg=0, invalid=96777 0669: dt=6.400000, rms=0.485 (0.097%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0670: dt=32.000000, rms=0.485 (0.035%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.485, neg=0, invalid=96777 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0671: dt=25.600000, rms=0.483 (0.437%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0672: dt=4.761905, rms=0.482 (0.167%), neg=0, invalid=96777 0673: dt=4.761905, rms=0.481 (0.131%), neg=0, invalid=96777 0674: dt=4.761905, rms=0.481 (0.127%), neg=0, invalid=96777 0675: dt=4.761905, rms=0.480 (0.141%), neg=0, invalid=96777 0676: dt=4.761905, rms=0.479 (0.162%), neg=0, invalid=96777 0677: dt=4.761905, rms=0.479 (0.152%), neg=0, invalid=96777 0678: dt=4.761905, rms=0.478 (0.141%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 5 iterations, nbhd size=1, neg = 0 0679: dt=4.761905, rms=0.477 (0.122%), neg=0, invalid=96777 0680: dt=4.761905, rms=0.477 (0.096%), neg=0, invalid=96777 0681: dt=19.200000, rms=0.477 (0.041%), neg=0, invalid=96777 0682: dt=19.200000, rms=0.477 (0.038%), neg=0, invalid=96777 0683: dt=19.200000, rms=0.476 (0.091%), neg=0, invalid=96777 0684: dt=19.200000, rms=0.475 (0.124%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0685: dt=19.200000, rms=0.476 (-0.168%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.479, neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0686: dt=2.304000, rms=0.479 (0.046%), neg=0, invalid=96777 iter 0, gcam->neg = 6 after 6 iterations, nbhd size=1, neg = 0 0687: dt=1.008000, rms=0.479 (0.040%), neg=0, invalid=96777 0688: dt=1.008000, rms=0.479 (0.033%), neg=0, invalid=96777 0689: dt=1.008000, rms=0.478 (0.054%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0690: dt=1.008000, rms=0.478 (0.031%), neg=0, invalid=96777 0691: dt=1.008000, rms=0.478 (-0.012%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.478, neg=0, invalid=96777 iter 0, gcam->neg = 16 after 8 iterations, nbhd size=1, neg = 0 0692: dt=2.880000, rms=0.478 (0.049%), neg=0, invalid=96777 iter 0, gcam->neg = 24 after 10 iterations, nbhd size=1, neg = 0 0693: dt=3.081967, rms=0.478 (0.090%), neg=0, invalid=96777 iter 0, gcam->neg = 19 after 8 iterations, nbhd size=1, neg = 0 0694: dt=2.880000, rms=0.477 (0.073%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0695: dt=2.880000, rms=0.477 (0.097%), neg=0, invalid=96777 iter 0, gcam->neg = 7 after 6 iterations, nbhd size=1, neg = 0 0696: dt=2.880000, rms=0.476 (0.154%), neg=0, invalid=96777 iter 0, gcam->neg = 32 after 13 iterations, nbhd size=1, neg = 0 0697: dt=2.880000, rms=0.475 (0.133%), neg=0, invalid=96777 iter 0, gcam->neg = 36 after 14 iterations, nbhd size=1, neg = 0 0698: dt=2.880000, rms=0.475 (0.148%), neg=0, invalid=96777 iter 0, gcam->neg = 92 after 23 iterations, nbhd size=1, neg = 0 0699: dt=2.880000, rms=0.474 (0.078%), neg=0, invalid=96777 iter 0, gcam->neg = 40 after 14 iterations, nbhd size=1, neg = 0 0700: dt=2.880000, rms=0.474 (0.133%), neg=0, invalid=96777 iter 0, gcam->neg = 35 after 10 iterations, nbhd size=1, neg = 0 0701: dt=2.880000, rms=0.473 (0.196%), neg=0, invalid=96777 iter 0, gcam->neg = 24 after 11 iterations, nbhd size=1, neg = 0 0702: dt=2.880000, rms=0.471 (0.286%), neg=0, invalid=96777 iter 0, gcam->neg = 22 after 9 iterations, nbhd size=1, neg = 0 0703: dt=2.880000, rms=0.470 (0.369%), neg=0, invalid=96777 iter 0, gcam->neg = 16 after 8 iterations, nbhd size=1, neg = 0 0704: dt=2.880000, rms=0.468 (0.366%), neg=0, invalid=96777 iter 0, gcam->neg = 40 after 8 iterations, nbhd size=1, neg = 0 0705: dt=2.880000, rms=0.467 (0.320%), neg=0, invalid=96777 iter 0, gcam->neg = 43 after 9 iterations, nbhd size=1, neg = 0 0706: dt=2.880000, rms=0.465 (0.251%), neg=0, invalid=96777 iter 0, gcam->neg = 52 after 11 iterations, nbhd size=1, neg = 0 0707: dt=2.880000, rms=0.464 (0.216%), neg=0, invalid=96777 iter 0, gcam->neg = 71 after 12 iterations, nbhd size=1, neg = 0 0708: dt=2.880000, rms=0.464 (0.135%), neg=0, invalid=96777 iter 0, gcam->neg = 79 after 13 iterations, nbhd size=1, neg = 0 0709: dt=2.880000, rms=0.463 (0.077%), neg=0, invalid=96777 iter 0, gcam->neg = 31 after 8 iterations, nbhd size=1, neg = 0 0710: dt=2.880000, rms=0.463 (-0.012%), neg=0, invalid=96777 0711: dt=0.000000, rms=0.463 (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=0.469, neg=0, invalid=96777 0712: dt=0.000000, rms=0.469 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.469, neg=0, invalid=96777 0713: dt=0.000000, rms=0.469 (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=0.460, neg=0, invalid=96777 iter 0, gcam->neg = 995 after 41 iterations, nbhd size=3, neg = 0 0714: dt=1.536000, rms=0.422 (8.230%), neg=0, invalid=96777 0715: dt=0.000016, rms=0.422 (-0.004%), neg=0, invalid=96777 0716: dt=0.000016, rms=0.422 (0.000%), neg=0, invalid=96777 0717: dt=0.000016, rms=0.422 (0.000%), neg=0, invalid=96777 0718: dt=0.000016, rms=0.422 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.422, neg=0, invalid=96777 0719: dt=0.000188, rms=0.422 (0.000%), neg=0, invalid=96777 0720: dt=0.000000, rms=0.422 (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=0.412, neg=0, invalid=96777 0721: dt=18.496000, rms=0.413 (-0.304%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.413, neg=0, invalid=96777 0722: dt=32.368000, rms=0.413 (0.003%), neg=0, invalid=96777 0723: dt=5.780000, rms=0.413 (0.000%), neg=0, invalid=96777 0724: dt=5.780000, rms=0.413 (-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=0.413, neg=0, invalid=96777 0725: dt=7.776000, rms=0.413 (0.006%), neg=0, invalid=96777 0726: dt=0.567000, rms=0.413 (0.000%), neg=0, invalid=96777 0727: dt=0.567000, rms=0.413 (0.000%), neg=0, invalid=96777 0728: dt=0.567000, rms=0.413 (0.000%), neg=0, invalid=96777 0729: dt=0.567000, rms=0.413 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.413, neg=0, invalid=96777 iter 0, gcam->neg = 1 after 200 iterations, nbhd size=1, neg = 2 starting rms=0.006, neg=2, removing folds in lattice.... iter 1, dt=0.000000: new neg 2, old_neg 2, delta 0, rms=0.006 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0730: dt=36.288000, rms=0.413 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.413, neg=0, invalid=96777 iter 0, gcam->neg = 13 after 200 iterations, nbhd size=2, neg = 2 starting rms=0.008, neg=2, removing folds in lattice.... iter 1, dt=0.000023: new neg 1, old_neg 2, delta 1, rms=0.006 (28.961%) iter 2, dt=0.000061: new neg 0, old_neg 1, delta 1, rms=0.003 (41.141%) 0731: dt=6.400000, rms=0.413 (0.002%), neg=0, invalid=96777 iter 0, gcam->neg = 20 after 200 iterations, nbhd size=4, neg = 2 starting rms=0.008, neg=2, removing folds in lattice.... iter 1, dt=0.000023: new neg 1, old_neg 2, delta 1, rms=0.005 (27.551%) iter 2, dt=0.000061: new neg 0, old_neg 1, delta 1, rms=0.003 (41.000%) 0732: dt=9.600000, rms=0.413 (-0.066%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.413, neg=0, invalid=96777 iter 0, gcam->neg = 46 after 200 iterations, nbhd size=2, neg = 5 starting rms=0.005, neg=5, removing folds in lattice.... iter 1, dt=0.000031: new neg 0, old_neg 5, delta 5, rms=0.003 (35.752%) 0733: dt=38.400000, rms=0.413 (0.208%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 26 iterations, nbhd size=4, neg = 0 0734: dt=4.800000, rms=0.413 (0.020%), neg=0, invalid=96777 0735: dt=4.800000, rms=0.412 (0.041%), neg=0, invalid=96777 0736: dt=4.800000, rms=0.412 (0.061%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 5 iterations, nbhd size=1, neg = 0 0737: dt=4.800000, rms=0.412 (0.077%), neg=0, invalid=96777 0738: dt=4.800000, rms=0.411 (0.087%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 14 iterations, nbhd size=2, neg = 0 0739: dt=4.800000, rms=0.411 (-0.002%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.413, neg=0, invalid=96777 0740: dt=0.001688, rms=0.413 (0.000%), neg=0, invalid=96777 iter 0, gcam->neg = 44 after 37 iterations, nbhd size=4, neg = 0 0741: dt=3.105882, rms=0.412 (0.207%), neg=0, invalid=96777 0742: dt=0.011248, rms=0.412 (0.000%), neg=0, invalid=96777 0743: dt=0.011248, rms=0.412 (0.001%), neg=0, invalid=96777 0744: dt=0.011248, rms=0.412 (0.002%), neg=0, invalid=96777 0745: dt=0.011248, rms=0.412 (0.002%), neg=0, invalid=96777 0746: dt=0.011248, rms=0.412 (0.003%), neg=0, invalid=96777 0747: dt=0.011248, rms=0.412 (0.004%), neg=0, invalid=96777 0748: dt=0.011248, rms=0.412 (0.004%), neg=0, invalid=96777 0749: dt=0.011248, rms=0.412 (0.005%), neg=0, invalid=96777 0750: dt=0.011248, rms=0.412 (0.005%), neg=0, invalid=96777 0751: dt=0.011248, rms=0.412 (0.006%), neg=0, invalid=96777 0752: dt=0.011248, rms=0.412 (0.006%), neg=0, invalid=96777 0753: dt=0.011248, rms=0.412 (0.007%), neg=0, invalid=96777 0754: dt=0.011248, rms=0.412 (0.007%), neg=0, invalid=96777 0755: dt=0.011248, rms=0.412 (0.007%), neg=0, invalid=96777 0756: dt=0.011248, rms=0.412 (0.007%), neg=0, invalid=96777 0757: dt=0.011248, rms=0.412 (0.008%), neg=0, invalid=96777 0758: dt=0.011248, rms=0.412 (0.008%), neg=0, invalid=96777 0759: dt=0.011248, rms=0.412 (0.008%), neg=0, invalid=96777 0760: dt=0.011248, rms=0.412 (0.008%), neg=0, invalid=96777 0761: dt=0.011248, rms=0.412 (0.008%), neg=0, invalid=96777 0762: dt=0.011248, rms=0.412 (0.008%), neg=0, invalid=96777 0763: dt=0.011248, rms=0.412 (0.008%), neg=0, invalid=96777 0764: dt=0.011248, rms=0.412 (0.008%), neg=0, invalid=96777 0765: dt=0.011248, rms=0.412 (0.008%), neg=0, invalid=96777 0766: dt=0.011248, rms=0.412 (0.008%), neg=0, invalid=96777 0767: dt=0.011248, rms=0.412 (0.008%), neg=0, invalid=96777 0768: dt=0.011248, rms=0.411 (0.008%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.411, neg=0, invalid=96777 iter 0, gcam->neg = 103 after 200 iterations, nbhd size=4, neg = 4 starting rms=0.005, neg=4, removing folds in lattice.... iter 1, dt=0.000047: new neg 0, old_neg 4, delta 4, rms=0.003 (45.413%) 0769: dt=9.216000, rms=0.409 (0.517%), neg=0, invalid=96777 0770: dt=0.045000, rms=0.409 (0.001%), neg=0, invalid=96777 0771: dt=0.045000, rms=0.409 (0.002%), neg=0, invalid=96777 0772: dt=0.045000, rms=0.409 (0.004%), neg=0, invalid=96777 0773: dt=0.045000, rms=0.409 (0.006%), neg=0, invalid=96777 0774: dt=0.045000, rms=0.409 (0.008%), neg=0, invalid=96777 0775: dt=0.045000, rms=0.409 (0.010%), neg=0, invalid=96777 0776: dt=0.045000, rms=0.409 (0.012%), neg=0, invalid=96777 0777: dt=0.045000, rms=0.409 (0.013%), neg=0, invalid=96777 0778: dt=0.045000, rms=0.409 (0.015%), neg=0, invalid=96777 0779: dt=0.045000, rms=0.409 (0.016%), neg=0, invalid=96777 0780: dt=0.045000, rms=0.409 (0.017%), neg=0, invalid=96777 0781: dt=0.045000, rms=0.409 (0.018%), neg=0, invalid=96777 0782: dt=0.045000, rms=0.409 (0.018%), neg=0, invalid=96777 0783: dt=0.045000, rms=0.409 (0.018%), neg=0, invalid=96777 0784: dt=0.045000, rms=0.409 (0.018%), neg=0, invalid=96777 0785: dt=0.045000, rms=0.409 (0.019%), neg=0, invalid=96777 0786: dt=0.045000, rms=0.408 (0.019%), neg=0, invalid=96777 0787: dt=0.045000, rms=0.408 (0.019%), neg=0, invalid=96777 0788: dt=0.045000, rms=0.408 (0.019%), neg=0, invalid=96777 0789: dt=0.045000, rms=0.408 (0.019%), neg=0, invalid=96777 0790: dt=0.045000, rms=0.408 (0.019%), neg=0, invalid=96777 iter 0, gcam->neg = 78 after 200 iterations, nbhd size=4, neg = 2 starting rms=0.003, neg=2, removing folds in lattice.... iter 1, dt=0.000039: new neg 0, old_neg 2, delta 2, rms=0.003 (25.772%) 0791: dt=9.072626, rms=0.408 (0.160%), neg=0, invalid=96777 0792: dt=0.003938, rms=0.408 (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=0.411, neg=0, invalid=96777 0793: dt=0.000000, rms=0.411 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.411, neg=0, invalid=96777 0794: dt=0.000000, rms=0.411 (0.000%), neg=0, invalid=96777 iter 0, gcam->neg = 11 after 200 iterations, nbhd size=1, neg = 2 starting rms=0.004, neg=2, removing folds in lattice.... iter 1, dt=0.000611: new neg 0, old_neg 2, delta 2, rms=0.002 (58.131%) 0795: dt=0.100000, rms=0.411 (-0.086%), 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=0.405, neg=0, invalid=96777 iter 0, gcam->neg = 421 after 31 iterations, nbhd size=3, neg = 0 0796: dt=0.506734, rms=0.395 (2.419%), neg=0, invalid=96777 0797: dt=0.000027, rms=0.395 (0.002%), neg=0, invalid=96777 0798: dt=0.000027, rms=0.395 (0.000%), neg=0, invalid=96777 0799: dt=0.000027, rms=0.395 (0.000%), neg=0, invalid=96777 0800: dt=0.000027, rms=0.395 (0.000%), neg=0, invalid=96777 0801: dt=0.000250, rms=0.395 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.395, neg=0, invalid=96777 iter 0, gcam->neg = 17 after 7 iterations, nbhd size=1, neg = 0 0802: dt=0.024000, rms=0.395 (0.053%), neg=0, invalid=96777 0803: dt=0.000060, rms=0.395 (0.000%), neg=0, invalid=96777 0804: dt=0.000060, rms=0.395 (0.000%), neg=0, invalid=96777 0805: dt=0.000060, rms=0.395 (0.000%), neg=0, invalid=96777 0806: dt=0.000060, rms=0.395 (0.001%), neg=0, invalid=96777 0807: dt=0.000060, rms=0.395 (0.001%), neg=0, invalid=96777 0808: dt=0.000060, rms=0.395 (0.001%), neg=0, invalid=96777 0809: dt=0.000060, rms=0.395 (0.001%), neg=0, invalid=96777 0810: dt=0.000060, rms=0.395 (0.001%), neg=0, invalid=96777 0811: dt=0.000060, rms=0.395 (0.001%), neg=0, invalid=96777 0812: dt=0.000060, rms=0.395 (0.001%), neg=0, invalid=96777 0813: dt=0.000060, rms=0.395 (0.001%), neg=0, invalid=96777 0814: dt=0.000060, rms=0.395 (0.001%), neg=0, invalid=96777 0815: dt=0.000060, rms=0.395 (0.001%), neg=0, invalid=96777 0816: dt=0.000060, rms=0.395 (0.001%), neg=0, invalid=96777 0817: dt=0.000060, rms=0.395 (0.001%), neg=0, invalid=96777 0818: dt=0.000060, rms=0.395 (0.001%), neg=0, invalid=96777 0819: dt=0.000060, rms=0.395 (0.001%), neg=0, invalid=96777 0820: dt=0.000060, rms=0.395 (0.001%), neg=0, invalid=96777 0821: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777 0822: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777 0823: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777 0824: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777 0825: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777 0826: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777 0827: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777 0828: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777 0829: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777 0830: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777 0831: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777 0832: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777 0833: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777 0834: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777 0835: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777 0836: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777 0837: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777 0838: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777 0839: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777 0840: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777 0841: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777 0842: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777 0843: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777 0844: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777 0845: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777 writing output transformation to transforms/talairach.m3z... GCAMwrite registration took 4 hours, 38 minutes and 37 seconds. #-------------------------------------- #@# CA Reg Inv Thu Aug 8 16:51:07 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 16:52:34 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... 11240145 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 1 minutes and 25 seconds. #-------------------------------------- #@# SkullLTA Thu Aug 8 16:54:00 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=11.0 skull bounding box = (55, 20, 16) --> (207, 204, 195) using (106, 81, 106) as brain centroid... mean wm in atlas = 126, using box (87,58,84) --> (124, 103,128) to find MRI wm before smoothing, mri peak at 109 after smoothing, mri peak at 110, scaling input intensities by 1.145 scaling channel 0 by 1.14545 **************************************** 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) 1.168 0.051 -0.020 -31.157; -0.035 1.106 0.358 -25.307; 0.070 -0.337 0.925 29.655; 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) 1.168 0.051 -0.020 -31.157; -0.035 1.106 0.358 -25.307; 0.070 -0.337 0.925 29.655; 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) 1.125 0.014 -0.028 -18.873; -0.001 1.105 0.290 -22.213; 0.071 -0.279 1.000 13.411; 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) 1.104 0.013 -0.028 -16.161; -0.003 1.134 0.262 -21.735; 0.070 -0.238 0.990 10.595; 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) 1.107 0.006 -0.038 -14.701; 0.005 1.132 0.252 -21.601; 0.079 -0.228 0.989 8.610; 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) 1.107 0.006 -0.038 -14.701; 0.005 1.132 0.252 -21.601; 0.079 -0.228 0.989 8.610; 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 1.10678 0.00590 -0.03797 -14.70059; 0.00517 1.13224 0.25242 -21.60137; 0.07881 -0.22815 0.98872 8.60961; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.10678 0.00590 -0.03797 -14.70059; 0.00517 1.13224 0.25242 -21.60137; 0.07881 -0.22815 0.98872 8.60961; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 007: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.107 0.006 -0.038 -14.701; 0.005 1.132 0.252 -21.601; 0.079 -0.228 0.989 8.610; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -4.0 (old=-4.2) transform before final EM align: 1.107 0.006 -0.038 -14.701; 0.005 1.132 0.252 -21.601; 0.079 -0.228 0.989 8.610; 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 1.10678 0.00590 -0.03797 -14.70059; 0.00517 1.13224 0.25242 -21.60137; 0.07881 -0.22815 0.98872 8.60961; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.10678 0.00590 -0.03797 -14.70059; 0.00517 1.13224 0.25242 -21.60137; 0.07881 -0.22815 0.98872 8.60961; 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: 1.107 0.006 -0.038 -14.701; 0.005 1.132 0.252 -21.601; 0.079 -0.228 0.989 8.610; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull_2.lta... registration took 29 minutes and 29 seconds. #-------------------------------------- #@# SubCort Seg Thu Aug 8 17:23:29 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 snake6 machine x86_64 setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 = 0.12812 ( 7) Left_Lateral_Ventricle (4): linear fit = 0.25 x + 0.0 (3501 voxels, overlap=0.007) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (3501 voxels, peak = 7), gca=10.8 gca peak = 0.14982 (20) mri peak = 0.12164 ( 7) Right_Lateral_Ventricle (43): linear fit = 0.31 x + 0.0 (3208 voxels, overlap=0.008) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (3208 voxels, peak = 6), gca=8.0 gca peak = 0.28003 (97) mri peak = 0.09887 (92) Right_Pallidum (52): linear fit = 0.94 x + 0.0 (123 voxels, overlap=0.826) Right_Pallidum (52): linear fit = 0.94 x + 0.0 (123 voxels, peak = 91), gca=90.7 gca peak = 0.18160 (96) mri peak = 0.08158 (92) Left_Pallidum (13): linear fit = 0.94 x + 0.0 (379 voxels, overlap=0.566) Left_Pallidum (13): linear fit = 0.94 x + 0.0 (379 voxels, peak = 91), gca=90.7 gca peak = 0.27536 (62) mri peak = 0.09023 (51) Right_Hippocampus (53): linear fit = 0.82 x + 0.0 (528 voxels, overlap=0.182) Right_Hippocampus (53): linear fit = 0.82 x + 0.0 (528 voxels, peak = 51), gca=51.1 gca peak = 0.32745 (63) mri peak = 0.10369 (58) Left_Hippocampus (17): linear fit = 0.90 x + 0.0 (498 voxels, overlap=0.606) Left_Hippocampus (17): linear fit = 0.90 x + 0.0 (498 voxels, peak = 57), gca=57.0 gca peak = 0.08597 (105) mri peak = 0.08517 (106) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (27442 voxels, overlap=0.743) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (27442 voxels, peak = 107), gca=106.6 gca peak = 0.09209 (106) mri peak = 0.08847 (108) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (28941 voxels, overlap=0.613) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (28941 voxels, peak = 109), gca=108.6 gca peak = 0.07826 (63) mri peak = 0.06440 (51) Left_Cerebral_Cortex (3): linear fit = 0.82 x + 0.0 (11820 voxels, overlap=0.307) Left_Cerebral_Cortex (3): linear fit = 0.82 x + 0.0 (11820 voxels, peak = 52), gca=52.0 gca peak = 0.08598 (64) mri peak = 0.06742 (51) Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (9630 voxels, overlap=0.266) Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (9630 voxels, peak = 53), gca=52.8 gca peak = 0.24164 (71) mri peak = 0.10762 (66) Right_Caudate (50): linear fit = 0.90 x + 0.0 (332 voxels, overlap=0.181) Right_Caudate (50): linear fit = 0.90 x + 0.0 (332 voxels, peak = 64), gca=64.3 gca peak = 0.18227 (75) mri peak = 0.08796 (68) Left_Caudate (11): linear fit = 0.87 x + 0.0 (689 voxels, overlap=0.452) Left_Caudate (11): linear fit = 0.87 x + 0.0 (689 voxels, peak = 65), gca=64.9 gca peak = 0.10629 (62) mri peak = 0.04888 (56) Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (6222 voxels, overlap=0.995) Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (6222 voxels, peak = 58), gca=58.0 gca peak = 0.11668 (59) mri peak = 0.05288 (56) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (7596 voxels, overlap=0.987) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (7596 voxels, peak = 57), gca=56.9 gca peak = 0.17849 (88) mri peak = 0.08781 (94) Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (5856 voxels, overlap=0.921) Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (5856 voxels, peak = 92), gca=92.0 gca peak = 0.16819 (86) mri peak = 0.09458 (93) Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (5069 voxels, overlap=0.973) Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (5069 voxels, peak = 90), gca=89.9 gca peak = 0.41688 (64) mri peak = 0.11359 (61) Left_Amygdala (18): linear fit = 0.94 x + 0.0 (244 voxels, overlap=1.037) Left_Amygdala (18): linear fit = 0.94 x + 0.0 (244 voxels, peak = 60), gca=59.8 gca peak = 0.42394 (62) mri peak = 0.10630 (58) Right_Amygdala (54): linear fit = 0.92 x + 0.0 (258 voxels, overlap=0.617) Right_Amygdala (54): linear fit = 0.92 x + 0.0 (258 voxels, peak = 57), gca=56.7 gca peak = 0.10041 (96) mri peak = 0.07153 (90) Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (3048 voxels, overlap=0.814) Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (3048 voxels, peak = 92), gca=91.7 gca peak = 0.13978 (88) mri peak = 0.06806 (89) Right_Thalamus_Proper (49): linear fit = 0.95 x + 0.0 (2683 voxels, overlap=0.920) Right_Thalamus_Proper (49): linear fit = 0.95 x + 0.0 (2683 voxels, peak = 84), gca=84.0 gca peak = 0.08514 (81) mri peak = 0.05583 (80) Left_Putamen (12): linear fit = 0.90 x + 0.0 (2027 voxels, overlap=0.673) Left_Putamen (12): linear fit = 0.90 x + 0.0 (2027 voxels, peak = 73), gca=73.3 gca peak = 0.09624 (82) mri peak = 0.05650 (72) Right_Putamen (51): linear fit = 0.93 x + 0.0 (2538 voxels, overlap=0.687) Right_Putamen (51): linear fit = 0.93 x + 0.0 (2538 voxels, peak = 76), gca=75.8 gca peak = 0.07543 (88) mri peak = 0.06768 (88) Brain_Stem (16): linear fit = 1.03 x + 0.0 (10689 voxels, overlap=0.765) Brain_Stem (16): linear fit = 1.03 x + 0.0 (10689 voxels, peak = 91), gca=91.1 gca peak = 0.12757 (95) mri peak = 0.06738 (93) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (878 voxels, overlap=0.822) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (878 voxels, peak = 96), gca=96.4 gca peak = 0.17004 (92) mri peak = 0.06801 (96) Left_VentralDC (28): linear fit = 1.03 x + 0.0 (987 voxels, overlap=0.843) Left_VentralDC (28): linear fit = 1.03 x + 0.0 (987 voxels, peak = 95), gca=95.2 gca peak = 0.21361 (36) mri peak = 0.17391 (11) gca peak = 0.26069 (23) mri peak = 0.17595 ( 8) Fourth_Ventricle (15): linear fit = 0.26 x + 0.0 (127 voxels, overlap=0.024) Fourth_Ventricle (15): linear fit = 0.26 x + 0.0 (127 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 0.87 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 = 0.12812 ( 7) Left_Lateral_Ventricle (4): linear fit = 0.70 x + 0.0 (3501 voxels, overlap=0.942) Left_Lateral_Ventricle (4): linear fit = 0.70 x + 0.0 (3501 voxels, peak = 8), gca=7.8 gca peak = 0.29325 ( 9) mri peak = 0.12164 ( 7) Right_Lateral_Ventricle (43): linear fit = 0.76 x + 0.0 (3208 voxels, overlap=0.969) Right_Lateral_Ventricle (43): linear fit = 0.76 x + 0.0 (3208 voxels, peak = 7), gca=6.9 gca peak = 0.30470 (91) mri peak = 0.09887 (92) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (123 voxels, overlap=1.010) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (123 voxels, peak = 91), gca=90.5 gca peak = 0.18129 (91) mri peak = 0.08158 (92) Left_Pallidum (13): linear fit = 0.99 x + 0.0 (379 voxels, overlap=1.007) Left_Pallidum (13): linear fit = 0.99 x + 0.0 (379 voxels, peak = 90), gca=89.6 gca peak = 0.32446 (51) mri peak = 0.09023 (51) Right_Hippocampus (53): linear fit = 0.98 x + 0.0 (528 voxels, overlap=1.002) Right_Hippocampus (53): linear fit = 0.98 x + 0.0 (528 voxels, peak = 50), gca=49.7 gca peak = 0.33359 (57) mri peak = 0.10369 (58) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (498 voxels, overlap=1.007) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (498 voxels, peak = 57), gca=57.0 gca peak = 0.08541 (107) mri peak = 0.08517 (106) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (27442 voxels, overlap=0.780) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (27442 voxels, peak = 106), gca=106.5 gca peak = 0.08551 (108) mri peak = 0.08847 (108) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (28941 voxels, overlap=0.708) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (28941 voxels, peak = 108), gca=108.0 gca peak = 0.09514 (52) mri peak = 0.06440 (51) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (11820 voxels, overlap=0.985) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (11820 voxels, peak = 53), gca=53.3 gca peak = 0.10560 (53) mri peak = 0.06742 (51) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (9630 voxels, overlap=0.987) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (9630 voxels, peak = 52), gca=52.2 gca peak = 0.26783 (64) mri peak = 0.10762 (66) Right_Caudate (50): linear fit = 0.99 x + 0.0 (332 voxels, overlap=0.993) Right_Caudate (50): linear fit = 0.99 x + 0.0 (332 voxels, peak = 63), gca=63.0 gca peak = 0.17966 (65) mri peak = 0.08796 (68) Left_Caudate (11): linear fit = 1.01 x + 0.0 (689 voxels, overlap=0.999) Left_Caudate (11): linear fit = 1.01 x + 0.0 (689 voxels, peak = 66), gca=66.0 gca peak = 0.11193 (57) mri peak = 0.04888 (56) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (6222 voxels, overlap=0.994) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (6222 voxels, peak = 58), gca=58.4 gca peak = 0.12335 (58) mri peak = 0.05288 (56) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (7596 voxels, overlap=1.000) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (7596 voxels, peak = 56), gca=56.0 gca peak = 0.17369 (92) mri peak = 0.08781 (94) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5856 voxels, overlap=0.994) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5856 voxels, peak = 92), gca=91.5 gca peak = 0.15955 (90) mri peak = 0.09458 (93) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5069 voxels, overlap=1.000) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5069 voxels, peak = 90), gca=89.6 gca peak = 0.34609 (59) mri peak = 0.11359 (61) Left_Amygdala (18): linear fit = 1.02 x + 0.0 (244 voxels, overlap=1.012) Left_Amygdala (18): linear fit = 1.02 x + 0.0 (244 voxels, peak = 60), gca=60.5 gca peak = 0.50707 (57) mri peak = 0.10630 (58) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (258 voxels, overlap=1.023) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (258 voxels, peak = 57), gca=57.0 gca peak = 0.10969 (90) mri peak = 0.07153 (90) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3048 voxels, overlap=0.997) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3048 voxels, peak = 90), gca=89.6 gca peak = 0.14487 (84) mri peak = 0.06806 (89) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (2683 voxels, overlap=1.000) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (2683 voxels, peak = 84), gca=83.6 gca peak = 0.09690 (79) mri peak = 0.05583 (80) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2027 voxels, overlap=0.997) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2027 voxels, peak = 79), gca=79.0 gca peak = 0.12049 (70) mri peak = 0.05650 (72) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2538 voxels, overlap=1.002) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2538 voxels, peak = 70), gca=69.7 gca peak = 0.07047 (88) mri peak = 0.06768 (88) Brain_Stem (16): linear fit = 1.00 x + 0.0 (10689 voxels, overlap=0.836) Brain_Stem (16): linear fit = 1.00 x + 0.0 (10689 voxels, peak = 88), gca=87.6 gca peak = 0.14090 (96) mri peak = 0.06738 (93) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (878 voxels, overlap=0.866) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (878 voxels, peak = 96), gca=95.5 gca peak = 0.13753 (96) mri peak = 0.06801 (96) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (987 voxels, overlap=0.914) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (987 voxels, peak = 96), gca=96.5 gca peak = 0.35640 (14) mri peak = 0.17391 (11) gca peak = 0.33827 ( 9) mri peak = 0.17595 ( 8) Fourth_Ventricle (15): linear fit = 0.68 x + 0.0 (127 voxels, overlap=0.932) Fourth_Ventricle (15): linear fit = 0.68 x + 0.0 (127 voxels, peak = 6), gca=6.1 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.27695 (32) gca peak Third_Ventricle = 0.35640 (14) gca peak CSF = 0.30128 (18) gca peak Left_Accumbens_area = 0.44858 (60) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.42679 (62) gca peak Left_choroid_plexus = 0.09164 (48) gca peak Right_Inf_Lat_Vent = 0.31192 (26) gca peak Right_Accumbens_area = 0.38912 (65) gca peak Right_vessel = 0.58264 (60) gca peak Right_choroid_plexus = 0.10280 (48) gca peak Fifth_Ventricle = 0.45329 (19) gca peak WM_hypointensities = 0.17302 (83) gca peak non_WM_hypointensities = 0.11232 (54) gca peak Optic_Chiasm = 0.34849 (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 0.71 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 11984 gm and wm labels changed (%13 to gray, %87 to white out of all changed labels) 311 hippocampal voxels changed. 7 amygdala voxels changed. pass 1: 91688 changed. image ll: -2.211, PF=1.000 pass 2: 16871 changed. image ll: -2.209, PF=1.000 pass 3: 6520 changed. pass 4: 3025 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 19 minutes and 14 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/cc_up.lta sub009 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/sub009/mri/transforms/cc_up.lta reading aseg from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/aseg.auto_noCCseg.mgz reading norm from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/norm.mgz 22980 voxels in left wm, 35154 in right wm, xrange [127, 135] searching rotation angles z=[-9 5], y=[-9 5] searching scale 1 Z rot -9.0 searching scale 1 Z rot -8.7 searching scale 1 Z rot -8.5 searching scale 1 Z rot -8.2 searching scale 1 Z rot -8.0 searching scale 1 Z rot -7.7 searching scale 1 Z rot -7.5 searching scale 1 Z rot -7.2 searching scale 1 Z rot -7.0 searching scale 1 Z rot -6.7 searching scale 1 Z rot -6.5 searching scale 1 Z rot -6.2 searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.7 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.2 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.2 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.2 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.2 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.2 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.0 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.3 searching scale 1 Z rot 4.5 searching scale 1 Z rot 4.8 global minimum found at slice 131.0, rotations (-1.91, -2.00) final transformation (x=131.0, yr=-1.915, zr=-1.998): 0.999 0.035 -0.033 -1.928; -0.035 0.999 0.001 53.484; 0.033 0.000 0.999 13.685; 0.000 0.000 0.000 1.000; updating x range to be [125, 131] in xformed coordinates best xformed slice 128 cc center is found at 128 154 110 eigenvectors: -0.000 -0.002 1.000; -0.223 -0.975 -0.002; 0.975 -0.223 -0.000; error in mid anterior detected - correcting... error in mid anterior detected - correcting... error in mid anterior detected - correcting... writing aseg with callosum to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/aseg.auto.mgz... corpus callosum matter segmentation took 0.8 minutes #-------------------------------------- #@# Merge ASeg Thu Aug 8 17:43:29 CEST 2013 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Thu Aug 8 17:43:29 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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... 2439 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 30 (30) 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 30 (30) 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 19 seconds. #-------------------------------------------- #@# Mask BFS Thu Aug 8 17:47:50 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1589890 voxels in mask (pct= 9.48) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Thu Aug 8 17:47:52 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 (108.0): 107.5 +- 4.6 [80.0 --> 125.0] GM (66.0) : 65.5 +- 9.6 [30.0 --> 96.0] setting bottom of white matter range to 75.0 setting top of gray matter range to 84.6 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 7605 sparsely connected voxels removed... thickening thin strands.... 20 segments, 8722 filled 751 bright non-wm voxels segmented. 4251 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 0.72 minutes reading wm segmentation from wm.seg.mgz... 195 voxels added to wm to prevent paths from MTL structures to cortex 1290 additional wm voxels added 0 additional wm voxels added SEG EDIT: 65476 voxels turned on, 47719 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+): 18 found - 18 modified | TOTAL: 18 pass 2 (xy+): 0 found - 18 modified | TOTAL: 18 pass 1 (xy-): 21 found - 21 modified | TOTAL: 39 pass 2 (xy-): 0 found - 21 modified | TOTAL: 39 pass 1 (yz+): 25 found - 25 modified | TOTAL: 64 pass 2 (yz+): 0 found - 25 modified | TOTAL: 64 pass 1 (yz-): 20 found - 20 modified | TOTAL: 84 pass 2 (yz-): 0 found - 20 modified | TOTAL: 84 pass 1 (xz+): 19 found - 19 modified | TOTAL: 103 pass 2 (xz+): 0 found - 19 modified | TOTAL: 103 pass 1 (xz-): 18 found - 18 modified | TOTAL: 121 pass 2 (xz-): 0 found - 18 modified | TOTAL: 121 Iteration Number : 1 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 pass 1 (+++): 6 found - 6 modified | TOTAL: 10 pass 2 (+++): 0 found - 6 modified | TOTAL: 10 pass 1 (+++): 2 found - 2 modified | TOTAL: 12 pass 2 (+++): 0 found - 2 modified | TOTAL: 12 pass 1 (+++): 16 found - 16 modified | TOTAL: 28 pass 2 (+++): 0 found - 16 modified | TOTAL: 28 Iteration Number : 1 pass 1 (++): 241 found - 241 modified | TOTAL: 241 pass 2 (++): 0 found - 241 modified | TOTAL: 241 pass 1 (+-): 226 found - 226 modified | TOTAL: 467 pass 2 (+-): 0 found - 226 modified | TOTAL: 467 pass 1 (--): 240 found - 240 modified | TOTAL: 707 pass 2 (--): 0 found - 240 modified | TOTAL: 707 pass 1 (-+): 210 found - 210 modified | TOTAL: 917 pass 2 (-+): 0 found - 210 modified | TOTAL: 917 Iteration Number : 2 pass 1 (xy+): 6 found - 6 modified | TOTAL: 6 pass 2 (xy+): 0 found - 6 modified | TOTAL: 6 pass 1 (xy-): 2 found - 2 modified | TOTAL: 8 pass 2 (xy-): 0 found - 2 modified | TOTAL: 8 pass 1 (yz+): 2 found - 2 modified | TOTAL: 10 pass 2 (yz+): 0 found - 2 modified | TOTAL: 10 pass 1 (yz-): 2 found - 2 modified | TOTAL: 12 pass 2 (yz-): 0 found - 2 modified | TOTAL: 12 pass 1 (xz+): 4 found - 4 modified | TOTAL: 16 pass 2 (xz+): 0 found - 4 modified | TOTAL: 16 pass 1 (xz-): 4 found - 4 modified | TOTAL: 20 pass 2 (xz-): 0 found - 4 modified | TOTAL: 20 Iteration Number : 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 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 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 1 found - 1 modified | TOTAL: 2 pass 2 (-+): 0 found - 1 modified | TOTAL: 2 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 1090 (out of 531379: 0.205127) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Thu Aug 8 17:50:27 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 1.086 0.047 -0.018 -20.209; -0.035 1.106 0.358 -25.307; 0.070 -0.337 0.925 29.655; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.086 0.047 -0.018 -20.209; -0.035 1.106 0.358 -25.307; 0.070 -0.337 0.925 29.655; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1112 (min = 350, max = 1400), aspect = 0.51 (min = 0.10, max = 0.75) no need to search using seed (125, 121, 151), TAL = (3.0, 23.0, 7.0) talairach voxel to voxel transform 0.918 -0.030 0.030 16.898; 0.046 0.807 -0.311 30.586; -0.053 0.297 0.965 -22.188; 0.000 0.000 0.000 1.000; segmentation indicates cc at (125, 121, 151) --> (3.0, 23.0, 7.0) done. writing output to filled.mgz... filling took 0.9 minutes talairach cc position changed to (3.00, 23.00, 7.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(21.00, 23.00, 7.00) SRC: (115.93, 86.18, 153.82) search lh wm seed point around talairach space (-15.00, 23.00, 7.00), SRC: (148.97, 87.83, 151.92) 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 17:51:25 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 4 found - 4 modified | TOTAL: 4 pass 2 (xy+): 0 found - 4 modified | TOTAL: 4 pass 1 (xy-): 1 found - 1 modified | TOTAL: 5 pass 2 (xy-): 0 found - 1 modified | TOTAL: 5 pass 1 (yz+): 0 found - 0 modified | TOTAL: 5 pass 1 (yz-): 1 found - 1 modified | TOTAL: 6 pass 2 (yz-): 0 found - 1 modified | TOTAL: 6 pass 1 (xz+): 2 found - 2 modified | TOTAL: 8 pass 2 (xz+): 0 found - 2 modified | TOTAL: 8 pass 1 (xz-): 1 found - 1 modified | TOTAL: 9 pass 2 (xz-): 0 found - 1 modified | TOTAL: 9 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 2 found - 2 modified | TOTAL: 3 pass 2 (--): 0 found - 2 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 = 13 (out of 255110: 0.005096) 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 40: 1168 vertices, 1282 faces slice 50: 7596 vertices, 7910 faces slice 60: 17706 vertices, 18109 faces slice 70: 29558 vertices, 29921 faces slice 80: 41414 vertices, 41840 faces slice 90: 53057 vertices, 53438 faces slice 100: 65191 vertices, 65598 faces slice 110: 77122 vertices, 77499 faces slice 120: 88225 vertices, 88598 faces slice 130: 98943 vertices, 99314 faces slice 140: 109309 vertices, 109688 faces slice 150: 118462 vertices, 118769 faces slice 160: 126731 vertices, 127041 faces slice 170: 134510 vertices, 134788 faces slice 180: 140690 vertices, 140900 faces slice 190: 145394 vertices, 145564 faces slice 200: 147202 vertices, 147234 faces slice 210: 147202 vertices, 147234 faces slice 220: 147202 vertices, 147234 faces slice 230: 147202 vertices, 147234 faces slice 240: 147202 vertices, 147234 faces slice 250: 147202 vertices, 147234 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... 147202 voxel in cpt #1: X=-32 [v=147202,e=441702,f=294468] located at (-29.049103, -19.310961, 36.435368) For the whole surface: X=-32 [v=147202,e=441702,f=294468] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Thu Aug 8 17:51:32 CEST 2013 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 17:51:37 CEST 2013 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts avg radius = 47.5 mm, total surface area = 75597 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.6 minutes Not saving sulc step 000: RMS=0.105 (target=0.015) step 005: RMS=0.077 (target=0.015) step 010: RMS=0.056 (target=0.015) step 015: RMS=0.046 (target=0.015) step 020: RMS=0.039 (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=0.025 (target=0.015) step 045: RMS=0.024 (target=0.015) step 050: RMS=0.023 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.022 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Thu Aug 8 17:52:11 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 0.94 +- 0.57 (0.00-->6.24) (max @ vno 60200 --> 61427) face area 0.02 +- 0.03 (-0.09-->0.68) scaling brain by 0.304... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.422, avgs=0 005/300: dt: 0.9000, rms radial error=176.162, avgs=0 010/300: dt: 0.9000, rms radial error=175.603, avgs=0 015/300: dt: 0.9000, rms radial error=174.875, avgs=0 020/300: dt: 0.9000, rms radial error=174.047, avgs=0 025/300: dt: 0.9000, rms radial error=173.161, avgs=0 030/300: dt: 0.9000, rms radial error=172.244, avgs=0 035/300: dt: 0.9000, rms radial error=171.311, avgs=0 040/300: dt: 0.9000, rms radial error=170.369, avgs=0 045/300: dt: 0.9000, rms radial error=169.426, avgs=0 050/300: dt: 0.9000, rms radial error=168.483, avgs=0 055/300: dt: 0.9000, rms radial error=167.542, avgs=0 060/300: dt: 0.9000, rms radial error=166.605, avgs=0 065/300: dt: 0.9000, rms radial error=165.673, avgs=0 070/300: dt: 0.9000, rms radial error=164.746, avgs=0 075/300: dt: 0.9000, rms radial error=163.823, avgs=0 080/300: dt: 0.9000, rms radial error=162.905, avgs=0 085/300: dt: 0.9000, rms radial error=161.992, avgs=0 090/300: dt: 0.9000, rms radial error=161.084, avgs=0 095/300: dt: 0.9000, rms radial error=160.181, avgs=0 100/300: dt: 0.9000, rms radial error=159.283, avgs=0 105/300: dt: 0.9000, rms radial error=158.389, avgs=0 110/300: dt: 0.9000, rms radial error=157.501, avgs=0 115/300: dt: 0.9000, rms radial error=156.617, avgs=0 120/300: dt: 0.9000, rms radial error=155.738, avgs=0 125/300: dt: 0.9000, rms radial error=154.864, avgs=0 130/300: dt: 0.9000, rms radial error=153.994, avgs=0 135/300: dt: 0.9000, rms radial error=153.129, avgs=0 140/300: dt: 0.9000, rms radial error=152.269, avgs=0 145/300: dt: 0.9000, rms radial error=151.413, avgs=0 150/300: dt: 0.9000, rms radial error=150.562, avgs=0 155/300: dt: 0.9000, rms radial error=149.716, avgs=0 160/300: dt: 0.9000, rms radial error=148.874, avgs=0 165/300: dt: 0.9000, rms radial error=148.036, avgs=0 170/300: dt: 0.9000, rms radial error=147.203, avgs=0 175/300: dt: 0.9000, rms radial error=146.375, avgs=0 180/300: dt: 0.9000, rms radial error=145.551, avgs=0 185/300: dt: 0.9000, rms radial error=144.732, avgs=0 190/300: dt: 0.9000, rms radial error=143.917, avgs=0 195/300: dt: 0.9000, rms radial error=143.107, avgs=0 200/300: dt: 0.9000, rms radial error=142.301, avgs=0 205/300: dt: 0.9000, rms radial error=141.500, avgs=0 210/300: dt: 0.9000, rms radial error=140.703, avgs=0 215/300: dt: 0.9000, rms radial error=139.910, avgs=0 220/300: dt: 0.9000, rms radial error=139.122, avgs=0 225/300: dt: 0.9000, rms radial error=138.338, avgs=0 230/300: dt: 0.9000, rms radial error=137.558, avgs=0 235/300: dt: 0.9000, rms radial error=136.783, avgs=0 240/300: dt: 0.9000, rms radial error=136.012, avgs=0 245/300: dt: 0.9000, rms radial error=135.246, avgs=0 250/300: dt: 0.9000, rms radial error=134.483, avgs=0 255/300: dt: 0.9000, rms radial error=133.725, avgs=0 260/300: dt: 0.9000, rms radial error=132.971, avgs=0 265/300: dt: 0.9000, rms radial error=132.222, avgs=0 270/300: dt: 0.9000, rms radial error=131.476, avgs=0 275/300: dt: 0.9000, rms radial error=130.735, avgs=0 280/300: dt: 0.9000, rms radial error=129.998, avgs=0 285/300: dt: 0.9000, rms radial error=129.265, avgs=0 290/300: dt: 0.9000, rms radial error=128.537, avgs=0 295/300: dt: 0.9000, rms radial error=127.812, avgs=0 300/300: dt: 0.9000, rms radial error=127.092, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 17467.02 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 = 3038.68 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00005 epoch 3 (K=160.0), pass 1, starting sse = 330.76 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/11 = 0.00711 epoch 4 (K=640.0), pass 1, starting sse = 18.04 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/12 = 0.00686 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 17:56:58 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/sub009/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub009 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=-32 (nv=147202, nf=294468, ne=441702, g=17) 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 9 iterations marking ambiguous vertices... 2257 ambiguous faces found in tessellation segmenting defects... 24 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 16 into 15 23 defects to be corrected 0 vertices coincident reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.8358 (-4.9179) -vertex loglikelihood: -6.7138 (-3.3569) -normal dot loglikelihood: -3.6666 (-3.6666) -quad curv loglikelihood: -6.0725 (-3.0363) Total Loglikelihood : -26.2887 CORRECTING DEFECT 0 (vertices=33, convex hull=63) After retessellation of defect 0, euler #=-21 (145827,436937,291089) : difference with theory (-20) = 1 CORRECTING DEFECT 1 (vertices=22, convex hull=75) After retessellation of defect 1, euler #=-20 (145835,436990,291135) : difference with theory (-19) = 1 CORRECTING DEFECT 2 (vertices=28, convex hull=62) After retessellation of defect 2, euler #=-19 (145846,437047,291182) : difference with theory (-18) = 1 CORRECTING DEFECT 3 (vertices=25, convex hull=57) After retessellation of defect 3, euler #=-18 (145861,437110,291231) : difference with theory (-17) = 1 CORRECTING DEFECT 4 (vertices=427, convex hull=194) After retessellation of defect 4, euler #=-17 (145884,437269,291368) : difference with theory (-16) = 1 CORRECTING DEFECT 5 (vertices=80, convex hull=79) After retessellation of defect 5, euler #=-16 (145918,437411,291477) : difference with theory (-15) = 1 CORRECTING DEFECT 6 (vertices=10, convex hull=22) After retessellation of defect 6, euler #=-15 (145919,437420,291486) : difference with theory (-14) = 1 CORRECTING DEFECT 7 (vertices=34, convex hull=46) After retessellation of defect 7, euler #=-14 (145929,437466,291523) : difference with theory (-13) = 1 CORRECTING DEFECT 8 (vertices=19, convex hull=48) After retessellation of defect 8, euler #=-13 (145935,437500,291552) : difference with theory (-12) = 1 CORRECTING DEFECT 9 (vertices=23, convex hull=22) Warning - incorrect dp selected!!!!(-80.689924 >= -80.689926 ) After retessellation of defect 9, euler #=-12 (145936,437510,291562) : difference with theory (-11) = 1 CORRECTING DEFECT 10 (vertices=32, convex hull=52) After retessellation of defect 10, euler #=-11 (145946,437562,291605) : difference with theory (-10) = 1 CORRECTING DEFECT 11 (vertices=63, convex hull=38) After retessellation of defect 11, euler #=-10 (145955,437601,291636) : difference with theory (-9) = 1 CORRECTING DEFECT 12 (vertices=32, convex hull=65) After retessellation of defect 12, euler #=-9 (145977,437695,291709) : difference with theory (-8) = 1 CORRECTING DEFECT 13 (vertices=42, convex hull=45) After retessellation of defect 13, euler #=-8 (145986,437738,291744) : difference with theory (-7) = 1 CORRECTING DEFECT 14 (vertices=103, convex hull=68) After retessellation of defect 14, euler #=-7 (146014,437850,291829) : difference with theory (-6) = 1 CORRECTING DEFECT 15 (vertices=27, convex hull=43) After retessellation of defect 15, euler #=-5 (146021,437892,291866) : difference with theory (-5) = 0 CORRECTING DEFECT 16 (vertices=7, convex hull=27) After retessellation of defect 16, euler #=-4 (146022,437902,291876) : difference with theory (-4) = 0 CORRECTING DEFECT 17 (vertices=121, convex hull=43) After retessellation of defect 17, euler #=-3 (146032,437950,291915) : difference with theory (-3) = 0 CORRECTING DEFECT 18 (vertices=16, convex hull=54) After retessellation of defect 18, euler #=-2 (146040,437993,291951) : difference with theory (-2) = 0 CORRECTING DEFECT 19 (vertices=20, convex hull=62) After retessellation of defect 19, euler #=-1 (146050,438045,291994) : difference with theory (-1) = 0 CORRECTING DEFECT 20 (vertices=51, convex hull=65) After retessellation of defect 20, euler #=0 (146069,438134,292065) : difference with theory (0) = 0 CORRECTING DEFECT 21 (vertices=145, convex hull=101) After retessellation of defect 21, euler #=1 (146103,438280,292178) : difference with theory (1) = 0 CORRECTING DEFECT 22 (vertices=32, convex hull=59) After retessellation of defect 22, euler #=2 (146118,438348,292232) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.21 (0.11-->7.41) (max @ vno 68747 --> 72328) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.21 (0.11-->7.41) (max @ vno 68747 --> 72328) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 90 mutations (33.2%), 181 crossovers (66.8%), 108 vertices were eliminated building final representation... 1084 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=146118, nf=292232, ne=438348, g=0) writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 18.9 minutes 0 defective edges removing intersecting faces 000: 125 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 146118 - 438348 + 292232 = 2 --> 0 holes F =2V-4: 292232 = 292236-4 (0) 2E=3F: 876696 = 876696 (0) total defect index = 0 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 21 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Thu Aug 8 18:15:59 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub009 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/sub009/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/wm.mgz... 18938 bright wm thresholded. 815 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.orig... computing class statistics... border white: 259466 voxels (1.55%) border gray 303507 voxels (1.81%) WM (91.0): 92.8 +- 10.6 [70.0 --> 110.0] GM (74.0) : 72.4 +- 12.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 46.1 (was 70) setting MAX_BORDER_WHITE to 115.6 (was 105) setting MIN_BORDER_WHITE to 59.0 (was 85) setting MAX_CSF to 33.3 (was 40) setting MAX_GRAY to 94.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 52.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 20.4 (was 40) repositioning cortical surface to gray/white boundary reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.22 (0.02-->3.23) (max @ vno 72318 --> 72328) face area 0.27 +- 0.12 (0.00-->2.15) mean absolute distance = 0.65 +- 0.76 3334 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=59 mean inside = 92.6, mean outside = 67.5 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=72.0, 185 (185) missing vertices, mean dist 0.3 [0.5 (%32.9)->0.7 (%67.1))] %67 local maxima, %28 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 +- 0.26 (0.11-->5.09) (max @ vno 72328 --> 69994) face area 0.27 +- 0.13 (0.00-->2.63) mean absolute distance = 0.29 +- 0.46 2565 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=8181313.0, rms=13.80 001: dt: 0.5000, sse=8284825.0, rms=9.980 (0.000%) 002: dt: 0.5000, sse=8638677.0, rms=7.805 (0.000%) 003: dt: 0.5000, sse=8709959.0, rms=6.394 (0.000%) 004: dt: 0.5000, sse=9058297.0, rms=5.564 (0.000%) 005: dt: 0.5000, sse=9033870.0, rms=5.081 (0.000%) 006: dt: 0.5000, sse=9298963.0, rms=4.838 (0.000%) 007: dt: 0.5000, sse=9143655.0, rms=4.682 (0.000%) 008: dt: 0.5000, sse=9303874.0, rms=4.605 (0.000%) 009: dt: 0.5000, sse=9127403.0, rms=4.541 (0.000%) rms = 4.50, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=9231868.0, rms=4.501 (0.000%) 011: dt: 0.2500, sse=5948398.5, rms=3.175 (0.000%) 012: dt: 0.2500, sse=5499109.5, rms=2.691 (0.000%) 013: dt: 0.2500, sse=5181864.0, rms=2.601 (0.000%) 014: dt: 0.2500, sse=5098457.0, rms=2.507 (0.000%) rms = 2.48, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=4977274.5, rms=2.478 (0.000%) 016: dt: 0.1250, sse=4707268.5, rms=2.202 (0.000%) rms = 2.17, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=4652214.0, rms=2.167 (0.000%) positioning took 2.3 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 removing 3 vertex label from ripped group mean border=76.4, 133 (52) missing vertices, mean dist -0.2 [0.3 (%77.4)->0.2 (%22.6))] %80 local maxima, %16 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 0.90 +- 0.26 (0.09-->5.30) (max @ vno 72328 --> 69994) face area 0.35 +- 0.17 (0.00-->3.81) mean absolute distance = 0.21 +- 0.28 2468 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5664017.0, rms=5.99 018: dt: 0.5000, sse=5908087.0, rms=4.141 (0.000%) rms = 4.67, time step reduction 1 of 3 to 0.250... 019: dt: 0.2500, sse=5362265.0, rms=2.966 (0.000%) 020: dt: 0.2500, sse=5184648.0, rms=2.442 (0.000%) 021: dt: 0.2500, sse=5103986.5, rms=2.045 (0.000%) rms = 2.02, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=5091900.0, rms=2.018 (0.000%) 023: dt: 0.1250, sse=4899920.0, rms=1.759 (0.000%) rms = 1.72, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=4848903.5, rms=1.719 (0.000%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group mean border=80.1, 85 (28) missing vertices, mean dist -0.1 [0.2 (%79.1)->0.2 (%20.9))] %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 (0.08-->5.42) (max @ vno 72328 --> 69994) face area 0.34 +- 0.16 (0.00-->3.96) mean absolute distance = 0.15 +- 0.23 2774 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5305572.5, rms=4.53 025: dt: 0.5000, sse=5513302.0, rms=4.234 (0.000%) rms = 4.45, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=5033679.0, rms=2.658 (0.000%) 027: dt: 0.2500, sse=4937652.0, rms=2.240 (0.000%) 028: dt: 0.2500, sse=5013818.0, rms=1.848 (0.000%) rms = 1.92, time step reduction 2 of 3 to 0.125... 029: dt: 0.1250, sse=4939601.5, rms=1.701 (0.000%) 030: dt: 0.1250, sse=4841204.5, rms=1.497 (0.000%) rms = 1.48, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=4807466.0, rms=1.476 (0.000%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... 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 3 vertex label from ripped group mean border=81.3, 75 (24) missing vertices, mean dist -0.0 [0.2 (%59.8)->0.2 (%40.2))] %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/sub009/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=4838137.5, rms=1.92 rms = 3.10, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=4908938.0, rms=1.213 (0.000%) 033: dt: 0.2500, sse=5051706.5, rms=1.117 (0.000%) rms = 1.12, time step reduction 2 of 3 to 0.125... rms = 1.10, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=5054505.0, rms=1.102 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 4 vertex label from ripped group generating cortex label... 13 non-cortical segments detected only using segment with 1519 vertices erasing segment 1 (vno[0] = 73398) erasing segment 2 (vno[0] = 76481) erasing segment 3 (vno[0] = 77591) erasing segment 4 (vno[0] = 85337) erasing segment 5 (vno[0] = 87185) erasing segment 6 (vno[0] = 94733) erasing segment 7 (vno[0] = 100948) erasing segment 8 (vno[0] = 102918) erasing segment 9 (vno[0] = 114820) erasing segment 10 (vno[0] = 115581) erasing segment 11 (vno[0] = 115607) erasing segment 12 (vno[0] = 117125) writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/label/lh.cortex.label... writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.curv writing smoothed area to lh.area writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.area vertex spacing 0.89 +- 0.25 (0.02-->5.47) (max @ vno 72328 --> 69994) face area 0.33 +- 0.16 (0.00-->4.05) refinement took 7.1 minutes #-------------------------------------------- #@# Smooth2 lh Thu Aug 8 18:23:07 CEST 2013 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 18:23:12 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 47.7 mm, total surface area = 88198 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=0.084 (target=0.015) step 010: RMS=0.061 (target=0.015) step 015: RMS=0.049 (target=0.015) step 020: RMS=0.041 (target=0.015) step 025: RMS=0.034 (target=0.015) step 030: RMS=0.028 (target=0.015) step 035: RMS=0.024 (target=0.015) step 040: RMS=0.021 (target=0.015) step 045: RMS=0.019 (target=0.015) step 050: RMS=0.017 (target=0.015) step 055: RMS=0.017 (target=0.015) step 060: 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/lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 178 vertices thresholded to be in k1 ~ [-1.06 0.29], k2 ~ [-0.24 0.14] total integrated curvature = 0.513*4pi (6.452) --> 0 handles ICI = 1.5, FI = 9.2, variation=157.807 146 vertices thresholded to be in [-0.04 0.02] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 111 vertices thresholded to be in [-0.26 0.15] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.016, std = 0.022 done. #----------------------------------------- #@# Curvature Stats lh Thu Aug 8 18:25:39 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub009 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 [ sub009/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 [ 292 ] Gb_filter = 0 WARN: S lookup min: -0.281872 WARN: S explicit min: 0.000000 vertex = 349 #-------------------------------------------- #@# Sphere lh Thu Aug 8 18:25:44 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 0.280... 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 %20.42 pass 1: epoch 2 of 3 starting distance error %20.30 unfolding complete - removing small folds... starting distance error %20.19 removing remaining folds... final distance error %20.21 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/lh.sphere spherical transformation took 0.99 hours #-------------------------------------------- #@# Surf Reg lh Thu Aug 8 19:25:24 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 = 0.576 curvature mean = 0.038, std = 0.934 curvature mean = 0.026, std = 0.845 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 0.00) sse = 357180.1, tmin=1.1687 d=32.00 min @ (8.00, 8.00, 0.00) sse = 295199.3, tmin=2.3467 d=16.00 min @ (0.00, -4.00, -4.00) sse = 287773.8, tmin=3.5194 d=8.00 min @ (0.00, 2.00, 2.00) sse = 285320.1, tmin=4.7325 d=4.00 min @ (-1.00, -1.00, 0.00) sse = 283934.3, tmin=5.9771 d=2.00 min @ (0.00, 0.00, -0.50) sse = 283738.5, tmin=7.2418 d=1.00 min @ (0.25, 0.00, 0.00) sse = 283649.9, tmin=8.5086 d=0.50 min @ (-0.12, -0.12, -0.12) sse = 283648.4, tmin=9.7731 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 9.77 min curvature mean = 0.014, std = 0.956 curvature mean = 0.014, std = 0.930 curvature mean = 0.014, std = 0.968 curvature mean = 0.007, std = 0.967 curvature mean = 0.013, std = 0.970 curvature mean = 0.002, std = 0.985 2 Reading smoothwm curvature mean = -0.025, std = 0.323 curvature mean = 0.004, std = 0.066 curvature mean = 0.078, std = 0.301 curvature mean = 0.003, std = 0.078 curvature mean = 0.036, std = 0.488 curvature mean = 0.003, std = 0.084 curvature mean = 0.022, std = 0.629 curvature mean = 0.003, std = 0.088 curvature mean = 0.008, std = 0.747 MRISregister() return, current seed 0 writing registered surface to ../surf/lh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white lh Thu Aug 8 19:53:51 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 19:53:54 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 19:53:56 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub009 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... 1620 labels changed using aseg relabeling using gibbs priors... 000: 3282 changed, 146118 examined... 001: 751 changed, 14004 examined... 002: 205 changed, 4211 examined... 003: 55 changed, 1157 examined... 004: 23 changed, 377 examined... 005: 8 changed, 132 examined... 006: 3 changed, 43 examined... 007: 1 changed, 20 examined... 008: 2 changed, 6 examined... 009: 1 changed, 10 examined... 010: 1 changed, 9 examined... 011: 0 changed, 5 examined... 225 labels changed using aseg 000: 151 total segments, 109 labels (675 vertices) changed 001: 44 total segments, 7 labels (46 vertices) changed 002: 37 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 32 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1710 vertices marked for relabeling... 1710 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 1 minutes and 7 seconds. #-------------------------------------------- #@# Make Pial Surf lh Thu Aug 8 19:55:03 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub009 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/sub009/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/wm.mgz... 18938 bright wm thresholded. 815 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.orig... computing class statistics... border white: 259466 voxels (1.55%) border gray 303507 voxels (1.81%) WM (91.0): 92.8 +- 10.6 [70.0 --> 110.0] GM (74.0) : 72.4 +- 12.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 46.1 (was 70) setting MAX_BORDER_WHITE to 115.6 (was 105) setting MIN_BORDER_WHITE to 59.0 (was 85) setting MAX_CSF to 33.3 (was 40) setting MAX_GRAY to 94.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 52.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 20.4 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=59 mean inside = 92.6, mean outside = 67.5 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/sub009/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.22 (0.02-->3.23) (max @ vno 72318 --> 72328) face area 0.27 +- 0.12 (0.00-->2.15) mean absolute distance = 0.65 +- 0.76 3346 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 1 with 11 points - only 0.00% unknown deleting segment 2 with 6 points - only 0.00% unknown deleting segment 3 with 654 points - only 0.00% unknown deleting segment 4 with 19 points - only 0.00% unknown deleting segment 5 with 19 points - only 0.00% unknown deleting segment 6 with 6 points - only 0.00% unknown deleting segment 7 with 18 points - only 0.00% unknown deleting segment 8 with 14 points - only 0.00% unknown mean border=72.0, 185 (185) missing vertices, mean dist 0.3 [0.5 (%32.9)->0.7 (%67.1))] %68 local maxima, %28 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 +- 0.26 (0.11-->5.09) (max @ vno 72328 --> 69994) face area 0.27 +- 0.13 (0.00-->2.63) mean absolute distance = 0.29 +- 0.45 2572 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=8202595.5, rms=13.78 001: dt: 0.5000, sse=8317187.0, rms=9.964 (0.000%) 002: dt: 0.5000, sse=8675203.0, rms=7.792 (0.000%) 003: dt: 0.5000, sse=8750276.0, rms=6.385 (0.000%) 004: dt: 0.5000, sse=9099968.0, rms=5.558 (0.000%) 005: dt: 0.5000, sse=9076132.0, rms=5.076 (0.000%) 006: dt: 0.5000, sse=9343738.0, rms=4.833 (0.000%) 007: dt: 0.5000, sse=9184572.0, rms=4.677 (0.000%) 008: dt: 0.5000, sse=9348068.0, rms=4.601 (0.000%) 009: dt: 0.5000, sse=9168776.0, rms=4.536 (0.000%) rms = 4.50, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=9275467.0, rms=4.497 (0.000%) 011: dt: 0.2500, sse=5971632.0, rms=3.170 (0.000%) 012: dt: 0.2500, sse=5520908.0, rms=2.688 (0.000%) 013: dt: 0.2500, sse=5201493.5, rms=2.597 (0.000%) 014: dt: 0.2500, sse=5117343.5, rms=2.503 (0.000%) rms = 2.47, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=4996641.5, rms=2.474 (0.000%) 016: dt: 0.1250, sse=4726252.5, rms=2.200 (0.000%) rms = 2.16, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=4671087.5, rms=2.165 (0.000%) positioning took 2.3 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 4 points - only 0.00% unknown deleting segment 5 with 569 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown deleting segment 10 with 6 points - only 0.00% unknown deleting segment 11 with 7 points - only 0.00% unknown deleting segment 12 with 19 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 15 with 11 points - only 0.00% unknown deleting segment 16 with 15 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 17 with 3 points - only 0.00% unknown mean border=76.4, 135 (52) missing vertices, mean dist -0.2 [0.3 (%77.3)->0.2 (%22.7))] %80 local maxima, %16 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 0.90 +- 0.25 (0.09-->5.30) (max @ vno 72328 --> 69994) face area 0.35 +- 0.16 (0.00-->3.81) mean absolute distance = 0.21 +- 0.28 2480 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5686639.0, rms=5.98 018: dt: 0.5000, sse=5928499.5, rms=4.134 (0.000%) rms = 4.66, time step reduction 1 of 3 to 0.250... 019: dt: 0.2500, sse=5382237.5, rms=2.961 (0.000%) 020: dt: 0.2500, sse=5206576.5, rms=2.437 (0.000%) 021: dt: 0.2500, sse=5124761.5, rms=2.042 (0.000%) rms = 2.01, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=5111591.0, rms=2.014 (0.000%) 023: dt: 0.1250, sse=4920777.0, rms=1.757 (0.000%) rms = 1.72, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=4869989.0, rms=1.717 (0.000%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 5 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 2 with 5 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 1 points - only 0.00% unknown deleting segment 4 with 7 points - only 0.00% unknown deleting segment 5 with 629 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown deleting segment 8 with 17 points - only 0.00% unknown deleting segment 9 with 20 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 10 with 4 points - only 0.00% unknown deleting segment 13 with 8 points - only 0.00% unknown deleting segment 14 with 14 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 15 with 3 points - only 0.00% unknown mean border=80.1, 90 (29) missing vertices, mean dist -0.1 [0.2 (%79.1)->0.2 (%20.9))] %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 (0.04-->5.42) (max @ vno 72328 --> 69994) face area 0.34 +- 0.16 (0.00-->3.96) mean absolute distance = 0.15 +- 0.23 2797 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5327450.0, rms=4.52 025: dt: 0.5000, sse=5535659.0, rms=4.227 (0.000%) rms = 4.45, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=5055721.5, rms=2.653 (0.000%) 027: dt: 0.2500, sse=4959688.0, rms=2.236 (0.000%) 028: dt: 0.2500, sse=5037968.5, rms=1.846 (0.000%) rms = 1.92, time step reduction 2 of 3 to 0.125... 029: dt: 0.1250, sse=4963726.0, rms=1.699 (0.000%) 030: dt: 0.1250, sse=4864778.0, rms=1.497 (0.000%) rms = 1.48, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=4831304.5, rms=1.477 (0.000%) positioning took 1.1 minutes 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 2 with 5 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 1 points - only 0.00% unknown deleting segment 4 with 7 points - only 0.00% unknown deleting segment 5 with 648 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown deleting segment 7 with 17 points - only 0.00% unknown deleting segment 8 with 19 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 9 with 4 points - only 0.00% unknown deleting segment 10 with 15 points - only 0.00% unknown deleting segment 11 with 14 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 12 with 3 points - only 0.00% unknown mean border=81.2, 86 (24) missing vertices, mean dist -0.0 [0.2 (%59.8)->0.2 (%40.2))] %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=4863136.0, rms=1.92 rms = 3.09, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=4935760.5, rms=1.215 (0.000%) 033: dt: 0.2500, sse=5081568.5, rms=1.118 (0.000%) rms = 1.12, time step reduction 2 of 3 to 0.125... rms = 1.10, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=5082797.5, rms=1.103 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 1 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 2 with 4 points - only 0.00% unknown smoothing surface for 5 iterations... mean border=49.1, 175 (175) missing vertices, mean dist 1.6 [0.1 (%0.0)->2.1 (%100.0))] %16 local maxima, %56 large gradients and %24 min vals, 1580 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=30720990.0, rms=31.38 001: dt: 0.5000, sse=21866200.0, rms=25.815 (0.000%) 002: dt: 0.5000, sse=15775913.0, rms=21.187 (0.000%) 003: dt: 0.5000, sse=11803336.0, rms=17.441 (0.000%) 004: dt: 0.5000, sse=9533108.0, rms=14.470 (0.000%) 005: dt: 0.5000, sse=8256870.0, rms=12.194 (0.000%) 006: dt: 0.5000, sse=7530437.5, rms=10.492 (0.000%) 007: dt: 0.5000, sse=7055526.5, rms=9.062 (0.000%) 008: dt: 0.5000, sse=6810970.0, rms=7.796 (0.000%) 009: dt: 0.5000, sse=6691887.0, rms=6.671 (0.000%) 010: dt: 0.5000, sse=6741076.0, rms=5.786 (0.000%) 011: dt: 0.5000, sse=6920722.0, rms=5.132 (0.000%) 012: dt: 0.5000, sse=7093514.5, rms=4.706 (0.000%) 013: dt: 0.5000, sse=7282325.0, rms=4.422 (0.000%) 014: dt: 0.5000, sse=7366286.5, rms=4.258 (0.000%) 015: dt: 0.5000, sse=7475775.0, rms=4.132 (0.000%) 016: dt: 0.5000, sse=7495378.0, rms=4.064 (0.000%) 017: dt: 0.5000, sse=7551958.0, rms=3.999 (0.000%) rms = 3.96, time step reduction 1 of 3 to 0.250... 018: dt: 0.5000, sse=7551811.5, rms=3.958 (0.000%) 019: dt: 0.2500, sse=5331480.0, rms=3.253 (0.000%) 020: dt: 0.2500, sse=5099851.0, rms=3.057 (0.000%) rms = 3.03, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=4986196.5, rms=3.034 (0.000%) 022: dt: 0.1250, sse=4792820.5, rms=2.940 (0.000%) rms = 2.93, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=4762591.0, rms=2.929 (0.000%) positioning took 3.0 minutes mean border=46.8, 793 (12) missing vertices, mean dist 0.2 [0.2 (%48.5)->0.6 (%51.5))] %33 local maxima, %43 large gradients and %19 min vals, 541 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=5474551.0, rms=5.04 024: dt: 0.5000, sse=5761867.5, rms=4.133 (0.000%) rms = 4.12, time step reduction 1 of 3 to 0.250... 025: dt: 0.5000, sse=7465571.5, rms=4.116 (0.000%) 026: dt: 0.2500, sse=5631418.0, rms=3.287 (0.000%) 027: dt: 0.2500, sse=5642405.0, rms=3.051 (0.000%) rms = 3.00, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=5502221.5, rms=3.004 (0.000%) 029: dt: 0.1250, sse=5307892.0, rms=2.853 (0.000%) rms = 2.82, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=5292795.5, rms=2.821 (0.000%) positioning took 0.9 minutes mean border=44.2, 992 (7) missing vertices, mean dist 0.1 [0.2 (%36.7)->0.4 (%63.3))] %54 local maxima, %22 large gradients and %19 min vals, 629 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=5655667.5, rms=4.45 031: dt: 0.5000, sse=5853190.5, rms=3.992 (0.000%) rms = 4.08, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=5500425.0, rms=3.226 (0.000%) 033: dt: 0.2500, sse=5725797.5, rms=2.917 (0.000%) 034: dt: 0.2500, sse=5645297.5, rms=2.840 (0.000%) rms = 2.80, time step reduction 2 of 3 to 0.125... 035: dt: 0.2500, sse=5700974.0, rms=2.802 (0.000%) 036: dt: 0.1250, sse=5498973.5, rms=2.674 (0.000%) rms = 2.65, time step reduction 3 of 3 to 0.062... 037: dt: 0.1250, sse=5487813.0, rms=2.647 (0.000%) positioning took 1.0 minutes mean border=42.9, 2039 (5) missing vertices, mean dist 0.1 [0.2 (%43.0)->0.3 (%57.0))] %59 local maxima, %17 large gradients and %18 min vals, 514 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/sub009/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=5567807.0, rms=3.14 rms = 3.78, time step reduction 1 of 3 to 0.250... 038: dt: 0.2500, sse=5401296.0, rms=2.806 (0.000%) 039: dt: 0.2500, sse=5550118.0, rms=2.697 (0.000%) rms = 2.67, time step reduction 2 of 3 to 0.125... 040: dt: 0.2500, sse=5639928.5, rms=2.672 (0.000%) 041: dt: 0.1250, sse=5526929.5, rms=2.556 (0.000%) rms = 2.53, time step reduction 3 of 3 to 0.062... 042: dt: 0.1250, sse=5536103.0, rms=2.530 (0.000%) positioning took 0.7 minutes writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.area.pial vertex spacing 1.00 +- 0.42 (0.07-->7.19) (max @ vno 98031 --> 96995) face area 0.40 +- 0.30 (0.00-->5.20) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 146118 vertices processed 25000 of 146118 vertices processed 50000 of 146118 vertices processed 75000 of 146118 vertices processed 100000 of 146118 vertices processed 125000 of 146118 vertices processed 0 of 146118 vertices processed 25000 of 146118 vertices processed 50000 of 146118 vertices processed 75000 of 146118 vertices processed 100000 of 146118 vertices processed 125000 of 146118 vertices processed thickness calculation complete, 263:496 truncations. 32479 vertices at 0 distance 100939 vertices at 1 distance 96911 vertices at 2 distance 36297 vertices at 3 distance 9817 vertices at 4 distance 2623 vertices at 5 distance 740 vertices at 6 distance 272 vertices at 7 distance 131 vertices at 8 distance 82 vertices at 9 distance 56 vertices at 10 distance 38 vertices at 11 distance 30 vertices at 12 distance 20 vertices at 13 distance 21 vertices at 14 distance 10 vertices at 15 distance 4 vertices at 16 distance 6 vertices at 17 distance 5 vertices at 18 distance 9 vertices at 19 distance 10 vertices at 20 distance writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.thickness positioning took 14.3 minutes #-------------------------------------------- #@# Surf Volume lh Thu Aug 8 20:09:20 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 20:09:20 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts pctsurfcon --s sub009 --lh-only Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts/pctsurfcon.log Thu Aug 8 20:09:20 CEST 2013 setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts /opt/freesurfer/5.3.0/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux snake6 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/sub009/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/tmp.pctsurfcon.8644/lh.wm.mgh --regheader sub009 --cortex srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/mri/orig.mgz as target reference. Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/label/lh.cortex.label Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 = 111541 Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/label/lh.cortex.label Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/tmp.pctsurfcon.8644/lh.wm.mgh Dim: 146118 1 1 mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/tmp.pctsurfcon.8644/lh.gm.mgh --projfrac 0.3 --regheader sub009 --cortex srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/mri/orig.mgz as target reference. Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/label/lh.cortex.label Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.white Done reading source surface Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 = 129823 Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/label/lh.cortex.label Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/tmp.pctsurfcon.8644/lh.gm.mgh Dim: 146118 1 1 mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/tmp.pctsurfcon.8644/lh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/tmp.pctsurfcon.8644/lh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/surf/lh.w-g.pct.mgh mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.w-g.pct.mgh --annot sub009 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/surf/lh.w-g.pct.mgh --annot sub009 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/stats/lh.w-g.pct.stats --snr sysname Linux hostname snake6 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/sub009/surf/lh.w-g.pct.mgh Vertex Area is 0.663559 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 1000 unknown 0 0.000 1 1001 bankssts 1387 995.230 2 1002 caudalanteriorcingulate 1626 1103.811 3 1003 caudalmiddlefrontal 3071 2022.123 4 1004 corpuscallosum 0 0.000 5 1005 cuneus 2101 1369.660 6 1006 entorhinal 758 516.569 7 1007 fusiform 5734 3788.897 8 1008 inferiorparietal 8907 5993.643 9 1009 inferiortemporal 5247 3557.660 10 1010 isthmuscingulate 1716 1104.740 11 1011 lateraloccipital 8358 5448.021 12 1012 lateralorbitofrontal 4001 2628.918 13 1013 lingual 3929 2727.612 14 1014 medialorbitofrontal 3404 2217.685 15 1015 middletemporal 4927 3422.167 16 1016 parahippocampal 1095 731.138 17 1017 paracentral 2194 1430.574 18 1018 parsopercularis 3344 2239.959 19 1019 parsorbitalis 1215 797.758 20 1020 parstriangularis 1773 1217.633 21 1021 pericalcarine 2164 1473.465 22 1022 postcentral 6120 4006.338 23 1023 posteriorcingulate 2209 1499.423 24 1024 precentral 7841 4942.984 25 1025 precuneus 6922 4586.249 26 1026 rostralanteriorcingulate 1820 1169.508 27 1027 rostralmiddlefrontal 8948 6107.701 28 1028 superiorfrontal 10472 7041.768 29 1029 superiorparietal 8961 5873.902 30 1030 superiortemporal 5536 3678.935 31 1031 supramarginal 6946 4625.763 32 1032 frontalpole 384 262.584 33 1033 temporalpole 959 630.734 34 1034 transversetemporal 787 487.875 35 1035 insula 3661 2414.259 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats lh Thu Aug 8 20:09:34 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 sub009 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 1387 995 2235 2.235 0.477 0.113 0.028 12 1.7 bankssts 1626 1104 3261 2.570 0.535 0.122 0.033 18 2.3 caudalanteriorcingulate 3071 2022 5110 2.379 0.416 0.138 0.113 47 22.3 caudalmiddlefrontal 2101 1370 3273 2.083 0.421 0.166 0.064 42 5.3 cuneus 758 517 2025 3.059 0.661 0.121 0.035 6 1.2 entorhinal 5734 3789 12012 2.692 0.598 0.165 0.088 240 22.3 fusiform 8907 5994 14437 2.195 0.446 0.148 0.056 168 20.2 inferiorparietal 5247 3558 10575 2.585 0.578 0.162 0.083 145 14.9 inferiortemporal 1716 1105 2951 2.471 0.678 0.167 0.087 47 6.6 isthmuscingulate 8358 5448 13029 2.116 0.486 0.163 0.068 171 20.4 lateraloccipital 4001 2629 6708 2.369 0.683 0.168 0.074 102 12.3 lateralorbitofrontal 3929 2728 6162 2.077 0.520 0.166 0.072 77 11.7 lingual 3404 2218 5612 2.183 0.699 0.147 0.116 167 10.7 medialorbitofrontal 4927 3422 10198 2.520 0.576 0.168 0.075 178 14.8 middletemporal 1095 731 1764 2.171 0.494 0.124 0.109 91 5.2 parahippocampal 2194 1431 3646 2.295 0.552 0.119 0.035 22 3.0 paracentral 3344 2240 6250 2.447 0.413 0.144 0.049 56 6.2 parsopercularis 1215 798 2373 2.400 0.525 0.185 0.082 34 4.1 parsorbitalis 1773 1218 2985 2.195 0.441 0.162 0.078 554 3.6 parstriangularis 2164 1473 2485 1.742 0.476 0.180 0.084 42 8.1 pericalcarine 6120 4006 8641 1.907 0.551 0.137 0.053 112 13.1 postcentral 2209 1499 4126 2.565 0.496 0.160 0.060 49 5.4 posteriorcingulate 7841 4943 13190 2.407 0.477 0.125 0.039 89 12.6 precentral 6922 4586 11437 2.321 0.467 0.150 0.058 140 14.6 precuneus 1820 1170 3307 2.524 0.595 0.153 0.078 38 6.9 rostralanteriorcingulate 8948 6108 15238 2.185 0.499 0.172 0.073 219 24.6 rostralmiddlefrontal 10472 7042 19699 2.440 0.512 0.147 0.050 171 20.8 superiorfrontal 8961 5874 13047 2.033 0.371 0.148 0.048 159 17.2 superiorparietal 5536 3679 11333 2.708 0.577 0.132 0.042 98 9.6 superiortemporal 6946 4626 11929 2.367 0.477 0.145 0.047 115 13.2 supramarginal 384 263 872 2.413 0.503 0.237 0.342 39 8.2 frontalpole 959 631 3408 3.699 0.690 0.164 0.075 21 2.8 temporalpole 787 488 1385 2.464 0.344 0.132 0.052 13 1.4 transversetemporal 3661 2414 7627 3.035 0.757 0.128 0.057 75 9.0 insula #----------------------------------------- #@# Cortical Parc 2 lh Thu Aug 8 20:09:53 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub009 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... 10 labels changed using aseg relabeling using gibbs priors... 000: 10264 changed, 146118 examined... 001: 2502 changed, 39264 examined... 002: 784 changed, 12919 examined... 003: 346 changed, 4393 examined... 004: 185 changed, 1924 examined... 005: 87 changed, 1026 examined... 006: 57 changed, 486 examined... 007: 25 changed, 325 examined... 008: 13 changed, 134 examined... 009: 9 changed, 66 examined... 010: 1 changed, 57 examined... 011: 1 changed, 8 examined... 012: 0 changed, 6 examined... 5 labels changed using aseg 000: 334 total segments, 247 labels (2782 vertices) changed 001: 105 total segments, 18 labels (37 vertices) changed 002: 87 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 109 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1071 vertices marked for relabeling... 1071 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 1 minutes and 13 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Thu Aug 8 20:11:07 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 sub009 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 1365 918 2157 2.068 0.585 0.186 0.111 48 4.6 G_and_S_frontomargin 2229 1475 3859 2.166 0.555 0.159 0.059 45 5.5 G_and_S_occipital_inf 1592 1003 2955 2.348 0.592 0.136 0.041 22 2.7 G_and_S_paracentral 1605 1086 3020 2.425 0.464 0.156 0.073 50 5.2 G_and_S_subcentral 872 627 1786 2.264 0.476 0.213 0.184 50 9.3 G_and_S_transv_frontopol 3429 2238 5679 2.374 0.481 0.140 0.057 55 9.0 G_and_S_cingul-Ant 1709 1135 3257 2.564 0.499 0.132 0.042 21 2.8 G_and_S_cingul-Mid-Ant 1672 1146 2867 2.428 0.361 0.139 0.046 25 3.2 G_and_S_cingul-Mid-Post 779 484 1792 2.990 0.525 0.189 0.084 22 2.7 G_cingul-Post-dorsal 264 160 402 2.151 0.684 0.166 0.093 8 0.8 G_cingul-Post-ventral 1928 1269 3030 2.018 0.441 0.178 0.074 43 5.6 G_cuneus 1889 1268 4274 2.556 0.412 0.157 0.060 44 4.3 G_front_inf-Opercular 503 327 1028 2.487 0.439 0.185 0.078 16 1.8 G_front_inf-Orbital 1466 983 2654 2.282 0.441 0.177 0.096 555 3.6 G_front_inf-Triangul 4437 2985 9047 2.382 0.468 0.175 0.068 112 12.2 G_front_middle 7530 5011 16116 2.548 0.527 0.153 0.056 142 16.8 G_front_sup 572 361 1294 3.109 0.631 0.142 0.100 18 2.7 G_Ins_lg_and_S_cent_ins 864 544 2622 3.787 0.620 0.152 0.079 41 3.1 G_insular_short 2050 1344 4383 2.509 0.401 0.192 0.086 69 6.4 G_occipital_middle 1382 883 2118 2.077 0.438 0.161 0.060 28 3.2 G_occipital_sup 2272 1435 5009 2.839 0.522 0.175 0.082 68 7.4 G_oc-temp_lat-fusifor 2631 1820 4534 2.054 0.539 0.184 0.104 66 9.7 G_oc-temp_med-Lingual 1355 887 3220 2.771 0.772 0.114 0.037 11 2.1 G_oc-temp_med-Parahip 2986 1938 5823 2.391 0.676 0.187 0.093 101 11.2 G_orbital 2960 1995 5474 2.232 0.400 0.165 0.072 75 9.3 G_pariet_inf-Angular 3825 2523 7701 2.527 0.446 0.158 0.058 84 8.6 G_pariet_inf-Supramar 3884 2557 6625 2.127 0.397 0.164 0.062 91 9.5 G_parietal_sup 2242 1435 3306 1.882 0.467 0.145 0.059 42 4.9 G_postcentral 3058 1833 6313 2.640 0.375 0.130 0.046 43 5.5 G_precentral 3345 2205 6455 2.384 0.480 0.164 0.078 95 8.7 G_precuneus 1264 836 2581 2.323 0.631 0.216 0.140 67 8.1 G_rectus 436 269 826 2.897 0.793 0.122 0.401 91 1.1 G_subcallosal 554 332 1113 2.542 0.259 0.136 0.059 11 1.1 G_temp_sup-G_T_transv 2173 1408 5507 2.867 0.563 0.161 0.058 66 5.0 G_temp_sup-Lateral 683 465 1907 3.653 0.595 0.120 0.035 6 1.0 G_temp_sup-Plan_polar 847 575 1546 2.442 0.461 0.105 0.027 6 1.0 G_temp_sup-Plan_tempo 2936 1981 7047 2.716 0.598 0.175 0.104 112 10.4 G_temporal_inf 2719 1902 6489 2.601 0.575 0.192 0.100 142 10.8 G_temporal_middle 313 213 429 2.158 0.409 0.118 0.027 3 0.3 Lat_Fis-ant-Horizont 287 192 405 2.545 0.440 0.144 0.051 3 0.5 Lat_Fis-ant-Vertical 1470 989 1955 2.258 0.392 0.129 0.037 13 2.4 Lat_Fis-post 2758 1736 4060 2.050 0.448 0.175 0.076 65 7.4 Pole_occipital 2495 1677 7344 3.124 0.711 0.167 0.092 132 9.4 Pole_temporal 2672 1813 3352 1.953 0.608 0.162 0.079 73 10.7 S_calcarine 2801 1858 3030 1.790 0.574 0.116 0.031 22 3.6 S_central 1182 783 1555 2.152 0.502 0.131 0.038 16 1.8 S_cingul-Marginalis 501 335 847 3.134 0.483 0.145 0.049 5 1.1 S_circular_insula_ant 1434 962 2262 2.733 0.502 0.092 0.025 7 1.5 S_circular_insula_inf 2045 1374 3034 2.452 0.496 0.119 0.033 15 2.9 S_circular_insula_sup 1126 767 2203 2.672 0.618 0.158 0.099 42 5.2 S_collat_transv_ant 393 256 413 2.020 0.355 0.159 0.059 5 0.9 S_collat_transv_post 2419 1659 3284 2.069 0.381 0.141 0.042 30 4.2 S_front_inf 1612 1084 2341 2.185 0.479 0.158 0.062 29 3.6 S_front_middle 2379 1624 3364 2.161 0.418 0.119 0.125 29 20.4 S_front_sup 434 298 576 2.038 0.280 0.118 0.030 3 0.6 S_interm_prim-Jensen 3646 2407 4459 1.953 0.301 0.126 0.032 40 5.0 S_intrapariet_and_P_trans 1320 903 1708 1.948 0.405 0.134 0.042 14 2.2 S_oc_middle_and_Lunatus 1524 1015 1907 2.017 0.428 0.128 0.036 15 2.2 S_oc_sup_and_transversal 1103 765 1470 2.151 0.425 0.143 0.047 16 2.0 S_occipital_ant 1297 860 1887 2.329 0.379 0.152 0.056 21 2.9 S_oc-temp_lat 2045 1457 3087 2.354 0.501 0.134 0.075 81 5.9 S_oc-temp_med_and_Lingual 428 300 589 2.000 0.375 0.166 0.052 7 1.0 S_orbital_lateral 917 615 1224 2.081 0.785 0.103 0.033 6 1.0 S_orbital_med-olfact 1416 955 2161 2.186 0.567 0.161 0.057 26 3.3 S_orbital-H_Shaped 2193 1422 2851 2.203 0.442 0.124 0.035 22 3.3 S_parieto_occipital 1399 933 1780 2.268 0.624 0.138 0.073 32 4.8 S_pericallosal 3225 2119 3933 1.994 0.384 0.125 0.037 34 4.9 S_postcentral 1419 935 2001 2.337 0.358 0.105 0.026 9 1.5 S_precentral-inf-part 1404 929 1856 2.253 0.431 0.138 0.041 16 2.2 S_precentral-sup-part 567 388 602 1.645 0.292 0.114 0.021 4 0.5 S_suborbital 1525 1058 2304 2.228 0.376 0.154 0.048 24 3.0 S_subparietal 1338 897 1869 2.314 0.532 0.137 0.049 18 2.6 S_temporal_inf 6793 4661 9959 2.213 0.469 0.131 0.038 89 10.4 S_temporal_sup 330 231 411 2.073 0.241 0.122 0.026 2 0.4 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Thu Aug 8 20:11:27 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub009 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... 830 labels changed using aseg relabeling using gibbs priors... 000: 3063 changed, 146118 examined... 001: 754 changed, 12773 examined... 002: 184 changed, 4121 examined... 003: 72 changed, 1135 examined... 004: 27 changed, 395 examined... 005: 9 changed, 125 examined... 006: 4 changed, 53 examined... 007: 3 changed, 25 examined... 008: 1 changed, 13 examined... 009: 0 changed, 5 examined... 47 labels changed using aseg 000: 70 total segments, 37 labels (417 vertices) changed 001: 35 total segments, 2 labels (3 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 33 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 974 vertices marked for relabeling... 974 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas40.annot... classification took 1 minutes and 5 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Thu Aug 8 20:12:31 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 sub009 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 2086 1428 3891 2.514 0.513 0.129 0.037 24 3.2 caudalanteriorcingulate 3203 2110 5335 2.393 0.427 0.138 0.110 48 22.5 caudalmiddlefrontal 2874 1879 4160 2.045 0.407 0.156 0.057 49 6.7 cuneus 690 464 1878 3.077 0.686 0.123 0.037 6 1.2 entorhinal 5215 3450 10385 2.665 0.584 0.165 0.089 225 20.7 fusiform 8189 5512 13053 2.162 0.426 0.146 0.056 152 18.5 inferiorparietal 5400 3668 11544 2.629 0.591 0.161 0.084 151 15.5 inferiortemporal 1709 1096 2930 2.469 0.687 0.167 0.088 47 6.7 isthmuscingulate 8516 5545 13322 2.118 0.490 0.164 0.069 178 21.1 lateraloccipital 4464 2936 7497 2.309 0.730 0.168 0.087 128 14.2 lateralorbitofrontal 3941 2734 6174 2.075 0.520 0.167 0.072 78 11.8 lingual 2558 1699 4373 2.140 0.668 0.165 0.156 167 12.1 medialorbitofrontal 6621 4606 13255 2.497 0.571 0.163 0.068 206 17.9 middletemporal 1048 698 1719 2.165 0.501 0.124 0.114 91 5.1 parahippocampal 2458 1604 4232 2.337 0.553 0.120 0.034 26 3.4 paracentral 3065 2046 5779 2.469 0.402 0.145 0.050 53 5.8 parsopercularis 1227 806 2306 2.445 0.521 0.157 0.054 22 2.9 parsorbitalis 2569 1738 4204 2.192 0.448 0.162 0.072 570 5.6 parstriangularis 2162 1475 2506 1.742 0.474 0.180 0.083 42 7.9 pericalcarine 6837 4495 9568 1.925 0.549 0.138 0.052 122 14.2 postcentral 2317 1577 4214 2.543 0.491 0.158 0.057 48 5.5 posteriorcingulate 7733 4870 13058 2.411 0.475 0.126 0.040 90 12.6 precentral 6699 4451 11347 2.335 0.466 0.154 0.062 144 14.8 precuneus 2347 1501 4001 2.481 0.594 0.141 0.055 39 5.3 rostralanteriorcingulate 6003 4097 10198 2.187 0.489 0.169 0.065 132 15.6 rostralmiddlefrontal 12354 8331 23469 2.398 0.520 0.156 0.064 260 34.5 superiorfrontal 7491 4891 11055 2.046 0.358 0.145 0.045 130 13.9 superiorparietal 7838 5198 16683 2.756 0.704 0.135 0.048 140 15.8 superiortemporal 6923 4612 11872 2.362 0.476 0.146 0.048 116 13.4 supramarginal 761 473 1347 2.454 0.344 0.133 0.053 13 1.4 transversetemporal 3219 2127 6977 3.125 0.716 0.124 0.050 62 6.7 insula #-------------------------------------------- #@# Tessellate rh Thu Aug 8 20:12:51 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 4 found - 4 modified | TOTAL: 4 pass 2 (xy+): 0 found - 4 modified | TOTAL: 4 pass 1 (xy-): 0 found - 0 modified | TOTAL: 4 pass 1 (yz+): 3 found - 3 modified | TOTAL: 7 pass 2 (yz+): 0 found - 3 modified | TOTAL: 7 pass 1 (yz-): 1 found - 1 modified | TOTAL: 8 pass 2 (yz-): 0 found - 1 modified | TOTAL: 8 pass 1 (xz+): 4 found - 4 modified | TOTAL: 12 pass 2 (xz+): 0 found - 4 modified | TOTAL: 12 pass 1 (xz-): 1 found - 1 modified | TOTAL: 13 pass 2 (xz-): 0 found - 1 modified | TOTAL: 13 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 (--): 4 found - 4 modified | TOTAL: 4 pass 2 (--): 0 found - 4 modified | TOTAL: 4 pass 1 (-+): 1 found - 1 modified | TOTAL: 5 pass 2 (-+): 0 found - 1 modified | TOTAL: 5 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 = 18 (out of 253619: 0.007097) 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: 297 vertices, 355 faces slice 50: 6084 vertices, 6352 faces slice 60: 15679 vertices, 16077 faces slice 70: 27718 vertices, 28118 faces slice 80: 39087 vertices, 39471 faces slice 90: 50806 vertices, 51217 faces slice 100: 62947 vertices, 63363 faces slice 110: 74553 vertices, 74945 faces slice 120: 85960 vertices, 86378 faces slice 130: 96968 vertices, 97362 faces slice 140: 107791 vertices, 108174 faces slice 150: 117190 vertices, 117512 faces slice 160: 125522 vertices, 125796 faces slice 170: 132989 vertices, 133271 faces slice 180: 139840 vertices, 140065 faces slice 190: 144792 vertices, 144961 faces slice 200: 147148 vertices, 147173 faces slice 210: 147156 vertices, 147176 faces slice 220: 147156 vertices, 147176 faces slice 230: 147156 vertices, 147176 faces slice 240: 147156 vertices, 147176 faces slice 250: 147156 vertices, 147176 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... 147156 voxel in cpt #1: X=-20 [v=147156,e=441528,f=294352] located at (24.144629, -17.471710, 38.149364) For the whole surface: X=-20 [v=147156,e=441528,f=294352] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Thu Aug 8 20:12:58 CEST 2013 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 20:13:03 CEST 2013 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts avg radius = 47.7 mm, total surface area = 75769 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=0.044 (target=0.015) step 020: RMS=0.037 (target=0.015) step 025: RMS=0.032 (target=0.015) step 030: RMS=0.029 (target=0.015) step 035: RMS=0.026 (target=0.015) step 040: RMS=0.023 (target=0.015) step 045: RMS=0.023 (target=0.015) step 050: RMS=0.021 (target=0.015) step 055: RMS=0.020 (target=0.015) step 060: RMS=0.020 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Thu Aug 8 20:13:44 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 0.95 +- 0.56 (0.00-->6.55) (max @ vno 109603 --> 109604) face area 0.02 +- 0.03 (-0.11-->0.64) scaling brain by 0.306... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.258, avgs=0 005/300: dt: 0.9000, rms radial error=175.998, avgs=0 010/300: dt: 0.9000, rms radial error=175.441, avgs=0 015/300: dt: 0.9000, rms radial error=174.711, avgs=0 020/300: dt: 0.9000, rms radial error=173.880, avgs=0 025/300: dt: 0.9000, rms radial error=172.991, avgs=0 030/300: dt: 0.9000, rms radial error=172.068, avgs=0 035/300: dt: 0.9000, rms radial error=171.129, avgs=0 040/300: dt: 0.9000, rms radial error=170.183, avgs=0 045/300: dt: 0.9000, rms radial error=169.235, avgs=0 050/300: dt: 0.9000, rms radial error=168.289, avgs=0 055/300: dt: 0.9000, rms radial error=167.346, avgs=0 060/300: dt: 0.9000, rms radial error=166.406, avgs=0 065/300: dt: 0.9000, rms radial error=165.471, avgs=0 070/300: dt: 0.9000, rms radial error=164.540, avgs=0 075/300: dt: 0.9000, rms radial error=163.614, avgs=0 080/300: dt: 0.9000, rms radial error=162.692, avgs=0 085/300: dt: 0.9000, rms radial error=161.778, avgs=0 090/300: dt: 0.9000, rms radial error=160.872, avgs=0 095/300: dt: 0.9000, rms radial error=159.970, avgs=0 100/300: dt: 0.9000, rms radial error=159.074, avgs=0 105/300: dt: 0.9000, rms radial error=158.182, avgs=0 110/300: dt: 0.9000, rms radial error=157.295, avgs=0 115/300: dt: 0.9000, rms radial error=156.414, avgs=0 120/300: dt: 0.9000, rms radial error=155.537, avgs=0 125/300: dt: 0.9000, rms radial error=154.666, avgs=0 130/300: dt: 0.9000, rms radial error=153.799, avgs=0 135/300: dt: 0.9000, rms radial error=152.937, avgs=0 140/300: dt: 0.9000, rms radial error=152.079, avgs=0 145/300: dt: 0.9000, rms radial error=151.226, avgs=0 150/300: dt: 0.9000, rms radial error=150.378, avgs=0 155/300: dt: 0.9000, rms radial error=149.534, avgs=0 160/300: dt: 0.9000, rms radial error=148.695, avgs=0 165/300: dt: 0.9000, rms radial error=147.861, avgs=0 170/300: dt: 0.9000, rms radial error=147.031, avgs=0 175/300: dt: 0.9000, rms radial error=146.206, avgs=0 180/300: dt: 0.9000, rms radial error=145.386, avgs=0 185/300: dt: 0.9000, rms radial error=144.570, avgs=0 190/300: dt: 0.9000, rms radial error=143.758, avgs=0 195/300: dt: 0.9000, rms radial error=142.951, avgs=0 200/300: dt: 0.9000, rms radial error=142.148, avgs=0 205/300: dt: 0.9000, rms radial error=141.350, avgs=0 210/300: dt: 0.9000, rms radial error=140.556, avgs=0 215/300: dt: 0.9000, rms radial error=139.767, avgs=0 220/300: dt: 0.9000, rms radial error=138.982, avgs=0 225/300: dt: 0.9000, rms radial error=138.201, avgs=0 230/300: dt: 0.9000, rms radial error=137.424, avgs=0 235/300: dt: 0.9000, rms radial error=136.652, avgs=0 240/300: dt: 0.9000, rms radial error=135.885, avgs=0 245/300: dt: 0.9000, rms radial error=135.121, avgs=0 250/300: dt: 0.9000, rms radial error=134.362, avgs=0 255/300: dt: 0.9000, rms radial error=133.607, avgs=0 260/300: dt: 0.9000, rms radial error=132.856, avgs=0 265/300: dt: 0.9000, rms radial error=132.109, avgs=0 270/300: dt: 0.9000, rms radial error=131.366, avgs=0 275/300: dt: 0.9000, rms radial error=130.628, avgs=0 280/300: dt: 0.9000, rms radial error=129.893, avgs=0 285/300: dt: 0.9000, rms radial error=129.163, avgs=0 290/300: dt: 0.9000, rms radial error=128.437, avgs=0 295/300: dt: 0.9000, rms radial error=127.715, avgs=0 300/300: dt: 0.9000, rms radial error=126.996, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 17388.32 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00016 epoch 2 (K=40.0), pass 1, starting sse = 2987.17 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00014 epoch 3 (K=160.0), pass 1, starting sse = 323.75 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.12/12 = 0.00964 epoch 4 (K=640.0), pass 1, starting sse = 18.55 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.25/22 = 0.01155 final writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.10 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Thu Aug 8 20:19:37 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/sub009/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub009 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=-20 (nv=147156, nf=294352, ne=441528, g=11) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations marking ambiguous vertices... 1820 ambiguous faces found in tessellation segmenting defects... 20 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 20 defects to be corrected 0 vertices coincident reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.9143 (-4.9571) -vertex loglikelihood: -6.7225 (-3.3612) -normal dot loglikelihood: -3.6256 (-3.6256) -quad curv loglikelihood: -6.5992 (-3.2996) Total Loglikelihood : -26.8615 CORRECTING DEFECT 0 (vertices=16, convex hull=56) After retessellation of defect 0, euler #=-17 (145994,437409,291398) : difference with theory (-17) = 0 CORRECTING DEFECT 1 (vertices=42, convex hull=77) After retessellation of defect 1, euler #=-16 (146017,437511,291478) : difference with theory (-16) = 0 CORRECTING DEFECT 2 (vertices=57, convex hull=101) After retessellation of defect 2, euler #=-15 (146049,437646,291582) : difference with theory (-15) = 0 CORRECTING DEFECT 3 (vertices=15, convex hull=30) After retessellation of defect 3, euler #=-14 (146053,437668,291601) : difference with theory (-14) = 0 CORRECTING DEFECT 4 (vertices=22, convex hull=73) After retessellation of defect 4, euler #=-13 (146068,437744,291663) : difference with theory (-13) = 0 CORRECTING DEFECT 5 (vertices=15, convex hull=31) After retessellation of defect 5, euler #=-12 (146072,437767,291683) : difference with theory (-12) = 0 CORRECTING DEFECT 6 (vertices=56, convex hull=131) After retessellation of defect 6, euler #=-11 (146100,437904,291793) : difference with theory (-11) = 0 CORRECTING DEFECT 7 (vertices=18, convex hull=24) After retessellation of defect 7, euler #=-10 (146103,437919,291806) : difference with theory (-10) = 0 CORRECTING DEFECT 8 (vertices=457, convex hull=274) After retessellation of defect 8, euler #=-9 (146119,438110,291982) : difference with theory (-9) = 0 CORRECTING DEFECT 9 (vertices=40, convex hull=20) After retessellation of defect 9, euler #=-8 (146123,438130,291999) : difference with theory (-8) = 0 CORRECTING DEFECT 10 (vertices=10, convex hull=13) After retessellation of defect 10, euler #=-7 (146124,438135,292004) : difference with theory (-7) = 0 CORRECTING DEFECT 11 (vertices=118, convex hull=165) After retessellation of defect 11, euler #=-6 (146166,438341,292169) : difference with theory (-6) = 0 CORRECTING DEFECT 12 (vertices=76, convex hull=70) After retessellation of defect 12, euler #=-5 (146200,438476,292271) : difference with theory (-5) = 0 CORRECTING DEFECT 13 (vertices=7, convex hull=24) After retessellation of defect 13, euler #=-4 (146202,438490,292284) : difference with theory (-4) = 0 CORRECTING DEFECT 14 (vertices=15, convex hull=14) After retessellation of defect 14, euler #=-3 (146203,438497,292291) : difference with theory (-3) = 0 CORRECTING DEFECT 15 (vertices=64, convex hull=46) After retessellation of defect 15, euler #=-2 (146208,438532,292322) : difference with theory (-2) = 0 CORRECTING DEFECT 16 (vertices=22, convex hull=26) After retessellation of defect 16, euler #=-1 (146209,438544,292334) : difference with theory (-1) = 0 CORRECTING DEFECT 17 (vertices=29, convex hull=77) After retessellation of defect 17, euler #=0 (146224,438619,292395) : difference with theory (0) = 0 CORRECTING DEFECT 18 (vertices=55, convex hull=80) After retessellation of defect 18, euler #=1 (146244,438714,292471) : difference with theory (1) = 0 CORRECTING DEFECT 19 (vertices=35, convex hull=33) After retessellation of defect 19, euler #=2 (146248,438738,292492) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.11-->7.99) (max @ vno 80780 --> 80800) 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 (0.11-->7.99) (max @ vno 80780 --> 80800) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 79 mutations (36.7%), 136 crossovers (63.3%), 164 vertices were eliminated building final representation... 908 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=146248, nf=292492, ne=438738, g=0) writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 27.0 minutes 0 defective edges removing intersecting faces 000: 153 intersecting 001: 2 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 146248 - 438738 + 292492 = 2 --> 0 holes F =2V-4: 292492 = 292496-4 (0) 2E=3F: 877476 = 877476 (0) total defect index = 0 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 16 intersecting 001: 4 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Thu Aug 8 20:46:44 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub009 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/sub009/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/wm.mgz... 19164 bright wm thresholded. 814 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.orig... computing class statistics... border white: 259466 voxels (1.55%) border gray 303507 voxels (1.81%) WM (92.0): 93.0 +- 10.6 [70.0 --> 110.0] GM (74.0) : 72.2 +- 13.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 44.0 (was 70) setting MAX_BORDER_WHITE to 115.6 (was 105) setting MIN_BORDER_WHITE to 57.0 (was 85) setting MAX_CSF to 30.9 (was 40) setting MAX_GRAY to 94.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 50.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 17.9 (was 40) repositioning cortical surface to gray/white boundary reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.22 (0.02-->2.66) (max @ vno 79769 --> 80799) face area 0.27 +- 0.12 (0.00-->1.76) mean absolute distance = 0.67 +- 0.76 3877 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 = 92.8, mean outside = 66.9 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=70.8, 60 (60) missing vertices, mean dist 0.4 [0.5 (%30.5)->0.8 (%69.5))] %70 local maxima, %25 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 (0.06-->4.62) (max @ vno 80799 --> 79769) face area 0.27 +- 0.13 (0.00-->2.93) mean absolute distance = 0.31 +- 0.45 2699 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=8750270.0, rms=14.49 001: dt: 0.5000, sse=8701720.0, rms=10.592 (0.000%) 002: dt: 0.5000, sse=8905935.0, rms=8.311 (0.000%) 003: dt: 0.5000, sse=8952658.0, rms=6.782 (0.000%) 004: dt: 0.5000, sse=9183209.0, rms=5.832 (0.000%) 005: dt: 0.5000, sse=9228581.0, rms=5.261 (0.000%) 006: dt: 0.5000, sse=9405899.0, rms=4.963 (0.000%) 007: dt: 0.5000, sse=9364875.0, rms=4.779 (0.000%) 008: dt: 0.5000, sse=9414885.0, rms=4.684 (0.000%) 009: dt: 0.5000, sse=9330527.0, rms=4.603 (0.000%) rms = 4.56, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=9347492.0, rms=4.560 (0.000%) 011: dt: 0.2500, sse=6068557.5, rms=3.252 (0.000%) 012: dt: 0.2500, sse=5611800.0, rms=2.777 (0.000%) 013: dt: 0.2500, sse=5301363.5, rms=2.682 (0.000%) 014: dt: 0.2500, sse=5209381.5, rms=2.584 (0.000%) rms = 2.55, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=5096611.5, rms=2.548 (0.000%) 016: dt: 0.1250, sse=4827331.5, rms=2.288 (0.000%) rms = 2.25, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=4771513.5, rms=2.251 (0.000%) positioning took 2.2 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group mean border=75.7, 61 (6) missing vertices, mean dist -0.2 [0.3 (%78.9)->0.2 (%21.1))] %81 local maxima, %14 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 0.90 +- 0.26 (0.06-->4.92) (max @ vno 80799 --> 79769) face area 0.35 +- 0.17 (0.00-->4.22) mean absolute distance = 0.21 +- 0.27 2522 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5950757.0, rms=6.43 018: dt: 0.5000, sse=6106958.5, rms=4.340 (0.000%) rms = 4.77, time step reduction 1 of 3 to 0.250... 019: dt: 0.2500, sse=5552593.0, rms=3.126 (0.000%) 020: dt: 0.2500, sse=5360413.0, rms=2.562 (0.000%) 021: dt: 0.2500, sse=5281753.0, rms=2.157 (0.000%) rms = 2.13, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=5269842.0, rms=2.132 (0.000%) 023: dt: 0.1250, sse=5055385.5, rms=1.847 (0.000%) rms = 1.80, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=4995741.0, rms=1.797 (0.000%) positioning took 1.0 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 mean border=79.7, 66 (3) missing vertices, mean dist -0.1 [0.2 (%80.5)->0.2 (%19.5))] %90 local maxima, % 5 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 (0.10-->5.10) (max @ vno 80799 --> 79769) face area 0.34 +- 0.16 (0.00-->4.34) mean absolute distance = 0.15 +- 0.22 2643 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5549135.0, rms=4.88 025: dt: 0.5000, sse=5665896.5, rms=4.369 (0.000%) rms = 4.56, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=5164925.0, rms=2.733 (0.000%) 027: dt: 0.2500, sse=5055262.5, rms=2.336 (0.000%) 028: dt: 0.2500, sse=5154182.0, rms=1.924 (0.000%) rms = 2.01, time step reduction 2 of 3 to 0.125... 029: dt: 0.1250, sse=5073879.0, rms=1.763 (0.000%) 030: dt: 0.1250, sse=4973509.0, rms=1.543 (0.000%) rms = 1.52, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=4934952.0, rms=1.518 (0.000%) positioning took 1.1 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 3 vertex label from ripped group mean border=81.0, 52 (1) missing vertices, mean dist -0.0 [0.2 (%60.3)->0.1 (%39.7))] %92 local maxima, % 3 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/sub009/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=4962267.5, rms=1.94 rms = 3.25, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=5031940.5, rms=1.215 (0.000%) 033: dt: 0.2500, sse=5172706.5, rms=1.143 (0.000%) rms = 1.14, time step reduction 2 of 3 to 0.125... 034: dt: 0.2500, sse=5274603.0, rms=1.143 (0.000%) rms = 1.12, time step reduction 3 of 3 to 0.062... 035: dt: 0.1250, sse=5311404.5, rms=1.116 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group generating cortex label... 13 non-cortical segments detected only using segment with 1610 vertices erasing segment 1 (vno[0] = 87431) erasing segment 2 (vno[0] = 90706) erasing segment 3 (vno[0] = 102106) erasing segment 4 (vno[0] = 103142) erasing segment 5 (vno[0] = 103149) erasing segment 6 (vno[0] = 103219) erasing segment 7 (vno[0] = 106604) erasing segment 8 (vno[0] = 107511) erasing segment 9 (vno[0] = 109450) erasing segment 10 (vno[0] = 113247) erasing segment 11 (vno[0] = 113282) erasing segment 12 (vno[0] = 116705) writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/label/rh.cortex.label... writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.curv writing smoothed area to rh.area writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.area vertex spacing 0.89 +- 0.25 (0.04-->5.20) (max @ vno 80799 --> 79769) face area 0.34 +- 0.16 (0.00-->4.40) refinement took 7.1 minutes #-------------------------------------------- #@# Smooth2 rh Thu Aug 8 20:53:51 CEST 2013 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 20:53:55 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 47.9 mm, total surface area = 88544 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.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=0.048 (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=0.023 (target=0.015) step 040: RMS=0.019 (target=0.015) step 045: RMS=0.017 (target=0.015) step 050: RMS=0.016 (target=0.015) inflation complete. inflation took 0.5 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 188 vertices thresholded to be in k1 ~ [-0.26 0.37], k2 ~ [-0.13 0.11] total integrated curvature = 0.465*4pi (5.845) --> 1 handles ICI = 1.6, FI = 11.9, variation=198.417 140 vertices thresholded to be in [-0.02 0.02] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 139 vertices thresholded to be in [-0.16 0.15] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.016, std = 0.024 done. #----------------------------------------- #@# Curvature Stats rh Thu Aug 8 20:56:18 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub009 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 [ sub009/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 [ 273 ] Gb_filter = 0 WARN: S lookup min: -0.238989 WARN: S explicit min: 0.000000 vertex = 170 #-------------------------------------------- #@# Sphere rh Thu Aug 8 20:56:24 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 0.283... 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 %19.30 pass 1: epoch 2 of 3 starting distance error %19.24 unfolding complete - removing small folds... starting distance error %19.19 removing remaining folds... final distance error %19.21 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/rh.sphere spherical transformation took 0.98 hours #-------------------------------------------- #@# Surf Reg rh Thu Aug 8 21:55:17 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 = 0.564 curvature mean = 0.014, std = 0.929 curvature mean = 0.025, std = 0.844 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 0.00) sse = 412168.3, tmin=1.3556 d=32.00 min @ (-8.00, -8.00, 0.00) sse = 327821.5, tmin=2.6979 d=16.00 min @ (-4.00, 0.00, 4.00) sse = 302534.3, tmin=4.0419 d=8.00 min @ (2.00, 2.00, 0.00) sse = 294141.2, tmin=5.4223 d=4.00 min @ (1.00, 0.00, -1.00) sse = 292668.7, tmin=6.8288 d=2.00 min @ (-0.50, -0.50, 0.50) sse = 292154.8, tmin=8.2403 d=1.00 min @ (-0.25, 0.00, -0.25) sse = 292002.5, tmin=9.6176 d=0.50 min @ (0.12, 0.12, 0.00) sse = 291966.3, tmin=11.0210 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 11.02 min curvature mean = -0.007, std = 0.932 curvature mean = 0.012, std = 0.930 curvature mean = -0.010, std = 0.941 curvature mean = 0.006, std = 0.966 curvature mean = -0.011, std = 0.940 curvature mean = 0.002, std = 0.984 2 Reading smoothwm curvature mean = -0.024, std = 0.309 curvature mean = 0.005, std = 0.069 curvature mean = 0.077, std = 0.314 curvature mean = 0.005, std = 0.083 curvature mean = 0.039, std = 0.507 curvature mean = 0.005, std = 0.088 curvature mean = 0.021, std = 0.656 curvature mean = 0.006, std = 0.091 curvature mean = 0.007, std = 0.776 MRISregister() return, current seed 0 writing registered surface to ../surf/rh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white rh Thu Aug 8 22:28:55 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 22:28:57 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 22:29:00 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub009 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... 1209 labels changed using aseg relabeling using gibbs priors... 000: 3289 changed, 146248 examined... 001: 798 changed, 13951 examined... 002: 197 changed, 4307 examined... 003: 88 changed, 1223 examined... 004: 46 changed, 528 examined... 005: 17 changed, 256 examined... 006: 9 changed, 98 examined... 007: 3 changed, 40 examined... 008: 2 changed, 16 examined... 009: 4 changed, 13 examined... 010: 3 changed, 23 examined... 011: 1 changed, 17 examined... 012: 0 changed, 9 examined... 170 labels changed using aseg 000: 129 total segments, 91 labels (443 vertices) changed 001: 42 total segments, 4 labels (21 vertices) changed 002: 38 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 42 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1931 vertices marked for relabeling... 1931 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 1 minutes and 11 seconds. #-------------------------------------------- #@# Make Pial Surf rh Thu Aug 8 22:30:11 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub009 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/sub009/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/wm.mgz... 19164 bright wm thresholded. 814 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.orig... computing class statistics... border white: 259466 voxels (1.55%) border gray 303507 voxels (1.81%) WM (92.0): 93.0 +- 10.6 [70.0 --> 110.0] GM (74.0) : 72.2 +- 13.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 44.0 (was 70) setting MAX_BORDER_WHITE to 115.6 (was 105) setting MIN_BORDER_WHITE to 57.0 (was 85) setting MAX_CSF to 30.9 (was 40) setting MAX_GRAY to 94.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 50.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 17.9 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=57 mean inside = 92.8, mean outside = 66.9 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.22 (0.02-->2.66) (max @ vno 79769 --> 80799) face area 0.27 +- 0.12 (0.00-->1.76) mean absolute distance = 0.67 +- 0.76 3914 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 15 points - only 0.00% unknown deleting segment 3 with 333 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown deleting segment 7 with 8 points - only 0.00% unknown deleting segment 8 with 7 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 9 with 3 points - only 0.00% unknown deleting segment 10 with 29 points - only 0.00% unknown mean border=70.8, 61 (61) missing vertices, mean dist 0.4 [0.5 (%30.5)->0.8 (%69.5))] %70 local maxima, %25 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 +- 0.26 (0.06-->4.62) (max @ vno 80799 --> 79769) face area 0.27 +- 0.13 (0.00-->2.93) mean absolute distance = 0.31 +- 0.45 2701 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=8763778.0, rms=14.48 001: dt: 0.5000, sse=8717599.0, rms=10.586 (0.000%) 002: dt: 0.5000, sse=8921043.0, rms=8.306 (0.000%) 003: dt: 0.5000, sse=8975575.0, rms=6.778 (0.000%) 004: dt: 0.5000, sse=9204313.0, rms=5.828 (0.000%) 005: dt: 0.5000, sse=9255857.0, rms=5.259 (0.000%) 006: dt: 0.5000, sse=9432396.0, rms=4.961 (0.000%) 007: dt: 0.5000, sse=9394983.0, rms=4.777 (0.000%) 008: dt: 0.5000, sse=9439806.0, rms=4.682 (0.000%) 009: dt: 0.5000, sse=9361114.0, rms=4.602 (0.000%) rms = 4.56, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=9373735.0, rms=4.559 (0.000%) 011: dt: 0.2500, sse=6083314.5, rms=3.252 (0.000%) 012: dt: 0.2500, sse=5624215.0, rms=2.777 (0.000%) 013: dt: 0.2500, sse=5313463.5, rms=2.682 (0.000%) 014: dt: 0.2500, sse=5220910.0, rms=2.585 (0.000%) rms = 2.55, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=5107566.0, rms=2.548 (0.000%) 016: dt: 0.1250, sse=4839035.5, rms=2.289 (0.000%) rms = 2.25, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=4783469.5, rms=2.252 (0.000%) positioning took 2.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 36 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 1 with 4 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 5 with 16 points - only 0.00% unknown deleting segment 6 with 297 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown deleting segment 8 with 11 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 10 with 18 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 11 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 12 with 3 points - only 0.00% unknown deleting segment 13 with 34 points - only 0.00% unknown mean border=75.7, 65 (8) missing vertices, mean dist -0.2 [0.3 (%78.9)->0.2 (%21.1))] %82 local maxima, %14 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 0.90 +- 0.25 (0.06-->4.92) (max @ vno 80799 --> 79769) face area 0.35 +- 0.17 (0.00-->4.22) mean absolute distance = 0.21 +- 0.27 2540 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5964654.0, rms=6.43 018: dt: 0.5000, sse=6123459.0, rms=4.336 (0.000%) rms = 4.76, time step reduction 1 of 3 to 0.250... 019: dt: 0.2500, sse=5567103.0, rms=3.123 (0.000%) 020: dt: 0.2500, sse=5374869.5, rms=2.560 (0.000%) 021: dt: 0.2500, sse=5296525.0, rms=2.156 (0.000%) rms = 2.13, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=5284441.0, rms=2.132 (0.000%) 023: dt: 0.1250, sse=5069048.5, rms=1.847 (0.000%) rms = 1.80, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=5009618.5, rms=1.797 (0.000%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 19 points - only 0.00% unknown deleting segment 1 with 13 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown deleting segment 3 with 294 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 4 points - only 0.00% unknown deleting segment 5 with 14 points - only 0.00% unknown deleting segment 7 with 33 points - only 0.00% unknown deleting segment 8 with 10 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 9 with 3 points - only 0.00% unknown deleting segment 10 with 40 points - only 0.00% unknown mean border=79.7, 69 (3) missing vertices, mean dist -0.1 [0.2 (%80.4)->0.2 (%19.6))] %91 local maxima, % 5 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 (0.10-->5.10) (max @ vno 80799 --> 79769) face area 0.34 +- 0.16 (0.00-->4.34) mean absolute distance = 0.15 +- 0.22 2666 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5564047.0, rms=4.88 025: dt: 0.5000, sse=5684758.5, rms=4.366 (0.000%) rms = 4.56, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=5182205.5, rms=2.732 (0.000%) 027: dt: 0.2500, sse=5070397.5, rms=2.336 (0.000%) 028: dt: 0.2500, sse=5170511.5, rms=1.924 (0.000%) rms = 2.01, time step reduction 2 of 3 to 0.125... 029: dt: 0.1250, sse=5089885.0, rms=1.763 (0.000%) 030: dt: 0.1250, sse=4988666.5, rms=1.544 (0.000%) rms = 1.52, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=4950042.0, rms=1.519 (0.000%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 22 points - only 0.00% unknown deleting segment 4 with 13 points - only 0.00% unknown deleting segment 5 with 307 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 4 points - only 0.00% unknown deleting segment 7 with 16 points - only 0.00% unknown deleting segment 8 with 21 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown deleting segment 10 with 10 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 11 with 3 points - only 0.00% unknown deleting segment 12 with 34 points - only 0.00% unknown mean border=80.9, 56 (1) missing vertices, mean dist -0.0 [0.2 (%60.2)->0.1 (%39.8))] %93 local maxima, % 3 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=4977131.0, rms=1.94 rms = 3.24, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=5048153.0, rms=1.214 (0.000%) 033: dt: 0.2500, sse=5190069.5, rms=1.144 (0.000%) rms = 1.14, time step reduction 2 of 3 to 0.125... 034: dt: 0.2500, sse=5292632.5, rms=1.144 (0.000%) rms = 1.12, time step reduction 3 of 3 to 0.062... 035: dt: 0.1250, sse=5328846.0, rms=1.117 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown smoothing surface for 5 iterations... mean border=47.1, 88 (88) missing vertices, mean dist 1.7 [0.1 (%0.0)->2.2 (%100.0))] %15 local maxima, %58 large gradients and %23 min vals, 1039 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=33695572.0, rms=32.95 001: dt: 0.5000, sse=24109036.0, rms=27.266 (0.000%) 002: dt: 0.5000, sse=17436482.0, rms=22.508 (0.000%) 003: dt: 0.5000, sse=12950371.0, rms=18.625 (0.000%) 004: dt: 0.5000, sse=10276401.0, rms=15.538 (0.000%) 005: dt: 0.5000, sse=8813430.0, rms=13.154 (0.000%) 006: dt: 0.5000, sse=7984159.0, rms=11.361 (0.000%) 007: dt: 0.5000, sse=7484004.5, rms=9.851 (0.000%) 008: dt: 0.5000, sse=7189707.5, rms=8.521 (0.000%) 009: dt: 0.5000, sse=7017868.5, rms=7.286 (0.000%) 010: dt: 0.5000, sse=7024291.5, rms=6.271 (0.000%) 011: dt: 0.5000, sse=7163269.0, rms=5.507 (0.000%) 012: dt: 0.5000, sse=7435373.0, rms=5.011 (0.000%) 013: dt: 0.5000, sse=7562700.5, rms=4.698 (0.000%) 014: dt: 0.5000, sse=7753237.5, rms=4.520 (0.000%) 015: dt: 0.5000, sse=7852165.5, rms=4.389 (0.000%) 016: dt: 0.5000, sse=7904825.0, rms=4.320 (0.000%) 017: dt: 0.5000, sse=7932647.0, rms=4.251 (0.000%) rms = 4.22, time step reduction 1 of 3 to 0.250... 018: dt: 0.5000, sse=7944391.5, rms=4.219 (0.000%) 019: dt: 0.2500, sse=5529934.0, rms=3.422 (0.000%) 020: dt: 0.2500, sse=5269636.5, rms=3.206 (0.000%) rms = 3.18, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=5108067.5, rms=3.180 (0.000%) 022: dt: 0.1250, sse=4893078.0, rms=3.057 (0.000%) rms = 3.04, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=4848967.5, rms=3.044 (0.000%) positioning took 3.0 minutes mean border=45.0, 745 (8) missing vertices, mean dist 0.1 [0.2 (%50.3)->0.5 (%49.7))] %32 local maxima, %45 large gradients and %19 min vals, 314 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=5475894.0, rms=4.77 024: dt: 0.5000, sse=5843607.0, rms=4.123 (0.000%) rms = 4.21, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=5424345.0, rms=3.471 (0.000%) 026: dt: 0.2500, sse=5570535.5, rms=3.199 (0.000%) 027: dt: 0.2500, sse=5477197.5, rms=3.092 (0.000%) 028: dt: 0.2500, sse=5540206.5, rms=3.038 (0.000%) rms = 3.01, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=5515802.0, rms=3.011 (0.000%) 030: dt: 0.1250, sse=5327823.0, rms=2.869 (0.000%) rms = 2.84, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=5312098.5, rms=2.843 (0.000%) positioning took 1.1 minutes mean border=42.5, 857 (5) missing vertices, mean dist 0.1 [0.2 (%37.7)->0.4 (%62.3))] %54 local maxima, %23 large gradients and %19 min vals, 471 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=5656001.0, rms=4.41 032: dt: 0.5000, sse=5915675.0, rms=4.144 (0.000%) rms = 4.25, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=5534863.0, rms=3.273 (0.000%) 034: dt: 0.2500, sse=5785543.5, rms=2.939 (0.000%) 035: dt: 0.2500, sse=5721019.0, rms=2.871 (0.000%) rms = 2.84, time step reduction 2 of 3 to 0.125... 036: dt: 0.2500, sse=5785428.0, rms=2.836 (0.000%) 037: dt: 0.1250, sse=5551452.5, rms=2.664 (0.000%) rms = 2.64, time step reduction 3 of 3 to 0.062... 038: dt: 0.1250, sse=5536021.0, rms=2.642 (0.000%) positioning took 1.0 minutes mean border=41.1, 1949 (2) missing vertices, mean dist 0.1 [0.2 (%44.6)->0.3 (%55.4))] %59 local maxima, %18 large gradients and %18 min vals, 406 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/sub009/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=5609083.0, rms=3.08 rms = 3.99, time step reduction 1 of 3 to 0.250... 039: dt: 0.2500, sse=5448987.0, rms=2.732 (0.000%) 040: dt: 0.2500, sse=5656892.0, rms=2.662 (0.000%) rms = 2.64, time step reduction 2 of 3 to 0.125... 041: dt: 0.2500, sse=5735981.5, rms=2.645 (0.000%) 042: dt: 0.1250, sse=5619942.5, rms=2.509 (0.000%) rms = 2.49, time step reduction 3 of 3 to 0.062... 043: dt: 0.1250, sse=5632522.0, rms=2.494 (0.000%) positioning took 0.7 minutes writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.area.pial vertex spacing 1.01 +- 0.41 (0.07-->8.67) (max @ vno 102156 --> 102155) face area 0.40 +- 0.30 (0.00-->6.82) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 146248 vertices processed 25000 of 146248 vertices processed 50000 of 146248 vertices processed 75000 of 146248 vertices processed 100000 of 146248 vertices processed 125000 of 146248 vertices processed 0 of 146248 vertices processed 25000 of 146248 vertices processed 50000 of 146248 vertices processed 75000 of 146248 vertices processed 100000 of 146248 vertices processed 125000 of 146248 vertices processed thickness calculation complete, 251:385 truncations. 33011 vertices at 0 distance 99243 vertices at 1 distance 97132 vertices at 2 distance 38100 vertices at 3 distance 9947 vertices at 4 distance 2514 vertices at 5 distance 792 vertices at 6 distance 278 vertices at 7 distance 118 vertices at 8 distance 71 vertices at 9 distance 50 vertices at 10 distance 34 vertices at 11 distance 32 vertices at 12 distance 24 vertices at 13 distance 18 vertices at 14 distance 23 vertices at 15 distance 17 vertices at 16 distance 14 vertices at 17 distance 10 vertices at 18 distance 7 vertices at 19 distance 15 vertices at 20 distance writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.thickness positioning took 14.6 minutes #-------------------------------------------- #@# Surf Volume rh Thu Aug 8 22:44:48 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 22:44:49 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts pctsurfcon --s sub009 --rh-only Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts/pctsurfcon.log Thu Aug 8 22:44:49 CEST 2013 setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts /opt/freesurfer/5.3.0/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux snake6 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/sub009/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/tmp.pctsurfcon.21186/rh.wm.mgh --regheader sub009 --cortex srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/mri/orig.mgz as target reference. Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/label/rh.cortex.label Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 = 111831 Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/label/rh.cortex.label Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/tmp.pctsurfcon.21186/rh.wm.mgh Dim: 146248 1 1 mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/tmp.pctsurfcon.21186/rh.gm.mgh --projfrac 0.3 --regheader sub009 --cortex srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/mri/orig.mgz as target reference. Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/label/rh.cortex.label Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.white Done reading source surface Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 = 130305 Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/label/rh.cortex.label Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/tmp.pctsurfcon.21186/rh.gm.mgh Dim: 146248 1 1 mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/tmp.pctsurfcon.21186/rh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/tmp.pctsurfcon.21186/rh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/surf/rh.w-g.pct.mgh mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.w-g.pct.mgh --annot sub009 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/surf/rh.w-g.pct.mgh --annot sub009 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/stats/rh.w-g.pct.stats --snr sysname Linux hostname snake6 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/sub009/surf/rh.w-g.pct.mgh Vertex Area is 0.666197 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 2000 unknown 0 0.000 1 2001 bankssts 1112 775.413 2 2002 caudalanteriorcingulate 981 688.921 3 2003 caudalmiddlefrontal 3731 2507.108 4 2004 corpuscallosum 0 0.000 5 2005 cuneus 2007 1316.870 6 2006 entorhinal 444 318.865 7 2007 fusiform 5076 3432.738 8 2008 inferiorparietal 8077 5455.833 9 2009 inferiortemporal 4898 3307.569 10 2010 isthmuscingulate 2076 1313.176 11 2011 lateraloccipital 8015 5289.354 12 2012 lateralorbitofrontal 4462 2926.592 13 2013 lingual 4273 2907.199 14 2014 medialorbitofrontal 2909 1908.565 15 2015 middletemporal 5190 3501.465 16 2016 parahippocampal 949 651.578 17 2017 paracentral 3230 2076.418 18 2018 parsopercularis 2120 1440.617 19 2019 parsorbitalis 1326 885.209 20 2020 parstriangularis 2291 1521.716 21 2021 pericalcarine 2025 1375.701 22 2022 postcentral 7665 5076.688 23 2023 posteriorcingulate 2332 1529.350 24 2024 precentral 7001 4552.345 25 2025 precuneus 6642 4384.634 26 2026 rostralanteriorcingulate 1180 755.048 27 2027 rostralmiddlefrontal 9506 6418.618 28 2028 superiorfrontal 11897 7992.842 29 2029 superiorparietal 9643 6390.857 30 2030 superiortemporal 5716 3874.690 31 2031 supramarginal 6513 4446.536 32 2032 frontalpole 426 289.887 33 2033 temporalpole 606 405.228 34 2034 transversetemporal 647 376.329 35 2035 insula 3907 2588.489 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats rh Thu Aug 8 22:45:14 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 sub009 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 1112 775 2055 2.592 0.403 0.127 0.040 13 1.8 bankssts 981 689 1862 2.283 0.665 0.153 0.035 19 1.5 caudalanteriorcingulate 3731 2507 6377 2.329 0.426 0.145 0.047 61 7.0 caudalmiddlefrontal 2007 1317 3048 2.033 0.438 0.171 0.066 42 5.2 cuneus 444 319 1695 3.408 0.704 0.147 0.063 6 1.3 entorhinal 5076 3433 9838 2.587 0.505 0.148 0.059 141 11.0 fusiform 8077 5456 13955 2.260 0.451 0.155 0.061 172 19.0 inferiorparietal 4898 3308 9558 2.422 0.703 0.164 0.073 141 14.1 inferiortemporal 2076 1313 3414 2.300 0.772 0.170 0.079 63 7.1 isthmuscingulate 8015 5289 13510 2.234 0.474 0.164 0.078 196 19.2 lateraloccipital 4462 2927 8009 2.526 0.661 0.169 0.086 113 15.3 lateralorbitofrontal 4273 2907 6715 2.100 0.549 0.168 0.070 89 11.6 lingual 2909 1909 5117 2.308 0.649 0.163 0.097 106 9.8 medialorbitofrontal 5190 3501 11531 2.688 0.618 0.156 0.064 120 13.3 middletemporal 949 652 1671 2.240 0.510 0.116 0.032 7 1.3 parahippocampal 3230 2076 5406 2.377 0.515 0.140 0.046 44 5.9 paracentral 2120 1441 3928 2.411 0.400 0.134 0.045 30 3.7 parsopercularis 1326 885 2655 2.349 0.528 0.167 0.096 41 3.2 parsorbitalis 2291 1522 3847 2.270 0.434 0.159 0.075 52 5.1 parstriangularis 2025 1376 2406 1.745 0.361 0.160 0.070 34 5.6 pericalcarine 7665 5077 11290 1.965 0.534 0.140 0.046 136 14.2 postcentral 2332 1529 4030 2.345 0.679 0.170 0.068 56 5.6 posteriorcingulate 7001 4552 12396 2.431 0.492 0.133 0.089 266 27.7 precentral 6642 4385 10711 2.275 0.457 0.156 0.070 144 14.7 precuneus 1180 755 2315 2.868 0.647 0.154 0.061 25 2.9 rostralanteriorcingulate 9506 6419 16447 2.269 0.459 0.171 0.071 233 25.7 rostralmiddlefrontal 11897 7993 23437 2.601 0.493 0.154 0.056 225 26.8 superiorfrontal 9643 6391 13990 1.981 0.418 0.152 0.048 179 18.8 superiorparietal 5716 3875 12325 2.793 0.542 0.145 0.058 110 11.8 superiortemporal 6513 4447 11256 2.311 0.450 0.141 0.056 140 13.3 supramarginal 426 290 1001 2.561 0.412 0.203 0.081 13 1.3 frontalpole 606 405 1891 3.464 0.740 0.182 0.126 33 3.9 temporalpole 647 376 1139 2.596 0.366 0.139 0.066 14 1.6 transversetemporal 3907 2588 7513 2.823 0.825 0.134 0.076 74 10.0 insula #----------------------------------------- #@# Cortical Parc 2 rh Thu Aug 8 22:45:45 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub009 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... 0 labels changed using aseg relabeling using gibbs priors... 000: 10805 changed, 146248 examined... 001: 2667 changed, 40876 examined... 002: 853 changed, 13541 examined... 003: 364 changed, 4664 examined... 004: 192 changed, 2025 examined... 005: 103 changed, 1083 examined... 006: 48 changed, 578 examined... 007: 17 changed, 258 examined... 008: 12 changed, 110 examined... 009: 5 changed, 51 examined... 010: 4 changed, 26 examined... 011: 4 changed, 20 examined... 012: 2 changed, 16 examined... 013: 0 changed, 9 examined... 0 labels changed using aseg 000: 341 total segments, 257 labels (2958 vertices) changed 001: 97 total segments, 15 labels (24 vertices) changed 002: 82 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 160 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1163 vertices marked for relabeling... 1163 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 1 minutes and 36 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Thu Aug 8 22:47:22 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 sub009 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 1101 743 1776 2.124 0.496 0.180 0.075 30 3.7 G_and_S_frontomargin 1548 1063 3003 2.446 0.421 0.153 0.050 27 3.2 G_and_S_occipital_inf 1810 1154 3351 2.421 0.557 0.148 0.047 27 3.5 G_and_S_paracentral 1607 1081 3279 2.617 0.442 0.160 0.053 31 3.3 G_and_S_subcentral 1030 710 2244 2.433 0.402 0.205 0.117 45 5.1 G_and_S_transv_frontopol 3657 2442 6734 2.562 0.582 0.145 0.051 60 7.7 G_and_S_cingul-Ant 1650 1149 3431 2.700 0.508 0.143 0.044 25 3.0 G_and_S_cingul-Mid-Ant 2012 1317 3462 2.434 0.472 0.154 0.064 38 4.4 G_and_S_cingul-Mid-Post 902 554 2064 2.847 0.624 0.199 0.089 33 3.1 G_cingul-Post-dorsal 352 225 837 2.811 0.691 0.165 0.092 10 1.2 G_cingul-Post-ventral 1757 1117 2624 2.002 0.453 0.186 0.080 44 5.9 G_cuneus 1657 1109 3745 2.617 0.466 0.154 0.059 33 3.7 G_front_inf-Opercular 306 197 594 2.295 0.365 0.146 0.177 10 0.5 G_front_inf-Orbital 1142 761 2329 2.450 0.420 0.179 0.067 31 3.1 G_front_inf-Triangul 4706 3200 9598 2.377 0.451 0.186 0.081 139 14.3 G_front_middle 7827 5157 16715 2.655 0.494 0.164 0.062 168 18.8 G_front_sup 577 376 1335 3.303 0.593 0.130 0.066 13 1.3 G_Ins_lg_and_S_cent_ins 707 475 2014 3.391 0.793 0.162 0.106 18 2.5 G_insular_short 2948 1955 6403 2.486 0.447 0.192 0.141 131 9.6 G_occipital_middle 2101 1342 3312 2.081 0.443 0.154 0.052 39 4.1 G_occipital_sup 2146 1360 4946 2.729 0.497 0.166 0.068 96 5.6 G_oc-temp_lat-fusifor 2860 1902 4840 2.154 0.574 0.185 0.086 76 9.5 G_oc-temp_med-Lingual 1340 858 3096 2.705 0.870 0.134 0.074 22 3.4 G_oc-temp_med-Parahip 3349 2170 7080 2.553 0.708 0.188 0.122 131 13.3 G_orbital 2605 1759 5175 2.315 0.424 0.171 0.076 75 8.1 G_pariet_inf-Angular 3300 2264 6909 2.444 0.433 0.161 0.075 108 8.7 G_pariet_inf-Supramar 3607 2409 5369 1.935 0.419 0.151 0.048 73 7.1 G_parietal_sup 2890 1856 4555 1.986 0.448 0.150 0.052 60 6.2 G_postcentral 2469 1537 5330 2.649 0.368 0.141 0.181 221 20.4 G_precentral 3072 1982 6044 2.428 0.427 0.181 0.102 105 8.5 G_precuneus 809 517 1632 2.380 0.630 0.211 0.194 60 4.9 G_rectus 435 293 890 2.695 0.715 0.139 0.120 13 1.5 G_subcallosal 505 287 1056 2.832 0.431 0.156 0.080 15 1.5 G_temp_sup-G_T_transv 2151 1420 5877 3.051 0.496 0.173 0.091 69 5.8 G_temp_sup-Lateral 597 441 1688 3.347 0.589 0.146 0.059 9 1.1 G_temp_sup-Plan_polar 681 467 1203 2.408 0.488 0.101 0.025 5 0.6 G_temp_sup-Plan_tempo 2266 1541 4791 2.444 0.770 0.182 0.089 89 7.7 G_temporal_inf 3027 2034 7962 2.849 0.574 0.173 0.079 91 9.8 G_temporal_middle 479 309 634 2.126 0.416 0.119 0.029 4 0.6 Lat_Fis-ant-Horizont 122 80 164 2.259 0.298 0.119 0.041 1 0.2 Lat_Fis-ant-Vertical 1665 1113 2151 2.231 0.432 0.117 0.037 14 2.6 Lat_Fis-post 3400 2238 5239 2.031 0.537 0.181 0.067 79 9.0 Pole_occipital 1972 1350 5553 3.001 0.736 0.181 0.111 81 9.3 Pole_temporal 2288 1602 2915 2.011 0.564 0.141 0.051 29 4.6 S_calcarine 2921 1983 3212 1.776 0.537 0.114 0.030 21 3.7 S_central 1657 1132 2382 2.173 0.371 0.133 0.041 21 2.6 S_cingul-Marginalis 534 354 1020 2.924 0.571 0.153 0.075 12 1.7 S_circular_insula_ant 1312 867 2026 2.581 0.532 0.096 0.023 7 1.4 S_circular_insula_inf 1336 894 1874 2.331 0.359 0.121 0.037 11 2.0 S_circular_insula_sup 919 630 1693 2.460 0.637 0.122 0.039 14 1.5 S_collat_transv_ant 383 254 427 2.034 0.383 0.165 0.053 6 0.8 S_collat_transv_post 2913 1951 4417 2.183 0.409 0.146 0.052 50 6.1 S_front_inf 2234 1522 3382 2.212 0.418 0.149 0.054 38 4.5 S_front_middle 2846 1926 4073 2.315 0.363 0.127 0.034 31 4.1 S_front_sup 788 540 1043 2.005 0.347 0.148 0.050 13 1.4 S_interm_prim-Jensen 3093 2080 3917 1.937 0.374 0.138 0.043 43 5.4 S_intrapariet_and_P_trans 1523 1013 1883 2.059 0.335 0.125 0.039 12 2.3 S_oc_middle_and_Lunatus 1193 841 1684 2.056 0.319 0.135 0.038 14 1.7 S_oc_sup_and_transversal 685 471 1073 2.292 0.347 0.138 0.052 11 1.4 S_occipital_ant 1546 1043 2368 2.419 0.513 0.151 0.057 28 3.2 S_oc-temp_lat 1873 1364 2731 2.221 0.358 0.118 0.029 12 2.3 S_oc-temp_med_and_Lingual 401 274 508 2.046 0.345 0.150 0.050 4 0.8 S_orbital_lateral 919 638 1258 2.184 0.752 0.120 0.042 11 1.9 S_orbital_med-olfact 1815 1211 2967 2.491 0.612 0.155 0.055 31 4.3 S_orbital-H_Shaped 2346 1566 3005 2.034 0.432 0.140 0.041 30 4.0 S_parieto_occipital 1901 1209 1910 1.817 0.745 0.151 0.055 42 4.7 S_pericallosal 3876 2607 4872 1.958 0.367 0.121 0.037 52 5.6 S_postcentral 1783 1188 2413 2.228 0.438 0.123 0.033 16 2.4 S_precentral-inf-part 946 645 1377 2.247 0.392 0.117 0.031 7 1.2 S_precentral-sup-part 81 58 123 2.189 0.839 0.122 0.025 1 0.1 S_suborbital 1558 1044 2228 2.165 0.355 0.146 0.049 23 2.9 S_subparietal 1534 1041 2261 2.267 0.530 0.135 0.041 19 2.5 S_temporal_inf 6194 4189 9727 2.388 0.436 0.136 0.042 83 10.9 S_temporal_sup 331 232 537 2.860 0.399 0.133 0.030 2 0.5 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 rh Thu Aug 8 22:49:10 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub009 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... 825 labels changed using aseg relabeling using gibbs priors... 000: 2826 changed, 146248 examined... 001: 650 changed, 12116 examined... 002: 159 changed, 3587 examined... 003: 62 changed, 936 examined... 004: 33 changed, 363 examined... 005: 21 changed, 186 examined... 006: 6 changed, 121 examined... 007: 3 changed, 37 examined... 008: 1 changed, 15 examined... 009: 0 changed, 7 examined... 76 labels changed using aseg 000: 63 total segments, 30 labels (172 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 41 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1150 vertices marked for relabeling... 1150 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas40.annot... classification took 1 minutes and 8 seconds. #----------------------------------------- #@# Parcellation Stats 3 rh Thu Aug 8 22:50:20 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 sub009 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 950 671 1813 2.288 0.670 0.157 0.036 19 1.5 caudalanteriorcingulate 3735 2508 6447 2.342 0.421 0.145 0.047 61 7.1 caudalmiddlefrontal 2626 1704 3888 1.993 0.455 0.164 0.061 52 6.4 cuneus 415 298 1644 3.421 0.721 0.148 0.066 6 1.2 entorhinal 4508 3026 8443 2.571 0.499 0.146 0.052 119 9.4 fusiform 7565 5137 13257 2.268 0.452 0.157 0.062 166 18.0 inferiorparietal 5406 3666 10731 2.450 0.693 0.166 0.078 163 15.8 inferiortemporal 2098 1332 3464 2.315 0.766 0.170 0.078 63 7.1 isthmuscingulate 8368 5525 14115 2.229 0.477 0.163 0.077 199 19.5 lateraloccipital 5155 3374 9106 2.440 0.700 0.167 0.087 137 17.8 lateralorbitofrontal 4245 2885 6666 2.100 0.548 0.169 0.070 89 11.5 lingual 2414 1577 4299 2.323 0.680 0.164 0.107 98 8.6 medialorbitofrontal 6045 4082 12948 2.646 0.594 0.151 0.059 130 14.4 middletemporal 954 652 1671 2.236 0.511 0.116 0.032 7 1.3 parahippocampal 3339 2146 5629 2.385 0.513 0.140 0.046 46 6.1 paracentral 2224 1505 4129 2.423 0.408 0.137 0.046 33 4.3 parsopercularis 1364 891 2533 2.347 0.523 0.156 0.094 39 3.3 parsorbitalis 2582 1713 4433 2.297 0.430 0.162 0.074 59 5.9 parstriangularis 2052 1400 2449 1.747 0.360 0.159 0.069 34 5.6 pericalcarine 8420 5563 12323 1.979 0.534 0.139 0.045 131 15.2 postcentral 2421 1586 4152 2.351 0.674 0.168 0.067 57 5.8 posteriorcingulate 6758 4389 11965 2.429 0.491 0.133 0.091 265 27.3 precentral 6616 4367 10782 2.284 0.453 0.157 0.071 147 14.7 precuneus 1290 844 2494 2.795 0.665 0.144 0.052 24 2.6 rostralanteriorcingulate 6249 4222 10699 2.234 0.428 0.172 0.072 156 16.8 rostralmiddlefrontal 15254 10279 29586 2.549 0.505 0.157 0.059 304 35.9 superiorfrontal 8189 5484 12051 1.986 0.409 0.151 0.048 155 15.8 superiorparietal 7418 5006 16243 2.835 0.598 0.149 0.068 168 18.7 superiortemporal 6295 4283 10588 2.275 0.456 0.143 0.058 150 13.4 supramarginal 640 372 1132 2.599 0.365 0.139 0.066 14 1.6 transversetemporal 3278 2194 6657 2.929 0.747 0.135 0.061 54 7.2 insula #-------------------------------------------- #@# Refine Pial Surfs w/ T2/FLAIR Thu Aug 8 22:50:42 CEST 2013 bbregister --s sub009 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/T2raw.lta --init-fsl --T2 Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/T2raw.dat.log Thu Aug 8 22:50:42 CEST 2013 setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts /opt/freesurfer/5.3.0/bin/bbregister --s sub009 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/T2raw.lta --init-fsl --T2 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ Linux snake6 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/sub009/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/template.nii mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/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/sub009/mri/orig/T2raw.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.995894, -0.015333, -0.0892185) j_ras = (-0.0248655, 0.993977, 0.106735) k_ras = (-0.0870445, -0.108515, 0.990277) writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/template.nii... fslregister --s sub009 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/fslregister --dof 6 --fsvol brainmask.mgz Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/reg.init.dat.fslregister.log Thu Aug 8 22:50:50 CEST 2013 --s sub009 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/fslregister --dof 6 --fsvol brainmask.mgz $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ snake6 Linux snake6 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/sub009/scripts mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/fslregister/refvol.fslregister.nii mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/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/sub009/mri/brainmask.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.86265e-09, 0) j_ras = (-7.45058e-09, 0, -1) k_ras = (-4.65661e-09, 1, 7.45058e-09) writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/fslregister/refvol.fslregister.nii... -------------------------------------- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/fslregister/movvol.fslregister.nii --frame 0 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/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/sub009/mri/transforms/tmp.bbregister.21801/template.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.995894, -0.015333, -0.0892184) j_ras = (-0.0248655, 0.993977, 0.106735) k_ras = (-0.0870445, -0.108515, 0.990277) keeping frame 0 writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/fslregister/movvol.fslregister.nii... Mov determinant is -0.311086 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/fslregister/movvol.fslregister.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/fslregister/reg0.21844.dat --regheader --fslregout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/reg.init.dat.fsl.mat0 --s sub009 --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/sub009/mri/transforms/tmp.bbregister.21801/fslregister/movvol.fslregister.nii reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/fslregister/reg0.21844.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/sub009/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/sub009/mri/transforms/tmp.bbregister.21801/fslregister/movvol.fslregister.nii Tmov: -------------------- -0.700 0.000 0.000 95.892; 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) -------- 0.996 0.015 0.089 -0.000; -0.087 -0.109 0.990 -0.000; 0.025 -0.994 -0.107 -0.000; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 0.996 0.015 0.089 -0.000; -0.087 -0.109 0.990 -0.000; 0.025 -0.994 -0.107 -0.000; 0.000 0.000 0.000 1.000; Determinant 1 subject = sub009 RegMat --------------------------- 0.996 0.015 0.089 -0.000; -0.087 -0.109 0.990 -0.000; 0.025 -0.994 -0.107 -0.000; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -0.311086, ref det = -1 Thu Aug 8 22:50:59 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/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/sub009/mri/transforms/tmp.bbregister.21801/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/reg.init.dat.fsl.mat0 Thu Aug 8 22:55:23 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/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/sub009/mri/transforms/tmp.bbregister.21801/reg.init.dat.fsl.mat -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/fslregister/fslmat0.trans.mat -schedule /opt/freesurfer/5.3.0/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s sub009 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/reg.init.dat --fslreg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/reg.init.dat.fsl.mat --noedit tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl ---- FSL registration matrix -------- 0.995 0.024 0.101 16.537; 0.103 -0.096 -0.990 257.759; -0.015 0.995 -0.098 13.660; 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/sub009/mri/transforms/tmp.bbregister.21801/template.nii reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/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/sub009/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/sub009/mri/transforms/tmp.bbregister.21801/template.nii Tmov: -------------------- -0.700 0.000 0.000 95.892; 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 = -0.311086, ref det = -1 ---- Input registration matrix (computed) -------- 0.995 0.015 0.103 0.059; -0.101 -0.098 0.990 0.554; 0.024 -0.995 -0.096 -0.937; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 0.995 0.015 0.103 0.059; -0.101 -0.098 0.990 0.554; 0.024 -0.995 -0.096 -0.937; 0.000 0.000 0.000 1.000; Determinant 0.999999 subject = sub009 RegMat --------------------------- 0.995 0.015 0.103 0.059; -0.101 -0.098 0.990 0.554; 0.024 -0.995 -0.096 -0.937; 0.000 0.000 0.000 1.000; Started at Thu Aug 8 22:50:50 CEST 2013 Ended at Thu Aug 8 23:01:48 CEST 2013 fslregister Done To check results, run: tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/reg.init.dat --surf orig mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/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/sub009/scripts mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/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 snake6 machine x86_64 user fkaule movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/template.nii regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/reg.init.dat subject sub009 dof 6 outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/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 1376322642 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.995 0.015 0.103 0.059; -0.101 -0.098 0.990 0.554; 0.024 -0.995 -0.096 -0.937; 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 1.033315 1 -25.0 -25.0 25.0 1.003318 2 -25.0 25.0 -25.0 1.012121 3 -25.0 25.0 25.0 1.004161 4 25.0 -25.0 -25.0 0.997893 5 25.0 -25.0 25.0 1.036592 6 25.0 25.0 -25.0 0.998662 7 25.0 25.0 25.0 1.021020 REL: 8 0.438956 8.107082 1.013385 rel = 0.433158 Initial costs ---------------- Number of surface hits 2772 WM Intensity 58.3193 +/- 11.9758 Ctx Intensity 69.8534 +/- 15.2890 Pct Contrast 17.2580 +/- 24.0963 Cost 0.4390 RelCost 0.4332 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 1.0064 1.0064 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.9726 0.9726 0.0 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.9475 0.9475 0.0 19 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.0000 0.9111 0.9111 0.0 21 -4.0000 -4.0000 -4.0000 4.0000 0.0000 -4.0000 0.8812 0.8812 0.0 39 -4.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.8571 0.8571 0.0 118 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.0000 0.8418 0.8418 0.0 120 -4.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.7935 0.7935 0.0 301 0.0000 -4.0000 4.0000 -4.0000 0.0000 0.0000 0.7808 0.7808 0.0 346 0.0000 0.0000 -4.0000 4.0000 0.0000 0.0000 0.6768 0.6768 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.4390 0.4390 0.0 Brute Force -------------------------- Min cost was 0.438956 Number of iterations 729 Search time 2.153000 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 5 -0.618 0.000 0.000 0.000 0.000 0.000 0.4240294907 7 -0.440 0.000 0.000 0.000 0.000 0.000 0.4209544114 8 -0.437 0.000 0.000 0.000 0.000 0.000 0.4209177264 10 -0.401 0.000 0.000 0.000 0.000 0.000 0.4207867888 12 -0.388 0.000 0.000 0.000 0.000 0.000 0.4207430928 14 -0.371 0.000 0.000 0.000 0.000 0.000 0.4207299772 15 -0.375 0.000 0.000 0.000 0.000 0.000 0.4207209116 17 -0.374 0.000 0.000 0.000 0.000 0.000 0.4207208115 21 -0.374 -1.618 0.000 0.000 0.000 0.000 0.2981514008 22 -0.374 -1.514 0.000 0.000 0.000 0.000 0.2917458273 25 -0.374 -1.293 0.000 0.000 0.000 0.000 0.2877179964 26 -0.374 -1.291 0.000 0.000 0.000 0.000 0.2875827155 27 -0.374 -1.155 0.000 0.000 0.000 0.000 0.2853981573 28 -0.374 -1.194 0.000 0.000 0.000 0.000 0.2852815210 29 -0.374 -1.182 0.000 0.000 0.000 0.000 0.2852194566 31 -0.374 -1.183 0.000 0.000 0.000 0.000 0.2852184333 32 -0.374 -1.184 0.000 0.000 0.000 0.000 0.2852181365 35 -0.374 -1.184 1.000 0.000 0.000 0.000 0.1932573450 43 -0.374 -1.184 1.090 0.000 0.000 0.000 0.1913017908 46 -0.374 -1.184 1.084 0.000 0.000 0.000 0.1912798821 55 -0.374 -1.184 1.084 0.133 0.000 0.000 0.1841702737 56 -0.374 -1.184 1.084 0.151 0.000 0.000 0.1839889615 58 -0.374 -1.184 1.084 0.148 0.000 0.000 0.1839844981 59 -0.374 -1.184 1.084 0.149 0.000 0.000 0.1839841188 66 -0.374 -1.184 1.084 0.149 -0.051 0.000 0.1830259769 68 -0.374 -1.184 1.084 0.149 -0.054 0.000 0.1830052049 70 -0.374 -1.184 1.084 0.149 -0.058 0.000 0.1829965795 78 -0.374 -1.184 1.084 0.149 -0.058 0.382 0.1630476874 79 -0.374 -1.184 1.084 0.149 -0.058 0.369 0.1628444379 81 -0.374 -1.184 1.084 0.149 -0.058 0.355 0.1628186469 82 -0.374 -1.184 1.084 0.149 -0.058 0.359 0.1627995908 83 -0.374 -1.184 1.084 0.149 -0.058 0.361 0.1627976520 92 -0.210 -1.184 1.084 0.149 -0.058 0.361 0.1584671673 94 -0.219 -1.184 1.084 0.149 -0.058 0.361 0.1584428926 96 -0.231 -1.184 1.084 0.149 -0.058 0.361 0.1584313808 97 -0.230 -1.184 1.084 0.149 -0.058 0.361 0.1584308908 106 -0.230 -1.141 1.084 0.149 -0.058 0.361 0.1579965593 119 -0.230 -1.141 0.875 0.149 -0.058 0.361 0.1536496762 122 -0.230 -1.141 0.834 0.149 -0.058 0.361 0.1531940783 123 -0.230 -1.141 0.836 0.149 -0.058 0.361 0.1531877192 124 -0.230 -1.141 0.840 0.149 -0.058 0.361 0.1531710905 127 -0.230 -1.141 0.842 0.149 -0.058 0.361 0.1531677108 128 -0.230 -1.141 0.843 0.149 -0.058 0.361 0.1531676964 135 -0.230 -1.141 0.843 0.531 -0.058 0.361 0.1473128666 136 -0.230 -1.141 0.843 0.380 -0.058 0.361 0.1403563629 139 -0.230 -1.141 0.843 0.378 -0.058 0.361 0.1403523950 141 -0.230 -1.141 0.843 0.377 -0.058 0.361 0.1403518831 149 -0.230 -1.141 0.843 0.377 -0.051 0.361 0.1403306435 153 -0.230 -1.141 0.843 0.377 -0.052 0.361 0.1403305798 160 -0.230 -1.141 0.843 0.377 -0.052 0.431 0.1400911137 161 -0.230 -1.141 0.843 0.377 -0.052 0.407 0.1399985170 162 -0.230 -1.141 0.843 0.377 -0.052 0.406 0.1399968466 164 -0.230 -1.141 0.843 0.377 -0.052 0.403 0.1399957568 165 -0.230 -1.141 0.843 0.377 -0.052 0.404 0.1399953869 167 -0.085 -1.098 0.602 0.606 -0.045 0.448 0.1343285674 173 -0.140 -1.115 0.694 0.519 -0.048 0.431 0.1339098551 174 -0.124 -1.110 0.666 0.545 -0.047 0.436 0.1333603664 175 -0.116 -1.108 0.654 0.557 -0.047 0.438 0.1333080120 176 -0.117 -1.108 0.654 0.556 -0.047 0.438 0.1333075260 177 -0.117 -1.108 0.655 0.555 -0.047 0.438 0.1333070076 178 -0.117 -1.108 0.655 0.555 -0.047 0.438 0.1333068951 186 -0.147 -1.108 0.655 0.555 -0.047 0.438 0.1322486410 188 -0.201 -1.108 0.655 0.555 -0.047 0.438 0.1313617889 190 -0.205 -1.108 0.655 0.555 -0.047 0.438 0.1313573967 199 -0.205 -1.041 0.655 0.555 -0.047 0.438 0.1304728631 201 -0.205 -1.056 0.655 0.555 -0.047 0.438 0.1303537402 203 -0.205 -1.062 0.655 0.555 -0.047 0.438 0.1303375048 204 -0.205 -1.063 0.655 0.555 -0.047 0.438 0.1303345283 205 -0.205 -1.068 0.655 0.555 -0.047 0.438 0.1303331739 206 -0.205 -1.066 0.655 0.555 -0.047 0.438 0.1303305412 215 -0.205 -1.066 0.497 0.555 -0.047 0.438 0.1273900231 216 -0.205 -1.066 0.504 0.555 -0.047 0.438 0.1273858699 221 -0.205 -1.066 0.508 0.555 -0.047 0.438 0.1273838560 222 -0.205 -1.066 0.507 0.555 -0.047 0.438 0.1273838362 230 -0.205 -1.066 0.507 0.555 -0.047 0.473 0.1265646605 232 -0.205 -1.066 0.507 0.555 -0.047 0.486 0.1264997243 233 -0.205 -1.066 0.507 0.555 -0.047 0.485 0.1264982170 241 -0.205 -1.066 0.507 0.555 -0.086 0.485 0.1258425191 245 -0.205 -1.066 0.507 0.555 -0.082 0.485 0.1258343048 253 -0.150 -1.050 0.414 0.643 -0.079 0.502 0.1257550182 254 -0.176 -1.057 0.459 0.601 -0.080 0.494 0.1251218396 256 -0.173 -1.057 0.454 0.605 -0.080 0.495 0.1251110666 258 -0.173 -1.056 0.453 0.606 -0.080 0.495 0.1251104986 260 -0.173 -1.056 0.453 0.606 -0.080 0.495 0.1251104486 272 -0.180 -1.056 0.453 0.606 -0.080 0.495 0.1250839290 274 -0.179 -1.056 0.453 0.606 -0.080 0.495 0.1250831880 285 -0.179 -1.035 0.453 0.606 -0.080 0.495 0.1249916686 286 -0.179 -1.038 0.453 0.606 -0.080 0.495 0.1249898323 287 -0.179 -1.037 0.453 0.606 -0.080 0.495 0.1249891314 296 -0.179 -1.037 0.451 0.606 -0.080 0.495 0.1249798103 297 -0.179 -1.037 0.445 0.606 -0.080 0.495 0.1249734194 299 -0.179 -1.037 0.443 0.606 -0.080 0.495 0.1249723968 300 -0.179 -1.037 0.442 0.606 -0.080 0.495 0.1249707811 301 -0.179 -1.037 0.440 0.606 -0.080 0.495 0.1249696578 303 -0.179 -1.037 0.441 0.606 -0.080 0.495 0.1249696544 310 -0.179 -1.037 0.441 0.606 -0.080 0.502 0.1249610311 312 -0.179 -1.037 0.441 0.606 -0.080 0.499 0.1249563349 321 -0.179 -1.037 0.441 0.606 -0.102 0.499 0.1247580194 323 -0.179 -1.037 0.441 0.606 -0.101 0.499 0.1247561821 324 -0.179 -1.037 0.441 0.606 -0.100 0.499 0.1247561150 332 -0.176 -1.036 0.436 0.610 -0.100 0.500 0.1247265205 334 -0.174 -1.036 0.433 0.613 -0.100 0.500 0.1247207955 335 -0.174 -1.036 0.433 0.613 -0.100 0.501 0.1247206597 350 -0.171 -1.036 0.433 0.613 -0.100 0.501 0.1247089616 363 -0.171 -1.037 0.433 0.613 -0.100 0.501 0.1247087942 373 -0.171 -1.037 0.438 0.613 -0.100 0.501 0.1247017144 374 -0.171 -1.037 0.437 0.613 -0.100 0.501 0.1247012166 394 -0.171 -1.037 0.437 0.613 -0.103 0.501 0.1246933981 408 -0.171 -1.037 0.437 0.613 -0.103 0.500 0.1246930870 421 -0.169 -1.037 0.437 0.613 -0.103 0.500 0.1246919227 423 -0.170 -1.037 0.437 0.613 -0.103 0.500 0.1246918112 434 -0.170 -1.035 0.437 0.613 -0.103 0.500 0.1246912973 444 -0.170 -1.035 0.438 0.613 -0.103 0.500 0.1246909621 464 -0.170 -1.035 0.438 0.613 -0.104 0.500 0.1246907325 Powell done niters = 5 Computing relative cost 0 -25.0 -25.0 -25.0 1.033704 1 -25.0 -25.0 25.0 0.994621 2 -25.0 25.0 -25.0 1.003955 3 -25.0 25.0 25.0 0.989554 4 25.0 -25.0 -25.0 1.024186 5 25.0 -25.0 25.0 1.047537 6 25.0 25.0 -25.0 1.035593 7 25.0 25.0 25.0 1.032315 REL: 8 0.124691 8.161465 1.020183 rel = 0.122224 Number of iterations 5 Min cost was 0.124691 Number of FunctionCalls 476 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 1.377000 sec Parameters at optimum (transmm) -0.16965 -1.03536 0.43834 Parameters at optimum (rotdeg) 0.61290 -0.10434 0.50048 Final costs ---------------- Number of surface hits 2772 WM Intensity 56.7404 +/- 11.0330 Ctx Intensity 69.2588 +/- 10.1336 Pct Contrast 20.2576 +/- 13.5904 Cost 0.1247 RelCost 0.4332 Reg at min cost was 0.995 0.017 0.094 -0.114; -0.093 -0.087 0.992 -0.471; 0.025 -0.996 -0.085 -0.493; 0.000 0.000 0.000 1.000; Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/bbr.pass1.dat, type = 14 Original Reg 0.995 0.015 0.103 0.059; -0.101 -0.098 0.990 0.554; 0.024 -0.995 -0.096 -0.937; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.001 -0.003 0.009 0.173; -0.008 -0.011 -0.002 1.025; -0.001 0.001 -0.011 -0.444; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 1.782706 Computing change in rh position Surface RMS Diff (mm) 1.619904 2.444892 mri_segreg done mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/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/sub009/scripts mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname snake6 machine x86_64 user fkaule movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/template.nii regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/bbr.pass1.dat subject sub009 dof 6 outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 1376026366 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.995 0.017 0.094 -0.114; -0.093 -0.087 0.992 -0.471; 0.025 -0.996 -0.085 -0.493; 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 1.016423 1 -25.0 -25.0 25.0 0.997811 2 -25.0 25.0 -25.0 0.994115 3 -25.0 25.0 25.0 0.997896 4 25.0 -25.0 -25.0 1.006045 5 25.0 -25.0 25.0 1.023716 6 25.0 25.0 -25.0 1.014273 7 25.0 25.0 25.0 1.015183 REL: 8 0.134087 8.065463 1.008183 rel = 0.132999 Initial costs ---------------- Number of surface hits 277390 WM Intensity 56.8589 +/- 10.5831 Ctx Intensity 69.3526 +/- 10.1667 Pct Contrast 20.1370 +/- 13.7599 Cost 0.1341 RelCost 0.1330 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1445 0.1445 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1394 0.1394 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.1363 0.1363 0.0 13 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.1325 0.1325 0.0 31 -0.1000 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.1323 0.1323 0.0 40 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.0000 0.1308 0.1308 0.0 58 -0.1000 -0.1000 0.1000 -0.1000 0.0000 0.0000 0.1300 0.1300 0.0 94 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.0000 0.1291 0.1291 0.0 120 -0.1000 0.0000 0.0000 0.0000 0.0000 -0.1000 0.1272 0.1272 0.0 121 -0.1000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1264 0.1264 0.0 184 -0.1000 0.1000 -0.1000 0.1000 0.0000 0.0000 0.1259 0.1259 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1247 0.1247 0.0 Brute Force -------------------------- Min cost was 0.124691 Number of iterations 729 Search time 2.098000 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 0.145 0.000 0.000 0.000 0.000 0.000 0.1316677242 9 0.152 0.000 0.000 0.000 0.000 0.000 0.1316635766 11 0.150 0.000 0.000 0.000 0.000 0.000 0.1316633193 19 0.150 0.055 0.000 0.000 0.000 0.000 0.1313455337 21 0.150 0.053 0.000 0.000 0.000 0.000 0.1313449322 29 0.150 0.053 -0.028 0.000 0.000 0.000 0.1312292684 32 0.150 0.053 -0.029 0.000 0.000 0.000 0.1312291729 39 0.150 0.053 -0.029 0.010 0.000 0.000 0.1311202670 40 0.150 0.053 -0.029 0.028 0.000 0.000 0.1310242261 41 0.150 0.053 -0.029 0.031 0.000 0.000 0.1310228484 42 0.150 0.053 -0.029 0.030 0.000 0.000 0.1310225481 50 0.150 0.053 -0.029 0.030 -0.014 0.000 0.1309972377 59 0.150 0.053 -0.029 0.030 -0.014 0.041 0.1308405624 60 0.150 0.053 -0.029 0.030 -0.014 0.035 0.1308394115 61 0.150 0.053 -0.029 0.030 -0.014 0.037 0.1308388734 70 0.208 0.074 -0.041 0.042 -0.019 0.051 0.1305962841 71 0.202 0.072 -0.039 0.041 -0.018 0.050 0.1305877315 73 0.201 0.071 -0.039 0.040 -0.018 0.049 0.1305873916 74 0.201 0.071 -0.039 0.040 -0.018 0.049 0.1305873201 76 0.201 0.071 -0.039 0.040 -0.018 0.049 0.1305873163 84 0.201 0.071 -0.039 0.040 -0.018 0.060 0.1305733172 85 0.201 0.071 -0.039 0.040 -0.018 0.059 0.1305730463 86 0.201 0.071 -0.039 0.040 -0.018 0.058 0.1305729202 96 0.201 0.070 -0.039 0.040 -0.018 0.058 0.1305728490 104 0.201 0.070 -0.064 0.040 -0.018 0.058 0.1304761187 106 0.201 0.070 -0.065 0.040 -0.018 0.058 0.1304759000 115 0.201 0.070 -0.065 0.049 -0.018 0.058 0.1304516466 116 0.201 0.070 -0.065 0.052 -0.018 0.058 0.1304494602 126 0.201 0.070 -0.065 0.052 -0.016 0.058 0.1304490328 136 0.205 0.072 -0.066 0.053 -0.016 0.059 0.1304467687 139 0.205 0.072 -0.066 0.053 -0.016 0.059 0.1304467412 149 0.205 0.072 -0.066 0.053 -0.016 0.064 0.1304450677 150 0.205 0.072 -0.066 0.053 -0.016 0.063 0.1304449994 151 0.205 0.072 -0.066 0.053 -0.016 0.062 0.1304449540 160 0.205 0.077 -0.066 0.053 -0.016 0.062 0.1304409792 162 0.205 0.078 -0.066 0.053 -0.016 0.062 0.1304405442 163 0.205 0.082 -0.066 0.053 -0.016 0.062 0.1304401267 165 0.205 0.081 -0.066 0.053 -0.016 0.062 0.1304398427 173 0.205 0.081 -0.075 0.053 -0.016 0.062 0.1304264829 174 0.205 0.081 -0.077 0.053 -0.016 0.062 0.1304255022 175 0.205 0.081 -0.078 0.053 -0.016 0.062 0.1304250495 186 0.205 0.081 -0.078 0.060 -0.016 0.062 0.1304060388 187 0.205 0.081 -0.078 0.063 -0.016 0.062 0.1304034358 206 0.205 0.081 -0.078 0.063 -0.016 0.063 0.1304033850 207 0.206 0.081 -0.078 0.063 -0.016 0.063 0.1304032411 211 0.207 0.081 -0.078 0.064 -0.016 0.063 0.1304032101 213 0.208 0.082 -0.079 0.064 -0.017 0.063 0.1304031668 217 0.211 0.091 -0.091 0.075 -0.017 0.067 0.1303761680 222 0.212 0.098 -0.099 0.082 -0.017 0.070 0.1303711430 224 0.212 0.097 -0.098 0.080 -0.017 0.069 0.1303711384 225 0.212 0.097 -0.098 0.081 -0.017 0.069 0.1303711251 227 0.212 0.097 -0.098 0.081 -0.017 0.069 0.1303710919 241 0.212 0.097 -0.098 0.081 -0.017 0.074 0.1303698309 251 0.212 0.095 -0.098 0.081 -0.017 0.073 0.1303694306 253 0.212 0.096 -0.098 0.081 -0.017 0.073 0.1303692453 260 0.212 0.096 -0.101 0.081 -0.017 0.073 0.1303668534 261 0.212 0.096 -0.104 0.081 -0.017 0.073 0.1303647895 264 0.212 0.096 -0.105 0.081 -0.017 0.073 0.1303644396 273 0.206 0.094 -0.104 0.080 -0.016 0.071 0.1303617292 275 0.206 0.093 -0.104 0.080 -0.016 0.071 0.1303617012 280 0.205 0.093 -0.103 0.080 -0.016 0.071 0.1303616720 288 0.205 0.093 -0.103 0.080 -0.023 0.071 0.1303598366 289 0.205 0.093 -0.103 0.080 -0.021 0.071 0.1303594426 290 0.205 0.093 -0.103 0.080 -0.022 0.071 0.1303594143 297 0.206 0.095 -0.106 0.082 -0.022 0.072 0.1303587789 298 0.206 0.095 -0.106 0.082 -0.022 0.072 0.1303587783 299 0.206 0.095 -0.106 0.082 -0.022 0.072 0.1303587650 319 0.206 0.097 -0.106 0.082 -0.022 0.072 0.1303587302 338 0.205 0.096 -0.106 0.082 -0.022 0.072 0.1303586955 405 0.205 0.096 -0.105 0.082 -0.022 0.071 0.1303586909 Powell done niters = 5 Computing relative cost 0 -25.0 -25.0 -25.0 1.016213 1 -25.0 -25.0 25.0 0.998353 2 -25.0 25.0 -25.0 0.994860 3 -25.0 25.0 25.0 0.997565 4 25.0 -25.0 -25.0 1.004759 5 25.0 -25.0 25.0 1.023781 6 25.0 25.0 -25.0 1.011973 7 25.0 25.0 25.0 1.014206 REL: 8 0.130359 8.061709 1.007714 rel = 0.129361 Number of iterations 5 Min cost was 0.130359 Number of FunctionCalls 429 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 62.251000 sec Parameters at optimum (transmm) 0.20508 0.09636 -0.10549 Parameters at optimum (rotdeg) 0.08156 -0.02152 0.07146 Final costs ---------------- Number of surface hits 277390 WM Intensity 56.8648 +/- 10.6213 Ctx Intensity 69.3155 +/- 10.1226 Pct Contrast 20.0837 +/- 13.7341 Cost 0.1304 RelCost 0.1330 Reg at min cost was 0.995 0.018 0.093 0.092; -0.091 -0.086 0.992 -0.374; 0.025 -0.996 -0.084 -0.599; 0.000 0.000 0.000 1.000; Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/T2raw.dat, type = 14 Original Reg 0.995 0.017 0.094 -0.114; -0.093 -0.087 0.992 -0.471; 0.025 -0.996 -0.085 -0.493; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.000 -0.000 0.001 -0.206; -0.001 -0.001 -0.000 -0.097; -0.000 0.000 -0.001 0.106; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.177186 Computing change in rh position Surface RMS Diff (mm) 0.189640 0.307027 mri_segreg done tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/T2raw.dat --noedit --ltaout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/mri/orig/T2raw.mgz reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 -------- 0.995 0.018 0.093 0.092; -0.091 -0.086 0.992 -0.374; 0.025 -0.996 -0.084 -0.599; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- INFO: loading target /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/mri/orig/T2raw.mgz Tmov: -------------------- -0.700 0.000 0.000 95.892; 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 -------- 0.995 0.018 0.093 0.092; -0.091 -0.086 0.992 -0.374; 0.025 -0.996 -0.084 -0.599; 0.000 0.000 0.000 1.000; Determinant 0.999999 subject = sub009 RegMat --------------------------- 0.995 0.018 0.093 0.092; -0.091 -0.086 0.992 -0.374; 0.025 -0.996 -0.084 -0.599; 0.000 0.000 0.000 1.000; transformed matrix: 1.000 -0.000 -0.004 -0.159; 0.000 1.000 0.023 -0.357; 0.004 -0.023 1.000 1.003; 0.000 0.000 0.000 1.000; transformed matrix: 0.697 0.017 0.061 17.690; 0.065 -0.056 -0.661 256.433; -0.012 0.664 -0.057 12.498; 0.000 0.000 0.000 1.000; Cleaning up Started at Thu Aug 8 22:50:42 CEST 2013 Ended at Thu Aug 8 23:03:44 CEST 2013 BBR-Run-Time-Sec 782 bbregister Done To check results, run: tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/T2raw.dat --surf mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/T2.mgz mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/mri/orig/T2raw.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.995894, -0.015333, -0.0892185) j_ras = (-0.0248655, 0.993977, 0.106735) k_ras = (-0.0870445, -0.108515, 0.990277) INFO: Reading transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/T2raw.lta... Reading transform with LTAreadEx() reading extra input line subject sub009 reading extra input line fscale 0.150000 reading template info from volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/orig.mgz... INFO: Applying transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/T2raw.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 1.000 -0.000 -0.004 -0.159; 0.000 1.000 0.023 -0.357; 0.004 -0.023 1.000 1.003; 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/sub009/mri/T2.mgz... mri_normalize -aseg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/aseg.mgz -sigma 4 -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.white identity.nofile -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.white identity.nofile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/T2.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/mri/T2.mgz... computing distance transform computing distance transform computing nonmaximum suppression 13976 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/sub009/mri/T2.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.woT2.pial `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.woT2.pial' mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub009 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/sub009/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/wm.mgz... 18938 bright wm thresholded. 815 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.orig... computing class statistics... border white: 259466 voxels (1.55%) border gray 303507 voxels (1.81%) WM (91.0): 92.8 +- 10.6 [70.0 --> 110.0] GM (74.0) : 72.4 +- 12.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 46.1 (was 70) setting MAX_BORDER_WHITE to 115.6 (was 105) setting MIN_BORDER_WHITE to 59.0 (was 85) setting MAX_CSF to 33.3 (was 40) setting MAX_GRAY to 94.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 52.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 20.4 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=59 mean inside = 92.6, mean outside = 67.5 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/sub009/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.89 +- 0.26 (0.02-->5.47) (max @ vno 69994 --> 72328) face area 0.33 +- 0.16 (0.00-->4.03) averaging target values for 5 iterations... 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 2 with 2 points - only 0.00% unknown deleting segment 3 with 11 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 4 with 1 points - only 0.00% unknown deleting segment 5 with 6 points - only 0.00% unknown deleting segment 6 with 654 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown deleting segment 9 with 19 points - only 0.00% unknown deleting segment 10 with 19 points - only 0.00% unknown deleting segment 11 with 6 points - only 0.00% unknown deleting segment 12 with 18 points - only 0.00% unknown deleting segment 13 with 14 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 14 with 1 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 15 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 16 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 17 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 18 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 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.89 +- 0.25 (0.02-->5.47) (max @ vno 72328 --> 69994) face area 0.33 +- 0.16 (0.00-->4.03) averaging target values for 5 iterations... 000: dt: 0.0000, sse=5036635.5, rms=0.00 rms = 1.17, time step reduction 1 of 3 to 0.250... rms = 0.30, 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=5036635.5, rms=0.000 (1.000%) positioning took 0.4 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 deleting segment 2 with 11 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 1 points - only 0.00% unknown deleting segment 4 with 6 points - only 0.00% unknown deleting segment 5 with 654 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown deleting segment 8 with 19 points - only 0.00% unknown deleting segment 9 with 19 points - only 0.00% unknown deleting segment 10 with 6 points - only 0.00% unknown deleting segment 11 with 18 points - only 0.00% unknown deleting segment 12 with 14 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 13 with 1 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 14 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 15 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 16 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 17 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 0.89 +- 0.25 (0.02-->5.47) (max @ vno 72328 --> 69994) face area 0.33 +- 0.16 (0.00-->4.03) averaging target values for 5 iterations... 000: dt: 0.0000, sse=5036635.5, rms=0.00 rms = 1.17, time step reduction 1 of 3 to 0.250... rms = 0.30, 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=5036635.5, 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 removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown deleting segment 2 with 11 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 1 points - only 0.00% unknown deleting segment 4 with 6 points - only 0.00% unknown deleting segment 5 with 654 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown deleting segment 8 with 19 points - only 0.00% unknown deleting segment 9 with 19 points - only 0.00% unknown deleting segment 10 with 6 points - only 0.00% unknown deleting segment 11 with 18 points - only 0.00% unknown deleting segment 12 with 14 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 13 with 1 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 14 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 15 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 16 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 17 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 0.89 +- 0.25 (0.02-->5.47) (max @ vno 72328 --> 69994) face area 0.33 +- 0.16 (0.00-->4.03) averaging target values for 5 iterations... 000: dt: 0.0000, sse=5036635.5, rms=0.00 rms = 1.17, time step reduction 1 of 3 to 0.250... rms = 0.30, 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=5036635.5, 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 removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown deleting segment 2 with 11 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 1 points - only 0.00% unknown deleting segment 4 with 6 points - only 0.00% unknown deleting segment 5 with 654 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown deleting segment 8 with 19 points - only 0.00% unknown deleting segment 9 with 19 points - only 0.00% unknown deleting segment 10 with 6 points - only 0.00% unknown deleting segment 11 with 18 points - only 0.00% unknown deleting segment 12 with 14 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 13 with 1 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 14 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 15 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 16 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 17 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=5036635.5, rms=0.00 rms = 1.17, time step reduction 1 of 3 to 0.250... rms = 0.30, 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=5036635.5, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 1 with 1 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown 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 [93.50 210.50], gm=152.00+-19.50, and vertices in regions > 142.2 49201 surface locations found to contain inconsistent values (3727 in, 45474 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=545821.2, rms=0.24 001: dt: 0.5000, sse=512763.5, rms=0.235 (0.000%) 002: dt: 0.5000, sse=492109.2, rms=0.221 (0.000%) 003: dt: 0.5000, sse=478890.5, rms=0.210 (0.000%) 004: dt: 0.5000, sse=468479.1, rms=0.201 (0.000%) 005: dt: 0.5000, sse=460928.7, rms=0.192 (0.000%) 006: dt: 0.5000, sse=454852.8, rms=0.185 (0.000%) 007: dt: 0.5000, sse=450161.5, rms=0.179 (0.000%) 008: dt: 0.5000, sse=446411.6, rms=0.174 (0.000%) 009: dt: 0.5000, sse=443463.4, rms=0.170 (0.000%) 010: dt: 0.5000, sse=440539.3, rms=0.166 (0.000%) 011: dt: 0.5000, sse=438160.5, rms=0.162 (0.000%) 012: dt: 0.5000, sse=435969.0, rms=0.160 (0.000%) 013: dt: 0.5000, sse=433968.7, rms=0.157 (0.000%) 014: dt: 0.5000, sse=431918.1, rms=0.156 (0.000%) 015: dt: 0.5000, sse=430199.5, rms=0.154 (0.000%) 016: dt: 0.5000, sse=428447.1, rms=0.153 (0.000%) 017: dt: 0.5000, sse=426984.7, rms=0.152 (0.000%) 018: dt: 0.5000, sse=425236.5, rms=0.151 (0.000%) 019: dt: 0.5000, sse=423691.1, rms=0.150 (0.000%) 020: dt: 0.5000, sse=422392.0, rms=0.150 (0.000%) 021: dt: 0.5000, sse=421291.2, rms=0.149 (0.000%) 022: dt: 0.5000, sse=419910.5, rms=0.149 (0.000%) 023: dt: 0.5000, sse=418554.5, rms=0.149 (0.000%) 024: dt: 0.5000, sse=417560.7, rms=0.149 (0.000%) 025: dt: 0.5000, sse=416196.1, rms=0.149 (0.000%) 026: dt: 0.5000, sse=415011.2, rms=0.149 (0.000%) 027: dt: 0.5000, sse=413737.7, rms=0.149 (0.000%) 028: dt: 0.5000, sse=412626.5, rms=0.149 (0.000%) 029: dt: 0.5000, sse=411409.8, rms=0.150 (0.000%) 030: dt: 0.5000, sse=410304.5, rms=0.150 (0.000%) positioning took 3.9 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [93.00 213.00], gm=153.00+-20.00, and vertices in regions > 143.0 41790 surface locations found to contain inconsistent values (1450 in, 40340 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=42761.6, rms=0.13 031: dt: 0.5000, sse=42489.0, rms=0.124 (0.000%) 032: dt: 0.5000, sse=43547.5, rms=0.112 (0.000%) 033: dt: 0.5000, sse=44796.3, rms=0.104 (0.000%) 034: dt: 0.5000, sse=45835.6, rms=0.099 (0.000%) 035: dt: 0.5000, sse=46688.0, rms=0.094 (0.000%) 036: dt: 0.5000, sse=47513.7, rms=0.089 (0.000%) 037: dt: 0.5000, sse=48284.1, rms=0.085 (0.000%) 038: dt: 0.5000, sse=49045.8, rms=0.081 (0.000%) 039: dt: 0.5000, sse=49766.2, rms=0.077 (0.000%) 040: dt: 0.5000, sse=50454.8, rms=0.074 (0.000%) 041: dt: 0.5000, sse=51093.2, rms=0.071 (0.000%) 042: dt: 0.5000, sse=51700.8, rms=0.068 (0.000%) 043: dt: 0.5000, sse=52256.1, rms=0.066 (0.000%) 044: dt: 0.5000, sse=52807.4, rms=0.063 (0.000%) 045: dt: 0.5000, sse=53337.2, rms=0.061 (0.000%) 046: dt: 0.5000, sse=53795.3, rms=0.059 (0.000%) 047: dt: 0.5000, sse=54250.1, rms=0.057 (0.000%) 048: dt: 0.5000, sse=54667.7, rms=0.056 (0.000%) 049: dt: 0.5000, sse=55090.1, rms=0.054 (0.000%) 050: dt: 0.5000, sse=55411.9, rms=0.053 (0.000%) 051: dt: 0.5000, sse=55740.8, rms=0.051 (0.000%) 052: dt: 0.5000, sse=56052.9, rms=0.050 (0.000%) 053: dt: 0.5000, sse=56331.7, rms=0.049 (0.000%) 054: dt: 0.5000, sse=56591.1, rms=0.048 (0.000%) 055: dt: 0.5000, sse=56808.3, rms=0.047 (0.000%) 056: dt: 0.5000, sse=57023.4, rms=0.046 (0.000%) 057: dt: 0.5000, sse=57233.9, rms=0.045 (0.000%) 058: dt: 0.5000, sse=57386.6, rms=0.045 (0.000%) 059: dt: 0.5000, sse=57561.9, rms=0.044 (0.000%) 060: dt: 0.5000, sse=57688.0, rms=0.043 (0.000%) positioning took 3.9 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [91.50 214.50], gm=153.00+-20.50, and vertices in regions > 142.7 40779 surface locations found to contain inconsistent values (255 in, 40524 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=6171.3, rms=0.05 061: dt: 0.5000, sse=6159.9, rms=0.053 (0.000%) 062: dt: 0.5000, sse=6243.5, rms=0.047 (0.000%) 063: dt: 0.5000, sse=6319.6, rms=0.043 (0.000%) 064: dt: 0.5000, sse=6379.4, rms=0.041 (0.000%) 065: dt: 0.5000, sse=6416.9, rms=0.039 (0.000%) 066: dt: 0.5000, sse=6437.3, rms=0.038 (0.000%) 067: dt: 0.5000, sse=6448.1, rms=0.037 (0.000%) 068: dt: 0.5000, sse=6457.0, rms=0.036 (0.000%) 069: dt: 0.5000, sse=6463.1, rms=0.035 (0.000%) 070: dt: 0.5000, sse=6472.0, rms=0.033 (0.000%) 071: dt: 0.5000, sse=6479.8, rms=0.033 (0.000%) 072: dt: 0.5000, sse=6487.4, rms=0.032 (0.000%) 073: dt: 0.5000, sse=6494.8, rms=0.031 (0.000%) 074: dt: 0.5000, sse=6500.6, rms=0.030 (0.000%) 075: dt: 0.5000, sse=6508.4, rms=0.030 (0.000%) 076: dt: 0.5000, sse=6513.4, rms=0.029 (0.000%) 077: dt: 0.5000, sse=6519.9, rms=0.029 (0.000%) 078: dt: 0.5000, sse=6527.2, rms=0.028 (0.000%) 079: dt: 0.5000, sse=6530.8, rms=0.028 (0.000%) 080: dt: 0.5000, sse=6534.9, rms=0.028 (0.000%) 081: dt: 0.5000, sse=6538.8, rms=0.027 (0.000%) 082: dt: 0.5000, sse=6543.6, rms=0.027 (0.000%) 083: dt: 0.5000, sse=6547.2, rms=0.027 (0.000%) 084: dt: 0.5000, sse=6550.2, rms=0.027 (0.000%) 085: dt: 0.5000, sse=6552.5, rms=0.026 (0.000%) 086: dt: 0.5000, sse=6555.2, rms=0.026 (0.000%) 087: dt: 0.5000, sse=6558.0, rms=0.026 (0.000%) 088: dt: 0.5000, sse=6560.3, rms=0.026 (0.000%) 089: dt: 0.5000, sse=6564.6, rms=0.026 (0.000%) 090: dt: 0.5000, sse=6565.5, rms=0.026 (0.000%) positioning took 3.8 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [91.50 214.50], gm=153.00+-20.50, and vertices in regions > 142.7 40410 surface locations found to contain inconsistent values (65 in, 40345 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/sub009/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=780.8, rms=0.03 091: dt: 0.5000, sse=781.5, rms=0.031 (0.000%) 092: dt: 0.5000, sse=771.2, rms=0.029 (0.000%) 093: dt: 0.5000, sse=764.6, rms=0.029 (0.000%) 094: dt: 0.5000, sse=758.2, rms=0.028 (0.000%) 095: dt: 0.5000, sse=752.9, rms=0.027 (0.000%) 096: dt: 0.5000, sse=748.3, rms=0.026 (0.000%) 097: dt: 0.5000, sse=745.5, rms=0.026 (0.000%) 098: dt: 0.5000, sse=743.0, rms=0.026 (0.000%) 099: dt: 0.5000, sse=740.3, rms=0.025 (0.000%) 100: dt: 0.5000, sse=737.5, rms=0.025 (0.000%) 101: dt: 0.5000, sse=736.0, rms=0.025 (0.000%) 102: dt: 0.5000, sse=733.7, rms=0.024 (0.000%) 103: dt: 0.5000, sse=732.3, rms=0.024 (0.000%) 104: dt: 0.5000, sse=729.8, rms=0.024 (0.000%) 105: dt: 0.5000, sse=728.5, rms=0.024 (0.000%) 106: dt: 0.5000, sse=726.5, rms=0.023 (0.000%) 107: dt: 0.5000, sse=724.8, rms=0.023 (0.000%) 108: dt: 0.5000, sse=723.3, rms=0.023 (0.000%) 109: dt: 0.5000, sse=723.5, rms=0.023 (0.000%) 110: dt: 0.5000, sse=721.8, rms=0.022 (0.000%) 111: dt: 0.5000, sse=720.9, rms=0.022 (0.000%) 112: dt: 0.5000, sse=721.7, rms=0.022 (0.000%) 113: dt: 0.5000, sse=720.4, rms=0.022 (0.000%) 114: dt: 0.5000, sse=719.6, rms=0.022 (0.000%) 115: dt: 0.5000, sse=719.1, rms=0.022 (0.000%) 116: dt: 0.5000, sse=718.0, rms=0.022 (0.000%) 117: dt: 0.5000, sse=717.3, rms=0.022 (0.000%) 118: dt: 0.5000, sse=717.8, rms=0.022 (0.000%) 119: dt: 0.5000, sse=717.7, rms=0.022 (0.000%) 120: dt: 0.5000, sse=717.9, rms=0.022 (0.000%) positioning took 3.7 minutes writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.area.pial vertex spacing 1.01 +- 0.43 (0.05-->7.19) (max @ vno 98031 --> 96995) face area 0.40 +- 0.31 (0.00-->5.22) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 146118 vertices processed 25000 of 146118 vertices processed 50000 of 146118 vertices processed 75000 of 146118 vertices processed 100000 of 146118 vertices processed 125000 of 146118 vertices processed 0 of 146118 vertices processed 25000 of 146118 vertices processed 50000 of 146118 vertices processed 75000 of 146118 vertices processed 100000 of 146118 vertices processed 125000 of 146118 vertices processed thickness calculation complete, 234:454 truncations. 31267 vertices at 0 distance 100158 vertices at 1 distance 97139 vertices at 2 distance 37480 vertices at 3 distance 10338 vertices at 4 distance 2816 vertices at 5 distance 812 vertices at 6 distance 264 vertices at 7 distance 122 vertices at 8 distance 85 vertices at 9 distance 50 vertices at 10 distance 40 vertices at 11 distance 23 vertices at 12 distance 19 vertices at 13 distance 12 vertices at 14 distance 13 vertices at 15 distance 8 vertices at 16 distance 5 vertices at 17 distance 6 vertices at 18 distance 10 vertices at 19 distance 9 vertices at 20 distance writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.thickness positioning took 19.4 minutes /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.woT2.pial `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.woT2.pial' mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub009 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/sub009/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/wm.mgz... 19164 bright wm thresholded. 814 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.orig... computing class statistics... border white: 259466 voxels (1.55%) border gray 303507 voxels (1.81%) WM (92.0): 93.0 +- 10.6 [70.0 --> 110.0] GM (74.0) : 72.2 +- 13.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 44.0 (was 70) setting MAX_BORDER_WHITE to 115.6 (was 105) setting MIN_BORDER_WHITE to 57.0 (was 85) setting MAX_CSF to 30.9 (was 40) setting MAX_GRAY to 94.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 50.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 17.9 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=57 mean inside = 92.8, mean outside = 66.9 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/sub009/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.89 +- 0.25 (0.02-->5.20) (max @ vno 79769 --> 80799) face area 0.33 +- 0.16 (0.00-->4.37) averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 15 points - only 0.00% unknown removing 2 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 17 points - only 0.00% unknown deleting segment 7 with 314 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 10 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 11 with 4 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 12 with 1 points - only 0.00% unknown deleting segment 13 with 5 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 14 with 1 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 15 with 3 points - only 0.00% unknown deleting segment 16 with 29 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 17 with 2 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 0.89 +- 0.25 (0.04-->5.20) (max @ vno 80799 --> 79769) face area 0.33 +- 0.16 (0.00-->4.37) averaging target values for 5 iterations... 000: dt: 0.0000, sse=5283345.5, rms=0.00 rms = 1.44, time step reduction 1 of 3 to 0.250... rms = 0.38, time step reduction 2 of 3 to 0.125... rms = 0.05, time step reduction 3 of 3 to 0.062... 001: dt: 0.1250, sse=5283345.5, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 15 points - only 0.00% unknown removing 2 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 17 points - only 0.00% unknown deleting segment 5 with 314 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 4 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 9 with 1 points - only 0.00% unknown deleting segment 10 with 5 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 11 with 1 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 12 with 3 points - only 0.00% unknown deleting segment 13 with 29 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 14 with 2 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 0.89 +- 0.25 (0.04-->5.20) (max @ vno 80799 --> 79769) face area 0.33 +- 0.16 (0.00-->4.37) averaging target values for 5 iterations... 000: dt: 0.0000, sse=5283345.5, rms=0.00 rms = 1.44, time step reduction 1 of 3 to 0.250... rms = 0.38, time step reduction 2 of 3 to 0.125... rms = 0.05, time step reduction 3 of 3 to 0.062... 002: dt: 0.1250, sse=5283345.5, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 15 points - only 0.00% unknown removing 2 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 17 points - only 0.00% unknown deleting segment 5 with 314 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 4 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 9 with 1 points - only 0.00% unknown deleting segment 10 with 5 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 11 with 1 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 12 with 3 points - only 0.00% unknown deleting segment 13 with 29 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 14 with 2 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 0.89 +- 0.25 (0.04-->5.20) (max @ vno 80799 --> 79769) face area 0.33 +- 0.16 (0.00-->4.37) averaging target values for 5 iterations... 000: dt: 0.0000, sse=5283345.5, rms=0.00 rms = 1.44, time step reduction 1 of 3 to 0.250... rms = 0.38, time step reduction 2 of 3 to 0.125... rms = 0.05, time step reduction 3 of 3 to 0.062... 003: dt: 0.1250, sse=5283345.5, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 15 points - only 0.00% unknown removing 2 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 17 points - only 0.00% unknown deleting segment 5 with 314 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 4 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 9 with 1 points - only 0.00% unknown deleting segment 10 with 5 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 11 with 1 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 12 with 3 points - only 0.00% unknown deleting segment 13 with 29 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 14 with 2 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=5283345.5, rms=0.00 rms = 1.44, time step reduction 1 of 3 to 0.250... rms = 0.38, time step reduction 2 of 3 to 0.125... rms = 0.05, time step reduction 3 of 3 to 0.062... 004: dt: 0.1250, sse=5283345.5, rms=0.000 (1.000%) positioning took 0.3 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 deleting segment 6 with 3 points - only 0.00% unknown 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 [92.00 212.00], gm=152.00+-20.00, and vertices in regions > 142.0 54992 surface locations found to contain inconsistent values (4218 in, 50774 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=553568.6, rms=0.23 001: dt: 0.5000, sse=517982.0, rms=0.224 (0.000%) 002: dt: 0.5000, sse=496008.7, rms=0.209 (0.000%) 003: dt: 0.5000, sse=482069.6, rms=0.197 (0.000%) 004: dt: 0.5000, sse=470726.9, rms=0.188 (0.000%) 005: dt: 0.5000, sse=462433.6, rms=0.180 (0.000%) 006: dt: 0.5000, sse=456190.8, rms=0.173 (0.000%) 007: dt: 0.5000, sse=451191.1, rms=0.167 (0.000%) 008: dt: 0.5000, sse=447166.4, rms=0.162 (0.000%) 009: dt: 0.5000, sse=443656.5, rms=0.157 (0.000%) 010: dt: 0.5000, sse=440653.6, rms=0.154 (0.000%) 011: dt: 0.5000, sse=438000.7, rms=0.151 (0.000%) 012: dt: 0.5000, sse=435878.2, rms=0.149 (0.000%) 013: dt: 0.5000, sse=433847.7, rms=0.147 (0.000%) 014: dt: 0.5000, sse=431588.1, rms=0.145 (0.000%) 015: dt: 0.5000, sse=429934.3, rms=0.144 (0.000%) 016: dt: 0.5000, sse=428059.9, rms=0.143 (0.000%) 017: dt: 0.5000, sse=426326.9, rms=0.142 (0.000%) 018: dt: 0.5000, sse=424761.1, rms=0.141 (0.000%) 019: dt: 0.5000, sse=422935.0, rms=0.141 (0.000%) 020: dt: 0.5000, sse=421328.0, rms=0.141 (0.000%) 021: dt: 0.5000, sse=419715.2, rms=0.140 (0.000%) 022: dt: 0.5000, sse=418351.8, rms=0.140 (0.000%) 023: dt: 0.5000, sse=417144.2, rms=0.140 (0.000%) 024: dt: 0.5000, sse=415696.4, rms=0.140 (0.000%) 025: dt: 0.5000, sse=414073.3, rms=0.141 (0.000%) 026: dt: 0.5000, sse=412813.5, rms=0.141 (0.000%) 027: dt: 0.5000, sse=411663.8, rms=0.141 (0.000%) 028: dt: 0.5000, sse=410353.9, rms=0.141 (0.000%) 029: dt: 0.5000, sse=409229.2, rms=0.142 (0.000%) 030: dt: 0.5000, sse=407916.7, rms=0.142 (0.000%) positioning took 4.0 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [95.00 209.00], gm=152.00+-19.00, and vertices in regions > 142.5 39232 surface locations found to contain inconsistent values (3272 in, 35960 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=42389.2, rms=0.12 031: dt: 0.5000, sse=42143.1, rms=0.120 (0.000%) 032: dt: 0.5000, sse=42833.0, rms=0.110 (0.000%) 033: dt: 0.5000, sse=43754.8, rms=0.102 (0.000%) 034: dt: 0.5000, sse=44552.0, rms=0.097 (0.000%) 035: dt: 0.5000, sse=45223.8, rms=0.092 (0.000%) 036: dt: 0.5000, sse=45882.4, rms=0.087 (0.000%) 037: dt: 0.5000, sse=46532.7, rms=0.083 (0.000%) 038: dt: 0.5000, sse=47153.7, rms=0.079 (0.000%) 039: dt: 0.5000, sse=47770.9, rms=0.075 (0.000%) 040: dt: 0.5000, sse=48403.9, rms=0.072 (0.000%) 041: dt: 0.5000, sse=48977.2, rms=0.069 (0.000%) 042: dt: 0.5000, sse=49550.5, rms=0.066 (0.000%) 043: dt: 0.5000, sse=50075.6, rms=0.063 (0.000%) 044: dt: 0.5000, sse=50585.0, rms=0.061 (0.000%) 045: dt: 0.5000, sse=51057.1, rms=0.059 (0.000%) 046: dt: 0.5000, sse=51506.5, rms=0.057 (0.000%) 047: dt: 0.5000, sse=51927.9, rms=0.055 (0.000%) 048: dt: 0.5000, sse=52297.9, rms=0.053 (0.000%) 049: dt: 0.5000, sse=52670.6, rms=0.052 (0.000%) 050: dt: 0.5000, sse=52984.2, rms=0.050 (0.000%) 051: dt: 0.5000, sse=53287.6, rms=0.049 (0.000%) 052: dt: 0.5000, sse=53577.7, rms=0.048 (0.000%) 053: dt: 0.5000, sse=53851.3, rms=0.047 (0.000%) 054: dt: 0.5000, sse=54110.2, rms=0.046 (0.000%) 055: dt: 0.5000, sse=54312.0, rms=0.045 (0.000%) 056: dt: 0.5000, sse=54524.5, rms=0.044 (0.000%) 057: dt: 0.5000, sse=54719.0, rms=0.043 (0.000%) 058: dt: 0.5000, sse=54878.2, rms=0.043 (0.000%) 059: dt: 0.5000, sse=55031.9, rms=0.042 (0.000%) 060: dt: 0.5000, sse=55190.9, rms=0.041 (0.000%) positioning took 3.9 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [87.50 216.50], gm=152.00+-21.50, and vertices in regions > 141.2 46443 surface locations found to contain inconsistent values (76 in, 46367 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=6303.0, rms=0.07 061: dt: 0.5000, sse=6212.9, rms=0.071 (0.000%) 062: dt: 0.5000, sse=6267.5, rms=0.060 (0.000%) 063: dt: 0.5000, sse=6378.5, rms=0.054 (0.000%) 064: dt: 0.5000, sse=6483.5, rms=0.051 (0.000%) 065: dt: 0.5000, sse=6559.6, rms=0.048 (0.000%) 066: dt: 0.5000, sse=6609.5, rms=0.045 (0.000%) 067: dt: 0.5000, sse=6643.6, rms=0.044 (0.000%) 068: dt: 0.5000, sse=6674.2, rms=0.042 (0.000%) 069: dt: 0.5000, sse=6704.0, rms=0.040 (0.000%) 070: dt: 0.5000, sse=6731.9, rms=0.039 (0.000%) 071: dt: 0.5000, sse=6756.5, rms=0.038 (0.000%) 072: dt: 0.5000, sse=6778.3, rms=0.037 (0.000%) 073: dt: 0.5000, sse=6796.7, rms=0.036 (0.000%) 074: dt: 0.5000, sse=6813.0, rms=0.035 (0.000%) 075: dt: 0.5000, sse=6827.6, rms=0.034 (0.000%) 076: dt: 0.5000, sse=6840.5, rms=0.033 (0.000%) 077: dt: 0.5000, sse=6850.6, rms=0.033 (0.000%) 078: dt: 0.5000, sse=6860.6, rms=0.032 (0.000%) 079: dt: 0.5000, sse=6868.9, rms=0.031 (0.000%) 080: dt: 0.5000, sse=6877.5, rms=0.031 (0.000%) 081: dt: 0.5000, sse=6884.9, rms=0.031 (0.000%) 082: dt: 0.5000, sse=6892.0, rms=0.030 (0.000%) 083: dt: 0.5000, sse=6897.8, rms=0.030 (0.000%) 084: dt: 0.5000, sse=6903.8, rms=0.030 (0.000%) 085: dt: 0.5000, sse=6909.2, rms=0.029 (0.000%) 086: dt: 0.5000, sse=6913.9, rms=0.029 (0.000%) 087: dt: 0.5000, sse=6918.3, rms=0.029 (0.000%) 088: dt: 0.5000, sse=6921.5, rms=0.029 (0.000%) 089: dt: 0.5000, sse=6924.7, rms=0.029 (0.000%) 090: dt: 0.5000, sse=6928.1, rms=0.029 (0.000%) positioning took 3.8 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [86.00 218.00], gm=152.00+-22.00, and vertices in regions > 141.0 46811 surface locations found to contain inconsistent values (17 in, 46794 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/sub009/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=920.2, rms=0.04 091: dt: 0.5000, sse=902.4, rms=0.039 (0.000%) 092: dt: 0.5000, sse=858.5, rms=0.034 (0.000%) 093: dt: 0.5000, sse=846.2, rms=0.032 (0.000%) 094: dt: 0.5000, sse=840.8, rms=0.031 (0.000%) 095: dt: 0.5000, sse=836.5, rms=0.030 (0.000%) 096: dt: 0.5000, sse=833.2, rms=0.030 (0.000%) 097: dt: 0.5000, sse=830.5, rms=0.030 (0.000%) 098: dt: 0.5000, sse=828.1, rms=0.029 (0.000%) 099: dt: 0.5000, sse=826.3, rms=0.029 (0.000%) 100: dt: 0.5000, sse=824.3, rms=0.029 (0.000%) 101: dt: 0.5000, sse=822.5, rms=0.028 (0.000%) 102: dt: 0.5000, sse=820.9, rms=0.028 (0.000%) 103: dt: 0.5000, sse=819.9, rms=0.028 (0.000%) 104: dt: 0.5000, sse=818.6, rms=0.028 (0.000%) 105: dt: 0.5000, sse=817.3, rms=0.028 (0.000%) 106: dt: 0.5000, sse=816.2, rms=0.027 (0.000%) 107: dt: 0.5000, sse=815.2, rms=0.027 (0.000%) 108: dt: 0.5000, sse=814.3, rms=0.027 (0.000%) 109: dt: 0.5000, sse=813.5, rms=0.027 (0.000%) 110: dt: 0.5000, sse=812.8, rms=0.027 (0.000%) 111: dt: 0.5000, sse=812.3, rms=0.027 (0.000%) 112: dt: 0.5000, sse=811.6, rms=0.027 (0.000%) 113: dt: 0.5000, sse=811.2, rms=0.027 (0.000%) 114: dt: 0.5000, sse=811.0, rms=0.027 (0.000%) 115: dt: 0.5000, sse=811.4, rms=0.027 (0.000%) 116: dt: 0.5000, sse=811.0, rms=0.027 (0.000%) 117: dt: 0.5000, sse=810.6, rms=0.027 (0.000%) 118: dt: 0.5000, sse=810.2, rms=0.026 (0.000%) 119: dt: 0.5000, sse=810.0, rms=0.026 (0.000%) 120: dt: 0.5000, sse=809.9, rms=0.026 (0.000%) positioning took 3.7 minutes writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.area.pial vertex spacing 1.02 +- 0.43 (0.08-->8.58) (max @ vno 102156 --> 102155) face area 0.41 +- 0.31 (0.00-->6.68) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 146248 vertices processed 25000 of 146248 vertices processed 50000 of 146248 vertices processed 75000 of 146248 vertices processed 100000 of 146248 vertices processed 125000 of 146248 vertices processed 0 of 146248 vertices processed 25000 of 146248 vertices processed 50000 of 146248 vertices processed 75000 of 146248 vertices processed 100000 of 146248 vertices processed 125000 of 146248 vertices processed thickness calculation complete, 284:405 truncations. 31600 vertices at 0 distance 98547 vertices at 1 distance 97474 vertices at 2 distance 38998 vertices at 3 distance 10460 vertices at 4 distance 2837 vertices at 5 distance 830 vertices at 6 distance 308 vertices at 7 distance 110 vertices at 8 distance 71 vertices at 9 distance 43 vertices at 10 distance 41 vertices at 11 distance 41 vertices at 12 distance 16 vertices at 13 distance 25 vertices at 14 distance 26 vertices at 15 distance 17 vertices at 16 distance 11 vertices at 17 distance 12 vertices at 18 distance 5 vertices at 19 distance 18 vertices at 20 distance writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.thickness positioning took 19.0 minutes #-------------------------------------------- #@# Surf Volume lh Thu Aug 8 23:43:47 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 23:43:48 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 23:43:48 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon sub009 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 = 5 writing volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/ribbon.mgz writing ribbon files #-------------------------------------------- #@# ASeg Stats Fri Aug 9 00:03:59 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009 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 sub009 $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 sub009 sysname Linux hostname snake6 machine x86_64 user fkaule UseRobust 0 atlas_icv (eTIV) = 1198514 mm^3 (det: 1.625434 ) Computing euler number orig.nofix lheno = -32, rheno = -20 orig.nofix lhholes = 17, rhholes = 11 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 250723.462 249908.000 diff= 815.5 pctdiff= 0.325 rhCtxGM: 256030.872 254885.000 diff= 1145.9 pctdiff= 0.448 lhCtxWM: 212144.737 211877.500 diff= 267.2 pctdiff= 0.126 rhCtxWM: 212485.812 212659.500 diff= -173.7 pctdiff=-0.082 SubCortGMVol 59766.000 SupraTentVol 1021635.883 (1018698.000) diff=2937.883 pctdiff=0.288 SupraTentVolNotVent 992174.883 (989237.000) diff=2937.883 pctdiff=0.296 BrainSegVol 1164260.000 (1161362.000) diff=2898.000 pctdiff=0.249 BrainSegVolNotVent 1130776.000 (1132546.883) diff=-1770.883 pctdiff=-0.157 BrainSegVolNotVent 1130776.000 CerebellumVol 141255.000 VentChorVol 29461.000 3rd4th5thCSF 4023.000 CSFVol 1142.000, OptChiasmVol 267.000 MaskVol 1709725.000 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 13306 13305.957 4 5 Left-Inf-Lat-Vent 238 237.695 5 7 Left-Cerebellum-White-Matter 18453 18452.689 6 8 Left-Cerebellum-Cortex 52582 52581.742 7 10 Left-Thalamus-Proper 6965 6965.113 8 11 Left-Caudate 3863 3863.370 9 12 Left-Putamen 6716 6716.408 10 13 Left-Pallidum 1892 1891.845 11 14 3rd-Ventricle 1460 1459.907 12 15 4th-Ventricle 1635 1634.819 13 16 Brain-Stem 23763 23762.811 14 17 Left-Hippocampus 3429 3428.875 15 18 Left-Amygdala 1480 1479.961 16 24 CSF 1144 1143.941 17 26 Left-Accumbens-area 856 855.577 18 28 Left-VentralDC 3880 3879.935 19 30 Left-vessel 29 29.245 20 31 Left-choroid-plexus 1099 1099.359 23 43 Right-Lateral-Ventricle 12914 12913.826 24 44 Right-Inf-Lat-Vent 217 216.662 25 46 Right-Cerebellum-White-Matter 18133 18133.016 26 47 Right-Cerebellum-Cortex 54267 54266.852 27 49 Right-Thalamus-Proper 6384 6383.620 28 50 Right-Caudate 3911 3911.343 29 51 Right-Putamen 7260 7260.207 30 52 Right-Pallidum 1645 1644.907 31 53 Right-Hippocampus 3514 3513.790 32 54 Right-Amygdala 1593 1593.034 33 58 Right-Accumbens-area 782 782.409 34 60 Right-VentralDC 3878 3877.557 35 62 Right-vessel 101 101.259 36 63 Right-choroid-plexus 1502 1501.959 37 72 5th-Ventricle 0 0.000 38 77 WM-hypointensities 1684 1684.251 39 78 Left-WM-hypointensities 0 0.000 40 79 Right-WM-hypointensities 0 0.000 41 80 non-WM-hypointensities 14 13.978 42 81 Left-non-WM-hypointensities 0 0.000 43 82 Right-non-WM-hypointensities 0 0.000 44 85 Optic-Chiasm 277 276.815 45 251 CC_Posterior 633 633.104 46 252 CC_Mid_Posterior 328 327.517 47 253 CC_Central 315 315.145 48 254 CC_Mid_Anterior 399 399.062 49 255 CC_Anterior 700 700.434 Reporting on 45 segmentations mri_segstats done #----------------------------------------- #@# AParc-to-ASeg Fri Aug 9 00:07:17 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009 mri_aparc2aseg --s sub009 --volmask SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer subject sub009 outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.white Reading lh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.pial Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/surf/rh.white Reading rh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.pial Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/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/sub009/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 = 503309 Used brute-force search on 0 voxels Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/aparc+aseg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009 mri_aparc2aseg --s sub009 --volmask --a2009s SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer subject sub009 outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.white Reading lh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.pial Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/surf/rh.white Reading rh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.pial Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/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/sub009/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 = 503309 Used brute-force search on 0 voxels Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# WMParc Fri Aug 9 00:12:12 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009 mri_aparc2aseg --s sub009 --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 sub009 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/sub009/mri/aparc+aseg.mgz Reading lh white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.white Reading lh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.pial Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/surf/rh.white Reading rh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.pial Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/mri/ribbon.mgz Loading filled from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/filled.mgz Ripping vertices labeled as unkown Ripped 7601 vertices from left hemi Ripped 7375 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/sub009/mri/aseg.mgz Loading Ctx Seg File /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 = 926878 Used brute-force search on 220 voxels Fixing Parahip LH WM Found 10 clusters 0 k 1672.000000 1 k 1.000000 2 k 1.000000 3 k 1.000000 4 k 1.000000 5 k 6.000000 6 k 2.000000 7 k 1.000000 8 k 32.000000 9 k 1.000000 Fixing Parahip RH WM Found 5 clusters 0 k 3.000000 1 k 2.000000 2 k 1.000000 3 k 1373.000000 4 k 2.000000 Writing output aseg to mri/wmparc.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009 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 sub009 --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 sub009 --surf-wm-vol --ctab /opt/freesurfer/5.3.0/WMParcStatsLUT.txt --etiv sysname Linux hostname snake6 machine x86_64 user fkaule UseRobust 0 atlas_icv (eTIV) = 1198514 mm^3 (det: 1.625434 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 250723.462 249908.000 diff= 815.5 pctdiff= 0.325 rhCtxGM: 256030.872 254885.000 diff= 1145.9 pctdiff= 0.448 lhCtxWM: 212144.737 211877.500 diff= 267.2 pctdiff= 0.126 rhCtxWM: 212485.812 212659.500 diff= -173.7 pctdiff=-0.082 SubCortGMVol 59766.000 SupraTentVol 1021635.883 (1018698.000) diff=2937.883 pctdiff=0.288 SupraTentVolNotVent 992174.883 (989237.000) diff=2937.883 pctdiff=0.296 BrainSegVol 1164260.000 (1161362.000) diff=2898.000 pctdiff=0.249 BrainSegVolNotVent 1130776.000 (1132546.883) diff=-1770.883 pctdiff=-0.157 BrainSegVolNotVent 1130776.000 CerebellumVol 141255.000 VentChorVol 29461.000 3rd4th5thCSF 4023.000 CSFVol 1142.000, OptChiasmVol 267.000 MaskVol 1709725.000 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 1805 1804.976 2 3002 wm-lh-caudalanteriorcingulate 3722 3722.377 3 3003 wm-lh-caudalmiddlefrontal 5819 5818.831 4 3004 wm-lh-corpuscallosum 0 0.000 5 3005 wm-lh-cuneus 1739 1739.438 6 3006 wm-lh-entorhinal 1174 1173.700 7 3007 wm-lh-fusiform 6099 6099.014 8 3008 wm-lh-inferiorparietal 10880 10880.184 9 3009 wm-lh-inferiortemporal 6232 6231.960 10 3010 wm-lh-isthmuscingulate 3386 3385.789 11 3011 wm-lh-lateraloccipital 9315 9315.484 12 3012 wm-lh-lateralorbitofrontal 6493 6493.025 13 3013 wm-lh-lingual 3892 3891.911 14 3014 wm-lh-medialorbitofrontal 3614 3613.732 15 3015 wm-lh-middletemporal 5669 5669.354 16 3016 wm-lh-parahippocampal 1681 1681.262 17 3017 wm-lh-paracentral 3500 3500.263 18 3018 wm-lh-parsopercularis 4456 4455.846 19 3019 wm-lh-parsorbitalis 1002 1001.512 20 3020 wm-lh-parstriangularis 2758 2758.121 21 3021 wm-lh-pericalcarine 2592 2592.143 22 3022 wm-lh-postcentral 6460 6459.997 23 3023 wm-lh-posteriorcingulate 4768 4768.479 24 3024 wm-lh-precentral 12316 12316.146 25 3025 wm-lh-precuneus 10587 10587.366 26 3026 wm-lh-rostralanteriorcingulate 2807 2807.190 27 3027 wm-lh-rostralmiddlefrontal 11997 11996.839 28 3028 wm-lh-superiorfrontal 15458 15458.268 29 3029 wm-lh-superiorparietal 10976 10976.164 30 3030 wm-lh-superiortemporal 6779 6779.273 31 3031 wm-lh-supramarginal 9299 9299.476 32 3032 wm-lh-frontalpole 242 241.536 33 3033 wm-lh-temporalpole 725 725.089 34 3034 wm-lh-transversetemporal 792 792.341 35 3035 wm-lh-insula 9900 9900.117 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 1754 1754.114 120 4002 wm-rh-caudalanteriorcingulate 2418 2417.562 121 4003 wm-rh-caudalmiddlefrontal 6421 6421.150 122 4004 wm-rh-corpuscallosum 0 0.000 123 4005 wm-rh-cuneus 1710 1709.773 124 4006 wm-rh-entorhinal 512 511.662 125 4007 wm-rh-fusiform 6470 6469.794 126 4008 wm-rh-inferiorparietal 10519 10519.486 127 4009 wm-rh-inferiortemporal 5595 5595.008 128 4010 wm-rh-isthmuscingulate 4005 4004.809 129 4011 wm-rh-lateraloccipital 8468 8467.862 130 4012 wm-rh-lateralorbitofrontal 6680 6680.200 131 4013 wm-rh-lingual 4140 4139.808 132 4014 wm-rh-medialorbitofrontal 3026 3025.862 133 4015 wm-rh-middletemporal 5180 5180.194 134 4016 wm-rh-parahippocampal 1393 1393.051 135 4017 wm-rh-paracentral 5542 5542.227 136 4018 wm-rh-parsopercularis 3170 3169.978 137 4019 wm-rh-parsorbitalis 1120 1120.104 138 4020 wm-rh-parstriangularis 3305 3305.098 139 4021 wm-rh-pericalcarine 2445 2445.323 140 4022 wm-rh-postcentral 8501 8500.583 141 4023 wm-rh-posteriorcingulate 4458 4458.224 142 4024 wm-rh-precentral 11362 11362.404 143 4025 wm-rh-precuneus 9609 9609.014 144 4026 wm-rh-rostralanteriorcingulate 2202 2202.296 145 4027 wm-rh-rostralmiddlefrontal 12301 12300.676 146 4028 wm-rh-superiorfrontal 17984 17984.150 147 4029 wm-rh-superiorparietal 12043 12043.066 148 4030 wm-rh-superiortemporal 6955 6954.842 149 4031 wm-rh-supramarginal 9802 9802.221 150 4032 wm-rh-frontalpole 272 271.942 151 4033 wm-rh-temporalpole 591 591.352 152 4034 wm-rh-transversetemporal 616 616.153 153 4035 wm-rh-insula 9805 9805.454 154 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 24313 24312.592 237 5002 Right-UnsegmentedWhiteMatter 23325 23325.129 238 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/sub009/label #-------------------------------------------- #@# BA Labels lh Fri Aug 9 00:22:49 CEST 2013 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.label --trgsubject sub009 --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 = sub009 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/sub009/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118 Number of reverse mapping hits = 243 Checking for and removing duplicates Writing label file ./lh.BA1.label 4372 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.label --trgsubject sub009 --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 = sub009 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/sub009/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118 Number of reverse mapping hits = 475 Checking for and removing duplicates Writing label file ./lh.BA2.label 8384 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.label --trgsubject sub009 --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 = sub009 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/sub009/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118 Number of reverse mapping hits = 134 Checking for and removing duplicates Writing label file ./lh.BA3a.label 4211 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.label --trgsubject sub009 --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 = sub009 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/sub009/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118 Number of reverse mapping hits = 303 Checking for and removing duplicates Writing label file ./lh.BA3b.label 6286 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.label --trgsubject sub009 --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 = sub009 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/sub009/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118 Number of reverse mapping hits = 626 Checking for and removing duplicates Writing label file ./lh.BA4a.label 6410 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.label --trgsubject sub009 --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 = sub009 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/sub009/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118 Number of reverse mapping hits = 350 Checking for and removing duplicates Writing label file ./lh.BA4p.label 4420 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.label --trgsubject sub009 --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 = sub009 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/sub009/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118 Number of reverse mapping hits = 1248 Checking for and removing duplicates Writing label file ./lh.BA6.label 14837 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.label --trgsubject sub009 --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 = sub009 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/sub009/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118 Number of reverse mapping hits = 863 Checking for and removing duplicates Writing label file ./lh.BA44.label 5044 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.label --trgsubject sub009 --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 = sub009 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/sub009/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118 Number of reverse mapping hits = 1296 Checking for and removing duplicates Writing label file ./lh.BA45.label 4718 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.label --trgsubject sub009 --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 = sub009 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/sub009/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118 Number of reverse mapping hits = 1647 Checking for and removing duplicates Writing label file ./lh.V1.label 6288 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.label --trgsubject sub009 --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 = sub009 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/sub009/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118 Number of reverse mapping hits = 2674 Checking for and removing duplicates Writing label file ./lh.V2.label 10788 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.label --trgsubject sub009 --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 = sub009 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/sub009/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118 Number of reverse mapping hits = 739 Checking for and removing duplicates Writing label file ./lh.MT.label 2757 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.perirhinal.label --trgsubject sub009 --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 = sub009 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/sub009/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118 Number of reverse mapping hits = 168 Checking for and removing duplicates Writing label file ./lh.perirhinal.label 1367 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.thresh.label --trgsubject sub009 --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 = sub009 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/sub009/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118 Number of reverse mapping hits = 82 Checking for and removing duplicates Writing label file ./lh.BA1.thresh.label 1096 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.thresh.label --trgsubject sub009 --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 = sub009 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/sub009/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118 Number of reverse mapping hits = 74 Checking for and removing duplicates Writing label file ./lh.BA2.thresh.label 2166 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.thresh.label --trgsubject sub009 --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 = sub009 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/sub009/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118 Number of reverse mapping hits = 15 Checking for and removing duplicates Writing label file ./lh.BA3a.thresh.label 1519 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.thresh.label --trgsubject sub009 --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 = sub009 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/sub009/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118 Number of reverse mapping hits = 82 Checking for and removing duplicates Writing label file ./lh.BA3b.thresh.label 2078 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.thresh.label --trgsubject sub009 --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 = sub009 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/sub009/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118 Number of reverse mapping hits = 247 Checking for and removing duplicates Writing label file ./lh.BA4a.thresh.label 2566 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.thresh.label --trgsubject sub009 --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 = sub009 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/sub009/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118 Number of reverse mapping hits = 126 Checking for and removing duplicates Writing label file ./lh.BA4p.thresh.label 1675 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.thresh.label --trgsubject sub009 --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 = sub009 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/sub009/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118 Number of reverse mapping hits = 604 Checking for and removing duplicates Writing label file ./lh.BA6.thresh.label 7639 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.thresh.label --trgsubject sub009 --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 = sub009 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/sub009/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118 Number of reverse mapping hits = 443 Checking for and removing duplicates Writing label file ./lh.BA44.thresh.label 2355 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.thresh.label --trgsubject sub009 --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 = sub009 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/sub009/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118 Number of reverse mapping hits = 633 Checking for and removing duplicates Writing label file ./lh.BA45.thresh.label 1784 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.thresh.label --trgsubject sub009 --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 = sub009 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/sub009/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118 Number of reverse mapping hits = 1212 Checking for and removing duplicates Writing label file ./lh.V1.thresh.label 4617 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.thresh.label --trgsubject sub009 --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 = sub009 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/sub009/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118 Number of reverse mapping hits = 1181 Checking for and removing duplicates Writing label file ./lh.V2.thresh.label 4515 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.thresh.label --trgsubject sub009 --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 = sub009 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/sub009/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118 Number of reverse mapping hits = 160 Checking for and removing duplicates Writing label file ./lh.MT.thresh.label 673 mri_label2label: Done mris_label2annot --s sub009 --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/sub009/label cmdline mris_label2annot --s sub009 --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 snake6 machine x86_64 user fkaule subject sub009 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/sub009/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 103427 unhit vertices Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/label/lh.BA.annot mris_label2annot --s sub009 --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/sub009/label cmdline mris_label2annot --s sub009 --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 snake6 machine x86_64 user fkaule subject sub009 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/sub009/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 121505 unhit vertices Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/label/lh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab sub009 lh white computing statistics for each annotation in ./lh.BA.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 1133 667 2086 2.282 0.490 0.173 0.074 31 3.4 BA1 3885 2607 6069 2.228 0.408 0.129 0.043 61 7.4 BA2 860 583 863 1.914 0.441 0.154 0.046 9 1.7 BA3a 2207 1513 3238 1.883 0.551 0.124 0.041 27 3.1 BA3b 1850 1146 4022 2.843 0.482 0.118 0.033 17 2.6 BA4a 1344 822 2168 2.596 0.459 0.099 0.030 9 1.6 BA4p 9292 6036 20367 2.710 0.528 0.135 0.042 120 15.7 BA6 2910 1966 5800 2.559 0.400 0.136 0.044 44 5.0 BA44 3682 2499 6445 2.296 0.437 0.161 0.068 592 8.0 BA45 3821 2607 5020 1.855 0.498 0.171 0.083 73 12.8 V1 8091 5275 12048 2.103 0.448 0.170 0.072 169 21.8 V2 2511 1712 4489 2.412 0.461 0.162 0.059 50 6.1 MT 1105 749 2333 2.690 0.648 0.126 0.080 65 2.5 perirhinal mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab sub009 lh white computing statistics for each annotation in ./lh.BA.thresh.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 714 414 1322 2.262 0.515 0.179 0.083 22 2.2 BA1 1382 922 2244 2.152 0.336 0.109 0.026 11 1.5 BA2 710 469 651 1.903 0.382 0.150 0.044 8 1.3 BA3a 1324 921 1579 1.564 0.337 0.114 0.030 12 1.6 BA3b 1786 1098 3916 2.880 0.482 0.115 0.030 15 2.5 BA4a 1095 689 1705 2.500 0.455 0.103 0.029 7 1.3 BA4p 5234 3357 11657 2.715 0.539 0.132 0.044 69 8.9 BA6 1990 1355 4155 2.608 0.374 0.138 0.043 29 3.4 BA44 1695 1114 3150 2.399 0.406 0.172 0.064 56 4.1 BA45 4041 2764 5343 1.849 0.486 0.170 0.082 76 13.5 V1 4023 2633 6097 2.114 0.441 0.185 0.088 95 12.5 V2 619 439 1091 2.273 0.490 0.167 0.061 12 1.5 MT #-------------------------------------------- #@# BA Labels rh Fri Aug 9 00:27:33 CEST 2013 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.label --trgsubject sub009 --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 = sub009 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/sub009/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248 Number of reverse mapping hits = 656 Checking for and removing duplicates Writing label file ./rh.BA1.label 4618 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.label --trgsubject sub009 --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 = sub009 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/sub009/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248 Number of reverse mapping hits = 1333 Checking for and removing duplicates Writing label file ./rh.BA2.label 8020 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.label --trgsubject sub009 --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 = sub009 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/sub009/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248 Number of reverse mapping hits = 188 Checking for and removing duplicates Writing label file ./rh.BA3a.label 4168 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.label --trgsubject sub009 --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 = sub009 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/sub009/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248 Number of reverse mapping hits = 341 Checking for and removing duplicates Writing label file ./rh.BA3b.label 4863 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.label --trgsubject sub009 --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 = sub009 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/sub009/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248 Number of reverse mapping hits = 393 Checking for and removing duplicates Writing label file ./rh.BA4a.label 6140 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.label --trgsubject sub009 --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 = sub009 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/sub009/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248 Number of reverse mapping hits = 218 Checking for and removing duplicates Writing label file ./rh.BA4p.label 4691 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.label --trgsubject sub009 --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 = sub009 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/sub009/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248 Number of reverse mapping hits = 1114 Checking for and removing duplicates Writing label file ./rh.BA6.label 13370 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.label --trgsubject sub009 --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 = sub009 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/sub009/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248 Number of reverse mapping hits = 1345 Checking for and removing duplicates Writing label file ./rh.BA44.label 8257 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.label --trgsubject sub009 --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 = sub009 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/sub009/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248 Number of reverse mapping hits = 1586 Checking for and removing duplicates Writing label file ./rh.BA45.label 6941 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.label --trgsubject sub009 --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 = sub009 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/sub009/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248 Number of reverse mapping hits = 1243 Checking for and removing duplicates Writing label file ./rh.V1.label 5970 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.label --trgsubject sub009 --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 = sub009 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/sub009/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248 Number of reverse mapping hits = 2681 Checking for and removing duplicates Writing label file ./rh.V2.label 10697 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.label --trgsubject sub009 --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 = sub009 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/sub009/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248 Number of reverse mapping hits = 636 Checking for and removing duplicates Writing label file ./rh.MT.label 2568 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.perirhinal.label --trgsubject sub009 --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 = sub009 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/sub009/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248 Number of reverse mapping hits = 43 Checking for and removing duplicates Writing label file ./rh.perirhinal.label 795 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.thresh.label --trgsubject sub009 --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 = sub009 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/sub009/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248 Number of reverse mapping hits = 200 Checking for and removing duplicates Writing label file ./rh.BA1.thresh.label 1076 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.thresh.label --trgsubject sub009 --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 = sub009 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/sub009/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248 Number of reverse mapping hits = 495 Checking for and removing duplicates Writing label file ./rh.BA2.thresh.label 3183 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.thresh.label --trgsubject sub009 --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 = sub009 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/sub009/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248 Number of reverse mapping hits = 62 Checking for and removing duplicates Writing label file ./rh.BA3a.thresh.label 1760 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.thresh.label --trgsubject sub009 --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 = sub009 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/sub009/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248 Number of reverse mapping hits = 182 Checking for and removing duplicates Writing label file ./rh.BA3b.thresh.label 2365 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.thresh.label --trgsubject sub009 --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 = sub009 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/sub009/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248 Number of reverse mapping hits = 163 Checking for and removing duplicates Writing label file ./rh.BA4a.thresh.label 1551 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.thresh.label --trgsubject sub009 --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 = sub009 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/sub009/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248 Number of reverse mapping hits = 75 Checking for and removing duplicates Writing label file ./rh.BA4p.thresh.label 1564 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.thresh.label --trgsubject sub009 --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 = sub009 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/sub009/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248 Number of reverse mapping hits = 452 Checking for and removing duplicates Writing label file ./rh.BA6.thresh.label 7411 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.thresh.label --trgsubject sub009 --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 = sub009 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/sub009/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248 Number of reverse mapping hits = 245 Checking for and removing duplicates Writing label file ./rh.BA44.thresh.label 1257 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.thresh.label --trgsubject sub009 --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 = sub009 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/sub009/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248 Number of reverse mapping hits = 238 Checking for and removing duplicates Writing label file ./rh.BA45.thresh.label 1416 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.thresh.label --trgsubject sub009 --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 = sub009 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/sub009/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248 Number of reverse mapping hits = 811 Checking for and removing duplicates Writing label file ./rh.V1.thresh.label 4043 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.thresh.label --trgsubject sub009 --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 = sub009 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/sub009/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248 Number of reverse mapping hits = 1126 Checking for and removing duplicates Writing label file ./rh.V2.thresh.label 4563 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.thresh.label --trgsubject sub009 --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 = sub009 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/sub009/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248 Number of reverse mapping hits = 82 Checking for and removing duplicates Writing label file ./rh.MT.thresh.label 350 mri_label2label: Done mris_label2annot --s sub009 --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/sub009/label cmdline mris_label2annot --s sub009 --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 snake6 machine x86_64 user fkaule subject sub009 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/sub009/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 102322 unhit vertices Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/label/rh.BA.annot mris_label2annot --s sub009 --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/sub009/label cmdline mris_label2annot --s sub009 --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 snake6 machine x86_64 user fkaule subject sub009 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/sub009/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 123231 unhit vertices Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/label/rh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab sub009 rh white computing statistics for each annotation in ./rh.BA.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 1201 752 2408 2.357 0.430 0.168 0.063 29 2.9 BA1 4871 3243 7867 2.233 0.367 0.129 0.042 83 8.0 BA2 1068 695 1123 1.974 0.421 0.135 0.042 10 1.8 BA3a 2069 1396 3072 1.864 0.539 0.126 0.036 27 3.1 BA3b 1682 1072 3660 2.838 0.485 0.123 0.034 17 2.4 BA4a 1195 786 1996 2.524 0.396 0.123 0.155 83 2.7 BA4p 8163 5331 18011 2.771 0.496 0.140 0.066 225 29.6 BA6 3864 2594 7764 2.573 0.452 0.139 0.046 56 6.9 BA44 5023 3345 9641 2.429 0.439 0.162 0.078 124 12.3 BA45 3665 2525 5299 1.957 0.425 0.168 0.069 70 10.1 V1 8214 5385 12922 2.169 0.489 0.172 0.069 176 21.8 V2 2352 1578 3926 2.397 0.405 0.134 0.105 60 4.2 MT 559 389 1634 2.852 0.748 0.143 0.054 7 1.4 perirhinal mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab sub009 rh white computing statistics for each annotation in ./rh.BA.thresh.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 845 525 1619 2.228 0.401 0.180 0.065 24 2.3 BA1 2627 1759 4183 2.179 0.331 0.124 0.040 33 4.3 BA2 907 605 862 1.915 0.391 0.143 0.045 8 1.8 BA3a 1707 1144 2170 1.706 0.426 0.115 0.031 19 2.1 BA3b 1121 689 2556 2.912 0.530 0.126 0.037 12 1.8 BA4a 942 621 1522 2.546 0.364 0.116 0.182 80 2.1 BA4p 4752 3056 10420 2.749 0.478 0.142 0.083 177 23.0 BA6 1051 712 2456 2.662 0.486 0.145 0.056 19 2.2 BA44 1181 799 2516 2.555 0.389 0.167 0.061 28 2.9 BA45 3502 2407 4947 1.944 0.423 0.163 0.065 62 9.2 V1 4069 2720 6184 2.063 0.522 0.184 0.078 99 12.3 V2 313 205 621 2.406 0.453 0.146 0.518 35 0.8 MT /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label lh Fri Aug 9 00:32:22 CEST 2013 mris_spherical_average -erode 1 -orig white -t 0.4 -o sub009 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject sub009. processing subject lh.EC_average... reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 1011 points to lh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label sub009 lh white limiting computations to label ./lh.entorhinal_exvivo.label. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 374 242 1174 3.103 0.694 0.111 0.030 3 0.6 ./lh.entorhinal_exvivo.label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label rh Fri Aug 9 00:32:37 CEST 2013 mris_spherical_average -erode 1 -orig white -t 0.4 -o sub009 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label painting output onto subject sub009. processing subject rh.EC_average... reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 753 points to rh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label sub009 rh white limiting computations to label ./rh.entorhinal_exvivo.label. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 288 182 1047 3.223 0.784 0.144 0.066 4 0.9 ./rh.entorhinal_exvivo.label #------------------------------------------ Started at Thu Aug 8 10:54:16 CEST 2013 Ended at Fri Aug 9 00:32:53 CEST 2013 #@#%# recon-all-run-time-hours 13.644 recon-all -s sub009 finished without error at Fri Aug 9 00:32:53 CEST 2013