Thu Aug 8 10:54:16 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010 /opt/freesurfer/5.3.0/bin/recon-all -i /home/data/exppsy/forrest_gump/openfmri.org/sub010/anatomy/highres001.nii.gz -cw256 -all -T2 /home/data/exppsy/forrest_gump/openfmri.org/sub010/anatomy/other/t2w001.nii.gz -T2pial -subjid sub010 -sd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer subjid sub010 setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Actual FREESURFER_HOME /opt/freesurfer/5.3.0 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux snake4 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc unlimited maxlocks unlimited maxsignal 16382 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 99201692 96606936 2594756 0 188544 94065044 -/+ buffers/cache: 2353348 96848344 Swap: 25165780 532 25165248 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:16-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:17-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:17-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:17-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:17-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:17-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:17-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:17-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:21-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/freesurfer/5.3.0/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /opt/freesurfer/5.3.0/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### -cw256 option is now persistent (remove with -clean-cw256) /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub010/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/orig/001.mgz mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub010/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/anatomy/highres001.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.996481, 0.0682576, -0.0486557) j_ras = (0.0655887, 0.996358, 0.0544886) k_ras = (-0.0521977, -0.0511056, 0.997328) writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/orig/001.mgz... #-------------------------------------------- #@# T2/FLAIR Input Thu Aug 8 10:54:34 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub010/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/orig/T2raw.mgz mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub010/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/anatomy/other/t2w001.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.996481, 0.0682576, -0.0486557) j_ras = (0.0655887, 0.996358, 0.0544886) k_ras = (-0.0521977, -0.0511056, 0.997328) writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/orig/T2raw.mgz... #-------------------------------------------- #@# MotionCor Thu Aug 8 10:54:48 CEST 2013 Found 1 runs /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/mri/orig/001.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/orig.mgz --conform --cw256 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.996481, 0.0682576, -0.0486557) j_ras = (0.0655887, 0.996358, 0.0544886) k_ras = (-0.0521977, -0.0511056, 0.997328) 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/sub010/mri/orig.mgz... mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/talairach.xfm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Aug 8 10:55:26 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 10:57:50 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6271, 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/sub010/mri/transforms/talairach_avi.log tal_QC_AZS /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/talairach_avi.log TalAviQA: 0.96447 z-score: -3 #-------------------------------------------- #@# Nu Intensity Correction Thu Aug 8 10:57:50 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/sub010/mri /opt/freesurfer/5.3.0/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux snake4 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux Thu Aug 8 10:57:50 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.19840 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.19840/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.19840/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, -1.07102e-08, 7.45058e-09) j_ras = (7.45058e-09, -3.72529e-09, -1) k_ras = (-4.42378e-09, 1, 7.45058e-09) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.19840/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Aug 8 10:57:54 CEST 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.19840/nu0.mnc ./tmp.mri_nu_correct.mni.19840/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.19840/0/ [fkaule@snake4:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/] [2013-08-08 10:57:54] 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.19840/0/ ./tmp.mri_nu_correct.mni.19840/nu0.mnc ./tmp.mri_nu_correct.mni.19840/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 Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 27 CV of field change: 0.000990656 [fkaule@snake4:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/] [2013-08-08 10:58:24] running: /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.19840/nu0.mnc ./tmp.mri_nu_correct.mni.19840/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Thu Aug 8 10:58:31 CEST 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.19840/nu1.mnc ./tmp.mri_nu_correct.mni.19840/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.19840/1/ [fkaule@snake4:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/] [2013-08-08 10:58:32] 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.19840/1/ ./tmp.mri_nu_correct.mni.19840/nu1.mnc ./tmp.mri_nu_correct.mni.19840/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done 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Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 25 CV of field change: 0.000996627 [fkaule@snake4:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/] [2013-08-08 10:59:00] running: /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.19840/nu1.mnc ./tmp.mri_nu_correct.mni.19840/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.19840/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.19840/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/sub010/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.19840/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.19840/ones.mgz sysname Linux hostname snake4 machine x86_64 user fkaule input ./tmp.mri_nu_correct.mni.19840/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.19840/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.19840/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.19840/sum.junk --avgwf ./tmp.mri_nu_correct.mni.19840/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.19840/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.19840/sum.junk --avgwf ./tmp.mri_nu_correct.mni.19840/input.mean.dat sysname Linux hostname snake4 machine x86_64 user fkaule UseRobust 0 Loading ./tmp.mri_nu_correct.mni.19840/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.19840/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.19840/ones.mgz --i ./tmp.mri_nu_correct.mni.19840/nu2.mnc --sum ./tmp.mri_nu_correct.mni.19840/sum.junk --avgwf ./tmp.mri_nu_correct.mni.19840/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.19840/ones.mgz --i ./tmp.mri_nu_correct.mni.19840/nu2.mnc --sum ./tmp.mri_nu_correct.mni.19840/sum.junk --avgwf ./tmp.mri_nu_correct.mni.19840/output.mean.dat sysname Linux hostname snake4 machine x86_64 user fkaule UseRobust 0 Loading ./tmp.mri_nu_correct.mni.19840/ones.mgz Loading ./tmp.mri_nu_correct.mni.19840/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.19840/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.19840/nu2.mnc ./tmp.mri_nu_correct.mni.19840/nu2.mnc mul .97908922083269502129 Saving result to './tmp.mri_nu_correct.mni.19840/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.19840/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.19840/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.19840/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.07102e-08, 7.45058e-09) j_ras = (7.45058e-09, -3.72529e-09, -1) k_ras = (-4.42378e-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 7 seconds. mapping (10, 205) to ( 3, 110) Thu Aug 8 10:59:46 CEST 2013 mri_nu_correct.mni done mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Thu Aug 8 10:59:47 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.292 -0.073 -0.004 4.202; 0.035 1.128 0.349 -34.304; -0.035 -0.435 1.307 -8.091; 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 = 14 Starting OpenSpline(): npoints = 14 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 46 (46), valley at 31 (31) csf peak at 23, setting threshold to 38 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 37 (37) csf peak at 24, setting threshold to 40 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 50 seconds. #-------------------------------------------- #@# Skull Stripping Thu Aug 8 11:02:38 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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=6.0 skull bounding box = (61, 27, 27) --> (195, 255, 198) using (106, 103, 113) as brain centroid... mean wm in atlas = 126, using box (90,75,92) --> (122, 131,134) to find MRI wm before smoothing, mri peak at 110 after smoothing, mri peak at 110, scaling input intensities by 1.145 scaling channel 0 by 1.14545 initial log_p = -4.9 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.763399 @ (-9.091, 9.091, -9.091) max log p = -4.729606 @ (13.636, 4.545, 4.545) max log p = -4.648008 @ (-6.818, -2.273, -2.273) max log p = -4.645391 @ (1.136, -3.409, -3.409) max log p = -4.636181 @ (1.705, 6.250, -1.705) max log p = -4.636181 @ (0.000, 0.000, 0.000) Found translation: (0.6, 14.2, -11.9): log p = -4.636 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.6 (thresh=-4.6) 1.236 0.000 0.000 -36.509; 0.000 1.194 0.320 -36.794; 0.000 -0.320 1.194 -0.626; 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) 1.422 0.000 0.000 -60.849; 0.000 1.194 0.320 -36.794; 0.000 -0.320 1.194 -0.626; 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) 1.365 0.009 0.086 -62.443; -0.050 1.249 0.379 -40.777; -0.093 -0.342 1.137 22.251; 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) 1.365 0.009 0.086 -62.443; -0.050 1.249 0.379 -40.777; -0.096 -0.355 1.180 19.109; 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) 1.365 0.009 0.086 -62.443; -0.050 1.249 0.379 -40.777; -0.096 -0.355 1.180 19.109; 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) 1.363 -0.004 0.093 -61.614; -0.038 1.255 0.371 -42.913; -0.107 -0.344 1.182 19.272; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.363 -0.004 0.093 -61.614; -0.038 1.258 0.372 -43.297; -0.107 -0.344 1.182 19.272; 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 1.36278 -0.00438 0.09280 -61.61366; -0.03776 1.25826 0.37192 -43.29714; -0.10746 -0.34419 1.18204 19.27242; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.36278 -0.00438 0.09280 -61.61366; -0.03776 1.25826 0.37192 -43.29714; -0.10746 -0.34419 1.18204 19.27242; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.363 -0.004 0.093 -61.614; -0.038 1.258 0.372 -43.297; -0.107 -0.344 1.182 19.272; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -4.0 (old=-4.9) transform before final EM align: 1.363 -0.004 0.093 -61.614; -0.038 1.258 0.372 -43.297; -0.107 -0.344 1.182 19.272; 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 1.36278 -0.00438 0.09280 -61.61366; -0.03776 1.25826 0.37192 -43.29714; -0.10746 -0.34419 1.18204 19.27242; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.36278 -0.00438 0.09280 -61.61366; -0.03776 1.25826 0.37192 -43.29714; -0.10746 -0.34419 1.18204 19.27242; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 010: -log(p) = 4.4 after pass:transform: ( 1.36, -0.00, 0.09, -61.61) ( -0.04, 1.26, 0.37, -43.30) ( -0.11, -0.34, 1.18, 19.27) dfp_em_step_func: 011: -log(p) = 4.4 after pass:transform: ( 1.36, -0.00, 0.09, -61.61) ( -0.04, 1.26, 0.37, -43.30) ( -0.11, -0.34, 1.18, 19.27) dfp_em_step_func: 012: -log(p) = 4.4 after pass:transform: ( 1.36, -0.00, 0.09, -61.61) ( -0.04, 1.26, 0.37, -43.30) ( -0.11, -0.34, 1.18, 19.27) dfp_em_step_func: 013: -log(p) = 4.4 after pass:transform: ( 1.36, -0.00, 0.09, -61.61) ( -0.04, 1.26, 0.37, -43.30) ( -0.11, -0.34, 1.18, 19.27) dfp_em_step_func: 014: -log(p) = 4.4 after pass:transform: ( 1.36, -0.00, 0.09, -61.61) ( -0.04, 1.26, 0.37, -43.30) ( -0.11, -0.34, 1.18, 19.27) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 016: -log(p) = 4.4 tol 0.000000 final transform: 1.363 -0.004 0.093 -61.614; -0.038 1.258 0.372 -43.297; -0.107 -0.344 1.182 19.272; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 34 minutes and 43 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=91 z=115 r=86 first estimation of the main basin volume: 2755782 voxels Looking for seedpoints 2 found in the cerebellum 11 found in the rest of the brain global maximum in x=148, y=88, z=86, 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=14613975146 voxels, voxel volume =1.000 = 14613975146 mmm3 = 14613975.040 cm3 done. PostAnalyze...Basin Prior 56 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=128,y=101, z=112, r=9755 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=9 , nb = 46017 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=26 , nb = -1034370054 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=19 , nb = 1090663681 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=9 , nb = -1074963069 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=9 , nb = 1077707658 OTHER CSF_MIN=0, CSF_intensity=6, CSF_MAX=22 , nb = 1071528312 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 9, 12, 22, 41 after analyzing : 9, 20, 25, 25 RIGHT_CER before analyzing : 26, 22, 15, 60 after analyzing : 22, 24, 25, 33 LEFT_CER before analyzing : 19, 17, 15, 61 after analyzing : 17, 22, 25, 31 RIGHT_BRAIN before analyzing : 9, 12, 22, 41 after analyzing : 9, 20, 25, 25 LEFT_BRAIN before analyzing : 9, 11, 21, 45 after analyzing : 9, 20, 25, 26 OTHER before analyzing : 22, 51, 79, 94 after analyzing : 22, 69, 79, 75 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...70 iterations *********************VALIDATION********************* curvature mean = -0.014, std = 0.013 curvature mean = 65.272, std = 8.437 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 1.57, sigma = 2.44 after rotation: sse = 1.57, sigma = 2.44 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 1.60, its var is 2.07 before Erosion-Dilatation 0.00% 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...39 iterations mri_strip_skull: done peeling brain Brain Size = 1394742 voxels, voxel volume = 1.000 mm3 = 1394742 mmm3 = 1394.742 cm3 ****************************** Saving brainmask.auto.mgz done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Thu Aug 8 11:37:48 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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=23.1 skull bounding box = (70, 43, 42) --> (186, 171, 200) using (109, 86, 121) as brain centroid... mean wm in atlas = 107, using box (95,70,102) --> (123, 101,140) 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 = -4.5 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.234900 @ (-9.091, 9.091, -9.091) max log p = -4.113619 @ (4.545, 4.545, -4.545) max log p = -4.087676 @ (2.273, -2.273, -2.273) max log p = -4.074259 @ (-1.136, 1.136, 1.136) max log p = -4.065760 @ (1.705, 0.568, -0.568) max log p = -4.065760 @ (0.000, 0.000, 0.000) Found translation: (-1.7, 13.1, -15.3): log p = -4.066 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.6, old_max_log_p =-4.1 (thresh=-4.1) 1.150 0.000 0.000 -20.982; 0.000 1.194 0.278 -33.543; 0.000 -0.320 1.038 21.380; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.6, old_max_log_p =-3.6 (thresh=-3.6) 1.150 0.000 0.000 -20.982; 0.000 1.194 0.278 -33.543; 0.000 -0.320 1.038 21.380; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.4, old_max_log_p =-3.6 (thresh=-3.6) 1.190 -0.019 0.071 -34.107; 0.003 1.217 0.284 -37.056; -0.072 -0.307 0.997 30.254; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4) 1.168 -0.018 0.070 -31.090; 0.003 1.217 0.284 -37.056; -0.072 -0.307 0.997 30.254; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.3, old_max_log_p =-3.4 (thresh=-3.4) 1.170 0.004 0.066 -33.669; -0.015 1.223 0.267 -32.903; -0.063 -0.289 1.006 27.154; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3) 1.167 0.004 0.066 -33.293; -0.015 1.224 0.267 -33.081; -0.063 -0.289 1.006 27.154; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3) 1.167 0.004 0.066 -33.293; -0.015 1.226 0.267 -33.259; -0.063 -0.289 1.006 27.623; 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 1.16713 0.00415 0.06623 -33.29273; -0.01545 1.22590 0.26728 -33.25930; -0.06331 -0.28872 1.00580 27.62313; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 1.16713 0.00415 0.06623 -33.29273; -0.01545 1.22590 0.26728 -33.25930; -0.06331 -0.28872 1.00580 27.62313; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.167 0.004 0.066 -33.293; -0.015 1.226 0.267 -33.259; -0.063 -0.289 1.006 27.623; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.3 (old=-4.5) transform before final EM align: 1.167 0.004 0.066 -33.293; -0.015 1.226 0.267 -33.259; -0.063 -0.289 1.006 27.623; 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 1.16713 0.00415 0.06623 -33.29273; -0.01545 1.22590 0.26728 -33.25930; -0.06331 -0.28872 1.00580 27.62313; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 1.16713 0.00415 0.06623 -33.29273; -0.01545 1.22590 0.26728 -33.25930; -0.06331 -0.28872 1.00580 27.62313; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 010: -log(p) = 3.9 after pass:transform: ( 1.17, 0.00, 0.07, -33.29) ( -0.02, 1.23, 0.27, -33.26) ( -0.06, -0.29, 1.01, 27.62) dfp_em_step_func: 011: -log(p) = 3.9 after pass:transform: ( 1.17, 0.00, 0.07, -33.29) ( -0.02, 1.23, 0.27, -33.26) ( -0.06, -0.29, 1.01, 27.62) dfp_em_step_func: 012: -log(p) = 3.8 after pass:transform: ( 1.17, 0.00, 0.07, -33.29) ( -0.02, 1.23, 0.27, -33.26) ( -0.06, -0.29, 1.01, 27.62) dfp_em_step_func: 013: -log(p) = 3.8 after pass:transform: ( 1.17, 0.00, 0.07, -33.29) ( -0.02, 1.23, 0.27, -33.26) ( -0.06, -0.29, 1.01, 27.62) dfp_em_step_func: 014: -log(p) = 3.8 after pass:transform: ( 1.17, 0.00, 0.07, -33.29) ( -0.02, 1.23, 0.27, -33.26) ( -0.06, -0.29, 1.01, 27.62) dfp_em_step_func: 015: -log(p) = 3.8 after pass:transform: ( 1.17, 0.00, 0.07, -33.29) ( -0.02, 1.23, 0.27, -33.26) ( -0.06, -0.29, 1.01, 27.62) dfp_em_step_func: 016: -log(p) = 3.8 after pass:transform: ( 1.17, 0.00, 0.07, -33.29) ( -0.02, 1.23, 0.27, -33.26) ( -0.06, -0.29, 1.01, 27.62) dfp_em_step_func: 017: -log(p) = 3.8 after pass:transform: ( 1.17, 0.00, 0.07, -33.29) ( -0.02, 1.23, 0.27, -33.26) ( -0.06, -0.29, 1.01, 27.62) dfp_em_step_func: 018: -log(p) = 3.8 after pass:transform: ( 1.17, 0.00, 0.07, -33.29) ( -0.02, 1.23, 0.27, -33.26) ( -0.06, -0.29, 1.01, 27.62) dfp_em_step_func: 019: -log(p) = 3.8 after pass:transform: ( 1.17, 0.01, 0.07, -33.29) ( -0.01, 1.23, 0.27, -33.26) ( -0.06, -0.28, 1.01, 27.62) dfp_em_step_func: 020: -log(p) = 3.8 after pass:transform: ( 1.17, 0.01, 0.07, -33.29) ( -0.01, 1.23, 0.28, -33.26) ( -0.06, -0.28, 1.01, 27.62) 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... dfp_em_step_func: 021: -log(p) = 3.8 after pass:transform: ( 1.17, 0.01, 0.07, -33.29) ( -0.01, 1.23, 0.28, -33.26) ( -0.06, -0.28, 1.01, 27.62) dfp_em_step_func: 022: -log(p) = 3.8 after pass:transform: ( 1.17, 0.01, 0.07, -33.29) ( -0.01, 1.23, 0.28, -33.26) ( -0.06, -0.28, 1.01, 27.62) dfp_em_step_func: 023: -log(p) = 3.8 after pass:transform: ( 1.17, 0.01, 0.07, -33.29) ( -0.01, 1.23, 0.28, -33.26) ( -0.06, -0.28, 1.01, 27.62) dfp_em_step_func: 024: -log(p) = 3.8 after pass:transform: ( 1.17, 0.01, 0.07, -33.29) ( -0.01, 1.23, 0.28, -33.26) ( -0.06, -0.28, 1.01, 27.62) 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 3 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 026: -log(p) = 3.8 tol 0.000000 final transform: 1.173 0.007 0.070 -33.293; -0.008 1.233 0.277 -33.259; -0.059 -0.284 1.012 27.623; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 26 minutes and 56 seconds. #-------------------------------------- #@# CA Normalize Thu Aug 8 12:04:43 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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=24.1 skull bounding box = (70, 43, 42) --> (185, 171, 200) using (108, 86, 121) as brain centroid... mean wm in atlas = 107, using box (94,70,102) --> (122, 101,140) to find MRI wm before smoothing, mri peak at 110 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 1.173 0.007 0.070 -33.293; -0.008 1.233 0.277 -33.259; -0.059 -0.284 1.012 27.623; 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, 46, 41) --> (185, 139, 197) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 130.0 0 of 56 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (73, 47, 38) --> (129, 135, 197) Right_Cerebral_White_Matter: limiting intensities to 99.0 --> 130.0 0 of 26 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (131, 117, 69) --> (172, 153, 119) Left_Cerebellum_White_Matter: limiting intensities to 103.0 --> 130.0 7 of 8 (87.5%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (90, 117, 64) --> (130, 152, 118) Right_Cerebellum_White_Matter: limiting intensities to 84.0 --> 130.0 0 of 10 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (114, 108, 100) --> (142, 163, 128) Brain_Stem: limiting intensities to 80.0 --> 130.0 1 of 8 (12.5%) samples deleted using 108 total control points for intensity normalization... bias field = 1.015 +- 0.055 0 of 100 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (127, 46, 41) --> (185, 139, 197) Left_Cerebral_White_Matter: limiting intensities to 99.0 --> 131.0 0 of 92 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (73, 47, 38) --> (129, 135, 197) Right_Cerebral_White_Matter: limiting intensities to 116.0 --> 131.0 69 of 89 (77.5%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (131, 117, 69) --> (172, 153, 119) Left_Cerebellum_White_Matter: limiting intensities to 80.0 --> 131.0 0 of 39 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (90, 117, 64) --> (130, 152, 118) Right_Cerebellum_White_Matter: limiting intensities to 91.0 --> 131.0 9 of 48 (18.8%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (114, 108, 100) --> (142, 163, 128) Brain_Stem: limiting intensities to 71.0 --> 131.0 0 of 68 (0.0%) samples deleted using 336 total control points for intensity normalization... bias field = 0.986 +- 0.066 0 of 258 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (127, 46, 41) --> (185, 139, 197) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 132.0 0 of 193 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (73, 47, 38) --> (129, 135, 197) Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 0 of 175 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (131, 117, 69) --> (172, 153, 119) Left_Cerebellum_White_Matter: limiting intensities to 75.0 --> 132.0 0 of 63 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (90, 117, 64) --> (130, 152, 118) Right_Cerebellum_White_Matter: limiting intensities to 74.0 --> 132.0 0 of 51 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (114, 108, 100) --> (142, 163, 128) Brain_Stem: limiting intensities to 67.0 --> 132.0 0 of 107 (0.0%) samples deleted using 589 total control points for intensity normalization... bias field = 1.027 +- 0.051 1 of 589 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 2 minutes and 1 seconds. #-------------------------------------- #@# CA Reg Thu Aug 8 12:06:45 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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) = 1.56 (predicted orig area = 5.1) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.879, neg=0, invalid=96777 0001: dt=129.472000, rms=0.813 (7.489%), neg=0, invalid=96777 0002: dt=221.952000, rms=0.786 (3.298%), neg=0, invalid=96777 0003: dt=55.488000, rms=0.782 (0.533%), neg=0, invalid=96777 0004: dt=221.952000, rms=0.777 (0.592%), neg=0, invalid=96777 0005: dt=129.472000, rms=0.769 (1.125%), neg=0, invalid=96777 0006: dt=32.368000, rms=0.768 (0.087%), neg=0, invalid=96777 0007: dt=32.368000, rms=0.767 (0.068%), neg=0, invalid=96777 0008: dt=32.368000, rms=0.766 (0.119%), neg=0, invalid=96777 0009: dt=32.368000, rms=0.765 (0.196%), neg=0, invalid=96777 0010: dt=32.368000, rms=0.762 (0.318%), neg=0, invalid=96777 0011: dt=32.368000, rms=0.759 (0.410%), neg=0, invalid=96777 0012: dt=32.368000, rms=0.756 (0.427%), neg=0, invalid=96777 0013: dt=32.368000, rms=0.753 (0.393%), neg=0, invalid=96777 0014: dt=32.368000, rms=0.751 (0.341%), neg=0, invalid=96777 0015: dt=32.368000, rms=0.748 (0.303%), neg=0, invalid=96777 0016: dt=32.368000, rms=0.746 (0.265%), neg=0, invalid=96777 0017: dt=32.368000, rms=0.744 (0.246%), neg=0, invalid=96777 0018: dt=32.368000, rms=0.743 (0.243%), neg=0, invalid=96777 0019: dt=32.368000, rms=0.741 (0.268%), neg=0, invalid=96777 0020: dt=32.368000, rms=0.739 (0.286%), neg=0, invalid=96777 0021: dt=32.368000, rms=0.737 (0.270%), neg=0, invalid=96777 0022: dt=32.368000, rms=0.735 (0.248%), neg=0, invalid=96777 0023: dt=32.368000, rms=0.733 (0.216%), neg=0, invalid=96777 0024: dt=32.368000, rms=0.732 (0.188%), neg=0, invalid=96777 0025: dt=32.368000, rms=0.731 (0.158%), neg=0, invalid=96777 0026: dt=32.368000, rms=0.729 (0.157%), neg=0, invalid=96777 0027: dt=32.368000, rms=0.728 (0.178%), neg=0, invalid=96777 0028: dt=32.368000, rms=0.727 (0.192%), neg=0, invalid=96777 0029: dt=32.368000, rms=0.725 (0.193%), neg=0, invalid=96777 0030: dt=32.368000, rms=0.724 (0.179%), neg=0, invalid=96777 0031: dt=32.368000, rms=0.723 (0.154%), neg=0, invalid=96777 0032: dt=32.368000, rms=0.722 (0.133%), neg=0, invalid=96777 0033: dt=32.368000, rms=0.721 (0.124%), neg=0, invalid=96777 0034: dt=32.368000, rms=0.720 (0.123%), neg=0, invalid=96777 0035: dt=517.888000, rms=0.718 (0.302%), neg=0, invalid=96777 0036: dt=27.744000, rms=0.718 (0.018%), neg=0, invalid=96777 0037: dt=27.744000, rms=0.718 (0.002%), neg=0, invalid=96777 0038: dt=27.744000, rms=0.718 (-0.022%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.718, neg=0, invalid=96777 0039: dt=32.368000, rms=0.718 (0.025%), neg=0, invalid=96777 0040: dt=92.480000, rms=0.717 (0.044%), neg=0, invalid=96777 0041: dt=369.920000, rms=0.716 (0.188%), neg=0, invalid=96777 0042: dt=32.368000, rms=0.716 (0.017%), neg=0, invalid=96777 0043: dt=32.368000, rms=0.716 (0.014%), neg=0, invalid=96777 0044: dt=32.368000, rms=0.716 (0.021%), neg=0, invalid=96777 0045: dt=32.368000, rms=0.715 (0.028%), neg=0, invalid=96777 0046: dt=32.368000, rms=0.715 (0.045%), neg=0, invalid=96777 0047: dt=32.368000, rms=0.715 (0.059%), neg=0, invalid=96777 0048: dt=32.368000, rms=0.714 (0.075%), neg=0, invalid=96777 0049: dt=32.368000, rms=0.714 (0.073%), neg=0, invalid=96777 0050: dt=32.368000, rms=0.713 (0.064%), neg=0, invalid=96777 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.718, neg=0, invalid=96777 0051: dt=145.152000, rms=0.694 (3.277%), neg=0, invalid=96777 0052: dt=124.416000, rms=0.680 (1.961%), neg=0, invalid=96777 0053: dt=36.288000, rms=0.675 (0.805%), neg=0, invalid=96777 0054: dt=103.680000, rms=0.671 (0.539%), neg=0, invalid=96777 0055: dt=31.104000, rms=0.667 (0.661%), neg=0, invalid=96777 0056: dt=36.288000, rms=0.665 (0.317%), neg=0, invalid=96777 0057: dt=124.416000, rms=0.660 (0.691%), neg=0, invalid=96777 0058: dt=20.736000, rms=0.658 (0.357%), neg=0, invalid=96777 0059: dt=580.608000, rms=0.643 (2.333%), neg=0, invalid=96777 0060: dt=25.920000, rms=0.638 (0.636%), neg=0, invalid=96777 0061: dt=36.288000, rms=0.637 (0.185%), neg=0, invalid=96777 0062: dt=36.288000, rms=0.636 (0.138%), neg=0, invalid=96777 0063: dt=36.288000, rms=0.636 (0.132%), neg=0, invalid=96777 0064: dt=36.288000, rms=0.635 (0.137%), neg=0, invalid=96777 0065: dt=36.288000, rms=0.634 (0.179%), neg=0, invalid=96777 0066: dt=36.288000, rms=0.632 (0.307%), neg=0, invalid=96777 0067: dt=36.288000, rms=0.630 (0.328%), neg=0, invalid=96777 0068: dt=36.288000, rms=0.627 (0.329%), neg=0, invalid=96777 0069: dt=36.288000, rms=0.626 (0.302%), neg=0, invalid=96777 0070: dt=36.288000, rms=0.623 (0.373%), neg=0, invalid=96777 0071: dt=36.288000, rms=0.621 (0.404%), neg=0, invalid=96777 0072: dt=36.288000, rms=0.619 (0.333%), neg=0, invalid=96777 0073: dt=36.288000, rms=0.617 (0.257%), neg=0, invalid=96777 0074: dt=36.288000, rms=0.615 (0.264%), neg=0, invalid=96777 0075: dt=36.288000, rms=0.613 (0.326%), neg=0, invalid=96777 0076: dt=36.288000, rms=0.612 (0.252%), neg=0, invalid=96777 0077: dt=36.288000, rms=0.611 (0.178%), neg=0, invalid=96777 0078: dt=36.288000, rms=0.610 (0.153%), neg=0, invalid=96777 0079: dt=36.288000, rms=0.609 (0.168%), neg=0, invalid=96777 0080: dt=36.288000, rms=0.608 (0.151%), neg=0, invalid=96777 0081: dt=36.288000, rms=0.607 (0.131%), neg=0, invalid=96777 0082: dt=36.288000, rms=0.606 (0.097%), neg=0, invalid=96777 0083: dt=36.288000, rms=0.606 (0.089%), neg=0, invalid=96777 0084: dt=36.288000, rms=0.606 (0.042%), neg=0, invalid=96777 0085: dt=36.288000, rms=0.606 (-0.019%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.606, neg=0, invalid=96777 0086: dt=20.736000, rms=0.606 (0.024%), neg=0, invalid=96777 0087: dt=20.736000, rms=0.606 (0.012%), neg=0, invalid=96777 0088: dt=20.736000, rms=0.605 (0.011%), neg=0, invalid=96777 0089: dt=20.736000, rms=0.605 (-0.029%), neg=0, invalid=96777 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.635, neg=0, invalid=96777 0090: dt=1.600000, rms=0.635 (0.006%), neg=0, invalid=96777 0091: dt=0.175000, rms=0.635 (0.003%), neg=0, invalid=96777 0092: dt=0.175000, rms=0.635 (0.000%), neg=0, invalid=96777 0093: dt=0.175000, rms=0.635 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.635, neg=0, invalid=96777 0094: dt=0.000000, rms=0.635 (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=0.719, neg=0, invalid=96777 0095: dt=4.467714, rms=0.698 (3.041%), neg=0, invalid=96777 0096: dt=3.180000, rms=0.696 (0.287%), neg=0, invalid=96777 0097: dt=0.864000, rms=0.695 (0.013%), neg=0, invalid=96777 0098: dt=0.864000, rms=0.695 (-0.006%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.695, neg=0, invalid=96777 0099: dt=0.000000, rms=0.695 (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=0.771, neg=0, invalid=96777 0100: dt=0.902222, rms=0.769 (0.376%), neg=0, invalid=96777 0101: dt=1.792000, rms=0.764 (0.625%), neg=0, invalid=96777 0102: dt=1.140187, rms=0.763 (0.147%), neg=0, invalid=96777 0103: dt=0.570093, rms=0.762 (0.078%), neg=0, invalid=96777 0104: dt=0.570093, rms=0.762 (0.046%), neg=0, invalid=96777 0105: dt=0.570093, rms=0.761 (0.028%), neg=0, invalid=96777 0106: dt=0.384000, rms=0.761 (0.005%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.761, neg=0, invalid=96777 0107: dt=1.584158, rms=0.760 (0.247%), neg=0, invalid=96777 0108: dt=0.000000, rms=0.760 (-0.001%), 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=0.712, neg=0, invalid=96777 0109: dt=0.161017, rms=0.703 (1.266%), neg=0, invalid=96777 0110: dt=0.000375, rms=0.703 (0.003%), neg=0, invalid=96777 0111: dt=0.000375, rms=0.703 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.703, neg=0, invalid=96777 0112: dt=0.028000, rms=0.702 (0.083%), neg=0, invalid=96777 0113: dt=0.112000, rms=0.701 (0.243%), neg=0, invalid=96777 0114: dt=0.028000, rms=0.700 (0.032%), neg=0, invalid=96777 0115: dt=0.028000, rms=0.700 (0.029%), neg=0, invalid=96777 0116: dt=0.028000, rms=0.700 (0.054%), neg=0, invalid=96777 0117: dt=0.028000, rms=0.699 (0.071%), neg=0, invalid=96777 0118: dt=0.028000, rms=0.699 (0.085%), neg=0, invalid=96777 0119: dt=0.028000, rms=0.698 (0.093%), neg=0, invalid=96777 0120: dt=0.028000, rms=0.697 (0.094%), neg=0, invalid=96777 0121: dt=0.028000, rms=0.697 (0.093%), neg=0, invalid=96777 0122: dt=0.028000, rms=0.696 (0.088%), neg=0, invalid=96777 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.15745 ( 7) Left_Lateral_Ventricle (4): linear fit = 0.22 x + 0.0 (1009 voxels, overlap=0.005) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (1009 voxels, peak = 5), gca=9.6 gca peak = 0.14022 (22) mri peak = 0.13549 ( 7) Right_Lateral_Ventricle (43): linear fit = 0.22 x + 0.0 (681 voxels, overlap=0.006) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (681 voxels, peak = 5), gca=8.8 gca peak = 0.24234 (100) mri peak = 0.08392 (90) Right_Pallidum (52): linear fit = 0.90 x + 0.0 (288 voxels, overlap=0.221) Right_Pallidum (52): linear fit = 0.90 x + 0.0 (288 voxels, peak = 90), gca=90.5 gca peak = 0.19192 (97) mri peak = 0.09211 (89) Left_Pallidum (13): linear fit = 0.92 x + 0.0 (232 voxels, overlap=0.421) Left_Pallidum (13): linear fit = 0.92 x + 0.0 (232 voxels, peak = 89), gca=88.8 gca peak = 0.24007 (63) mri peak = 0.11170 (56) Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (369 voxels, overlap=0.299) Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (369 voxels, peak = 55), gca=55.1 gca peak = 0.29892 (64) mri peak = 0.07546 (56) Left_Hippocampus (17): linear fit = 0.85 x + 0.0 (245 voxels, overlap=0.150) Left_Hippocampus (17): linear fit = 0.85 x + 0.0 (245 voxels, peak = 54), gca=54.1 gca peak = 0.12541 (104) mri peak = 0.08353 (106) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (44473 voxels, overlap=0.696) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (44473 voxels, peak = 108), gca=107.6 gca peak = 0.13686 (104) mri peak = 0.08740 (108) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (44250 voxels, overlap=0.583) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (44250 voxels, peak = 109), gca=108.7 gca peak = 0.11691 (63) mri peak = 0.06456 (53) Left_Cerebral_Cortex (3): linear fit = 0.80 x + 0.0 (12646 voxels, overlap=0.067) Left_Cerebral_Cortex (3): linear fit = 0.80 x + 0.0 (12646 voxels, peak = 50), gca=50.1 gca peak = 0.13270 (63) mri peak = 0.06113 (53) Right_Cerebral_Cortex (42): linear fit = 0.80 x + 0.0 (13572 voxels, overlap=0.030) Right_Cerebral_Cortex (42): linear fit = 0.80 x + 0.0 (13572 voxels, peak = 50), gca=50.1 gca peak = 0.15182 (70) mri peak = 0.08264 (65) Right_Caudate (50): linear fit = 0.87 x + 0.0 (408 voxels, overlap=0.217) Right_Caudate (50): linear fit = 0.87 x + 0.0 (408 voxels, peak = 61), gca=60.5 gca peak = 0.14251 (76) mri peak = 0.06446 (56) Left_Caudate (11): linear fit = 0.82 x + 0.0 (554 voxels, overlap=0.024) Left_Caudate (11): linear fit = 0.82 x + 0.0 (554 voxels, peak = 63), gca=62.7 gca peak = 0.12116 (60) mri peak = 0.04686 (53) Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (6784 voxels, overlap=0.981) Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (6784 voxels, peak = 56), gca=56.1 gca peak = 0.12723 (61) mri peak = 0.04360 (58) Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (8805 voxels, overlap=0.974) Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (8805 voxels, peak = 57), gca=57.0 gca peak = 0.22684 (88) mri peak = 0.08989 (90) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (5690 voxels, overlap=0.904) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (5690 voxels, peak = 90), gca=90.2 gca peak = 0.21067 (87) mri peak = 0.07613 (89) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (5630 voxels, overlap=0.965) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (5630 voxels, peak = 90), gca=90.0 gca peak = 0.25455 (62) mri peak = 0.15449 (54) Left_Amygdala (18): linear fit = 0.86 x + 0.0 (250 voxels, overlap=0.367) Left_Amygdala (18): linear fit = 0.86 x + 0.0 (250 voxels, peak = 53), gca=53.0 gca peak = 0.39668 (62) mri peak = 0.09836 (59) Right_Amygdala (54): linear fit = 0.94 x + 0.0 (246 voxels, overlap=1.004) Right_Amygdala (54): linear fit = 0.94 x + 0.0 (246 voxels, peak = 58), gca=58.0 gca peak = 0.10129 (93) mri peak = 0.05466 (87) Left_Thalamus_Proper (10): linear fit = 0.92 x + 0.0 (3847 voxels, overlap=0.681) Left_Thalamus_Proper (10): linear fit = 0.92 x + 0.0 (3847 voxels, peak = 85), gca=85.1 gca peak = 0.12071 (89) mri peak = 0.06454 (80) Right_Thalamus_Proper (49): linear fit = 0.95 x + 0.0 (3298 voxels, overlap=0.842) Right_Thalamus_Proper (49): linear fit = 0.95 x + 0.0 (3298 voxels, peak = 85), gca=85.0 gca peak = 0.13716 (82) mri peak = 0.05280 (75) Left_Putamen (12): linear fit = 0.93 x + 0.0 (1846 voxels, overlap=0.877) Left_Putamen (12): linear fit = 0.93 x + 0.0 (1846 voxels, peak = 76), gca=75.8 gca peak = 0.15214 (84) mri peak = 0.05720 (74) Right_Putamen (51): linear fit = 0.88 x + 0.0 (1623 voxels, overlap=0.454) Right_Putamen (51): linear fit = 0.88 x + 0.0 (1623 voxels, peak = 74), gca=74.3 gca peak = 0.08983 (85) mri peak = 0.08109 (83) Brain_Stem (16): linear fit = 1.02 x + 0.0 (8543 voxels, overlap=0.777) Brain_Stem (16): linear fit = 1.02 x + 0.0 (8543 voxels, peak = 87), gca=87.1 gca peak = 0.11809 (92) mri peak = 0.06588 (97) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (666 voxels, overlap=0.876) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (666 voxels, peak = 94), gca=94.3 gca peak = 0.12914 (94) mri peak = 0.06316 (95) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (845 voxels, overlap=0.889) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (845 voxels, peak = 96), gca=96.3 gca peak = 0.21100 (36) mri peak = 0.44444 (10) gca peak = 0.13542 (27) mri peak = 0.13841 ( 5) Fourth_Ventricle (15): linear fit = 0.19 x + 0.0 (173 voxels, overlap=0.018) Fourth_Ventricle (15): linear fit = 0.19 x + 0.0 (173 voxels, peak = 5), gca=5.0 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 0.85 x + 0.0 estimating mean wm scale to be 1.04 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=0.726, neg=0, invalid=96777 0123: dt=129.472000, rms=0.721 (0.780%), neg=0, invalid=96777 0124: dt=110.976000, rms=0.717 (0.472%), neg=0, invalid=96777 0125: dt=55.488000, rms=0.716 (0.151%), neg=0, invalid=96777 0126: dt=517.888000, rms=0.712 (0.560%), neg=0, invalid=96777 0127: dt=32.368000, rms=0.711 (0.128%), neg=0, invalid=96777 0128: dt=110.976000, rms=0.711 (0.095%), neg=0, invalid=96777 0129: dt=129.472000, rms=0.710 (0.143%), neg=0, invalid=96777 0130: dt=55.488000, rms=0.709 (0.065%), neg=0, invalid=96777 0131: dt=1479.680000, rms=0.704 (0.689%), neg=0, invalid=96777 0132: dt=32.368000, rms=0.703 (0.200%), neg=0, invalid=96777 0133: dt=32.368000, rms=0.703 (0.031%), neg=0, invalid=96777 0134: dt=32.368000, rms=0.703 (0.013%), neg=0, invalid=96777 0135: dt=32.368000, rms=0.703 (0.011%), neg=0, invalid=96777 0136: dt=32.368000, rms=0.702 (0.030%), neg=0, invalid=96777 0137: dt=32.368000, rms=0.702 (0.040%), neg=0, invalid=96777 0138: dt=32.368000, rms=0.702 (0.054%), neg=0, invalid=96777 0139: dt=32.368000, rms=0.701 (0.055%), neg=0, invalid=96777 0140: dt=32.368000, rms=0.701 (0.061%), neg=0, invalid=96777 0141: dt=32.368000, rms=0.700 (0.066%), neg=0, invalid=96777 0142: dt=32.368000, rms=0.700 (0.065%), neg=0, invalid=96777 0143: dt=32.368000, rms=0.699 (0.065%), neg=0, invalid=96777 0144: dt=32.368000, rms=0.699 (0.078%), neg=0, invalid=96777 0145: dt=32.368000, rms=0.698 (0.084%), neg=0, invalid=96777 0146: dt=32.368000, rms=0.698 (0.078%), neg=0, invalid=96777 0147: dt=32.368000, rms=0.697 (0.082%), neg=0, invalid=96777 0148: dt=32.368000, rms=0.697 (0.078%), neg=0, invalid=96777 0149: dt=32.368000, rms=0.696 (0.074%), neg=0, invalid=96777 0150: dt=32.368000, rms=0.696 (0.072%), neg=0, invalid=96777 0151: dt=32.368000, rms=0.695 (0.060%), neg=0, invalid=96777 0152: dt=32.368000, rms=0.695 (0.061%), neg=0, invalid=96777 0153: dt=32.368000, rms=0.694 (0.059%), neg=0, invalid=96777 0154: dt=32.368000, rms=0.694 (0.056%), neg=0, invalid=96777 0155: dt=32.368000, rms=0.694 (0.049%), neg=0, invalid=96777 0156: dt=32.368000, rms=0.693 (0.049%), neg=0, invalid=96777 0157: dt=32.368000, rms=0.693 (0.051%), neg=0, invalid=96777 0158: dt=32.368000, rms=0.693 (0.051%), neg=0, invalid=96777 0159: dt=32.368000, rms=0.692 (0.052%), neg=0, invalid=96777 0160: dt=32.368000, rms=0.692 (0.047%), neg=0, invalid=96777 0161: dt=32.368000, rms=0.692 (0.049%), neg=0, invalid=96777 0162: dt=32.368000, rms=0.691 (0.048%), neg=0, invalid=96777 0163: dt=32.368000, rms=0.691 (0.048%), neg=0, invalid=96777 0164: dt=32.368000, rms=0.691 (0.047%), neg=0, invalid=96777 0165: dt=32.368000, rms=0.690 (0.044%), neg=0, invalid=96777 0166: dt=32.368000, rms=0.690 (0.044%), neg=0, invalid=96777 0167: dt=32.368000, rms=0.690 (0.046%), neg=0, invalid=96777 0168: dt=32.368000, rms=0.689 (0.044%), neg=0, invalid=96777 0169: dt=32.368000, rms=0.689 (0.045%), neg=0, invalid=96777 0170: dt=32.368000, rms=0.689 (0.042%), neg=0, invalid=96777 0171: dt=32.368000, rms=0.689 (0.039%), neg=0, invalid=96777 0172: dt=32.368000, rms=0.688 (0.039%), neg=0, invalid=96777 0173: dt=32.368000, rms=0.688 (0.036%), neg=0, invalid=96777 0174: dt=32.368000, rms=0.688 (0.038%), neg=0, invalid=96777 0175: dt=32.368000, rms=0.687 (0.035%), neg=0, invalid=96777 0176: dt=32.368000, rms=0.687 (0.033%), neg=0, invalid=96777 0177: dt=32.368000, rms=0.687 (0.034%), neg=0, invalid=96777 0178: dt=32.368000, rms=0.687 (0.034%), neg=0, invalid=96777 0179: dt=32.368000, rms=0.687 (0.033%), neg=0, invalid=96777 0180: dt=32.368000, rms=0.686 (0.032%), neg=0, invalid=96777 0181: dt=32.368000, rms=0.686 (0.033%), neg=0, invalid=96777 0182: dt=32.368000, rms=0.686 (0.032%), neg=0, invalid=96777 0183: dt=32.368000, rms=0.686 (0.030%), neg=0, invalid=96777 0184: dt=32.368000, rms=0.685 (0.031%), neg=0, invalid=96777 0185: dt=32.368000, rms=0.685 (0.030%), neg=0, invalid=96777 0186: dt=32.368000, rms=0.685 (0.029%), neg=0, invalid=96777 0187: dt=32.368000, rms=0.685 (0.028%), neg=0, invalid=96777 0188: dt=32.368000, rms=0.685 (0.029%), neg=0, invalid=96777 0189: dt=32.368000, rms=0.684 (0.028%), neg=0, invalid=96777 0190: dt=32.368000, rms=0.684 (0.029%), neg=0, invalid=96777 0191: dt=32.368000, rms=0.684 (0.028%), neg=0, invalid=96777 0192: dt=32.368000, rms=0.684 (0.028%), neg=0, invalid=96777 0193: dt=32.368000, rms=0.684 (0.024%), neg=0, invalid=96777 0194: dt=32.368000, rms=0.684 (0.023%), neg=0, invalid=96777 0195: dt=517.888000, rms=0.683 (0.043%), neg=0, invalid=96777 0196: dt=27.744000, rms=0.683 (0.004%), neg=0, invalid=96777 0197: dt=27.744000, rms=0.683 (0.001%), neg=0, invalid=96777 0198: dt=27.744000, rms=0.683 (0.002%), neg=0, invalid=96777 0199: dt=27.744000, rms=0.683 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.683, neg=0, invalid=96777 0200: dt=110.976000, rms=0.683 (0.052%), neg=0, invalid=96777 0201: dt=369.920000, rms=0.682 (0.112%), neg=0, invalid=96777 0202: dt=129.472000, rms=0.682 (0.071%), neg=0, invalid=96777 0203: dt=32.368000, rms=0.682 (0.004%), neg=0, invalid=96777 0204: dt=32.368000, rms=0.682 (0.007%), neg=0, invalid=96777 0205: dt=32.368000, rms=0.681 (0.012%), neg=0, invalid=96777 0206: dt=32.368000, rms=0.681 (0.019%), neg=0, invalid=96777 0207: dt=32.368000, rms=0.681 (0.026%), neg=0, invalid=96777 0208: dt=32.368000, rms=0.681 (0.028%), neg=0, invalid=96777 0209: dt=32.368000, rms=0.681 (0.026%), neg=0, invalid=96777 0210: dt=32.368000, rms=0.681 (0.026%), neg=0, invalid=96777 0211: dt=32.368000, rms=0.680 (0.021%), neg=0, invalid=96777 0212: dt=32.368000, rms=0.680 (0.021%), neg=0, invalid=96777 0213: dt=32.368000, rms=0.680 (0.022%), neg=0, invalid=96777 0214: dt=32.368000, rms=0.680 (0.021%), neg=0, invalid=96777 0215: dt=295.936000, rms=0.680 (0.032%), neg=0, invalid=96777 0216: dt=32.368000, rms=0.680 (0.010%), neg=0, invalid=96777 0217: dt=32.368000, rms=0.680 (-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=0.680, neg=0, invalid=96777 0218: dt=145.152000, rms=0.669 (1.692%), neg=0, invalid=96777 0219: dt=36.288000, rms=0.664 (0.677%), neg=0, invalid=96777 0220: dt=331.776000, rms=0.653 (1.696%), neg=0, invalid=96777 0221: dt=31.104000, rms=0.647 (0.976%), neg=0, invalid=96777 0222: dt=36.288000, rms=0.644 (0.347%), neg=0, invalid=96777 0223: dt=36.288000, rms=0.643 (0.161%), neg=0, invalid=96777 0224: dt=36.288000, rms=0.642 (0.209%), neg=0, invalid=96777 0225: dt=36.288000, rms=0.641 (0.143%), neg=0, invalid=96777 0226: dt=62.208000, rms=0.640 (0.225%), neg=0, invalid=96777 0227: dt=25.920000, rms=0.639 (0.155%), neg=0, invalid=96777 0228: dt=36.288000, rms=0.638 (0.167%), neg=0, invalid=96777 0229: dt=331.776000, rms=0.633 (0.692%), neg=0, invalid=96777 0230: dt=7.776000, rms=0.631 (0.322%), neg=0, invalid=96777 0231: dt=1.944000, rms=0.631 (0.055%), neg=0, invalid=96777 0232: dt=0.141750, rms=0.631 (0.000%), neg=0, invalid=96777 0233: dt=0.035437, rms=0.631 (0.003%), neg=0, invalid=96777 0234: dt=0.004430, rms=0.631 (0.000%), neg=0, invalid=96777 0235: dt=0.000277, rms=0.631 (0.000%), neg=0, invalid=96777 0236: dt=0.000000, rms=0.631 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.631, neg=0, invalid=96777 0237: dt=0.000000, rms=0.631 (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=0.635, neg=0, invalid=96777 0238: dt=0.000000, rms=0.635 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.635, neg=0, invalid=96777 0239: dt=0.000000, rms=0.635 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.647, neg=0, invalid=96777 0240: dt=1.008000, rms=0.641 (0.924%), neg=0, invalid=96777 0241: dt=1.008000, rms=0.635 (0.862%), neg=0, invalid=96777 0242: dt=4.032000, rms=0.615 (3.109%), neg=0, invalid=96777 0243: dt=3.456000, rms=0.603 (1.958%), neg=0, invalid=96777 0244: dt=11.520000, rms=0.574 (4.800%), neg=0, invalid=96777 0245: dt=4.032000, rms=0.571 (0.589%), neg=0, invalid=96777 0246: dt=16.128000, rms=0.560 (1.891%), neg=0, invalid=96777 0247: dt=5.244444, rms=0.559 (0.237%), neg=0, invalid=96777 0248: dt=4.595745, rms=0.558 (0.196%), neg=0, invalid=96777 0249: dt=5.000000, rms=0.557 (0.179%), neg=0, invalid=96777 0250: dt=4.186047, rms=0.556 (0.149%), neg=0, invalid=96777 0251: dt=5.600000, rms=0.555 (0.156%), neg=0, invalid=96777 0252: dt=4.689655, rms=0.554 (0.129%), neg=0, invalid=96777 0253: dt=4.242424, rms=0.554 (0.106%), neg=0, invalid=96777 0254: dt=5.066667, rms=0.553 (0.118%), neg=0, invalid=96777 0255: dt=4.521739, rms=0.553 (0.083%), neg=0, invalid=96777 0256: dt=11.520000, rms=0.552 (0.101%), neg=0, invalid=96777 0257: dt=3.692308, rms=0.551 (0.136%), neg=0, invalid=96777 0258: dt=11.520000, rms=0.551 (0.117%), neg=0, invalid=96777 0259: dt=2.924731, rms=0.550 (0.096%), neg=0, invalid=96777 0260: dt=11.520000, rms=0.550 (0.111%), neg=0, invalid=96777 0261: dt=3.456000, rms=0.549 (0.071%), neg=0, invalid=96777 0262: dt=9.216000, rms=0.549 (0.076%), neg=0, invalid=96777 0263: dt=4.032000, rms=0.548 (0.059%), neg=0, invalid=96777 0264: dt=4.032000, rms=0.548 (0.045%), neg=0, invalid=96777 0265: dt=4.032000, rms=0.548 (0.030%), neg=0, invalid=96777 0266: dt=4.032000, rms=0.548 (0.067%), neg=0, invalid=96777 0267: dt=4.032000, rms=0.547 (0.098%), neg=0, invalid=96777 0268: dt=4.032000, rms=0.547 (0.101%), neg=0, invalid=96777 0269: dt=4.032000, rms=0.546 (0.120%), neg=0, invalid=96777 0270: dt=4.032000, rms=0.545 (0.109%), neg=0, invalid=96777 0271: dt=4.032000, rms=0.545 (0.140%), neg=0, invalid=96777 0272: dt=4.032000, rms=0.544 (0.130%), neg=0, invalid=96777 0273: dt=4.032000, rms=0.543 (0.109%), neg=0, invalid=96777 0274: dt=4.032000, rms=0.543 (0.096%), neg=0, invalid=96777 0275: dt=4.032000, rms=0.542 (0.095%), neg=0, invalid=96777 0276: dt=4.032000, rms=0.542 (0.084%), neg=0, invalid=96777 0277: dt=4.032000, rms=0.541 (0.082%), neg=0, invalid=96777 0278: dt=4.032000, rms=0.541 (0.071%), neg=0, invalid=96777 0279: dt=4.032000, rms=0.541 (0.056%), neg=0, invalid=96777 0280: dt=4.032000, rms=0.540 (0.060%), neg=0, invalid=96777 0281: dt=4.032000, rms=0.540 (0.045%), neg=0, invalid=96777 0282: dt=4.032000, rms=0.540 (0.060%), neg=0, invalid=96777 0283: dt=4.032000, rms=0.539 (0.058%), neg=0, invalid=96777 0284: dt=4.032000, rms=0.539 (0.046%), neg=0, invalid=96777 0285: dt=4.032000, rms=0.539 (0.040%), neg=0, invalid=96777 0286: dt=4.032000, rms=0.539 (0.030%), neg=0, invalid=96777 0287: dt=4.032000, rms=0.539 (0.029%), neg=0, invalid=96777 0288: dt=4.032000, rms=0.539 (0.023%), neg=0, invalid=96777 0289: dt=4.032000, rms=0.538 (0.027%), neg=0, invalid=96777 0290: dt=4.032000, rms=0.538 (0.037%), neg=0, invalid=96777 0291: dt=4.032000, rms=0.538 (0.029%), neg=0, invalid=96777 0292: dt=4.032000, rms=0.538 (0.027%), neg=0, invalid=96777 0293: dt=4.032000, rms=0.538 (0.027%), neg=0, invalid=96777 0294: dt=4.032000, rms=0.538 (0.032%), neg=0, invalid=96777 0295: dt=4.032000, rms=0.537 (0.020%), neg=0, invalid=96777 0296: dt=4.032000, rms=0.537 (0.014%), neg=0, invalid=96777 0297: dt=2.880000, rms=0.537 (0.002%), neg=0, invalid=96777 0298: dt=2.880000, rms=0.537 (0.004%), neg=0, invalid=96777 0299: dt=2.880000, rms=0.537 (-0.003%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.537, neg=0, invalid=96777 0300: dt=1.008000, rms=0.537 (0.001%), neg=0, invalid=96777 0301: dt=0.063000, rms=0.537 (-0.002%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.559, neg=0, invalid=96777 0302: dt=0.000000, rms=0.559 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.559, neg=0, invalid=96777 0303: dt=0.000000, rms=0.559 (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=0.523, neg=0, invalid=96777 0304: dt=0.179097, rms=0.514 (1.572%), neg=0, invalid=96777 0305: dt=0.028000, rms=0.514 (0.169%), neg=0, invalid=96777 0306: dt=0.143858, rms=0.509 (0.800%), neg=0, invalid=96777 0307: dt=0.320000, rms=0.503 (1.334%), neg=0, invalid=96777 0308: dt=0.007000, rms=0.503 (0.018%), neg=0, invalid=96777 0309: dt=0.007000, rms=0.502 (0.015%), neg=0, invalid=96777 0310: dt=0.007000, rms=0.502 (0.027%), neg=0, invalid=96777 0311: dt=0.007000, rms=0.502 (0.039%), neg=0, invalid=96777 0312: dt=0.007000, rms=0.502 (0.047%), neg=0, invalid=96777 0313: dt=0.007000, rms=0.502 (0.059%), neg=0, invalid=96777 0314: dt=0.007000, rms=0.501 (0.061%), neg=0, invalid=96777 0315: dt=0.007000, rms=0.501 (0.069%), neg=0, invalid=96777 0316: dt=0.007000, rms=0.501 (0.073%), neg=0, invalid=96777 0317: dt=0.007000, rms=0.500 (0.081%), neg=0, invalid=96777 0318: dt=0.007000, rms=0.500 (0.081%), neg=0, invalid=96777 0319: dt=0.007000, rms=0.499 (0.081%), neg=0, invalid=96777 0320: dt=0.007000, rms=0.499 (0.083%), neg=0, invalid=96777 0321: dt=0.007000, rms=0.499 (0.083%), neg=0, invalid=96777 0322: dt=0.007000, rms=0.498 (0.083%), neg=0, invalid=96777 0323: dt=0.007000, rms=0.498 (0.079%), neg=0, invalid=96777 0324: dt=0.007000, rms=0.497 (0.077%), neg=0, invalid=96777 0325: dt=0.007000, rms=0.497 (0.076%), neg=0, invalid=96777 0326: dt=0.007000, rms=0.497 (0.075%), neg=0, invalid=96777 0327: dt=0.007000, rms=0.496 (0.075%), neg=0, invalid=96777 0328: dt=0.007000, rms=0.496 (0.068%), neg=0, invalid=96777 0329: dt=0.007000, rms=0.496 (0.066%), neg=0, invalid=96777 0330: dt=0.007000, rms=0.495 (0.063%), neg=0, invalid=96777 0331: dt=0.007000, rms=0.495 (0.060%), neg=0, invalid=96777 0332: dt=0.007000, rms=0.495 (0.056%), neg=0, invalid=96777 0333: dt=0.007000, rms=0.494 (0.051%), neg=0, invalid=96777 0334: dt=0.007000, rms=0.494 (0.052%), neg=0, invalid=96777 0335: dt=0.007000, rms=0.494 (0.047%), neg=0, invalid=96777 0336: dt=0.007000, rms=0.494 (0.044%), neg=0, invalid=96777 0337: dt=0.007000, rms=0.494 (0.040%), neg=0, invalid=96777 0338: dt=0.007000, rms=0.493 (0.038%), neg=0, invalid=96777 0339: dt=0.007000, rms=0.493 (0.036%), neg=0, invalid=96777 0340: dt=0.007000, rms=0.493 (0.033%), neg=0, invalid=96777 0341: dt=0.007000, rms=0.493 (0.031%), neg=0, invalid=96777 0342: dt=0.007000, rms=0.493 (0.027%), neg=0, invalid=96777 0343: dt=0.007000, rms=0.493 (0.030%), neg=0, invalid=96777 0344: dt=0.007000, rms=0.493 (0.001%), neg=0, invalid=96777 0345: dt=0.007000, rms=0.493 (0.002%), neg=0, invalid=96777 0346: dt=0.007000, rms=0.493 (0.002%), neg=0, invalid=96777 0347: dt=0.320000, rms=0.492 (0.046%), neg=0, invalid=96777 0348: dt=0.005001, rms=0.492 (0.003%), neg=0, invalid=96777 0349: dt=0.005001, rms=0.492 (0.000%), neg=0, invalid=96777 0350: dt=0.005001, rms=0.492 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.492, neg=0, invalid=96777 0351: dt=0.112778, rms=0.491 (0.324%), neg=0, invalid=96777 0352: dt=0.112000, rms=0.490 (0.244%), neg=0, invalid=96777 0353: dt=0.028000, rms=0.489 (0.047%), neg=0, invalid=96777 0354: dt=0.028000, rms=0.489 (0.044%), neg=0, invalid=96777 0355: dt=0.028000, rms=0.489 (0.086%), neg=0, invalid=96777 0356: dt=0.028000, rms=0.488 (0.109%), neg=0, invalid=96777 0357: dt=0.028000, rms=0.488 (0.128%), neg=0, invalid=96777 0358: dt=0.028000, rms=0.487 (0.142%), neg=0, invalid=96777 0359: dt=0.007000, rms=0.487 (0.000%), neg=0, invalid=96777 0360: dt=0.007000, rms=0.487 (0.006%), neg=0, invalid=96777 0361: dt=0.007000, rms=0.487 (0.007%), neg=0, invalid=96777 0362: dt=0.007000, rms=0.487 (0.010%), neg=0, invalid=96777 0363: dt=0.007000, rms=0.487 (0.015%), neg=0, invalid=96777 0364: dt=0.007000, rms=0.487 (0.017%), neg=0, invalid=96777 0365: dt=0.007000, rms=0.486 (0.018%), neg=0, invalid=96777 0366: dt=0.007000, rms=0.486 (0.022%), neg=0, invalid=96777 0367: dt=0.007000, rms=0.486 (0.018%), neg=0, invalid=96777 0368: dt=0.112000, rms=0.486 (0.046%), neg=0, invalid=96777 0369: dt=0.096000, rms=0.486 (0.030%), neg=0, invalid=96777 0370: dt=0.001500, rms=0.486 (0.004%), neg=0, invalid=96777 0371: dt=0.001500, rms=0.486 (0.000%), neg=0, invalid=96777 0372: dt=0.001500, rms=0.486 (0.001%), neg=0, invalid=96777 0373: dt=0.001500, rms=0.486 (0.001%), neg=0, invalid=96777 0374: dt=0.001500, rms=0.486 (-0.000%), 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=0.484, neg=0, invalid=96777 0375: dt=32.368000, rms=0.484 (0.004%), neg=0, invalid=96777 0376: dt=73.984000, rms=0.484 (0.009%), neg=0, invalid=96777 0377: dt=1.734000, rms=0.484 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.484, neg=0, invalid=96777 0378: dt=92.480000, rms=0.484 (0.039%), neg=0, invalid=96777 0379: dt=129.472000, rms=0.483 (0.062%), neg=0, invalid=96777 0380: dt=27.744000, rms=0.483 (0.009%), neg=0, invalid=96777 0381: dt=27.744000, rms=0.483 (0.011%), neg=0, invalid=96777 0382: dt=27.744000, rms=0.483 (0.014%), neg=0, invalid=96777 0383: dt=27.744000, rms=0.483 (0.017%), neg=0, invalid=96777 0384: dt=27.744000, rms=0.483 (0.025%), neg=0, invalid=96777 0385: dt=27.744000, rms=0.483 (0.026%), neg=0, invalid=96777 0386: dt=27.744000, rms=0.483 (0.022%), neg=0, invalid=96777 0387: dt=27.744000, rms=0.483 (0.019%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.483, neg=0, invalid=96777 0388: dt=36.288000, rms=0.482 (0.227%), neg=0, invalid=96777 0389: dt=36.288000, rms=0.481 (0.112%), neg=0, invalid=96777 0390: dt=36.288000, rms=0.481 (0.073%), neg=0, invalid=96777 0391: dt=36.288000, rms=0.480 (0.077%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0392: dt=36.288000, rms=0.480 (0.014%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0393: dt=36.288000, rms=0.480 (-0.067%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.480, neg=0, invalid=96777 0394: dt=82.944000, rms=0.478 (0.529%), neg=0, invalid=96777 0395: dt=31.104000, rms=0.477 (0.158%), neg=0, invalid=96777 0396: dt=31.104000, rms=0.477 (0.052%), neg=0, invalid=96777 0397: dt=31.104000, rms=0.476 (0.138%), neg=0, invalid=96777 0398: dt=31.104000, rms=0.475 (0.172%), neg=0, invalid=96777 0399: dt=31.104000, rms=0.475 (0.163%), neg=0, invalid=96777 0400: dt=31.104000, rms=0.474 (0.109%), neg=0, invalid=96777 0401: dt=31.104000, rms=0.473 (0.127%), neg=0, invalid=96777 0402: dt=31.104000, rms=0.473 (0.111%), neg=0, invalid=96777 0403: dt=31.104000, rms=0.472 (0.136%), neg=0, invalid=96777 0404: dt=31.104000, rms=0.472 (0.083%), neg=0, invalid=96777 0405: dt=31.104000, rms=0.471 (0.082%), neg=0, invalid=96777 0406: dt=25.920000, rms=0.471 (0.018%), neg=0, invalid=96777 0407: dt=25.920000, rms=0.471 (0.023%), neg=0, invalid=96777 0408: dt=25.920000, rms=0.471 (0.019%), neg=0, invalid=96777 0409: dt=25.920000, rms=0.471 (0.019%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.471, neg=0, invalid=96777 iter 0, gcam->neg = 9 after 1 iterations, nbhd size=0, neg = 0 0410: dt=32.000000, rms=0.469 (0.610%), neg=0, invalid=96777 0411: dt=19.200000, rms=0.467 (0.263%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0412: dt=11.200000, rms=0.466 (0.220%), neg=0, invalid=96777 0413: dt=11.200000, rms=0.466 (0.033%), neg=0, invalid=96777 0414: dt=11.200000, rms=0.465 (0.282%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 7 iterations, nbhd size=1, neg = 0 0415: dt=11.200000, rms=0.464 (0.262%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 1 iterations, nbhd size=0, neg = 0 0416: dt=11.200000, rms=0.462 (0.269%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0417: dt=11.200000, rms=0.461 (0.226%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0418: dt=11.200000, rms=0.460 (0.218%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0419: dt=11.200000, rms=0.459 (0.186%), neg=0, invalid=96777 0420: dt=11.200000, rms=0.459 (0.189%), neg=0, invalid=96777 0421: dt=11.200000, rms=0.458 (0.198%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0422: dt=11.200000, rms=0.457 (0.180%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0423: dt=11.200000, rms=0.456 (0.177%), neg=0, invalid=96777 0424: dt=11.200000, rms=0.455 (0.145%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0425: dt=11.200000, rms=0.455 (0.125%), neg=0, invalid=96777 0426: dt=11.200000, rms=0.454 (0.142%), neg=0, invalid=96777 0427: dt=11.200000, rms=0.454 (0.126%), neg=0, invalid=96777 0428: dt=11.200000, rms=0.453 (0.157%), neg=0, invalid=96777 0429: dt=11.200000, rms=0.452 (0.111%), neg=0, invalid=96777 0430: dt=11.200000, rms=0.452 (0.109%), neg=0, invalid=96777 0431: dt=11.200000, rms=0.452 (0.036%), neg=0, invalid=96777 0432: dt=11.200000, rms=0.452 (0.034%), neg=0, invalid=96777 0433: dt=11.200000, rms=0.451 (0.037%), neg=0, invalid=96777 0434: dt=11.200000, rms=0.451 (0.046%), neg=0, invalid=96777 0435: dt=11.200000, rms=0.451 (0.042%), neg=0, invalid=96777 0436: dt=11.200000, rms=0.451 (0.026%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.451, neg=0, invalid=96777 iter 0, gcam->neg = 12 after 10 iterations, nbhd size=1, neg = 0 0437: dt=44.800000, rms=0.448 (0.712%), neg=0, invalid=96777 0438: dt=9.600000, rms=0.447 (0.157%), neg=0, invalid=96777 0439: dt=9.600000, rms=0.447 (0.094%), neg=0, invalid=96777 0440: dt=9.600000, rms=0.446 (0.120%), neg=0, invalid=96777 0441: dt=9.600000, rms=0.445 (0.136%), neg=0, invalid=96777 0442: dt=9.600000, rms=0.445 (0.120%), neg=0, invalid=96777 0443: dt=9.600000, rms=0.444 (0.110%), neg=0, invalid=96777 0444: dt=11.200000, rms=0.444 (0.046%), neg=0, invalid=96777 0445: dt=11.200000, rms=0.444 (0.024%), neg=0, invalid=96777 0446: dt=11.200000, rms=0.444 (0.041%), neg=0, invalid=96777 0447: dt=11.200000, rms=0.444 (0.040%), neg=0, invalid=96777 0448: dt=11.200000, rms=0.444 (0.055%), neg=0, invalid=96777 0449: dt=11.200000, rms=0.443 (0.067%), neg=0, invalid=96777 0450: dt=11.200000, rms=0.443 (0.058%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.449, neg=0, invalid=96777 0451: dt=0.864000, rms=0.449 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.449, neg=0, invalid=96777 0452: dt=2.424242, rms=0.448 (0.040%), neg=0, invalid=96777 0453: dt=2.880000, rms=0.448 (0.022%), neg=0, invalid=96777 0454: dt=2.880000, rms=0.448 (-0.011%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.458, neg=0, invalid=96777 0455: dt=0.448000, rms=0.458 (0.027%), neg=0, invalid=96777 0456: dt=0.312500, rms=0.458 (0.007%), neg=0, invalid=96777 0457: dt=0.312500, rms=0.458 (-0.009%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.458, neg=0, invalid=96777 iter 0, gcam->neg = 9 after 7 iterations, nbhd size=1, neg = 0 0458: dt=1.173333, rms=0.457 (0.167%), neg=0, invalid=96777 0459: dt=0.004000, rms=0.457 (0.000%), neg=0, invalid=96777 0460: dt=0.004000, rms=0.457 (0.000%), neg=0, invalid=96777 0461: dt=0.004000, rms=0.457 (0.000%), neg=0, invalid=96777 0462: dt=0.004000, rms=0.457 (0.001%), neg=0, invalid=96777 0463: dt=0.004000, rms=0.457 (0.001%), neg=0, invalid=96777 0464: dt=0.004000, rms=0.457 (-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=0.446, neg=0, invalid=96777 iter 0, gcam->neg = 919 after 11 iterations, nbhd size=1, neg = 0 0465: dt=1.441713, rms=0.412 (7.562%), neg=0, invalid=96777 0466: dt=0.000094, rms=0.412 (-0.014%), neg=0, invalid=96777 0467: dt=0.000094, rms=0.412 (0.001%), neg=0, invalid=96777 0468: dt=0.000094, rms=0.412 (-0.003%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.412, neg=0, invalid=96777 0469: dt=0.000109, rms=0.412 (0.000%), neg=0, invalid=96777 0470: dt=0.000000, rms=0.412 (0.000%), neg=0, invalid=96777 0471: dt=0.000000, rms=0.412 (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=0.404, neg=0, invalid=96777 0472: dt=0.003613, rms=0.405 (-0.262%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.405, neg=0, invalid=96777 0473: dt=8.092000, rms=0.405 (0.001%), neg=0, invalid=96777 0474: dt=8.092000, rms=0.405 (0.000%), neg=0, invalid=96777 0475: dt=8.092000, rms=0.405 (-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=0.405, neg=0, invalid=96777 0476: dt=0.000000, rms=0.405 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.405, neg=0, invalid=96777 0477: dt=31.104000, rms=0.405 (0.026%), neg=0, invalid=96777 0478: dt=82.944000, rms=0.405 (0.030%), neg=0, invalid=96777 0479: dt=145.152000, rms=0.405 (0.049%), neg=0, invalid=96777 0480: dt=36.288000, rms=0.405 (0.007%), neg=0, invalid=96777 0481: dt=36.288000, rms=0.405 (0.005%), neg=0, invalid=96777 0482: dt=36.288000, rms=0.405 (0.009%), neg=0, invalid=96777 0483: dt=36.288000, rms=0.405 (0.014%), neg=0, invalid=96777 0484: dt=36.288000, rms=0.404 (0.015%), neg=0, invalid=96777 0485: dt=36.288000, rms=0.404 (0.013%), neg=0, invalid=96777 0486: dt=36.288000, rms=0.404 (0.009%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.405, neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0487: dt=11.200000, rms=0.405 (0.067%), neg=0, invalid=96777 0488: dt=2.800000, rms=0.404 (0.004%), neg=0, invalid=96777 0489: dt=2.800000, rms=0.404 (0.011%), neg=0, invalid=96777 0490: dt=2.800000, rms=0.404 (0.012%), neg=0, invalid=96777 0491: dt=2.800000, rms=0.404 (0.000%), neg=0, invalid=96777 0492: dt=2.800000, rms=0.404 (-0.023%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.404, neg=0, invalid=96777 iter 0, gcam->neg = 16 after 9 iterations, nbhd size=1, neg = 0 0493: dt=19.200000, rms=0.404 (0.183%), neg=0, invalid=96777 0494: dt=11.200000, rms=0.403 (0.121%), neg=0, invalid=96777 0495: dt=11.200000, rms=0.403 (0.129%), neg=0, invalid=96777 0496: dt=11.200000, rms=0.402 (0.192%), neg=0, invalid=96777 iter 0, gcam->neg = 5 after 8 iterations, nbhd size=1, neg = 0 0497: dt=11.200000, rms=0.401 (0.188%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0498: dt=11.200000, rms=0.401 (0.150%), neg=0, invalid=96777 iter 0, gcam->neg = 6 after 24 iterations, nbhd size=3, neg = 0 0499: dt=11.200000, rms=0.400 (0.043%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 7 iterations, nbhd size=1, neg = 0 0500: dt=11.200000, rms=0.400 (0.052%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0501: dt=11.200000, rms=0.400 (0.041%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 8 iterations, nbhd size=1, neg = 0 0502: dt=25.600000, rms=0.399 (0.162%), neg=0, invalid=96777 0503: dt=11.200000, rms=0.399 (0.045%), neg=0, invalid=96777 0504: dt=11.200000, rms=0.399 (0.052%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0505: dt=11.200000, rms=0.399 (0.076%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 14 iterations, nbhd size=2, neg = 0 0506: dt=11.200000, rms=0.398 (0.052%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 11 iterations, nbhd size=1, neg = 0 0507: dt=11.200000, rms=0.398 (0.019%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.400, neg=0, invalid=96777 0508: dt=0.044792, rms=0.400 (0.000%), neg=0, invalid=96777 iter 0, gcam->neg = 29 after 18 iterations, nbhd size=2, neg = 0 0509: dt=4.516129, rms=0.400 (0.142%), neg=0, invalid=96777 0510: dt=0.003375, rms=0.400 (0.000%), neg=0, invalid=96777 0511: dt=0.003375, rms=0.400 (0.000%), neg=0, invalid=96777 0512: dt=0.003375, rms=0.400 (0.000%), neg=0, invalid=96777 0513: dt=0.003375, rms=0.400 (0.000%), neg=0, invalid=96777 0514: dt=0.003375, rms=0.400 (0.000%), neg=0, invalid=96777 0515: dt=0.003375, rms=0.400 (0.000%), neg=0, invalid=96777 0516: dt=0.003375, rms=0.400 (0.000%), neg=0, invalid=96777 0517: dt=0.003375, rms=0.400 (0.000%), neg=0, invalid=96777 0518: dt=0.003375, rms=0.400 (0.000%), neg=0, invalid=96777 0519: dt=0.003375, rms=0.400 (0.000%), neg=0, invalid=96777 0520: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777 0521: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777 0522: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777 0523: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777 0524: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777 0525: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777 0526: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777 0527: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777 0528: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777 0529: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777 0530: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777 0531: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777 0532: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777 0533: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777 0534: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777 0535: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777 0536: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777 0537: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777 0538: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777 0539: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777 0540: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777 0541: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777 0542: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777 0543: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777 0544: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777 0545: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777 0546: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777 0547: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777 0548: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.400, neg=0, invalid=96777 iter 0, gcam->neg = 140 after 31 iterations, nbhd size=3, neg = 0 0549: dt=10.698413, rms=0.398 (0.379%), neg=0, invalid=96777 0550: dt=0.002811, rms=0.398 (0.000%), neg=0, invalid=96777 0551: dt=0.002811, rms=0.398 (-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=0.402, neg=0, invalid=96777 0552: dt=0.000438, rms=0.402 (0.000%), neg=0, invalid=96777 0553: dt=0.000000, rms=0.402 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.402, neg=0, invalid=96777 0554: dt=0.000375, rms=0.402 (0.000%), neg=0, invalid=96777 0555: dt=0.000000, rms=0.402 (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=0.396, neg=0, invalid=96777 iter 0, gcam->neg = 315 after 21 iterations, nbhd size=2, neg = 0 0556: dt=0.384000, rms=0.388 (1.811%), neg=0, invalid=96777 0557: dt=0.000020, rms=0.388 (0.002%), neg=0, invalid=96777 0558: dt=0.000020, rms=0.388 (0.000%), neg=0, invalid=96777 0559: dt=0.000020, rms=0.388 (0.000%), neg=0, invalid=96777 0560: dt=0.000020, rms=0.388 (0.000%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0561: dt=0.001000, rms=0.388 (0.001%), neg=0, invalid=96777 0562: dt=0.000109, rms=0.388 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.388, neg=0, invalid=96777 iter 0, gcam->neg = 72 after 17 iterations, nbhd size=2, neg = 0 0563: dt=0.079545, rms=0.387 (0.267%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0564: dt=0.000012, rms=0.387 (0.001%), neg=0, invalid=96777 0565: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777 0566: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777 0567: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777 0568: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777 0569: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777 0570: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777 0571: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777 0572: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777 0573: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777 0574: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777 0575: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777 0576: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777 0577: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777 0578: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777 0579: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777 0580: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777 0581: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777 0582: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777 0583: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777 0584: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777 0585: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777 0586: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777 0587: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777 0588: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777 0589: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777 0590: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777 0591: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777 0592: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777 0593: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777 0594: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777 0595: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777 0596: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777 0597: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777 0598: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777 0599: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777 0600: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777 0601: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777 0602: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777 0603: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777 iter 0, gcam->neg = 59 after 16 iterations, nbhd size=2, neg = 0 0604: dt=0.079545, rms=0.386 (0.217%), neg=0, invalid=96777 0605: dt=0.000012, rms=0.386 (0.001%), neg=0, invalid=96777 writing output transformation to transforms/talairach.m3z... GCAMwrite registration took 3 hours, 45 minutes and 10 seconds. #-------------------------------------- #@# CA Reg Inv Thu Aug 8 15:51:55 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 15:53:50 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... 11996396 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 1 minutes and 47 seconds. #-------------------------------------- #@# SkullLTA Thu Aug 8 15:55:38 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=31.3 skull bounding box = (71, 45, 30) --> (189, 182, 194) using (110, 91, 112) as brain centroid... mean wm in atlas = 126, using box (96,74,92) --> (124, 107,132) to find MRI wm before smoothing, mri peak at 110 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=-4.0, old_max_log_p =-4.2 (thresh=-4.2) 1.248 0.007 0.074 -43.432; -0.008 1.233 0.277 -33.259; -0.063 -0.306 1.088 21.742; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.248 0.007 0.074 -43.432; -0.008 1.233 0.277 -33.259; -0.063 -0.306 1.088 21.742; 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 =-4.0 (thresh=-4.0) 1.273 0.019 0.041 -43.984; -0.010 1.245 0.316 -38.566; -0.020 -0.342 1.058 21.291; 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) 1.296 0.019 0.042 -47.167; -0.010 1.245 0.316 -38.566; -0.020 -0.342 1.058 21.291; 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) 1.296 0.019 0.042 -47.167; -0.010 1.245 0.316 -38.566; -0.020 -0.342 1.058 21.291; 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) 1.291 -0.008 0.053 -46.566; 0.011 1.239 0.334 -44.203; -0.041 -0.363 1.055 26.091; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.290 -0.008 0.053 -46.364; 0.011 1.239 0.334 -44.203; -0.041 -0.363 1.055 26.091; 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 1.28985 -0.00767 0.05333 -46.36439; 0.01112 1.23927 0.33371 -44.20263; -0.04089 -0.36328 1.05452 26.09148; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.28985 -0.00767 0.05333 -46.36439; 0.01112 1.23927 0.33371 -44.20263; -0.04089 -0.36328 1.05452 26.09148; 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: 1.290 -0.008 0.053 -46.364; 0.011 1.239 0.334 -44.203; -0.041 -0.363 1.055 26.091; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -4.0 (old=-4.2) transform before final EM align: 1.290 -0.008 0.053 -46.364; 0.011 1.239 0.334 -44.203; -0.041 -0.363 1.055 26.091; 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 1.28985 -0.00767 0.05333 -46.36439; 0.01112 1.23927 0.33371 -44.20263; -0.04089 -0.36328 1.05452 26.09148; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.28985 -0.00767 0.05333 -46.36439; 0.01112 1.23927 0.33371 -44.20263; -0.04089 -0.36328 1.05452 26.09148; 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: 010: -log(p) = 4.4 tol 0.000000 final transform: 1.290 -0.008 0.053 -46.364; 0.011 1.239 0.334 -44.203; -0.041 -0.363 1.055 26.091; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull_2.lta... registration took 40 minutes and 31 seconds. #-------------------------------------- #@# SubCort Seg Thu Aug 8 16:36:09 CEST 2013 mri_ca_label -align norm.mgz transforms/talairach.m3z /opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz sysname Linux hostname snake4 machine x86_64 setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 = 0.12811 ( 8) Left_Lateral_Ventricle (4): linear fit = 0.25 x + 0.0 (1304 voxels, overlap=0.006) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (1304 voxels, peak = 7), gca=10.8 gca peak = 0.14982 (20) mri peak = 0.10835 ( 6) Right_Lateral_Ventricle (43): linear fit = 0.25 x + 0.0 (642 voxels, overlap=0.008) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (642 voxels, peak = 5), gca=8.0 gca peak = 0.28003 (97) mri peak = 0.06855 (87) Right_Pallidum (52): linear fit = 0.93 x + 0.0 (253 voxels, overlap=0.332) Right_Pallidum (52): linear fit = 0.93 x + 0.0 (253 voxels, peak = 90), gca=89.7 gca peak = 0.18160 (96) mri peak = 0.08019 (92) Left_Pallidum (13): linear fit = 0.93 x + 0.0 (251 voxels, overlap=0.258) Left_Pallidum (13): linear fit = 0.93 x + 0.0 (251 voxels, peak = 89), gca=88.8 gca peak = 0.27536 (62) mri peak = 0.10516 (56) Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (502 voxels, overlap=0.199) Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (502 voxels, peak = 54), gca=54.2 gca peak = 0.32745 (63) mri peak = 0.09957 (54) Left_Hippocampus (17): linear fit = 0.83 x + 0.0 (576 voxels, overlap=0.386) Left_Hippocampus (17): linear fit = 0.83 x + 0.0 (576 voxels, peak = 53), gca=52.6 gca peak = 0.08597 (105) mri peak = 0.08652 (109) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (20917 voxels, overlap=0.608) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (20917 voxels, peak = 109), gca=108.7 gca peak = 0.09209 (106) mri peak = 0.10326 (111) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (19493 voxels, overlap=0.564) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (19493 voxels, peak = 111), gca=110.8 gca peak = 0.07826 (63) mri peak = 0.06236 (53) Left_Cerebral_Cortex (3): linear fit = 0.80 x + 0.0 (10571 voxels, overlap=0.170) Left_Cerebral_Cortex (3): linear fit = 0.80 x + 0.0 (10571 voxels, peak = 50), gca=50.1 gca peak = 0.08598 (64) mri peak = 0.06339 (52) Right_Cerebral_Cortex (42): linear fit = 0.80 x + 0.0 (9805 voxels, overlap=0.110) Right_Cerebral_Cortex (42): linear fit = 0.80 x + 0.0 (9805 voxels, peak = 51), gca=50.9 gca peak = 0.24164 (71) mri peak = 0.10212 (65) Right_Caudate (50): linear fit = 0.88 x + 0.0 (519 voxels, overlap=0.025) Right_Caudate (50): linear fit = 0.88 x + 0.0 (519 voxels, peak = 62), gca=62.1 gca peak = 0.18227 (75) mri peak = 0.10526 (64) Left_Caudate (11): linear fit = 0.81 x + 0.0 (665 voxels, overlap=0.024) Left_Caudate (11): linear fit = 0.81 x + 0.0 (665 voxels, peak = 61), gca=61.1 gca peak = 0.10629 (62) mri peak = 0.04847 (58) Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (5630 voxels, overlap=0.971) Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (5630 voxels, peak = 58), gca=58.0 gca peak = 0.11668 (59) mri peak = 0.05438 (58) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (6967 voxels, overlap=0.971) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (6967 voxels, peak = 57), gca=56.9 gca peak = 0.17849 (88) mri peak = 0.10071 (90) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (4265 voxels, overlap=0.960) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (4265 voxels, peak = 90), gca=90.2 gca peak = 0.16819 (86) mri peak = 0.08158 (89) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (3935 voxels, overlap=0.973) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (3935 voxels, peak = 89), gca=89.0 gca peak = 0.41688 (64) mri peak = 0.10000 (54) Left_Amygdala (18): linear fit = 0.88 x + 0.0 (217 voxels, overlap=1.036) Left_Amygdala (18): linear fit = 0.88 x + 0.0 (217 voxels, peak = 56), gca=56.0 gca peak = 0.42394 (62) mri peak = 0.08115 (64) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (196 voxels, overlap=1.036) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (196 voxels, peak = 62), gca=62.0 gca peak = 0.10041 (96) mri peak = 0.06387 (84) Left_Thalamus_Proper (10): linear fit = 0.92 x + 0.0 (2782 voxels, overlap=0.652) Left_Thalamus_Proper (10): linear fit = 0.92 x + 0.0 (2782 voxels, peak = 88), gca=87.8 gca peak = 0.13978 (88) mri peak = 0.07066 (80) Right_Thalamus_Proper (49): linear fit = 0.95 x + 0.0 (2740 voxels, overlap=0.821) Right_Thalamus_Proper (49): linear fit = 0.95 x + 0.0 (2740 voxels, peak = 84), gca=84.0 gca peak = 0.08514 (81) mri peak = 0.05775 (70) Left_Putamen (12): linear fit = 0.88 x + 0.0 (1709 voxels, overlap=0.538) Left_Putamen (12): linear fit = 0.88 x + 0.0 (1709 voxels, peak = 71), gca=70.9 gca peak = 0.09624 (82) mri peak = 0.07085 (72) Right_Putamen (51): linear fit = 0.88 x + 0.0 (1732 voxels, overlap=0.477) Right_Putamen (51): linear fit = 0.88 x + 0.0 (1732 voxels, peak = 73), gca=72.6 gca peak = 0.07543 (88) mri peak = 0.07695 (83) Brain_Stem (16): linear fit = 1.00 x + 0.0 (8303 voxels, overlap=0.764) Brain_Stem (16): linear fit = 1.00 x + 0.0 (8303 voxels, peak = 88), gca=87.6 gca peak = 0.12757 (95) mri peak = 0.07749 (92) Right_VentralDC (60): linear fit = 1.03 x + 0.0 (638 voxels, overlap=0.823) Right_VentralDC (60): linear fit = 1.03 x + 0.0 (638 voxels, peak = 98), gca=98.3 gca peak = 0.17004 (92) mri peak = 0.06553 (96) Left_VentralDC (28): linear fit = 1.03 x + 0.0 (733 voxels, overlap=0.903) Left_VentralDC (28): linear fit = 1.03 x + 0.0 (733 voxels, peak = 95), gca=95.2 gca peak = 0.21361 (36) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.26069 (23) mri peak = 0.12656 ( 6) Fourth_Ventricle (15): linear fit = 0.22 x + 0.0 (107 voxels, overlap=0.029) Fourth_Ventricle (15): linear fit = 0.22 x + 0.0 (107 voxels, peak = 5), gca=4.9 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak Third_Ventricle = 0.21361 (36) gca peak Fourth_Ventricle = 0.26069 (23) gca peak CSF = 0.14367 (38) gca peak Left_Accumbens_area = 0.57033 (70) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65201 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.31129 (32) gca peak Right_Accumbens_area = 0.30219 (72) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.72939 (42) gca peak WM_hypointensities = 0.14821 (82) gca peak non_WM_hypointensities = 0.10354 (53) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means estimating mean gm scale to be 0.86 x + 0.0 estimating mean wm scale to be 1.04 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 = 0.12811 ( 8) Left_Lateral_Ventricle (4): linear fit = 0.52 x + 0.0 (1304 voxels, overlap=0.465) Left_Lateral_Ventricle (4): linear fit = 0.52 x + 0.0 (1304 voxels, peak = 6), gca=5.8 gca peak = 0.29325 ( 9) mri peak = 0.10835 ( 6) Right_Lateral_Ventricle (43): linear fit = 0.64 x + 0.0 (642 voxels, overlap=0.831) Right_Lateral_Ventricle (43): linear fit = 0.64 x + 0.0 (642 voxels, peak = 6), gca=5.8 gca peak = 0.32313 (90) mri peak = 0.06855 (87) Right_Pallidum (52): linear fit = 0.95 x + 0.0 (253 voxels, overlap=1.028) Right_Pallidum (52): linear fit = 0.95 x + 0.0 (253 voxels, peak = 86), gca=85.9 gca peak = 0.18461 (89) mri peak = 0.08019 (92) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (251 voxels, overlap=1.003) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (251 voxels, peak = 89), gca=88.6 gca peak = 0.29894 (54) mri peak = 0.10516 (56) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (502 voxels, overlap=1.003) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (502 voxels, peak = 54), gca=54.0 gca peak = 0.28418 (53) mri peak = 0.09957 (54) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (576 voxels, overlap=1.006) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (576 voxels, peak = 53), gca=53.0 gca peak = 0.08268 (109) mri peak = 0.08652 (109) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (20917 voxels, overlap=0.755) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (20917 voxels, peak = 110), gca=109.5 gca peak = 0.08584 (111) mri peak = 0.10326 (111) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (19493 voxels, overlap=0.743) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (19493 voxels, peak = 111), gca=111.0 gca peak = 0.09713 (50) mri peak = 0.06236 (53) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (10571 voxels, overlap=0.989) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (10571 voxels, peak = 50), gca=50.0 gca peak = 0.11022 (51) mri peak = 0.06339 (52) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (9805 voxels, overlap=0.974) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (9805 voxels, peak = 50), gca=50.2 gca peak = 0.24028 (64) mri peak = 0.10212 (65) Right_Caudate (50): linear fit = 1.01 x + 0.0 (519 voxels, overlap=1.002) Right_Caudate (50): linear fit = 1.01 x + 0.0 (519 voxels, peak = 65), gca=65.0 gca peak = 0.18407 (61) mri peak = 0.10526 (64) Left_Caudate (11): linear fit = 1.02 x + 0.0 (665 voxels, overlap=0.984) Left_Caudate (11): linear fit = 1.02 x + 0.0 (665 voxels, peak = 63), gca=62.5 gca peak = 0.11245 (58) mri peak = 0.04847 (58) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (5630 voxels, overlap=0.998) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (5630 voxels, peak = 59), gca=59.4 gca peak = 0.12331 (58) mri peak = 0.05438 (58) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (6967 voxels, overlap=1.000) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (6967 voxels, peak = 57), gca=57.1 gca peak = 0.16635 (89) mri peak = 0.10071 (90) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4265 voxels, overlap=0.990) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4265 voxels, peak = 89), gca=88.6 gca peak = 0.16437 (89) mri peak = 0.08158 (89) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (3935 voxels, overlap=0.998) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (3935 voxels, peak = 89), gca=88.6 gca peak = 0.54117 (56) mri peak = 0.10000 (54) Left_Amygdala (18): linear fit = 1.04 x + 0.0 (217 voxels, overlap=1.027) Left_Amygdala (18): linear fit = 1.04 x + 0.0 (217 voxels, peak = 59), gca=58.5 gca peak = 0.38630 (63) mri peak = 0.08115 (64) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (196 voxels, overlap=1.016) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (196 voxels, peak = 63), gca=63.0 gca peak = 0.10601 (88) mri peak = 0.06387 (84) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (2782 voxels, overlap=0.997) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (2782 voxels, peak = 89), gca=89.3 gca peak = 0.14353 (84) mri peak = 0.07066 (80) Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (2740 voxels, overlap=0.989) Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (2740 voxels, peak = 83), gca=82.7 gca peak = 0.09324 (72) mri peak = 0.05775 (70) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1709 voxels, overlap=1.000) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1709 voxels, peak = 72), gca=72.0 gca peak = 0.12381 (67) mri peak = 0.07085 (72) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1732 voxels, overlap=1.000) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1732 voxels, peak = 67), gca=67.0 gca peak = 0.07578 (85) mri peak = 0.07695 (83) Brain_Stem (16): linear fit = 1.00 x + 0.0 (8303 voxels, overlap=0.755) Brain_Stem (16): linear fit = 1.00 x + 0.0 (8303 voxels, peak = 85), gca=84.6 gca peak = 0.13169 (98) mri peak = 0.07749 (92) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (638 voxels, overlap=0.872) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (638 voxels, peak = 98), gca=98.5 gca peak = 0.13795 (96) mri peak = 0.06553 (96) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (733 voxels, overlap=0.928) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (733 voxels, peak = 96), gca=96.5 gca peak = 0.35640 (14) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.33827 ( 9) mri peak = 0.12656 ( 6) Fourth_Ventricle (15): linear fit = 0.57 x + 0.0 (107 voxels, overlap=0.470) Fourth_Ventricle (15): linear fit = 0.57 x + 0.0 (107 voxels, peak = 5), gca=5.2 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.24968 (29) gca peak Third_Ventricle = 0.35640 (14) gca peak Fourth_Ventricle = 0.33827 ( 9) gca peak CSF = 0.30128 (18) gca peak Left_Accumbens_area = 0.68077 (57) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.43860 (61) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.33086 (28) gca peak Right_Accumbens_area = 0.31095 (63) gca peak Right_vessel = 0.53048 (60) gca peak Right_choroid_plexus = 0.10423 (48) gca peak Fifth_Ventricle = 0.45329 (19) gca peak WM_hypointensities = 0.17031 (85) gca peak non_WM_hypointensities = 0.11439 (55) gca peak Optic_Chiasm = 0.34840 (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 0.58 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 8974 gm and wm labels changed (%11 to gray, %89 to white out of all changed labels) 180 hippocampal voxels changed. 1 amygdala voxels changed. pass 1: 74924 changed. image ll: -2.124, PF=1.000 pass 2: 14199 changed. image ll: -2.122, PF=1.000 pass 3: 5409 changed. pass 4: 2603 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 18 minutes and 52 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/cc_up.lta sub010 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/sub010/mri/transforms/cc_up.lta reading aseg from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/aseg.auto_noCCseg.mgz reading norm from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/norm.mgz 20559 voxels in left wm, 30231 in right wm, xrange [125, 133] searching rotation angles z=[-7 7], y=[-4 10] 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 searching scale 1 Z rot 5.0 searching scale 1 Z rot 5.3 searching scale 1 Z rot 5.5 searching scale 1 Z rot 5.8 searching scale 1 Z rot 6.0 searching scale 1 Z rot 6.3 global minimum found at slice 129.6, rotations (2.65, -0.46) final transformation (x=129.6, yr=2.650, zr=-0.463): 0.999 0.008 0.046 -6.994; -0.008 1.000 -0.000 45.088; -0.046 -0.000 0.999 28.104; 0.000 0.000 0.000 1.000; updating x range to be [126, 130] in xformed coordinates best xformed slice 128 cc center is found at 128 148 117 eigenvectors: -0.001 0.000 1.000; -0.137 -0.991 0.000; 0.991 -0.137 0.001; writing aseg with callosum to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/aseg.auto.mgz... corpus callosum matter segmentation took 0.7 minutes #-------------------------------------- #@# Merge ASeg Thu Aug 8 16:55:43 CEST 2013 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Thu Aug 8 16:55:43 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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... 1432 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 55 (55), valley at 23 (23) csf peak at 27, setting threshold to 45 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 24 (24) 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 24 seconds. #-------------------------------------------- #@# Mask BFS Thu Aug 8 17:00:10 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1279546 voxels in mask (pct= 7.63) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Thu Aug 8 17:00:12 CEST 2013 mri_segment brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (107.0): 107.2 +- 4.8 [80.0 --> 125.0] GM (66.0) : 65.2 +- 10.0 [30.0 --> 96.0] setting bottom of white matter range to 75.2 setting top of gray matter range to 85.2 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... 5920 sparsely connected voxels removed... thickening thin strands.... 20 segments, 7387 filled 179 bright non-wm voxels segmented. 3370 diagonally connected voxels added... white matter segmentation took 1.7 minutes writing output to wm.seg.mgz... mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.62 minutes reading wm segmentation from wm.seg.mgz... 82 voxels added to wm to prevent paths from MTL structures to cortex 1099 additional wm voxels added 0 additional wm voxels added SEG EDIT: 47958 voxels turned on, 33998 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+): 19 found - 19 modified | TOTAL: 19 pass 2 (xy+): 0 found - 19 modified | TOTAL: 19 pass 1 (xy-): 15 found - 15 modified | TOTAL: 34 pass 2 (xy-): 0 found - 15 modified | TOTAL: 34 pass 1 (yz+): 27 found - 27 modified | TOTAL: 61 pass 2 (yz+): 0 found - 27 modified | TOTAL: 61 pass 1 (yz-): 17 found - 17 modified | TOTAL: 78 pass 2 (yz-): 0 found - 17 modified | TOTAL: 78 pass 1 (xz+): 12 found - 12 modified | TOTAL: 90 pass 2 (xz+): 0 found - 12 modified | TOTAL: 90 pass 1 (xz-): 11 found - 11 modified | TOTAL: 101 pass 2 (xz-): 0 found - 11 modified | TOTAL: 101 Iteration Number : 1 pass 1 (+++): 11 found - 11 modified | TOTAL: 11 pass 2 (+++): 0 found - 11 modified | TOTAL: 11 pass 1 (+++): 13 found - 13 modified | TOTAL: 24 pass 2 (+++): 0 found - 13 modified | TOTAL: 24 pass 1 (+++): 12 found - 12 modified | TOTAL: 36 pass 2 (+++): 0 found - 12 modified | TOTAL: 36 pass 1 (+++): 15 found - 15 modified | TOTAL: 51 pass 2 (+++): 0 found - 15 modified | TOTAL: 51 Iteration Number : 1 pass 1 (++): 188 found - 188 modified | TOTAL: 188 pass 2 (++): 0 found - 188 modified | TOTAL: 188 pass 1 (+-): 146 found - 146 modified | TOTAL: 334 pass 2 (+-): 0 found - 146 modified | TOTAL: 334 pass 1 (--): 171 found - 171 modified | TOTAL: 505 pass 2 (--): 1 found - 172 modified | TOTAL: 506 pass 3 (--): 0 found - 172 modified | TOTAL: 506 pass 1 (-+): 166 found - 166 modified | TOTAL: 672 pass 2 (-+): 0 found - 166 modified | TOTAL: 672 Iteration Number : 2 pass 1 (xy+): 5 found - 5 modified | TOTAL: 5 pass 2 (xy+): 0 found - 5 modified | TOTAL: 5 pass 1 (xy-): 4 found - 4 modified | TOTAL: 9 pass 2 (xy-): 0 found - 4 modified | TOTAL: 9 pass 1 (yz+): 6 found - 6 modified | TOTAL: 15 pass 2 (yz+): 0 found - 6 modified | TOTAL: 15 pass 1 (yz-): 5 found - 5 modified | TOTAL: 20 pass 2 (yz-): 0 found - 5 modified | TOTAL: 20 pass 1 (xz+): 2 found - 2 modified | TOTAL: 22 pass 2 (xz+): 0 found - 2 modified | TOTAL: 22 pass 1 (xz-): 5 found - 5 modified | TOTAL: 27 pass 2 (xz-): 0 found - 5 modified | TOTAL: 27 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 (++): 2 found - 2 modified | TOTAL: 2 pass 2 (++): 0 found - 2 modified | TOTAL: 2 pass 1 (+-): 4 found - 4 modified | TOTAL: 6 pass 2 (+-): 0 found - 4 modified | TOTAL: 6 pass 1 (--): 1 found - 1 modified | TOTAL: 7 pass 2 (--): 0 found - 1 modified | TOTAL: 7 pass 1 (-+): 2 found - 2 modified | TOTAL: 9 pass 2 (-+): 0 found - 2 modified | TOTAL: 9 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 = 860 (out of 401720: 0.214079) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Thu Aug 8 17:02:36 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 1.173 0.007 0.070 -33.293; -0.008 1.233 0.277 -33.259; -0.059 -0.284 1.012 27.623; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.173 0.007 0.070 -33.293; -0.008 1.233 0.277 -33.259; -0.059 -0.284 1.012 27.623; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1226 (min = 350, max = 1400), aspect = 0.45 (min = 0.10, max = 0.75) no need to search using seed (127, 107, 95), TAL = (1.0, -33.0, 21.0) talairach voxel to voxel transform 0.850 -0.017 -0.054 29.210; -0.005 0.763 -0.209 30.967; 0.048 0.213 0.927 -16.909; 0.000 0.000 0.000 1.000; segmentation indicates cc at (127, 107, 95) --> (1.0, -33.0, 21.0) done. writing output to filled.mgz... filling took 0.9 minutes talairach cc position changed to (1.00, -33.00, 21.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(19.00, -33.00, 21.00) SRC: (114.86, 92.23, 99.16) search lh wm seed point around talairach space (-17.00, -33.00, 21.00), SRC: (145.45, 92.04, 100.88) 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 17:03:30 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 3 found - 3 modified | TOTAL: 4 pass 2 (xy-): 0 found - 3 modified | TOTAL: 4 pass 1 (yz+): 1 found - 1 modified | TOTAL: 5 pass 2 (yz+): 0 found - 1 modified | TOTAL: 5 pass 1 (yz-): 2 found - 2 modified | TOTAL: 7 pass 2 (yz-): 0 found - 2 modified | TOTAL: 7 pass 1 (xz+): 0 found - 0 modified | TOTAL: 7 pass 1 (xz-): 1 found - 1 modified | TOTAL: 8 pass 2 (xz-): 0 found - 1 modified | TOTAL: 8 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 1 found - 1 modified | TOTAL: 2 pass 2 (--): 0 found - 1 modified | TOTAL: 2 pass 1 (-+): 0 found - 0 modified | TOTAL: 2 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 = 10 (out of 192890: 0.005184) 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 50: 3401 vertices, 3592 faces slice 60: 10727 vertices, 11043 faces slice 70: 20151 vertices, 20468 faces slice 80: 29887 vertices, 30243 faces slice 90: 38894 vertices, 39231 faces slice 100: 48437 vertices, 48774 faces slice 110: 57589 vertices, 57925 faces slice 120: 66648 vertices, 67010 faces slice 130: 75605 vertices, 75952 faces slice 140: 85146 vertices, 85508 faces slice 150: 93160 vertices, 93476 faces slice 160: 99455 vertices, 99705 faces slice 170: 105051 vertices, 105292 faces slice 180: 109818 vertices, 110015 faces slice 190: 112861 vertices, 112993 faces slice 200: 113880 vertices, 113928 faces slice 210: 113880 vertices, 113928 faces slice 220: 113880 vertices, 113928 faces slice 230: 113880 vertices, 113928 faces slice 240: 113880 vertices, 113928 faces slice 250: 113880 vertices, 113928 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... 113880 voxel in cpt #1: X=-48 [v=113880,e=341784,f=227856] located at (-26.027784, -18.012205, 33.335861) For the whole surface: X=-48 [v=113880,e=341784,f=227856] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Thu Aug 8 17:03:38 CEST 2013 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 17:03:42 CEST 2013 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts avg radius = 44.8 mm, total surface area = 59841 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.5 minutes Not saving sulc step 000: RMS=0.102 (target=0.015) step 005: RMS=0.076 (target=0.015) step 010: RMS=0.055 (target=0.015) step 015: RMS=0.048 (target=0.015) step 020: RMS=0.041 (target=0.015) step 025: RMS=0.036 (target=0.015) step 030: RMS=0.032 (target=0.015) step 035: RMS=0.030 (target=0.015) step 040: RMS=0.028 (target=0.015) step 045: RMS=0.027 (target=0.015) step 050: RMS=0.026 (target=0.015) step 055: RMS=0.026 (target=0.015) step 060: RMS=0.025 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Thu Aug 8 17:04:09 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.07 +- 0.65 (0.00-->7.38) (max @ vno 51981 --> 52877) face area 0.03 +- 0.04 (-0.29-->0.61) scaling brain by 0.329... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.712, avgs=0 005/300: dt: 0.9000, rms radial error=176.454, avgs=0 010/300: dt: 0.9000, rms radial error=175.900, avgs=0 015/300: dt: 0.9000, rms radial error=175.172, avgs=0 020/300: dt: 0.9000, rms radial error=174.341, avgs=0 025/300: dt: 0.9000, rms radial error=173.456, avgs=0 030/300: dt: 0.9000, rms radial error=172.541, avgs=0 035/300: dt: 0.9000, rms radial error=171.607, avgs=0 040/300: dt: 0.9000, rms radial error=170.666, avgs=0 045/300: dt: 0.9000, rms radial error=169.722, avgs=0 050/300: dt: 0.9000, rms radial error=168.777, avgs=0 055/300: dt: 0.9000, rms radial error=167.835, avgs=0 060/300: dt: 0.9000, rms radial error=166.902, avgs=0 065/300: dt: 0.9000, rms radial error=165.973, avgs=0 070/300: dt: 0.9000, rms radial error=165.048, avgs=0 075/300: dt: 0.9000, rms radial error=164.128, avgs=0 080/300: dt: 0.9000, rms radial error=163.212, avgs=0 085/300: dt: 0.9000, rms radial error=162.301, avgs=0 090/300: dt: 0.9000, rms radial error=161.394, avgs=0 095/300: dt: 0.9000, rms radial error=160.492, avgs=0 100/300: dt: 0.9000, rms radial error=159.594, avgs=0 105/300: dt: 0.9000, rms radial error=158.701, avgs=0 110/300: dt: 0.9000, rms radial error=157.813, avgs=0 115/300: dt: 0.9000, rms radial error=156.930, avgs=0 120/300: dt: 0.9000, rms radial error=156.051, avgs=0 125/300: dt: 0.9000, rms radial error=155.176, avgs=0 130/300: dt: 0.9000, rms radial error=154.307, avgs=0 135/300: dt: 0.9000, rms radial error=153.441, avgs=0 140/300: dt: 0.9000, rms radial error=152.581, avgs=0 145/300: dt: 0.9000, rms radial error=151.725, avgs=0 150/300: dt: 0.9000, rms radial error=150.873, avgs=0 155/300: dt: 0.9000, rms radial error=150.026, avgs=0 160/300: dt: 0.9000, rms radial error=149.184, avgs=0 165/300: dt: 0.9000, rms radial error=148.346, avgs=0 170/300: dt: 0.9000, rms radial error=147.512, avgs=0 175/300: dt: 0.9000, rms radial error=146.684, avgs=0 180/300: dt: 0.9000, rms radial error=145.859, avgs=0 185/300: dt: 0.9000, rms radial error=145.039, avgs=0 190/300: dt: 0.9000, rms radial error=144.224, avgs=0 195/300: dt: 0.9000, rms radial error=143.413, avgs=0 200/300: dt: 0.9000, rms radial error=142.606, avgs=0 205/300: dt: 0.9000, rms radial error=141.804, avgs=0 210/300: dt: 0.9000, rms radial error=141.006, avgs=0 215/300: dt: 0.9000, rms radial error=140.213, avgs=0 220/300: dt: 0.9000, rms radial error=139.424, avgs=0 225/300: dt: 0.9000, rms radial error=138.639, avgs=0 230/300: dt: 0.9000, rms radial error=137.859, avgs=0 235/300: dt: 0.9000, rms radial error=137.082, avgs=0 240/300: dt: 0.9000, rms radial error=136.311, avgs=0 245/300: dt: 0.9000, rms radial error=135.544, avgs=0 250/300: dt: 0.9000, rms radial error=134.781, avgs=0 255/300: dt: 0.9000, rms radial error=134.022, avgs=0 260/300: dt: 0.9000, rms radial error=133.268, avgs=0 265/300: dt: 0.9000, rms radial error=132.518, avgs=0 270/300: dt: 0.9000, rms radial error=131.772, avgs=0 275/300: dt: 0.9000, rms radial error=131.030, avgs=0 280/300: dt: 0.9000, rms radial error=130.292, avgs=0 285/300: dt: 0.9000, rms radial error=129.558, avgs=0 290/300: dt: 0.9000, rms radial error=128.829, avgs=0 295/300: dt: 0.9000, rms radial error=128.103, avgs=0 300/300: dt: 0.9000, rms radial error=127.382, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 13112.08 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00017 epoch 2 (K=40.0), pass 1, starting sse = 2164.42 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00016 epoch 3 (K=160.0), pass 1, starting sse = 231.75 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.09/11 = 0.00782 epoch 4 (K=640.0), pass 1, starting sse = 15.39 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/13 = 0.00536 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.07 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Thu Aug 8 17:08:04 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/sub010/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub010 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=-48 (nv=113880, nf=227856, ne=341784, g=25) 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... 2877 ambiguous faces found in tessellation segmenting defects... 34 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 11 into 8 33 defects to be corrected 0 vertices coincident reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.7635 (-4.8818) -vertex loglikelihood: -6.9151 (-3.4575) -normal dot loglikelihood: -3.6436 (-3.6436) -quad curv loglikelihood: -6.5325 (-3.2663) Total Loglikelihood : -26.8548 CORRECTING DEFECT 0 (vertices=5, convex hull=26) After retessellation of defect 0, euler #=-30 (112015,335104,223059) : difference with theory (-30) = 0 CORRECTING DEFECT 1 (vertices=46, convex hull=86) After retessellation of defect 1, euler #=-29 (112037,335207,223141) : difference with theory (-29) = 0 CORRECTING DEFECT 2 (vertices=338, convex hull=131) After retessellation of defect 2, euler #=-29 (112073,335396,223294) : difference with theory (-28) = 1 CORRECTING DEFECT 3 (vertices=14, convex hull=27) After retessellation of defect 3, euler #=-28 (112075,335411,223308) : difference with theory (-27) = 1 CORRECTING DEFECT 4 (vertices=30, convex hull=64) After retessellation of defect 4, euler #=-27 (112090,335483,223366) : difference with theory (-26) = 1 CORRECTING DEFECT 5 (vertices=38, convex hull=87) After retessellation of defect 5, euler #=-26 (112105,335566,223435) : difference with theory (-25) = 1 CORRECTING DEFECT 6 (vertices=31, convex hull=71) After retessellation of defect 6, euler #=-25 (112120,335642,223497) : difference with theory (-24) = 1 CORRECTING DEFECT 7 (vertices=60, convex hull=90) After retessellation of defect 7, euler #=-24 (112152,335773,223597) : difference with theory (-23) = 1 CORRECTING DEFECT 8 (vertices=41, convex hull=83) After retessellation of defect 8, euler #=-22 (112165,335849,223662) : difference with theory (-22) = 0 CORRECTING DEFECT 9 (vertices=173, convex hull=179) After retessellation of defect 9, euler #=-21 (112188,335999,223790) : difference with theory (-21) = 0 CORRECTING DEFECT 10 (vertices=41, convex hull=80) After retessellation of defect 10, euler #=-20 (112217,336117,223880) : difference with theory (-20) = 0 CORRECTING DEFECT 11 (vertices=50, convex hull=74) After retessellation of defect 11, euler #=-19 (112238,336210,223953) : difference with theory (-19) = 0 CORRECTING DEFECT 12 (vertices=27, convex hull=49) After retessellation of defect 12, euler #=-18 (112256,336283,224009) : difference with theory (-18) = 0 CORRECTING DEFECT 13 (vertices=26, convex hull=81) After retessellation of defect 13, euler #=-17 (112269,336353,224067) : difference with theory (-17) = 0 CORRECTING DEFECT 14 (vertices=88, convex hull=76) After retessellation of defect 14, euler #=-16 (112288,336442,224138) : difference with theory (-16) = 0 CORRECTING DEFECT 15 (vertices=46, convex hull=85) After retessellation of defect 15, euler #=-15 (112298,336504,224191) : difference with theory (-15) = 0 CORRECTING DEFECT 16 (vertices=17, convex hull=20) After retessellation of defect 16, euler #=-14 (112302,336521,224205) : difference with theory (-14) = 0 CORRECTING DEFECT 17 (vertices=16, convex hull=46) After retessellation of defect 17, euler #=-13 (112311,336566,224242) : difference with theory (-13) = 0 CORRECTING DEFECT 18 (vertices=38, convex hull=38) After retessellation of defect 18, euler #=-12 (112319,336602,224271) : difference with theory (-12) = 0 CORRECTING DEFECT 19 (vertices=41, convex hull=30) After retessellation of defect 19, euler #=-11 (112326,336634,224297) : difference with theory (-11) = 0 CORRECTING DEFECT 20 (vertices=25, convex hull=62) After retessellation of defect 20, euler #=-10 (112335,336683,224338) : difference with theory (-10) = 0 CORRECTING DEFECT 21 (vertices=15, convex hull=19) After retessellation of defect 21, euler #=-9 (112337,336697,224351) : difference with theory (-9) = 0 CORRECTING DEFECT 22 (vertices=9, convex hull=25) After retessellation of defect 22, euler #=-8 (112343,336722,224371) : difference with theory (-8) = 0 CORRECTING DEFECT 23 (vertices=61, convex hull=61) After retessellation of defect 23, euler #=-7 (112349,336764,224408) : difference with theory (-7) = 0 CORRECTING DEFECT 24 (vertices=252, convex hull=150) After retessellation of defect 24, euler #=-6 (112395,336974,224573) : difference with theory (-6) = 0 CORRECTING DEFECT 25 (vertices=25, convex hull=53) After retessellation of defect 25, euler #=-5 (112407,337035,224623) : difference with theory (-5) = 0 CORRECTING DEFECT 26 (vertices=21, convex hull=26) After retessellation of defect 26, euler #=-4 (112414,337063,224645) : difference with theory (-4) = 0 CORRECTING DEFECT 27 (vertices=6, convex hull=28) After retessellation of defect 27, euler #=-3 (112416,337077,224658) : difference with theory (-3) = 0 CORRECTING DEFECT 28 (vertices=33, convex hull=69) After retessellation of defect 28, euler #=-2 (112432,337151,224717) : difference with theory (-2) = 0 CORRECTING DEFECT 29 (vertices=37, convex hull=46) After retessellation of defect 29, euler #=-1 (112441,337198,224756) : difference with theory (-1) = 0 CORRECTING DEFECT 30 (vertices=72, convex hull=78) After retessellation of defect 30, euler #=0 (112470,337317,224847) : difference with theory (0) = 0 CORRECTING DEFECT 31 (vertices=98, convex hull=109) After retessellation of defect 31, euler #=1 (112497,337448,224952) : difference with theory (1) = 0 CORRECTING DEFECT 32 (vertices=45, convex hull=89) After retessellation of defect 32, euler #=2 (112521,337557,225038) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.24 (0.04-->11.42) (max @ vno 86901 --> 94849) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.24 (0.04-->11.42) (max @ vno 86901 --> 94849) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 145 mutations (37.1%), 246 crossovers (62.9%), 222 vertices were eliminated building final representation... 1359 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=112521, nf=225038, ne=337557, g=0) writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 23.2 minutes 0 defective edges removing intersecting faces 000: 247 intersecting 001: 14 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 112521 - 337557 + 225038 = 2 --> 0 holes F =2V-4: 225038 = 225042-4 (0) 2E=3F: 675114 = 675114 (0) total defect index = 0 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 33 intersecting 001: 4 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Thu Aug 8 17:31:24 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub010 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/sub010/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/wm.mgz... 13095 bright wm thresholded. 240 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.orig... computing class statistics... border white: 201670 voxels (1.20%) border gray 234473 voxels (1.40%) WM (91.0): 92.1 +- 10.7 [70.0 --> 110.0] GM (73.0) : 71.4 +- 13.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 43.8 (was 70) setting MAX_BORDER_WHITE to 115.7 (was 105) setting MIN_BORDER_WHITE to 57.0 (was 85) setting MAX_CSF to 30.6 (was 40) setting MAX_GRAY to 94.3 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 50.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 17.4 (was 40) repositioning cortical surface to gray/white boundary reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->3.89) (max @ vno 15970 --> 17848) face area 0.28 +- 0.12 (0.00-->2.64) mean absolute distance = 0.64 +- 0.76 2829 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 = 91.7, mean outside = 66.6 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group mean border=70.6, 73 (73) missing vertices, mean dist 0.4 [0.4 (%29.9)->0.7 (%70.1))] %69 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 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.27 (0.08-->5.86) (max @ vno 49307 --> 52883) face area 0.28 +- 0.14 (0.00-->5.09) mean absolute distance = 0.31 +- 0.47 1959 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=6201876.5, rms=13.93 001: dt: 0.5000, sse=6300535.0, rms=10.162 (0.000%) 002: dt: 0.5000, sse=6480750.5, rms=8.034 (0.000%) 003: dt: 0.5000, sse=6603552.0, rms=6.726 (0.000%) 004: dt: 0.5000, sse=6743813.5, rms=5.930 (0.000%) 005: dt: 0.5000, sse=6841023.0, rms=5.489 (0.000%) 006: dt: 0.5000, sse=6893624.5, rms=5.219 (0.000%) 007: dt: 0.5000, sse=6924194.5, rms=5.080 (0.000%) 008: dt: 0.5000, sse=6928049.0, rms=4.941 (0.000%) 009: dt: 0.5000, sse=6892103.0, rms=4.876 (0.000%) 010: dt: 0.5000, sse=6868757.5, rms=4.797 (0.000%) rms = 4.77, time step reduction 1 of 3 to 0.250... 011: dt: 0.5000, sse=6846176.0, rms=4.766 (0.000%) 012: dt: 0.2500, sse=4494396.0, rms=3.470 (0.000%) 013: dt: 0.2500, sse=4136003.0, rms=3.041 (0.000%) 014: dt: 0.2500, sse=3924544.2, rms=2.960 (0.000%) 015: dt: 0.2500, sse=3860050.8, rms=2.866 (0.000%) rms = 2.84, time step reduction 2 of 3 to 0.125... 016: dt: 0.2500, sse=3781857.2, rms=2.843 (0.000%) 017: dt: 0.1250, sse=3528814.0, rms=2.519 (0.000%) 018: dt: 0.1250, sse=3482855.5, rms=2.466 (0.000%) rms = 2.45, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=3453897.2, rms=2.451 (0.000%) positioning took 1.9 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group mean border=75.3, 92 (10) missing vertices, mean dist -0.2 [0.3 (%77.9)->0.3 (%22.1))] %81 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.26 (0.08-->6.05) (max @ vno 49307 --> 52883) face area 0.35 +- 0.17 (0.00-->6.88) mean absolute distance = 0.22 +- 0.31 2809 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4269646.0, rms=6.34 020: dt: 0.5000, sse=4491872.5, rms=4.382 (0.000%) rms = 4.77, time step reduction 1 of 3 to 0.250... 021: dt: 0.2500, sse=4064394.2, rms=3.159 (0.000%) 022: dt: 0.2500, sse=3890573.5, rms=2.627 (0.000%) 023: dt: 0.2500, sse=3841361.5, rms=2.188 (0.000%) rms = 2.18, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=3835740.2, rms=2.182 (0.000%) 025: dt: 0.1250, sse=3668682.2, rms=1.851 (0.000%) 026: dt: 0.1250, sse=3629452.0, rms=1.800 (0.000%) rms = 1.80, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=3602583.0, rms=1.800 (0.000%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group mean border=78.9, 104 (7) missing vertices, mean dist -0.1 [0.2 (%76.8)->0.2 (%23.2))] %88 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 0.91 +- 0.26 (0.09-->6.33) (max @ vno 49307 --> 52883) face area 0.34 +- 0.17 (0.00-->7.12) mean absolute distance = 0.17 +- 0.26 2301 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3951063.5, rms=4.54 028: dt: 0.5000, sse=4325509.0, rms=4.440 (0.000%) rms = 4.54, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=3903438.8, rms=2.806 (0.000%) 030: dt: 0.2500, sse=3766594.8, rms=2.387 (0.000%) 031: dt: 0.2500, sse=3835299.5, rms=2.014 (0.000%) rms = 2.10, time step reduction 2 of 3 to 0.125... 032: dt: 0.1250, sse=3770415.0, rms=1.833 (0.000%) 033: dt: 0.1250, sse=3685747.2, rms=1.575 (0.000%) rms = 1.54, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=3655808.0, rms=1.540 (0.000%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group mean border=80.0, 96 (6) missing vertices, mean dist -0.0 [0.2 (%58.8)->0.2 (%41.2))] %90 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/sub010/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=3681861.5, rms=1.97 rms = 3.05, time step reduction 1 of 3 to 0.250... 035: dt: 0.2500, sse=3760503.0, rms=1.311 (0.000%) 036: dt: 0.2500, sse=3910438.5, rms=1.152 (0.000%) rms = 1.15, time step reduction 2 of 3 to 0.125... 037: dt: 0.2500, sse=3993506.0, rms=1.145 (0.000%) rms = 1.12, time step reduction 3 of 3 to 0.062... 038: dt: 0.1250, sse=4022768.0, rms=1.120 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 10 non-cortical segments detected only using segment with 1669 vertices erasing segment 1 (vno[0] = 70696) erasing segment 2 (vno[0] = 80752) erasing segment 3 (vno[0] = 80816) erasing segment 4 (vno[0] = 88329) erasing segment 5 (vno[0] = 89005) erasing segment 6 (vno[0] = 89818) erasing segment 7 (vno[0] = 91477) erasing segment 8 (vno[0] = 92922) erasing segment 9 (vno[0] = 93559) writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/label/lh.cortex.label... writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.curv writing smoothed area to lh.area writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.area vertex spacing 0.90 +- 0.26 (0.08-->6.42) (max @ vno 49307 --> 52883) face area 0.34 +- 0.17 (0.00-->7.20) refinement took 5.8 minutes #-------------------------------------------- #@# Smooth2 lh Thu Aug 8 17:37:09 CEST 2013 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 17:37:12 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 45.0 mm, total surface area = 69548 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.119 (target=0.015) step 005: RMS=0.081 (target=0.015) step 010: RMS=0.059 (target=0.015) step 015: RMS=0.048 (target=0.015) step 020: RMS=0.040 (target=0.015) step 025: RMS=0.033 (target=0.015) step 030: RMS=0.027 (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=0.018 (target=0.015) step 055: RMS=0.016 (target=0.015) step 060: 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/lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 100 vertices thresholded to be in k1 ~ [-0.76 0.46], k2 ~ [-0.30 0.12] total integrated curvature = 0.531*4pi (6.670) --> 0 handles ICI = 1.4, FI = 8.4, variation=143.686 112 vertices thresholded to be in [-0.05 0.05] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 79 vertices thresholded to be in [-0.26 0.14] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.019, std = 0.023 done. #----------------------------------------- #@# Curvature Stats lh Thu Aug 8 17:39:11 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub010 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 [ sub010/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 [ 235 ] Gb_filter = 0 WARN: S lookup min: -0.685159 WARN: S explicit min: 0.000000 vertex = 1663 #-------------------------------------------- #@# Sphere lh Thu Aug 8 17:39:15 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 0.305... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=snake, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %21.17 pass 1: epoch 2 of 3 starting distance error %21.11 unfolding complete - removing small folds... starting distance error %20.98 removing remaining folds... final distance error %21.01 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/lh.sphere spherical transformation took 0.84 hours #-------------------------------------------- #@# Surf Reg lh Thu Aug 8 18:29:35 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 = 0.575 curvature mean = 0.036, std = 0.938 curvature mean = 0.021, std = 0.867 Starting MRISrigidBodyAlignGlobal() d=32.00 min @ (0.00, -8.00, 0.00) sse = 200972.6, tmin=1.7917 d=8.00 min @ (2.00, 2.00, -2.00) sse = 194728.5, tmin=3.5916 d=4.00 min @ (-1.00, 0.00, 0.00) sse = 193221.5, tmin=4.5166 d=2.00 min @ (0.00, 0.00, 0.50) sse = 193141.8, tmin=5.4543 d=0.50 min @ (0.00, -0.12, -0.12) sse = 193114.1, tmin=7.3045 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 7.30 min curvature mean = 0.028, std = 0.968 curvature mean = 0.009, std = 0.944 curvature mean = 0.026, std = 0.981 curvature mean = 0.004, std = 0.975 curvature mean = 0.026, std = 0.985 curvature mean = 0.001, std = 0.990 2 Reading smoothwm curvature mean = -0.028, std = 0.316 curvature mean = 0.004, std = 0.068 curvature mean = 0.069, std = 0.341 curvature mean = 0.004, std = 0.080 curvature mean = 0.035, std = 0.524 curvature mean = 0.005, std = 0.087 curvature mean = 0.019, std = 0.663 curvature mean = 0.005, std = 0.090 curvature mean = 0.006, std = 0.776 MRISregister() return, current seed 0 writing registered surface to ../surf/lh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white lh Thu Aug 8 18:52:14 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 18:52:16 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 18:52:18 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub010 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... 894 labels changed using aseg relabeling using gibbs priors... 000: 2612 changed, 112521 examined... 001: 561 changed, 11320 examined... 002: 116 changed, 3159 examined... 003: 35 changed, 675 examined... 004: 11 changed, 211 examined... 005: 5 changed, 70 examined... 006: 2 changed, 24 examined... 007: 3 changed, 13 examined... 008: 2 changed, 10 examined... 009: 3 changed, 10 examined... 010: 0 changed, 13 examined... 164 labels changed using aseg 000: 108 total segments, 65 labels (199 vertices) changed 001: 43 total segments, 1 labels (2 vertices) changed 002: 42 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... 1051 vertices marked for relabeling... 1051 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 50 seconds. #-------------------------------------------- #@# Make Pial Surf lh Thu Aug 8 18:53:08 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub010 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/sub010/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/wm.mgz... 13095 bright wm thresholded. 240 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.orig... computing class statistics... border white: 201670 voxels (1.20%) border gray 234473 voxels (1.40%) WM (91.0): 92.1 +- 10.7 [70.0 --> 110.0] GM (73.0) : 71.4 +- 13.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 43.8 (was 70) setting MAX_BORDER_WHITE to 115.7 (was 105) setting MIN_BORDER_WHITE to 57.0 (was 85) setting MAX_CSF to 30.6 (was 40) setting MAX_GRAY to 94.3 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 50.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 17.4 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=57 mean inside = 91.7, mean outside = 66.6 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->3.89) (max @ vno 15970 --> 17848) face area 0.28 +- 0.12 (0.00-->2.64) mean absolute distance = 0.65 +- 0.77 2940 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 23 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 3 with 950 points - only 4.74% unknown deleting segment 4 with 19 points - only 0.00% unknown deleting segment 6 with 6 points - only 0.00% unknown deleting segment 7 with 7 points - only 0.00% unknown deleting segment 8 with 13 points - only 0.00% unknown deleting segment 9 with 17 points - only 0.00% unknown deleting segment 10 with 30 points - only 0.00% unknown deleting segment 11 with 5 points - only 0.00% unknown mean border=70.6, 75 (73) missing vertices, mean dist 0.4 [0.5 (%29.9)->0.7 (%70.1))] %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 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.27 (0.08-->5.86) (max @ vno 49307 --> 52883) face area 0.28 +- 0.14 (0.00-->5.08) mean absolute distance = 0.31 +- 0.48 1990 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=6236135.5, rms=13.89 001: dt: 0.5000, sse=6337606.0, rms=10.134 (0.000%) 002: dt: 0.5000, sse=6519611.5, rms=8.011 (0.000%) 003: dt: 0.5000, sse=6643135.5, rms=6.709 (0.000%) 004: dt: 0.5000, sse=6789308.0, rms=5.916 (0.000%) 005: dt: 0.5000, sse=6884693.0, rms=5.478 (0.000%) 006: dt: 0.5000, sse=6943840.0, rms=5.208 (0.000%) 007: dt: 0.5000, sse=6971964.0, rms=5.070 (0.000%) 008: dt: 0.5000, sse=6980964.0, rms=4.933 (0.000%) 009: dt: 0.5000, sse=6943480.0, rms=4.871 (0.000%) 010: dt: 0.5000, sse=6926897.0, rms=4.792 (0.000%) rms = 4.76, time step reduction 1 of 3 to 0.250... 011: dt: 0.5000, sse=6898367.0, rms=4.763 (0.000%) 012: dt: 0.2500, sse=4528130.5, rms=3.470 (0.000%) 013: dt: 0.2500, sse=4167583.8, rms=3.038 (0.000%) 014: dt: 0.2500, sse=3953588.5, rms=2.957 (0.000%) 015: dt: 0.2500, sse=3887498.2, rms=2.860 (0.000%) rms = 2.83, time step reduction 2 of 3 to 0.125... 016: dt: 0.2500, sse=3807576.8, rms=2.835 (0.000%) 017: dt: 0.1250, sse=3555130.5, rms=2.512 (0.000%) 018: dt: 0.1250, sse=3509869.0, rms=2.461 (0.000%) rms = 2.45, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=3481148.2, rms=2.449 (0.000%) positioning took 1.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 19 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 1 with 1 points - only 0.00% unknown deleting segment 7 with 857 points - only 5.25% unknown removing 4 vertex label from ripped group deleting segment 12 with 5 points - only 0.00% unknown deleting segment 13 with 15 points - only 0.00% unknown deleting segment 14 with 35 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 15 with 4 points - only 0.00% unknown mean border=75.3, 93 (9) missing vertices, mean dist -0.2 [0.3 (%77.9)->0.3 (%22.1))] %82 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.26 (0.12-->6.05) (max @ vno 49307 --> 52883) face area 0.35 +- 0.17 (0.00-->6.88) mean absolute distance = 0.22 +- 0.32 2227 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4306171.0, rms=6.34 020: dt: 0.5000, sse=4528531.0, rms=4.384 (0.000%) rms = 4.76, time step reduction 1 of 3 to 0.250... 021: dt: 0.2500, sse=4098567.5, rms=3.164 (0.000%) 022: dt: 0.2500, sse=3926800.0, rms=2.635 (0.000%) 023: dt: 0.2500, sse=3875310.2, rms=2.198 (0.000%) rms = 2.19, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=3872115.0, rms=2.194 (0.000%) 025: dt: 0.1250, sse=3703568.0, rms=1.867 (0.000%) 026: dt: 0.1250, sse=3667082.5, rms=1.817 (0.000%) rms = 1.82, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=3638557.8, rms=1.815 (0.000%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 15 points - only 0.00% unknown deleting segment 1 with 36 points - only 11.11% unknown removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown deleting segment 3 with 933 points - only 4.82% unknown deleting segment 5 with 7 points - only 0.00% unknown deleting segment 6 with 11 points - only 0.00% unknown deleting segment 7 with 15 points - only 0.00% unknown deleting segment 8 with 20 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 5 points - only 0.00% unknown mean border=78.8, 109 (5) missing vertices, mean dist -0.1 [0.2 (%76.8)->0.2 (%23.2))] %89 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 0.91 +- 0.26 (0.09-->6.33) (max @ vno 49307 --> 52883) face area 0.34 +- 0.17 (0.00-->7.12) mean absolute distance = 0.17 +- 0.26 2322 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3987435.2, rms=4.52 028: dt: 0.5000, sse=4360479.5, rms=4.443 (0.000%) rms = 4.54, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=3937313.8, rms=2.815 (0.000%) 030: dt: 0.2500, sse=3801524.8, rms=2.401 (0.000%) 031: dt: 0.2500, sse=3871084.0, rms=2.033 (0.000%) rms = 2.12, time step reduction 2 of 3 to 0.125... 032: dt: 0.1250, sse=3806410.5, rms=1.855 (0.000%) 033: dt: 0.1250, sse=3722069.0, rms=1.601 (0.000%) rms = 1.56, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=3689253.5, rms=1.565 (0.000%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 11 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 6 points - only 0.00% unknown deleting segment 4 with 940 points - only 4.79% unknown deleting segment 5 with 6 points - only 0.00% unknown deleting segment 6 with 11 points - only 0.00% unknown deleting segment 7 with 16 points - only 0.00% unknown deleting segment 8 with 19 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 5 points - only 0.00% unknown mean border=79.9, 118 (4) missing vertices, mean dist -0.0 [0.2 (%58.8)->0.2 (%41.2))] %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=3715870.0, rms=1.99 rms = 3.05, time step reduction 1 of 3 to 0.250... 035: dt: 0.2500, sse=3797065.5, rms=1.340 (0.000%) 036: dt: 0.2500, sse=3951858.5, rms=1.168 (0.000%) rms = 1.16, time step reduction 2 of 3 to 0.125... 037: dt: 0.2500, sse=4035628.5, rms=1.157 (0.000%) rms = 1.13, time step reduction 3 of 3 to 0.062... 038: dt: 0.1250, sse=4063921.5, rms=1.127 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... smoothing surface for 5 iterations... mean border=46.7, 55 (55) missing vertices, mean dist 1.8 [0.1 (%0.0)->2.3 (%100.0))] %17 local maxima, %57 large gradients and %21 min vals, 1181 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=24858422.0, rms=32.46 001: dt: 0.5000, sse=17687736.0, rms=26.747 (0.000%) 002: dt: 0.5000, sse=12847571.0, rms=22.106 (0.000%) 003: dt: 0.5000, sse=9726175.0, rms=18.430 (0.000%) 004: dt: 0.5000, sse=7884176.5, rms=15.524 (0.000%) 005: dt: 0.5000, sse=6842810.0, rms=13.231 (0.000%) 006: dt: 0.5000, sse=6196642.5, rms=11.439 (0.000%) 007: dt: 0.5000, sse=5854193.0, rms=9.979 (0.000%) 008: dt: 0.5000, sse=5617719.5, rms=8.722 (0.000%) 009: dt: 0.5000, sse=5504031.5, rms=7.647 (0.000%) 010: dt: 0.5000, sse=5451949.0, rms=6.765 (0.000%) 011: dt: 0.5000, sse=5531929.5, rms=6.077 (0.000%) 012: dt: 0.5000, sse=5561197.5, rms=5.522 (0.000%) 013: dt: 0.5000, sse=5675990.0, rms=5.123 (0.000%) 014: dt: 0.5000, sse=5757143.0, rms=4.848 (0.000%) 015: dt: 0.5000, sse=5825581.5, rms=4.640 (0.000%) 016: dt: 0.5000, sse=5866411.5, rms=4.477 (0.000%) 017: dt: 0.5000, sse=5892094.0, rms=4.367 (0.000%) 018: dt: 0.5000, sse=5916866.5, rms=4.278 (0.000%) rms = 4.23, time step reduction 1 of 3 to 0.250... 019: dt: 0.5000, sse=5972314.5, rms=4.232 (0.000%) 020: dt: 0.2500, sse=4336481.5, rms=3.580 (0.000%) 021: dt: 0.2500, sse=4182995.8, rms=3.401 (0.000%) rms = 3.38, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=4078695.0, rms=3.382 (0.000%) 023: dt: 0.1250, sse=3912956.0, rms=3.278 (0.000%) rms = 3.27, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=3889524.8, rms=3.266 (0.000%) positioning took 2.3 minutes mean border=44.1, 612 (13) missing vertices, mean dist 0.2 [0.2 (%46.6)->0.6 (%53.4))] %35 local maxima, %42 large gradients and %18 min vals, 490 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=4512922.5, rms=5.42 025: dt: 0.5000, sse=4742340.5, rms=4.582 (0.000%) 026: dt: 0.5000, sse=5974030.5, rms=4.442 (0.000%) rms = 4.40, time step reduction 1 of 3 to 0.250... 027: dt: 0.5000, sse=5956478.0, rms=4.404 (0.000%) 028: dt: 0.2500, sse=4828224.0, rms=3.590 (0.000%) 029: dt: 0.2500, sse=4726922.5, rms=3.337 (0.000%) rms = 3.31, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=4622455.0, rms=3.309 (0.000%) 031: dt: 0.1250, sse=4461873.0, rms=3.163 (0.000%) rms = 3.14, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=4438586.0, rms=3.138 (0.000%) positioning took 0.8 minutes mean border=41.7, 769 (7) missing vertices, mean dist 0.1 [0.2 (%36.9)->0.4 (%63.1))] %55 local maxima, %21 large gradients and %18 min vals, 557 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=4684454.0, rms=4.47 033: dt: 0.5000, sse=4887963.0, rms=4.203 (0.000%) rms = 4.25, time step reduction 1 of 3 to 0.250... 034: dt: 0.2500, sse=4608592.5, rms=3.488 (0.000%) 035: dt: 0.2500, sse=4814211.5, rms=3.192 (0.000%) 036: dt: 0.2500, sse=4767194.0, rms=3.131 (0.000%) rms = 3.09, time step reduction 2 of 3 to 0.125... 037: dt: 0.2500, sse=4817374.5, rms=3.089 (0.000%) 038: dt: 0.1250, sse=4633848.5, rms=2.952 (0.000%) rms = 2.93, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=4628728.0, rms=2.930 (0.000%) positioning took 0.8 minutes mean border=40.4, 1523 (3) missing vertices, mean dist 0.1 [0.2 (%44.4)->0.3 (%55.6))] %59 local maxima, %17 large gradients and %18 min vals, 401 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/sub010/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=4673022.5, rms=3.26 rms = 3.94, time step reduction 1 of 3 to 0.250... 040: dt: 0.2500, sse=4550543.5, rms=2.969 (0.000%) 041: dt: 0.2500, sse=4697228.0, rms=2.882 (0.000%) rms = 2.85, time step reduction 2 of 3 to 0.125... 042: dt: 0.2500, sse=4765246.5, rms=2.846 (0.000%) 043: dt: 0.1250, sse=4665466.0, rms=2.730 (0.000%) rms = 2.71, time step reduction 3 of 3 to 0.062... 044: dt: 0.1250, sse=4681510.0, rms=2.711 (0.000%) positioning took 0.6 minutes writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.area.pial vertex spacing 1.05 +- 0.45 (0.08-->8.25) (max @ vno 79788 --> 78779) face area 0.44 +- 0.33 (0.00-->9.19) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 112521 vertices processed 25000 of 112521 vertices processed 50000 of 112521 vertices processed 75000 of 112521 vertices processed 100000 of 112521 vertices processed 0 of 112521 vertices processed 25000 of 112521 vertices processed 50000 of 112521 vertices processed 75000 of 112521 vertices processed 100000 of 112521 vertices processed thickness calculation complete, 288:998 truncations. 24574 vertices at 0 distance 73812 vertices at 1 distance 71442 vertices at 2 distance 31784 vertices at 3 distance 8764 vertices at 4 distance 2130 vertices at 5 distance 632 vertices at 6 distance 216 vertices at 7 distance 83 vertices at 8 distance 57 vertices at 9 distance 28 vertices at 10 distance 13 vertices at 11 distance 18 vertices at 12 distance 18 vertices at 13 distance 6 vertices at 14 distance 15 vertices at 15 distance 20 vertices at 16 distance 10 vertices at 17 distance 8 vertices at 18 distance 1 vertices at 19 distance 15 vertices at 20 distance writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.thickness positioning took 11.4 minutes #-------------------------------------------- #@# Surf Volume lh Thu Aug 8 19:04:31 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.volume lh.area.mid mul lh.thickness Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# WM/GM Contrast lh Thu Aug 8 19:04:31 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts pctsurfcon --s sub010 --lh-only Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts/pctsurfcon.log Thu Aug 8 19:04:31 CEST 2013 setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts /opt/freesurfer/5.3.0/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux snake4 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux FREESURFER_HOME /opt/freesurfer/5.3.0 mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/tmp.pctsurfcon.31166/lh.wm.mgh --regheader sub010 --cortex srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/mri/orig.mgz as target reference. Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/label/lh.cortex.label Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 = 87112 Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/label/lh.cortex.label Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/tmp.pctsurfcon.31166/lh.wm.mgh Dim: 112521 1 1 mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/tmp.pctsurfcon.31166/lh.gm.mgh --projfrac 0.3 --regheader sub010 --cortex srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/mri/orig.mgz as target reference. Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/label/lh.cortex.label Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.white Done reading source surface Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 = 100596 Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/label/lh.cortex.label Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/tmp.pctsurfcon.31166/lh.gm.mgh Dim: 112521 1 1 mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/tmp.pctsurfcon.31166/lh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/tmp.pctsurfcon.31166/lh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/surf/lh.w-g.pct.mgh mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.w-g.pct.mgh --annot sub010 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/surf/lh.w-g.pct.mgh --annot sub010 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/stats/lh.w-g.pct.stats --snr sysname Linux hostname snake4 machine x86_64 user fkaule UseRobust 0 Constructing seg from annotation Reading annotation reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Seg base 1000 Loading /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.w-g.pct.mgh Vertex Area is 0.677656 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 1000 unknown 0 0.000 1 1001 bankssts 1374 950.297 2 1002 caudalanteriorcingulate 831 560.371 3 1003 caudalmiddlefrontal 2328 1552.597 4 1004 corpuscallosum 0 0.000 5 1005 cuneus 2341 1516.038 6 1006 entorhinal 463 358.715 7 1007 fusiform 4034 2769.124 8 1008 inferiorparietal 6246 4317.512 9 1009 inferiortemporal 4634 3226.471 10 1010 isthmuscingulate 1325 885.830 11 1011 lateraloccipital 6344 4063.706 12 1012 lateralorbitofrontal 2862 1972.734 13 1013 lingual 4100 2872.105 14 1014 medialorbitofrontal 2135 1399.892 15 1015 middletemporal 3674 2670.622 16 1016 parahippocampal 786 547.957 17 1017 paracentral 1577 1051.674 18 1018 parsopercularis 1879 1318.475 19 1019 parsorbitalis 789 544.669 20 1020 parstriangularis 1446 994.055 21 1021 pericalcarine 2116 1423.561 22 1022 postcentral 5135 3403.305 23 1023 posteriorcingulate 1407 926.874 24 1024 precentral 6317 4196.049 25 1025 precuneus 4869 3313.008 26 1026 rostralanteriorcingulate 1071 731.814 27 1027 rostralmiddlefrontal 7023 4899.621 28 1028 superiorfrontal 8194 5685.728 29 1029 superiorparietal 7149 4715.262 30 1030 superiortemporal 4004 2770.111 31 1031 supramarginal 4432 3006.804 32 1032 frontalpole 271 168.141 33 1033 temporalpole 682 490.979 34 1034 transversetemporal 488 311.560 35 1035 insula 2715 1748.682 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats lh Thu Aug 8 19:04:42 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 sub010 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 1374 950 2563 2.703 0.409 0.124 0.031 13 1.7 bankssts 831 560 2102 3.156 0.651 0.190 0.073 27 2.3 caudalanteriorcingulate 2328 1553 4236 2.449 0.544 0.135 0.045 32 4.2 caudalmiddlefrontal 2341 1516 3529 2.124 0.489 0.170 0.071 52 6.7 cuneus 463 359 1737 3.685 1.063 0.148 0.049 7 0.8 entorhinal 4034 2769 8812 2.683 0.618 0.161 0.064 97 11.2 fusiform 6246 4318 12853 2.547 0.508 0.155 0.062 142 14.8 inferiorparietal 4634 3226 10068 2.477 0.687 0.163 0.080 137 12.8 inferiortemporal 1325 886 2627 2.721 0.812 0.165 0.091 29 3.3 isthmuscingulate 6344 4064 9327 2.052 0.488 0.150 0.053 108 12.9 lateraloccipital 2862 1973 6305 2.690 0.709 0.154 0.070 72 7.4 lateralorbitofrontal 4100 2872 7176 2.214 0.553 0.180 0.095 140 13.1 lingual 2135 1400 4339 2.460 0.829 0.191 0.135 159 11.5 medialorbitofrontal 3674 2671 9393 2.749 0.686 0.166 0.070 105 10.8 middletemporal 786 548 2286 3.504 0.676 0.147 0.056 20 1.6 parahippocampal 1577 1052 2775 2.365 0.523 0.126 0.040 17 2.4 paracentral 1879 1318 3832 2.517 0.452 0.141 0.055 39 4.0 parsopercularis 789 545 2240 2.916 0.676 0.165 0.068 20 2.1 parsorbitalis 1446 994 3095 2.606 0.522 0.156 0.061 31 3.0 parstriangularis 2116 1424 2394 1.745 0.447 0.148 0.064 44 5.0 pericalcarine 5135 3403 8437 2.127 0.587 0.137 0.049 87 9.8 postcentral 1407 927 2665 2.703 0.505 0.149 0.045 28 2.6 posteriorcingulate 6317 4196 12756 2.638 0.510 0.125 0.046 83 10.0 precentral 4869 3313 8841 2.357 0.568 0.146 0.060 101 12.0 precuneus 1071 732 2430 2.798 0.701 0.172 0.075 26 3.2 rostralanteriorcingulate 7023 4900 14490 2.405 0.595 0.172 0.072 178 19.4 rostralmiddlefrontal 8194 5686 19182 2.757 0.617 0.153 0.068 207 17.3 superiorfrontal 7149 4715 11812 2.209 0.464 0.133 0.046 115 13.3 superiorparietal 4004 2770 9678 2.808 0.675 0.127 0.044 83 7.4 superiortemporal 4432 3007 8834 2.510 0.557 0.157 0.069 112 10.3 supramarginal 271 168 770 3.257 0.494 0.205 0.117 10 1.1 frontalpole 682 491 2810 3.642 0.928 0.189 0.098 20 2.8 temporalpole 488 312 875 2.600 0.319 0.155 0.053 8 1.1 transversetemporal 2715 1749 5996 2.927 0.917 0.118 0.136 59 7.4 insula #----------------------------------------- #@# Cortical Parc 2 lh Thu Aug 8 19:04:55 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub010 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... 27 labels changed using aseg relabeling using gibbs priors... 000: 7893 changed, 112521 examined... 001: 1975 changed, 30181 examined... 002: 569 changed, 10037 examined... 003: 242 changed, 3209 examined... 004: 87 changed, 1304 examined... 005: 61 changed, 506 examined... 006: 35 changed, 342 examined... 007: 20 changed, 183 examined... 008: 12 changed, 121 examined... 009: 8 changed, 72 examined... 010: 3 changed, 48 examined... 011: 0 changed, 18 examined... 20 labels changed using aseg 000: 229 total segments, 146 labels (1364 vertices) changed 001: 91 total segments, 8 labels (63 vertices) changed 002: 84 total segments, 1 labels (7 vertices) changed 003: 83 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 112 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 556 vertices marked for relabeling... 556 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 57 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Thu Aug 8 19:05:53 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 sub010 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 1109 739 2276 2.563 0.677 0.179 0.092 32 3.8 G_and_S_frontomargin 1131 789 1972 2.216 0.490 0.144 0.041 17 1.9 G_and_S_occipital_inf 1218 789 2462 2.438 0.503 0.139 0.090 23 2.1 G_and_S_paracentral 1387 924 3095 2.652 0.518 0.167 0.079 39 3.7 G_and_S_subcentral 577 383 1472 2.789 0.591 0.191 0.093 19 1.9 G_and_S_transv_frontopol 2197 1513 4613 2.698 0.614 0.155 0.073 45 5.6 G_and_S_cingul-Ant 1226 858 2707 2.698 0.817 0.155 0.054 23 2.5 G_and_S_cingul-Mid-Ant 1111 756 2055 2.573 0.506 0.123 0.037 13 1.7 G_and_S_cingul-Mid-Post 371 250 1046 3.132 0.477 0.205 0.083 13 1.3 G_cingul-Post-dorsal 263 169 487 2.624 0.928 0.184 0.238 9 0.9 G_cingul-Post-ventral 2136 1360 3236 1.987 0.494 0.176 0.088 58 6.9 G_cuneus 1068 746 2703 2.742 0.437 0.172 0.085 36 3.7 G_front_inf-Opercular 258 175 717 3.165 0.477 0.164 0.067 6 0.7 G_front_inf-Orbital 823 582 2088 2.683 0.486 0.169 0.070 22 1.7 G_front_inf-Triangul 3410 2450 8766 2.672 0.573 0.197 0.077 111 11.2 G_front_middle 5447 3756 14261 2.896 0.584 0.164 0.083 222 13.5 G_front_sup 444 269 1350 3.355 0.906 0.158 0.155 27 2.7 G_Ins_lg_and_S_cent_ins 545 334 1878 3.827 0.736 0.123 0.404 13 1.4 G_insular_short 1850 1182 3931 2.508 0.426 0.179 0.065 56 4.8 G_occipital_middle 1371 869 2231 2.213 0.441 0.152 0.059 31 3.0 G_occipital_sup 1637 1071 4041 2.847 0.520 0.182 0.081 53 6.2 G_oc-temp_lat-fusifor 2779 1923 4986 2.134 0.538 0.190 0.113 105 10.0 G_oc-temp_med-Lingual 1045 749 3417 3.597 0.783 0.143 0.048 21 1.8 G_oc-temp_med-Parahip 2031 1393 5750 2.936 0.649 0.182 0.093 72 6.7 G_orbital 2199 1536 5634 2.727 0.461 0.188 0.094 77 7.2 G_pariet_inf-Angular 2133 1481 5325 2.679 0.569 0.179 0.093 79 6.2 G_pariet_inf-Supramar 2642 1714 5334 2.379 0.483 0.149 0.057 55 6.2 G_parietal_sup 1889 1232 3588 2.284 0.490 0.145 0.051 37 4.1 G_postcentral 2303 1482 5924 2.958 0.376 0.137 0.048 39 4.6 G_precentral 2202 1495 5003 2.569 0.573 0.173 0.079 70 7.4 G_precuneus 907 568 2217 2.714 0.788 0.236 0.178 70 7.5 G_rectus 198 117 349 2.880 1.127 0.133 0.084 4 0.3 G_subcallosal 399 251 894 2.759 0.368 0.165 0.087 27 1.0 G_temp_sup-G_T_transv 1572 1073 5180 3.209 0.601 0.169 0.068 50 4.9 G_temp_sup-Lateral 328 244 1213 3.999 0.888 0.114 0.038 3 0.4 G_temp_sup-Plan_polar 763 547 1583 2.500 0.392 0.095 0.021 5 0.7 G_temp_sup-Plan_tempo 2843 1986 6968 2.565 0.696 0.181 0.098 110 9.3 G_temporal_inf 2091 1540 6671 2.983 0.677 0.191 0.096 80 8.2 G_temporal_middle 315 210 639 2.818 0.415 0.143 0.049 6 0.6 Lat_Fis-ant-Horizont 106 82 161 2.171 0.272 0.116 0.022 1 0.1 Lat_Fis-ant-Vertical 843 557 1141 2.407 0.481 0.130 0.038 7 1.3 Lat_Fis-post 2061 1265 2505 1.718 0.458 0.152 0.067 35 4.8 Pole_occipital 1529 1118 5501 3.161 0.912 0.207 0.124 63 7.7 Pole_temporal 2880 1993 3874 2.034 0.611 0.151 0.062 62 7.3 S_calcarine 2585 1764 3191 1.983 0.579 0.111 0.029 16 3.2 S_central 936 642 1346 2.216 0.460 0.112 0.026 7 1.1 S_cingul-Marginalis 448 310 872 2.735 0.648 0.105 0.026 2 0.5 S_circular_insula_ant 1183 798 1860 2.457 0.581 0.103 0.045 13 2.4 S_circular_insula_inf 1680 1116 2315 2.343 0.394 0.097 0.027 10 1.7 S_circular_insula_sup 1091 776 1909 2.439 0.537 0.108 0.022 8 1.1 S_collat_transv_ant 286 186 310 2.002 0.475 0.171 0.052 5 0.5 S_collat_transv_post 1682 1140 2476 2.170 0.386 0.126 0.034 16 2.2 S_front_inf 1401 964 2130 2.071 0.513 0.143 0.072 22 3.2 S_front_middle 2034 1397 3730 2.416 0.528 0.131 0.043 28 3.2 S_front_sup 319 207 340 1.937 0.259 0.134 0.035 3 0.5 S_interm_prim-Jensen 2941 1970 4126 2.166 0.414 0.113 0.029 25 3.7 S_intrapariet_and_P_trans 1077 711 1305 2.026 0.338 0.121 0.034 8 1.4 S_oc_middle_and_Lunatus 1085 731 1532 2.204 0.380 0.130 0.038 12 1.7 S_oc_sup_and_transversal 582 397 784 2.066 0.327 0.142 0.048 8 1.0 S_occipital_ant 809 532 1141 2.448 0.525 0.129 0.036 8 1.3 S_oc-temp_lat 1529 1086 3056 2.730 0.724 0.153 0.050 31 3.2 S_oc-temp_med_and_Lingual 301 203 432 2.092 0.514 0.129 0.038 3 0.4 S_orbital_lateral 545 380 1021 2.363 1.010 0.119 0.045 12 1.0 S_orbital_med-olfact 892 628 1505 2.381 0.598 0.144 0.049 12 1.9 S_orbital-H_Shaped 1993 1361 2884 2.241 0.467 0.123 0.035 20 2.9 S_parieto_occipital 982 607 1308 2.623 0.898 0.166 0.045 24 1.7 S_pericallosal 2504 1678 3367 2.074 0.444 0.124 0.040 31 3.8 S_postcentral 1490 1013 2427 2.462 0.411 0.118 0.032 16 1.9 S_precentral-inf-part 1052 720 1464 2.237 0.366 0.107 0.024 6 1.2 S_precentral-sup-part 580 384 999 2.189 0.690 0.178 0.099 28 2.3 S_suborbital 846 575 1364 2.304 0.522 0.126 0.039 8 1.3 S_subparietal 1372 961 1812 2.054 0.425 0.138 0.040 19 2.1 S_temporal_inf 4864 3383 8492 2.556 0.485 0.124 0.036 56 7.2 S_temporal_sup 315 225 524 2.518 0.297 0.095 0.018 1 0.3 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Thu Aug 8 19:06:06 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub010 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... 779 labels changed using aseg relabeling using gibbs priors... 000: 2351 changed, 112521 examined... 001: 571 changed, 10363 examined... 002: 147 changed, 3186 examined... 003: 48 changed, 848 examined... 004: 23 changed, 286 examined... 005: 12 changed, 137 examined... 006: 8 changed, 68 examined... 007: 8 changed, 47 examined... 008: 6 changed, 30 examined... 009: 2 changed, 24 examined... 010: 2 changed, 12 examined... 011: 2 changed, 13 examined... 012: 0 changed, 14 examined... 163 labels changed using aseg 000: 66 total segments, 33 labels (220 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 20 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 399 vertices marked for relabeling... 399 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas40.annot... classification took 0 minutes and 50 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Thu Aug 8 19:06:56 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 sub010 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 1373 935 3202 3.001 0.628 0.166 0.060 32 3.2 caudalanteriorcingulate 2337 1569 4298 2.452 0.545 0.134 0.045 32 4.2 caudalmiddlefrontal 3150 2057 4686 2.117 0.475 0.153 0.060 61 7.5 cuneus 430 330 1473 3.587 1.046 0.149 0.046 6 0.8 entorhinal 3635 2476 7715 2.674 0.598 0.155 0.055 77 9.1 fusiform 5747 3975 11756 2.525 0.512 0.156 0.062 131 13.7 inferiorparietal 4697 3290 10433 2.495 0.699 0.163 0.083 139 12.8 inferiortemporal 1341 899 2660 2.723 0.811 0.165 0.091 29 3.3 isthmuscingulate 6430 4118 9550 2.058 0.490 0.149 0.053 111 12.9 lateraloccipital 3092 2107 7305 2.765 0.749 0.161 0.074 83 8.6 lateralorbitofrontal 4079 2865 7164 2.216 0.549 0.179 0.095 135 12.8 lingual 1805 1184 3827 2.509 0.851 0.201 0.132 105 10.1 medialorbitofrontal 5076 3623 12132 2.702 0.662 0.163 0.067 136 14.7 middletemporal 845 590 2468 3.509 0.670 0.149 0.057 21 1.8 parahippocampal 1774 1189 3226 2.402 0.539 0.124 0.038 19 2.6 paracentral 1743 1217 3563 2.552 0.434 0.145 0.059 39 4.0 parsopercularis 926 626 2186 2.805 0.636 0.151 0.052 17 2.1 parsorbitalis 1773 1215 3401 2.429 0.522 0.145 0.052 32 3.1 parstriangularis 2161 1443 2433 1.740 0.446 0.151 0.069 46 5.7 pericalcarine 5674 3757 9270 2.135 0.582 0.138 0.049 97 10.7 postcentral 1519 1001 2797 2.665 0.515 0.147 0.044 29 2.8 posteriorcingulate 6223 4123 12531 2.644 0.506 0.126 0.046 82 10.1 precentral 4635 3157 8648 2.373 0.572 0.153 0.064 107 12.3 precuneus 1413 962 3154 2.775 0.698 0.171 0.087 37 4.1 rostralanteriorcingulate 4721 3341 10284 2.430 0.600 0.178 0.080 135 14.1 rostralmiddlefrontal 9453 6528 21475 2.673 0.637 0.157 0.070 289 21.6 superiorfrontal 5816 3854 9805 2.228 0.469 0.132 0.045 91 10.8 superiorparietal 5861 4077 14803 2.891 0.750 0.134 0.054 129 12.5 superiortemporal 4390 2974 8599 2.495 0.553 0.159 0.070 111 10.3 supramarginal 490 313 879 2.594 0.323 0.154 0.052 8 1.1 transversetemporal 2432 1568 5544 2.979 0.875 0.111 0.132 38 5.9 insula #-------------------------------------------- #@# Tessellate rh Thu Aug 8 19:07:09 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 2 found - 2 modified | TOTAL: 3 pass 2 (yz-): 0 found - 2 modified | TOTAL: 3 pass 1 (xz+): 1 found - 1 modified | TOTAL: 4 pass 2 (xz+): 0 found - 1 modified | TOTAL: 4 pass 1 (xz-): 0 found - 0 modified | TOTAL: 4 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 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 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 1 found - 1 modified | TOTAL: 2 pass 2 (-+): 0 found - 1 modified | TOTAL: 2 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 1 found - 1 modified | TOTAL: 1 pass 2 (yz-): 0 found - 1 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 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 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 = 9 (out of 191312: 0.004704) 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: 43 vertices, 56 faces slice 50: 2777 vertices, 2965 faces slice 60: 9379 vertices, 9649 faces slice 70: 18315 vertices, 18627 faces slice 80: 27980 vertices, 28318 faces slice 90: 36998 vertices, 37320 faces slice 100: 46874 vertices, 47191 faces slice 110: 56310 vertices, 56626 faces slice 120: 65253 vertices, 65590 faces slice 130: 74150 vertices, 74489 faces slice 140: 83222 vertices, 83549 faces slice 150: 90932 vertices, 91213 faces slice 160: 97616 vertices, 97883 faces slice 170: 103226 vertices, 103427 faces slice 180: 108200 vertices, 108368 faces slice 190: 111397 vertices, 111511 faces slice 200: 112292 vertices, 112326 faces slice 210: 112292 vertices, 112326 faces slice 220: 112292 vertices, 112326 faces slice 230: 112292 vertices, 112326 faces slice 240: 112292 vertices, 112326 faces slice 250: 112292 vertices, 112326 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... 112292 voxel in cpt #1: X=-34 [v=112292,e=336978,f=224652] located at (23.270029, -17.063156, 35.209133) For the whole surface: X=-34 [v=112292,e=336978,f=224652] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Thu Aug 8 19:07:16 CEST 2013 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 19:07:20 CEST 2013 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts avg radius = 44.2 mm, total surface area = 59007 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.5 minutes Not saving sulc step 000: RMS=0.102 (target=0.015) step 005: RMS=0.075 (target=0.015) step 010: RMS=0.055 (target=0.015) step 015: RMS=0.046 (target=0.015) step 020: RMS=0.040 (target=0.015) step 025: RMS=0.035 (target=0.015) step 030: RMS=0.032 (target=0.015) step 035: RMS=0.029 (target=0.015) step 040: RMS=0.027 (target=0.015) step 045: RMS=0.026 (target=0.015) step 050: RMS=0.025 (target=0.015) step 055: RMS=0.024 (target=0.015) step 060: RMS=0.024 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Thu Aug 8 19:07:48 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 1.08 +- 0.64 (0.00-->6.24) (max @ vno 84528 --> 84556) face area 0.03 +- 0.04 (-0.05-->0.60) scaling brain by 0.333... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.635, avgs=0 005/300: dt: 0.9000, rms radial error=176.376, avgs=0 010/300: dt: 0.9000, rms radial error=175.821, avgs=0 015/300: dt: 0.9000, rms radial error=175.093, avgs=0 020/300: dt: 0.9000, rms radial error=174.262, avgs=0 025/300: dt: 0.9000, rms radial error=173.372, avgs=0 030/300: dt: 0.9000, rms radial error=172.450, avgs=0 035/300: dt: 0.9000, rms radial error=171.512, avgs=0 040/300: dt: 0.9000, rms radial error=170.566, avgs=0 045/300: dt: 0.9000, rms radial error=169.619, avgs=0 050/300: dt: 0.9000, rms radial error=168.680, avgs=0 055/300: dt: 0.9000, rms radial error=167.743, avgs=0 060/300: dt: 0.9000, rms radial error=166.810, avgs=0 065/300: dt: 0.9000, rms radial error=165.881, avgs=0 070/300: dt: 0.9000, rms radial error=164.956, avgs=0 075/300: dt: 0.9000, rms radial error=164.036, avgs=0 080/300: dt: 0.9000, rms radial error=163.121, avgs=0 085/300: dt: 0.9000, rms radial error=162.210, avgs=0 090/300: dt: 0.9000, rms radial error=161.304, avgs=0 095/300: dt: 0.9000, rms radial error=160.403, avgs=0 100/300: dt: 0.9000, rms radial error=159.506, avgs=0 105/300: dt: 0.9000, rms radial error=158.614, avgs=0 110/300: dt: 0.9000, rms radial error=157.726, avgs=0 115/300: dt: 0.9000, rms radial error=156.843, avgs=0 120/300: dt: 0.9000, rms radial error=155.965, avgs=0 125/300: dt: 0.9000, rms radial error=155.092, avgs=0 130/300: dt: 0.9000, rms radial error=154.222, avgs=0 135/300: dt: 0.9000, rms radial error=153.358, avgs=0 140/300: dt: 0.9000, rms radial error=152.498, avgs=0 145/300: dt: 0.9000, rms radial error=151.643, avgs=0 150/300: dt: 0.9000, rms radial error=150.792, avgs=0 155/300: dt: 0.9000, rms radial error=149.946, avgs=0 160/300: dt: 0.9000, rms radial error=149.104, avgs=0 165/300: dt: 0.9000, rms radial error=148.267, avgs=0 170/300: dt: 0.9000, rms radial error=147.434, avgs=0 175/300: dt: 0.9000, rms radial error=146.606, avgs=0 180/300: dt: 0.9000, rms radial error=145.782, avgs=0 185/300: dt: 0.9000, rms radial error=144.963, avgs=0 190/300: dt: 0.9000, rms radial error=144.148, avgs=0 195/300: dt: 0.9000, rms radial error=143.337, avgs=0 200/300: dt: 0.9000, rms radial error=142.531, avgs=0 205/300: dt: 0.9000, rms radial error=141.730, avgs=0 210/300: dt: 0.9000, rms radial error=140.932, avgs=0 215/300: dt: 0.9000, rms radial error=140.139, avgs=0 220/300: dt: 0.9000, rms radial error=139.351, avgs=0 225/300: dt: 0.9000, rms radial error=138.567, avgs=0 230/300: dt: 0.9000, rms radial error=137.787, avgs=0 235/300: dt: 0.9000, rms radial error=137.011, avgs=0 240/300: dt: 0.9000, rms radial error=136.240, avgs=0 245/300: dt: 0.9000, rms radial error=135.473, avgs=0 250/300: dt: 0.9000, rms radial error=134.710, avgs=0 255/300: dt: 0.9000, rms radial error=133.951, avgs=0 260/300: dt: 0.9000, rms radial error=133.197, avgs=0 265/300: dt: 0.9000, rms radial error=132.446, avgs=0 270/300: dt: 0.9000, rms radial error=131.700, avgs=0 275/300: dt: 0.9000, rms radial error=130.958, avgs=0 280/300: dt: 0.9000, rms radial error=130.220, avgs=0 285/300: dt: 0.9000, rms radial error=129.487, avgs=0 290/300: dt: 0.9000, rms radial error=128.757, avgs=0 295/300: dt: 0.9000, rms radial error=128.032, avgs=0 300/300: dt: 0.9000, rms radial error=127.310, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 12847.82 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00017 epoch 2 (K=40.0), pass 1, starting sse = 2075.19 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00021 epoch 3 (K=160.0), pass 1, starting sse = 210.97 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.12/11 = 0.01123 epoch 4 (K=640.0), pass 1, starting sse = 11.41 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.26/18 = 0.01451 final writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.07 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Thu Aug 8 19:11:42 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/sub010/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub010 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=-34 (nv=112292, nf=224652, ne=336978, g=18) 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 11 iterations marking ambiguous vertices... 2041 ambiguous faces found in tessellation segmenting defects... 27 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 27 defects to be corrected 0 vertices coincident reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.8867 (-4.9434) -vertex loglikelihood: -6.9117 (-3.4559) -normal dot loglikelihood: -3.6465 (-3.6465) -quad curv loglikelihood: -6.1500 (-3.0750) Total Loglikelihood : -26.5949 CORRECTING DEFECT 0 (vertices=33, convex hull=71) After retessellation of defect 0, euler #=-23 (111025,332513,221465) : difference with theory (-24) = -1 CORRECTING DEFECT 1 (vertices=53, convex hull=101) After retessellation of defect 1, euler #=-22 (111056,332649,221571) : difference with theory (-23) = -1 CORRECTING DEFECT 2 (vertices=16, convex hull=48) After retessellation of defect 2, euler #=-21 (111063,332690,221606) : difference with theory (-22) = -1 CORRECTING DEFECT 3 (vertices=76, convex hull=73) After retessellation of defect 3, euler #=-20 (111081,332782,221681) : difference with theory (-21) = -1 CORRECTING DEFECT 4 (vertices=57, convex hull=83) After retessellation of defect 4, euler #=-19 (111100,332874,221755) : difference with theory (-20) = -1 CORRECTING DEFECT 5 (vertices=27, convex hull=63) After retessellation of defect 5, euler #=-18 (111118,332950,221814) : difference with theory (-19) = -1 CORRECTING DEFECT 6 (vertices=12, convex hull=20) After retessellation of defect 6, euler #=-17 (111119,332958,221822) : difference with theory (-18) = -1 CORRECTING DEFECT 7 (vertices=45, convex hull=77) After retessellation of defect 7, euler #=-16 (111136,333039,221887) : difference with theory (-17) = -1 CORRECTING DEFECT 8 (vertices=55, convex hull=42) After retessellation of defect 8, euler #=-15 (111146,333087,221926) : difference with theory (-16) = -1 CORRECTING DEFECT 9 (vertices=36, convex hull=75) After retessellation of defect 9, euler #=-14 (111162,333165,221989) : difference with theory (-15) = -1 CORRECTING DEFECT 10 (vertices=32, convex hull=57) After retessellation of defect 10, euler #=-13 (111175,333225,222037) : difference with theory (-14) = -1 CORRECTING DEFECT 11 (vertices=83, convex hull=31) After retessellation of defect 11, euler #=-12 (111183,333259,222064) : difference with theory (-13) = -1 CORRECTING DEFECT 12 (vertices=32, convex hull=42) After retessellation of defect 12, euler #=-11 (111194,333307,222102) : difference with theory (-12) = -1 CORRECTING DEFECT 13 (vertices=6, convex hull=29) After retessellation of defect 13, euler #=-10 (111196,333321,222115) : difference with theory (-11) = -1 CORRECTING DEFECT 14 (vertices=25, convex hull=22) After retessellation of defect 14, euler #=-9 (111200,333337,222128) : difference with theory (-10) = -1 CORRECTING DEFECT 15 (vertices=84, convex hull=87) After retessellation of defect 15, euler #=-8 (111244,333502,222250) : difference with theory (-9) = -1 CORRECTING DEFECT 16 (vertices=48, convex hull=61) After retessellation of defect 16, euler #=-7 (111258,333567,222302) : difference with theory (-8) = -1 CORRECTING DEFECT 17 (vertices=19, convex hull=30) After retessellation of defect 17, euler #=-6 (111260,333580,222314) : difference with theory (-7) = -1 CORRECTING DEFECT 18 (vertices=32, convex hull=56) After retessellation of defect 18, euler #=-5 (111279,333656,222372) : difference with theory (-6) = -1 CORRECTING DEFECT 19 (vertices=31, convex hull=29) Warning - incorrect dp selected!!!!(-104.593326 >= -104.593328 ) After retessellation of defect 19, euler #=-4 (111280,333669,222385) : difference with theory (-5) = -1 CORRECTING DEFECT 20 (vertices=252, convex hull=79) After retessellation of defect 20, euler #=-4 (111315,333813,222494) : difference with theory (-4) = 0 CORRECTING DEFECT 21 (vertices=18, convex hull=46) After retessellation of defect 21, euler #=-3 (111326,333861,222532) : difference with theory (-3) = 0 CORRECTING DEFECT 22 (vertices=90, convex hull=49) After retessellation of defect 22, euler #=-2 (111338,333914,222574) : difference with theory (-2) = 0 CORRECTING DEFECT 23 (vertices=5, convex hull=38) After retessellation of defect 23, euler #=-1 (111340,333932,222591) : difference with theory (-1) = 0 CORRECTING DEFECT 24 (vertices=35, convex hull=61) After retessellation of defect 24, euler #=0 (111353,333995,222642) : difference with theory (0) = 0 CORRECTING DEFECT 25 (vertices=32, convex hull=56) After retessellation of defect 25, euler #=1 (111366,334057,222692) : difference with theory (1) = 0 CORRECTING DEFECT 26 (vertices=44, convex hull=81) After retessellation of defect 26, euler #=2 (111391,334167,222778) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.05-->4.93) (max @ vno 5340 --> 7264) 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 (0.05-->4.93) (max @ vno 5340 --> 7264) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 97 mutations (35.8%), 174 crossovers (64.2%), 70 vertices were eliminated building final representation... 901 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=111391, nf=222778, ne=334167, g=0) writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 14.7 minutes 0 defective edges removing intersecting faces 000: 118 intersecting 001: 12 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 111391 - 334167 + 222778 = 2 --> 0 holes F =2V-4: 222778 = 222782-4 (0) 2E=3F: 668334 = 668334 (0) total defect index = 0 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 5 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Thu Aug 8 19:26:28 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub010 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/sub010/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/wm.mgz... 12290 bright wm thresholded. 241 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.orig... computing class statistics... border white: 201670 voxels (1.20%) border gray 234473 voxels (1.40%) WM (91.0): 91.9 +- 10.6 [70.0 --> 110.0] GM (73.0) : 71.3 +- 13.5 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 42.5 (was 70) setting MAX_BORDER_WHITE to 115.6 (was 105) setting MIN_BORDER_WHITE to 56.0 (was 85) setting MAX_CSF to 29.1 (was 40) setting MAX_GRAY to 94.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 49.3 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 15.6 (was 40) repositioning cortical surface to gray/white boundary reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.03-->2.73) (max @ vno 8619 --> 10263) face area 0.28 +- 0.12 (0.00-->1.33) mean absolute distance = 0.64 +- 0.71 3225 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=56 mean inside = 91.3, mean outside = 66.0 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 1 vertex label from ripped group mean border=70.1, 49 (49) missing vertices, mean dist 0.4 [0.4 (%30.1)->0.7 (%69.9))] %71 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.93 +- 0.27 (0.13-->3.59) (max @ vno 88410 --> 89070) face area 0.28 +- 0.14 (0.00-->1.54) mean absolute distance = 0.31 +- 0.47 2338 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=6263519.5, rms=14.16 001: dt: 0.5000, sse=6245345.0, rms=10.374 (0.000%) 002: dt: 0.5000, sse=6399585.0, rms=8.201 (0.000%) 003: dt: 0.5000, sse=6475290.5, rms=6.821 (0.000%) 004: dt: 0.5000, sse=6640219.5, rms=5.985 (0.000%) 005: dt: 0.5000, sse=6712765.5, rms=5.476 (0.000%) 006: dt: 0.5000, sse=6791901.0, rms=5.198 (0.000%) 007: dt: 0.5000, sse=6837379.0, rms=5.009 (0.000%) 008: dt: 0.5000, sse=6846357.0, rms=4.907 (0.000%) 009: dt: 0.5000, sse=6843883.5, rms=4.824 (0.000%) 010: dt: 0.5000, sse=6829250.5, rms=4.773 (0.000%) 011: dt: 0.5000, sse=6802085.5, rms=4.716 (0.000%) rms = 4.68, time step reduction 1 of 3 to 0.250... 012: dt: 0.5000, sse=6778209.0, rms=4.683 (0.000%) 013: dt: 0.2500, sse=4421098.5, rms=3.302 (0.000%) 014: dt: 0.2500, sse=4074072.5, rms=2.871 (0.000%) 015: dt: 0.2500, sse=3852660.5, rms=2.789 (0.000%) 016: dt: 0.2500, sse=3800534.8, rms=2.710 (0.000%) rms = 2.70, time step reduction 2 of 3 to 0.125... 017: dt: 0.2500, sse=3720320.8, rms=2.695 (0.000%) 018: dt: 0.1250, sse=3456618.2, rms=2.333 (0.000%) 019: dt: 0.1250, sse=3420086.8, rms=2.281 (0.000%) rms = 2.27, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=3391328.2, rms=2.273 (0.000%) positioning took 2.0 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 1 vertex label from ripped group mean border=74.8, 45 (7) missing vertices, mean dist -0.2 [0.3 (%78.4)->0.3 (%21.6))] %82 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.26 (0.09-->3.47) (max @ vno 89159 --> 88482) face area 0.35 +- 0.17 (0.00-->2.01) mean absolute distance = 0.22 +- 0.33 2303 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4232823.5, rms=6.34 021: dt: 0.5000, sse=4461567.5, rms=4.430 (0.000%) rms = 4.78, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=4019862.2, rms=3.180 (0.000%) 023: dt: 0.2500, sse=3836859.8, rms=2.626 (0.000%) 024: dt: 0.2500, sse=3785870.2, rms=2.205 (0.000%) rms = 2.20, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=3775824.5, rms=2.199 (0.000%) 026: dt: 0.1250, sse=3604553.8, rms=1.842 (0.000%) 027: dt: 0.1250, sse=3567259.2, rms=1.790 (0.000%) rms = 1.79, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=3542844.8, rms=1.789 (0.000%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 1 vertex label from ripped group mean border=78.2, 42 (7) missing vertices, mean dist -0.1 [0.2 (%75.6)->0.2 (%24.4))] %88 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 0.91 +- 0.26 (0.13-->3.47) (max @ vno 89159 --> 88482) face area 0.35 +- 0.17 (0.00-->1.98) mean absolute distance = 0.17 +- 0.27 2375 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3847400.0, rms=4.31 rms = 4.44, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=3688419.0, rms=2.969 (0.000%) 030: dt: 0.2500, sse=3616075.2, rms=1.973 (0.000%) 031: dt: 0.2500, sse=3644289.8, rms=1.850 (0.000%) 032: dt: 0.2500, sse=3676542.5, rms=1.774 (0.000%) rms = 1.86, time step reduction 2 of 3 to 0.125... 033: dt: 0.1250, sse=3626170.8, rms=1.674 (0.000%) 034: dt: 0.1250, sse=3554452.8, rms=1.553 (0.000%) rms = 1.55, time step reduction 3 of 3 to 0.062... 035: dt: 0.1250, sse=3532614.8, rms=1.546 (0.000%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group mean border=79.3, 66 (7) missing vertices, mean dist -0.0 [0.2 (%58.4)->0.2 (%41.6))] %89 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/sub010/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=3554496.5, rms=1.98 rms = 2.99, time step reduction 1 of 3 to 0.250... 036: dt: 0.2500, sse=3647274.8, rms=1.307 (0.000%) 037: dt: 0.2500, sse=3806872.8, rms=1.124 (0.000%) rms = 1.12, time step reduction 2 of 3 to 0.125... 038: dt: 0.2500, sse=3878057.8, rms=1.123 (0.000%) rms = 1.09, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=3904920.2, rms=1.091 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 13 non-cortical segments detected only using segment with 1747 vertices erasing segment 1 (vno[0] = 67108) erasing segment 2 (vno[0] = 69658) erasing segment 3 (vno[0] = 80395) erasing segment 4 (vno[0] = 82178) erasing segment 5 (vno[0] = 86152) erasing segment 6 (vno[0] = 86160) erasing segment 7 (vno[0] = 86197) erasing segment 8 (vno[0] = 89141) erasing segment 9 (vno[0] = 89757) erasing segment 10 (vno[0] = 89802) erasing segment 11 (vno[0] = 89809) erasing segment 12 (vno[0] = 90446) writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/label/rh.cortex.label... writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.curv writing smoothed area to rh.area writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.area vertex spacing 0.90 +- 0.26 (0.04-->3.59) (max @ vno 89070 --> 88410) face area 0.34 +- 0.16 (0.00-->2.15) refinement took 5.9 minutes #-------------------------------------------- #@# Smooth2 rh Thu Aug 8 19:32:21 CEST 2013 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 19:32:25 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 44.4 mm, total surface area = 69078 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.118 (target=0.015) step 005: RMS=0.082 (target=0.015) step 010: RMS=0.059 (target=0.015) step 015: RMS=0.047 (target=0.015) step 020: RMS=0.040 (target=0.015) step 025: RMS=0.033 (target=0.015) step 030: RMS=0.028 (target=0.015) step 035: RMS=0.024 (target=0.015) step 040: RMS=0.020 (target=0.015) step 045: RMS=0.018 (target=0.015) step 050: RMS=0.016 (target=0.015) step 055: RMS=0.015 (target=0.015) inflation complete. inflation took 0.4 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 107 vertices thresholded to be in k1 ~ [-0.24 0.64], k2 ~ [-0.17 0.10] total integrated curvature = 0.614*4pi (7.721) --> 0 handles ICI = 1.4, FI = 8.3, variation=142.901 114 vertices thresholded to be in [-0.05 0.02] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 102 vertices thresholded to be in [-0.16 0.23] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.018, std = 0.023 done. #----------------------------------------- #@# Curvature Stats rh Thu Aug 8 19:34:14 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub010 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 [ sub010/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 [ 233 ] Gb_filter = 0 WARN: S lookup min: -0.262075 WARN: S explicit min: 0.000000 vertex = 790 #-------------------------------------------- #@# Sphere rh Thu Aug 8 19:34:18 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 0.307... 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 %20.35 pass 1: epoch 2 of 3 starting distance error %20.28 unfolding complete - removing small folds... starting distance error %20.24 removing remaining folds... final distance error %20.26 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/rh.sphere spherical transformation took 0.74 hours #-------------------------------------------- #@# Surf Reg rh Thu Aug 8 20:18:43 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 = 0.578 curvature mean = 0.030, std = 0.941 curvature mean = 0.021, std = 0.872 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 0.00) sse = 311886.0, tmin=0.8804 d=32.00 min @ (0.00, 8.00, 0.00) sse = 258786.6, tmin=1.7659 d=16.00 min @ (4.00, 0.00, 4.00) sse = 244398.9, tmin=2.6545 d=8.00 min @ (-2.00, 0.00, 0.00) sse = 241030.0, tmin=3.6574 d=4.00 min @ (0.00, -1.00, 0.00) sse = 240748.2, tmin=4.7330 d=2.00 min @ (0.50, 0.50, 0.00) sse = 240329.7, tmin=5.8162 d=0.50 min @ (-0.12, -0.12, -0.12) sse = 240299.9, tmin=7.9474 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 7.95 min curvature mean = 0.006, std = 0.960 curvature mean = 0.009, std = 0.946 curvature mean = 0.004, std = 0.973 curvature mean = 0.004, std = 0.976 curvature mean = 0.002, std = 0.976 curvature mean = 0.001, std = 0.990 2 Reading smoothwm curvature mean = -0.028, std = 0.311 curvature mean = 0.006, std = 0.071 curvature mean = 0.068, std = 0.349 curvature mean = 0.005, std = 0.085 curvature mean = 0.034, std = 0.528 curvature mean = 0.005, std = 0.093 curvature mean = 0.018, std = 0.660 curvature mean = 0.005, std = 0.096 curvature mean = 0.006, std = 0.769 MRISregister() return, current seed 0 writing registered surface to ../surf/rh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white rh Thu Aug 8 20:44:27 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 20:44:29 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 20:44:30 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub010 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... 885 labels changed using aseg relabeling using gibbs priors... 000: 2560 changed, 111391 examined... 001: 575 changed, 10957 examined... 002: 134 changed, 3173 examined... 003: 48 changed, 826 examined... 004: 15 changed, 282 examined... 005: 11 changed, 92 examined... 006: 4 changed, 59 examined... 007: 0 changed, 17 examined... 144 labels changed using aseg 000: 87 total segments, 50 labels (208 vertices) changed 001: 37 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 48 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 931 vertices marked for relabeling... 931 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 51 seconds. #-------------------------------------------- #@# Make Pial Surf rh Thu Aug 8 20:45:21 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub010 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/sub010/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/wm.mgz... 12290 bright wm thresholded. 241 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.orig... computing class statistics... border white: 201670 voxels (1.20%) border gray 234473 voxels (1.40%) WM (91.0): 91.9 +- 10.6 [70.0 --> 110.0] GM (73.0) : 71.3 +- 13.5 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 42.5 (was 70) setting MAX_BORDER_WHITE to 115.6 (was 105) setting MIN_BORDER_WHITE to 56.0 (was 85) setting MAX_CSF to 29.1 (was 40) setting MAX_GRAY to 94.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 49.3 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 15.6 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=56 mean inside = 91.3, mean outside = 66.0 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/sub010/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.03-->2.73) (max @ vno 8619 --> 10263) face area 0.28 +- 0.12 (0.00-->1.33) mean absolute distance = 0.64 +- 0.73 3313 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 20 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown deleting segment 2 with 10 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 784 points - only 0.00% unknown deleting segment 6 with 7 points - only 0.00% unknown mean border=70.1, 49 (49) missing vertices, mean dist 0.4 [0.4 (%30.0)->0.7 (%70.0))] %72 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.93 +- 0.27 (0.13-->3.59) (max @ vno 88410 --> 89070) face area 0.28 +- 0.13 (0.00-->1.56) mean absolute distance = 0.31 +- 0.48 2063 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=6294467.0, rms=14.14 001: dt: 0.5000, sse=6276941.5, rms=10.358 (0.000%) 002: dt: 0.5000, sse=6440930.5, rms=8.189 (0.000%) 003: dt: 0.5000, sse=6518812.0, rms=6.812 (0.000%) 004: dt: 0.5000, sse=6692514.5, rms=5.979 (0.000%) 005: dt: 0.5000, sse=6763652.0, rms=5.471 (0.000%) 006: dt: 0.5000, sse=6850346.0, rms=5.190 (0.000%) 007: dt: 0.5000, sse=6889043.5, rms=5.003 (0.000%) 008: dt: 0.5000, sse=6903848.5, rms=4.901 (0.000%) 009: dt: 0.5000, sse=6898054.0, rms=4.816 (0.000%) 010: dt: 0.5000, sse=6886989.0, rms=4.765 (0.000%) 011: dt: 0.5000, sse=6855885.0, rms=4.709 (0.000%) rms = 4.68, time step reduction 1 of 3 to 0.250... 012: dt: 0.5000, sse=6834797.5, rms=4.676 (0.000%) 013: dt: 0.2500, sse=4457324.0, rms=3.299 (0.000%) 014: dt: 0.2500, sse=4109140.8, rms=2.870 (0.000%) 015: dt: 0.2500, sse=3886174.5, rms=2.786 (0.000%) 016: dt: 0.2500, sse=3832405.0, rms=2.706 (0.000%) rms = 2.69, time step reduction 2 of 3 to 0.125... 017: dt: 0.2500, sse=3750530.8, rms=2.692 (0.000%) 018: dt: 0.1250, sse=3486635.0, rms=2.332 (0.000%) 019: dt: 0.1250, sse=3450738.5, rms=2.281 (0.000%) rms = 2.27, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=3421693.5, rms=2.273 (0.000%) positioning took 2.0 minutes inhibiting deformation at non-cortical midline structures... deleting segment 1 with 46 points - only 23.91% unknown removing 4 vertex label from ripped group deleting segment 2 with 4 points - only 0.00% unknown deleting segment 3 with 14 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 6 with 1 points - only 0.00% unknown deleting segment 7 with 563 points - only 0.00% unknown deleting segment 9 with 6 points - only 0.00% unknown deleting segment 11 with 5 points - only 0.00% unknown mean border=74.8, 50 (7) missing vertices, mean dist -0.2 [0.3 (%78.4)->0.3 (%21.6))] %82 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.26 (0.11-->3.46) (max @ vno 89159 --> 88482) face area 0.35 +- 0.17 (0.00-->2.01) mean absolute distance = 0.22 +- 0.33 2403 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4272208.5, rms=6.34 021: dt: 0.5000, sse=4503166.5, rms=4.429 (0.000%) rms = 4.79, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=4059610.0, rms=3.188 (0.000%) 023: dt: 0.2500, sse=3878794.2, rms=2.641 (0.000%) 024: dt: 0.2500, sse=3828278.8, rms=2.229 (0.000%) rms = 2.22, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=3819842.2, rms=2.225 (0.000%) 026: dt: 0.1250, sse=3646417.5, rms=1.879 (0.000%) rms = 1.83, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=3609318.8, rms=1.833 (0.000%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 1 with 62 points - only 29.03% unknown removing 4 vertex label from ripped group deleting segment 2 with 4 points - only 0.00% unknown deleting segment 4 with 13 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 5 with 1 points - only 0.00% unknown deleting segment 6 with 706 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 8 with 5 points - only 0.00% unknown deleting segment 9 with 6 points - only 0.00% unknown mean border=78.1, 43 (7) missing vertices, mean dist -0.1 [0.2 (%75.4)->0.2 (%24.6))] %88 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 0.91 +- 0.26 (0.12-->3.42) (max @ vno 89159 --> 88482) face area 0.35 +- 0.16 (0.00-->1.99) mean absolute distance = 0.18 +- 0.27 2435 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3915584.0, rms=4.32 rms = 4.46, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=3749633.0, rms=2.989 (0.000%) 029: dt: 0.2500, sse=3669072.8, rms=2.004 (0.000%) 030: dt: 0.2500, sse=3690236.2, rms=1.880 (0.000%) 031: dt: 0.2500, sse=3725850.8, rms=1.799 (0.000%) rms = 1.89, time step reduction 2 of 3 to 0.125... 032: dt: 0.1250, sse=3673796.2, rms=1.698 (0.000%) 033: dt: 0.1250, sse=3605017.2, rms=1.579 (0.000%) rms = 1.57, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=3577784.2, rms=1.570 (0.000%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 0 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 62 points - only 29.03% unknown deleting segment 3 with 6 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 5 with 14 points - only 0.00% unknown deleting segment 6 with 737 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 8 with 5 points - only 0.00% unknown deleting segment 9 with 5 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 10 with 3 points - only 0.00% unknown mean border=79.3, 67 (7) missing vertices, mean dist -0.0 [0.2 (%58.5)->0.2 (%41.5))] %90 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=3604920.8, rms=2.01 rms = 3.02, time step reduction 1 of 3 to 0.250... 035: dt: 0.2500, sse=3700839.2, rms=1.347 (0.000%) 036: dt: 0.2500, sse=3864579.0, rms=1.161 (0.000%) rms = 1.16, time step reduction 2 of 3 to 0.125... rms = 1.14, time step reduction 3 of 3 to 0.062... 037: dt: 0.1250, sse=3866826.5, rms=1.144 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... smoothing surface for 5 iterations... mean border=45.7, 24 (24) missing vertices, mean dist 1.8 [0.1 (%0.0)->2.3 (%100.0))] %14 local maxima, %58 large gradients and %23 min vals, 1314 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=25179400.0, rms=32.85 001: dt: 0.5000, sse=17927304.0, rms=27.109 (0.000%) 002: dt: 0.5000, sse=12997613.0, rms=22.420 (0.000%) 003: dt: 0.5000, sse=9794399.0, rms=18.679 (0.000%) 004: dt: 0.5000, sse=7898608.5, rms=15.718 (0.000%) 005: dt: 0.5000, sse=6833644.0, rms=13.386 (0.000%) 006: dt: 0.5000, sse=6199615.0, rms=11.583 (0.000%) 007: dt: 0.5000, sse=5835691.5, rms=10.118 (0.000%) 008: dt: 0.5000, sse=5583771.0, rms=8.853 (0.000%) 009: dt: 0.5000, sse=5490532.0, rms=7.755 (0.000%) 010: dt: 0.5000, sse=5434232.0, rms=6.837 (0.000%) 011: dt: 0.5000, sse=5495971.5, rms=6.133 (0.000%) 012: dt: 0.5000, sse=5562216.5, rms=5.566 (0.000%) 013: dt: 0.5000, sse=5669598.0, rms=5.150 (0.000%) 014: dt: 0.5000, sse=5748345.0, rms=4.846 (0.000%) 015: dt: 0.5000, sse=5847945.5, rms=4.646 (0.000%) 016: dt: 0.5000, sse=5871751.5, rms=4.487 (0.000%) 017: dt: 0.5000, sse=5920825.5, rms=4.385 (0.000%) 018: dt: 0.5000, sse=5928871.0, rms=4.298 (0.000%) rms = 4.25, time step reduction 1 of 3 to 0.250... 019: dt: 0.5000, sse=5999224.0, rms=4.249 (0.000%) 020: dt: 0.2500, sse=4356141.5, rms=3.631 (0.000%) 021: dt: 0.2500, sse=4218046.5, rms=3.472 (0.000%) rms = 3.46, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=4109447.2, rms=3.457 (0.000%) 023: dt: 0.1250, sse=3955508.8, rms=3.368 (0.000%) rms = 3.36, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=3928717.8, rms=3.360 (0.000%) positioning took 2.4 minutes mean border=43.4, 624 (9) missing vertices, mean dist 0.2 [0.2 (%48.8)->0.6 (%51.2))] %33 local maxima, %43 large gradients and %19 min vals, 486 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=4482038.5, rms=5.20 025: dt: 0.5000, sse=4748793.5, rms=4.491 (0.000%) 026: dt: 0.5000, sse=5937889.5, rms=4.380 (0.000%) 027: dt: 0.5000, sse=5859295.5, rms=4.323 (0.000%) rms = 4.29, time step reduction 1 of 3 to 0.250... 028: dt: 0.5000, sse=6508248.0, rms=4.292 (0.000%) 029: dt: 0.2500, sse=4775004.5, rms=3.476 (0.000%) 030: dt: 0.2500, sse=4748277.0, rms=3.241 (0.000%) rms = 3.23, time step reduction 2 of 3 to 0.125... 031: dt: 0.2500, sse=4613001.0, rms=3.232 (0.000%) 032: dt: 0.1250, sse=4475820.0, rms=3.102 (0.000%) rms = 3.08, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=4452397.5, rms=3.084 (0.000%) positioning took 0.9 minutes mean border=41.1, 678 (7) missing vertices, mean dist 0.1 [0.2 (%38.4)->0.4 (%61.6))] %54 local maxima, %22 large gradients and %19 min vals, 577 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=4682343.5, rms=4.34 034: dt: 0.5000, sse=4873798.0, rms=4.086 (0.000%) rms = 4.14, time step reduction 1 of 3 to 0.250... 035: dt: 0.2500, sse=4615343.5, rms=3.440 (0.000%) 036: dt: 0.2500, sse=4785714.0, rms=3.160 (0.000%) 037: dt: 0.2500, sse=4737580.5, rms=3.103 (0.000%) rms = 3.07, time step reduction 2 of 3 to 0.125... 038: dt: 0.2500, sse=4786241.0, rms=3.070 (0.000%) 039: dt: 0.1250, sse=4629978.0, rms=2.955 (0.000%) rms = 2.94, time step reduction 3 of 3 to 0.062... 040: dt: 0.1250, sse=4620575.5, rms=2.942 (0.000%) positioning took 0.8 minutes mean border=39.8, 1486 (6) missing vertices, mean dist 0.1 [0.2 (%45.1)->0.3 (%54.9))] %59 local maxima, %17 large gradients and %18 min vals, 414 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/sub010/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=4664351.5, rms=3.26 rms = 3.87, time step reduction 1 of 3 to 0.250... 041: dt: 0.2500, sse=4547328.5, rms=2.994 (0.000%) 042: dt: 0.2500, sse=4691075.0, rms=2.916 (0.000%) rms = 2.88, time step reduction 2 of 3 to 0.125... 043: dt: 0.2500, sse=4743708.0, rms=2.884 (0.000%) 044: dt: 0.1250, sse=4668799.5, rms=2.780 (0.000%) rms = 2.76, time step reduction 3 of 3 to 0.062... 045: dt: 0.1250, sse=4683887.0, rms=2.764 (0.000%) positioning took 0.6 minutes writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.area.pial vertex spacing 1.05 +- 0.45 (0.09-->7.19) (max @ vno 50964 --> 49869) face area 0.44 +- 0.33 (0.00-->5.79) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 111391 vertices processed 25000 of 111391 vertices processed 50000 of 111391 vertices processed 75000 of 111391 vertices processed 100000 of 111391 vertices processed 0 of 111391 vertices processed 25000 of 111391 vertices processed 50000 of 111391 vertices processed 75000 of 111391 vertices processed 100000 of 111391 vertices processed thickness calculation complete, 340:1064 truncations. 23571 vertices at 0 distance 71398 vertices at 1 distance 71309 vertices at 2 distance 32185 vertices at 3 distance 9374 vertices at 4 distance 2387 vertices at 5 distance 766 vertices at 6 distance 244 vertices at 7 distance 92 vertices at 8 distance 45 vertices at 9 distance 23 vertices at 10 distance 32 vertices at 11 distance 15 vertices at 12 distance 13 vertices at 13 distance 23 vertices at 14 distance 24 vertices at 15 distance 14 vertices at 16 distance 13 vertices at 17 distance 8 vertices at 18 distance 7 vertices at 19 distance 5 vertices at 20 distance writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.thickness positioning took 11.6 minutes #-------------------------------------------- #@# Surf Volume rh Thu Aug 8 20:56:57 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 20:56:57 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts pctsurfcon --s sub010 --rh-only Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts/pctsurfcon.log Thu Aug 8 20:56:57 CEST 2013 setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts /opt/freesurfer/5.3.0/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux snake4 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux FREESURFER_HOME /opt/freesurfer/5.3.0 mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/tmp.pctsurfcon.978/rh.wm.mgh --regheader sub010 --cortex srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/mri/orig.mgz as target reference. Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/label/rh.cortex.label Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 = 86344 Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/label/rh.cortex.label Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/tmp.pctsurfcon.978/rh.wm.mgh Dim: 111391 1 1 mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/tmp.pctsurfcon.978/rh.gm.mgh --projfrac 0.3 --regheader sub010 --cortex srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/mri/orig.mgz as target reference. Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/label/rh.cortex.label Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.white Done reading source surface Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 = 99452 Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/label/rh.cortex.label Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/tmp.pctsurfcon.978/rh.gm.mgh Dim: 111391 1 1 mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/tmp.pctsurfcon.978/rh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/tmp.pctsurfcon.978/rh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/surf/rh.w-g.pct.mgh mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.w-g.pct.mgh --annot sub010 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/surf/rh.w-g.pct.mgh --annot sub010 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/stats/rh.w-g.pct.stats --snr sysname Linux hostname snake4 machine x86_64 user fkaule UseRobust 0 Constructing seg from annotation Reading annotation reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Seg base 2000 Loading /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.w-g.pct.mgh Vertex Area is 0.679864 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 2000 unknown 0 0.000 1 2001 bankssts 1491 1053.074 2 2002 caudalanteriorcingulate 972 688.321 3 2003 caudalmiddlefrontal 2081 1399.162 4 2004 corpuscallosum 0 0.000 5 2005 cuneus 2409 1575.154 6 2006 entorhinal 487 352.277 7 2007 fusiform 3287 2291.558 8 2008 inferiorparietal 7236 5051.799 9 2009 inferiortemporal 3875 2637.674 10 2010 isthmuscingulate 1181 779.891 11 2011 lateraloccipital 5789 3729.210 12 2012 lateralorbitofrontal 3333 2220.578 13 2013 lingual 3959 2721.951 14 2014 medialorbitofrontal 1903 1315.260 15 2015 middletemporal 4185 2969.861 16 2016 parahippocampal 649 469.661 17 2017 paracentral 1792 1190.402 18 2018 parsopercularis 1498 1043.138 19 2019 parsorbitalis 896 632.190 20 2020 parstriangularis 2141 1451.833 21 2021 pericalcarine 2141 1553.410 22 2022 postcentral 5066 3373.560 23 2023 posteriorcingulate 1409 963.851 24 2024 precentral 6364 4293.731 25 2025 precuneus 4994 3444.563 26 2026 rostralanteriorcingulate 801 578.226 27 2027 rostralmiddlefrontal 7005 4895.054 28 2028 superiorfrontal 8022 5489.056 29 2029 superiorparietal 7019 4653.616 30 2030 superiortemporal 4274 2960.927 31 2031 supramarginal 3732 2655.914 32 2032 frontalpole 323 234.243 33 2033 temporalpole 637 427.150 34 2034 transversetemporal 377 237.177 35 2035 insula 2486 1607.757 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats rh Thu Aug 8 20:57:09 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 sub010 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 1491 1053 2634 2.391 0.509 0.144 0.040 22 2.5 bankssts 972 688 2398 2.885 0.693 0.168 0.052 21 2.1 caudalanteriorcingulate 2081 1399 3887 2.507 0.528 0.137 0.058 32 4.3 caudalmiddlefrontal 2409 1575 3505 1.925 0.526 0.173 0.081 59 8.0 cuneus 487 352 1487 2.883 1.163 0.172 0.092 11 1.9 entorhinal 3287 2292 6738 2.574 0.575 0.151 0.055 61 7.0 fusiform 7236 5052 14159 2.418 0.589 0.150 0.052 133 15.3 inferiorparietal 3875 2638 8060 2.405 0.671 0.155 0.068 119 10.1 inferiortemporal 1181 780 2499 2.882 0.681 0.153 0.058 24 2.8 isthmuscingulate 5789 3729 9053 2.137 0.527 0.164 0.069 122 14.2 lateraloccipital 3333 2221 7179 2.771 0.738 0.165 0.082 118 11.0 lateralorbitofrontal 3959 2722 6580 2.202 0.594 0.181 0.089 106 13.4 lingual 1903 1315 4226 2.595 0.725 0.177 0.145 107 14.9 medialorbitofrontal 4185 2970 11210 2.784 0.787 0.148 0.054 91 8.4 middletemporal 649 470 1779 3.143 0.706 0.146 0.053 10 1.3 parahippocampal 1792 1190 3318 2.457 0.593 0.131 0.048 26 2.8 paracentral 1498 1043 3356 2.688 0.472 0.146 0.057 31 3.7 parsopercularis 896 632 2289 2.688 0.544 0.175 0.067 27 2.6 parsorbitalis 2141 1452 4330 2.580 0.564 0.136 0.042 31 3.7 parstriangularis 2141 1553 2589 1.784 0.423 0.165 0.065 35 5.9 pericalcarine 5066 3374 8328 2.105 0.624 0.133 0.040 64 8.9 postcentral 1409 964 2957 2.674 0.623 0.166 0.053 30 3.0 posteriorcingulate 6364 4294 12788 2.645 0.509 0.130 0.039 72 10.4 precentral 4994 3445 9228 2.422 0.544 0.144 0.049 93 10.1 precuneus 801 578 2415 3.264 0.715 0.174 0.088 28 2.6 rostralanteriorcingulate 7005 4895 15053 2.512 0.640 0.171 0.074 179 19.0 rostralmiddlefrontal 8022 5489 18327 2.828 0.578 0.149 0.053 151 16.2 superiorfrontal 7019 4654 11696 2.204 0.485 0.145 0.052 132 14.7 superiorparietal 4274 2961 10144 2.818 0.636 0.115 0.034 56 6.1 superiortemporal 3732 2656 8262 2.554 0.597 0.157 0.066 81 9.4 supramarginal 323 234 1061 2.891 0.522 0.273 0.195 21 1.9 frontalpole 637 427 2555 3.932 0.725 0.166 0.072 15 1.9 temporalpole 377 237 656 2.533 0.352 0.125 0.039 5 0.6 transversetemporal 2486 1608 5598 3.081 0.936 0.115 0.059 36 5.4 insula #----------------------------------------- #@# Cortical Parc 2 rh Thu Aug 8 20:57:21 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub010 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... 8 labels changed using aseg relabeling using gibbs priors... 000: 8222 changed, 111391 examined... 001: 1987 changed, 31328 examined... 002: 546 changed, 10066 examined... 003: 225 changed, 3081 examined... 004: 117 changed, 1272 examined... 005: 73 changed, 645 examined... 006: 24 changed, 414 examined... 007: 16 changed, 155 examined... 008: 8 changed, 82 examined... 009: 1 changed, 40 examined... 010: 0 changed, 7 examined... 10 labels changed using aseg 000: 255 total segments, 174 labels (1677 vertices) changed 001: 100 total segments, 19 labels (82 vertices) changed 002: 83 total segments, 2 labels (3 vertices) changed 003: 81 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 89 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 598 vertices marked for relabeling... 598 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 58 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Thu Aug 8 20:58:19 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 sub010 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 904 620 1854 2.377 0.659 0.170 0.095 23 2.5 G_and_S_frontomargin 669 489 1404 2.334 0.510 0.185 0.080 18 1.9 G_and_S_occipital_inf 1334 846 2625 2.430 0.557 0.145 0.059 25 2.5 G_and_S_paracentral 1115 750 2456 2.698 0.449 0.157 0.061 20 3.2 G_and_S_subcentral 955 699 2654 2.724 0.671 0.223 0.129 46 4.1 G_and_S_transv_frontopol 2280 1594 5294 2.888 0.641 0.157 0.066 54 5.3 G_and_S_cingul-Ant 1205 836 2642 2.865 0.527 0.137 0.041 17 1.9 G_and_S_cingul-Mid-Ant 1232 841 2458 2.672 0.492 0.134 0.039 16 2.0 G_and_S_cingul-Mid-Post 458 305 1236 3.139 0.507 0.191 0.074 13 1.4 G_cingul-Post-dorsal 241 157 614 2.960 0.595 0.154 0.075 6 0.7 G_cingul-Post-ventral 2221 1497 3237 1.888 0.464 0.177 0.079 52 6.6 G_cuneus 986 695 2783 2.865 0.482 0.157 0.068 25 2.9 G_front_inf-Opercular 302 204 785 2.682 0.426 0.175 0.067 10 0.9 G_front_inf-Orbital 949 633 2397 2.888 0.529 0.175 0.068 26 2.4 G_front_inf-Triangul 2754 1898 7082 2.739 0.559 0.192 0.096 92 9.8 G_front_middle 5353 3667 14158 2.945 0.591 0.176 0.073 144 15.3 G_front_sup 444 266 1314 3.969 0.788 0.118 0.097 8 0.9 G_Ins_lg_and_S_cent_ins 551 336 1835 3.543 0.785 0.137 0.089 16 2.4 G_insular_short 1897 1292 4684 2.802 0.540 0.203 0.099 69 6.1 G_occipital_middle 2088 1325 3248 2.081 0.480 0.161 0.058 41 4.9 G_occipital_sup 1184 781 2720 2.771 0.563 0.167 0.072 29 3.2 G_oc-temp_lat-fusifor 2574 1753 4722 2.325 0.587 0.201 0.106 84 10.3 G_oc-temp_med-Lingual 885 634 2526 3.066 1.065 0.148 0.060 13 2.1 G_oc-temp_med-Parahip 2374 1627 6604 2.884 0.727 0.201 0.110 124 10.7 G_orbital 2455 1738 6016 2.618 0.584 0.175 0.086 64 7.7 G_pariet_inf-Angular 1706 1240 4903 2.810 0.648 0.188 0.084 54 5.8 G_pariet_inf-Supramar 1977 1299 4146 2.434 0.500 0.161 0.071 62 6.2 G_parietal_sup 1790 1190 3508 2.274 0.551 0.141 0.041 27 3.0 G_postcentral 2373 1608 6076 2.877 0.460 0.146 0.047 37 4.7 G_precentral 2250 1554 4988 2.476 0.553 0.163 0.061 57 5.5 G_precuneus 503 339 1204 2.645 0.662 0.217 0.138 28 3.0 G_rectus 317 195 757 3.252 0.777 0.076 0.344 38 8.1 G_subcallosal 258 165 536 2.776 0.239 0.120 0.040 3 0.4 G_temp_sup-G_T_transv 1455 997 4427 3.053 0.560 0.153 0.058 41 3.3 G_temp_sup-Lateral 594 423 1684 3.482 0.777 0.102 0.031 4 0.7 G_temp_sup-Plan_polar 476 355 1072 2.495 0.544 0.121 0.034 5 0.7 G_temp_sup-Plan_tempo 2333 1597 5898 2.589 0.691 0.179 0.093 105 7.9 G_temporal_inf 2491 1792 7858 2.974 0.737 0.166 0.059 72 5.9 G_temporal_middle 423 283 704 2.392 0.505 0.101 0.020 2 0.4 Lat_Fis-ant-Horizont 165 124 251 2.191 0.354 0.116 0.022 1 0.1 Lat_Fis-ant-Vertical 1144 784 1640 2.345 0.393 0.122 0.035 10 1.7 Lat_Fis-post 3219 2024 4483 1.950 0.562 0.165 0.071 68 9.5 Pole_occipital 1544 1062 5244 3.334 0.843 0.177 0.094 41 5.5 Pole_temporal 2345 1689 3225 2.024 0.629 0.164 0.072 48 7.2 S_calcarine 2607 1778 3244 1.977 0.609 0.120 0.033 18 3.6 S_central 988 695 1560 2.276 0.499 0.122 0.034 12 1.3 S_cingul-Marginalis 517 336 978 2.939 0.697 0.118 0.033 4 0.7 S_circular_insula_ant 976 648 1505 2.509 0.542 0.081 0.016 3 0.7 S_circular_insula_inf 1032 715 1466 2.355 0.362 0.096 0.029 6 1.2 S_circular_insula_sup 1038 741 1771 2.309 0.518 0.127 0.035 13 1.5 S_collat_transv_ant 484 331 713 2.115 0.462 0.143 0.041 6 0.9 S_collat_transv_post 1830 1275 3055 2.248 0.526 0.127 0.036 21 2.8 S_front_inf 1701 1200 2754 2.326 0.496 0.143 0.044 21 3.0 S_front_middle 1502 1047 2934 2.612 0.569 0.119 0.029 16 1.8 S_front_sup 415 276 733 2.390 0.440 0.136 0.040 6 0.7 S_interm_prim-Jensen 2613 1743 3543 2.077 0.419 0.116 0.032 21 3.4 S_intrapariet_and_P_trans 799 554 960 1.863 0.360 0.128 0.034 6 1.1 S_oc_middle_and_Lunatus 1388 955 1919 2.067 0.398 0.135 0.036 17 2.0 S_oc_sup_and_transversal 723 468 906 2.134 0.375 0.141 0.045 9 1.5 S_occipital_ant 598 394 890 2.206 0.479 0.113 0.034 7 0.7 S_oc-temp_lat 1254 905 2344 2.571 0.602 0.121 0.028 11 1.5 S_oc-temp_med_and_Lingual 487 318 683 2.274 0.528 0.145 0.053 8 0.9 S_orbital_lateral 598 426 942 2.168 0.613 0.116 0.031 7 0.7 S_orbital_med-olfact 1254 844 2384 2.747 0.681 0.144 0.051 19 2.4 S_orbital-H_Shaped 2020 1388 3023 2.316 0.460 0.125 0.034 20 2.9 S_parieto_occipital 1188 766 1753 2.586 0.813 0.146 0.040 23 1.9 S_pericallosal 2052 1385 2638 1.989 0.461 0.113 0.029 15 2.5 S_postcentral 1204 791 1809 2.589 0.494 0.119 0.033 11 1.6 S_precentral-inf-part 1371 938 2214 2.501 0.429 0.121 0.037 13 1.9 S_precentral-sup-part 287 197 503 2.257 0.641 0.157 0.076 11 1.1 S_suborbital 1051 714 1792 2.397 0.536 0.128 0.034 12 1.5 S_subparietal 1029 699 1227 1.873 0.489 0.129 0.038 10 1.3 S_temporal_inf 5880 4098 9805 2.370 0.494 0.120 0.031 60 7.7 S_temporal_sup 155 113 344 2.638 0.375 0.111 0.023 1 0.2 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 rh Thu Aug 8 20:58:32 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub010 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... 880 labels changed using aseg relabeling using gibbs priors... 000: 2279 changed, 111391 examined... 001: 529 changed, 9872 examined... 002: 124 changed, 2865 examined... 003: 45 changed, 779 examined... 004: 26 changed, 246 examined... 005: 14 changed, 117 examined... 006: 13 changed, 76 examined... 007: 12 changed, 58 examined... 008: 6 changed, 57 examined... 009: 4 changed, 37 examined... 010: 3 changed, 18 examined... 011: 3 changed, 15 examined... 012: 4 changed, 15 examined... 013: 2 changed, 16 examined... 014: 2 changed, 10 examined... 015: 1 changed, 9 examined... 016: 1 changed, 9 examined... 017: 1 changed, 7 examined... 018: 0 changed, 5 examined... 212 labels changed using aseg 000: 69 total segments, 36 labels (141 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 57 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 276 vertices marked for relabeling... 276 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas40.annot... classification took 0 minutes and 50 seconds. #----------------------------------------- #@# Parcellation Stats 3 rh Thu Aug 8 20:59:23 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 sub010 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 1024 720 2470 2.881 0.674 0.166 0.051 21 2.2 caudalanteriorcingulate 2148 1442 3962 2.520 0.522 0.136 0.055 32 4.3 caudalmiddlefrontal 2860 1896 4163 1.951 0.509 0.168 0.073 64 8.5 cuneus 544 395 1498 2.790 1.102 0.167 0.078 11 1.8 entorhinal 2834 1957 5736 2.562 0.575 0.147 0.051 51 5.5 fusiform 6786 4716 13282 2.418 0.585 0.150 0.053 126 14.3 inferiorparietal 4306 2941 9149 2.445 0.676 0.158 0.072 132 11.8 inferiortemporal 1181 784 2505 2.876 0.672 0.154 0.058 24 2.7 isthmuscingulate 6046 3906 9408 2.133 0.521 0.164 0.067 124 15.0 lateraloccipital 3721 2495 8294 2.744 0.755 0.175 0.086 138 13.0 lateralorbitofrontal 3962 2731 6658 2.207 0.598 0.181 0.089 107 13.3 lingual 1567 1071 3502 2.637 0.770 0.172 0.154 94 13.6 medialorbitofrontal 5395 3849 13400 2.701 0.759 0.146 0.051 106 10.2 middletemporal 651 468 1752 3.124 0.727 0.143 0.052 10 1.4 parahippocampal 1909 1261 3599 2.499 0.604 0.131 0.047 28 3.0 paracentral 1533 1069 3391 2.684 0.474 0.145 0.061 32 4.0 parsopercularis 978 678 2269 2.596 0.581 0.145 0.045 19 1.9 parsorbitalis 2227 1526 4536 2.558 0.574 0.140 0.047 36 4.1 parstriangularis 2154 1558 2588 1.779 0.424 0.165 0.065 35 5.9 pericalcarine 5434 3625 8899 2.104 0.625 0.133 0.040 67 9.5 postcentral 1460 999 3011 2.659 0.626 0.165 0.052 30 3.1 posteriorcingulate 6052 4092 12351 2.650 0.514 0.131 0.040 70 10.0 precentral 5007 3454 9342 2.418 0.551 0.143 0.049 93 10.1 precuneus 825 605 2454 3.181 0.743 0.180 0.088 29 2.7 rostralanteriorcingulate 4628 3223 10070 2.529 0.631 0.172 0.075 116 12.7 rostralmiddlefrontal 10477 7202 23659 2.765 0.602 0.156 0.062 229 24.1 superiorfrontal 6062 4011 10312 2.230 0.489 0.146 0.053 119 13.3 superiorparietal 5720 3945 14107 2.899 0.748 0.126 0.041 86 9.9 superiortemporal 3545 2520 7877 2.564 0.590 0.160 0.067 80 9.2 supramarginal 359 227 632 2.537 0.352 0.126 0.039 5 0.6 transversetemporal 2419 1576 5468 3.041 0.913 0.112 0.054 33 4.8 insula #-------------------------------------------- #@# Refine Pial Surfs w/ T2/FLAIR Thu Aug 8 20:59:35 CEST 2013 bbregister --s sub010 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/T2raw.lta --init-fsl --T2 Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/T2raw.dat.log Thu Aug 8 20:59:35 CEST 2013 setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts /opt/freesurfer/5.3.0/bin/bbregister --s sub010 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/T2raw.lta --init-fsl --T2 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ Linux snake4 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux FREESURFER_HOME /opt/freesurfer/5.3.0 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/template.nii mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/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/sub010/mri/orig/T2raw.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.996481, 0.0682576, -0.0486557) j_ras = (0.0655887, 0.996358, 0.0544886) k_ras = (-0.0521977, -0.0511056, 0.997328) writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/template.nii... fslregister --s sub010 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/fslregister --dof 6 --fsvol brainmask.mgz Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/reg.init.dat.fslregister.log Thu Aug 8 20:59:40 CEST 2013 --s sub010 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/fslregister --dof 6 --fsvol brainmask.mgz $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ snake4 Linux snake4 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux nIters 1 -------------------------------------- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/fslregister/refvol.fslregister.nii mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/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/sub010/mri/brainmask.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.07102e-08, 7.45058e-09) j_ras = (7.45058e-09, -3.72529e-09, -1) k_ras = (-4.42378e-09, 1, 7.45058e-09) writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/fslregister/refvol.fslregister.nii... -------------------------------------- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/fslregister/movvol.fslregister.nii --frame 0 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/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/sub010/mri/transforms/tmp.bbregister.1178/template.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.996481, 0.0682576, -0.0486557) j_ras = (0.0655887, 0.996358, 0.0544886) k_ras = (-0.0521977, -0.0511056, 0.997328) keeping frame 0 writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/fslregister/movvol.fslregister.nii... Mov determinant is -0.311086 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/fslregister/movvol.fslregister.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/fslregister/reg0.1218.dat --regheader --fslregout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/reg.init.dat.fsl.mat0 --s sub010 --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/sub010/mri/transforms/tmp.bbregister.1178/fslregister/movvol.fslregister.nii reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/fslregister/reg0.1218.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/sub010/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/sub010/mri/transforms/tmp.bbregister.1178/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 -0.068 0.049 0.000; -0.052 -0.051 0.997 0.000; -0.066 -0.996 -0.054 -0.000; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 0.996 -0.068 0.049 0.000; -0.052 -0.051 0.997 0.000; -0.066 -0.996 -0.054 -0.000; 0.000 0.000 0.000 1.000; Determinant 1 subject = sub010 RegMat --------------------------- 0.996 -0.068 0.049 0.000; -0.052 -0.051 0.997 0.000; -0.066 -0.996 -0.054 -0.000; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -0.311086, ref det = -1 Thu Aug 8 20:59:49 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/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/sub010/mri/transforms/tmp.bbregister.1178/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/reg.init.dat.fsl.mat0 Thu Aug 8 21:04:13 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/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/sub010/mri/transforms/tmp.bbregister.1178/reg.init.dat.fsl.mat -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/fslregister/fslmat0.trans.mat -schedule /opt/freesurfer/5.3.0/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s sub010 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/reg.init.dat --fslreg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/reg.init.dat.fsl.mat --noedit tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl ---- FSL registration matrix -------- 0.997 -0.060 0.056 32.987; 0.053 -0.050 -0.997 258.619; 0.063 0.997 -0.047 -0.014; 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/sub010/mri/transforms/tmp.bbregister.1178/template.nii reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/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/sub010/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/sub010/mri/transforms/tmp.bbregister.1178/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) -------- 0.997 -0.063 0.053 0.084; -0.056 -0.047 0.997 1.598; -0.060 -0.997 -0.050 -0.458; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 0.997 -0.063 0.053 0.084; -0.056 -0.047 0.997 1.598; -0.060 -0.997 -0.050 -0.458; 0.000 0.000 0.000 1.000; Determinant 1 subject = sub010 RegMat --------------------------- 0.997 -0.063 0.053 0.084; -0.056 -0.047 0.997 1.598; -0.060 -0.997 -0.050 -0.458; 0.000 0.000 0.000 1.000; Started at Thu Aug 8 20:59:40 CEST 2013 Ended at Thu Aug 8 21:10:10 CEST 2013 fslregister Done To check results, run: tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/reg.init.dat --surf orig mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/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/sub010/scripts mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Linux hostname snake4 machine x86_64 user fkaule movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/template.nii regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/reg.init.dat subject sub010 dof 6 outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/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 1376658733 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.997 -0.063 0.053 0.084; -0.056 -0.047 0.997 1.598; -0.060 -0.997 -0.050 -0.458; 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 1.045764 1 -25.0 -25.0 25.0 1.015950 2 -25.0 25.0 -25.0 1.038444 3 -25.0 25.0 25.0 1.048401 4 25.0 -25.0 -25.0 1.016484 5 25.0 -25.0 25.0 1.008765 6 25.0 25.0 -25.0 1.021521 7 25.0 25.0 25.0 1.024672 REL: 8 0.282323 8.220002 1.027500 rel = 0.274766 Initial costs ---------------- Number of surface hits 2105 WM Intensity 55.1658 +/- 10.0304 Ctx Intensity 67.4505 +/- 11.3538 Pct Contrast 19.9782 +/- 18.5298 Cost 0.2823 RelCost 0.2748 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9763 0.9763 0.0 6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.9580 0.9580 0.0 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.9550 0.9550 0.0 19 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.0000 0.9120 0.9120 0.0 21 -4.0000 -4.0000 -4.0000 4.0000 0.0000 -4.0000 0.8799 0.8799 0.0 39 -4.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.8730 0.8730 0.0 61 -4.0000 -4.0000 4.0000 -4.0000 4.0000 0.0000 0.8555 0.8555 0.0 102 -4.0000 0.0000 -4.0000 4.0000 0.0000 -4.0000 0.7866 0.7866 0.0 120 -4.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.7115 0.7115 0.0 346 0.0000 0.0000 -4.0000 4.0000 0.0000 0.0000 0.6763 0.6763 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.2823 0.2823 0.0 Brute Force -------------------------- Min cost was 0.282323 Number of iterations 729 Search time 2.071000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 7 0.081 0.000 0.000 0.000 0.000 0.000 0.2798987473 8 0.117 0.000 0.000 0.000 0.000 0.000 0.2798302787 9 0.103 0.000 0.000 0.000 0.000 0.000 0.2797153885 10 0.101 0.000 0.000 0.000 0.000 0.000 0.2797103372 11 0.098 0.000 0.000 0.000 0.000 0.000 0.2797057770 17 0.098 -1.618 0.000 0.000 0.000 0.000 0.2547975036 18 0.098 -0.900 0.000 0.000 0.000 0.000 0.1916273660 22 0.098 -0.882 0.000 0.000 0.000 0.000 0.1913300169 24 0.098 -0.842 0.000 0.000 0.000 0.000 0.1911925005 27 0.098 -0.841 0.000 0.000 0.000 0.000 0.1911923798 37 0.098 -0.841 0.382 0.000 0.000 0.000 0.1623420136 38 0.098 -0.841 0.534 0.000 0.000 0.000 0.1610038547 42 0.098 -0.841 0.554 0.000 0.000 0.000 0.1607820018 43 0.098 -0.841 0.559 0.000 0.000 0.000 0.1607775623 44 0.098 -0.841 0.557 0.000 0.000 0.000 0.1607767615 51 0.098 -0.841 0.557 0.382 0.000 0.000 0.1481033577 54 0.098 -0.841 0.557 0.368 0.000 0.000 0.1480194385 56 0.098 -0.841 0.557 0.369 0.000 0.000 0.1480192152 64 0.098 -0.841 0.557 0.369 -0.046 0.000 0.1478097685 65 0.098 -0.841 0.557 0.369 -0.041 0.000 0.1477535978 66 0.098 -0.841 0.557 0.369 -0.028 0.000 0.1476978174 68 0.098 -0.841 0.557 0.369 -0.027 0.000 0.1476965434 69 0.098 -0.841 0.557 0.369 -0.026 0.000 0.1476955927 81 0.098 -0.841 0.557 0.369 -0.026 0.001 0.1476955197 92 0.072 -0.841 0.557 0.369 -0.026 0.001 0.1475872601 94 0.077 -0.841 0.557 0.369 -0.026 0.001 0.1475710673 96 0.079 -0.841 0.557 0.369 -0.026 0.001 0.1475692659 97 0.080 -0.841 0.557 0.369 -0.026 0.001 0.1475686265 98 0.081 -0.841 0.557 0.369 -0.026 0.001 0.1475685489 109 0.081 -0.776 0.557 0.369 -0.026 0.001 0.1462220455 111 0.081 -0.775 0.557 0.369 -0.026 0.001 0.1462206692 117 0.081 -0.775 -0.061 0.369 -0.026 0.001 0.1452707646 119 0.081 -0.775 0.243 0.369 -0.026 0.001 0.1393047025 122 0.081 -0.775 0.299 0.369 -0.026 0.001 0.1388997789 126 0.081 -0.775 0.300 0.369 -0.026 0.001 0.1388984067 127 0.081 -0.775 0.301 0.369 -0.026 0.001 0.1388976555 133 0.081 -0.775 0.301 0.751 -0.026 0.001 0.1377324858 134 0.081 -0.775 0.301 0.573 -0.026 0.001 0.1365577488 135 0.081 -0.775 0.301 0.592 -0.026 0.001 0.1361116141 136 0.081 -0.775 0.301 0.645 -0.026 0.001 0.1355918373 137 0.081 -0.775 0.301 0.646 -0.026 0.001 0.1355870667 140 0.081 -0.775 0.301 0.649 -0.026 0.001 0.1355825748 141 0.081 -0.775 0.301 0.648 -0.026 0.001 0.1355823258 151 0.081 -0.775 0.301 0.648 -0.113 0.001 0.1354293954 152 0.081 -0.775 0.301 0.648 -0.074 0.001 0.1352418161 153 0.081 -0.775 0.301 0.648 -0.076 0.001 0.1352339243 154 0.081 -0.775 0.301 0.648 -0.082 0.001 0.1352173427 156 0.081 -0.775 0.301 0.648 -0.087 0.001 0.1352098561 157 0.081 -0.775 0.301 0.648 -0.088 0.001 0.1352096761 165 0.081 -0.775 0.301 0.648 -0.088 -0.043 0.1329868884 167 0.081 -0.775 0.301 0.648 -0.088 -0.108 0.1322049734 168 0.081 -0.775 0.301 0.648 -0.088 -0.093 0.1321036264 169 0.081 -0.775 0.301 0.648 -0.088 -0.092 0.1321001253 170 0.081 -0.775 0.301 0.648 -0.088 -0.087 0.1320964693 183 0.091 -0.775 0.301 0.648 -0.088 -0.087 0.1320573402 184 0.098 -0.775 0.301 0.648 -0.088 -0.087 0.1320448085 194 0.098 -0.639 0.301 0.648 -0.088 -0.087 0.1314103741 195 0.098 -0.681 0.301 0.648 -0.088 -0.087 0.1311697645 196 0.098 -0.686 0.301 0.648 -0.088 -0.087 0.1311353890 199 0.098 -0.691 0.301 0.648 -0.088 -0.087 0.1311227919 208 0.098 -0.691 0.129 0.648 -0.088 -0.087 0.1298426937 212 0.098 -0.691 0.102 0.648 -0.088 -0.087 0.1295425843 221 0.098 -0.691 0.102 0.654 -0.088 -0.087 0.1293195956 222 0.098 -0.691 0.102 0.737 -0.088 -0.087 0.1261612594 225 0.098 -0.691 0.102 0.750 -0.088 -0.087 0.1259277404 227 0.098 -0.691 0.102 0.752 -0.088 -0.087 0.1259261497 235 0.098 -0.691 0.102 0.752 -0.106 -0.087 0.1256318091 236 0.098 -0.691 0.102 0.752 -0.173 -0.087 0.1256208305 239 0.098 -0.691 0.102 0.752 -0.251 -0.087 0.1253173438 243 0.098 -0.691 0.102 0.752 -0.242 -0.087 0.1252707117 244 0.098 -0.691 0.102 0.752 -0.240 -0.087 0.1252664345 245 0.098 -0.691 0.102 0.752 -0.238 -0.087 0.1252650436 254 0.098 -0.691 0.102 0.752 -0.238 -0.096 0.1251763466 256 0.098 -0.691 0.102 0.752 -0.238 -0.110 0.1251064648 257 0.098 -0.691 0.102 0.752 -0.238 -0.113 0.1251023519 269 0.077 -0.691 0.102 0.752 -0.238 -0.113 0.1245388016 271 0.046 -0.691 0.102 0.752 -0.238 -0.113 0.1241281190 282 0.046 -0.677 0.102 0.752 -0.238 -0.113 0.1241026310 283 0.046 -0.682 0.102 0.752 -0.238 -0.113 0.1240853142 285 0.046 -0.681 0.102 0.752 -0.238 -0.113 0.1240852242 293 0.046 -0.681 0.050 0.752 -0.238 -0.113 0.1237052012 294 0.046 -0.681 0.052 0.752 -0.238 -0.113 0.1236906944 295 0.046 -0.681 0.065 0.752 -0.238 -0.113 0.1236583896 297 0.046 -0.681 0.061 0.752 -0.238 -0.113 0.1236475157 307 0.046 -0.681 0.061 0.781 -0.238 -0.113 0.1233281206 309 0.046 -0.681 0.061 0.773 -0.238 -0.113 0.1232717663 319 0.046 -0.681 0.061 0.773 -0.229 -0.113 0.1232119749 321 0.046 -0.681 0.061 0.773 -0.223 -0.113 0.1231926702 322 0.046 -0.681 0.061 0.773 -0.222 -0.113 0.1231922379 330 0.046 -0.681 0.061 0.773 -0.222 -0.128 0.1231715191 331 0.046 -0.681 0.061 0.773 -0.222 -0.125 0.1231532928 332 0.046 -0.681 0.061 0.773 -0.222 -0.122 0.1231455990 333 0.046 -0.681 0.061 0.773 -0.222 -0.121 0.1231455575 345 0.044 -0.681 0.061 0.773 -0.222 -0.121 0.1231266858 346 0.021 -0.681 0.061 0.773 -0.222 -0.121 0.1230944926 348 0.030 -0.681 0.061 0.773 -0.222 -0.121 0.1230583475 349 0.031 -0.681 0.061 0.773 -0.222 -0.121 0.1230580732 359 0.031 -0.669 0.061 0.773 -0.222 -0.121 0.1229931675 360 0.031 -0.671 0.061 0.773 -0.222 -0.121 0.1229877195 361 0.031 -0.672 0.061 0.773 -0.222 -0.121 0.1229865998 362 0.031 -0.673 0.061 0.773 -0.222 -0.121 0.1229862162 373 0.031 -0.673 0.055 0.773 -0.222 -0.121 0.1229802391 374 0.031 -0.673 0.057 0.773 -0.222 -0.121 0.1229782452 386 0.031 -0.673 0.057 0.774 -0.222 -0.121 0.1229760006 387 0.031 -0.673 0.057 0.776 -0.222 -0.121 0.1229747743 399 0.031 -0.673 0.057 0.776 -0.218 -0.121 0.1229714520 408 0.031 -0.673 0.057 0.776 -0.218 -0.135 0.1229628292 409 0.031 -0.673 0.057 0.776 -0.218 -0.130 0.1229276960 412 0.017 -0.665 0.053 0.778 -0.215 -0.139 0.1229066164 436 0.026 -0.669 0.057 0.776 -0.218 -0.130 0.1229040328 437 0.026 -0.670 0.057 0.776 -0.218 -0.130 0.1229031392 460 0.026 -0.670 0.057 0.777 -0.218 -0.130 0.1229017014 473 0.026 -0.670 0.057 0.777 -0.216 -0.130 0.1229006552 484 0.026 -0.670 0.057 0.777 -0.216 -0.131 0.1228965156 485 0.026 -0.670 0.057 0.777 -0.216 -0.132 0.1228956624 487 0.020 -0.668 0.057 0.778 -0.214 -0.135 0.1228938820 493 0.022 -0.669 0.057 0.778 -0.215 -0.134 0.1228919303 514 0.022 -0.669 0.057 0.778 -0.215 -0.135 0.1228910971 525 0.022 -0.668 0.057 0.778 -0.215 -0.135 0.1228902165 537 0.022 -0.668 0.056 0.778 -0.215 -0.135 0.1228893177 560 0.022 -0.668 0.056 0.778 -0.216 -0.135 0.1228888567 569 0.022 -0.668 0.056 0.778 -0.216 -0.135 0.1228886972 Powell done niters = 6 Computing relative cost 0 -25.0 -25.0 -25.0 1.014050 1 -25.0 -25.0 25.0 1.046470 2 -25.0 25.0 -25.0 1.028936 3 -25.0 25.0 25.0 1.007599 4 25.0 -25.0 -25.0 1.027513 5 25.0 -25.0 25.0 1.044016 6 25.0 25.0 -25.0 0.991669 7 25.0 25.0 25.0 1.022222 REL: 8 0.122889 8.182476 1.022810 rel = 0.120148 Number of iterations 6 Min cost was 0.122889 Number of FunctionCalls 579 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 1.456000 sec Parameters at optimum (transmm) 0.02230 -0.66767 0.05609 Parameters at optimum (rotdeg) 0.77765 -0.21625 -0.13502 Final costs ---------------- Number of surface hits 2105 WM Intensity 54.7066 +/- 8.9338 Ctx Intensity 67.3044 +/- 9.6627 Pct Contrast 20.7461 +/- 14.3771 Cost 0.1229 RelCost 0.2748 Reg at min cost was 0.997 -0.059 0.055 0.112; -0.057 -0.033 0.998 0.936; -0.057 -0.998 -0.036 -0.380; 0.000 0.000 0.000 1.000; Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/bbr.pass1.dat, type = 14 Original Reg 0.997 -0.063 0.053 0.084; -0.056 -0.047 0.997 1.598; -0.060 -0.997 -0.050 -0.458; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.000 -0.004 -0.002 -0.028; 0.002 -0.014 -0.000 0.662; -0.003 0.001 -0.014 -0.078; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 1.091263 Computing change in rh position Surface RMS Diff (mm) 1.156741 1.927655 mri_segreg done mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/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/sub010/scripts mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname snake4 machine x86_64 user fkaule movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/template.nii regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/bbr.pass1.dat subject sub010 dof 6 outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 1376400309 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.997 -0.059 0.055 0.112; -0.057 -0.033 0.998 0.936; -0.057 -0.998 -0.036 -0.380; 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 1.022829 1 -25.0 -25.0 25.0 1.011391 2 -25.0 25.0 -25.0 1.008765 3 -25.0 25.0 25.0 1.014969 4 25.0 -25.0 -25.0 1.019751 5 25.0 -25.0 25.0 1.026475 6 25.0 25.0 -25.0 1.021876 7 25.0 25.0 25.0 1.034910 REL: 8 0.146833 8.160967 1.020121 rel = 0.143937 Initial costs ---------------- Number of surface hits 208855 WM Intensity 54.9470 +/- 9.6295 Ctx Intensity 67.1138 +/- 9.7123 Pct Contrast 20.1534 +/- 14.6898 Cost 0.1468 RelCost 0.1439 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1500 0.1500 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1487 0.1487 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.1437 0.1437 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.1420 0.1420 0.0 6 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 0.1405 0.1405 0.0 7 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.0000 0.1383 0.1383 0.0 8 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.1000 0.1373 0.1373 0.0 30 -0.1000 -0.1000 0.0000 -0.1000 0.0000 -0.1000 0.1368 0.1368 0.0 31 -0.1000 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.1354 0.1354 0.0 34 -0.1000 -0.1000 0.0000 -0.1000 0.1000 0.0000 0.1351 0.1351 0.0 35 -0.1000 -0.1000 0.0000 -0.1000 0.1000 0.1000 0.1345 0.1345 0.0 88 -0.1000 0.0000 -0.1000 -0.1000 0.1000 0.0000 0.1331 0.1331 0.0 93 -0.1000 0.0000 -0.1000 0.0000 0.0000 -0.1000 0.1323 0.1323 0.0 94 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.0000 0.1303 0.1303 0.0 97 -0.1000 0.0000 -0.1000 0.0000 0.1000 0.0000 0.1302 0.1302 0.0 112 -0.1000 0.0000 0.0000 -0.1000 0.0000 0.0000 0.1290 0.1290 0.0 120 -0.1000 0.0000 0.0000 0.0000 0.0000 -0.1000 0.1287 0.1287 0.0 121 -0.1000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1273 0.1273 0.0 337 0.0000 0.0000 -0.1000 0.0000 0.0000 0.0000 0.1253 0.1253 0.0 340 0.0000 0.0000 -0.1000 0.0000 0.1000 0.0000 0.1248 0.1248 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1229 0.1229 0.0 Brute Force -------------------------- Min cost was 0.122889 Number of iterations 729 Search time 1.554000 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 0.082 0.000 0.000 0.000 0.000 0.000 0.1458149024 8 0.088 0.000 0.000 0.000 0.000 0.000 0.1458117233 9 0.087 0.000 0.000 0.000 0.000 0.000 0.1458113466 17 0.087 0.076 0.000 0.000 0.000 0.000 0.1450888197 18 0.087 0.074 0.000 0.000 0.000 0.000 0.1450850635 19 0.087 0.070 0.000 0.000 0.000 0.000 0.1450798674 22 0.087 0.068 0.000 0.000 0.000 0.000 0.1450794793 30 0.087 0.068 -0.056 0.000 0.000 0.000 0.1449826744 31 0.087 0.068 -0.034 0.000 0.000 0.000 0.1449470763 32 0.087 0.068 -0.036 0.000 0.000 0.000 0.1449468939 34 0.087 0.068 -0.035 0.000 0.000 0.000 0.1449468147 41 0.087 0.068 -0.035 -0.132 0.000 0.000 0.1411851936 42 0.087 0.068 -0.035 -0.141 0.000 0.000 0.1411503358 43 0.087 0.068 -0.035 -0.147 0.000 0.000 0.1411466191 44 0.087 0.068 -0.035 -0.145 0.000 0.000 0.1411462036 52 0.087 0.068 -0.035 -0.145 0.069 0.000 0.1403739620 54 0.087 0.068 -0.035 -0.145 0.067 0.000 0.1403726556 55 0.087 0.068 -0.035 -0.145 0.066 0.000 0.1403725136 63 0.087 0.068 -0.035 -0.145 0.066 0.065 0.1394880703 65 0.087 0.068 -0.035 -0.145 0.066 0.067 0.1394874522 74 0.086 0.068 -0.035 -0.145 0.066 0.067 0.1394860558 75 0.082 0.068 -0.035 -0.145 0.066 0.067 0.1394840013 85 0.082 0.025 -0.035 -0.145 0.066 0.067 0.1392971198 86 0.082 0.031 -0.035 -0.145 0.066 0.067 0.1392769580 87 0.082 0.036 -0.035 -0.145 0.066 0.067 0.1392707865 96 0.082 0.036 0.048 -0.145 0.066 0.067 0.1381593300 97 0.082 0.036 0.055 -0.145 0.066 0.067 0.1381503630 98 0.082 0.036 0.056 -0.145 0.066 0.067 0.1381501840 106 0.082 0.036 0.056 -0.192 0.066 0.067 0.1377376363 108 0.082 0.036 0.056 -0.191 0.066 0.067 0.1377373318 117 0.082 0.036 0.056 -0.191 0.087 0.067 0.1376926263 118 0.082 0.036 0.056 -0.191 0.084 0.067 0.1376899590 119 0.082 0.036 0.056 -0.191 0.083 0.067 0.1376897722 127 0.082 0.036 0.056 -0.191 0.083 0.065 0.1376896304 129 0.078 0.004 0.148 -0.236 0.100 0.064 0.1375617851 135 0.079 0.016 0.113 -0.219 0.093 0.064 0.1374614070 136 0.079 0.016 0.113 -0.219 0.093 0.064 0.1374612031 139 0.080 0.018 0.109 -0.217 0.093 0.065 0.1374601702 142 0.080 0.018 0.108 -0.217 0.092 0.065 0.1374601302 153 0.069 0.018 0.108 -0.217 0.092 0.065 0.1374349690 154 0.065 0.018 0.108 -0.217 0.092 0.065 0.1374341590 155 0.066 0.018 0.108 -0.217 0.092 0.065 0.1374341327 163 0.066 0.002 0.108 -0.217 0.092 0.065 0.1373749651 164 0.066 -0.004 0.108 -0.217 0.092 0.065 0.1373704933 174 0.066 -0.004 0.108 -0.217 0.092 0.063 0.1373698675 182 0.066 -0.004 0.108 -0.232 0.092 0.063 0.1373562652 183 0.066 -0.004 0.108 -0.227 0.092 0.063 0.1373526036 185 0.066 -0.004 0.108 -0.226 0.092 0.063 0.1373525238 194 0.066 -0.004 0.108 -0.226 0.096 0.063 0.1373501648 195 0.066 -0.004 0.108 -0.226 0.097 0.063 0.1373498926 204 0.066 -0.004 0.107 -0.225 0.096 0.063 0.1373497704 217 0.065 -0.004 0.107 -0.225 0.096 0.063 0.1373484880 218 0.061 -0.004 0.107 -0.225 0.096 0.063 0.1373459604 221 0.059 -0.004 0.107 -0.225 0.096 0.063 0.1373455571 232 0.059 -0.009 0.107 -0.225 0.096 0.063 0.1373429361 234 0.059 -0.008 0.107 -0.225 0.096 0.063 0.1373428382 252 0.059 -0.008 0.107 -0.228 0.096 0.063 0.1373409880 261 0.059 -0.008 0.107 -0.228 0.099 0.063 0.1373399094 262 0.059 -0.008 0.107 -0.228 0.100 0.063 0.1373398462 263 0.059 -0.008 0.107 -0.228 0.101 0.063 0.1373398352 272 0.059 -0.009 0.109 -0.230 0.101 0.063 0.1373391978 273 0.059 -0.009 0.110 -0.230 0.101 0.063 0.1373391866 275 0.059 -0.009 0.110 -0.230 0.101 0.063 0.1373391574 279 0.059 -0.009 0.111 -0.230 0.101 0.063 0.1373391439 280 0.059 -0.009 0.110 -0.230 0.101 0.063 0.1373390156 283 0.051 -0.014 0.114 -0.235 0.106 0.062 0.1373388598 291 0.055 -0.009 0.110 -0.230 0.101 0.063 0.1373373201 301 0.055 -0.013 0.110 -0.230 0.101 0.063 0.1373353841 303 0.055 -0.012 0.110 -0.230 0.101 0.063 0.1373352866 330 0.055 -0.012 0.110 -0.230 0.104 0.063 0.1373349217 343 0.055 -0.012 0.110 -0.230 0.104 0.063 0.1373348630 355 0.054 -0.012 0.110 -0.230 0.104 0.063 0.1373346052 Powell done niters = 6 Computing relative cost 0 -25.0 -25.0 -25.0 1.023859 1 -25.0 -25.0 25.0 1.009395 2 -25.0 25.0 -25.0 1.009667 3 -25.0 25.0 25.0 1.012653 4 25.0 -25.0 -25.0 1.018492 5 25.0 -25.0 25.0 1.026773 6 25.0 25.0 -25.0 1.018917 7 25.0 25.0 25.0 1.033462 REL: 8 0.137335 8.153219 1.019152 rel = 0.134754 Number of iterations 6 Min cost was 0.137335 Number of FunctionCalls 460 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 39.149000 sec Parameters at optimum (transmm) 0.05420 -0.01155 0.11035 Parameters at optimum (rotdeg) -0.23004 0.10394 0.06253 Final costs ---------------- Number of surface hits 208855 WM Intensity 54.9646 +/- 9.6236 Ctx Intensity 67.1014 +/- 9.6266 Pct Contrast 20.1181 +/- 14.5150 Cost 0.1373 RelCost 0.1439 Reg at min cost was 0.997 -0.061 0.054 0.165; -0.056 -0.037 0.998 0.923; -0.058 -0.997 -0.040 -0.273; 0.000 0.000 0.000 1.000; Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/T2raw.dat, type = 14 Original Reg 0.997 -0.059 0.055 0.112; -0.057 -0.033 0.998 0.936; -0.057 -0.998 -0.036 -0.380; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg 0.000 0.002 0.001 -0.052; -0.001 0.004 0.000 0.013; 0.002 -0.000 0.004 -0.106; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.192862 Computing change in rh position Surface RMS Diff (mm) 0.200435 0.406761 mri_segreg done tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/T2raw.dat --noedit --ltaout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/mri/orig/T2raw.mgz reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 -------- 0.997 -0.061 0.054 0.165; -0.056 -0.037 0.998 0.923; -0.058 -0.997 -0.040 -0.273; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- INFO: loading target /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/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 -------- 0.997 -0.061 0.054 0.165; -0.056 -0.037 0.998 0.923; -0.058 -0.997 -0.040 -0.273; 0.000 0.000 0.000 1.000; Determinant 1 subject = sub010 RegMat --------------------------- 0.997 -0.061 0.054 0.165; -0.056 -0.037 0.998 0.923; -0.058 -0.997 -0.040 -0.273; 0.000 0.000 0.000 1.000; transformed matrix: 1.000 -0.007 -0.005 -0.052; 0.007 1.000 0.014 0.003; 0.004 -0.014 1.000 -0.630; 0.000 0.000 0.000 1.000; transformed matrix: 0.698 -0.039 0.038 32.819; 0.038 -0.027 -0.665 256.625; 0.042 0.665 -0.025 -0.977; 0.000 0.000 0.000 1.000; Cleaning up Started at Thu Aug 8 20:59:35 CEST 2013 Ended at Thu Aug 8 21:11:37 CEST 2013 BBR-Run-Time-Sec 722 bbregister Done To check results, run: tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/T2raw.dat --surf mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/T2.mgz mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/mri/orig/T2raw.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.996481, 0.0682576, -0.0486557) j_ras = (0.0655887, 0.996358, 0.0544886) k_ras = (-0.0521977, -0.0511056, 0.997328) INFO: Reading transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/T2raw.lta... Reading transform with LTAreadEx() reading extra input line subject sub010 reading extra input line fscale 0.150000 reading template info from volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/orig.mgz... INFO: Applying transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/T2raw.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 1.000 -0.007 -0.005 -0.052; 0.007 1.000 0.014 0.003; 0.004 -0.014 1.000 -0.630; 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/sub010/mri/T2.mgz... mri_normalize -aseg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/aseg.mgz -sigma 4 -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.white identity.nofile -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.white identity.nofile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/T2.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/mri/T2.mgz... computing distance transform computing distance transform computing nonmaximum suppression 8132 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/sub010/mri/T2.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.woT2.pial `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.woT2.pial' mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub010 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/sub010/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/wm.mgz... 13095 bright wm thresholded. 240 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.orig... computing class statistics... border white: 201670 voxels (1.20%) border gray 234473 voxels (1.40%) WM (91.0): 92.1 +- 10.7 [70.0 --> 110.0] GM (73.0) : 71.4 +- 13.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 43.8 (was 70) setting MAX_BORDER_WHITE to 115.7 (was 105) setting MIN_BORDER_WHITE to 57.0 (was 85) setting MAX_CSF to 30.6 (was 40) setting MAX_GRAY to 94.3 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 50.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 17.4 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=57 mean inside = 91.7, mean outside = 66.6 smoothing surface for 5 iterations... reading initial white vertex positions from white... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.90 +- 0.26 (0.02-->6.42) (max @ vno 49307 --> 52883) face area 0.34 +- 0.16 (0.00-->7.16) averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 24 points - only 0.00% unknown deleting segment 2 with 6 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 924 points - only 4.87% unknown deleting segment 7 with 12 points - only 0.00% unknown deleting segment 8 with 19 points - only 0.00% unknown deleting segment 10 with 6 points - only 0.00% unknown deleting segment 11 with 9 points - only 0.00% unknown deleting segment 12 with 13 points - only 0.00% unknown deleting segment 13 with 17 points - only 0.00% unknown deleting segment 14 with 30 points - only 0.00% unknown deleting segment 15 with 5 points - only 0.00% unknown tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.90 +- 0.26 (0.05-->6.42) (max @ vno 49307 --> 52883) face area 0.34 +- 0.16 (0.00-->7.16) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4024837.5, rms=0.00 rms = 1.07, time step reduction 1 of 3 to 0.250... rms = 0.27, time step reduction 2 of 3 to 0.125... rms = 0.03, time step reduction 3 of 3 to 0.062... 001: dt: 0.1250, sse=4024837.5, rms=0.000 (1.000%) positioning took 0.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 24 points - only 0.00% unknown deleting segment 1 with 6 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 3 with 924 points - only 4.87% unknown deleting segment 4 with 12 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 9 points - only 0.00% unknown deleting segment 8 with 13 points - only 0.00% unknown deleting segment 9 with 17 points - only 0.00% unknown deleting segment 10 with 30 points - only 0.00% unknown deleting segment 11 with 5 points - only 0.00% unknown tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.26 (0.05-->6.42) (max @ vno 49307 --> 52883) face area 0.34 +- 0.16 (0.00-->7.16) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4024837.5, rms=0.00 rms = 1.07, time step reduction 1 of 3 to 0.250... rms = 0.27, time step reduction 2 of 3 to 0.125... rms = 0.03, time step reduction 3 of 3 to 0.062... 002: dt: 0.1250, sse=4024837.5, rms=0.000 (1.000%) positioning took 0.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 24 points - only 0.00% unknown deleting segment 1 with 6 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 3 with 924 points - only 4.87% unknown deleting segment 4 with 12 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 9 points - only 0.00% unknown deleting segment 8 with 13 points - only 0.00% unknown deleting segment 9 with 17 points - only 0.00% unknown deleting segment 10 with 30 points - only 0.00% unknown deleting segment 11 with 5 points - only 0.00% unknown tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.26 (0.05-->6.42) (max @ vno 49307 --> 52883) face area 0.34 +- 0.16 (0.00-->7.16) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4024837.5, rms=0.00 rms = 1.07, time step reduction 1 of 3 to 0.250... rms = 0.27, time step reduction 2 of 3 to 0.125... rms = 0.03, time step reduction 3 of 3 to 0.062... 003: dt: 0.1250, sse=4024837.5, rms=0.000 (1.000%) positioning took 0.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 24 points - only 0.00% unknown deleting segment 1 with 6 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 3 with 924 points - only 4.87% unknown deleting segment 4 with 12 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 9 points - only 0.00% unknown deleting segment 8 with 13 points - only 0.00% unknown deleting segment 9 with 17 points - only 0.00% unknown deleting segment 10 with 30 points - only 0.00% unknown deleting segment 11 with 5 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=4024837.5, rms=0.00 rms = 1.07, time step reduction 1 of 3 to 0.250... rms = 0.27, time step reduction 2 of 3 to 0.125... rms = 0.03, time step reduction 3 of 3 to 0.062... 004: dt: 0.1250, sse=4024837.5, rms=0.000 (1.000%) positioning took 0.2 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group smoothing surface for 5 iterations... reading initial pial vertex positions from woT2.pial... repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [89.10 222.90], gm=156.00+-22.30, and vertices in regions > 144.8 25335 surface locations found to contain inconsistent values (1995 in, 23340 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=458774.4, rms=0.22 001: dt: 0.5000, sse=430848.8, rms=0.215 (0.000%) 002: dt: 0.5000, sse=413732.2, rms=0.203 (0.000%) 003: dt: 0.5000, sse=402526.7, rms=0.194 (0.000%) 004: dt: 0.5000, sse=394554.8, rms=0.186 (0.000%) 005: dt: 0.5000, sse=388978.8, rms=0.178 (0.000%) 006: dt: 0.5000, sse=384655.2, rms=0.172 (0.000%) 007: dt: 0.5000, sse=380914.8, rms=0.167 (0.000%) 008: dt: 0.5000, sse=377920.1, rms=0.163 (0.000%) 009: dt: 0.5000, sse=375961.9, rms=0.160 (0.000%) 010: dt: 0.5000, sse=373370.3, rms=0.157 (0.000%) 011: dt: 0.5000, sse=371330.9, rms=0.154 (0.000%) 012: dt: 0.5000, sse=369542.8, rms=0.152 (0.000%) 013: dt: 0.5000, sse=367807.3, rms=0.151 (0.000%) 014: dt: 0.5000, sse=366092.6, rms=0.149 (0.000%) 015: dt: 0.5000, sse=364371.3, rms=0.148 (0.000%) 016: dt: 0.5000, sse=362689.0, rms=0.148 (0.000%) 017: dt: 0.5000, sse=361575.8, rms=0.147 (0.000%) 018: dt: 0.5000, sse=359866.9, rms=0.147 (0.000%) 019: dt: 0.5000, sse=358425.4, rms=0.147 (0.000%) 020: dt: 0.5000, sse=357066.3, rms=0.147 (0.000%) 021: dt: 0.5000, sse=356190.8, rms=0.147 (0.000%) 022: dt: 0.5000, sse=354647.8, rms=0.148 (0.000%) 023: dt: 0.5000, sse=352928.2, rms=0.148 (0.000%) 024: dt: 0.5000, sse=351970.6, rms=0.148 (0.000%) 025: dt: 0.5000, sse=351171.3, rms=0.149 (0.000%) 026: dt: 0.5000, sse=350023.2, rms=0.149 (0.000%) 027: dt: 0.5000, sse=348805.7, rms=0.149 (0.000%) 028: dt: 0.5000, sse=347812.3, rms=0.150 (0.000%) 029: dt: 0.5000, sse=346543.6, rms=0.150 (0.000%) 030: dt: 0.5000, sse=345773.7, rms=0.151 (0.000%) positioning took 3.0 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [88.00 226.00], gm=157.00+-23.00, and vertices in regions > 145.5 20901 surface locations found to contain inconsistent values (661 in, 20240 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=35700.3, rms=0.12 031: dt: 0.5000, sse=35536.3, rms=0.117 (0.000%) 032: dt: 0.5000, sse=36263.8, rms=0.107 (0.000%) 033: dt: 0.5000, sse=37104.3, rms=0.099 (0.000%) 034: dt: 0.5000, sse=37836.9, rms=0.094 (0.000%) 035: dt: 0.5000, sse=38481.9, rms=0.089 (0.000%) 036: dt: 0.5000, sse=39140.8, rms=0.085 (0.000%) 037: dt: 0.5000, sse=39729.2, rms=0.081 (0.000%) 038: dt: 0.5000, sse=40321.2, rms=0.077 (0.000%) 039: dt: 0.5000, sse=40881.0, rms=0.073 (0.000%) 040: dt: 0.5000, sse=41432.2, rms=0.070 (0.000%) 041: dt: 0.5000, sse=41917.3, rms=0.067 (0.000%) 042: dt: 0.5000, sse=42402.4, rms=0.065 (0.000%) 043: dt: 0.5000, sse=42878.4, rms=0.062 (0.000%) 044: dt: 0.5000, sse=43283.0, rms=0.060 (0.000%) 045: dt: 0.5000, sse=43690.0, rms=0.058 (0.000%) 046: dt: 0.5000, sse=44037.4, rms=0.056 (0.000%) 047: dt: 0.5000, sse=44377.8, rms=0.055 (0.000%) 048: dt: 0.5000, sse=44708.8, rms=0.053 (0.000%) 049: dt: 0.5000, sse=45008.6, rms=0.052 (0.000%) 050: dt: 0.5000, sse=45324.1, rms=0.050 (0.000%) 051: dt: 0.5000, sse=45599.2, rms=0.049 (0.000%) 052: dt: 0.5000, sse=45824.9, rms=0.048 (0.000%) 053: dt: 0.5000, sse=46064.4, rms=0.047 (0.000%) 054: dt: 0.5000, sse=46290.4, rms=0.046 (0.000%) 055: dt: 0.5000, sse=46508.7, rms=0.046 (0.000%) 056: dt: 0.5000, sse=46718.5, rms=0.045 (0.000%) 057: dt: 0.5000, sse=46902.8, rms=0.045 (0.000%) 058: dt: 0.5000, sse=47088.3, rms=0.044 (0.000%) 059: dt: 0.5000, sse=47216.6, rms=0.043 (0.000%) 060: dt: 0.5000, sse=47301.2, rms=0.043 (0.000%) positioning took 2.9 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [103.10 206.90], gm=155.00+-17.30, and vertices in regions > 146.3 13736 surface locations found to contain inconsistent values (5496 in, 8240 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=8089.1, rms=0.18 061: dt: 0.5000, sse=7955.0, rms=0.174 (0.000%) 062: dt: 0.5000, sse=7539.9, rms=0.163 (0.000%) 063: dt: 0.5000, sse=7220.5, rms=0.153 (0.000%) 064: dt: 0.5000, sse=6976.5, rms=0.144 (0.000%) 065: dt: 0.5000, sse=6799.2, rms=0.137 (0.000%) 066: dt: 0.5000, sse=6676.5, rms=0.130 (0.000%) 067: dt: 0.5000, sse=6567.2, rms=0.125 (0.000%) 068: dt: 0.5000, sse=6474.5, rms=0.120 (0.000%) 069: dt: 0.5000, sse=6389.2, rms=0.115 (0.000%) 070: dt: 0.5000, sse=6330.9, rms=0.110 (0.000%) 071: dt: 0.5000, sse=6282.3, rms=0.105 (0.000%) 072: dt: 0.5000, sse=6247.6, rms=0.101 (0.000%) 073: dt: 0.5000, sse=6219.6, rms=0.097 (0.000%) 074: dt: 0.5000, sse=6204.7, rms=0.093 (0.000%) 075: dt: 0.5000, sse=6191.0, rms=0.089 (0.000%) 076: dt: 0.5000, sse=6186.2, rms=0.086 (0.000%) 077: dt: 0.5000, sse=6182.3, rms=0.083 (0.000%) 078: dt: 0.5000, sse=6187.0, rms=0.079 (0.000%) 079: dt: 0.5000, sse=6194.9, rms=0.077 (0.000%) 080: dt: 0.5000, sse=6204.8, rms=0.074 (0.000%) 081: dt: 0.5000, sse=6215.7, rms=0.071 (0.000%) 082: dt: 0.5000, sse=6235.3, rms=0.069 (0.000%) 083: dt: 0.5000, sse=6246.4, rms=0.067 (0.000%) 084: dt: 0.5000, sse=6263.7, rms=0.064 (0.000%) 085: dt: 0.5000, sse=6278.4, rms=0.062 (0.000%) 086: dt: 0.5000, sse=6290.3, rms=0.060 (0.000%) 087: dt: 0.5000, sse=6302.3, rms=0.058 (0.000%) 088: dt: 0.5000, sse=6316.3, rms=0.057 (0.000%) 089: dt: 0.5000, sse=6324.7, rms=0.055 (0.000%) 090: dt: 0.5000, sse=6337.0, rms=0.054 (0.000%) positioning took 2.8 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [112.80 199.20], gm=156.00+-14.40, and vertices in regions > 148.8 21619 surface locations found to contain inconsistent values (16444 in, 5175 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/sub010/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=9710.2, rms=0.29 091: dt: 0.5000, sse=9270.5, rms=0.285 (0.000%) 092: dt: 0.5000, sse=8617.0, rms=0.274 (0.000%) 093: dt: 0.5000, sse=8057.5, rms=0.264 (0.000%) 094: dt: 0.5000, sse=7554.5, rms=0.255 (0.000%) 095: dt: 0.5000, sse=7106.7, rms=0.247 (0.000%) 096: dt: 0.5000, sse=6699.3, rms=0.239 (0.000%) 097: dt: 0.5000, sse=6327.3, rms=0.231 (0.000%) 098: dt: 0.5000, sse=5978.0, rms=0.224 (0.000%) 099: dt: 0.5000, sse=5641.3, rms=0.217 (0.000%) 100: dt: 0.5000, sse=5311.4, rms=0.209 (0.000%) 101: dt: 0.5000, sse=5000.9, rms=0.202 (0.000%) 102: dt: 0.5000, sse=4706.1, rms=0.195 (0.000%) 103: dt: 0.5000, sse=4434.0, rms=0.188 (0.000%) 104: dt: 0.5000, sse=4177.8, rms=0.182 (0.000%) 105: dt: 0.5000, sse=3936.6, rms=0.175 (0.000%) 106: dt: 0.5000, sse=3710.8, rms=0.169 (0.000%) 107: dt: 0.5000, sse=3498.0, rms=0.163 (0.000%) 108: dt: 0.5000, sse=3296.7, rms=0.157 (0.000%) 109: dt: 0.5000, sse=3108.9, rms=0.151 (0.000%) 110: dt: 0.5000, sse=2931.8, rms=0.145 (0.000%) 111: dt: 0.5000, sse=2766.5, rms=0.139 (0.000%) 112: dt: 0.5000, sse=2612.9, rms=0.134 (0.000%) 113: dt: 0.5000, sse=2471.7, rms=0.128 (0.000%) 114: dt: 0.5000, sse=2340.8, rms=0.123 (0.000%) 115: dt: 0.5000, sse=2218.6, rms=0.118 (0.000%) 116: dt: 0.5000, sse=2109.3, rms=0.113 (0.000%) 117: dt: 0.5000, sse=2005.6, rms=0.109 (0.000%) 118: dt: 0.5000, sse=1910.7, rms=0.104 (0.000%) 119: dt: 0.5000, sse=1824.0, rms=0.100 (0.000%) 120: dt: 0.5000, sse=1744.3, rms=0.096 (0.000%) positioning took 2.8 minutes writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.area.pial vertex spacing 1.07 +- 0.47 (0.08-->8.17) (max @ vno 79788 --> 78779) face area 0.44 +- 0.35 (0.00-->7.69) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 112521 vertices processed 25000 of 112521 vertices processed 50000 of 112521 vertices processed 75000 of 112521 vertices processed 100000 of 112521 vertices processed 0 of 112521 vertices processed 25000 of 112521 vertices processed 50000 of 112521 vertices processed 75000 of 112521 vertices processed 100000 of 112521 vertices processed thickness calculation complete, 229:1031 truncations. 25308 vertices at 0 distance 74701 vertices at 1 distance 70921 vertices at 2 distance 31005 vertices at 3 distance 8480 vertices at 4 distance 2183 vertices at 5 distance 674 vertices at 6 distance 207 vertices at 7 distance 66 vertices at 8 distance 44 vertices at 9 distance 26 vertices at 10 distance 15 vertices at 11 distance 20 vertices at 12 distance 18 vertices at 13 distance 12 vertices at 14 distance 8 vertices at 15 distance 15 vertices at 16 distance 10 vertices at 17 distance 11 vertices at 18 distance 4 vertices at 19 distance 6 vertices at 20 distance writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.thickness positioning took 14.5 minutes /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.woT2.pial `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.woT2.pial' mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub010 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/sub010/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/wm.mgz... 12290 bright wm thresholded. 241 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.orig... computing class statistics... border white: 201670 voxels (1.20%) border gray 234473 voxels (1.40%) WM (91.0): 91.9 +- 10.6 [70.0 --> 110.0] GM (73.0) : 71.3 +- 13.5 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 42.5 (was 70) setting MAX_BORDER_WHITE to 115.6 (was 105) setting MIN_BORDER_WHITE to 56.0 (was 85) setting MAX_CSF to 29.1 (was 40) setting MAX_GRAY to 94.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 49.3 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 15.6 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=56 mean inside = 91.3, mean outside = 66.0 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/sub010/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.90 +- 0.26 (0.03-->3.59) (max @ vno 88410 --> 89070) face area 0.34 +- 0.16 (0.00-->2.13) averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 1 with 59 points - only 30.51% unknown deleting segment 2 with 6 points - only 0.00% unknown deleting segment 4 with 10 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 9 with 810 points - only 0.00% unknown deleting segment 10 with 7 points - only 0.00% unknown deleting segment 11 with 6 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 12 with 1 points - only 0.00% unknown tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.90 +- 0.26 (0.07-->3.46) (max @ vno 60920 --> 61814) face area 0.34 +- 0.16 (0.00-->2.13) averaging target values for 5 iterations... 000: dt: 0.0000, sse=3904294.5, rms=0.00 rms = 1.47, 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=3904294.5, rms=0.000 (1.000%) positioning took 0.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 59 points - only 30.51% unknown deleting segment 1 with 6 points - only 0.00% unknown deleting segment 2 with 10 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 5 with 810 points - only 0.00% unknown deleting segment 6 with 7 points - only 0.00% unknown deleting segment 7 with 6 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 8 with 1 points - only 0.00% unknown tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.26 (0.07-->3.46) (max @ vno 60920 --> 61814) face area 0.34 +- 0.16 (0.00-->2.13) averaging target values for 5 iterations... 000: dt: 0.0000, sse=3904294.5, rms=0.00 rms = 1.47, 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=3904294.5, rms=0.000 (1.000%) positioning took 0.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 59 points - only 30.51% unknown deleting segment 1 with 6 points - only 0.00% unknown deleting segment 2 with 10 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 5 with 810 points - only 0.00% unknown deleting segment 6 with 7 points - only 0.00% unknown deleting segment 7 with 6 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 8 with 1 points - only 0.00% unknown tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.26 (0.07-->3.46) (max @ vno 60920 --> 61814) face area 0.34 +- 0.16 (0.00-->2.13) averaging target values for 5 iterations... 000: dt: 0.0000, sse=3904294.5, rms=0.00 rms = 1.47, 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=3904294.5, rms=0.000 (1.000%) positioning took 0.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 59 points - only 30.51% unknown deleting segment 1 with 6 points - only 0.00% unknown deleting segment 2 with 10 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 5 with 810 points - only 0.00% unknown deleting segment 6 with 7 points - only 0.00% unknown deleting segment 7 with 6 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 8 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=3904294.5, rms=0.00 rms = 1.47, 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=3904294.5, rms=0.000 (1.000%) positioning took 0.2 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group smoothing surface for 5 iterations... reading initial pial vertex positions from woT2.pial... repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [102.60 203.40], gm=153.00+-16.80, and vertices in regions > 144.6 32499 surface locations found to contain inconsistent values (6526 in, 25973 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=461334.0, rms=0.25 001: dt: 0.5000, sse=433240.8, rms=0.246 (0.000%) 002: dt: 0.5000, sse=415716.5, rms=0.232 (0.000%) 003: dt: 0.5000, sse=404683.8, rms=0.222 (0.000%) 004: dt: 0.5000, sse=396047.9, rms=0.212 (0.000%) 005: dt: 0.5000, sse=389515.8, rms=0.204 (0.000%) 006: dt: 0.5000, sse=384523.5, rms=0.197 (0.000%) 007: dt: 0.5000, sse=380656.6, rms=0.191 (0.000%) 008: dt: 0.5000, sse=377785.3, rms=0.185 (0.000%) 009: dt: 0.5000, sse=375323.8, rms=0.181 (0.000%) 010: dt: 0.5000, sse=373274.1, rms=0.177 (0.000%) 011: dt: 0.5000, sse=371203.3, rms=0.174 (0.000%) 012: dt: 0.5000, sse=369271.0, rms=0.171 (0.000%) 013: dt: 0.5000, sse=367494.1, rms=0.169 (0.000%) 014: dt: 0.5000, sse=365989.0, rms=0.167 (0.000%) 015: dt: 0.5000, sse=364516.8, rms=0.166 (0.000%) 016: dt: 0.5000, sse=363190.2, rms=0.164 (0.000%) 017: dt: 0.5000, sse=361709.2, rms=0.163 (0.000%) 018: dt: 0.5000, sse=360423.2, rms=0.163 (0.000%) 019: dt: 0.5000, sse=358982.1, rms=0.162 (0.000%) 020: dt: 0.5000, sse=357685.2, rms=0.162 (0.000%) 021: dt: 0.5000, sse=356452.5, rms=0.161 (0.000%) 022: dt: 0.5000, sse=355091.5, rms=0.161 (0.000%) 023: dt: 0.5000, sse=353877.5, rms=0.161 (0.000%) 024: dt: 0.5000, sse=352503.6, rms=0.161 (0.000%) 025: dt: 0.5000, sse=351754.4, rms=0.161 (0.000%) 026: dt: 0.5000, sse=350467.2, rms=0.161 (0.000%) 027: dt: 0.5000, sse=349278.9, rms=0.161 (0.000%) 028: dt: 0.5000, sse=348301.2, rms=0.162 (0.000%) 029: dt: 0.5000, sse=347300.8, rms=0.162 (0.000%) 030: dt: 0.5000, sse=346608.0, rms=0.162 (0.000%) positioning took 2.9 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [100.30 207.70], gm=154.00+-17.90, and vertices in regions > 145.0 25001 surface locations found to contain inconsistent values (1723 in, 23278 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=36143.1, rms=0.14 031: dt: 0.5000, sse=35900.4, rms=0.133 (0.000%) 032: dt: 0.5000, sse=36564.6, rms=0.122 (0.000%) 033: dt: 0.5000, sse=37401.6, rms=0.115 (0.000%) 034: dt: 0.5000, sse=38133.3, rms=0.109 (0.000%) 035: dt: 0.5000, sse=38771.1, rms=0.104 (0.000%) 036: dt: 0.5000, sse=39402.9, rms=0.099 (0.000%) 037: dt: 0.5000, sse=39998.6, rms=0.095 (0.000%) 038: dt: 0.5000, sse=40606.3, rms=0.091 (0.000%) 039: dt: 0.5000, sse=41163.0, rms=0.087 (0.000%) 040: dt: 0.5000, sse=41728.7, rms=0.084 (0.000%) 041: dt: 0.5000, sse=42245.6, rms=0.081 (0.000%) 042: dt: 0.5000, sse=42753.1, rms=0.078 (0.000%) 043: dt: 0.5000, sse=43218.8, rms=0.075 (0.000%) 044: dt: 0.5000, sse=43656.8, rms=0.073 (0.000%) 045: dt: 0.5000, sse=44066.9, rms=0.070 (0.000%) 046: dt: 0.5000, sse=44477.1, rms=0.068 (0.000%) 047: dt: 0.5000, sse=44858.4, rms=0.066 (0.000%) 048: dt: 0.5000, sse=45200.9, rms=0.064 (0.000%) 049: dt: 0.5000, sse=45558.4, rms=0.062 (0.000%) 050: dt: 0.5000, sse=45869.6, rms=0.060 (0.000%) 051: dt: 0.5000, sse=46134.1, rms=0.059 (0.000%) 052: dt: 0.5000, sse=46403.9, rms=0.057 (0.000%) 053: dt: 0.5000, sse=46670.9, rms=0.056 (0.000%) 054: dt: 0.5000, sse=46913.3, rms=0.055 (0.000%) 055: dt: 0.5000, sse=47112.3, rms=0.054 (0.000%) 056: dt: 0.5000, sse=47303.3, rms=0.053 (0.000%) 057: dt: 0.5000, sse=47512.1, rms=0.051 (0.000%) 058: dt: 0.5000, sse=47700.1, rms=0.050 (0.000%) 059: dt: 0.5000, sse=47851.7, rms=0.050 (0.000%) 060: dt: 0.5000, sse=48009.2, rms=0.049 (0.000%) positioning took 2.9 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [97.30 210.70], gm=154.00+-18.90, and vertices in regions > 144.5 23565 surface locations found to contain inconsistent values (251 in, 23314 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=5207.5, rms=0.06 061: dt: 0.5000, sse=5182.6, rms=0.061 (0.000%) 062: dt: 0.5000, sse=5255.6, rms=0.054 (0.000%) 063: dt: 0.5000, sse=5333.7, rms=0.050 (0.000%) 064: dt: 0.5000, sse=5399.6, rms=0.047 (0.000%) 065: dt: 0.5000, sse=5442.4, rms=0.045 (0.000%) 066: dt: 0.5000, sse=5466.1, rms=0.044 (0.000%) 067: dt: 0.5000, sse=5479.7, rms=0.042 (0.000%) 068: dt: 0.5000, sse=5493.1, rms=0.041 (0.000%) 069: dt: 0.5000, sse=5506.1, rms=0.040 (0.000%) 070: dt: 0.5000, sse=5517.8, rms=0.039 (0.000%) 071: dt: 0.5000, sse=5528.1, rms=0.038 (0.000%) 072: dt: 0.5000, sse=5539.3, rms=0.037 (0.000%) 073: dt: 0.5000, sse=5548.8, rms=0.036 (0.000%) 074: dt: 0.5000, sse=5558.5, rms=0.036 (0.000%) 075: dt: 0.5000, sse=5567.3, rms=0.035 (0.000%) 076: dt: 0.5000, sse=5571.2, rms=0.035 (0.000%) 077: dt: 0.5000, sse=5575.4, rms=0.034 (0.000%) 078: dt: 0.5000, sse=5580.0, rms=0.034 (0.000%) 079: dt: 0.5000, sse=5584.9, rms=0.033 (0.000%) 080: dt: 0.5000, sse=5589.2, rms=0.033 (0.000%) 081: dt: 0.5000, sse=5594.5, rms=0.033 (0.000%) 082: dt: 0.5000, sse=5599.1, rms=0.032 (0.000%) 083: dt: 0.5000, sse=5602.4, rms=0.032 (0.000%) 084: dt: 0.5000, sse=5605.8, rms=0.032 (0.000%) 085: dt: 0.5000, sse=5607.8, rms=0.032 (0.000%) 086: dt: 0.5000, sse=5608.6, rms=0.031 (0.000%) 087: dt: 0.5000, sse=5611.4, rms=0.031 (0.000%) 088: dt: 0.5000, sse=5613.7, rms=0.031 (0.000%) 089: dt: 0.5000, sse=5616.2, rms=0.031 (0.000%) 090: dt: 0.5000, sse=5616.1, rms=0.031 (0.000%) positioning took 2.9 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [102.10 205.90], gm=154.00+-17.30, and vertices in regions > 145.3 11360 surface locations found to contain inconsistent values (1534 in, 9826 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/sub010/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=945.3, rms=0.06 091: dt: 0.5000, sse=937.7, rms=0.060 (0.000%) 092: dt: 0.5000, sse=899.3, rms=0.057 (0.000%) 093: dt: 0.5000, sse=872.7, rms=0.055 (0.000%) 094: dt: 0.5000, sse=848.8, rms=0.052 (0.000%) 095: dt: 0.5000, sse=829.0, rms=0.050 (0.000%) 096: dt: 0.5000, sse=814.6, rms=0.049 (0.000%) 097: dt: 0.5000, sse=803.5, rms=0.048 (0.000%) 098: dt: 0.5000, sse=793.9, rms=0.047 (0.000%) 099: dt: 0.5000, sse=785.3, rms=0.046 (0.000%) 100: dt: 0.5000, sse=776.8, rms=0.045 (0.000%) 101: dt: 0.5000, sse=768.7, rms=0.044 (0.000%) 102: dt: 0.5000, sse=760.4, rms=0.043 (0.000%) 103: dt: 0.5000, sse=753.0, rms=0.042 (0.000%) 104: dt: 0.5000, sse=747.5, rms=0.042 (0.000%) 105: dt: 0.5000, sse=741.8, rms=0.041 (0.000%) 106: dt: 0.5000, sse=735.7, rms=0.040 (0.000%) 107: dt: 0.5000, sse=731.4, rms=0.039 (0.000%) 108: dt: 0.5000, sse=727.6, rms=0.039 (0.000%) 109: dt: 0.5000, sse=723.2, rms=0.038 (0.000%) 110: dt: 0.5000, sse=718.4, rms=0.038 (0.000%) 111: dt: 0.5000, sse=715.4, rms=0.037 (0.000%) 112: dt: 0.5000, sse=711.7, rms=0.037 (0.000%) 113: dt: 0.5000, sse=709.7, rms=0.036 (0.000%) 114: dt: 0.5000, sse=706.9, rms=0.036 (0.000%) 115: dt: 0.5000, sse=703.8, rms=0.036 (0.000%) 116: dt: 0.5000, sse=701.3, rms=0.035 (0.000%) 117: dt: 0.5000, sse=699.9, rms=0.035 (0.000%) 118: dt: 0.5000, sse=699.6, rms=0.035 (0.000%) 119: dt: 0.5000, sse=696.8, rms=0.035 (0.000%) 120: dt: 0.5000, sse=694.5, rms=0.034 (0.000%) positioning took 2.9 minutes writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.area.pial vertex spacing 1.06 +- 0.46 (0.03-->7.43) (max @ vno 50964 --> 49869) face area 0.44 +- 0.34 (0.00-->5.41) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 111391 vertices processed 25000 of 111391 vertices processed 50000 of 111391 vertices processed 75000 of 111391 vertices processed 100000 of 111391 vertices processed 0 of 111391 vertices processed 25000 of 111391 vertices processed 50000 of 111391 vertices processed 75000 of 111391 vertices processed 100000 of 111391 vertices processed thickness calculation complete, 355:1226 truncations. 23172 vertices at 0 distance 71146 vertices at 1 distance 71592 vertices at 2 distance 32643 vertices at 3 distance 9256 vertices at 4 distance 2482 vertices at 5 distance 776 vertices at 6 distance 263 vertices at 7 distance 107 vertices at 8 distance 50 vertices at 9 distance 29 vertices at 10 distance 12 vertices at 11 distance 14 vertices at 12 distance 5 vertices at 13 distance 19 vertices at 14 distance 11 vertices at 15 distance 14 vertices at 16 distance 9 vertices at 17 distance 5 vertices at 18 distance 12 vertices at 19 distance 7 vertices at 20 distance writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.thickness positioning took 14.4 minutes #-------------------------------------------- #@# Surf Volume lh Thu Aug 8 21:42:01 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 21:42:01 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 21:42:01 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon sub010 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 = 49 writing volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/ribbon.mgz writing ribbon files #-------------------------------------------- #@# ASeg Stats Thu Aug 8 21:55:18 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010 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 sub010 $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 sub010 sysname Linux hostname snake4 machine x86_64 user fkaule UseRobust 0 atlas_icv (eTIV) = 925308 mm^3 (det: 2.105359 ) Computing euler number orig.nofix lheno = -48, rheno = -34 orig.nofix lhholes = 25, rhholes = 18 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 215045.047 214126.000 diff= 919.0 pctdiff= 0.427 rhCtxGM: 216453.318 215813.000 diff= 640.3 pctdiff= 0.296 lhCtxWM: 159951.796 159955.000 diff= -3.2 pctdiff=-0.002 rhCtxWM: 161933.369 161722.000 diff= 211.4 pctdiff= 0.131 SubCortGMVol 57131.000 SupraTentVol 827705.530 (825177.000) diff=2528.530 pctdiff=0.305 SupraTentVolNotVent 811627.530 (809099.000) diff=2528.530 pctdiff=0.312 BrainSegVol 932519.000 (930794.000) diff=1725.000 pctdiff=0.185 BrainSegVolNotVent 913858.000 (915337.530) diff=-1479.530 pctdiff=-0.162 BrainSegVolNotVent 913858.000 CerebellumVol 104471.000 VentChorVol 16078.000 3rd4th5thCSF 2583.000 CSFVol 897.000, OptChiasmVol 249.000 MaskVol 1374696.000 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 7829 7829.426 4 5 Left-Inf-Lat-Vent 339 339.366 5 7 Left-Cerebellum-White-Matter 12932 12931.568 6 8 Left-Cerebellum-Cortex 39955 39954.531 7 10 Left-Thalamus-Proper 6620 6620.007 8 11 Left-Caudate 3656 3655.936 9 12 Left-Putamen 6330 6329.792 10 13 Left-Pallidum 1725 1725.390 11 14 3rd-Ventricle 733 733.176 12 15 4th-Ventricle 1097 1097.076 13 16 Brain-Stem 19373 19373.477 14 17 Left-Hippocampus 3640 3640.310 15 18 Left-Amygdala 1499 1498.651 16 24 CSF 897 897.245 17 26 Left-Accumbens-area 736 735.534 18 28 Left-VentralDC 3573 3572.699 19 30 Left-vessel 188 187.965 20 31 Left-choroid-plexus 962 961.815 23 43 Right-Lateral-Ventricle 5416 5416.328 24 44 Right-Inf-Lat-Vent 307 307.397 25 46 Right-Cerebellum-White-Matter 13244 13243.784 26 47 Right-Cerebellum-Cortex 40491 40490.508 27 49 Right-Thalamus-Proper 6326 6325.789 28 50 Right-Caudate 3626 3625.609 29 51 Right-Putamen 6094 6093.857 30 52 Right-Pallidum 1871 1871.403 31 53 Right-Hippocampus 3529 3529.014 32 54 Right-Amygdala 1769 1769.435 33 58 Right-Accumbens-area 758 757.725 34 60 Right-VentralDC 3511 3511.233 35 62 Right-vessel 124 124.474 36 63 Right-choroid-plexus 1168 1167.699 37 72 5th-Ventricle 0 0.000 38 77 WM-hypointensities 723 723.212 39 78 Left-WM-hypointensities 0 0.000 40 79 Right-WM-hypointensities 0 0.000 41 80 non-WM-hypointensities 61 60.620 42 81 Left-non-WM-hypointensities 0 0.000 43 82 Right-non-WM-hypointensities 0 0.000 44 85 Optic-Chiasm 242 242.300 45 251 CC_Posterior 850 850.278 46 252 CC_Mid_Posterior 349 348.652 47 253 CC_Central 307 306.991 48 254 CC_Mid_Anterior 266 265.577 49 255 CC_Anterior 615 614.942 Reporting on 45 segmentations mri_segstats done #----------------------------------------- #@# AParc-to-ASeg Thu Aug 8 21:58:44 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010 mri_aparc2aseg --s sub010 --volmask SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer subject sub010 outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.white Reading lh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.pial Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/surf/rh.white Reading rh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.pial Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/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/sub010/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 = 428041 Used brute-force search on 0 voxels Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/aparc+aseg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010 mri_aparc2aseg --s sub010 --volmask --a2009s SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer subject sub010 outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.white Reading lh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.pial Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/surf/rh.white Reading rh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.pial Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/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/sub010/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 = 428041 Used brute-force search on 0 voxels Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# WMParc Thu Aug 8 22:02:45 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010 mri_aparc2aseg --s sub010 --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 sub010 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/sub010/mri/aparc+aseg.mgz Reading lh white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.white Reading lh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.pial Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/surf/rh.white Reading rh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.pial Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/mri/ribbon.mgz Loading filled from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/filled.mgz Ripping vertices labeled as unkown Ripped 7480 vertices from left hemi Ripped 7577 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/sub010/mri/aseg.mgz Loading Ctx Seg File /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 = 749163 Used brute-force search on 32 voxels Fixing Parahip LH WM Found 5 clusters 0 k 9.000000 1 k 1194.000000 2 k 2.000000 3 k 4.000000 4 k 49.000000 Fixing Parahip RH WM Found 6 clusters 0 k 2.000000 1 k 1.000000 2 k 2.000000 3 k 1.000000 4 k 1.000000 5 k 1061.000000 Writing output aseg to mri/wmparc.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010 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 sub010 --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 sub010 --surf-wm-vol --ctab /opt/freesurfer/5.3.0/WMParcStatsLUT.txt --etiv sysname Linux hostname snake4 machine x86_64 user fkaule UseRobust 0 atlas_icv (eTIV) = 925308 mm^3 (det: 2.105359 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 215045.047 214126.000 diff= 919.0 pctdiff= 0.427 rhCtxGM: 216453.318 215813.000 diff= 640.3 pctdiff= 0.296 lhCtxWM: 159951.796 159955.000 diff= -3.2 pctdiff=-0.002 rhCtxWM: 161933.369 161722.000 diff= 211.4 pctdiff= 0.131 SubCortGMVol 57131.000 SupraTentVol 827705.530 (825177.000) diff=2528.530 pctdiff=0.305 SupraTentVolNotVent 811627.530 (809099.000) diff=2528.530 pctdiff=0.312 BrainSegVol 932519.000 (930794.000) diff=1725.000 pctdiff=0.185 BrainSegVolNotVent 913858.000 (915337.530) diff=-1479.530 pctdiff=-0.162 BrainSegVolNotVent 913858.000 CerebellumVol 104471.000 VentChorVol 16078.000 3rd4th5thCSF 2583.000 CSFVol 897.000, OptChiasmVol 249.000 MaskVol 1374696.000 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 3007 3007.497 2 3002 wm-lh-caudalanteriorcingulate 1815 1814.583 3 3003 wm-lh-caudalmiddlefrontal 4416 4416.122 4 3004 wm-lh-corpuscallosum 0 0.000 5 3005 wm-lh-cuneus 2213 2212.622 6 3006 wm-lh-entorhinal 700 700.151 7 3007 wm-lh-fusiform 5229 5229.411 8 3008 wm-lh-inferiorparietal 7393 7393.180 9 3009 wm-lh-inferiortemporal 4544 4544.138 10 3010 wm-lh-isthmuscingulate 3195 3194.569 11 3011 wm-lh-lateraloccipital 7121 7120.542 12 3012 wm-lh-lateralorbitofrontal 4504 4504.396 13 3013 wm-lh-lingual 4379 4378.711 14 3014 wm-lh-medialorbitofrontal 2391 2391.337 15 3015 wm-lh-middletemporal 3822 3821.702 16 3016 wm-lh-parahippocampal 1263 1263.064 17 3017 wm-lh-paracentral 2899 2899.385 18 3018 wm-lh-parsopercularis 2360 2360.028 19 3019 wm-lh-parsorbitalis 632 632.361 20 3020 wm-lh-parstriangularis 2051 2050.875 21 3021 wm-lh-pericalcarine 2653 2652.559 22 3022 wm-lh-postcentral 5421 5421.239 23 3023 wm-lh-posteriorcingulate 3201 3201.417 24 3024 wm-lh-precentral 10281 10281.124 25 3025 wm-lh-precuneus 6670 6670.213 26 3026 wm-lh-rostralanteriorcingulate 2855 2854.854 27 3027 wm-lh-rostralmiddlefrontal 9121 9120.788 28 3028 wm-lh-superiorfrontal 12124 12124.131 29 3029 wm-lh-superiorparietal 8530 8529.941 30 3030 wm-lh-superiortemporal 4345 4344.885 31 3031 wm-lh-supramarginal 5673 5673.487 32 3032 wm-lh-frontalpole 125 125.029 33 3033 wm-lh-temporalpole 501 500.944 34 3034 wm-lh-transversetemporal 598 598.409 35 3035 wm-lh-insula 6063 6063.475 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 3059 3058.928 120 4002 wm-rh-caudalanteriorcingulate 2345 2345.101 121 4003 wm-rh-caudalmiddlefrontal 3739 3738.853 122 4004 wm-rh-corpuscallosum 0 0.000 123 4005 wm-rh-cuneus 2023 2022.947 124 4006 wm-rh-entorhinal 568 568.484 125 4007 wm-rh-fusiform 4504 4503.506 126 4008 wm-rh-inferiorparietal 9271 9271.327 127 4009 wm-rh-inferiortemporal 4136 4135.960 128 4010 wm-rh-isthmuscingulate 2671 2671.055 129 4011 wm-rh-lateraloccipital 6333 6333.224 130 4012 wm-rh-lateralorbitofrontal 4706 4706.465 131 4013 wm-rh-lingual 4280 4280.259 132 4014 wm-rh-medialorbitofrontal 2523 2523.001 133 4015 wm-rh-middletemporal 4412 4412.409 134 4016 wm-rh-parahippocampal 1130 1129.912 135 4017 wm-rh-paracentral 3348 3348.097 136 4018 wm-rh-parsopercularis 2198 2198.048 137 4019 wm-rh-parsorbitalis 750 749.881 138 4020 wm-rh-parstriangularis 2763 2762.996 139 4021 wm-rh-pericalcarine 2843 2843.098 140 4022 wm-rh-postcentral 5877 5877.005 141 4023 wm-rh-posteriorcingulate 3024 3023.799 142 4024 wm-rh-precentral 10984 10983.681 143 4025 wm-rh-precuneus 7561 7561.242 144 4026 wm-rh-rostralanteriorcingulate 1612 1612.110 145 4027 wm-rh-rostralmiddlefrontal 9128 9128.189 146 4028 wm-rh-superiorfrontal 11986 11985.799 147 4029 wm-rh-superiorparietal 8349 8348.782 148 4030 wm-rh-superiortemporal 4035 4034.939 149 4031 wm-rh-supramarginal 5576 5575.699 150 4032 wm-rh-frontalpole 187 186.517 151 4033 wm-rh-temporalpole 568 568.127 152 4034 wm-rh-transversetemporal 397 397.337 153 4035 wm-rh-insula 6007 6006.890 154 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 18696 18696.154 237 5002 Right-UnsegmentedWhiteMatter 19159 19158.822 238 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/sub010/label #-------------------------------------------- #@# BA Labels lh Thu Aug 8 22:12:37 CEST 2013 INFO: fsaverage subject does not exist in SUBJECTS_DIR INFO: Creating symlink to fsaverage subject... cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer; ln -s /opt/freesurfer/5.3.0/subjects/fsaverage; cd - mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.label --trgsubject sub010 --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 = sub010 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/sub010/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521 Number of reverse mapping hits = 96 Checking for and removing duplicates Writing label file ./lh.BA1.label 4225 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.label --trgsubject sub010 --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 = sub010 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/sub010/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521 Number of reverse mapping hits = 212 Checking for and removing duplicates Writing label file ./lh.BA2.label 8121 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.label --trgsubject sub010 --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 = sub010 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/sub010/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521 Number of reverse mapping hits = 77 Checking for and removing duplicates Writing label file ./lh.BA3a.label 4154 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.label --trgsubject sub010 --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 = sub010 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/sub010/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521 Number of reverse mapping hits = 183 Checking for and removing duplicates Writing label file ./lh.BA3b.label 6166 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.label --trgsubject sub010 --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 = sub010 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/sub010/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521 Number of reverse mapping hits = 84 Checking for and removing duplicates Writing label file ./lh.BA4a.label 5868 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.label --trgsubject sub010 --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 = sub010 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/sub010/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521 Number of reverse mapping hits = 59 Checking for and removing duplicates Writing label file ./lh.BA4p.label 4129 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.label --trgsubject sub010 --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 = sub010 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/sub010/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521 Number of reverse mapping hits = 410 Checking for and removing duplicates Writing label file ./lh.BA6.label 13999 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.label --trgsubject sub010 --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 = sub010 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/sub010/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521 Number of reverse mapping hits = 285 Checking for and removing duplicates Writing label file ./lh.BA44.label 4466 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.label --trgsubject sub010 --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 = sub010 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/sub010/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521 Number of reverse mapping hits = 319 Checking for and removing duplicates Writing label file ./lh.BA45.label 3741 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.label --trgsubject sub010 --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 = sub010 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/sub010/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521 Number of reverse mapping hits = 1439 Checking for and removing duplicates Writing label file ./lh.V1.label 6080 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.label --trgsubject sub010 --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 = sub010 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/sub010/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521 Number of reverse mapping hits = 2375 Checking for and removing duplicates Writing label file ./lh.V2.label 10489 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.label --trgsubject sub010 --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 = sub010 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/sub010/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521 Number of reverse mapping hits = 238 Checking for and removing duplicates Writing label file ./lh.MT.label 2256 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.perirhinal.label --trgsubject sub010 --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 = sub010 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/sub010/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521 Number of reverse mapping hits = 110 Checking for and removing duplicates Writing label file ./lh.perirhinal.label 1309 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.thresh.label --trgsubject sub010 --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 = sub010 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/sub010/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521 Number of reverse mapping hits = 13 Checking for and removing duplicates Writing label file ./lh.BA1.thresh.label 1027 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.thresh.label --trgsubject sub010 --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 = sub010 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/sub010/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521 Number of reverse mapping hits = 29 Checking for and removing duplicates Writing label file ./lh.BA2.thresh.label 2121 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.thresh.label --trgsubject sub010 --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 = sub010 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/sub010/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521 Number of reverse mapping hits = 26 Checking for and removing duplicates Writing label file ./lh.BA3a.thresh.label 1530 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.thresh.label --trgsubject sub010 --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 = sub010 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/sub010/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521 Number of reverse mapping hits = 104 Checking for and removing duplicates Writing label file ./lh.BA3b.thresh.label 2100 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.thresh.label --trgsubject sub010 --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 = sub010 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/sub010/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521 Number of reverse mapping hits = 33 Checking for and removing duplicates Writing label file ./lh.BA4a.thresh.label 2352 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.thresh.label --trgsubject sub010 --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 = sub010 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/sub010/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521 Number of reverse mapping hits = 22 Checking for and removing duplicates Writing label file ./lh.BA4p.thresh.label 1571 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.thresh.label --trgsubject sub010 --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 = sub010 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/sub010/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521 Number of reverse mapping hits = 148 Checking for and removing duplicates Writing label file ./lh.BA6.thresh.label 7183 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.thresh.label --trgsubject sub010 --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 = sub010 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/sub010/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521 Number of reverse mapping hits = 115 Checking for and removing duplicates Writing label file ./lh.BA44.thresh.label 2027 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.thresh.label --trgsubject sub010 --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 = sub010 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/sub010/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521 Number of reverse mapping hits = 138 Checking for and removing duplicates Writing label file ./lh.BA45.thresh.label 1289 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.thresh.label --trgsubject sub010 --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 = sub010 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/sub010/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521 Number of reverse mapping hits = 1056 Checking for and removing duplicates Writing label file ./lh.V1.thresh.label 4461 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.thresh.label --trgsubject sub010 --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 = sub010 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/sub010/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521 Number of reverse mapping hits = 1262 Checking for and removing duplicates Writing label file ./lh.V2.thresh.label 4596 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.thresh.label --trgsubject sub010 --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 = sub010 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/sub010/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521 Number of reverse mapping hits = 39 Checking for and removing duplicates Writing label file ./lh.MT.thresh.label 552 mri_label2label: Done mris_label2annot --s sub010 --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/sub010/label cmdline mris_label2annot --s sub010 --hemi lh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --l lh.perirhinal.label --a BA --maxstatwinner --noverbose sysname Linux hostname snake4 machine x86_64 user fkaule subject sub010 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/sub010/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 77718 unhit vertices Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/label/lh.BA.annot mris_label2annot --s sub010 --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/sub010/label cmdline mris_label2annot --s sub010 --hemi lh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l lh.BA1.thresh.label --l lh.BA2.thresh.label --l lh.BA3a.thresh.label --l lh.BA3b.thresh.label --l lh.BA4a.thresh.label --l lh.BA4p.thresh.label --l lh.BA6.thresh.label --l lh.BA44.thresh.label --l lh.BA45.thresh.label --l lh.V1.thresh.label --l lh.V2.thresh.label --l lh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose sysname Linux hostname snake4 machine x86_64 user fkaule subject sub010 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/sub010/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 92228 unhit vertices Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/label/lh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab sub010 lh white computing statistics for each annotation in ./lh.BA.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 829 507 1405 1.881 0.756 0.177 0.074 24 2.7 BA1 3158 2139 5435 2.277 0.506 0.128 0.038 39 4.9 BA2 852 579 838 1.918 0.393 0.134 0.037 7 1.2 BA3a 2016 1368 3325 1.977 0.588 0.125 0.045 30 3.3 BA3b 1213 776 2944 2.878 0.523 0.109 0.072 15 1.6 BA4a 1058 705 1884 2.622 0.506 0.105 0.029 6 1.4 BA4p 7180 4860 18198 2.851 0.631 0.141 0.053 127 12.9 BA6 2042 1415 4510 2.713 0.461 0.138 0.053 40 4.5 BA44 2380 1665 5167 2.549 0.517 0.148 0.052 42 4.1 BA45 3648 2441 4555 1.730 0.490 0.156 0.075 76 10.2 V1 7807 5115 11855 2.093 0.508 0.169 0.069 168 21.0 V2 1723 1182 2922 2.275 0.400 0.153 0.049 30 3.5 MT 897 662 3188 3.610 0.865 0.167 0.073 27 2.4 perirhinal mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab sub010 lh white computing statistics for each annotation in ./lh.BA.thresh.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 507 282 654 1.511 0.555 0.185 0.085 16 2.0 BA1 1119 761 1926 2.151 0.501 0.117 0.031 11 1.3 BA2 678 454 634 1.948 0.381 0.146 0.043 6 1.2 BA3a 1317 907 1778 1.723 0.430 0.105 0.028 9 1.6 BA3b 1204 769 2880 2.933 0.471 0.103 0.071 14 1.6 BA4a 876 589 1558 2.629 0.467 0.103 0.029 6 1.1 BA4p 3855 2591 9579 2.815 0.617 0.139 0.042 53 6.6 BA6 1277 879 2896 2.766 0.466 0.147 0.068 33 3.6 BA44 983 692 2592 2.764 0.534 0.170 0.048 23 2.0 BA45 3888 2602 5015 1.755 0.478 0.156 0.070 68 10.4 V1 4162 2704 5731 1.893 0.435 0.176 0.081 110 12.8 V2 427 315 797 2.192 0.433 0.154 0.047 7 0.8 MT #-------------------------------------------- #@# BA Labels rh Thu Aug 8 22:16:23 CEST 2013 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.label --trgsubject sub010 --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 = sub010 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/sub010/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391 Number of reverse mapping hits = 98 Checking for and removing duplicates Writing label file ./rh.BA1.label 4060 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.label --trgsubject sub010 --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 = sub010 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/sub010/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391 Number of reverse mapping hits = 139 Checking for and removing duplicates Writing label file ./rh.BA2.label 6826 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.label --trgsubject sub010 --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 = sub010 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/sub010/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391 Number of reverse mapping hits = 87 Checking for and removing duplicates Writing label file ./rh.BA3a.label 4067 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.label --trgsubject sub010 --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 = sub010 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/sub010/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391 Number of reverse mapping hits = 120 Checking for and removing duplicates Writing label file ./rh.BA3b.label 4642 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.label --trgsubject sub010 --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 = sub010 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/sub010/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391 Number of reverse mapping hits = 220 Checking for and removing duplicates Writing label file ./rh.BA4a.label 5967 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.label --trgsubject sub010 --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 = sub010 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/sub010/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391 Number of reverse mapping hits = 160 Checking for and removing duplicates Writing label file ./rh.BA4p.label 4633 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.label --trgsubject sub010 --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 = sub010 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/sub010/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391 Number of reverse mapping hits = 457 Checking for and removing duplicates Writing label file ./rh.BA6.label 12713 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.label --trgsubject sub010 --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 = sub010 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/sub010/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391 Number of reverse mapping hits = 406 Checking for and removing duplicates Writing label file ./rh.BA44.label 7318 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.label --trgsubject sub010 --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 = sub010 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/sub010/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391 Number of reverse mapping hits = 741 Checking for and removing duplicates Writing label file ./rh.BA45.label 6096 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.label --trgsubject sub010 --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 = sub010 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/sub010/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391 Number of reverse mapping hits = 1665 Checking for and removing duplicates Writing label file ./rh.V1.label 6392 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.label --trgsubject sub010 --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 = sub010 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/sub010/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391 Number of reverse mapping hits = 2499 Checking for and removing duplicates Writing label file ./rh.V2.label 10515 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.label --trgsubject sub010 --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 = sub010 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/sub010/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391 Number of reverse mapping hits = 249 Checking for and removing duplicates Writing label file ./rh.MT.label 2181 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.perirhinal.label --trgsubject sub010 --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 = sub010 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/sub010/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391 Number of reverse mapping hits = 65 Checking for and removing duplicates Writing label file ./rh.perirhinal.label 817 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.thresh.label --trgsubject sub010 --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 = sub010 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/sub010/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391 Number of reverse mapping hits = 33 Checking for and removing duplicates Writing label file ./rh.BA1.thresh.label 909 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.thresh.label --trgsubject sub010 --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 = sub010 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/sub010/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391 Number of reverse mapping hits = 61 Checking for and removing duplicates Writing label file ./rh.BA2.thresh.label 2749 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.thresh.label --trgsubject sub010 --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 = sub010 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/sub010/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391 Number of reverse mapping hits = 26 Checking for and removing duplicates Writing label file ./rh.BA3a.thresh.label 1724 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.thresh.label --trgsubject sub010 --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 = sub010 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/sub010/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391 Number of reverse mapping hits = 71 Checking for and removing duplicates Writing label file ./rh.BA3b.thresh.label 2254 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.thresh.label --trgsubject sub010 --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 = sub010 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/sub010/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391 Number of reverse mapping hits = 41 Checking for and removing duplicates Writing label file ./rh.BA4a.thresh.label 1429 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.thresh.label --trgsubject sub010 --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 = sub010 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/sub010/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391 Number of reverse mapping hits = 58 Checking for and removing duplicates Writing label file ./rh.BA4p.thresh.label 1547 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.thresh.label --trgsubject sub010 --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 = sub010 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/sub010/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391 Number of reverse mapping hits = 287 Checking for and removing duplicates Writing label file ./rh.BA6.thresh.label 7246 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.thresh.label --trgsubject sub010 --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 = sub010 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/sub010/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391 Number of reverse mapping hits = 46 Checking for and removing duplicates Writing label file ./rh.BA44.thresh.label 1058 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.thresh.label --trgsubject sub010 --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 = sub010 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/sub010/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391 Number of reverse mapping hits = 165 Checking for and removing duplicates Writing label file ./rh.BA45.thresh.label 1343 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.thresh.label --trgsubject sub010 --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 = sub010 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/sub010/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391 Number of reverse mapping hits = 1139 Checking for and removing duplicates Writing label file ./rh.V1.thresh.label 4371 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.thresh.label --trgsubject sub010 --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 = sub010 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/sub010/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391 Number of reverse mapping hits = 1271 Checking for and removing duplicates Writing label file ./rh.V2.thresh.label 4708 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.thresh.label --trgsubject sub010 --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 = sub010 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/sub010/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391 Number of reverse mapping hits = 48 Checking for and removing duplicates Writing label file ./rh.MT.thresh.label 316 mri_label2label: Done mris_label2annot --s sub010 --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/sub010/label cmdline mris_label2annot --s sub010 --hemi rh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --l rh.perirhinal.label --a BA --maxstatwinner --noverbose sysname Linux hostname snake4 machine x86_64 user fkaule subject sub010 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/sub010/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 75955 unhit vertices Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/label/rh.BA.annot mris_label2annot --s sub010 --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/sub010/label cmdline mris_label2annot --s sub010 --hemi rh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l rh.BA1.thresh.label --l rh.BA2.thresh.label --l rh.BA3a.thresh.label --l rh.BA3b.thresh.label --l rh.BA4a.thresh.label --l rh.BA4p.thresh.label --l rh.BA6.thresh.label --l rh.BA44.thresh.label --l rh.BA45.thresh.label --l rh.V1.thresh.label --l rh.V2.thresh.label --l rh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose sysname Linux hostname snake4 machine x86_64 user fkaule subject sub010 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/sub010/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 91276 unhit vertices Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/label/rh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab sub010 rh white computing statistics for each annotation in ./rh.BA.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 745 436 1729 2.718 0.406 0.163 0.047 15 1.5 BA1 2634 1796 4579 2.288 0.530 0.115 0.034 23 4.1 BA2 901 588 923 2.072 0.471 0.133 0.041 8 1.4 BA3a 1696 1176 2812 2.012 0.594 0.135 0.038 21 2.9 BA3b 1334 862 3320 2.935 0.578 0.134 0.058 21 2.3 BA4a 1122 780 2129 2.656 0.464 0.119 0.035 9 1.6 BA4p 6421 4340 15619 2.902 0.617 0.136 0.040 84 10.7 BA6 2715 1866 6069 2.772 0.524 0.135 0.043 41 5.1 BA44 3989 2752 9154 2.676 0.596 0.152 0.053 78 8.6 BA45 4011 2750 5592 1.926 0.523 0.171 0.074 85 13.4 V1 7620 5035 11666 2.131 0.589 0.176 0.078 184 22.4 V2 1701 1175 2843 2.316 0.472 0.161 0.070 32 4.1 MT 547 400 1651 2.934 1.124 0.176 0.086 13 1.9 perirhinal mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab sub010 rh white computing statistics for each annotation in ./rh.BA.thresh.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 520 294 1118 2.597 0.377 0.170 0.054 11 1.2 BA1 1541 1041 2780 2.272 0.523 0.104 0.027 11 1.7 BA2 815 535 801 2.064 0.438 0.136 0.038 7 1.4 BA3a 1388 994 2021 1.817 0.488 0.123 0.029 12 1.7 BA3b 759 485 2005 3.028 0.568 0.132 0.071 15 1.3 BA4a 880 614 1718 2.703 0.470 0.116 0.038 6 1.2 BA4p 4205 2836 10451 2.933 0.603 0.140 0.043 60 7.4 BA6 717 505 1859 2.751 0.497 0.150 0.067 18 2.0 BA44 1040 722 2689 2.888 0.638 0.163 0.056 23 2.4 BA45 3823 2617 5263 1.927 0.530 0.170 0.074 82 12.5 V1 4172 2802 6222 2.029 0.575 0.187 0.091 108 14.6 V2 255 169 523 2.620 0.442 0.157 0.062 4 0.6 MT /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label lh Thu Aug 8 22:20:09 CEST 2013 INFO: lh.EC_average subject does not exist in SUBJECTS_DIR INFO: Creating symlink to lh.EC_average subject... cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer; ln -s /opt/freesurfer/5.3.0/subjects/lh.EC_average; cd - mris_spherical_average -erode 1 -orig white -t 0.4 -o sub010 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject sub010. processing subject lh.EC_average... reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 804 points to lh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label sub010 lh white limiting computations to label ./lh.entorhinal_exvivo.label. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 275 197 971 2.926 0.840 0.124 0.081 9 0.5 ./lh.entorhinal_exvivo.label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label rh Thu Aug 8 22:20:22 CEST 2013 INFO: rh.EC_average subject does not exist in SUBJECTS_DIR INFO: Creating symlink to rh.EC_average subject... cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer; ln -s /opt/freesurfer/5.3.0/subjects/rh.EC_average; cd - mris_spherical_average -erode 1 -orig white -t 0.4 -o sub010 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label painting output onto subject sub010. processing subject rh.EC_average... reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 734 points to rh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label sub010 rh white limiting computations to label ./rh.entorhinal_exvivo.label. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 268 189 829 2.798 1.185 0.125 0.045 3 0.5 ./rh.entorhinal_exvivo.label #------------------------------------------ Started at Thu Aug 8 10:54:16 CEST 2013 Ended at Thu Aug 8 22:20:36 CEST 2013 #@#%# recon-all-run-time-hours 11.439 recon-all -s sub010 finished without error at Thu Aug 8 22:20:36 CEST 2013