Thu Aug 8 10:53:55 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003 /opt/freesurfer/5.3.0/bin/recon-all -i /home/data/exppsy/forrest_gump/openfmri.org/sub003/anatomy/highres001.nii.gz -cw256 -all -T2 /home/data/exppsy/forrest_gump/openfmri.org/sub003/anatomy/other/t2w001.nii.gz -T2pial -subjid sub003 -sd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer subjid sub003 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 snake5 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 96468108 2733584 0 177872 94401912 -/+ buffers/cache: 1888324 97313368 Swap: 25165780 3620 25162160 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:56-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: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:56-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: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:56-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: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:56-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: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:56-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: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:56-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: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:56-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: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:56-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: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:57-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: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:57-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: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:57-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: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:57-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: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:57-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: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:57-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: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:57-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: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:57-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: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:57-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: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:57-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: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:58-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: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:58-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: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:58-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: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:58-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: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:58-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: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:58-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: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:58-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: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:58-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: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:58-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: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:58-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: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:59-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: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:59-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: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:59-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: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:59-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: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:59-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: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:59-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: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:59-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: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:59-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: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:59-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: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:59-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: snake5 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/sub003 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub003/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/orig/001.mgz mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub003/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/anatomy/highres001.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.99822, -0.0508489, 0.0311494) j_ras = (-0.0512259, 0.998622, -0.0114243) k_ras = (0.0305256, 0.0129996, 0.999449) writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/orig/001.mgz... #-------------------------------------------- #@# T2/FLAIR Input Thu Aug 8 10:54:14 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub003/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/orig/T2raw.mgz mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub003/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/anatomy/other/t2w001.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.99822, -0.0508489, 0.0311494) j_ras = (-0.0512259, 0.998622, -0.0114243) k_ras = (0.0305256, 0.0129996, 0.999449) writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/orig/T2raw.mgz... #-------------------------------------------- #@# MotionCor Thu Aug 8 10:54:27 CEST 2013 Found 1 runs /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/mri/orig/001.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/orig.mgz --conform --cw256 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.99822, -0.0508489, 0.0311494) j_ras = (-0.0512259, 0.998622, -0.0114243) k_ras = (0.0305256, 0.0129996, 0.999449) Original Data has (0.699959, 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/sub003/mri/orig.mgz... mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/talairach.xfm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Aug 8 10:55:06 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 10:57:51 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7490, pval=0.6675 >= threshold=0.0050) awk -f /opt/freesurfer/5.3.0/bin/extract_talairach_avi_QA.awk /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/talairach_avi.log tal_QC_AZS /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/talairach_avi.log TalAviQA: 0.96561 z-score: -2 #-------------------------------------------- #@# Nu Intensity Correction Thu Aug 8 10:57:51 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/sub003/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 snake5 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux Thu Aug 8 10:57:51 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.12223 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.12223/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.12223/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 4.65661e-09, -1.86265e-09) j_ras = (1.86265e-09, 2.79397e-09, -1) k_ras = (-8.3528e-09, 1, -9.31323e-10) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.12223/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Aug 8 10:57:56 CEST 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.12223/nu0.mnc ./tmp.mri_nu_correct.mni.12223/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.12223/0/ [fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/] [2013-08-08 10:57:56] 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.12223/0/ ./tmp.mri_nu_correct.mni.12223/nu0.mnc ./tmp.mri_nu_correct.mni.12223/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 Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 31 CV of field change: 0.000976255 [fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/] [2013-08-08 10:58:35] running: /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.12223/nu0.mnc ./tmp.mri_nu_correct.mni.12223/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Thu Aug 8 10:58:43 CEST 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.12223/nu1.mnc ./tmp.mri_nu_correct.mni.12223/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.12223/1/ [fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/] [2013-08-08 10:58:43] 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.12223/1/ ./tmp.mri_nu_correct.mni.12223/nu1.mnc ./tmp.mri_nu_correct.mni.12223/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 23 CV of field change: 0.000975575 [fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/] [2013-08-08 10:59:19] running: /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.12223/nu1.mnc ./tmp.mri_nu_correct.mni.12223/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.12223/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.12223/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/sub003/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.12223/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.12223/ones.mgz sysname Linux hostname snake5 machine x86_64 user fkaule input ./tmp.mri_nu_correct.mni.12223/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.12223/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.12223/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.12223/sum.junk --avgwf ./tmp.mri_nu_correct.mni.12223/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.12223/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.12223/sum.junk --avgwf ./tmp.mri_nu_correct.mni.12223/input.mean.dat sysname Linux hostname snake5 machine x86_64 user fkaule UseRobust 0 Loading ./tmp.mri_nu_correct.mni.12223/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.12223/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.12223/ones.mgz --i ./tmp.mri_nu_correct.mni.12223/nu2.mnc --sum ./tmp.mri_nu_correct.mni.12223/sum.junk --avgwf ./tmp.mri_nu_correct.mni.12223/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.12223/ones.mgz --i ./tmp.mri_nu_correct.mni.12223/nu2.mnc --sum ./tmp.mri_nu_correct.mni.12223/sum.junk --avgwf ./tmp.mri_nu_correct.mni.12223/output.mean.dat sysname Linux hostname snake5 machine x86_64 user fkaule UseRobust 0 Loading ./tmp.mri_nu_correct.mni.12223/ones.mgz Loading ./tmp.mri_nu_correct.mni.12223/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.12223/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.12223/nu2.mnc ./tmp.mri_nu_correct.mni.12223/nu2.mnc mul .96234187965292691773 Saving result to './tmp.mri_nu_correct.mni.12223/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.12223/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.12223/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.12223/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 4.65661e-09, -1.86265e-09) j_ras = (1.86265e-09, 2.79397e-09, -1) k_ras = (-8.3528e-09, 1, -9.31322e-10) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 8 seconds. mapping (12, 204) to ( 3, 110) Thu Aug 8 11:00:10 CEST 2013 mri_nu_correct.mni done mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Thu Aug 8 11:00:12 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.180 0.077 -0.031 -0.003; -0.080 1.219 0.135 -38.645; 0.045 -0.260 1.294 -20.863; 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 = 15 Starting OpenSpline(): npoints = 15 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 50 (50), valley at 32 (32) csf peak at 25, setting threshold to 41 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 51 (51), valley at 32 (32) csf peak at 15, setting threshold to 39 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 53 seconds. #-------------------------------------------- #@# Skull Stripping Thu Aug 8 11:03:07 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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=34.4 skull bounding box = (62, 39, 43) --> (188, 211, 179) using (104, 96, 111) as brain centroid... mean wm in atlas = 126, using box (89,75,94) --> (119, 117,127) to find MRI wm before smoothing, mri peak at 113 after smoothing, mri peak at 112, scaling input intensities by 1.125 scaling channel 0 by 1.125 initial log_p = -5.0 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.747513 @ (-9.091, 27.273, -9.091) max log p = -4.604891 @ (4.545, -13.636, -4.545) max log p = -4.542052 @ (6.818, 2.273, 2.273) max log p = -4.533968 @ (-3.409, -1.136, -1.136) max log p = -4.520561 @ (1.705, 1.705, 1.705) max log p = -4.520561 @ (0.000, 0.000, 0.000) Found translation: (0.6, 16.5, -10.8): log p = -4.521 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.5 (thresh=-4.5) 1.064 0.000 0.000 -7.413; 0.000 1.226 0.161 -17.501; 0.000 -0.150 1.140 -9.507; 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) 1.064 0.000 0.000 -7.413; 0.000 1.226 0.161 -17.501; 0.000 -0.150 1.140 -9.507; 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) 1.083 -0.037 -0.043 -3.155; 0.036 1.197 0.195 -23.161; 0.038 -0.199 1.198 -21.787; 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) 1.078 0.013 -0.117 3.144; -0.000 1.225 0.162 -17.451; 0.108 -0.159 1.176 -30.076; 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) 1.061 0.007 -0.077 1.138; -0.000 1.225 0.162 -17.451; 0.074 -0.162 1.201 -28.466; 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) 1.061 0.019 -0.086 0.502; -0.009 1.221 0.163 -15.941; 0.082 -0.162 1.197 -29.460; 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) 1.061 0.017 -0.076 -0.451; -0.009 1.225 0.163 -16.423; 0.073 -0.162 1.196 -27.802; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.061 0.017 -0.076 -0.451; -0.009 1.225 0.163 -16.423; 0.073 -0.162 1.196 -27.802; 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 1.06086 0.01736 -0.07570 -0.45149; -0.00881 1.22506 0.16318 -16.42283; 0.07348 -0.16174 1.19586 -27.80207; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.06086 0.01736 -0.07570 -0.45149; -0.00881 1.22506 0.16318 -16.42283; 0.07348 -0.16174 1.19586 -27.80207; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.061 0.017 -0.076 -0.451; -0.009 1.225 0.163 -16.423; 0.073 -0.162 1.196 -27.802; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -4.0 (old=-5.0) transform before final EM align: 1.061 0.017 -0.076 -0.451; -0.009 1.225 0.163 -16.423; 0.073 -0.162 1.196 -27.802; 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 1.06086 0.01736 -0.07570 -0.45149; -0.00881 1.22506 0.16318 -16.42283; 0.07348 -0.16174 1.19586 -27.80207; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.06086 0.01736 -0.07570 -0.45149; -0.00881 1.22506 0.16318 -16.42283; 0.07348 -0.16174 1.19586 -27.80207; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 012: -log(p) = 4.4 tol 0.000000 final transform: 1.061 0.017 -0.076 -0.451; -0.009 1.225 0.163 -16.423; 0.073 -0.162 1.196 -27.802; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 39 minutes and 19 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=125 y=86 z=122 r=86 first estimation of the main basin volume: 2692528 voxels Looking for seedpoints 2 found in the cerebellum 15 found in the rest of the brain global maximum in x=152, y=86, z=87, 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=19354074114 voxels, voxel volume =1.000 = 19354074114 mmm3 = 19354075.136 cm3 done. PostAnalyze...Basin Prior 162 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=126,y=97, z=115, r=9457 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=7 , nb = 45566 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=9 , nb = -1037164009 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=12 , nb = 1094733289 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=7 , nb = 1059422609 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1079664476 OTHER CSF_MIN=0, CSF_intensity=6, CSF_MAX=36 , nb = -1112638672 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 7, 11, 29, 49 after analyzing : 7, 23, 29, 29 RIGHT_CER before analyzing : 9, 11, 23, 59 after analyzing : 9, 20, 25, 29 LEFT_CER before analyzing : 12, 14, 24, 60 after analyzing : 12, 21, 25, 30 RIGHT_BRAIN before analyzing : 7, 10, 27, 49 after analyzing : 7, 21, 27, 28 LEFT_BRAIN before analyzing : 4, 6, 29, 49 after analyzing : 4, 21, 29, 28 OTHER before analyzing : 36, 78, 89, 96 after analyzing : 36, 85, 89, 87 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...69 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.012 curvature mean = 67.488, std = 7.941 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 2.30, sigma = 4.07 after rotation: sse = 2.30, sigma = 4.07 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 2.35, its var is 3.31 before Erosion-Dilatation 0.32% 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...46 iterations mri_strip_skull: done peeling brain Brain Size = 1519485 voxels, voxel volume = 1.000 mm3 = 1519485 mmm3 = 1519.485 cm3 ****************************** Saving brainmask.auto.mgz done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Thu Aug 8 11:42:55 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca transforms/talairach.lta ======= NUMBER OF OPENMP THREADS = 1 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca'... average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.4 (994 zeros) ************************************************ spacing=8, using 2772 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2772, passno 0, spacing 8 resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=21.0 skull bounding box = (60, 39, 40) --> (189, 160, 204) using (103, 79, 122) as brain centroid... mean wm in atlas = 107, using box (87,64,102) --> (118, 93,142) 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 = -4.6 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.050945 @ (-9.091, 27.273, -9.091) max log p = -3.907736 @ (4.545, -4.545, -4.545) max log p = -3.852608 @ (2.273, -2.273, -2.273) max log p = -3.845421 @ (-1.136, -1.136, -1.136) max log p = -3.822341 @ (2.841, 0.568, 2.841) max log p = -3.822341 @ (0.000, 0.000, 0.000) Found translation: (-0.6, 19.9, -14.2): log p = -3.822 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p =-3.8 (thresh=-3.8) 1.150 0.000 0.000 -19.675; 0.000 1.150 0.000 5.040; 0.000 0.000 1.000 -14.205; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p =-3.5 (thresh=-3.5) 1.150 0.000 0.000 -19.675; 0.000 1.150 0.000 5.040; 0.000 0.000 1.000 -14.205; 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=-3.3, old_max_log_p =-3.5 (thresh=-3.5) 1.126 -0.028 -0.067 -5.862; 0.034 1.165 0.098 -8.804; 0.079 -0.119 1.050 -18.373; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3) 1.100 -0.062 -0.102 4.833; 0.072 1.185 0.096 -15.413; 0.118 -0.122 1.067 -23.172; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3) 1.100 -0.062 -0.102 4.833; 0.072 1.185 0.096 -15.413; 0.118 -0.122 1.067 -23.172; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.3 (thresh=-3.3) 1.103 -0.027 -0.064 -3.969; 0.036 1.185 0.099 -12.067; 0.082 -0.120 1.068 -19.353; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2) 1.105 -0.027 -0.064 -4.123; 0.036 1.188 0.090 -11.195; 0.083 -0.111 1.069 -20.889; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2) 1.106 -0.027 -0.064 -4.276; 0.036 1.189 0.090 -11.347; 0.083 -0.111 1.069 -20.889; 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 1.10592 -0.02670 -0.06425 -4.27603; 0.03566 1.18895 0.09021 -11.34732; 0.08259 -0.11063 1.06874 -20.88874; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 1.10592 -0.02670 -0.06425 -4.27603; 0.03566 1.18895 0.09021 -11.34732; 0.08259 -0.11063 1.06874 -20.88874; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.106 -0.027 -0.064 -4.276; 0.036 1.189 0.090 -11.347; 0.083 -0.111 1.069 -20.889; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.2 (old=-4.6) transform before final EM align: 1.106 -0.027 -0.064 -4.276; 0.036 1.189 0.090 -11.347; 0.083 -0.111 1.069 -20.889; 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 1.10592 -0.02670 -0.06425 -4.27603; 0.03566 1.18895 0.09021 -11.34732; 0.08259 -0.11063 1.06874 -20.88874; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 1.10592 -0.02670 -0.06425 -4.27603; 0.03566 1.18895 0.09021 -11.34732; 0.08259 -0.11063 1.06874 -20.88874; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 011: -log(p) = 3.8 after pass:transform: ( 1.11, -0.03, -0.06, -4.28) ( 0.04, 1.19, 0.09, -11.35) ( 0.08, -0.11, 1.07, -20.89) dfp_em_step_func: 012: -log(p) = 3.8 after pass:transform: ( 1.11, -0.03, -0.06, -4.28) ( 0.04, 1.19, 0.09, -11.35) ( 0.08, -0.11, 1.07, -20.89) 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: 014: -log(p) = 3.8 tol 0.000000 final transform: 1.106 -0.027 -0.064 -4.276; 0.036 1.189 0.090 -11.347; 0.083 -0.111 1.069 -20.889; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 32 minutes and 13 seconds. #-------------------------------------- #@# CA Normalize Thu Aug 8 12:15:08 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=21.0 skull bounding box = (60, 39, 40) --> (189, 161, 204) using (103, 80, 122) as brain centroid... mean wm in atlas = 107, using box (87,65,102) --> (118, 94,142) to find MRI wm before smoothing, mri peak at 109 after smoothing, mri peak at 109, scaling input intensities by 0.982 scaling channel 0 by 0.981651 using 244171 sample points... INFO: compute sample coordinates transform 1.106 -0.027 -0.064 -4.276; 0.036 1.189 0.090 -11.347; 0.083 -0.111 1.069 -20.889; 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 (122, 40, 45) --> (186, 137, 200) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 133.0 0 of 78 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (68, 42, 46) --> (130, 139, 202) Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 133.0 0 of 57 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (127, 112, 67) --> (172, 148, 118) Left_Cerebellum_White_Matter: limiting intensities to 89.0 --> 133.0 0 of 8 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (85, 112, 68) --> (127, 149, 120) Right_Cerebellum_White_Matter: limiting intensities to 82.0 --> 133.0 0 of 9 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (113, 106, 100) --> (142, 164, 130) Brain_Stem: limiting intensities to 74.0 --> 133.0 0 of 12 (0.0%) samples deleted using 164 total control points for intensity normalization... bias field = 1.005 +- 0.050 0 of 164 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (122, 40, 45) --> (186, 137, 200) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 130.0 0 of 130 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (68, 42, 46) --> (130, 139, 202) Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 130.0 0 of 134 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (127, 112, 67) --> (172, 148, 118) Left_Cerebellum_White_Matter: limiting intensities to 78.0 --> 130.0 0 of 33 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (85, 112, 68) --> (127, 149, 120) Right_Cerebellum_White_Matter: limiting intensities to 83.0 --> 130.0 0 of 32 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (113, 106, 100) --> (142, 164, 130) Brain_Stem: limiting intensities to 72.0 --> 130.0 0 of 64 (0.0%) samples deleted using 393 total control points for intensity normalization... bias field = 1.001 +- 0.058 0 of 393 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (122, 40, 45) --> (186, 137, 200) Left_Cerebral_White_Matter: limiting intensities to 90.0 --> 128.0 0 of 249 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (68, 42, 46) --> (130, 139, 202) Right_Cerebral_White_Matter: limiting intensities to 94.0 --> 128.0 0 of 183 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (127, 112, 67) --> (172, 148, 118) Left_Cerebellum_White_Matter: limiting intensities to 83.0 --> 128.0 3 of 31 (9.7%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (85, 112, 68) --> (127, 149, 120) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 128.0 9 of 40 (22.5%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (113, 106, 100) --> (142, 164, 130) Brain_Stem: limiting intensities to 69.0 --> 128.0 0 of 93 (0.0%) samples deleted using 596 total control points for intensity normalization... bias field = 1.015 +- 0.048 0 of 584 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 2 minutes and 4 seconds. #-------------------------------------- #@# CA Reg Thu Aug 8 12:17:12 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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) = 1.42 (predicted orig area = 5.6) 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=0.904, neg=0, invalid=96777 0001: dt=129.472000, rms=0.802 (11.269%), neg=0, invalid=96777 0002: dt=129.472000, rms=0.783 (2.392%), neg=0, invalid=96777 0003: dt=129.472000, rms=0.770 (1.636%), neg=0, invalid=96777 0004: dt=110.976000, rms=0.765 (0.593%), neg=0, invalid=96777 0005: dt=129.472000, rms=0.759 (0.815%), neg=0, invalid=96777 0006: dt=110.976000, rms=0.757 (0.337%), neg=0, invalid=96777 0007: dt=295.936000, rms=0.751 (0.740%), neg=0, invalid=96777 0008: dt=55.488000, rms=0.748 (0.412%), neg=0, invalid=96777 0009: dt=369.920000, rms=0.745 (0.435%), neg=0, invalid=96777 0010: dt=110.976000, rms=0.740 (0.570%), neg=0, invalid=96777 0011: dt=73.984000, rms=0.740 (0.076%), neg=0, invalid=96777 0012: dt=73.984000, rms=0.739 (0.147%), neg=0, invalid=96777 0013: dt=73.984000, rms=0.737 (0.230%), neg=0, invalid=96777 0014: dt=73.984000, rms=0.735 (0.291%), neg=0, invalid=96777 0015: dt=73.984000, rms=0.733 (0.315%), neg=0, invalid=96777 0016: dt=73.984000, rms=0.730 (0.333%), neg=0, invalid=96777 0017: dt=73.984000, rms=0.728 (0.359%), neg=0, invalid=96777 0018: dt=73.984000, rms=0.725 (0.382%), neg=0, invalid=96777 0019: dt=73.984000, rms=0.722 (0.340%), neg=0, invalid=96777 0020: dt=73.984000, rms=0.720 (0.286%), neg=0, invalid=96777 0021: dt=73.984000, rms=0.719 (0.247%), neg=0, invalid=96777 0022: dt=73.984000, rms=0.717 (0.247%), neg=0, invalid=96777 0023: dt=73.984000, rms=0.715 (0.273%), neg=0, invalid=96777 0024: dt=73.984000, rms=0.713 (0.279%), neg=0, invalid=96777 0025: dt=73.984000, rms=0.711 (0.235%), neg=0, invalid=96777 0026: dt=73.984000, rms=0.710 (0.180%), neg=0, invalid=96777 0027: dt=73.984000, rms=0.709 (0.158%), neg=0, invalid=96777 0028: dt=73.984000, rms=0.707 (0.199%), neg=0, invalid=96777 0029: dt=73.984000, rms=0.706 (0.210%), neg=0, invalid=96777 0030: dt=73.984000, rms=0.705 (0.175%), neg=0, invalid=96777 0031: dt=73.984000, rms=0.704 (0.148%), neg=0, invalid=96777 0032: dt=73.984000, rms=0.703 (0.127%), neg=0, invalid=96777 0033: dt=73.984000, rms=0.702 (0.131%), neg=0, invalid=96777 0034: dt=73.984000, rms=0.701 (0.154%), neg=0, invalid=96777 0035: dt=73.984000, rms=0.700 (0.140%), neg=0, invalid=96777 0036: dt=73.984000, rms=0.699 (0.113%), neg=0, invalid=96777 0037: dt=73.984000, rms=0.698 (0.104%), neg=0, invalid=96777 0038: dt=1183.744000, rms=0.697 (0.167%), neg=0, invalid=96777 0039: dt=27.744000, rms=0.697 (0.020%), neg=0, invalid=96777 0040: dt=27.744000, rms=0.697 (0.011%), neg=0, invalid=96777 0041: dt=27.744000, rms=0.697 (-0.029%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.697, neg=0, invalid=96777 0042: dt=73.984000, rms=0.696 (0.053%), neg=0, invalid=96777 0043: dt=92.480000, rms=0.696 (0.040%), neg=0, invalid=96777 0044: dt=92.480000, rms=0.696 (0.038%), neg=0, invalid=96777 0045: dt=92.480000, rms=0.696 (0.043%), neg=0, invalid=96777 0046: dt=92.480000, rms=0.695 (0.015%), neg=0, invalid=96777 0047: dt=92.480000, rms=0.695 (0.020%), neg=0, invalid=96777 0048: dt=92.480000, rms=0.695 (0.075%), neg=0, invalid=96777 0049: dt=92.480000, rms=0.694 (0.086%), neg=0, invalid=96777 0050: dt=92.480000, rms=0.694 (0.030%), neg=0, invalid=96777 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.700, neg=0, invalid=96777 0051: dt=145.152000, rms=0.689 (1.620%), neg=0, invalid=96777 0052: dt=62.208000, rms=0.683 (0.846%), neg=0, invalid=96777 0053: dt=62.208000, rms=0.677 (0.856%), neg=0, invalid=96777 0054: dt=9.072000, rms=0.676 (0.166%), neg=0, invalid=96777 0055: dt=9.072000, rms=0.675 (0.109%), neg=0, invalid=96777 0056: dt=9.072000, rms=0.674 (0.099%), neg=0, invalid=96777 0057: dt=9.072000, rms=0.674 (0.119%), neg=0, invalid=96777 0058: dt=9.072000, rms=0.672 (0.196%), neg=0, invalid=96777 0059: dt=9.072000, rms=0.670 (0.318%), neg=0, invalid=96777 0060: dt=9.072000, rms=0.667 (0.410%), neg=0, invalid=96777 0061: dt=9.072000, rms=0.665 (0.409%), neg=0, invalid=96777 0062: dt=9.072000, rms=0.662 (0.381%), neg=0, invalid=96777 0063: dt=9.072000, rms=0.660 (0.339%), neg=0, invalid=96777 0064: dt=9.072000, rms=0.658 (0.320%), neg=0, invalid=96777 0065: dt=9.072000, rms=0.656 (0.291%), neg=0, invalid=96777 0066: dt=9.072000, rms=0.654 (0.258%), neg=0, invalid=96777 0067: dt=9.072000, rms=0.652 (0.251%), neg=0, invalid=96777 0068: dt=9.072000, rms=0.651 (0.283%), neg=0, invalid=96777 0069: dt=9.072000, rms=0.649 (0.315%), neg=0, invalid=96777 0070: dt=9.072000, rms=0.647 (0.311%), neg=0, invalid=96777 0071: dt=9.072000, rms=0.645 (0.276%), neg=0, invalid=96777 0072: dt=9.072000, rms=0.643 (0.239%), neg=0, invalid=96777 0073: dt=9.072000, rms=0.642 (0.213%), neg=0, invalid=96777 0074: dt=9.072000, rms=0.641 (0.193%), neg=0, invalid=96777 0075: dt=9.072000, rms=0.640 (0.169%), neg=0, invalid=96777 0076: dt=9.072000, rms=0.639 (0.158%), neg=0, invalid=96777 0077: dt=9.072000, rms=0.637 (0.164%), neg=0, invalid=96777 0078: dt=9.072000, rms=0.636 (0.175%), neg=0, invalid=96777 0079: dt=9.072000, rms=0.635 (0.189%), neg=0, invalid=96777 0080: dt=9.072000, rms=0.634 (0.176%), neg=0, invalid=96777 0081: dt=9.072000, rms=0.633 (0.160%), neg=0, invalid=96777 0082: dt=9.072000, rms=0.632 (0.137%), neg=0, invalid=96777 0083: dt=9.072000, rms=0.631 (0.114%), neg=0, invalid=96777 0084: dt=9.072000, rms=0.631 (0.100%), neg=0, invalid=96777 0085: dt=145.152000, rms=0.631 (0.035%), neg=0, invalid=96777 0086: dt=145.152000, rms=0.631 (-0.007%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.631, neg=0, invalid=96777 0087: dt=36.288000, rms=0.629 (0.199%), neg=0, invalid=96777 0088: dt=20.736000, rms=0.629 (0.010%), neg=0, invalid=96777 0089: dt=20.736000, rms=0.629 (0.013%), neg=0, invalid=96777 0090: dt=20.736000, rms=0.629 (0.004%), neg=0, invalid=96777 0091: dt=20.736000, rms=0.629 (-0.033%), neg=0, invalid=96777 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.653, neg=0, invalid=96777 0092: dt=11.636364, rms=0.651 (0.215%), neg=0, invalid=96777 0093: dt=9.600000, rms=0.651 (0.052%), neg=0, invalid=96777 0094: dt=9.600000, rms=0.651 (0.054%), neg=0, invalid=96777 0095: dt=9.600000, rms=0.651 (-0.017%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.651, neg=0, invalid=96777 0096: dt=0.000000, rms=0.651 (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=0.705, neg=0, invalid=96777 0097: dt=4.198895, rms=0.699 (0.862%), neg=0, invalid=96777 0098: dt=1.008000, rms=0.699 (0.026%), neg=0, invalid=96777 0099: dt=1.008000, rms=0.699 (0.007%), neg=0, invalid=96777 0100: dt=1.008000, rms=0.699 (-0.026%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.699, neg=0, invalid=96777 0101: dt=0.000000, rms=0.699 (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 0102: dt=0.848718, rms=0.768 (0.294%), neg=0, invalid=96777 0103: dt=1.659722, rms=0.765 (0.404%), neg=0, invalid=96777 0104: dt=1.792000, rms=0.764 (0.227%), neg=0, invalid=96777 0105: dt=1.792000, rms=0.763 (0.074%), neg=0, invalid=96777 0106: dt=1.792000, rms=0.763 (-0.138%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.763, neg=0, invalid=96777 0107: dt=0.882006, rms=0.761 (0.256%), neg=0, invalid=96777 0108: dt=0.256000, rms=0.761 (0.005%), neg=0, invalid=96777 0109: dt=0.256000, rms=0.761 (-0.000%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.706, neg=0, invalid=96777 0110: dt=0.320000, rms=0.690 (2.279%), neg=0, invalid=96777 0111: dt=0.000000, rms=0.690 (0.006%), neg=0, invalid=96777 0112: dt=0.050000, rms=0.690 (-0.329%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.690, neg=0, invalid=96777 0113: dt=0.000000, rms=0.690 (0.000%), neg=0, invalid=96777 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.08748 ( 5) Left_Lateral_Ventricle (4): linear fit = 0.17 x + 0.0 (1345 voxels, overlap=0.137) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (1345 voxels, peak = 4), gca=9.6 gca peak = 0.14022 (22) mri peak = 0.13408 (55) Right_Lateral_Ventricle (43): linear fit = 0.20 x + 0.0 (755 voxels, overlap=0.004) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (755 voxels, peak = 5), gca=8.8 gca peak = 0.24234 (100) mri peak = 0.07578 (75) Right_Pallidum (52): linear fit = 0.82 x + 0.0 (280 voxels, overlap=0.045) Right_Pallidum (52): linear fit = 0.82 x + 0.0 (280 voxels, peak = 82), gca=82.5 gca peak = 0.19192 (97) mri peak = 0.10324 (80) Left_Pallidum (13): linear fit = 0.79 x + 0.0 (154 voxels, overlap=0.034) Left_Pallidum (13): linear fit = 0.79 x + 0.0 (154 voxels, peak = 76), gca=76.1 gca peak = 0.24007 (63) mri peak = 0.09007 (53) Right_Hippocampus (53): linear fit = 0.85 x + 0.0 (442 voxels, overlap=0.537) Right_Hippocampus (53): linear fit = 0.85 x + 0.0 (442 voxels, peak = 53), gca=53.2 gca peak = 0.29892 (64) mri peak = 0.08799 (54) Left_Hippocampus (17): linear fit = 0.88 x + 0.0 (498 voxels, overlap=0.429) Left_Hippocampus (17): linear fit = 0.88 x + 0.0 (498 voxels, peak = 56), gca=56.0 gca peak = 0.12541 (104) mri peak = 0.08176 (107) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (49751 voxels, overlap=0.696) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (49751 voxels, peak = 109), gca=108.7 gca peak = 0.13686 (104) mri peak = 0.08587 (108) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (54124 voxels, overlap=0.651) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (54124 voxels, peak = 110), gca=109.7 gca peak = 0.11691 (63) mri peak = 0.06253 (52) Left_Cerebral_Cortex (3): linear fit = 0.77 x + 0.0 (13695 voxels, overlap=0.013) Left_Cerebral_Cortex (3): linear fit = 0.77 x + 0.0 (13695 voxels, peak = 49), gca=48.8 gca peak = 0.13270 (63) mri peak = 0.07149 (51) Right_Cerebral_Cortex (42): linear fit = 0.80 x + 0.0 (13348 voxels, overlap=0.014) Right_Cerebral_Cortex (42): linear fit = 0.80 x + 0.0 (13348 voxels, peak = 50), gca=50.1 gca peak = 0.15182 (70) mri peak = 0.08434 (64) Right_Caudate (50): linear fit = 0.90 x + 0.0 (433 voxels, overlap=0.471) Right_Caudate (50): linear fit = 0.90 x + 0.0 (433 voxels, peak = 63), gca=63.3 gca peak = 0.14251 (76) mri peak = 0.07703 (63) Left_Caudate (11): linear fit = 0.82 x + 0.0 (446 voxels, overlap=0.061) Left_Caudate (11): linear fit = 0.82 x + 0.0 (446 voxels, peak = 63), gca=62.7 gca peak = 0.12116 (60) mri peak = 0.04763 (59) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (9930 voxels, overlap=0.983) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (9930 voxels, peak = 59), gca=59.1 gca peak = 0.12723 (61) mri peak = 0.05089 (57) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (10376 voxels, overlap=0.974) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (10376 voxels, peak = 59), gca=58.9 gca peak = 0.22684 (88) mri peak = 0.07078 (91) Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (5273 voxels, overlap=0.904) Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (5273 voxels, peak = 92), gca=92.0 gca peak = 0.21067 (87) mri peak = 0.07103 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (4739 voxels, overlap=0.965) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (4739 voxels, peak = 90), gca=90.0 gca peak = 0.25455 (62) mri peak = 0.13688 (53) Left_Amygdala (18): linear fit = 0.83 x + 0.0 (280 voxels, overlap=0.315) Left_Amygdala (18): linear fit = 0.83 x + 0.0 (280 voxels, peak = 52), gca=51.8 gca peak = 0.39668 (62) mri peak = 0.11325 (54) Right_Amygdala (54): linear fit = 0.86 x + 0.0 (233 voxels, overlap=0.684) Right_Amygdala (54): linear fit = 0.86 x + 0.0 (233 voxels, peak = 53), gca=53.0 gca peak = 0.10129 (93) mri peak = 0.04470 (96) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4274 voxels, overlap=0.970) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4274 voxels, peak = 93), gca=93.5 gca peak = 0.12071 (89) mri peak = 0.05443 (82) Right_Thalamus_Proper (49): linear fit = 0.94 x + 0.0 (3020 voxels, overlap=0.942) Right_Thalamus_Proper (49): linear fit = 0.94 x + 0.0 (3020 voxels, peak = 83), gca=83.2 gca peak = 0.13716 (82) mri peak = 0.05156 (70) Left_Putamen (12): linear fit = 0.92 x + 0.0 (1505 voxels, overlap=0.755) Left_Putamen (12): linear fit = 0.92 x + 0.0 (1505 voxels, peak = 75), gca=75.0 gca peak = 0.15214 (84) mri peak = 0.06922 (72) Right_Putamen (51): linear fit = 0.88 x + 0.0 (1590 voxels, overlap=0.415) Right_Putamen (51): linear fit = 0.88 x + 0.0 (1590 voxels, peak = 74), gca=74.3 gca peak = 0.08983 (85) mri peak = 0.07526 (89) Brain_Stem (16): linear fit = 1.03 x + 0.0 (8419 voxels, overlap=0.777) Brain_Stem (16): linear fit = 1.03 x + 0.0 (8419 voxels, peak = 88), gca=88.0 gca peak = 0.11809 (92) mri peak = 0.07792 (87) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (544 voxels, overlap=0.898) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (544 voxels, peak = 94), gca=94.3 gca peak = 0.12914 (94) mri peak = 0.07407 (85) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (632 voxels, overlap=0.856) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (632 voxels, peak = 94), gca=94.0 gca peak = 0.21100 (36) mri peak = 0.02731 ( 7) gca peak = 0.13542 (27) mri peak = 0.11213 ( 9) Fourth_Ventricle (15): linear fit = 0.28 x + 0.0 (173 voxels, overlap=0.022) Fourth_Ventricle (15): linear fit = 0.28 x + 0.0 (173 voxels, peak = 7), gca=7.4 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak Third_Ventricle = 0.21100 (36) gca peak Fourth_Ventricle = 0.13542 (27) gca peak CSF = 0.17123 (45) gca peak Left_Accumbens_area = 0.25875 (69) gca peak Left_undetermined = 0.96240 (36) gca peak Left_vessel = 0.33262 (65) gca peak Left_choroid_plexus = 0.09846 (46) gca peak Right_Inf_Lat_Vent = 0.28113 (34) gca peak Right_Accumbens_area = 0.27120 (72) gca peak Right_vessel = 0.61915 (60) gca peak Right_choroid_plexus = 0.12775 (51) gca peak Fifth_Ventricle = 0.45329 (44) gca peak WM_hypointensities = 0.11729 (81) gca peak non_WM_hypointensities = 0.10912 (56) gca peak Optic_Chiasm = 0.33287 (75) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 0.83 x + 0.0 estimating mean wm scale to be 1.05 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=0.732, neg=0, invalid=96777 0114: dt=129.472000, rms=0.725 (1.009%), neg=0, invalid=96777 0115: dt=129.472000, rms=0.722 (0.411%), neg=0, invalid=96777 0116: dt=92.480000, rms=0.721 (0.135%), neg=0, invalid=96777 0117: dt=129.472000, rms=0.719 (0.276%), neg=0, invalid=96777 0118: dt=55.488000, rms=0.718 (0.068%), neg=0, invalid=96777 0119: dt=1183.744000, rms=0.713 (0.749%), neg=0, invalid=96777 0120: dt=32.368000, rms=0.712 (0.106%), neg=0, invalid=96777 0121: dt=55.488000, rms=0.712 (0.045%), neg=0, invalid=96777 0122: dt=55.488000, rms=0.711 (0.056%), neg=0, invalid=96777 0123: dt=55.488000, rms=0.711 (0.087%), neg=0, invalid=96777 0124: dt=55.488000, rms=0.710 (0.099%), neg=0, invalid=96777 0125: dt=55.488000, rms=0.709 (0.103%), neg=0, invalid=96777 0126: dt=55.488000, rms=0.709 (0.106%), neg=0, invalid=96777 0127: dt=55.488000, rms=0.708 (0.107%), neg=0, invalid=96777 0128: dt=55.488000, rms=0.707 (0.106%), neg=0, invalid=96777 0129: dt=55.488000, rms=0.706 (0.098%), neg=0, invalid=96777 0130: dt=55.488000, rms=0.706 (0.090%), neg=0, invalid=96777 0131: dt=55.488000, rms=0.705 (0.083%), neg=0, invalid=96777 0132: dt=55.488000, rms=0.705 (0.085%), neg=0, invalid=96777 0133: dt=55.488000, rms=0.704 (0.087%), neg=0, invalid=96777 0134: dt=55.488000, rms=0.703 (0.077%), neg=0, invalid=96777 0135: dt=55.488000, rms=0.703 (0.070%), neg=0, invalid=96777 0136: dt=55.488000, rms=0.702 (0.063%), neg=0, invalid=96777 0137: dt=55.488000, rms=0.702 (0.059%), neg=0, invalid=96777 0138: dt=55.488000, rms=0.702 (0.065%), neg=0, invalid=96777 0139: dt=55.488000, rms=0.701 (0.067%), neg=0, invalid=96777 0140: dt=55.488000, rms=0.701 (0.061%), neg=0, invalid=96777 0141: dt=55.488000, rms=0.700 (0.057%), neg=0, invalid=96777 0142: dt=55.488000, rms=0.700 (0.054%), neg=0, invalid=96777 0143: dt=55.488000, rms=0.700 (0.054%), neg=0, invalid=96777 0144: dt=55.488000, rms=0.699 (0.060%), neg=0, invalid=96777 0145: dt=55.488000, rms=0.699 (0.055%), neg=0, invalid=96777 0146: dt=55.488000, rms=0.698 (0.055%), neg=0, invalid=96777 0147: dt=55.488000, rms=0.698 (0.051%), neg=0, invalid=96777 0148: dt=55.488000, rms=0.698 (0.043%), neg=0, invalid=96777 0149: dt=55.488000, rms=0.697 (0.041%), neg=0, invalid=96777 0150: dt=55.488000, rms=0.697 (0.050%), neg=0, invalid=96777 0151: dt=55.488000, rms=0.697 (0.048%), neg=0, invalid=96777 0152: dt=55.488000, rms=0.696 (0.047%), neg=0, invalid=96777 0153: dt=55.488000, rms=0.696 (0.044%), neg=0, invalid=96777 0154: dt=55.488000, rms=0.696 (0.043%), neg=0, invalid=96777 0155: dt=55.488000, rms=0.696 (0.043%), neg=0, invalid=96777 0156: dt=55.488000, rms=0.695 (0.044%), neg=0, invalid=96777 0157: dt=55.488000, rms=0.695 (0.044%), neg=0, invalid=96777 0158: dt=55.488000, rms=0.695 (0.042%), neg=0, invalid=96777 0159: dt=55.488000, rms=0.694 (0.038%), neg=0, invalid=96777 0160: dt=55.488000, rms=0.694 (0.034%), neg=0, invalid=96777 0161: dt=55.488000, rms=0.694 (0.032%), neg=0, invalid=96777 0162: dt=55.488000, rms=0.694 (0.032%), neg=0, invalid=96777 0163: dt=55.488000, rms=0.693 (0.039%), neg=0, invalid=96777 0164: dt=55.488000, rms=0.693 (0.040%), neg=0, invalid=96777 0165: dt=55.488000, rms=0.693 (0.036%), neg=0, invalid=96777 0166: dt=55.488000, rms=0.693 (0.029%), neg=0, invalid=96777 0167: dt=55.488000, rms=0.692 (0.030%), neg=0, invalid=96777 0168: dt=55.488000, rms=0.692 (0.034%), neg=0, invalid=96777 0169: dt=55.488000, rms=0.692 (0.034%), neg=0, invalid=96777 0170: dt=55.488000, rms=0.692 (0.027%), neg=0, invalid=96777 0171: dt=55.488000, rms=0.692 (0.023%), neg=0, invalid=96777 0172: dt=55.488000, rms=0.691 (0.023%), neg=0, invalid=96777 0173: dt=517.888000, rms=0.691 (0.064%), neg=0, invalid=96777 0174: dt=0.000903, rms=0.691 (-0.004%), neg=0, invalid=96777 0175: dt=0.000903, rms=0.691 (0.000%), neg=0, invalid=96777 0176: dt=0.000903, rms=0.691 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.691, neg=0, invalid=96777 0177: dt=32.368000, rms=0.691 (0.021%), neg=0, invalid=96777 0178: dt=32.368000, rms=0.691 (0.014%), neg=0, invalid=96777 0179: dt=32.368000, rms=0.691 (0.009%), neg=0, invalid=96777 0180: dt=32.368000, rms=0.691 (0.008%), neg=0, invalid=96777 0181: dt=32.368000, rms=0.691 (0.007%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.691, neg=0, invalid=96777 0182: dt=103.680000, rms=0.685 (0.929%), neg=0, invalid=96777 0183: dt=36.288000, rms=0.679 (0.823%), neg=0, invalid=96777 0184: dt=124.416000, rms=0.674 (0.826%), neg=0, invalid=96777 0185: dt=9.072000, rms=0.671 (0.335%), neg=0, invalid=96777 0186: dt=9.072000, rms=0.670 (0.163%), neg=0, invalid=96777 0187: dt=9.072000, rms=0.670 (0.088%), neg=0, invalid=96777 0188: dt=6.480000, rms=0.669 (0.046%), neg=0, invalid=96777 0189: dt=0.405000, rms=0.669 (0.007%), neg=0, invalid=96777 0190: dt=0.012656, rms=0.669 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.669, neg=0, invalid=96777 0191: dt=0.008859, rms=0.669 (0.000%), neg=0, invalid=96777 0192: dt=0.008859, rms=0.669 (0.000%), neg=0, invalid=96777 0193: dt=0.002215, rms=0.669 (0.000%), neg=0, invalid=96777 0194: dt=0.001107, rms=0.669 (0.000%), neg=0, invalid=96777 0195: dt=0.000554, rms=0.669 (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=0.672, neg=0, invalid=96777 0196: dt=0.000000, rms=0.672 (0.000%), neg=0, invalid=96777 0197: dt=0.000031, rms=0.672 (0.000%), neg=0, invalid=96777 0198: dt=0.000031, rms=0.672 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.672, neg=0, invalid=96777 0199: dt=0.000000, rms=0.672 (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=0.680, neg=0, invalid=96777 0200: dt=11.520000, rms=0.612 (10.080%), neg=0, invalid=96777 0201: dt=4.032000, rms=0.604 (1.237%), neg=0, invalid=96777 0202: dt=4.032000, rms=0.598 (0.953%), neg=0, invalid=96777 0203: dt=4.032000, rms=0.593 (0.805%), neg=0, invalid=96777 0204: dt=4.032000, rms=0.590 (0.651%), neg=0, invalid=96777 0205: dt=11.520000, rms=0.580 (1.542%), neg=0, invalid=96777 0206: dt=4.032000, rms=0.579 (0.281%), neg=0, invalid=96777 0207: dt=4.032000, rms=0.577 (0.269%), neg=0, invalid=96777 0208: dt=4.032000, rms=0.576 (0.221%), neg=0, invalid=96777 0209: dt=16.128000, rms=0.571 (0.792%), neg=0, invalid=96777 0210: dt=2.880000, rms=0.571 (0.080%), neg=0, invalid=96777 0211: dt=16.128000, rms=0.569 (0.368%), neg=0, invalid=96777 0212: dt=3.456000, rms=0.568 (0.097%), neg=0, invalid=96777 0213: dt=5.473684, rms=0.568 (0.130%), neg=0, invalid=96777 0214: dt=4.032000, rms=0.567 (0.059%), neg=0, invalid=96777 0215: dt=6.000000, rms=0.567 (0.108%), neg=0, invalid=96777 0216: dt=3.456000, rms=0.566 (0.055%), neg=0, invalid=96777 0217: dt=6.000000, rms=0.566 (0.102%), neg=0, invalid=96777 0218: dt=3.456000, rms=0.566 (0.036%), neg=0, invalid=96777 0219: dt=3.456000, rms=0.565 (0.070%), neg=0, invalid=96777 0220: dt=3.456000, rms=0.565 (0.079%), neg=0, invalid=96777 0221: dt=3.456000, rms=0.564 (0.115%), neg=0, invalid=96777 0222: dt=3.456000, rms=0.563 (0.130%), neg=0, invalid=96777 0223: dt=3.456000, rms=0.562 (0.171%), neg=0, invalid=96777 0224: dt=3.456000, rms=0.561 (0.167%), neg=0, invalid=96777 0225: dt=3.456000, rms=0.560 (0.162%), neg=0, invalid=96777 0226: dt=3.456000, rms=0.560 (0.153%), neg=0, invalid=96777 0227: dt=3.456000, rms=0.559 (0.148%), neg=0, invalid=96777 0228: dt=3.456000, rms=0.558 (0.142%), neg=0, invalid=96777 0229: dt=3.456000, rms=0.557 (0.127%), neg=0, invalid=96777 0230: dt=3.456000, rms=0.557 (0.109%), neg=0, invalid=96777 0231: dt=3.456000, rms=0.556 (0.087%), neg=0, invalid=96777 0232: dt=3.456000, rms=0.556 (0.084%), neg=0, invalid=96777 0233: dt=3.456000, rms=0.555 (0.078%), neg=0, invalid=96777 0234: dt=3.456000, rms=0.555 (0.066%), neg=0, invalid=96777 0235: dt=3.456000, rms=0.555 (0.053%), neg=0, invalid=96777 0236: dt=3.456000, rms=0.554 (0.042%), neg=0, invalid=96777 0237: dt=3.456000, rms=0.554 (0.043%), neg=0, invalid=96777 0238: dt=3.456000, rms=0.554 (0.046%), neg=0, invalid=96777 0239: dt=3.456000, rms=0.554 (0.043%), neg=0, invalid=96777 0240: dt=3.456000, rms=0.554 (0.030%), neg=0, invalid=96777 0241: dt=3.456000, rms=0.553 (0.029%), neg=0, invalid=96777 0242: dt=3.456000, rms=0.553 (0.040%), neg=0, invalid=96777 0243: dt=3.456000, rms=0.553 (0.032%), neg=0, invalid=96777 0244: dt=3.456000, rms=0.553 (0.025%), neg=0, invalid=96777 0245: dt=3.456000, rms=0.553 (0.032%), neg=0, invalid=96777 0246: dt=3.456000, rms=0.552 (0.028%), neg=0, invalid=96777 0247: dt=3.456000, rms=0.552 (0.019%), neg=0, invalid=96777 0248: dt=3.456000, rms=0.552 (0.023%), neg=0, invalid=96777 0249: dt=3.456000, rms=0.552 (0.019%), neg=0, invalid=96777 0250: dt=11.520000, rms=0.552 (0.012%), neg=0, invalid=96777 0251: dt=11.520000, rms=0.552 (-0.030%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.552, neg=0, invalid=96777 0252: dt=4.032000, rms=0.552 (0.061%), neg=0, invalid=96777 0253: dt=0.063000, rms=0.552 (0.002%), neg=0, invalid=96777 0254: dt=0.063000, rms=0.552 (-0.000%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.572, neg=0, invalid=96777 0255: dt=0.000000, rms=0.572 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.572, neg=0, invalid=96777 0256: dt=0.000000, rms=0.572 (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=0.538, neg=0, invalid=96777 0257: dt=0.112000, rms=0.532 (0.967%), neg=0, invalid=96777 0258: dt=0.028000, rms=0.531 (0.193%), neg=0, invalid=96777 0259: dt=0.153646, rms=0.526 (0.992%), neg=0, invalid=96777 0260: dt=0.131198, rms=0.523 (0.616%), neg=0, invalid=96777 0261: dt=0.121324, rms=0.521 (0.443%), neg=0, invalid=96777 0262: dt=0.114316, rms=0.519 (0.340%), neg=0, invalid=96777 0263: dt=0.028000, rms=0.518 (0.066%), neg=0, invalid=96777 0264: dt=0.080000, rms=0.517 (0.190%), neg=0, invalid=96777 0265: dt=0.112000, rms=0.516 (0.234%), neg=0, invalid=96777 0266: dt=0.112000, rms=0.515 (0.200%), neg=0, invalid=96777 0267: dt=0.028000, rms=0.515 (0.041%), neg=0, invalid=96777 0268: dt=0.028000, rms=0.515 (0.043%), neg=0, invalid=96777 0269: dt=0.028000, rms=0.514 (0.074%), neg=0, invalid=96777 0270: dt=0.028000, rms=0.514 (0.110%), neg=0, invalid=96777 0271: dt=0.028000, rms=0.513 (0.128%), neg=0, invalid=96777 0272: dt=0.028000, rms=0.512 (0.144%), neg=0, invalid=96777 0273: dt=0.028000, rms=0.512 (0.157%), neg=0, invalid=96777 0274: dt=0.028000, rms=0.511 (0.156%), neg=0, invalid=96777 0275: dt=0.028000, rms=0.510 (0.158%), neg=0, invalid=96777 0276: dt=0.007000, rms=0.510 (0.003%), neg=0, invalid=96777 0277: dt=0.007000, rms=0.510 (0.007%), neg=0, invalid=96777 0278: dt=0.007000, rms=0.510 (0.006%), neg=0, invalid=96777 0279: dt=0.112000, rms=0.510 (0.045%), neg=0, invalid=96777 0280: dt=0.096000, rms=0.510 (0.037%), neg=0, invalid=96777 0281: dt=0.006000, rms=0.510 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.510, neg=0, invalid=96777 0282: dt=0.007000, rms=0.509 (0.022%), neg=0, invalid=96777 0283: dt=0.001750, rms=0.509 (0.005%), neg=0, invalid=96777 0284: dt=0.001750, rms=0.509 (0.005%), neg=0, invalid=96777 0285: dt=0.001750, rms=0.509 (0.010%), neg=0, invalid=96777 0286: dt=0.001750, rms=0.509 (0.018%), neg=0, invalid=96777 0287: dt=0.001750, rms=0.509 (0.019%), neg=0, invalid=96777 0288: dt=0.001750, rms=0.509 (0.021%), neg=0, invalid=96777 0289: dt=0.001750, rms=0.509 (0.025%), neg=0, invalid=96777 0290: dt=0.001750, rms=0.509 (0.027%), neg=0, invalid=96777 0291: dt=0.001750, rms=0.509 (0.030%), neg=0, invalid=96777 0292: dt=0.001750, rms=0.508 (0.032%), neg=0, invalid=96777 0293: dt=0.001750, rms=0.508 (0.034%), neg=0, invalid=96777 0294: dt=0.001750, rms=0.508 (0.036%), neg=0, invalid=96777 0295: dt=0.001750, rms=0.508 (0.037%), neg=0, invalid=96777 0296: dt=0.001750, rms=0.508 (0.037%), neg=0, invalid=96777 0297: dt=0.001750, rms=0.508 (0.037%), neg=0, invalid=96777 0298: dt=0.001750, rms=0.507 (0.036%), neg=0, invalid=96777 0299: dt=0.001750, rms=0.507 (0.038%), neg=0, invalid=96777 0300: dt=0.001750, rms=0.507 (0.038%), neg=0, invalid=96777 0301: dt=0.001750, rms=0.507 (0.038%), neg=0, invalid=96777 0302: dt=0.001750, rms=0.507 (0.039%), neg=0, invalid=96777 0303: dt=0.001750, rms=0.506 (0.039%), neg=0, invalid=96777 0304: dt=0.001750, rms=0.506 (0.037%), neg=0, invalid=96777 0305: dt=0.001750, rms=0.506 (0.037%), neg=0, invalid=96777 0306: dt=0.001750, rms=0.506 (0.035%), neg=0, invalid=96777 0307: dt=0.001750, rms=0.506 (0.037%), neg=0, invalid=96777 0308: dt=0.001750, rms=0.505 (0.034%), neg=0, invalid=96777 0309: dt=0.001750, rms=0.505 (0.032%), neg=0, invalid=96777 0310: dt=0.001750, rms=0.505 (0.031%), neg=0, invalid=96777 0311: dt=0.001750, rms=0.505 (0.035%), neg=0, invalid=96777 0312: dt=0.001750, rms=0.505 (0.033%), neg=0, invalid=96777 0313: dt=0.001750, rms=0.505 (0.029%), neg=0, invalid=96777 0314: dt=0.001750, rms=0.505 (0.030%), neg=0, invalid=96777 0315: dt=0.001750, rms=0.504 (0.028%), neg=0, invalid=96777 0316: dt=0.001750, rms=0.504 (0.029%), neg=0, invalid=96777 0317: dt=0.001750, rms=0.504 (0.028%), neg=0, invalid=96777 0318: dt=0.001750, rms=0.504 (0.025%), neg=0, invalid=96777 0319: dt=0.001750, rms=0.504 (0.025%), neg=0, invalid=96777 0320: dt=0.001750, rms=0.504 (0.026%), neg=0, invalid=96777 0321: dt=0.001750, rms=0.504 (0.025%), neg=0, invalid=96777 0322: dt=0.001750, rms=0.503 (0.023%), neg=0, invalid=96777 0323: dt=0.448000, rms=0.502 (0.370%), neg=0, invalid=96777 0324: dt=0.096000, rms=0.502 (0.020%), neg=0, invalid=96777 0325: dt=0.006000, rms=0.502 (0.001%), neg=0, invalid=96777 0326: dt=0.006000, rms=0.502 (0.001%), neg=0, invalid=96777 0327: dt=0.006000, rms=0.501 (0.003%), neg=0, invalid=96777 0328: dt=0.006000, rms=0.501 (0.004%), neg=0, invalid=96777 0329: dt=0.006000, rms=0.501 (0.005%), neg=0, invalid=96777 0330: dt=0.006000, rms=0.501 (0.007%), neg=0, invalid=96777 0331: dt=0.006000, rms=0.501 (0.008%), neg=0, invalid=96777 0332: dt=0.006000, rms=0.501 (0.008%), neg=0, invalid=96777 0333: dt=0.006000, rms=0.501 (0.009%), neg=0, invalid=96777 0334: dt=0.006000, rms=0.501 (0.008%), neg=0, invalid=96777 0335: dt=0.112000, rms=0.501 (0.024%), neg=0, invalid=96777 0336: dt=0.028000, rms=0.501 (0.007%), neg=0, invalid=96777 label assignment complete, 0 changed (0.00%) ********************************************************************************************* ********************************************************************************************* ********************************************************************************************* ********************* ALLOWING NEGATIVE NODES IN DEFORMATION ******************************** ********************************************************************************************* ********************************************************************************************* ********************************************************************************************* **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.499, neg=0, invalid=96777 0337: dt=8.092000, rms=0.499 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.499, neg=0, invalid=96777 0338: dt=73.984000, rms=0.499 (0.047%), neg=0, invalid=96777 0339: dt=92.480000, rms=0.499 (0.030%), neg=0, invalid=96777 0340: dt=92.480000, rms=0.499 (0.023%), neg=0, invalid=96777 0341: dt=92.480000, rms=0.498 (0.056%), neg=0, invalid=96777 0342: dt=92.480000, rms=0.498 (0.029%), neg=0, invalid=96777 0343: dt=92.480000, rms=0.498 (0.037%), neg=0, invalid=96777 0344: dt=92.480000, rms=0.498 (0.021%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.498, neg=0, invalid=96777 0345: dt=25.920000, rms=0.497 (0.137%), neg=0, invalid=96777 0346: dt=36.288000, rms=0.497 (0.057%), neg=0, invalid=96777 0347: dt=36.288000, rms=0.497 (0.036%), neg=0, invalid=96777 0348: dt=36.288000, rms=0.497 (-0.008%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.497, neg=0, invalid=96777 0349: dt=36.288000, rms=0.495 (0.300%), neg=0, invalid=96777 0350: dt=124.416000, rms=0.494 (0.318%), neg=0, invalid=96777 0351: dt=25.920000, rms=0.493 (0.177%), neg=0, invalid=96777 0352: dt=25.920000, rms=0.493 (0.029%), neg=0, invalid=96777 0353: dt=25.920000, rms=0.493 (0.057%), neg=0, invalid=96777 0354: dt=25.920000, rms=0.492 (0.116%), neg=0, invalid=96777 0355: dt=25.920000, rms=0.491 (0.111%), neg=0, invalid=96777 0356: dt=25.920000, rms=0.491 (0.107%), neg=0, invalid=96777 0357: dt=145.152000, rms=0.491 (0.067%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.491, neg=0, invalid=96777 iter 0, gcam->neg = 4 after 9 iterations, nbhd size=1, neg = 0 0358: dt=19.200000, rms=0.488 (0.551%), neg=0, invalid=96777 0359: dt=8.744186, rms=0.487 (0.148%), neg=0, invalid=96777 0360: dt=8.744186, rms=0.486 (0.229%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 5 iterations, nbhd size=1, neg = 0 0361: dt=8.744186, rms=0.485 (0.259%), neg=0, invalid=96777 0362: dt=8.744186, rms=0.484 (0.277%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0363: dt=8.744186, rms=0.483 (0.206%), neg=0, invalid=96777 0364: dt=8.744186, rms=0.482 (0.225%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0365: dt=8.744186, rms=0.481 (0.195%), neg=0, invalid=96777 iter 0, gcam->neg = 6 after 2 iterations, nbhd size=0, neg = 0 0366: dt=8.744186, rms=0.480 (0.185%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 2 iterations, nbhd size=0, neg = 0 0367: dt=8.744186, rms=0.479 (0.218%), neg=0, invalid=96777 0368: dt=8.744186, rms=0.478 (0.216%), neg=0, invalid=96777 0369: dt=8.744186, rms=0.476 (0.253%), neg=0, invalid=96777 0370: dt=8.744186, rms=0.475 (0.230%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0371: dt=8.744186, rms=0.474 (0.211%), neg=0, invalid=96777 0372: dt=8.744186, rms=0.474 (0.174%), neg=0, invalid=96777 0373: dt=8.744186, rms=0.473 (0.165%), neg=0, invalid=96777 0374: dt=8.744186, rms=0.472 (0.152%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0375: dt=8.744186, rms=0.471 (0.146%), neg=0, invalid=96777 0376: dt=8.744186, rms=0.471 (0.137%), neg=0, invalid=96777 0377: dt=8.744186, rms=0.470 (0.109%), neg=0, invalid=96777 0378: dt=8.744186, rms=0.470 (0.120%), neg=0, invalid=96777 0379: dt=8.744186, rms=0.469 (0.110%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 8 iterations, nbhd size=1, neg = 0 0380: dt=25.600000, rms=0.469 (0.052%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0381: dt=25.600000, rms=0.469 (-0.138%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.469, neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0382: dt=25.600000, rms=0.467 (0.501%), neg=0, invalid=96777 0383: dt=7.265700, rms=0.465 (0.268%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0384: dt=19.200000, rms=0.464 (0.238%), neg=0, invalid=96777 iter 0, gcam->neg = 6 after 1 iterations, nbhd size=0, neg = 0 0385: dt=19.200000, rms=0.464 (-0.152%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.473, neg=0, invalid=96777 iter 0, gcam->neg = 23 after 8 iterations, nbhd size=1, neg = 0 0386: dt=4.521739, rms=0.471 (0.296%), neg=0, invalid=96777 iter 0, gcam->neg = 11 after 8 iterations, nbhd size=1, neg = 0 0387: dt=1.500000, rms=0.471 (0.036%), neg=0, invalid=96777 0388: dt=1.500000, rms=0.471 (0.057%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0389: dt=1.500000, rms=0.470 (0.080%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0390: dt=1.500000, rms=0.470 (0.019%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0391: dt=1.500000, rms=0.470 (-0.009%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.470, neg=0, invalid=96777 iter 0, gcam->neg = 57 after 34 iterations, nbhd size=3, neg = 0 0392: dt=8.356506, rms=0.468 (0.417%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0393: dt=2.133333, rms=0.468 (0.050%), neg=0, invalid=96777 0394: dt=2.133333, rms=0.467 (0.146%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0395: dt=2.133333, rms=0.466 (0.195%), neg=0, invalid=96777 iter 0, gcam->neg = 18 after 7 iterations, nbhd size=1, neg = 0 0396: dt=2.133333, rms=0.466 (0.183%), neg=0, invalid=96777 iter 0, gcam->neg = 16 after 18 iterations, nbhd size=2, neg = 0 0397: dt=2.133333, rms=0.465 (0.101%), neg=0, invalid=96777 iter 0, gcam->neg = 22 after 9 iterations, nbhd size=1, neg = 0 0398: dt=2.133333, rms=0.465 (0.026%), neg=0, invalid=96777 iter 0, gcam->neg = 10 after 7 iterations, nbhd size=1, neg = 0 0399: dt=5.600000, rms=0.464 (0.121%), neg=0, invalid=96777 iter 0, gcam->neg = 85 after 20 iterations, nbhd size=2, neg = 0 0400: dt=13.824000, rms=0.463 (0.328%), neg=0, invalid=96777 0401: dt=0.036000, rms=0.463 (0.000%), neg=0, invalid=96777 0402: dt=0.036000, rms=0.463 (0.001%), neg=0, invalid=96777 0403: dt=0.036000, rms=0.463 (0.002%), neg=0, invalid=96777 0404: dt=0.036000, rms=0.463 (-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=0.468, neg=0, invalid=96777 0405: dt=0.000000, rms=0.468 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.468, neg=0, invalid=96777 0406: dt=0.000000, rms=0.468 (0.000%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.460, neg=0, invalid=96777 iter 0, gcam->neg = 929 after 24 iterations, nbhd size=2, neg = 0 0407: dt=1.497678, rms=0.424 (7.722%), neg=0, invalid=96777 0408: dt=0.000047, rms=0.424 (0.007%), neg=0, invalid=96777 0409: dt=0.000047, rms=0.424 (0.000%), neg=0, invalid=96777 0410: dt=0.000047, rms=0.424 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.424, neg=0, invalid=96777 0411: dt=0.000188, rms=0.424 (0.000%), neg=0, invalid=96777 0412: dt=0.000000, rms=0.424 (-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=0.414, neg=0, invalid=96777 0413: dt=0.000000, rms=0.416 (-0.304%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.416, neg=0, invalid=96777 0414: dt=32.368000, rms=0.416 (0.023%), neg=0, invalid=96777 0415: dt=55.488000, rms=0.415 (0.007%), neg=0, invalid=96777 0416: dt=55.488000, rms=0.415 (0.001%), neg=0, invalid=96777 0417: dt=55.488000, rms=0.415 (-0.001%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.416, neg=0, invalid=96777 0418: dt=0.000000, rms=0.416 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.416, neg=0, invalid=96777 0419: dt=62.208000, rms=0.415 (0.050%), neg=0, invalid=96777 0420: dt=124.416000, rms=0.415 (0.046%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0421: dt=124.416000, rms=0.415 (-0.046%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.416, neg=0, invalid=96777 iter 0, gcam->neg = 9 after 23 iterations, nbhd size=3, neg = 0 0422: dt=9.600000, rms=0.415 (0.052%), neg=0, invalid=96777 0423: dt=0.010937, rms=0.415 (0.000%), neg=0, invalid=96777 0424: dt=0.010937, rms=0.415 (0.000%), neg=0, invalid=96777 0425: dt=0.010937, rms=0.415 (0.000%), neg=0, invalid=96777 0426: dt=0.010937, rms=0.415 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.415, neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0427: dt=11.200000, rms=0.415 (0.131%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 14 iterations, nbhd size=2, neg = 0 0428: dt=2.800000, rms=0.415 (0.019%), neg=0, invalid=96777 0429: dt=2.800000, rms=0.415 (0.045%), neg=0, invalid=96777 0430: dt=2.800000, rms=0.414 (0.081%), neg=0, invalid=96777 0431: dt=2.800000, rms=0.414 (0.105%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 8 iterations, nbhd size=1, neg = 0 0432: dt=2.800000, rms=0.413 (0.112%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0433: dt=2.800000, rms=0.413 (0.091%), neg=0, invalid=96777 iter 0, gcam->neg = 8 after 50 iterations, nbhd size=3, neg = 0 0434: dt=2.800000, rms=0.413 (0.014%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.415, neg=0, invalid=96777 0435: dt=0.002813, rms=0.415 (0.000%), neg=0, invalid=96777 iter 0, gcam->neg = 65 after 31 iterations, nbhd size=3, neg = 0 0436: dt=5.361702, rms=0.413 (0.302%), neg=0, invalid=96777 0437: dt=0.002250, rms=0.413 (0.000%), neg=0, invalid=96777 0438: dt=0.002250, rms=0.413 (0.000%), neg=0, invalid=96777 0439: dt=0.002250, rms=0.413 (0.000%), neg=0, invalid=96777 0440: dt=0.002250, rms=0.413 (0.000%), neg=0, invalid=96777 0441: dt=0.002250, rms=0.413 (0.000%), neg=0, invalid=96777 0442: dt=0.002250, rms=0.413 (0.000%), neg=0, invalid=96777 0443: dt=0.002250, rms=0.413 (0.000%), neg=0, invalid=96777 0444: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777 0445: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777 0446: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777 0447: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777 0448: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777 0449: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777 0450: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777 0451: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777 0452: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777 0453: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777 0454: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777 0455: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777 0456: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777 0457: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777 0458: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777 0459: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777 0460: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777 0461: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777 0462: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777 0463: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777 0464: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777 0465: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777 0466: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777 0467: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777 0468: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777 0469: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777 0470: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777 0471: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777 0472: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777 0473: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777 0474: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777 0475: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777 0476: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777 0477: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777 0478: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777 0479: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777 0480: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777 0481: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777 0482: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777 iter 0, gcam->neg = 84 after 200 iterations, nbhd size=2, neg = 1 starting rms=0.004, neg=1, removing folds in lattice.... iter 1, dt=0.000094: new neg 1, old_neg 1, delta 0, rms=0.003 (29.848%) iter 2, dt=0.000143: new neg 0, old_neg 1, delta 1, rms=0.002 (14.394%) 0483: dt=6.583333, rms=0.412 (0.174%), neg=0, invalid=96777 iter 0, gcam->neg = 10 after 15 iterations, nbhd size=2, neg = 0 0484: dt=1.728000, rms=0.412 (0.016%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.412, neg=0, invalid=96777 0485: dt=0.002250, rms=0.412 (0.000%), neg=0, invalid=96777 iter 0, gcam->neg = 26 after 27 iterations, nbhd size=3, neg = 0 0486: dt=1.728000, rms=0.412 (0.099%), neg=0, invalid=96777 iter 0, gcam->neg = 16 after 11 iterations, nbhd size=1, neg = 0 0487: dt=2.304000, rms=0.411 (0.141%), neg=0, invalid=96777 iter 0, gcam->neg = 34 after 43 iterations, nbhd size=2, neg = 0 0488: dt=4.032000, rms=0.411 (0.121%), neg=0, invalid=96777 iter 0, gcam->neg = 206 after 27 iterations, nbhd size=2, neg = 0 0489: dt=4.032000, rms=0.411 (-0.036%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.415, neg=0, invalid=96777 0490: dt=0.000050, rms=0.415 (0.000%), neg=0, invalid=96777 0491: dt=0.000000, rms=0.415 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.415, neg=0, invalid=96777 0492: dt=0.000250, rms=0.415 (0.000%), neg=0, invalid=96777 0493: dt=0.000000, rms=0.415 (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=0.408, neg=0, invalid=96777 iter 0, gcam->neg = 651 after 34 iterations, nbhd size=4, neg = 0 0494: dt=0.737864, rms=0.395 (3.217%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0495: dt=0.000063, rms=0.395 (0.003%), neg=0, invalid=96777 0496: dt=0.000063, rms=0.395 (0.000%), neg=0, invalid=96777 0497: dt=0.000063, rms=0.395 (0.000%), neg=0, invalid=96777 0498: dt=0.000063, rms=0.395 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.395, neg=0, invalid=96777 0499: dt=0.001750, rms=0.395 (0.001%), neg=0, invalid=96777 iter 0, gcam->neg = 5 after 7 iterations, nbhd size=1, neg = 0 0500: dt=0.028000, rms=0.395 (0.028%), neg=0, invalid=96777 0501: dt=0.000003, rms=0.395 (0.000%), neg=0, invalid=96777 0502: dt=0.000003, rms=0.395 (0.000%), neg=0, invalid=96777 0503: dt=0.000003, rms=0.395 (0.000%), neg=0, invalid=96777 0504: dt=0.000003, rms=0.395 (0.000%), neg=0, invalid=96777 0505: dt=0.000003, rms=0.395 (0.000%), neg=0, invalid=96777 0506: dt=0.000003, rms=0.395 (0.000%), neg=0, invalid=96777 writing output transformation to transforms/talairach.m3z... GCAMwrite registration took 3 hours, 47 minutes and 8 seconds. #-------------------------------------- #@# CA Reg Inv Thu Aug 8 16:04:20 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Thu Aug 8 16:06:02 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... 11654984 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 1 minutes and 43 seconds. #-------------------------------------- #@# SkullLTA Thu Aug 8 16:07:46 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=15.0 skull bounding box = (52, 23, 26) --> (200, 194, 218) using (101, 80, 122) as brain centroid... mean wm in atlas = 126, using box (83,59,98) --> (119, 101,145) to find MRI wm before smoothing, mri peak at 109 after smoothing, mri peak at 109, scaling input intensities by 1.156 scaling channel 0 by 1.15596 **************************************** 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) 1.189 -0.029 -0.069 -14.029; 0.036 1.189 0.090 -11.347; 0.089 -0.119 1.149 -30.408; 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) 1.189 -0.029 -0.069 -14.029; 0.036 1.189 0.090 -11.347; 0.089 -0.119 1.149 -30.408; 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) 1.212 -0.034 -0.035 -20.437; 0.039 1.206 0.132 -16.648; 0.043 -0.147 1.084 -10.317; 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) 1.146 0.006 -0.028 -16.785; 0.003 1.201 0.168 -15.701; 0.043 -0.189 1.099 -7.844; 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) 1.146 0.006 -0.028 -16.785; 0.003 1.201 0.168 -15.701; 0.043 -0.189 1.099 -7.844; 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) 1.144 -0.012 -0.039 -13.427; 0.021 1.209 0.150 -16.126; 0.052 -0.170 1.101 -10.763; 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) 1.142 0.001 -0.056 -11.985; 0.011 1.210 0.151 -14.689; 0.071 -0.170 1.101 -13.494; 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 1.14160 0.00070 -0.05573 -11.98465; 0.01126 1.20996 0.15055 -14.68894; 0.07067 -0.16981 1.10053 -13.49355; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.14160 0.00070 -0.05573 -11.98465; 0.01126 1.20996 0.15055 -14.68894; 0.07067 -0.16981 1.10053 -13.49355; 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: 1.142 0.001 -0.056 -11.985; 0.011 1.210 0.151 -14.689; 0.071 -0.170 1.101 -13.494; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -4.0 (old=-4.2) transform before final EM align: 1.142 0.001 -0.056 -11.985; 0.011 1.210 0.151 -14.689; 0.071 -0.170 1.101 -13.494; 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 1.14160 0.00070 -0.05573 -11.98465; 0.01126 1.20996 0.15055 -14.68894; 0.07067 -0.16981 1.10053 -13.49355; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.14160 0.00070 -0.05573 -11.98465; 0.01126 1.20996 0.15055 -14.68894; 0.07067 -0.16981 1.10053 -13.49355; 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: 1.142 0.001 -0.056 -11.985; 0.011 1.210 0.151 -14.689; 0.071 -0.170 1.101 -13.494; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull_2.lta... registration took 39 minutes and 41 seconds. #-------------------------------------- #@# SubCort Seg Thu Aug 8 16:47:27 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 snake5 machine x86_64 setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 = 0.09295 ( 4) Left_Lateral_Ventricle (4): linear fit = 0.12 x + 0.0 (160 voxels, overlap=0.007) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (160 voxels, peak = 3), gca=10.8 gca peak = 0.14982 (20) mri peak = 0.09989 ( 6) Right_Lateral_Ventricle (43): linear fit = 0.14 x + 0.0 (99 voxels, overlap=0.057) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (99 voxels, peak = 3), gca=8.0 gca peak = 0.28003 (97) mri peak = 0.11307 (88) Right_Pallidum (52): linear fit = 0.88 x + 0.0 (282 voxels, overlap=0.042) Right_Pallidum (52): linear fit = 0.88 x + 0.0 (282 voxels, peak = 85), gca=84.9 gca peak = 0.18160 (96) mri peak = 0.14844 (88) Left_Pallidum (13): linear fit = 0.88 x + 0.0 (251 voxels, overlap=0.041) Left_Pallidum (13): linear fit = 0.88 x + 0.0 (251 voxels, peak = 85), gca=85.0 gca peak = 0.27536 (62) mri peak = 0.14191 (56) Right_Hippocampus (53): linear fit = 0.86 x + 0.0 (451 voxels, overlap=0.457) Right_Hippocampus (53): linear fit = 0.86 x + 0.0 (451 voxels, peak = 53), gca=53.0 gca peak = 0.32745 (63) mri peak = 0.10251 (54) Left_Hippocampus (17): linear fit = 0.85 x + 0.0 (514 voxels, overlap=0.347) Left_Hippocampus (17): linear fit = 0.85 x + 0.0 (514 voxels, peak = 53), gca=53.2 gca peak = 0.08597 (105) mri peak = 0.07945 (107) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (24517 voxels, overlap=0.608) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (24517 voxels, peak = 110), gca=109.7 gca peak = 0.09209 (106) mri peak = 0.09088 (108) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (23723 voxels, overlap=0.564) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (23723 voxels, peak = 111), gca=110.8 gca peak = 0.07826 (63) mri peak = 0.06574 (52) Left_Cerebral_Cortex (3): linear fit = 0.80 x + 0.0 (11644 voxels, overlap=0.170) Left_Cerebral_Cortex (3): linear fit = 0.80 x + 0.0 (11644 voxels, peak = 50), gca=50.1 gca peak = 0.08598 (64) mri peak = 0.06639 (53) Right_Cerebral_Cortex (42): linear fit = 0.80 x + 0.0 (9724 voxels, overlap=0.067) Right_Cerebral_Cortex (42): linear fit = 0.80 x + 0.0 (9724 voxels, peak = 51), gca=50.9 gca peak = 0.24164 (71) mri peak = 0.09369 (67) Right_Caudate (50): linear fit = 0.94 x + 0.0 (274 voxels, overlap=0.583) Right_Caudate (50): linear fit = 0.94 x + 0.0 (274 voxels, peak = 67), gca=67.1 gca peak = 0.18227 (75) mri peak = 0.09580 (66) Left_Caudate (11): linear fit = 0.86 x + 0.0 (595 voxels, overlap=0.031) Left_Caudate (11): linear fit = 0.86 x + 0.0 (595 voxels, peak = 64), gca=64.1 gca peak = 0.10629 (62) mri peak = 0.05526 (61) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (9316 voxels, overlap=0.999) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (9316 voxels, peak = 61), gca=61.1 gca peak = 0.11668 (59) mri peak = 0.05718 (57) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (8907 voxels, overlap=0.959) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (8907 voxels, peak = 57), gca=56.9 gca peak = 0.17849 (88) mri peak = 0.07904 (91) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (3949 voxels, overlap=0.980) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (3949 voxels, peak = 91), gca=91.1 gca peak = 0.16819 (86) mri peak = 0.08305 (89) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (3771 voxels, overlap=0.984) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (3771 voxels, peak = 89), gca=89.0 gca peak = 0.41688 (64) mri peak = 0.13552 (54) Left_Amygdala (18): linear fit = 0.82 x + 0.0 (250 voxels, overlap=0.831) Left_Amygdala (18): linear fit = 0.82 x + 0.0 (250 voxels, peak = 53), gca=52.8 gca peak = 0.42394 (62) mri peak = 0.11791 (56) Right_Amygdala (54): linear fit = 0.88 x + 0.0 (219 voxels, overlap=0.622) Right_Amygdala (54): linear fit = 0.88 x + 0.0 (219 voxels, peak = 55), gca=54.9 gca peak = 0.10041 (96) mri peak = 0.06043 (85) Left_Thalamus_Proper (10): linear fit = 0.94 x + 0.0 (2887 voxels, overlap=0.769) Left_Thalamus_Proper (10): linear fit = 0.94 x + 0.0 (2887 voxels, peak = 91), gca=90.7 gca peak = 0.13978 (88) mri peak = 0.07904 (82) Right_Thalamus_Proper (49): linear fit = 0.93 x + 0.0 (3127 voxels, overlap=0.754) Right_Thalamus_Proper (49): linear fit = 0.93 x + 0.0 (3127 voxels, peak = 81), gca=81.4 gca peak = 0.08514 (81) mri peak = 0.06416 (70) Left_Putamen (12): linear fit = 0.88 x + 0.0 (1674 voxels, overlap=0.610) Left_Putamen (12): linear fit = 0.88 x + 0.0 (1674 voxels, peak = 71), gca=70.9 gca peak = 0.09624 (82) mri peak = 0.08647 (72) Right_Putamen (51): linear fit = 0.90 x + 0.0 (1432 voxels, overlap=0.475) Right_Putamen (51): linear fit = 0.90 x + 0.0 (1432 voxels, peak = 74), gca=74.2 gca peak = 0.07543 (88) mri peak = 0.07404 (89) Brain_Stem (16): linear fit = 1.01 x + 0.0 (7608 voxels, overlap=0.765) Brain_Stem (16): linear fit = 1.01 x + 0.0 (7608 voxels, peak = 89), gca=89.3 gca peak = 0.12757 (95) mri peak = 0.08062 (93) Right_VentralDC (60): linear fit = 0.99 x + 0.0 (715 voxels, overlap=0.837) Right_VentralDC (60): linear fit = 0.99 x + 0.0 (715 voxels, peak = 94), gca=93.6 gca peak = 0.17004 (92) mri peak = 0.07068 (96) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (731 voxels, overlap=0.933) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (731 voxels, peak = 91), gca=90.6 gca peak = 0.21361 (36) mri peak = 0.25018 ( 3) gca peak = 0.26069 (23) mri peak = 0.11236 ( 4) Fourth_Ventricle (15): linear fit = 0.26 x + 0.0 (83 voxels, overlap=0.029) Fourth_Ventricle (15): linear fit = 0.26 x + 0.0 (83 voxels, peak = 6), gca=6.1 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak Third_Ventricle = 0.21361 (36) gca peak Fourth_Ventricle = 0.26069 (23) gca peak CSF = 0.14367 (38) gca peak Left_Accumbens_area = 0.57033 (70) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65201 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.31129 (32) gca peak Right_Accumbens_area = 0.30219 (72) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.72939 (42) gca peak WM_hypointensities = 0.14821 (82) gca peak non_WM_hypointensities = 0.10354 (53) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means estimating mean gm scale to be 0.83 x + 0.0 estimating mean wm scale to be 1.04 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 = 0.09295 ( 4) Left_Lateral_Ventricle (4): linear fit = 0.52 x + 0.0 (160 voxels, overlap=0.761) Left_Lateral_Ventricle (4): linear fit = 0.52 x + 0.0 (160 voxels, peak = 6), gca=5.8 gca peak = 0.29325 ( 9) mri peak = 0.09989 ( 6) Right_Lateral_Ventricle (43): linear fit = 0.38 x + 0.0 (99 voxels, overlap=0.260) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (99 voxels, peak = 3), gca=3.6 gca peak = 0.26184 (85) mri peak = 0.11307 (88) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (282 voxels, overlap=1.005) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (282 voxels, peak = 85), gca=85.0 gca peak = 0.18578 (85) mri peak = 0.14844 (88) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (251 voxels, overlap=1.003) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (251 voxels, peak = 86), gca=86.3 gca peak = 0.33434 (53) mri peak = 0.14191 (56) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (451 voxels, overlap=1.008) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (451 voxels, peak = 53), gca=53.0 gca peak = 0.29127 (53) mri peak = 0.10251 (54) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (514 voxels, overlap=1.001) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (514 voxels, peak = 53), gca=53.0 gca peak = 0.08168 (110) mri peak = 0.07945 (107) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (24517 voxels, overlap=0.771) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (24517 voxels, peak = 110), gca=110.0 gca peak = 0.08583 (111) mri peak = 0.09088 (108) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (23723 voxels, overlap=0.719) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (23723 voxels, peak = 111), gca=111.0 gca peak = 0.09719 (50) mri peak = 0.06574 (52) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (11644 voxels, overlap=0.988) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (11644 voxels, peak = 50), gca=50.0 gca peak = 0.11022 (51) mri peak = 0.06639 (53) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (9724 voxels, overlap=0.936) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (9724 voxels, peak = 50), gca=50.2 gca peak = 0.23446 (69) mri peak = 0.09369 (67) Right_Caudate (50): linear fit = 1.00 x + 0.0 (274 voxels, overlap=1.010) Right_Caudate (50): linear fit = 1.00 x + 0.0 (274 voxels, peak = 69), gca=69.0 gca peak = 0.18422 (64) mri peak = 0.09580 (66) Left_Caudate (11): linear fit = 0.99 x + 0.0 (595 voxels, overlap=0.975) Left_Caudate (11): linear fit = 0.99 x + 0.0 (595 voxels, peak = 63), gca=63.0 gca peak = 0.11091 (61) mri peak = 0.05526 (61) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (9316 voxels, overlap=0.997) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (9316 voxels, peak = 63), gca=62.5 gca peak = 0.12326 (57) mri peak = 0.05718 (57) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (8907 voxels, overlap=1.000) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (8907 voxels, peak = 56), gca=56.1 gca peak = 0.16819 (91) mri peak = 0.07904 (91) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (3949 voxels, overlap=1.000) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (3949 voxels, peak = 91), gca=90.5 gca peak = 0.16430 (89) mri peak = 0.08305 (89) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (3771 voxels, overlap=1.000) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (3771 voxels, peak = 89), gca=88.6 gca peak = 0.34863 (52) mri peak = 0.13552 (54) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (250 voxels, overlap=1.031) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (250 voxels, peak = 52), gca=52.0 gca peak = 0.54141 (55) mri peak = 0.11791 (56) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (219 voxels, overlap=1.023) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (219 voxels, peak = 55), gca=55.0 gca peak = 0.10948 (89) mri peak = 0.06043 (85) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (2887 voxels, overlap=0.894) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (2887 voxels, peak = 89), gca=88.6 gca peak = 0.11263 (81) mri peak = 0.07904 (82) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3127 voxels, overlap=0.987) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3127 voxels, peak = 81), gca=80.6 gca peak = 0.09324 (72) mri peak = 0.06416 (70) Left_Putamen (12): linear fit = 1.03 x + 0.0 (1674 voxels, overlap=1.000) Left_Putamen (12): linear fit = 1.03 x + 0.0 (1674 voxels, peak = 75), gca=74.5 gca peak = 0.10809 (69) mri peak = 0.08647 (72) Right_Putamen (51): linear fit = 1.01 x + 0.0 (1432 voxels, overlap=0.985) Right_Putamen (51): linear fit = 1.01 x + 0.0 (1432 voxels, peak = 70), gca=70.0 gca peak = 0.07498 (87) mri peak = 0.07404 (89) Brain_Stem (16): linear fit = 1.00 x + 0.0 (7608 voxels, overlap=0.797) Brain_Stem (16): linear fit = 1.00 x + 0.0 (7608 voxels, peak = 87), gca=86.6 gca peak = 0.13759 (93) mri peak = 0.08062 (93) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (715 voxels, overlap=0.816) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (715 voxels, peak = 94), gca=94.4 gca peak = 0.16758 (91) mri peak = 0.07068 (96) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (731 voxels, overlap=0.912) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (731 voxels, peak = 91), gca=90.5 gca peak = 0.35640 (14) mri peak = 0.25018 ( 3) gca peak = 0.33827 ( 9) mri peak = 0.11236 ( 4) Fourth_Ventricle (15): linear fit = 0.70 x + 0.0 (83 voxels, overlap=0.845) Fourth_Ventricle (15): linear fit = 0.70 x + 0.0 (83 voxels, peak = 6), gca=6.3 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.27462 (30) gca peak Third_Ventricle = 0.35640 (14) gca peak CSF = 0.30128 (18) gca peak Left_Accumbens_area = 0.51723 (60) 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 = 0.31195 (27) gca peak Right_Accumbens_area = 0.31042 (68) gca peak Right_vessel = 0.53014 (60) gca peak Right_choroid_plexus = 0.10423 (48) gca peak Fifth_Ventricle = 0.45329 (19) gca peak WM_hypointensities = 0.16060 (85) gca peak non_WM_hypointensities = 0.11646 (55) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.54 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 10266 gm and wm labels changed (%10 to gray, %90 to white out of all changed labels) 241 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 83197 changed. image ll: -2.166, PF=1.000 pass 2: 16100 changed. image ll: -2.164, PF=1.000 pass 3: 6390 changed. pass 4: 3087 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 21 minutes and 16 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/cc_up.lta sub003 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/sub003/mri/transforms/cc_up.lta reading aseg from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/aseg.auto_noCCseg.mgz reading norm from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/norm.mgz 28093 voxels in left wm, 39898 in right wm, xrange [121, 131] searching rotation angles z=[-6 8], y=[-11 3] searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.8 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.3 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.8 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.3 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.8 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.3 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.8 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.3 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.8 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.3 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.8 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.3 searching scale 1 Z rot -0.0 searching scale 1 Z rot 0.2 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.7 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.2 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.7 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.2 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.7 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.2 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.7 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.2 searching scale 1 Z rot 4.5 searching scale 1 Z rot 4.7 searching scale 1 Z rot 5.0 searching scale 1 Z rot 5.2 searching scale 1 Z rot 5.5 searching scale 1 Z rot 5.7 searching scale 1 Z rot 6.0 searching scale 1 Z rot 6.2 searching scale 1 Z rot 6.5 searching scale 1 Z rot 6.7 searching scale 1 Z rot 7.0 searching scale 1 Z rot 7.2 searching scale 1 Z rot 7.5 searching scale 1 Z rot 7.7 global minimum found at slice 126.1, rotations (-3.60, 0.99) final transformation (x=126.1, yr=-3.601, zr=0.994): 0.998 -0.017 -0.063 10.978; 0.017 1.000 -0.001 45.958; 0.063 -0.000 0.998 2.314; 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 128 147 160 eigenvectors: -0.002 0.001 1.000; 0.022 -1.000 0.001; 1.000 0.022 0.001; error in mid anterior detected - correcting... writing aseg with callosum to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/aseg.auto.mgz... corpus callosum matter segmentation took 1.0 minutes #-------------------------------------- #@# Merge ASeg Thu Aug 8 17:09:40 CEST 2013 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Thu Aug 8 17:09:40 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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... 2558 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 30 (30) 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 40 seconds. #-------------------------------------------- #@# Mask BFS Thu Aug 8 17:14:22 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1383897 voxels in mask (pct= 8.25) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Thu Aug 8 17:14:25 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): 107.0 +- 4.9 [80.0 --> 125.0] GM (66.0) : 65.3 +- 9.9 [30.0 --> 96.0] setting bottom of white matter range to 75.1 setting top of gray matter range to 85.0 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 6982 sparsely connected voxels removed... thickening thin strands.... 20 segments, 6893 filled 187 bright non-wm voxels segmented. 3746 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 0.67 minutes reading wm segmentation from wm.seg.mgz... 58 voxels added to wm to prevent paths from MTL structures to cortex 1127 additional wm voxels added 0 additional wm voxels added SEG EDIT: 34372 voxels turned on, 37121 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+): 23 found - 23 modified | TOTAL: 23 pass 2 (xy+): 0 found - 23 modified | TOTAL: 23 pass 1 (xy-): 25 found - 25 modified | TOTAL: 48 pass 2 (xy-): 0 found - 25 modified | TOTAL: 48 pass 1 (yz+): 27 found - 27 modified | TOTAL: 75 pass 2 (yz+): 0 found - 27 modified | TOTAL: 75 pass 1 (yz-): 16 found - 16 modified | TOTAL: 91 pass 2 (yz-): 0 found - 16 modified | TOTAL: 91 pass 1 (xz+): 24 found - 24 modified | TOTAL: 115 pass 2 (xz+): 0 found - 24 modified | TOTAL: 115 pass 1 (xz-): 24 found - 24 modified | TOTAL: 139 pass 2 (xz-): 0 found - 24 modified | TOTAL: 139 Iteration Number : 1 pass 1 (+++): 18 found - 18 modified | TOTAL: 18 pass 2 (+++): 0 found - 18 modified | TOTAL: 18 pass 1 (+++): 8 found - 8 modified | TOTAL: 26 pass 2 (+++): 0 found - 8 modified | TOTAL: 26 pass 1 (+++): 6 found - 6 modified | TOTAL: 32 pass 2 (+++): 0 found - 6 modified | TOTAL: 32 pass 1 (+++): 13 found - 13 modified | TOTAL: 45 pass 2 (+++): 0 found - 13 modified | TOTAL: 45 Iteration Number : 1 pass 1 (++): 162 found - 162 modified | TOTAL: 162 pass 2 (++): 0 found - 162 modified | TOTAL: 162 pass 1 (+-): 238 found - 238 modified | TOTAL: 400 pass 2 (+-): 1 found - 239 modified | TOTAL: 401 pass 3 (+-): 0 found - 239 modified | TOTAL: 401 pass 1 (--): 144 found - 144 modified | TOTAL: 545 pass 2 (--): 0 found - 144 modified | TOTAL: 545 pass 1 (-+): 190 found - 190 modified | TOTAL: 735 pass 2 (-+): 0 found - 190 modified | TOTAL: 735 Iteration Number : 2 pass 1 (xy+): 7 found - 7 modified | TOTAL: 7 pass 2 (xy+): 0 found - 7 modified | TOTAL: 7 pass 1 (xy-): 2 found - 2 modified | TOTAL: 9 pass 2 (xy-): 0 found - 2 modified | TOTAL: 9 pass 1 (yz+): 2 found - 2 modified | TOTAL: 11 pass 2 (yz+): 0 found - 2 modified | TOTAL: 11 pass 1 (yz-): 6 found - 6 modified | TOTAL: 17 pass 2 (yz-): 0 found - 6 modified | TOTAL: 17 pass 1 (xz+): 5 found - 5 modified | TOTAL: 22 pass 2 (xz+): 0 found - 5 modified | TOTAL: 22 pass 1 (xz-): 3 found - 3 modified | TOTAL: 25 pass 2 (xz-): 0 found - 3 modified | TOTAL: 25 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 (-+): 1 found - 1 modified | TOTAL: 1 pass 2 (-+): 0 found - 1 modified | TOTAL: 1 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 945 (out of 449892: 0.210050) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Thu Aug 8 17:16:53 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 1.106 -0.027 -0.064 -4.276; 0.036 1.189 0.090 -11.347; 0.083 -0.111 1.069 -20.889; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.106 -0.027 -0.064 -4.276; 0.036 1.189 0.090 -11.347; 0.083 -0.111 1.069 -20.889; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1194 (min = 350, max = 1400), aspect = 0.52 (min = 0.10, max = 0.75) no need to search using seed (126, 115, 145), TAL = (2.0, 17.0, 13.0) talairach voxel to voxel transform 0.900 0.025 0.052 5.216; -0.022 0.834 -0.072 7.873; -0.072 0.084 0.924 19.957; 0.000 0.000 0.000 1.000; segmentation indicates cc at (126, 115, 145) --> (2.0, 17.0, 13.0) done. writing output to filled.mgz... filling took 1.0 minutes talairach cc position changed to (2.00, 17.00, 13.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, 17.00, 13.00) SRC: (112.78, 91.05, 155.93) search lh wm seed point around talairach space (-16.00, 17.00, 13.00), SRC: (145.16, 90.28, 153.35) 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 17:17:56 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 1 found - 1 modified | TOTAL: 3 pass 2 (xy-): 0 found - 1 modified | TOTAL: 3 pass 1 (yz+): 1 found - 1 modified | TOTAL: 4 pass 2 (yz+): 0 found - 1 modified | TOTAL: 4 pass 1 (yz-): 0 found - 0 modified | TOTAL: 4 pass 1 (xz+): 0 found - 0 modified | TOTAL: 4 pass 1 (xz-): 0 found - 0 modified | TOTAL: 4 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 4 (out of 216070: 0.001851) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 40: 16 vertices, 22 faces slice 50: 3802 vertices, 3997 faces slice 60: 10981 vertices, 11263 faces slice 70: 20573 vertices, 20908 faces slice 80: 31321 vertices, 31695 faces slice 90: 41789 vertices, 42139 faces slice 100: 52568 vertices, 52941 faces slice 110: 64298 vertices, 64702 faces slice 120: 75278 vertices, 75667 faces slice 130: 86018 vertices, 86379 faces slice 140: 96250 vertices, 96551 faces slice 150: 104805 vertices, 105079 faces slice 160: 111797 vertices, 112055 faces slice 170: 118318 vertices, 118529 faces slice 180: 124034 vertices, 124223 faces slice 190: 128211 vertices, 128332 faces slice 200: 129694 vertices, 129710 faces slice 210: 129694 vertices, 129710 faces slice 220: 129694 vertices, 129710 faces slice 230: 129694 vertices, 129710 faces slice 240: 129694 vertices, 129710 faces slice 250: 129694 vertices, 129710 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... 129694 voxel in cpt #1: X=-16 [v=129694,e=389130,f=259420] located at (-24.568037, -16.476614, 38.646660) For the whole surface: X=-16 [v=129694,e=389130,f=259420] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Thu Aug 8 17:18:04 CEST 2013 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 17:18:09 CEST 2013 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts avg radius = 45.2 mm, total surface area = 67371 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.7 minutes Not saving sulc step 000: RMS=0.103 (target=0.015) step 005: RMS=0.075 (target=0.015) step 010: RMS=0.055 (target=0.015) step 015: RMS=0.046 (target=0.015) step 020: RMS=0.039 (target=0.015) step 025: RMS=0.035 (target=0.015) step 030: RMS=0.031 (target=0.015) step 035: RMS=0.028 (target=0.015) step 040: RMS=0.027 (target=0.015) step 045: RMS=0.025 (target=0.015) step 050: RMS=0.024 (target=0.015) step 055: RMS=0.024 (target=0.015) step 060: RMS=0.023 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Thu Aug 8 17:18:51 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 1.00 +- 0.59 (0.00-->8.39) (max @ vno 91160 --> 92232) face area 0.03 +- 0.03 (-0.13-->1.03) scaling brain by 0.316... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.813, avgs=0 005/300: dt: 0.9000, rms radial error=176.555, avgs=0 010/300: dt: 0.9000, rms radial error=176.000, avgs=0 015/300: dt: 0.9000, rms radial error=175.271, avgs=0 020/300: dt: 0.9000, rms radial error=174.442, avgs=0 025/300: dt: 0.9000, rms radial error=173.556, avgs=0 030/300: dt: 0.9000, rms radial error=172.637, avgs=0 035/300: dt: 0.9000, rms radial error=171.701, avgs=0 040/300: dt: 0.9000, rms radial error=170.758, avgs=0 045/300: dt: 0.9000, rms radial error=169.811, avgs=0 050/300: dt: 0.9000, rms radial error=168.864, avgs=0 055/300: dt: 0.9000, rms radial error=167.920, avgs=0 060/300: dt: 0.9000, rms radial error=166.979, avgs=0 065/300: dt: 0.9000, rms radial error=166.041, avgs=0 070/300: dt: 0.9000, rms radial error=165.109, avgs=0 075/300: dt: 0.9000, rms radial error=164.180, avgs=0 080/300: dt: 0.9000, rms radial error=163.257, avgs=0 085/300: dt: 0.9000, rms radial error=162.338, avgs=0 090/300: dt: 0.9000, rms radial error=161.424, avgs=0 095/300: dt: 0.9000, rms radial error=160.515, avgs=0 100/300: dt: 0.9000, rms radial error=159.611, avgs=0 105/300: dt: 0.9000, rms radial error=158.711, avgs=0 110/300: dt: 0.9000, rms radial error=157.817, avgs=0 115/300: dt: 0.9000, rms radial error=156.927, avgs=0 120/300: dt: 0.9000, rms radial error=156.044, avgs=0 125/300: dt: 0.9000, rms radial error=155.166, avgs=0 130/300: dt: 0.9000, rms radial error=154.293, avgs=0 135/300: dt: 0.9000, rms radial error=153.425, avgs=0 140/300: dt: 0.9000, rms radial error=152.562, avgs=0 145/300: dt: 0.9000, rms radial error=151.704, avgs=0 150/300: dt: 0.9000, rms radial error=150.850, avgs=0 155/300: dt: 0.9000, rms radial error=150.000, avgs=0 160/300: dt: 0.9000, rms radial error=149.155, avgs=0 165/300: dt: 0.9000, rms radial error=148.315, avgs=0 170/300: dt: 0.9000, rms radial error=147.480, avgs=0 175/300: dt: 0.9000, rms radial error=146.649, avgs=0 180/300: dt: 0.9000, rms radial error=145.823, avgs=0 185/300: dt: 0.9000, rms radial error=145.001, avgs=0 190/300: dt: 0.9000, rms radial error=144.184, avgs=0 195/300: dt: 0.9000, rms radial error=143.371, avgs=0 200/300: dt: 0.9000, rms radial error=142.563, avgs=0 205/300: dt: 0.9000, rms radial error=141.759, avgs=0 210/300: dt: 0.9000, rms radial error=140.959, avgs=0 215/300: dt: 0.9000, rms radial error=140.165, avgs=0 220/300: dt: 0.9000, rms radial error=139.374, avgs=0 225/300: dt: 0.9000, rms radial error=138.589, avgs=0 230/300: dt: 0.9000, rms radial error=137.807, avgs=0 235/300: dt: 0.9000, rms radial error=137.030, avgs=0 240/300: dt: 0.9000, rms radial error=136.257, avgs=0 245/300: dt: 0.9000, rms radial error=135.489, avgs=0 250/300: dt: 0.9000, rms radial error=134.725, avgs=0 255/300: dt: 0.9000, rms radial error=133.965, avgs=0 260/300: dt: 0.9000, rms radial error=133.209, avgs=0 265/300: dt: 0.9000, rms radial error=132.458, avgs=0 270/300: dt: 0.9000, rms radial error=131.710, avgs=0 275/300: dt: 0.9000, rms radial error=130.968, avgs=0 280/300: dt: 0.9000, rms radial error=130.229, avgs=0 285/300: dt: 0.9000, rms radial error=129.495, avgs=0 290/300: dt: 0.9000, rms radial error=128.764, avgs=0 295/300: dt: 0.9000, rms radial error=128.038, avgs=0 300/300: dt: 0.9000, rms radial error=127.316, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 15148.56 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00015 epoch 2 (K=40.0), pass 1, starting sse = 2533.04 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00009 epoch 3 (K=160.0), pass 1, starting sse = 264.64 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.09/11 = 0.00857 epoch 4 (K=640.0), pass 1, starting sse = 14.98 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.14/16 = 0.00905 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.08 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Thu Aug 8 17:23:35 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/sub003/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub003 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=-16 (nv=129694, nf=259420, ne=389130, g=9) 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 8 iterations marking ambiguous vertices... 1837 ambiguous faces found in tessellation segmenting defects... 19 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 19 defects to be corrected 0 vertices coincident reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.8374 (-4.9187) -vertex loglikelihood: -6.7649 (-3.3824) -normal dot loglikelihood: -3.6152 (-3.6152) -quad curv loglikelihood: -6.5526 (-3.2763) Total Loglikelihood : -26.7701 CORRECTING DEFECT 0 (vertices=20, convex hull=76) After retessellation of defect 0, euler #=-16 (128575,385286,256695) : difference with theory (-16) = 0 CORRECTING DEFECT 1 (vertices=60, convex hull=97) After retessellation of defect 1, euler #=-15 (128590,385373,256768) : difference with theory (-15) = 0 CORRECTING DEFECT 2 (vertices=224, convex hull=194) After retessellation of defect 2, euler #=-14 (128647,385632,256971) : difference with theory (-14) = 0 CORRECTING DEFECT 3 (vertices=11, convex hull=24) After retessellation of defect 3, euler #=-13 (128651,385650,256986) : difference with theory (-13) = 0 CORRECTING DEFECT 4 (vertices=89, convex hull=42) After retessellation of defect 4, euler #=-12 (128658,385696,257026) : difference with theory (-12) = 0 CORRECTING DEFECT 5 (vertices=120, convex hull=73) After retessellation of defect 5, euler #=-11 (128683,385803,257109) : difference with theory (-11) = 0 CORRECTING DEFECT 6 (vertices=59, convex hull=29) After retessellation of defect 6, euler #=-10 (128691,385837,257136) : difference with theory (-10) = 0 CORRECTING DEFECT 7 (vertices=10, convex hull=26) After retessellation of defect 7, euler #=-9 (128695,385857,257153) : difference with theory (-9) = 0 CORRECTING DEFECT 8 (vertices=161, convex hull=64) After retessellation of defect 8, euler #=-8 (128704,385915,257203) : difference with theory (-8) = 0 CORRECTING DEFECT 9 (vertices=12, convex hull=29) After retessellation of defect 9, euler #=-7 (128709,385941,257225) : difference with theory (-7) = 0 CORRECTING DEFECT 10 (vertices=22, convex hull=28) After retessellation of defect 10, euler #=-6 (128712,385961,257243) : difference with theory (-6) = 0 CORRECTING DEFECT 11 (vertices=6, convex hull=23) After retessellation of defect 11, euler #=-5 (128714,385974,257255) : difference with theory (-5) = 0 CORRECTING DEFECT 12 (vertices=46, convex hull=86) After retessellation of defect 12, euler #=-4 (128740,386083,257339) : difference with theory (-4) = 0 CORRECTING DEFECT 13 (vertices=18, convex hull=25) After retessellation of defect 13, euler #=-3 (128743,386098,257352) : difference with theory (-3) = 0 CORRECTING DEFECT 14 (vertices=28, convex hull=49) After retessellation of defect 14, euler #=-2 (128755,386156,257399) : difference with theory (-2) = 0 CORRECTING DEFECT 15 (vertices=28, convex hull=75) After retessellation of defect 15, euler #=-1 (128772,386237,257464) : difference with theory (-1) = 0 CORRECTING DEFECT 16 (vertices=9, convex hull=18) After retessellation of defect 16, euler #=0 (128773,386245,257472) : difference with theory (0) = 0 CORRECTING DEFECT 17 (vertices=174, convex hull=102) After retessellation of defect 17, euler #=1 (128805,386384,257580) : difference with theory (1) = 0 CORRECTING DEFECT 18 (vertices=33, convex hull=66) After retessellation of defect 18, euler #=2 (128814,386436,257624) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.07-->7.78) (max @ vno 125265 --> 127336) 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 (0.07-->7.78) (max @ vno 125265 --> 127336) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 69 mutations (34.0%), 134 crossovers (66.0%), 71 vertices were eliminated building final representation... 880 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=128814, nf=257624, ne=386436, g=0) writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 11.9 minutes 0 defective edges removing intersecting faces 000: 104 intersecting 001: 8 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 128814 - 386436 + 257624 = 2 --> 0 holes F =2V-4: 257624 = 257628-4 (0) 2E=3F: 772872 = 772872 (0) total defect index = 0 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 14 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Thu Aug 8 17:35:36 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub003 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/sub003/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/wm.mgz... 15061 bright wm thresholded. 302 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.orig... computing class statistics... border white: 229356 voxels (1.37%) border gray 266114 voxels (1.59%) WM (92.0): 92.8 +- 10.6 [70.0 --> 110.0] GM (74.0) : 72.1 +- 13.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 43.9 (was 70) setting MAX_BORDER_WHITE to 115.6 (was 105) setting MIN_BORDER_WHITE to 57.0 (was 85) setting MAX_CSF to 30.8 (was 40) setting MAX_GRAY to 94.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 50.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 17.6 (was 40) repositioning cortical surface to gray/white boundary reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.22 (0.00-->3.59) (max @ vno 56572 --> 128641) face area 0.27 +- 0.12 (0.00-->1.50) mean absolute distance = 0.66 +- 0.75 3216 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=57 mean inside = 92.8, mean outside = 67.3 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group mean border=70.6, 37 (37) missing vertices, mean dist 0.4 [0.4 (%29.2)->0.8 (%70.8))] %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 (0.07-->4.54) (max @ vno 128641 --> 61076) face area 0.27 +- 0.13 (0.00-->2.13) mean absolute distance = 0.31 +- 0.46 2364 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=7465953.0, rms=14.40 001: dt: 0.5000, sse=7262134.0, rms=10.477 (0.000%) 002: dt: 0.5000, sse=7351785.0, rms=8.228 (0.000%) 003: dt: 0.5000, sse=7413903.5, rms=6.769 (0.000%) 004: dt: 0.5000, sse=7597030.0, rms=5.886 (0.000%) 005: dt: 0.5000, sse=7659898.0, rms=5.350 (0.000%) 006: dt: 0.5000, sse=7772073.5, rms=5.077 (0.000%) 007: dt: 0.5000, sse=7755777.5, rms=4.889 (0.000%) 008: dt: 0.5000, sse=7801354.0, rms=4.794 (0.000%) 009: dt: 0.5000, sse=7751140.0, rms=4.702 (0.000%) rms = 4.66, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=7755212.5, rms=4.664 (0.000%) 011: dt: 0.2500, sse=4943071.0, rms=3.317 (0.000%) 012: dt: 0.2500, sse=4577469.5, rms=2.876 (0.000%) 013: dt: 0.2500, sse=4314085.0, rms=2.788 (0.000%) 014: dt: 0.2500, sse=4268909.5, rms=2.701 (0.000%) rms = 2.68, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=4162221.5, rms=2.675 (0.000%) 016: dt: 0.1250, sse=3871362.5, rms=2.326 (0.000%) 017: dt: 0.1250, sse=3831868.2, rms=2.273 (0.000%) rms = 2.26, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=3800823.0, rms=2.263 (0.000%) positioning took 2.1 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=75.5, 19 (3) missing vertices, mean dist -0.2 [0.3 (%78.8)->0.2 (%21.2))] %81 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 (0.10-->4.77) (max @ vno 128641 --> 61076) face area 0.35 +- 0.17 (0.00-->2.79) mean absolute distance = 0.21 +- 0.29 2665 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4803874.0, rms=6.41 019: dt: 0.5000, sse=4962588.0, rms=4.328 (0.000%) rms = 4.76, time step reduction 1 of 3 to 0.250... 020: dt: 0.2500, sse=4493959.0, rms=3.071 (0.000%) 021: dt: 0.2500, sse=4333171.0, rms=2.534 (0.000%) 022: dt: 0.2500, sse=4261336.5, rms=2.121 (0.000%) rms = 2.12, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=4262324.0, rms=2.116 (0.000%) 024: dt: 0.1250, sse=4062707.8, rms=1.769 (0.000%) 025: dt: 0.1250, sse=4015600.2, rms=1.716 (0.000%) rms = 1.72, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=4015600.2, rms=1.716 (0.000%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=79.3, 22 (2) missing vertices, mean dist -0.1 [0.2 (%78.9)->0.2 (%21.1))] %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 0.90 +- 0.25 (0.11-->4.90) (max @ vno 128641 --> 61076) face area 0.34 +- 0.16 (0.00-->2.77) mean absolute distance = 0.15 +- 0.23 2784 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4474704.0, rms=4.76 027: dt: 0.5000, sse=4776922.5, rms=4.468 (0.000%) rms = 4.55, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=4306562.0, rms=2.805 (0.000%) 029: dt: 0.2500, sse=4177830.8, rms=2.405 (0.000%) 030: dt: 0.2500, sse=4245258.0, rms=2.000 (0.000%) rms = 2.10, time step reduction 2 of 3 to 0.125... 031: dt: 0.1250, sse=4171524.5, rms=1.801 (0.000%) 032: dt: 0.1250, sse=4077918.5, rms=1.518 (0.000%) rms = 1.47, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=4045932.8, rms=1.475 (0.000%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=80.5, 30 (1) missing vertices, mean dist -0.0 [0.2 (%59.7)->0.1 (%40.3))] %91 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=4080045.0, rms=1.97 rms = 3.07, time step reduction 1 of 3 to 0.250... 034: dt: 0.2500, sse=4151119.0, rms=1.280 (0.000%) 035: dt: 0.2500, sse=4290692.0, rms=1.100 (0.000%) rms = 1.10, time step reduction 2 of 3 to 0.125... 036: dt: 0.2500, sse=4374876.0, rms=1.096 (0.000%) rms = 1.07, time step reduction 3 of 3 to 0.062... 037: dt: 0.1250, sse=4403312.5, rms=1.070 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 14 non-cortical segments detected only using segment with 1770 vertices erasing segment 1 (vno[0] = 74553) erasing segment 2 (vno[0] = 76852) erasing segment 3 (vno[0] = 77980) erasing segment 4 (vno[0] = 83191) erasing segment 5 (vno[0] = 87211) erasing segment 6 (vno[0] = 87222) erasing segment 7 (vno[0] = 91656) erasing segment 8 (vno[0] = 94452) erasing segment 9 (vno[0] = 96138) erasing segment 10 (vno[0] = 96140) erasing segment 11 (vno[0] = 100554) erasing segment 12 (vno[0] = 101378) erasing segment 13 (vno[0] = 102157) writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/label/lh.cortex.label... writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.curv writing smoothed area to lh.area writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.area vertex spacing 0.90 +- 0.25 (0.03-->4.88) (max @ vno 128641 --> 61076) face area 0.34 +- 0.16 (0.00-->2.78) refinement took 6.6 minutes #-------------------------------------------- #@# Smooth2 lh Thu Aug 8 17:42:15 CEST 2013 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 17:42:19 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 45.4 mm, total surface area = 78610 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=0.082 (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=0.034 (target=0.015) step 030: RMS=0.028 (target=0.015) step 035: RMS=0.024 (target=0.015) step 040: RMS=0.021 (target=0.015) step 045: RMS=0.019 (target=0.015) step 050: RMS=0.017 (target=0.015) step 055: RMS=0.016 (target=0.015) step 060: RMS=0.015 (target=0.015) inflation complete. inflation took 0.5 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 111 vertices thresholded to be in k1 ~ [-0.23 0.79], k2 ~ [-0.14 0.08] total integrated curvature = 0.588*4pi (7.387) --> 0 handles ICI = 1.5, FI = 8.0, variation=145.885 116 vertices thresholded to be in [-0.04 0.02] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 95 vertices thresholded to be in [-0.15 0.15] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.017, std = 0.021 done. #----------------------------------------- #@# Curvature Stats lh Thu Aug 8 17:44:29 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub003 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 [ sub003/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 [ 211 ] Gb_filter = 0 WARN: S lookup min: -1.156500 WARN: S explicit min: 0.000000 vertex = 678 #-------------------------------------------- #@# Sphere lh Thu Aug 8 17:44:33 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 0.292... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=snake, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %20.77 pass 1: epoch 2 of 3 starting distance error %20.75 unfolding complete - removing small folds... starting distance error %20.68 removing remaining folds... final distance error %20.69 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/lh.sphere spherical transformation took 0.90 hours #-------------------------------------------- #@# Surf Reg lh Thu Aug 8 18:38:41 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 = 0.596 curvature mean = 0.030, std = 0.936 curvature mean = 0.023, std = 0.864 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 0.00) sse = 321607.3, tmin=1.0430 d=32.00 min @ (0.00, 8.00, 0.00) sse = 270092.5, tmin=2.0947 d=16.00 min @ (4.00, 0.00, 0.00) sse = 248718.9, tmin=3.1583 d=4.00 min @ (0.00, 1.00, 1.00) sse = 247261.0, tmin=5.3649 d=0.50 min @ (-0.12, 0.00, 0.12) sse = 247231.8, tmin=8.5913 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 8.59 min curvature mean = 0.018, std = 0.961 curvature mean = 0.012, std = 0.941 curvature mean = 0.018, std = 0.973 curvature mean = 0.006, std = 0.973 curvature mean = 0.016, std = 0.975 curvature mean = 0.002, std = 0.988 2 Reading smoothwm curvature mean = -0.026, std = 0.313 curvature mean = 0.004, std = 0.067 curvature mean = 0.076, std = 0.326 curvature mean = 0.004, std = 0.080 curvature mean = 0.036, std = 0.517 curvature mean = 0.004, std = 0.086 curvature mean = 0.020, std = 0.657 curvature mean = 0.004, std = 0.089 curvature mean = 0.008, std = 0.769 MRISregister() return, current seed 0 writing registered surface to ../surf/lh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white lh Thu Aug 8 19:04:44 CEST 2013 mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Thu Aug 8 19:04:47 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts mrisp_paint -a 5 /opt/freesurfer/5.3.0/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /opt/freesurfer/5.3.0/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Thu Aug 8 19:04:49 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub003 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... 1095 labels changed using aseg relabeling using gibbs priors... 000: 2699 changed, 128814 examined... 001: 578 changed, 11878 examined... 002: 132 changed, 3273 examined... 003: 47 changed, 791 examined... 004: 21 changed, 291 examined... 005: 5 changed, 122 examined... 006: 3 changed, 36 examined... 007: 2 changed, 19 examined... 008: 1 changed, 10 examined... 009: 0 changed, 7 examined... 212 labels changed using aseg 000: 120 total segments, 80 labels (246 vertices) changed 001: 41 total segments, 1 labels (1 vertices) changed 002: 40 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 51 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1129 vertices marked for relabeling... 1129 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 59 seconds. #-------------------------------------------- #@# Make Pial Surf lh Thu Aug 8 19:05:48 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub003 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/sub003/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/wm.mgz... 15061 bright wm thresholded. 302 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.orig... computing class statistics... border white: 229356 voxels (1.37%) border gray 266114 voxels (1.59%) WM (92.0): 92.8 +- 10.6 [70.0 --> 110.0] GM (74.0) : 72.1 +- 13.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 43.9 (was 70) setting MAX_BORDER_WHITE to 115.6 (was 105) setting MIN_BORDER_WHITE to 57.0 (was 85) setting MAX_CSF to 30.8 (was 40) setting MAX_GRAY to 94.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 50.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 17.6 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=57 mean inside = 92.8, mean outside = 67.3 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.22 (0.00-->3.59) (max @ vno 56572 --> 128641) face area 0.27 +- 0.12 (0.00-->1.50) mean absolute distance = 0.66 +- 0.75 3216 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 94 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown deleting segment 4 with 5 points - only 0.00% unknown deleting segment 5 with 10 points - only 0.00% unknown deleting segment 7 with 7 points - only 0.00% unknown deleting segment 8 with 14 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 9 with 4 points - only 0.00% unknown deleting segment 10 with 21 points - only 0.00% unknown deleting segment 11 with 7 points - only 0.00% unknown mean border=70.6, 37 (37) missing vertices, mean dist 0.4 [0.4 (%29.2)->0.8 (%70.8))] %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 (0.07-->4.54) (max @ vno 128641 --> 61076) face area 0.27 +- 0.13 (0.00-->2.13) mean absolute distance = 0.31 +- 0.46 2365 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=7473539.0, rms=14.40 001: dt: 0.5000, sse=7271485.5, rms=10.476 (0.000%) 002: dt: 0.5000, sse=7357718.5, rms=8.228 (0.000%) 003: dt: 0.5000, sse=7421993.5, rms=6.769 (0.000%) 004: dt: 0.5000, sse=7602813.5, rms=5.887 (0.000%) 005: dt: 0.5000, sse=7667546.0, rms=5.351 (0.000%) 006: dt: 0.5000, sse=7780513.5, rms=5.078 (0.000%) 007: dt: 0.5000, sse=7763787.0, rms=4.890 (0.000%) 008: dt: 0.5000, sse=7811158.0, rms=4.794 (0.000%) 009: dt: 0.5000, sse=7760282.0, rms=4.702 (0.000%) rms = 4.66, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=7765007.5, rms=4.663 (0.000%) 011: dt: 0.2500, sse=4947214.5, rms=3.316 (0.000%) 012: dt: 0.2500, sse=4581080.5, rms=2.875 (0.000%) 013: dt: 0.2500, sse=4317435.0, rms=2.787 (0.000%) 014: dt: 0.2500, sse=4272544.5, rms=2.701 (0.000%) rms = 2.67, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=4165785.5, rms=2.675 (0.000%) 016: dt: 0.1250, sse=3874189.8, rms=2.325 (0.000%) 017: dt: 0.1250, sse=3834696.5, rms=2.273 (0.000%) rms = 2.26, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=3803987.5, rms=2.262 (0.000%) positioning took 2.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 91 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 3 points - only 0.00% unknown deleting segment 5 with 6 points - only 0.00% unknown removing 1 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 8 with 5 points - only 0.00% unknown deleting segment 10 with 11 points - only 0.00% unknown deleting segment 11 with 40 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 12 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 13 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 14 with 4 points - only 0.00% unknown mean border=75.5, 19 (3) missing vertices, mean dist -0.2 [0.3 (%78.8)->0.2 (%21.2))] %81 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.26 (0.10-->4.77) (max @ vno 128641 --> 61076) face area 0.35 +- 0.17 (0.00-->2.79) mean absolute distance = 0.21 +- 0.29 2679 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4809469.5, rms=6.41 019: dt: 0.5000, sse=4968671.0, rms=4.324 (0.000%) rms = 4.76, time step reduction 1 of 3 to 0.250... 020: dt: 0.2500, sse=4499053.0, rms=3.068 (0.000%) 021: dt: 0.2500, sse=4337635.0, rms=2.532 (0.000%) 022: dt: 0.2500, sse=4267446.5, rms=2.120 (0.000%) rms = 2.11, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=4267548.0, rms=2.115 (0.000%) 024: dt: 0.1250, sse=4067736.2, rms=1.768 (0.000%) 025: dt: 0.1250, sse=4020981.5, rms=1.715 (0.000%) rms = 1.72, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=4020981.5, rms=1.715 (0.000%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 80 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 3 with 2 points - only 0.00% unknown deleting segment 5 with 6 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown deleting segment 7 with 11 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 10 with 11 points - only 0.00% unknown deleting segment 11 with 14 points - only 0.00% unknown deleting segment 12 with 40 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 13 with 3 points - only 0.00% unknown deleting segment 14 with 8 points - only 0.00% unknown deleting segment 15 with 9 points - only 0.00% unknown deleting segment 16 with 5 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 17 with 4 points - only 0.00% unknown mean border=79.3, 22 (2) missing vertices, mean dist -0.1 [0.2 (%79.0)->0.2 (%21.0))] %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 0.90 +- 0.25 (0.11-->4.90) (max @ vno 128641 --> 61076) face area 0.34 +- 0.16 (0.00-->2.77) mean absolute distance = 0.15 +- 0.24 2805 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4481905.0, rms=4.77 027: dt: 0.5000, sse=4780509.0, rms=4.467 (0.000%) rms = 4.54, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=4309538.5, rms=2.804 (0.000%) 029: dt: 0.2500, sse=4180369.0, rms=2.402 (0.000%) 030: dt: 0.2500, sse=4248919.5, rms=1.999 (0.000%) rms = 2.09, time step reduction 2 of 3 to 0.125... 031: dt: 0.1250, sse=4175122.8, rms=1.801 (0.000%) 032: dt: 0.1250, sse=4081150.5, rms=1.517 (0.000%) rms = 1.47, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=4049539.2, rms=1.474 (0.000%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 72 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 3 points - only 0.00% unknown deleting segment 4 with 6 points - only 0.00% unknown deleting segment 5 with 7 points - only 0.00% unknown deleting segment 6 with 11 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 8 with 9 points - only 0.00% unknown deleting segment 9 with 15 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 10 with 4 points - only 0.00% unknown deleting segment 11 with 40 points - only 0.00% unknown deleting segment 12 with 8 points - only 0.00% unknown deleting segment 13 with 15 points - only 0.00% unknown deleting segment 14 with 5 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 15 with 3 points - only 0.00% unknown mean border=80.5, 30 (1) missing vertices, mean dist -0.0 [0.2 (%59.7)->0.2 (%40.3))] %91 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4083266.5, rms=1.96 rms = 3.06, time step reduction 1 of 3 to 0.250... 034: dt: 0.2500, sse=4155235.5, rms=1.276 (0.000%) 035: dt: 0.2500, sse=4295353.5, rms=1.099 (0.000%) rms = 1.10, time step reduction 2 of 3 to 0.125... 036: dt: 0.2500, sse=4380404.5, rms=1.096 (0.000%) rms = 1.07, time step reduction 3 of 3 to 0.062... 037: dt: 0.1250, sse=4409607.5, rms=1.070 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... smoothing surface for 5 iterations... mean border=46.8, 24 (24) missing vertices, mean dist 1.7 [0.4 (%0.0)->2.2 (%100.0))] %15 local maxima, %60 large gradients and %21 min vals, 1201 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=29363298.0, rms=32.90 001: dt: 0.5000, sse=20971844.0, rms=27.211 (0.000%) 002: dt: 0.5000, sse=15249326.0, rms=22.545 (0.000%) 003: dt: 0.5000, sse=11478462.0, rms=18.803 (0.000%) 004: dt: 0.5000, sse=9214643.0, rms=15.820 (0.000%) 005: dt: 0.5000, sse=7897537.5, rms=13.450 (0.000%) 006: dt: 0.5000, sse=7129650.0, rms=11.618 (0.000%) 007: dt: 0.5000, sse=6673061.5, rms=10.072 (0.000%) 008: dt: 0.5000, sse=6358933.0, rms=8.702 (0.000%) 009: dt: 0.5000, sse=6158782.5, rms=7.503 (0.000%) 010: dt: 0.5000, sse=6165566.5, rms=6.532 (0.000%) 011: dt: 0.5000, sse=6199794.5, rms=5.790 (0.000%) 012: dt: 0.5000, sse=6300519.5, rms=5.234 (0.000%) 013: dt: 0.5000, sse=6415731.0, rms=4.880 (0.000%) 014: dt: 0.5000, sse=6515793.5, rms=4.658 (0.000%) 015: dt: 0.5000, sse=6607865.5, rms=4.524 (0.000%) 016: dt: 0.5000, sse=6635672.5, rms=4.422 (0.000%) 017: dt: 0.5000, sse=6702909.0, rms=4.355 (0.000%) 018: dt: 0.5000, sse=6709572.5, rms=4.295 (0.000%) rms = 4.26, time step reduction 1 of 3 to 0.250... 019: dt: 0.5000, sse=6738862.0, rms=4.262 (0.000%) 020: dt: 0.2500, sse=4781606.5, rms=3.500 (0.000%) 021: dt: 0.2500, sse=4594213.5, rms=3.283 (0.000%) rms = 3.25, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=4463428.5, rms=3.252 (0.000%) 023: dt: 0.1250, sse=4246123.0, rms=3.096 (0.000%) rms = 3.07, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=4218790.0, rms=3.075 (0.000%) positioning took 3.0 minutes mean border=44.4, 720 (4) missing vertices, mean dist 0.2 [0.2 (%49.8)->0.6 (%50.2))] %32 local maxima, %46 large gradients and %17 min vals, 415 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=4865797.0, rms=5.11 025: dt: 0.5000, sse=5170906.5, rms=4.379 (0.000%) rms = 4.39, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=4789324.5, rms=3.738 (0.000%) 027: dt: 0.2500, sse=4849623.0, rms=3.427 (0.000%) 028: dt: 0.2500, sse=4790957.5, rms=3.294 (0.000%) 029: dt: 0.2500, sse=4861055.0, rms=3.214 (0.000%) rms = 3.18, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=4867138.5, rms=3.176 (0.000%) 031: dt: 0.1250, sse=4687796.0, rms=3.000 (0.000%) rms = 2.96, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=4680468.5, rms=2.962 (0.000%) positioning took 1.1 minutes mean border=41.6, 891 (3) missing vertices, mean dist 0.1 [0.2 (%36.1)->0.4 (%63.9))] %55 local maxima, %23 large gradients and %17 min vals, 509 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=5026844.0, rms=4.66 033: dt: 0.5000, sse=5225649.5, rms=4.280 (0.000%) rms = 4.33, time step reduction 1 of 3 to 0.250... 034: dt: 0.2500, sse=4863804.5, rms=3.401 (0.000%) 035: dt: 0.2500, sse=5017575.5, rms=3.058 (0.000%) 036: dt: 0.2500, sse=4992551.0, rms=2.982 (0.000%) rms = 2.94, time step reduction 2 of 3 to 0.125... 037: dt: 0.2500, sse=5046519.0, rms=2.939 (0.000%) 038: dt: 0.1250, sse=4847981.0, rms=2.742 (0.000%) rms = 2.71, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=4834373.5, rms=2.711 (0.000%) positioning took 0.9 minutes mean border=40.2, 1678 (2) missing vertices, mean dist 0.1 [0.2 (%43.6)->0.3 (%56.4))] %60 local maxima, %17 large gradients and %17 min vals, 371 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/sub003/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=4912659.0, rms=3.24 rms = 4.20, time step reduction 1 of 3 to 0.250... 040: dt: 0.2500, sse=4756649.5, rms=2.849 (0.000%) 041: dt: 0.2500, sse=4882015.5, rms=2.749 (0.000%) rms = 2.72, time step reduction 2 of 3 to 0.125... 042: dt: 0.2500, sse=4955121.5, rms=2.717 (0.000%) 043: dt: 0.1250, sse=4865108.5, rms=2.585 (0.000%) rms = 2.57, time step reduction 3 of 3 to 0.062... 044: dt: 0.1250, sse=4866558.0, rms=2.568 (0.000%) positioning took 0.7 minutes writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.area.pial vertex spacing 1.03 +- 0.43 (0.11-->8.33) (max @ vno 102151 --> 101354) face area 0.42 +- 0.31 (0.00-->6.35) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 128814 vertices processed 25000 of 128814 vertices processed 50000 of 128814 vertices processed 75000 of 128814 vertices processed 100000 of 128814 vertices processed 125000 of 128814 vertices processed 0 of 128814 vertices processed 25000 of 128814 vertices processed 50000 of 128814 vertices processed 75000 of 128814 vertices processed 100000 of 128814 vertices processed 125000 of 128814 vertices processed thickness calculation complete, 344:1057 truncations. 29578 vertices at 0 distance 87298 vertices at 1 distance 83046 vertices at 2 distance 34244 vertices at 3 distance 9081 vertices at 4 distance 2194 vertices at 5 distance 679 vertices at 6 distance 224 vertices at 7 distance 59 vertices at 8 distance 32 vertices at 9 distance 39 vertices at 10 distance 30 vertices at 11 distance 16 vertices at 12 distance 20 vertices at 13 distance 12 vertices at 14 distance 7 vertices at 15 distance 17 vertices at 16 distance 14 vertices at 17 distance 6 vertices at 18 distance 4 vertices at 19 distance 16 vertices at 20 distance writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.thickness positioning took 13.9 minutes #-------------------------------------------- #@# Surf Volume lh Thu Aug 8 19:19:44 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 19:19:45 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts pctsurfcon --s sub003 --lh-only Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts/pctsurfcon.log Thu Aug 8 19:19:45 CEST 2013 setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts /opt/freesurfer/5.3.0/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux snake5 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/sub003/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/tmp.pctsurfcon.1521/lh.wm.mgh --regheader sub003 --cortex srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/mri/orig.mgz as target reference. Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/label/lh.cortex.label Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 = 99517 Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/label/lh.cortex.label Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/tmp.pctsurfcon.1521/lh.wm.mgh Dim: 128814 1 1 mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/tmp.pctsurfcon.1521/lh.gm.mgh --projfrac 0.3 --regheader sub003 --cortex srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/mri/orig.mgz as target reference. Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/label/lh.cortex.label Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.white Done reading source surface Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 = 114982 Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/label/lh.cortex.label Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/tmp.pctsurfcon.1521/lh.gm.mgh Dim: 128814 1 1 mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/tmp.pctsurfcon.1521/lh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/tmp.pctsurfcon.1521/lh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/surf/lh.w-g.pct.mgh mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.w-g.pct.mgh --annot sub003 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/surf/lh.w-g.pct.mgh --annot sub003 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/stats/lh.w-g.pct.stats --snr sysname Linux hostname snake5 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/sub003/surf/lh.w-g.pct.mgh Vertex Area is 0.668935 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 1000 unknown 0 0.000 1 1001 bankssts 1313 912.526 2 1002 caudalanteriorcingulate 1207 797.752 3 1003 caudalmiddlefrontal 3048 2076.126 4 1004 corpuscallosum 0 0.000 5 1005 cuneus 2385 1534.899 6 1006 entorhinal 642 439.147 7 1007 fusiform 4680 3118.398 8 1008 inferiorparietal 8019 5422.172 9 1009 inferiortemporal 4652 3183.842 10 1010 isthmuscingulate 1397 920.880 11 1011 lateraloccipital 7688 4947.458 12 1012 lateralorbitofrontal 3472 2351.095 13 1013 lingual 4989 3368.609 14 1014 medialorbitofrontal 2458 1637.896 15 1015 middletemporal 4026 2802.262 16 1016 parahippocampal 943 632.615 17 1017 paracentral 1806 1199.072 18 1018 parsopercularis 2289 1564.207 19 1019 parsorbitalis 861 574.945 20 1020 parstriangularis 1942 1297.889 21 1021 pericalcarine 2546 1710.734 22 1022 postcentral 5594 3713.786 23 1023 posteriorcingulate 1802 1215.047 24 1024 precentral 6059 4011.424 25 1025 precuneus 5795 3903.047 26 1026 rostralanteriorcingulate 1151 752.602 27 1027 rostralmiddlefrontal 7838 5340.084 28 1028 superiorfrontal 9528 6568.189 29 1029 superiorparietal 8197 5422.492 30 1030 superiortemporal 4968 3300.387 31 1031 supramarginal 5392 3678.488 32 1032 frontalpole 336 229.860 33 1033 temporalpole 610 421.463 34 1034 transversetemporal 701 449.925 35 1035 insula 3025 1921.944 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats lh Thu Aug 8 19:19:58 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 sub003 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 1313 913 2183 2.297 0.409 0.121 0.031 13 1.6 bankssts 1207 798 2356 2.720 0.709 0.175 0.068 31 3.4 caudalanteriorcingulate 3048 2076 5891 2.507 0.452 0.133 0.038 40 4.8 caudalmiddlefrontal 2385 1535 3593 1.999 0.562 0.164 0.071 48 7.5 cuneus 642 439 1862 2.952 0.902 0.159 0.068 18 2.0 entorhinal 4680 3118 10090 2.782 0.570 0.159 0.076 123 13.0 fusiform 8019 5422 15214 2.473 0.473 0.143 0.046 132 15.2 inferiorparietal 4652 3184 9405 2.452 0.618 0.144 0.060 94 10.5 inferiortemporal 1397 921 2659 2.629 0.845 0.161 0.066 32 3.1 isthmuscingulate 7688 4947 11816 2.150 0.442 0.155 0.059 143 18.1 lateraloccipital 3472 2351 6651 2.490 0.603 0.164 0.078 103 10.5 lateralorbitofrontal 4989 3369 8147 2.189 0.563 0.170 0.075 106 15.0 lingual 2458 1638 4697 2.393 0.745 0.162 0.091 83 8.7 medialorbitofrontal 4026 2802 9497 2.683 0.601 0.153 0.055 87 8.2 middletemporal 943 633 2299 3.027 0.681 0.129 0.052 13 2.2 parahippocampal 1806 1199 3117 2.288 0.520 0.118 0.029 18 2.2 paracentral 2289 1564 4977 2.676 0.504 0.131 0.041 34 3.7 parsopercularis 861 575 1979 2.662 0.571 0.158 0.055 17 1.7 parsorbitalis 1942 1298 3766 2.470 0.441 0.152 0.056 42 4.0 parstriangularis 2546 1711 3160 1.914 0.471 0.136 0.058 34 4.6 pericalcarine 5594 3714 8680 2.060 0.558 0.136 0.048 91 10.3 postcentral 1802 1215 3319 2.474 0.639 0.168 0.051 42 3.9 posteriorcingulate 6059 4011 11803 2.567 0.517 0.121 0.032 63 8.1 precentral 5795 3903 10220 2.342 0.455 0.159 0.065 122 14.2 precuneus 1151 753 2653 2.890 0.797 0.158 0.066 27 2.8 rostralanteriorcingulate 7838 5340 14208 2.277 0.542 0.171 0.083 222 22.6 rostralmiddlefrontal 9528 6568 21005 2.659 0.551 0.147 0.055 182 20.6 superiorfrontal 8197 5422 12474 2.077 0.407 0.135 0.043 130 14.5 superiorparietal 4968 3300 10547 2.647 0.630 0.144 0.060 190 14.4 superiortemporal 5392 3678 10196 2.409 0.472 0.149 0.049 97 10.5 supramarginal 336 230 693 2.333 0.480 0.255 0.158 18 2.4 frontalpole 610 421 2332 3.637 0.960 0.182 0.084 15 2.3 temporalpole 701 450 1347 2.485 0.322 0.113 0.042 6 1.1 transversetemporal 3025 1922 6705 3.230 0.903 0.119 0.066 60 7.5 insula #----------------------------------------- #@# Cortical Parc 2 lh Thu Aug 8 19:20:16 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub003 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... 34 labels changed using aseg relabeling using gibbs priors... 000: 9137 changed, 128814 examined... 001: 2210 changed, 34529 examined... 002: 682 changed, 11259 examined... 003: 321 changed, 3790 examined... 004: 164 changed, 1763 examined... 005: 74 changed, 913 examined... 006: 32 changed, 409 examined... 007: 14 changed, 175 examined... 008: 8 changed, 85 examined... 009: 4 changed, 33 examined... 010: 3 changed, 24 examined... 011: 1 changed, 16 examined... 012: 0 changed, 6 examined... 8 labels changed using aseg 000: 275 total segments, 194 labels (2471 vertices) changed 001: 99 total segments, 19 labels (44 vertices) changed 002: 80 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 109 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 698 vertices marked for relabeling... 698 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 1 minutes and 8 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Thu Aug 8 19:21:24 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 sub003 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 1283 876 2219 2.152 0.591 0.174 0.081 33 3.8 G_and_S_frontomargin 1722 1148 3448 2.506 0.479 0.167 0.060 35 3.9 G_and_S_occipital_inf 1509 973 2744 2.334 0.524 0.126 0.033 19 2.1 G_and_S_paracentral 1323 902 2836 2.655 0.483 0.154 0.056 25 2.9 G_and_S_subcentral 851 591 1821 2.395 0.469 0.227 0.112 38 3.9 G_and_S_transv_frontopol 2248 1539 4781 2.708 0.695 0.157 0.066 49 5.8 G_and_S_cingul-Ant 1733 1184 3348 2.617 0.583 0.148 0.062 28 3.3 G_and_S_cingul-Mid-Ant 1375 942 2573 2.495 0.478 0.145 0.043 23 2.5 G_and_S_cingul-Mid-Post 490 325 1204 2.878 0.561 0.217 0.094 19 1.8 G_cingul-Post-dorsal 361 221 760 2.874 0.993 0.166 0.079 11 0.9 G_cingul-Post-ventral 2163 1400 3365 1.931 0.556 0.166 0.084 47 7.1 G_cuneus 1256 882 3590 2.927 0.399 0.170 0.060 34 3.1 G_front_inf-Opercular 291 198 696 2.670 0.553 0.228 0.133 16 1.1 G_front_inf-Orbital 1102 715 2524 2.643 0.433 0.137 0.041 19 1.9 G_front_inf-Triangul 4358 3011 9617 2.498 0.525 0.176 0.093 144 13.3 G_front_middle 6152 4245 15510 2.809 0.557 0.164 0.062 148 15.6 G_front_sup 439 267 1093 3.545 0.670 0.125 0.082 9 1.1 G_Ins_lg_and_S_cent_ins 630 369 2126 4.092 0.730 0.129 0.129 28 3.5 G_insular_short 2194 1443 4532 2.504 0.465 0.174 0.067 53 5.9 G_occipital_middle 1622 1062 2501 2.019 0.455 0.150 0.047 28 3.2 G_occipital_sup 1478 921 3679 3.063 0.480 0.173 0.077 45 4.7 G_oc-temp_lat-fusifor 3359 2224 5807 2.166 0.572 0.184 0.084 81 11.5 G_oc-temp_med-Lingual 1133 772 3384 3.154 0.821 0.149 0.064 22 3.0 G_oc-temp_med-Parahip 2252 1516 5406 2.686 0.646 0.181 0.094 90 8.1 G_orbital 2624 1741 5368 2.497 0.421 0.143 0.043 47 4.8 G_pariet_inf-Angular 3002 2049 6580 2.589 0.435 0.166 0.061 69 6.9 G_pariet_inf-Supramar 2955 1982 5554 2.214 0.434 0.153 0.053 72 6.7 G_parietal_sup 1995 1278 3380 2.118 0.513 0.148 0.066 45 4.6 G_postcentral 2371 1525 5689 2.804 0.435 0.136 0.039 34 3.9 G_precentral 2924 1947 6143 2.458 0.493 0.183 0.086 88 9.1 G_precuneus 929 642 2188 2.421 0.705 0.226 0.161 64 6.3 G_rectus 244 143 402 2.791 0.501 0.089 0.043 2 0.4 G_subcallosal 552 336 1149 2.582 0.284 0.119 0.047 6 0.9 G_temp_sup-G_T_transv 1960 1319 5560 2.910 0.652 0.193 0.096 166 9.0 G_temp_sup-Lateral 451 335 1562 3.703 0.805 0.160 0.060 9 1.2 G_temp_sup-Plan_polar 730 510 1425 2.398 0.445 0.109 0.027 6 0.8 G_temp_sup-Plan_tempo 2628 1770 6096 2.556 0.649 0.162 0.074 76 8.1 G_temporal_inf 2437 1725 6895 2.882 0.581 0.167 0.061 64 5.6 G_temporal_middle 375 255 582 2.213 0.353 0.157 0.055 7 0.9 Lat_Fis-ant-Horizont 329 221 522 2.481 0.609 0.104 0.027 2 0.3 Lat_Fis-ant-Vertical 1407 930 1778 2.216 0.408 0.123 0.033 12 2.0 Lat_Fis-post 2513 1537 3348 1.939 0.463 0.163 0.080 62 7.9 Pole_occipital 1811 1271 5452 2.993 0.865 0.189 0.117 72 8.0 Pole_temporal 2997 2058 3919 2.047 0.534 0.133 0.051 39 5.4 S_calcarine 2701 1827 3323 1.983 0.558 0.101 0.023 14 2.7 S_central 1011 676 1412 2.195 0.459 0.109 0.026 7 1.0 S_cingul-Marginalis 460 308 818 2.880 0.515 0.111 0.029 3 0.6 S_circular_insula_ant 1341 874 2267 2.794 0.720 0.087 0.027 10 1.2 S_circular_insula_inf 1696 1139 2570 2.535 0.461 0.116 0.030 13 2.1 S_circular_insula_sup 1133 779 2064 2.510 0.570 0.133 0.074 19 2.0 S_collat_transv_ant 565 375 751 2.163 0.376 0.124 0.035 5 0.8 S_collat_transv_post 2113 1422 3247 2.208 0.462 0.139 0.041 29 3.5 S_front_inf 1138 763 1562 2.004 0.444 0.152 0.061 20 2.5 S_front_middle 2165 1482 3353 2.342 0.333 0.099 0.023 12 2.1 S_front_sup 248 164 465 2.358 0.353 0.099 0.034 3 0.4 S_interm_prim-Jensen 3488 2317 4596 2.069 0.377 0.118 0.031 30 4.5 S_intrapariet_and_P_trans 1651 1092 2163 2.116 0.360 0.146 0.047 21 3.1 S_oc_middle_and_Lunatus 1407 935 1967 2.150 0.405 0.116 0.030 12 1.7 S_oc_sup_and_transversal 687 460 881 2.291 0.376 0.127 0.042 6 1.1 S_occipital_ant 972 668 1490 2.451 0.393 0.122 0.031 8 1.3 S_oc-temp_lat 2177 1494 3517 2.540 0.440 0.130 0.045 25 3.6 S_oc-temp_med_and_Lingual 480 318 708 2.295 0.380 0.150 0.055 7 1.1 S_orbital_lateral 752 507 1087 2.019 0.805 0.109 0.048 8 0.8 S_orbital_med-olfact 1349 902 2261 2.367 0.486 0.155 0.065 25 3.2 S_orbital-H_Shaped 2204 1481 3186 2.254 0.414 0.141 0.047 31 4.3 S_parieto_occipital 1187 739 1250 2.079 0.860 0.148 0.043 21 2.0 S_pericallosal 2641 1773 3454 1.957 0.395 0.131 0.038 31 3.8 S_postcentral 1540 1029 2435 2.458 0.387 0.108 0.027 12 1.7 S_precentral-inf-part 806 566 1097 2.108 0.363 0.099 0.018 4 0.7 S_precentral-sup-part 664 433 1363 2.780 0.659 0.175 0.084 19 2.2 S_suborbital 1078 741 1690 2.262 0.438 0.145 0.053 15 2.1 S_subparietal 1406 951 1822 2.128 0.436 0.123 0.033 14 2.0 S_temporal_inf 5364 3661 9133 2.396 0.469 0.129 0.041 68 9.7 S_temporal_sup 377 244 453 2.096 0.265 0.096 0.022 2 0.4 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Thu Aug 8 19:21:43 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub003 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... 917 labels changed using aseg relabeling using gibbs priors... 000: 2665 changed, 128814 examined... 001: 605 changed, 11425 examined... 002: 169 changed, 3300 examined... 003: 63 changed, 995 examined... 004: 30 changed, 385 examined... 005: 8 changed, 158 examined... 006: 4 changed, 45 examined... 007: 3 changed, 25 examined... 008: 1 changed, 17 examined... 009: 1 changed, 9 examined... 010: 1 changed, 7 examined... 011: 1 changed, 7 examined... 012: 2 changed, 6 examined... 013: 2 changed, 12 examined... 014: 2 changed, 12 examined... 015: 2 changed, 15 examined... 016: 4 changed, 13 examined... 017: 5 changed, 18 examined... 018: 5 changed, 23 examined... 019: 2 changed, 28 examined... 020: 5 changed, 13 examined... 021: 3 changed, 21 examined... 022: 2 changed, 17 examined... 023: 0 changed, 14 examined... 124 labels changed using aseg 000: 61 total segments, 28 labels (160 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 40 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 504 vertices marked for relabeling... 504 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas40.annot... classification took 1 minutes and 0 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Thu Aug 8 19:22:42 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 sub003 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 1727 1161 3341 2.648 0.680 0.168 0.076 39 4.3 caudalanteriorcingulate 3077 2087 5894 2.502 0.452 0.132 0.038 40 4.9 caudalmiddlefrontal 3280 2135 4940 2.042 0.519 0.155 0.063 59 8.8 cuneus 570 384 1513 2.835 0.902 0.132 0.038 5 0.9 entorhinal 4154 2757 8674 2.771 0.549 0.149 0.058 86 9.4 fusiform 7518 5070 14114 2.461 0.468 0.141 0.044 121 13.7 inferiorparietal 4907 3361 10333 2.491 0.636 0.155 0.080 134 14.3 inferiortemporal 1344 883 2577 2.638 0.831 0.163 0.067 32 3.0 isthmuscingulate 7882 5068 12119 2.145 0.459 0.156 0.060 149 18.6 lateraloccipital 3841 2598 7497 2.456 0.657 0.173 0.085 128 12.8 lateralorbitofrontal 5004 3382 8171 2.183 0.557 0.169 0.074 104 14.6 lingual 2174 1442 4253 2.402 0.753 0.173 0.105 84 8.9 medialorbitofrontal 5701 3978 12799 2.618 0.597 0.149 0.052 113 11.3 middletemporal 961 642 2334 3.053 0.691 0.132 0.060 16 2.7 parahippocampal 2079 1381 3637 2.318 0.530 0.118 0.029 20 2.5 paracentral 1976 1353 4389 2.740 0.466 0.131 0.042 30 3.3 parsopercularis 933 637 1915 2.504 0.538 0.152 0.065 22 2.0 parsorbitalis 2421 1601 4543 2.453 0.444 0.146 0.047 42 4.5 parstriangularis 2537 1698 3144 1.917 0.471 0.136 0.058 34 4.7 pericalcarine 6427 4267 10016 2.085 0.549 0.137 0.048 105 12.2 postcentral 2026 1358 3591 2.447 0.621 0.160 0.049 43 4.1 posteriorcingulate 6105 4038 11845 2.575 0.519 0.121 0.032 64 8.2 precentral 5624 3808 10117 2.333 0.464 0.161 0.067 122 14.2 precuneus 1433 948 3185 2.857 0.765 0.154 0.063 31 3.3 rostralanteriorcingulate 5558 3774 10227 2.287 0.558 0.160 0.071 137 14.2 rostralmiddlefrontal 10530 7277 22903 2.602 0.559 0.159 0.066 244 26.3 superiorfrontal 6501 4295 9810 2.079 0.398 0.133 0.042 105 11.0 superiorparietal 6515 4367 14464 2.716 0.736 0.148 0.061 220 18.4 superiortemporal 5205 3554 9820 2.409 0.476 0.150 0.050 92 10.1 supramarginal 697 449 1342 2.485 0.320 0.114 0.042 6 1.1 transversetemporal 2652 1670 6037 3.282 0.889 0.112 0.064 51 6.4 insula #-------------------------------------------- #@# Tessellate rh Thu Aug 8 19:22:59 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 1 found - 1 modified | TOTAL: 4 pass 2 (xy-): 0 found - 1 modified | TOTAL: 4 pass 1 (yz+): 1 found - 1 modified | TOTAL: 5 pass 2 (yz+): 0 found - 1 modified | TOTAL: 5 pass 1 (yz-): 0 found - 0 modified | TOTAL: 5 pass 1 (xz+): 1 found - 1 modified | TOTAL: 6 pass 2 (xz+): 0 found - 1 modified | TOTAL: 6 pass 1 (xz-): 1 found - 1 modified | TOTAL: 7 pass 2 (xz-): 0 found - 1 modified | TOTAL: 7 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 = 9 (out of 216437: 0.004158) 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 50: 1381 vertices, 1487 faces slice 60: 6522 vertices, 6713 faces slice 70: 14552 vertices, 14911 faces slice 80: 24424 vertices, 24790 faces slice 90: 34974 vertices, 35317 faces slice 100: 45064 vertices, 45394 faces slice 110: 56376 vertices, 56740 faces slice 120: 67383 vertices, 67766 faces slice 130: 78824 vertices, 79204 faces slice 140: 89653 vertices, 90034 faces slice 150: 99678 vertices, 99995 faces slice 160: 107250 vertices, 107518 faces slice 170: 114617 vertices, 114868 faces slice 180: 120756 vertices, 120997 faces slice 190: 125574 vertices, 125731 faces slice 200: 128227 vertices, 128278 faces slice 210: 128276 vertices, 128300 faces slice 220: 128276 vertices, 128300 faces slice 230: 128276 vertices, 128300 faces slice 240: 128276 vertices, 128300 faces slice 250: 128276 vertices, 128300 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... 128276 voxel in cpt #1: X=-24 [v=128276,e=384900,f=256600] located at (28.519100, -10.943598, 38.935242) For the whole surface: X=-24 [v=128276,e=384900,f=256600] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Thu Aug 8 19:23:07 CEST 2013 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 19:23:11 CEST 2013 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts avg radius = 44.3 mm, total surface area = 66756 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.5 minutes Not saving sulc step 000: RMS=0.103 (target=0.015) step 005: RMS=0.075 (target=0.015) step 010: RMS=0.054 (target=0.015) step 015: RMS=0.045 (target=0.015) step 020: RMS=0.039 (target=0.015) step 025: RMS=0.034 (target=0.015) step 030: RMS=0.031 (target=0.015) step 035: RMS=0.028 (target=0.015) step 040: RMS=0.026 (target=0.015) step 045: RMS=0.024 (target=0.015) step 050: RMS=0.023 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.022 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Thu Aug 8 19:23:43 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 1.01 +- 0.59 (0.00-->7.25) (max @ vno 46638 --> 47748) face area 0.03 +- 0.03 (-0.03-->0.82) scaling brain by 0.318... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.937, avgs=0 005/300: dt: 0.9000, rms radial error=176.678, avgs=0 010/300: dt: 0.9000, rms radial error=176.121, avgs=0 015/300: dt: 0.9000, rms radial error=175.390, avgs=0 020/300: dt: 0.9000, rms radial error=174.559, avgs=0 025/300: dt: 0.9000, rms radial error=173.669, avgs=0 030/300: dt: 0.9000, rms radial error=172.747, avgs=0 035/300: dt: 0.9000, rms radial error=171.808, avgs=0 040/300: dt: 0.9000, rms radial error=170.864, avgs=0 045/300: dt: 0.9000, rms radial error=169.916, avgs=0 050/300: dt: 0.9000, rms radial error=168.969, avgs=0 055/300: dt: 0.9000, rms radial error=168.025, avgs=0 060/300: dt: 0.9000, rms radial error=167.083, avgs=0 065/300: dt: 0.9000, rms radial error=166.146, avgs=0 070/300: dt: 0.9000, rms radial error=165.214, avgs=0 075/300: dt: 0.9000, rms radial error=164.286, avgs=0 080/300: dt: 0.9000, rms radial error=163.362, avgs=0 085/300: dt: 0.9000, rms radial error=162.444, avgs=0 090/300: dt: 0.9000, rms radial error=161.530, avgs=0 095/300: dt: 0.9000, rms radial error=160.622, avgs=0 100/300: dt: 0.9000, rms radial error=159.718, avgs=0 105/300: dt: 0.9000, rms radial error=158.820, avgs=0 110/300: dt: 0.9000, rms radial error=157.926, avgs=0 115/300: dt: 0.9000, rms radial error=157.037, avgs=0 120/300: dt: 0.9000, rms radial error=156.154, avgs=0 125/300: dt: 0.9000, rms radial error=155.275, avgs=0 130/300: dt: 0.9000, rms radial error=154.400, avgs=0 135/300: dt: 0.9000, rms radial error=153.531, avgs=0 140/300: dt: 0.9000, rms radial error=152.666, avgs=0 145/300: dt: 0.9000, rms radial error=151.807, avgs=0 150/300: dt: 0.9000, rms radial error=150.951, avgs=0 155/300: dt: 0.9000, rms radial error=150.101, avgs=0 160/300: dt: 0.9000, rms radial error=149.255, avgs=0 165/300: dt: 0.9000, rms radial error=148.414, avgs=0 170/300: dt: 0.9000, rms radial error=147.578, avgs=0 175/300: dt: 0.9000, rms radial error=146.746, avgs=0 180/300: dt: 0.9000, rms radial error=145.920, avgs=0 185/300: dt: 0.9000, rms radial error=145.097, avgs=0 190/300: dt: 0.9000, rms radial error=144.280, avgs=0 195/300: dt: 0.9000, rms radial error=143.467, avgs=0 200/300: dt: 0.9000, rms radial error=142.658, avgs=0 205/300: dt: 0.9000, rms radial error=141.854, avgs=0 210/300: dt: 0.9000, rms radial error=141.055, avgs=0 215/300: dt: 0.9000, rms radial error=140.259, avgs=0 220/300: dt: 0.9000, rms radial error=139.469, avgs=0 225/300: dt: 0.9000, rms radial error=138.683, avgs=0 230/300: dt: 0.9000, rms radial error=137.901, avgs=0 235/300: dt: 0.9000, rms radial error=137.123, avgs=0 240/300: dt: 0.9000, rms radial error=136.350, avgs=0 245/300: dt: 0.9000, rms radial error=135.581, avgs=0 250/300: dt: 0.9000, rms radial error=134.817, avgs=0 255/300: dt: 0.9000, rms radial error=134.056, avgs=0 260/300: dt: 0.9000, rms radial error=133.300, avgs=0 265/300: dt: 0.9000, rms radial error=132.549, avgs=0 270/300: dt: 0.9000, rms radial error=131.801, avgs=0 275/300: dt: 0.9000, rms radial error=131.057, avgs=0 280/300: dt: 0.9000, rms radial error=130.318, avgs=0 285/300: dt: 0.9000, rms radial error=129.583, avgs=0 290/300: dt: 0.9000, rms radial error=128.852, avgs=0 295/300: dt: 0.9000, rms radial error=128.125, avgs=0 300/300: dt: 0.9000, rms radial error=127.402, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 14934.66 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00015 epoch 2 (K=40.0), pass 1, starting sse = 2467.32 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00011 epoch 3 (K=160.0), pass 1, starting sse = 252.81 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.15/13 = 0.01180 epoch 4 (K=640.0), pass 1, starting sse = 12.93 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.36/27 = 0.01348 final writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.09 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Thu Aug 8 19:29:11 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/sub003/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub003 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=-24 (nv=128276, nf=256600, ne=384900, g=13) 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... 1864 ambiguous faces found in tessellation segmenting defects... 23 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 3 into 2 -merging segment 10 into 9 -merging segment 21 into 20 20 defects to be corrected 0 vertices coincident reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.9022 (-4.9511) -vertex loglikelihood: -6.7965 (-3.3982) -normal dot loglikelihood: -3.6210 (-3.6210) -quad curv loglikelihood: -6.5603 (-3.2802) Total Loglikelihood : -26.8800 CORRECTING DEFECT 0 (vertices=18, convex hull=26) After retessellation of defect 0, euler #=-20 (127094,380724,253610) : difference with theory (-17) = 3 CORRECTING DEFECT 1 (vertices=127, convex hull=118) After retessellation of defect 1, euler #=-19 (127134,380894,253741) : difference with theory (-16) = 3 CORRECTING DEFECT 2 (vertices=97, convex hull=88) After retessellation of defect 2, euler #=-17 (127155,380994,253822) : difference with theory (-15) = 2 CORRECTING DEFECT 3 (vertices=20, convex hull=58) After retessellation of defect 3, euler #=-16 (127168,381054,253870) : difference with theory (-14) = 2 CORRECTING DEFECT 4 (vertices=6, convex hull=27) After retessellation of defect 4, euler #=-15 (127169,381065,253881) : difference with theory (-13) = 2 CORRECTING DEFECT 5 (vertices=26, convex hull=35) After retessellation of defect 5, euler #=-14 (127173,381095,253908) : difference with theory (-12) = 2 CORRECTING DEFECT 6 (vertices=41, convex hull=68) After retessellation of defect 6, euler #=-13 (127191,381175,253971) : difference with theory (-11) = 2 CORRECTING DEFECT 7 (vertices=72, convex hull=73) After retessellation of defect 7, euler #=-12 (127221,381297,254064) : difference with theory (-10) = 2 CORRECTING DEFECT 8 (vertices=32, convex hull=67) After retessellation of defect 8, euler #=-10 (127227,381345,254108) : difference with theory (-9) = 1 CORRECTING DEFECT 9 (vertices=5, convex hull=15) After retessellation of defect 9, euler #=-9 (127228,381352,254115) : difference with theory (-8) = 1 CORRECTING DEFECT 10 (vertices=11, convex hull=29) After retessellation of defect 10, euler #=-8 (127232,381373,254133) : difference with theory (-7) = 1 CORRECTING DEFECT 11 (vertices=39, convex hull=30) After retessellation of defect 11, euler #=-7 (127237,381399,254155) : difference with theory (-6) = 1 CORRECTING DEFECT 12 (vertices=12, convex hull=42) After retessellation of defect 12, euler #=-6 (127238,381415,254171) : difference with theory (-5) = 1 CORRECTING DEFECT 13 (vertices=85, convex hull=99) After retessellation of defect 13, euler #=-5 (127275,381567,254287) : difference with theory (-4) = 1 CORRECTING DEFECT 14 (vertices=203, convex hull=71) After retessellation of defect 14, euler #=-4 (127294,381657,254359) : difference with theory (-3) = 1 CORRECTING DEFECT 15 (vertices=14, convex hull=16) After retessellation of defect 15, euler #=-3 (127296,381666,254367) : difference with theory (-2) = 1 CORRECTING DEFECT 16 (vertices=187, convex hull=185) After retessellation of defect 16, euler #=-2 (127375,381993,254616) : difference with theory (-1) = 1 CORRECTING DEFECT 17 (vertices=50, convex hull=91) After retessellation of defect 17, euler #=-1 (127396,382097,254700) : difference with theory (0) = 1 CORRECTING DEFECT 18 (vertices=78, convex hull=114) After retessellation of defect 18, euler #=1 (127430,382250,254821) : difference with theory (1) = 0 CORRECTING DEFECT 19 (vertices=61, convex hull=87) After retessellation of defect 19, euler #=2 (127449,382341,254894) : 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-->9.06) (max @ vno 41533 --> 51218) 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-->9.06) (max @ vno 41533 --> 51218) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 75 mutations (35.9%), 134 crossovers (64.1%), 39 vertices were eliminated building final representation... 827 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=127449, nf=254894, ne=382341, g=0) writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 12.6 minutes 0 defective edges removing intersecting faces 000: 115 intersecting 001: 4 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 127449 - 382341 + 254894 = 2 --> 0 holes F =2V-4: 254894 = 254898-4 (0) 2E=3F: 764682 = 764682 (0) total defect index = 0 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 15 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Thu Aug 8 19:41:56 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub003 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/sub003/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/wm.mgz... 14678 bright wm thresholded. 302 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.orig... computing class statistics... border white: 229356 voxels (1.37%) border gray 266114 voxels (1.59%) WM (92.0): 92.8 +- 10.5 [70.0 --> 110.0] GM (74.0) : 72.0 +- 13.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 42.7 (was 70) setting MAX_BORDER_WHITE to 115.5 (was 105) setting MIN_BORDER_WHITE to 56.0 (was 85) setting MAX_CSF to 29.3 (was 40) setting MAX_GRAY to 94.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 49.3 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 16.0 (was 40) repositioning cortical surface to gray/white boundary reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.22 (0.02-->3.76) (max @ vno 41533 --> 51218) face area 0.28 +- 0.12 (0.00-->2.00) mean absolute distance = 0.65 +- 0.74 4220 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 = 92.5, mean outside = 66.6 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=70.2, 21 (21) missing vertices, mean dist 0.4 [0.4 (%29.6)->0.8 (%70.4))] %73 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 0.92 +- 0.27 (0.11-->3.96) (max @ vno 96770 --> 127334) face area 0.28 +- 0.13 (0.00-->2.35) mean absolute distance = 0.30 +- 0.46 2092 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=7453672.0, rms=14.48 001: dt: 0.5000, sse=7266450.0, rms=10.620 (0.000%) 002: dt: 0.5000, sse=7384190.5, rms=8.387 (0.000%) 003: dt: 0.5000, sse=7452752.5, rms=6.883 (0.000%) 004: dt: 0.5000, sse=7611918.0, rms=5.946 (0.000%) 005: dt: 0.5000, sse=7699602.0, rms=5.375 (0.000%) 006: dt: 0.5000, sse=7802816.0, rms=5.080 (0.000%) 007: dt: 0.5000, sse=7835676.5, rms=4.899 (0.000%) 008: dt: 0.5000, sse=7859050.0, rms=4.804 (0.000%) 009: dt: 0.5000, sse=7816631.0, rms=4.720 (0.000%) rms = 4.68, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=7805371.0, rms=4.679 (0.000%) 011: dt: 0.2500, sse=5051549.5, rms=3.290 (0.000%) 012: dt: 0.2500, sse=4662302.0, rms=2.825 (0.000%) 013: dt: 0.2500, sse=4407076.0, rms=2.735 (0.000%) 014: dt: 0.2500, sse=4338599.5, rms=2.650 (0.000%) rms = 2.62, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=4240810.5, rms=2.619 (0.000%) 016: dt: 0.1250, sse=3950006.2, rms=2.266 (0.000%) 017: dt: 0.1250, sse=3901774.2, rms=2.215 (0.000%) rms = 2.21, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=3869343.0, rms=2.206 (0.000%) positioning took 2.1 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=75.0, 31 (2) missing vertices, mean dist -0.2 [0.3 (%78.3)->0.2 (%21.7))] %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 (0.10-->3.84) (max @ vno 96770 --> 127334) face area 0.35 +- 0.17 (0.00-->2.85) mean absolute distance = 0.21 +- 0.29 2502 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4856976.5, rms=6.35 019: dt: 0.5000, sse=5106578.0, rms=4.306 (0.000%) rms = 4.80, time step reduction 1 of 3 to 0.250... 020: dt: 0.2500, sse=4610242.0, rms=3.023 (0.000%) 021: dt: 0.2500, sse=4436322.0, rms=2.517 (0.000%) 022: dt: 0.2500, sse=4377291.5, rms=2.127 (0.000%) rms = 2.14, time step reduction 2 of 3 to 0.125... 023: dt: 0.1250, sse=4301798.5, rms=1.991 (0.000%) 024: dt: 0.1250, sse=4192281.2, rms=1.793 (0.000%) rms = 1.76, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=4143849.2, rms=1.761 (0.000%) positioning took 1.0 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 mean border=78.6, 35 (1) missing vertices, mean dist -0.1 [0.2 (%78.2)->0.2 (%21.8))] %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.91 +- 0.25 (0.05-->4.00) (max @ vno 96851 --> 95998) face area 0.34 +- 0.16 (0.00-->2.73) mean absolute distance = 0.15 +- 0.22 2514 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4570445.0, rms=4.64 026: dt: 0.5000, sse=4903614.0, rms=4.524 (0.000%) rms = 4.60, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=4414154.5, rms=2.841 (0.000%) 028: dt: 0.2500, sse=4273651.0, rms=2.455 (0.000%) 029: dt: 0.2500, sse=4337364.0, rms=2.036 (0.000%) rms = 2.14, time step reduction 2 of 3 to 0.125... 030: dt: 0.1250, sse=4262148.5, rms=1.834 (0.000%) 031: dt: 0.1250, sse=4165483.2, rms=1.547 (0.000%) rms = 1.50, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=4131703.0, rms=1.503 (0.000%) positioning took 0.9 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 mean border=79.8, 33 (1) missing vertices, mean dist -0.0 [0.2 (%59.4)->0.2 (%40.6))] %92 local maxima, % 2 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=4160251.8, rms=1.96 rms = 3.14, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=4243662.5, rms=1.257 (0.000%) 034: dt: 0.2500, sse=4395133.0, rms=1.123 (0.000%) rms = 1.13, time step reduction 2 of 3 to 0.125... rms = 1.11, time step reduction 3 of 3 to 0.062... 035: dt: 0.1250, sse=4400362.0, rms=1.106 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 15 non-cortical segments detected only using segment with 2136 vertices erasing segment 1 (vno[0] = 74662) erasing segment 2 (vno[0] = 80162) erasing segment 3 (vno[0] = 81298) erasing segment 4 (vno[0] = 81312) erasing segment 5 (vno[0] = 85521) erasing segment 6 (vno[0] = 88554) erasing segment 7 (vno[0] = 88589) erasing segment 8 (vno[0] = 88598) erasing segment 9 (vno[0] = 88669) erasing segment 10 (vno[0] = 89652) erasing segment 11 (vno[0] = 89754) erasing segment 12 (vno[0] = 98381) erasing segment 13 (vno[0] = 98436) erasing segment 14 (vno[0] = 99160) writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/label/rh.cortex.label... writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.curv writing smoothed area to rh.area writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.area vertex spacing 0.90 +- 0.26 (0.04-->4.00) (max @ vno 95998 --> 96851) face area 0.34 +- 0.16 (0.00-->2.74) refinement took 6.7 minutes #-------------------------------------------- #@# Smooth2 rh Thu Aug 8 19:48:36 CEST 2013 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 19:48:40 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 44.5 mm, total surface area = 78549 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.120 (target=0.015) step 005: RMS=0.082 (target=0.015) step 010: RMS=0.060 (target=0.015) step 015: RMS=0.049 (target=0.015) step 020: RMS=0.040 (target=0.015) step 025: RMS=0.034 (target=0.015) step 030: RMS=0.029 (target=0.015) step 035: RMS=0.024 (target=0.015) step 040: RMS=0.021 (target=0.015) step 045: RMS=0.018 (target=0.015) step 050: RMS=0.017 (target=0.015) step 055: RMS=0.016 (target=0.015) step 060: RMS=0.015 (target=0.015) inflation complete. inflation took 0.6 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 134 vertices thresholded to be in k1 ~ [-0.14 1.18], k2 ~ [-0.10 0.07] total integrated curvature = 0.603*4pi (7.578) --> 0 handles ICI = 1.5, FI = 7.9, variation=142.226 96 vertices thresholded to be in [-0.03 0.01] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 81 vertices thresholded to be in [-0.11 0.22] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.017, std = 0.021 done. #----------------------------------------- #@# Curvature Stats rh Thu Aug 8 19:50:58 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub003 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 [ sub003/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 [ 235 ] Gb_filter = 0 WARN: S lookup min: -0.673576 WARN: S explicit min: 0.000000 vertex = 120 #-------------------------------------------- #@# Sphere rh Thu Aug 8 19:51:03 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 0.292... 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 %20.93 pass 1: epoch 2 of 3 starting distance error %20.88 unfolding complete - removing small folds... starting distance error %20.73 removing remaining folds... final distance error %20.75 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/rh.sphere spherical transformation took 1.01 hours #-------------------------------------------- #@# Surf Reg rh Thu Aug 8 20:51:48 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 = 0.603 curvature mean = 0.029, std = 0.923 curvature mean = 0.020, std = 0.864 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 0.00) sse = 358105.3, tmin=1.0184 d=32.00 min @ (0.00, -8.00, 8.00) sse = 294718.3, tmin=2.0409 d=16.00 min @ (-4.00, 4.00, 0.00) sse = 260841.7, tmin=3.0736 d=8.00 min @ (2.00, -2.00, 2.00) sse = 248670.1, tmin=4.1391 d=4.00 min @ (0.00, 1.00, 0.00) sse = 248486.3, tmin=5.2322 d=2.00 min @ (0.00, -0.50, 0.00) sse = 247984.5, tmin=6.3537 d=1.00 min @ (-0.25, 0.00, -0.25) sse = 247894.1, tmin=7.4741 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 8.61 min curvature mean = 0.022, std = 0.949 curvature mean = 0.011, std = 0.943 curvature mean = 0.020, std = 0.961 curvature mean = 0.005, std = 0.974 curvature mean = 0.019, std = 0.963 curvature mean = 0.001, std = 0.989 2 Reading smoothwm curvature mean = -0.020, std = 0.311 curvature mean = 0.006, std = 0.070 curvature mean = 0.065, std = 0.328 curvature mean = 0.006, std = 0.084 curvature mean = 0.028, std = 0.514 curvature mean = 0.007, std = 0.090 curvature mean = 0.016, std = 0.650 curvature mean = 0.007, std = 0.093 curvature mean = 0.005, std = 0.762 MRISregister() return, current seed 0 writing registered surface to ../surf/rh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white rh Thu Aug 8 21:17:53 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 21:17:55 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 21:17:57 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub003 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... 1189 labels changed using aseg relabeling using gibbs priors... 000: 2829 changed, 127449 examined... 001: 676 changed, 11956 examined... 002: 172 changed, 3793 examined... 003: 75 changed, 1036 examined... 004: 25 changed, 411 examined... 005: 12 changed, 146 examined... 006: 7 changed, 61 examined... 007: 1 changed, 33 examined... 008: 2 changed, 8 examined... 009: 2 changed, 12 examined... 010: 0 changed, 12 examined... 260 labels changed using aseg 000: 92 total segments, 55 labels (419 vertices) changed 001: 41 total segments, 4 labels (10 vertices) changed 002: 37 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 44 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 664 vertices marked for relabeling... 664 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 1 minutes and 0 seconds. #-------------------------------------------- #@# Make Pial Surf rh Thu Aug 8 21:18:58 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub003 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/sub003/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/wm.mgz... 14678 bright wm thresholded. 302 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.orig... computing class statistics... border white: 229356 voxels (1.37%) border gray 266114 voxels (1.59%) WM (92.0): 92.8 +- 10.5 [70.0 --> 110.0] GM (74.0) : 72.0 +- 13.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 42.7 (was 70) setting MAX_BORDER_WHITE to 115.5 (was 105) setting MIN_BORDER_WHITE to 56.0 (was 85) setting MAX_CSF to 29.3 (was 40) setting MAX_GRAY to 94.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 49.3 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 16.0 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=56 mean inside = 92.5, 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/sub003/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.22 (0.02-->3.76) (max @ vno 41533 --> 51218) face area 0.28 +- 0.12 (0.00-->2.00) mean absolute distance = 0.66 +- 0.75 3563 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 4 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown deleting segment 7 with 469 points - only 2.56% unknown removing 2 vertex label from ripped group deleting segment 9 with 13 points - only 0.00% unknown deleting segment 10 with 72 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 11 with 2 points - only 0.00% unknown mean border=70.2, 27 (23) missing vertices, mean dist 0.4 [0.4 (%29.6)->0.8 (%70.4))] %73 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 0.92 +- 0.27 (0.11-->3.65) (max @ vno 103328 --> 127415) face area 0.28 +- 0.13 (0.00-->2.35) mean absolute distance = 0.30 +- 0.47 2173 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=7474115.0, rms=14.45 001: dt: 0.5000, sse=7295226.5, rms=10.605 (0.000%) 002: dt: 0.5000, sse=7421282.5, rms=8.377 (0.000%) 003: dt: 0.5000, sse=7495878.0, rms=6.876 (0.000%) 004: dt: 0.5000, sse=7654546.0, rms=5.941 (0.000%) 005: dt: 0.5000, sse=7742302.0, rms=5.372 (0.000%) 006: dt: 0.5000, sse=7848051.0, rms=5.077 (0.000%) 007: dt: 0.5000, sse=7878429.5, rms=4.896 (0.000%) 008: dt: 0.5000, sse=7900173.0, rms=4.800 (0.000%) 009: dt: 0.5000, sse=7862075.0, rms=4.717 (0.000%) rms = 4.67, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=7849494.0, rms=4.675 (0.000%) 011: dt: 0.2500, sse=5083620.5, rms=3.290 (0.000%) 012: dt: 0.2500, sse=4693034.5, rms=2.826 (0.000%) 013: dt: 0.2500, sse=4436248.0, rms=2.736 (0.000%) 014: dt: 0.2500, sse=4368500.5, rms=2.651 (0.000%) rms = 2.62, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=4270207.0, rms=2.620 (0.000%) 016: dt: 0.1250, sse=3979691.8, rms=2.269 (0.000%) 017: dt: 0.1250, sse=3929857.2, rms=2.219 (0.000%) rms = 2.21, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=3897658.2, rms=2.210 (0.000%) positioning took 2.1 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 2 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown deleting segment 8 with 12 points - only 0.00% unknown deleting segment 10 with 368 points - only 3.26% unknown removing 2 vertex label from ripped group deleting segment 12 with 17 points - only 0.00% unknown deleting segment 13 with 36 points - only 0.00% unknown mean border=74.9, 40 (3) missing vertices, mean dist -0.2 [0.3 (%78.3)->0.2 (%21.7))] %83 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.26 (0.10-->3.81) (max @ vno 96851 --> 95998) face area 0.35 +- 0.17 (0.00-->2.85) mean absolute distance = 0.21 +- 0.29 2583 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4887542.5, rms=6.34 019: dt: 0.5000, sse=5136694.5, rms=4.305 (0.000%) rms = 4.80, time step reduction 1 of 3 to 0.250... 020: dt: 0.2500, sse=4640588.0, rms=3.026 (0.000%) 021: dt: 0.2500, sse=4466881.5, rms=2.522 (0.000%) 022: dt: 0.2500, sse=4408578.5, rms=2.134 (0.000%) rms = 2.15, time step reduction 2 of 3 to 0.125... 023: dt: 0.1250, sse=4332940.5, rms=1.999 (0.000%) 024: dt: 0.1250, sse=4223839.0, rms=1.802 (0.000%) rms = 1.77, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=4175795.8, rms=1.771 (0.000%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 2 with 4 points - only 0.00% unknown deleting segment 3 with 13 points - only 0.00% unknown deleting segment 4 with 395 points - only 3.04% unknown deleting segment 5 with 24 points - only 0.00% unknown deleting segment 6 with 41 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 8 with 1 points - only 0.00% unknown mean border=78.6, 43 (2) missing vertices, mean dist -0.1 [0.2 (%78.1)->0.2 (%21.9))] %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.91 +- 0.25 (0.10-->4.00) (max @ vno 96851 --> 95998) face area 0.34 +- 0.16 (0.00-->2.62) mean absolute distance = 0.15 +- 0.23 2617 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4603211.5, rms=4.64 026: dt: 0.5000, sse=4940450.5, rms=4.521 (0.000%) rms = 4.59, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=4449440.0, rms=2.843 (0.000%) 028: dt: 0.2500, sse=4309617.0, rms=2.459 (0.000%) 029: dt: 0.2500, sse=4373618.5, rms=2.041 (0.000%) rms = 2.15, time step reduction 2 of 3 to 0.125... 030: dt: 0.1250, sse=4298228.5, rms=1.840 (0.000%) 031: dt: 0.1250, sse=4201184.0, rms=1.556 (0.000%) rms = 1.51, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=4166465.8, rms=1.512 (0.000%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 1 with 4 points - only 0.00% unknown deleting segment 2 with 14 points - only 0.00% unknown deleting segment 3 with 391 points - only 3.07% unknown deleting segment 5 with 24 points - only 0.00% unknown deleting segment 6 with 41 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 8 with 1 points - only 0.00% unknown mean border=79.8, 44 (2) missing vertices, mean dist -0.0 [0.2 (%59.4)->0.2 (%40.6))] %92 local maxima, % 2 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4196169.0, rms=1.96 rms = 3.14, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=4281657.5, rms=1.266 (0.000%) 034: dt: 0.2500, sse=4438970.0, rms=1.132 (0.000%) rms = 1.14, time step reduction 2 of 3 to 0.125... rms = 1.12, time step reduction 3 of 3 to 0.062... 035: dt: 0.1250, sse=4444141.5, rms=1.116 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... deleting segment 5 with 28 points - only 42.86% unknown smoothing surface for 5 iterations... mean border=45.8, 58 (58) missing vertices, mean dist 1.7 [0.1 (%0.0)->2.2 (%100.0))] %13 local maxima, %60 large gradients and %22 min vals, 1243 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=29410856.0, rms=33.14 001: dt: 0.5000, sse=20951966.0, rms=27.374 (0.000%) 002: dt: 0.5000, sse=15182975.0, rms=22.647 (0.000%) 003: dt: 0.5000, sse=11382203.0, rms=18.876 (0.000%) 004: dt: 0.5000, sse=9104711.0, rms=15.903 (0.000%) 005: dt: 0.5000, sse=7896732.5, rms=13.591 (0.000%) 006: dt: 0.5000, sse=7130652.5, rms=11.796 (0.000%) 007: dt: 0.5000, sse=6644975.0, rms=10.244 (0.000%) 008: dt: 0.5000, sse=6305187.0, rms=8.853 (0.000%) 009: dt: 0.5000, sse=6140117.5, rms=7.620 (0.000%) 010: dt: 0.5000, sse=6092370.5, rms=6.639 (0.000%) 011: dt: 0.5000, sse=6168638.0, rms=5.882 (0.000%) 012: dt: 0.5000, sse=6215960.0, rms=5.294 (0.000%) 013: dt: 0.5000, sse=6383658.0, rms=4.901 (0.000%) 014: dt: 0.5000, sse=6485862.0, rms=4.643 (0.000%) 015: dt: 0.5000, sse=6604944.0, rms=4.485 (0.000%) 016: dt: 0.5000, sse=6663277.0, rms=4.375 (0.000%) 017: dt: 0.5000, sse=6727157.0, rms=4.286 (0.000%) 018: dt: 0.5000, sse=6710818.5, rms=4.227 (0.000%) rms = 4.19, time step reduction 1 of 3 to 0.250... 019: dt: 0.5000, sse=6764291.0, rms=4.186 (0.000%) 020: dt: 0.2500, sse=4741081.5, rms=3.422 (0.000%) 021: dt: 0.2500, sse=4537224.5, rms=3.206 (0.000%) rms = 3.18, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=4421609.5, rms=3.180 (0.000%) 023: dt: 0.1250, sse=4215136.0, rms=3.047 (0.000%) rms = 3.03, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=4182074.2, rms=3.031 (0.000%) positioning took 2.7 minutes mean border=43.5, 703 (4) missing vertices, mean dist 0.2 [0.2 (%49.8)->0.5 (%50.2))] %31 local maxima, %46 large gradients and %18 min vals, 303 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=4780434.5, rms=4.91 025: dt: 0.5000, sse=5050464.0, rms=4.208 (0.000%) rms = 4.30, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=4701266.5, rms=3.589 (0.000%) 027: dt: 0.2500, sse=4782997.0, rms=3.318 (0.000%) 028: dt: 0.2500, sse=4728798.0, rms=3.201 (0.000%) 029: dt: 0.2500, sse=4782871.0, rms=3.148 (0.000%) rms = 3.12, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=4783259.5, rms=3.119 (0.000%) 031: dt: 0.1250, sse=4631725.0, rms=2.979 (0.000%) rms = 2.95, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=4627159.5, rms=2.953 (0.000%) positioning took 1.0 minutes mean border=40.8, 847 (1) missing vertices, mean dist 0.1 [0.2 (%36.9)->0.4 (%63.1))] %54 local maxima, %22 large gradients and %18 min vals, 406 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=4955397.0, rms=4.60 033: dt: 0.5000, sse=5138247.0, rms=4.200 (0.000%) rms = 4.32, time step reduction 1 of 3 to 0.250... 034: dt: 0.2500, sse=4822962.0, rms=3.363 (0.000%) 035: dt: 0.2500, sse=5020140.0, rms=3.046 (0.000%) 036: dt: 0.2500, sse=4977545.5, rms=2.977 (0.000%) rms = 2.94, time step reduction 2 of 3 to 0.125... 037: dt: 0.2500, sse=5045740.5, rms=2.945 (0.000%) 038: dt: 0.1250, sse=4856544.5, rms=2.782 (0.000%) rms = 2.76, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=4844206.5, rms=2.760 (0.000%) positioning took 0.9 minutes mean border=39.3, 1701 (0) missing vertices, mean dist 0.1 [0.2 (%44.3)->0.3 (%55.7))] %59 local maxima, %17 large gradients and %18 min vals, 326 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/sub003/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=4916712.5, rms=3.24 rms = 4.16, time step reduction 1 of 3 to 0.250... 040: dt: 0.2500, sse=4767624.0, rms=2.852 (0.000%) 041: dt: 0.2500, sse=4913418.0, rms=2.766 (0.000%) rms = 2.72, time step reduction 2 of 3 to 0.125... 042: dt: 0.2500, sse=4985712.5, rms=2.720 (0.000%) 043: dt: 0.1250, sse=4899711.5, rms=2.591 (0.000%) rms = 2.57, time step reduction 3 of 3 to 0.062... 044: dt: 0.1250, sse=4897560.0, rms=2.572 (0.000%) positioning took 0.6 minutes writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.area.pial vertex spacing 1.03 +- 0.43 (0.08-->6.12) (max @ vno 83570 --> 83557) face area 0.42 +- 0.31 (0.00-->4.77) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 127449 vertices processed 25000 of 127449 vertices processed 50000 of 127449 vertices processed 75000 of 127449 vertices processed 100000 of 127449 vertices processed 125000 of 127449 vertices processed 0 of 127449 vertices processed 25000 of 127449 vertices processed 50000 of 127449 vertices processed 75000 of 127449 vertices processed 100000 of 127449 vertices processed 125000 of 127449 vertices processed thickness calculation complete, 398:665 truncations. 29618 vertices at 0 distance 83784 vertices at 1 distance 83372 vertices at 2 distance 34131 vertices at 3 distance 8808 vertices at 4 distance 2301 vertices at 5 distance 629 vertices at 6 distance 239 vertices at 7 distance 113 vertices at 8 distance 60 vertices at 9 distance 36 vertices at 10 distance 54 vertices at 11 distance 49 vertices at 12 distance 35 vertices at 13 distance 29 vertices at 14 distance 20 vertices at 15 distance 10 vertices at 16 distance 13 vertices at 17 distance 15 vertices at 18 distance 12 vertices at 19 distance 6 vertices at 20 distance writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.thickness positioning took 13.1 minutes #-------------------------------------------- #@# Surf Volume rh Thu Aug 8 21:32:06 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 21:32:07 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts pctsurfcon --s sub003 --rh-only Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts/pctsurfcon.log Thu Aug 8 21:32:07 CEST 2013 setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts /opt/freesurfer/5.3.0/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux snake5 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/sub003/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/tmp.pctsurfcon.7121/rh.wm.mgh --regheader sub003 --cortex srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/mri/orig.mgz as target reference. Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/label/rh.cortex.label Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 = 99332 Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/label/rh.cortex.label Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/tmp.pctsurfcon.7121/rh.wm.mgh Dim: 127449 1 1 mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/tmp.pctsurfcon.7121/rh.gm.mgh --projfrac 0.3 --regheader sub003 --cortex srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/mri/orig.mgz as target reference. Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/label/rh.cortex.label Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.white Done reading source surface Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 = 113777 Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/label/rh.cortex.label Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/tmp.pctsurfcon.7121/rh.gm.mgh Dim: 127449 1 1 mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/tmp.pctsurfcon.7121/rh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/tmp.pctsurfcon.7121/rh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/surf/rh.w-g.pct.mgh mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.w-g.pct.mgh --annot sub003 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/surf/rh.w-g.pct.mgh --annot sub003 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/stats/rh.w-g.pct.stats --snr sysname Linux hostname snake5 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/sub003/surf/rh.w-g.pct.mgh Vertex Area is 0.676693 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 2000 unknown 0 0.000 1 2001 bankssts 1331 939.548 2 2002 caudalanteriorcingulate 1036 681.329 3 2003 caudalmiddlefrontal 2272 1530.222 4 2004 corpuscallosum 0 0.000 5 2005 cuneus 2425 1607.873 6 2006 entorhinal 448 309.408 7 2007 fusiform 4200 2877.131 8 2008 inferiorparietal 8944 6206.092 9 2009 inferiortemporal 4353 3039.652 10 2010 isthmuscingulate 1357 906.082 11 2011 lateraloccipital 6960 4565.230 12 2012 lateralorbitofrontal 3815 2582.281 13 2013 lingual 4639 3196.726 14 2014 medialorbitofrontal 2210 1547.753 15 2015 middletemporal 4284 3010.956 16 2016 parahippocampal 1040 706.010 17 2017 paracentral 2081 1378.797 18 2018 parsopercularis 1724 1200.683 19 2019 parsorbitalis 1150 769.446 20 2020 parstriangularis 2205 1527.890 21 2021 pericalcarine 2356 1639.314 22 2022 postcentral 5115 3459.484 23 2023 posteriorcingulate 1711 1180.435 24 2024 precentral 6288 4162.129 25 2025 precuneus 6136 4148.881 26 2026 rostralanteriorcingulate 835 551.488 27 2027 rostralmiddlefrontal 8318 5772.868 28 2028 superiorfrontal 9184 6405.801 29 2029 superiorparietal 8255 5460.278 30 2030 superiortemporal 4572 3057.099 31 2031 supramarginal 5507 3739.162 32 2032 frontalpole 425 298.237 33 2033 temporalpole 516 368.095 34 2034 transversetemporal 499 305.694 35 2035 insula 2873 1900.918 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats rh Thu Aug 8 21:32:23 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 sub003 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 1331 940 2400 2.449 0.420 0.131 0.038 14 1.8 bankssts 1036 681 1939 2.412 0.724 0.139 0.037 16 1.5 caudalanteriorcingulate 2272 1530 4074 2.426 0.456 0.129 0.040 28 3.5 caudalmiddlefrontal 2425 1608 3740 2.054 0.396 0.186 0.087 63 7.7 cuneus 448 309 1494 3.344 0.801 0.170 0.094 14 1.5 entorhinal 4200 2877 8339 2.467 0.592 0.159 0.063 114 10.4 fusiform 8944 6206 17221 2.375 0.517 0.150 0.071 751 31.8 inferiorparietal 4353 3040 8827 2.356 0.700 0.156 0.074 114 15.0 inferiortemporal 1357 906 2654 2.455 0.780 0.165 0.140 157 7.3 isthmuscingulate 6960 4565 10937 2.113 0.493 0.160 0.086 181 16.1 lateraloccipital 3815 2582 7673 2.731 0.622 0.164 0.082 129 11.9 lateralorbitofrontal 4639 3197 7320 2.095 0.505 0.171 0.073 112 12.7 lingual 2210 1548 4498 2.532 0.657 0.175 0.098 97 8.4 medialorbitofrontal 4284 3011 10626 2.807 0.632 0.159 0.060 97 10.4 middletemporal 1040 706 2286 2.752 0.711 0.130 0.045 13 1.7 parahippocampal 2081 1379 3486 2.265 0.523 0.120 0.029 21 2.6 paracentral 1724 1201 3368 2.544 0.359 0.127 0.041 24 2.8 parsopercularis 1150 769 2765 2.809 0.578 0.172 0.081 27 2.9 parsorbitalis 2205 1528 4561 2.509 0.479 0.154 0.049 46 4.2 parstriangularis 2356 1639 3093 1.931 0.427 0.148 0.056 35 5.1 pericalcarine 5115 3459 7961 2.033 0.594 0.125 0.041 68 8.3 postcentral 1711 1180 3380 2.486 0.785 0.168 0.159 46 4.4 posteriorcingulate 6288 4162 12009 2.551 0.510 0.128 0.035 72 9.5 precentral 6136 4149 10373 2.296 0.465 0.153 0.059 133 14.7 precuneus 835 551 2074 3.163 0.698 0.165 0.061 19 2.0 rostralanteriorcingulate 8318 5773 16683 2.421 0.520 0.166 0.082 213 33.1 rostralmiddlefrontal 9184 6406 20741 2.760 0.553 0.146 0.047 148 17.8 superiorfrontal 8255 5460 12778 2.057 0.427 0.141 0.046 147 15.7 superiorparietal 4572 3057 10532 2.911 0.637 0.127 0.041 55 8.0 superiortemporal 5507 3739 9971 2.381 0.553 0.146 0.048 101 10.2 supramarginal 425 298 1170 2.836 0.445 0.231 0.102 19 2.0 frontalpole 516 368 1814 3.595 0.767 0.164 0.071 10 1.4 temporalpole 499 306 867 2.505 0.325 0.143 0.044 7 0.9 transversetemporal 2873 1901 6519 3.099 0.831 0.138 0.083 79 7.5 insula #----------------------------------------- #@# Cortical Parc 2 rh Thu Aug 8 21:32:43 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub003 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... 69 labels changed using aseg relabeling using gibbs priors... 000: 9200 changed, 127449 examined... 001: 2120 changed, 35285 examined... 002: 673 changed, 10882 examined... 003: 309 changed, 3770 examined... 004: 131 changed, 1729 examined... 005: 71 changed, 775 examined... 006: 35 changed, 381 examined... 007: 11 changed, 188 examined... 008: 8 changed, 73 examined... 009: 3 changed, 46 examined... 010: 6 changed, 22 examined... 011: 3 changed, 25 examined... 012: 3 changed, 18 examined... 013: 1 changed, 15 examined... 014: 2 changed, 7 examined... 015: 2 changed, 10 examined... 016: 0 changed, 8 examined... 3 labels changed using aseg 000: 242 total segments, 156 labels (1981 vertices) changed 001: 94 total segments, 9 labels (94 vertices) changed 002: 85 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 106 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 436 vertices marked for relabeling... 436 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 1 minutes and 11 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Thu Aug 8 21:33:53 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 sub003 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 1208 839 2507 2.489 0.608 0.188 0.076 35 3.9 G_and_S_frontomargin 1233 846 2450 2.320 0.501 0.156 0.054 25 2.5 G_and_S_occipital_inf 1194 783 2204 2.305 0.491 0.135 0.037 17 1.9 G_and_S_paracentral 1151 801 2560 2.851 0.435 0.145 0.045 18 2.1 G_and_S_subcentral 1030 741 2207 2.396 0.482 0.191 0.209 42 14.1 G_and_S_transv_frontopol 2337 1626 5089 2.845 0.557 0.149 0.062 44 5.0 G_and_S_cingul-Ant 1415 978 2974 2.779 0.504 0.139 0.040 21 2.2 G_and_S_cingul-Mid-Ant 1195 839 2405 2.572 0.522 0.160 0.055 23 2.7 G_and_S_cingul-Mid-Post 537 360 1597 3.282 0.522 0.218 0.419 29 2.0 G_cingul-Post-dorsal 241 152 570 2.737 0.658 0.178 0.096 9 0.9 G_cingul-Post-ventral 2168 1493 3394 1.976 0.442 0.196 0.094 61 7.4 G_cuneus 1089 777 2814 2.738 0.335 0.156 0.059 27 2.7 G_front_inf-Opercular 348 236 938 2.818 0.342 0.182 0.072 11 1.0 G_front_inf-Orbital 1021 708 2539 2.658 0.422 0.179 0.067 30 2.6 G_front_inf-Triangul 3591 2499 9253 2.702 0.464 0.178 0.074 109 10.6 G_front_middle 6449 4485 16580 2.867 0.555 0.159 0.055 129 14.4 G_front_sup 490 314 1188 3.226 0.891 0.140 0.133 27 2.0 G_Ins_lg_and_S_cent_ins 578 389 2124 3.885 0.721 0.207 0.178 32 3.1 G_insular_short 2283 1519 4824 2.471 0.474 0.183 0.075 67 7.0 G_occipital_middle 1641 1088 2807 2.149 0.377 0.162 0.056 33 3.8 G_occipital_sup 1575 1001 3598 2.745 0.451 0.168 0.073 55 4.6 G_oc-temp_lat-fusifor 2931 1998 5095 2.133 0.545 0.188 0.091 92 9.6 G_oc-temp_med-Lingual 806 534 2481 3.200 0.763 0.148 0.062 12 1.8 G_oc-temp_med-Parahip 2576 1739 6702 2.891 0.657 0.198 0.122 132 11.2 G_orbital 3399 2387 8059 2.575 0.522 0.180 0.124 681 22.7 G_pariet_inf-Angular 2648 1800 5949 2.600 0.530 0.163 0.057 66 5.8 G_pariet_inf-Supramar 2450 1635 4572 2.223 0.441 0.165 0.064 64 6.3 G_parietal_sup 2007 1343 3613 2.156 0.450 0.144 0.057 38 4.4 G_postcentral 2373 1556 5957 2.858 0.431 0.138 0.039 34 3.9 G_precentral 2790 1868 5820 2.431 0.473 0.173 0.073 77 8.1 G_precuneus 604 414 1361 2.509 0.689 0.207 0.142 57 4.2 G_rectus 112 71 261 3.226 0.436 0.133 0.126 2 0.4 G_subcallosal 358 211 679 2.503 0.271 0.145 0.046 6 0.7 G_temp_sup-G_T_transv 1564 1061 4895 3.243 0.599 0.161 0.063 32 4.3 G_temp_sup-Lateral 448 309 1335 3.609 0.712 0.123 0.042 4 0.6 G_temp_sup-Plan_polar 779 547 1596 2.621 0.328 0.106 0.025 6 0.8 G_temp_sup-Plan_tempo 2345 1642 5469 2.487 0.697 0.181 0.110 92 12.2 G_temporal_inf 2535 1838 7398 2.942 0.619 0.178 0.076 74 7.5 G_temporal_middle 375 268 663 2.360 0.510 0.118 0.024 3 0.3 Lat_Fis-ant-Horizont 183 135 279 2.239 0.384 0.093 0.017 1 0.1 Lat_Fis-ant-Vertical 1376 922 1946 2.394 0.381 0.128 0.039 15 2.1 Lat_Fis-post 3600 2322 5228 2.043 0.527 0.169 0.067 76 9.7 Pole_occipital 1792 1291 5628 3.103 0.720 0.181 0.080 60 5.8 Pole_temporal 2505 1725 3465 2.073 0.494 0.145 0.055 41 5.3 S_calcarine 2487 1652 2847 1.899 0.585 0.099 0.023 12 2.6 S_central 1333 889 1794 2.026 0.448 0.106 0.026 9 1.4 S_cingul-Marginalis 733 480 1270 2.853 0.535 0.122 0.032 6 1.0 S_circular_insula_ant 1220 768 2079 2.824 0.659 0.079 0.020 5 1.0 S_circular_insula_inf 1197 813 1812 2.553 0.437 0.113 0.029 8 1.5 S_circular_insula_sup 854 598 1486 2.190 0.632 0.119 0.034 11 1.2 S_collat_transv_ant 447 300 544 2.132 0.390 0.174 0.061 7 1.1 S_collat_transv_post 2335 1562 3406 2.225 0.392 0.123 0.035 24 3.1 S_front_inf 1791 1251 2728 2.184 0.439 0.149 0.060 32 4.5 S_front_middle 1857 1298 2822 2.289 0.385 0.119 0.030 15 2.4 S_front_sup 807 540 966 2.133 0.388 0.124 0.037 8 1.2 S_interm_prim-Jensen 3351 2188 4186 1.953 0.374 0.114 0.028 33 3.9 S_intrapariet_and_P_trans 1232 856 1530 1.881 0.322 0.130 0.035 13 1.8 S_oc_middle_and_Lunatus 1684 1154 2226 1.980 0.358 0.130 0.034 17 2.3 S_oc_sup_and_transversal 667 465 938 2.030 0.332 0.142 0.337 56 1.0 S_occipital_ant 1042 713 1274 1.838 0.431 0.140 0.050 18 1.7 S_oc-temp_lat 2239 1571 3425 2.338 0.516 0.124 0.031 19 2.9 S_oc-temp_med_and_Lingual 523 353 776 2.332 0.416 0.147 0.049 7 1.0 S_orbital_lateral 526 386 759 2.270 0.541 0.125 0.027 4 0.6 S_orbital_med-olfact 1628 1097 2830 2.641 0.605 0.142 0.050 26 3.3 S_orbital-H_Shaped 2292 1538 3128 2.160 0.351 0.139 0.051 46 5.3 S_parieto_occipital 1652 1041 1714 1.952 0.711 0.140 0.096 148 6.5 S_pericallosal 2408 1598 2760 1.787 0.368 0.121 0.033 24 3.1 S_postcentral 1538 1021 2212 2.369 0.311 0.112 0.029 13 1.8 S_precentral-inf-part 951 640 1285 2.261 0.397 0.126 0.034 8 1.3 S_precentral-sup-part 384 265 682 2.419 0.898 0.163 0.069 7 1.1 S_suborbital 1357 939 2007 2.172 0.368 0.134 0.039 17 2.1 S_subparietal 1100 741 1529 2.281 0.575 0.115 0.026 8 1.4 S_temporal_inf 5859 4049 9697 2.364 0.482 0.123 0.034 57 8.3 S_temporal_sup 240 175 389 3.015 0.546 0.146 0.030 2 0.3 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 rh Thu Aug 8 21:34:14 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub003 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... 1033 labels changed using aseg relabeling using gibbs priors... 000: 2644 changed, 127449 examined... 001: 574 changed, 11321 examined... 002: 154 changed, 3158 examined... 003: 51 changed, 922 examined... 004: 24 changed, 291 examined... 005: 20 changed, 135 examined... 006: 14 changed, 117 examined... 007: 10 changed, 65 examined... 008: 10 changed, 50 examined... 009: 15 changed, 55 examined... 010: 8 changed, 63 examined... 011: 6 changed, 39 examined... 012: 4 changed, 26 examined... 013: 1 changed, 18 examined... 014: 0 changed, 5 examined... 190 labels changed using aseg 000: 65 total segments, 32 labels (362 vertices) changed 001: 34 total segments, 1 labels (2 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 35 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 495 vertices marked for relabeling... 495 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas40.annot... classification took 1 minutes and 1 seconds. #----------------------------------------- #@# Parcellation Stats 3 rh Thu Aug 8 21:35:15 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 sub003 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 1107 725 2134 2.471 0.726 0.143 0.039 18 1.8 caudalanteriorcingulate 2332 1575 4244 2.441 0.459 0.132 0.039 30 3.8 caudalmiddlefrontal 2976 1982 4491 2.042 0.377 0.176 0.078 68 8.6 cuneus 428 306 1465 3.342 0.778 0.166 0.094 13 1.3 entorhinal 3603 2448 6762 2.433 0.577 0.149 0.055 81 7.6 fusiform 8563 5937 16372 2.367 0.525 0.150 0.096 792 31.3 inferiorparietal 4839 3379 10123 2.397 0.710 0.161 0.078 142 17.6 inferiortemporal 1364 912 2664 2.452 0.779 0.165 0.139 157 7.3 isthmuscingulate 7323 4810 11504 2.108 0.494 0.159 0.057 141 17.0 lateraloccipital 4171 2858 9086 2.764 0.629 0.178 0.089 159 14.3 lateralorbitofrontal 4664 3213 7370 2.096 0.503 0.170 0.072 111 12.6 lingual 1722 1192 3468 2.499 0.699 0.183 0.109 85 7.3 medialorbitofrontal 5384 3764 12480 2.718 0.619 0.154 0.057 112 11.9 middletemporal 1026 700 2256 2.754 0.714 0.130 0.045 13 1.6 parahippocampal 2160 1438 3663 2.272 0.521 0.119 0.028 22 2.7 paracentral 1766 1217 3404 2.549 0.363 0.130 0.042 26 2.9 parsopercularis 1260 843 2822 2.719 0.524 0.156 0.068 23 2.8 parsorbitalis 2387 1658 4815 2.450 0.470 0.152 0.049 50 4.6 parstriangularis 2339 1630 3068 1.930 0.422 0.149 0.057 35 5.2 pericalcarine 5697 3830 8875 2.051 0.595 0.128 0.042 78 9.5 postcentral 1750 1206 3411 2.478 0.775 0.168 0.157 47 4.5 posteriorcingulate 6104 4046 11851 2.564 0.512 0.127 0.035 70 9.2 precentral 6157 4168 10586 2.305 0.463 0.153 0.059 135 14.7 precuneus 986 651 2349 3.120 0.676 0.161 0.062 21 2.3 rostralanteriorcingulate 5340 3670 10751 2.447 0.527 0.164 0.068 129 14.4 rostralmiddlefrontal 12079 8448 26332 2.666 0.565 0.150 0.062 226 36.0 superiorfrontal 6947 4591 10815 2.061 0.433 0.143 0.047 127 13.2 superiorparietal 6152 4215 14531 2.895 0.680 0.135 0.046 86 11.3 superiortemporal 5035 3398 9103 2.393 0.545 0.144 0.046 90 9.2 supramarginal 498 304 858 2.500 0.323 0.142 0.044 7 0.9 transversetemporal 2905 1918 6518 3.093 0.822 0.137 0.080 77 7.6 insula #-------------------------------------------- #@# Refine Pial Surfs w/ T2/FLAIR Thu Aug 8 21:35:33 CEST 2013 bbregister --s sub003 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/T2raw.lta --init-fsl --T2 Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/T2raw.dat.log Thu Aug 8 21:35:33 CEST 2013 setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts /opt/freesurfer/5.3.0/bin/bbregister --s sub003 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/T2raw.lta --init-fsl --T2 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ Linux snake5 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/sub003/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/template.nii mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/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/sub003/mri/orig/T2raw.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.99822, -0.0508489, 0.0311494) j_ras = (-0.0512259, 0.998622, -0.0114243) k_ras = (0.0305256, 0.0129996, 0.999449) writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/template.nii... fslregister --s sub003 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/fslregister --dof 6 --fsvol brainmask.mgz Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/reg.init.dat.fslregister.log Thu Aug 8 21:35:38 CEST 2013 --s sub003 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/fslregister --dof 6 --fsvol brainmask.mgz $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ snake5 Linux snake5 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/sub003/scripts mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/fslregister/refvol.fslregister.nii mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/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/sub003/mri/brainmask.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 4.65661e-09, -1.86265e-09) j_ras = (1.86265e-09, 2.79397e-09, -1) k_ras = (-8.3528e-09, 1, -9.31323e-10) writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/fslregister/refvol.fslregister.nii... -------------------------------------- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/fslregister/movvol.fslregister.nii --frame 0 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/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/sub003/mri/transforms/tmp.bbregister.7576/template.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.99822, -0.0508489, 0.0311494) j_ras = (-0.0512259, 0.998622, -0.0114243) k_ras = (0.0305256, 0.0129996, 0.999449) keeping frame 0 writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/fslregister/movvol.fslregister.nii... Mov determinant is -0.311093 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/fslregister/movvol.fslregister.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/fslregister/reg0.7616.dat --regheader --fslregout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/reg.init.dat.fsl.mat0 --s sub003 --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/sub003/mri/transforms/tmp.bbregister.7576/fslregister/movvol.fslregister.nii reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/fslregister/reg0.7616.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/sub003/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/sub003/mri/transforms/tmp.bbregister.7576/fslregister/movvol.fslregister.nii Tmov: -------------------- -0.700 0.000 0.000 95.894; 0.000 0.000 0.667 -128.000; 0.000 -0.667 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 0.998 0.051 -0.031 -0.000; 0.031 0.013 0.999 0.000; 0.051 -0.999 0.011 0.000; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 0.998 0.051 -0.031 -0.000; 0.031 0.013 0.999 0.000; 0.051 -0.999 0.011 0.000; 0.000 0.000 0.000 1.000; Determinant 1 subject = sub003 RegMat --------------------------- 0.998 0.051 -0.031 -0.000; 0.031 0.013 0.999 0.000; 0.051 -0.999 0.011 0.000; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -0.311093, ref det = -1 Thu Aug 8 21:35:47 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/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/sub003/mri/transforms/tmp.bbregister.7576/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/reg.init.dat.fsl.mat0 Thu Aug 8 21:40:24 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/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/sub003/mri/transforms/tmp.bbregister.7576/reg.init.dat.fsl.mat -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/fslregister/fslmat0.trans.mat -schedule /opt/freesurfer/5.3.0/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s sub003 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/reg.init.dat --fslreg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/reg.init.dat.fsl.mat --noedit tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl ---- FSL registration matrix -------- 0.998 0.051 -0.033 30.148; -0.033 -0.006 -0.999 260.830; -0.051 0.999 -0.004 5.216; 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/sub003/mri/transforms/tmp.bbregister.7576/template.nii reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/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/sub003/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/sub003/mri/transforms/tmp.bbregister.7576/template.nii Tmov: -------------------- -0.700 0.000 0.000 95.894; 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 = -0.311093, ref det = -1 ---- Input registration matrix (computed) -------- 0.998 0.051 -0.033 0.150; 0.033 -0.004 0.999 1.026; 0.051 -0.999 -0.006 -0.374; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 0.998 0.051 -0.033 0.150; 0.033 -0.004 0.999 1.026; 0.051 -0.999 -0.006 -0.374; 0.000 0.000 0.000 1.000; Determinant 1 subject = sub003 RegMat --------------------------- 0.998 0.051 -0.033 0.150; 0.033 -0.004 0.999 1.026; 0.051 -0.999 -0.006 -0.374; 0.000 0.000 0.000 1.000; Started at Thu Aug 8 21:35:38 CEST 2013 Ended at Thu Aug 8 21:47:22 CEST 2013 fslregister Done To check results, run: tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/reg.init.dat --surf orig mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/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/sub003/scripts mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/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 snake5 machine x86_64 user fkaule movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/template.nii regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/reg.init.dat subject sub003 dof 6 outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/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 1376059224 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.998 0.051 -0.033 0.150; 0.033 -0.004 0.999 1.026; 0.051 -0.999 -0.006 -0.374; 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 0.986576 1 -25.0 -25.0 25.0 0.983247 2 -25.0 25.0 -25.0 1.007463 3 -25.0 25.0 25.0 1.044004 4 25.0 -25.0 -25.0 1.036276 5 25.0 -25.0 25.0 1.040975 6 25.0 25.0 -25.0 1.013110 7 25.0 25.0 25.0 1.034280 REL: 8 0.467633 8.145932 1.018241 rel = 0.459255 Initial costs ---------------- Number of surface hits 2411 WM Intensity 67.2941 +/- 13.0305 Ctx Intensity 80.6970 +/- 18.9236 Pct Contrast 17.0092 +/- 23.6115 Cost 0.4676 RelCost 0.4593 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9902 0.9902 0.0 3 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 -4.0000 0.9857 0.9857 0.0 4 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.0000 0.9724 0.9724 0.0 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.8944 0.8944 0.0 21 -4.0000 -4.0000 -4.0000 4.0000 0.0000 -4.0000 0.8910 0.8910 0.0 39 -4.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.8550 0.8550 0.0 102 -4.0000 0.0000 -4.0000 4.0000 0.0000 -4.0000 0.7523 0.7523 0.0 120 -4.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.7029 0.7029 0.0 346 0.0000 0.0000 -4.0000 4.0000 0.0000 0.0000 0.5969 0.5969 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.4676 0.4676 0.0 Brute Force -------------------------- Min cost was 0.467633 Number of iterations 729 Search time 2.660000 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 11 0.019 0.000 0.000 0.000 0.000 0.000 0.4675131428 12 0.025 0.000 0.000 0.000 0.000 0.000 0.4674809813 13 0.036 0.000 0.000 0.000 0.000 0.000 0.4674561091 14 0.035 0.000 0.000 0.000 0.000 0.000 0.4674542680 15 0.033 0.000 0.000 0.000 0.000 0.000 0.4674534706 21 0.033 -1.618 0.000 0.000 0.000 0.000 0.4053029209 22 0.033 -1.331 0.000 0.000 0.000 0.000 0.3953529608 24 0.033 -0.823 0.000 0.000 0.000 0.000 0.3941499489 26 0.033 -1.058 0.000 0.000 0.000 0.000 0.3931425806 30 0.033 -1.069 0.000 0.000 0.000 0.000 0.3930436256 31 0.033 -1.073 0.000 0.000 0.000 0.000 0.3930194551 33 0.033 -1.075 0.000 0.000 0.000 0.000 0.3930114613 35 0.033 -1.076 0.000 0.000 0.000 0.000 0.3930113406 37 0.033 -1.076 1.000 0.000 0.000 0.000 0.2670190595 40 0.033 -1.076 1.618 0.000 0.000 0.000 0.2610119080 42 0.033 -1.076 1.345 0.000 0.000 0.000 0.2531224902 43 0.033 -1.076 1.352 0.000 0.000 0.000 0.2528559976 44 0.033 -1.076 1.423 0.000 0.000 0.000 0.2525060895 46 0.033 -1.076 1.394 0.000 0.000 0.000 0.2522172948 56 0.033 -1.076 1.394 0.382 0.000 0.000 0.2357375372 57 0.033 -1.076 1.394 0.336 0.000 0.000 0.2341538128 58 0.033 -1.076 1.394 0.284 0.000 0.000 0.2328213725 60 0.033 -1.076 1.394 0.243 0.000 0.000 0.2326645563 61 0.033 -1.076 1.394 0.255 0.000 0.000 0.2323784493 62 0.033 -1.076 1.394 0.261 0.000 0.000 0.2323630026 63 0.033 -1.076 1.394 0.260 0.000 0.000 0.2323600515 71 0.033 -1.076 1.394 0.260 0.046 0.000 0.2321164858 73 0.033 -1.076 1.394 0.260 0.039 0.000 0.2320909955 76 0.033 -1.076 1.394 0.260 0.038 0.000 0.2320871752 84 0.033 -1.076 1.394 0.260 0.038 -0.255 0.2288025977 85 0.033 -1.076 1.394 0.260 0.038 -0.226 0.2286803540 86 0.033 -1.076 1.394 0.260 0.038 -0.213 0.2286702508 88 0.033 -1.076 1.394 0.260 0.038 -0.131 0.2283463921 90 0.033 -1.076 1.394 0.260 0.038 -0.163 0.2283462069 91 0.033 -1.076 1.394 0.260 0.038 -0.147 0.2282822144 92 0.033 -1.076 1.394 0.260 0.038 -0.146 0.2282811641 93 0.033 -1.076 1.394 0.260 0.038 -0.144 0.2282744338 107 0.015 -1.076 1.394 0.260 0.038 -0.144 0.2280284491 108 0.016 -1.076 1.394 0.260 0.038 -0.144 0.2280243147 109 0.017 -1.076 1.394 0.260 0.038 -0.144 0.2280232614 117 0.017 -0.694 1.394 0.260 0.038 -0.144 0.2050094028 119 0.017 -0.730 1.394 0.260 0.038 -0.144 0.2047954990 120 0.017 -0.727 1.394 0.260 0.038 -0.144 0.2047353044 121 0.017 -0.715 1.394 0.260 0.038 -0.144 0.2046219815 123 0.017 -0.716 1.394 0.260 0.038 -0.144 0.2046207957 132 0.017 -0.716 1.155 0.260 0.038 -0.144 0.2001881173 133 0.017 -0.716 1.177 0.260 0.038 -0.144 0.2000120596 134 0.017 -0.716 1.199 0.260 0.038 -0.144 0.1999988262 135 0.017 -0.716 1.189 0.260 0.038 -0.144 0.1999617517 143 0.017 -0.716 1.189 0.642 0.038 -0.144 0.1836026879 144 0.017 -0.716 1.189 0.571 0.038 -0.144 0.1826210799 145 0.017 -0.716 1.189 0.568 0.038 -0.144 0.1825894435 146 0.017 -0.716 1.189 0.450 0.038 -0.144 0.1817752020 148 0.017 -0.716 1.189 0.495 0.038 -0.144 0.1817290746 149 0.017 -0.716 1.189 0.478 0.038 -0.144 0.1816493584 151 0.017 -0.716 1.189 0.481 0.038 -0.144 0.1816467865 153 0.017 -0.716 1.189 0.480 0.038 -0.144 0.1816464746 162 0.017 -0.716 1.189 0.480 0.066 -0.144 0.1816448783 163 0.017 -0.716 1.189 0.480 0.052 -0.144 0.1816346052 165 0.017 -0.716 1.189 0.480 0.047 -0.144 0.1816325051 166 0.017 -0.716 1.189 0.480 0.049 -0.144 0.1816295590 175 0.017 -0.716 1.189 0.480 0.049 -0.258 0.1812482422 176 0.017 -0.716 1.189 0.480 0.049 -0.211 0.1808579081 177 0.017 -0.716 1.189 0.480 0.049 -0.210 0.1808553024 178 0.017 -0.716 1.189 0.480 0.049 -0.200 0.1808404900 180 0.017 -0.716 1.189 0.480 0.049 -0.198 0.1808404695 181 0.017 -0.716 1.189 0.480 0.049 -0.197 0.1808401222 182 0.017 -0.716 1.189 0.480 0.049 -0.190 0.1808362096 186 0.017 -0.716 1.189 0.480 0.049 -0.191 0.1808355393 187 0.001 -0.357 0.985 0.700 0.061 -0.238 0.1722128821 194 0.003 -0.391 1.004 0.679 0.060 -0.233 0.1718116350 196 0.003 -0.383 1.000 0.684 0.060 -0.234 0.1717705390 206 -0.109 -0.383 1.000 0.684 0.060 -0.234 0.1709969041 221 -0.109 -0.383 1.000 0.684 0.060 -0.211 0.1702856055 222 -0.109 -0.383 1.000 0.684 0.060 -0.139 0.1688426579 225 -0.109 -0.383 1.000 0.684 0.060 -0.133 0.1687721311 226 -0.109 -0.383 1.000 0.684 0.060 -0.123 0.1687097224 236 -0.109 -0.383 0.737 0.684 0.060 -0.123 0.1573634780 239 -0.109 -0.383 0.734 0.684 0.060 -0.123 0.1573594472 249 -0.109 -0.383 0.734 0.860 0.060 -0.123 0.1490910204 251 -0.109 -0.383 0.734 0.840 0.060 -0.123 0.1490776266 253 -0.109 -0.383 0.734 0.849 0.060 -0.123 0.1490195326 254 -0.109 -0.383 0.734 0.848 0.060 -0.123 0.1490181004 263 -0.109 -0.383 0.734 0.848 0.033 -0.123 0.1486217550 264 -0.109 -0.383 0.734 0.848 0.024 -0.123 0.1486186896 265 -0.109 -0.383 0.734 0.848 0.028 -0.123 0.1486107347 267 -0.109 -0.383 0.734 0.848 0.029 -0.123 0.1486103046 275 -0.106 -0.453 0.774 0.806 0.027 -0.114 0.1481831611 289 -0.064 -0.453 0.774 0.806 0.027 -0.114 0.1481664275 290 -0.084 -0.453 0.774 0.806 0.027 -0.114 0.1480575169 301 -0.084 -0.453 0.774 0.806 0.027 -0.153 0.1477852686 302 -0.084 -0.453 0.774 0.806 0.027 -0.145 0.1477742506 303 -0.084 -0.453 0.774 0.806 0.027 -0.147 0.1477712237 304 -0.084 -0.453 0.774 0.806 0.027 -0.148 0.1477709643 312 -0.084 -0.453 0.586 0.806 0.027 -0.148 0.1405570570 314 -0.084 -0.453 0.592 0.806 0.027 -0.148 0.1405391024 315 -0.084 -0.453 0.599 0.806 0.027 -0.148 0.1405186979 320 -0.084 -0.453 0.598 0.806 0.027 -0.148 0.1405164413 322 -0.084 -0.453 0.597 0.806 0.027 -0.148 0.1405156542 329 -0.084 -0.453 0.597 0.938 0.027 -0.148 0.1372059596 332 -0.084 -0.453 0.597 0.953 0.027 -0.148 0.1372033284 333 -0.084 -0.453 0.597 0.945 0.027 -0.148 0.1371705124 336 -0.084 -0.453 0.597 0.944 0.027 -0.148 0.1371703173 346 -0.084 -0.453 0.597 0.944 0.055 -0.148 0.1363851946 347 -0.084 -0.453 0.597 0.944 0.062 -0.148 0.1363652232 348 -0.084 -0.453 0.597 0.944 0.061 -0.148 0.1363640171 356 -0.080 -0.533 0.643 0.895 0.058 -0.137 0.1347476246 357 -0.080 -0.533 0.643 0.895 0.058 -0.137 0.1347362534 358 -0.081 -0.516 0.633 0.906 0.059 -0.139 0.1346805271 360 -0.081 -0.522 0.637 0.902 0.059 -0.139 0.1346635519 361 -0.081 -0.521 0.636 0.902 0.059 -0.139 0.1346634868 363 -0.055 -0.590 0.498 0.999 0.091 -0.163 0.1306214095 370 -0.058 -0.581 0.516 0.987 0.087 -0.160 0.1305123469 371 -0.058 -0.581 0.516 0.987 0.087 -0.160 0.1305109192 372 -0.058 -0.583 0.512 0.989 0.087 -0.161 0.1305000663 374 -0.057 -0.583 0.511 0.990 0.088 -0.161 0.1304990943 384 -0.094 -0.583 0.511 0.990 0.088 -0.161 0.1303908439 385 -0.085 -0.583 0.511 0.990 0.088 -0.161 0.1303653723 386 -0.082 -0.583 0.511 0.990 0.088 -0.161 0.1303601038 388 -0.080 -0.583 0.511 0.990 0.088 -0.161 0.1303589313 389 -0.081 -0.583 0.511 0.990 0.088 -0.161 0.1303587661 397 -0.081 -0.583 0.511 0.990 0.088 -0.189 0.1302129309 398 -0.081 -0.583 0.511 0.990 0.088 -0.188 0.1302124721 399 -0.081 -0.583 0.511 0.990 0.088 -0.187 0.1302111751 409 -0.080 -0.590 0.515 0.986 0.087 -0.186 0.1300492376 411 -0.079 -0.617 0.530 0.970 0.087 -0.182 0.1298577719 412 -0.079 -0.610 0.526 0.974 0.087 -0.183 0.1298386809 415 -0.080 -0.607 0.524 0.976 0.087 -0.184 0.1298362414 416 -0.079 -0.607 0.525 0.975 0.087 -0.184 0.1298354730 417 -0.079 -0.608 0.525 0.975 0.087 -0.184 0.1298353065 425 -0.079 -0.608 0.525 0.948 0.087 -0.184 0.1294352107 427 -0.079 -0.608 0.525 0.951 0.087 -0.184 0.1294232040 430 -0.079 -0.608 0.525 0.952 0.087 -0.184 0.1294205362 438 -0.079 -0.608 0.525 0.952 0.063 -0.184 0.1290539386 439 -0.079 -0.608 0.525 0.952 0.054 -0.184 0.1289878445 440 -0.079 -0.608 0.525 0.952 0.037 -0.184 0.1289744422 441 -0.079 -0.608 0.525 0.952 0.044 -0.184 0.1289537906 442 -0.079 -0.608 0.525 0.952 0.045 -0.184 0.1289526990 449 -0.070 -0.634 0.472 0.989 0.057 -0.193 0.1289489272 450 -0.075 -0.621 0.498 0.970 0.051 -0.188 0.1284704510 452 -0.074 -0.621 0.498 0.971 0.051 -0.188 0.1284703164 465 -0.077 -0.621 0.498 0.971 0.051 -0.188 0.1284661953 466 -0.078 -0.621 0.498 0.971 0.051 -0.188 0.1284656516 475 -0.078 -0.621 0.498 0.971 0.051 -0.203 0.1283631135 476 -0.078 -0.621 0.498 0.971 0.051 -0.208 0.1283598454 480 -0.078 -0.621 0.498 0.971 0.051 -0.212 0.1283589260 481 -0.078 -0.621 0.498 0.971 0.051 -0.211 0.1283587004 482 -0.078 -0.621 0.498 0.971 0.051 -0.210 0.1283582946 491 -0.078 -0.619 0.497 0.972 0.051 -0.210 0.1283545845 492 -0.078 -0.619 0.497 0.972 0.051 -0.210 0.1283536503 502 -0.078 -0.619 0.497 0.963 0.051 -0.210 0.1282398325 505 -0.078 -0.619 0.497 0.958 0.051 -0.210 0.1282233966 516 -0.078 -0.619 0.497 0.958 0.043 -0.210 0.1281501180 518 -0.078 -0.619 0.497 0.958 0.039 -0.210 0.1281414781 519 -0.078 -0.619 0.497 0.958 0.038 -0.210 0.1281369757 520 -0.078 -0.619 0.497 0.958 0.034 -0.210 0.1281365397 522 -0.078 -0.619 0.497 0.958 0.035 -0.210 0.1281323452 530 -0.076 -0.624 0.486 0.966 0.038 -0.212 0.1280227170 531 -0.076 -0.626 0.482 0.968 0.039 -0.213 0.1280155175 532 -0.076 -0.626 0.483 0.968 0.039 -0.213 0.1280147430 533 -0.076 -0.626 0.484 0.968 0.038 -0.212 0.1280140471 537 -0.076 -0.626 0.483 0.968 0.038 -0.212 0.1280139666 548 -0.079 -0.626 0.483 0.968 0.038 -0.212 0.1280115701 549 -0.078 -0.626 0.483 0.968 0.038 -0.212 0.1280099384 550 -0.077 -0.626 0.483 0.968 0.038 -0.212 0.1280093167 559 -0.077 -0.626 0.483 0.968 0.038 -0.211 0.1280093009 569 -0.077 -0.619 0.480 0.972 0.039 -0.211 0.1279943915 571 -0.077 -0.620 0.480 0.971 0.039 -0.211 0.1279942885 581 -0.077 -0.620 0.480 0.966 0.039 -0.211 0.1279674828 582 -0.077 -0.620 0.480 0.967 0.039 -0.211 0.1279674502 592 -0.077 -0.620 0.480 0.967 0.038 -0.211 0.1279614525 593 -0.077 -0.620 0.480 0.967 0.034 -0.211 0.1279500962 595 -0.077 -0.620 0.480 0.967 0.033 -0.211 0.1279493426 603 -0.076 -0.623 0.473 0.972 0.034 -0.213 0.1279196292 605 -0.076 -0.623 0.474 0.971 0.034 -0.212 0.1279175584 606 -0.076 -0.623 0.474 0.970 0.034 -0.212 0.1279173460 610 -0.077 -0.620 0.465 0.973 0.029 -0.212 0.1278815070 617 -0.077 -0.620 0.466 0.973 0.030 -0.212 0.1278798259 623 -0.077 -0.620 0.466 0.973 0.030 -0.212 0.1278796220 636 -0.079 -0.620 0.466 0.973 0.030 -0.212 0.1278790959 638 -0.078 -0.620 0.466 0.973 0.030 -0.212 0.1278787608 646 -0.078 -0.620 0.466 0.973 0.030 -0.207 0.1278720852 657 -0.078 -0.621 0.467 0.972 0.030 -0.207 0.1278699518 680 -0.078 -0.621 0.467 0.972 0.031 -0.207 0.1278692602 688 -0.078 -0.620 0.466 0.973 0.031 -0.206 0.1278674976 694 -0.078 -0.620 0.466 0.973 0.031 -0.206 0.1278673395 Powell done niters = 7 Computing relative cost 0 -25.0 -25.0 -25.0 0.968830 1 -25.0 -25.0 25.0 1.022399 2 -25.0 25.0 -25.0 1.010376 3 -25.0 25.0 25.0 1.027400 4 25.0 -25.0 -25.0 1.051955 5 25.0 -25.0 25.0 1.018903 6 25.0 25.0 -25.0 1.019751 7 25.0 25.0 25.0 1.046903 REL: 8 0.127867 8.166515 1.020814 rel = 0.12526 Number of iterations 7 Min cost was 0.127867 Number of FunctionCalls 696 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 2.516000 sec Parameters at optimum (transmm) -0.07808 -0.62048 0.46589 Parameters at optimum (rotdeg) 0.97265 0.03053 -0.20650 Final costs ---------------- Number of surface hits 2411 WM Intensity 65.1866 +/- 11.3468 Ctx Intensity 79.9800 +/- 13.1774 Pct Contrast 20.3501 +/- 13.6723 Cost 0.1279 RelCost 0.4593 Reg at min cost was 0.998 0.051 -0.029 0.075; 0.029 0.013 1.000 0.411; 0.051 -0.999 0.011 0.109; 0.000 0.000 0.000 1.000; Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/bbr.pass1.dat, type = 14 Original Reg 0.998 0.051 -0.033 0.150; 0.033 -0.004 0.999 1.026; 0.051 -0.999 -0.006 -0.374; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.000 0.000 -0.004 0.075; 0.004 -0.017 -0.000 0.615; -0.000 -0.000 -0.017 -0.483; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 1.517281 Computing change in rh position Surface RMS Diff (mm) 1.555715 2.412896 mri_segreg done mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/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/sub003/scripts mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname snake5 machine x86_64 user fkaule movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/template.nii regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/bbr.pass1.dat subject sub003 dof 6 outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 1376293067 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.998 0.051 -0.029 0.075; 0.029 0.013 1.000 0.411; 0.051 -0.999 0.011 0.109; 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 1.012628 1 -25.0 -25.0 25.0 1.010317 2 -25.0 25.0 -25.0 1.013781 3 -25.0 25.0 25.0 1.026243 4 25.0 -25.0 -25.0 1.035852 5 25.0 -25.0 25.0 1.031547 6 25.0 25.0 -25.0 1.028321 7 25.0 25.0 25.0 1.031602 REL: 8 0.133532 8.190292 1.023786 rel = 0.130429 Initial costs ---------------- Number of surface hits 240423 WM Intensity 64.9359 +/- 11.1877 Ctx Intensity 79.7729 +/- 12.9062 Pct Contrast 20.4782 +/- 13.8817 Cost 0.1335 RelCost 0.1304 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1323 0.1323 0.0 9 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 -0.1000 0.1284 0.1284 0.0 21 -0.1000 -0.1000 -0.1000 0.1000 0.0000 -0.1000 0.1280 0.1280 0.0 99 -0.1000 0.0000 -0.1000 0.1000 -0.1000 -0.1000 0.1271 0.1271 0.0 Brute Force -------------------------- Min cost was 0.127104 Number of iterations 729 Search time 2.645000 sec Parameters at best (transmm, rotdeg) -0.100 0.000 -0.100 0.100 -0.100 -0.100 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 -0.1 1 0 2 -0.1 3 0.1 4 -0.1 5 -0.1 7 -0.042 0.000 -0.100 0.100 -0.100 -0.100 0.1307987305 8 -0.030 0.000 -0.100 0.100 -0.100 -0.100 0.1307770674 9 -0.029 0.000 -0.100 0.100 -0.100 -0.100 0.1307765224 10 -0.027 0.000 -0.100 0.100 -0.100 -0.100 0.1307761312 11 -0.026 0.000 -0.100 0.100 -0.100 -0.100 0.1307759415 14 -0.025 0.000 -0.100 0.100 -0.100 -0.100 0.1307759274 22 -0.025 0.075 -0.100 0.100 -0.100 -0.100 0.1300930603 23 -0.025 0.070 -0.100 0.100 -0.100 -0.100 0.1300780848 24 -0.025 0.063 -0.100 0.100 -0.100 -0.100 0.1300697692 25 -0.025 0.064 -0.100 0.100 -0.100 -0.100 0.1300695851 33 -0.025 0.064 -0.191 0.100 -0.100 -0.100 0.1288568820 34 -0.025 0.064 -0.201 0.100 -0.100 -0.100 0.1288540792 35 -0.025 0.064 -0.197 0.100 -0.100 -0.100 0.1288519871 44 -0.025 0.064 -0.197 0.160 -0.100 -0.100 0.1282988494 45 -0.025 0.064 -0.197 0.152 -0.100 -0.100 0.1282747727 46 -0.025 0.064 -0.197 0.149 -0.100 -0.100 0.1282723798 47 -0.025 0.064 -0.197 0.148 -0.100 -0.100 0.1282721881 55 -0.025 0.064 -0.197 0.148 -0.038 -0.100 0.1277993515 57 -0.025 0.064 -0.197 0.148 -0.042 -0.100 0.1277987802 59 -0.025 0.064 -0.197 0.148 -0.040 -0.100 0.1277982290 67 -0.025 0.064 -0.197 0.148 -0.040 -0.034 0.1275387248 68 -0.025 0.064 -0.197 0.148 -0.040 -0.051 0.1274734378 69 -0.025 0.064 -0.197 0.148 -0.040 -0.055 0.1274698060 70 -0.025 0.064 -0.197 0.148 -0.040 -0.056 0.1274694474 80 -0.012 0.064 -0.197 0.148 -0.040 -0.056 0.1274541905 82 -0.014 0.064 -0.197 0.148 -0.040 -0.056 0.1274531144 91 -0.014 0.087 -0.197 0.148 -0.040 -0.056 0.1274297659 92 -0.014 0.079 -0.197 0.148 -0.040 -0.056 0.1274225386 93 -0.014 0.080 -0.197 0.148 -0.040 -0.056 0.1274222259 94 -0.014 0.081 -0.197 0.148 -0.040 -0.056 0.1274222185 103 -0.014 0.081 -0.231 0.148 -0.040 -0.056 0.1272575196 113 -0.014 0.081 -0.231 0.185 -0.040 -0.056 0.1271104372 114 -0.014 0.081 -0.231 0.176 -0.040 -0.056 0.1270789392 115 -0.014 0.081 -0.231 0.174 -0.040 -0.056 0.1270777567 124 -0.014 0.081 -0.231 0.174 -0.038 -0.056 0.1270736522 126 -0.014 0.081 -0.231 0.174 -0.036 -0.056 0.1270728425 135 -0.014 0.081 -0.231 0.174 -0.036 -0.045 0.1270528137 138 -0.004 0.099 -0.266 0.200 -0.031 -0.033 0.1269067538 145 -0.003 0.101 -0.270 0.204 -0.031 -0.032 0.1269045210 146 -0.003 0.101 -0.271 0.204 -0.031 -0.032 0.1269043616 148 -0.002 0.102 -0.272 0.205 -0.030 -0.031 0.1269041834 171 -0.002 0.106 -0.272 0.205 -0.030 -0.031 0.1269024512 173 -0.002 0.107 -0.272 0.205 -0.030 -0.031 0.1269023307 182 -0.002 0.107 -0.279 0.205 -0.030 -0.031 0.1268956505 183 -0.002 0.107 -0.280 0.205 -0.030 -0.031 0.1268956258 200 -0.002 0.107 -0.280 0.205 -0.039 -0.031 0.1268924465 201 -0.002 0.107 -0.280 0.205 -0.036 -0.031 0.1268905816 210 -0.004 0.104 -0.274 0.201 -0.037 -0.033 0.1268869372 216 -0.004 0.104 -0.273 0.200 -0.037 -0.033 0.1268869206 231 -0.002 0.104 -0.273 0.200 -0.037 -0.033 0.1268861339 247 -0.002 0.104 -0.275 0.200 -0.037 -0.033 0.1268854410 248 -0.002 0.104 -0.276 0.200 -0.037 -0.033 0.1268853028 274 -0.002 0.103 -0.275 0.200 -0.037 -0.034 0.1268852642 275 -0.002 0.103 -0.275 0.200 -0.037 -0.034 0.1268852221 331 -0.002 0.103 -0.275 0.200 -0.037 -0.034 0.1268851593 344 -0.003 0.103 -0.275 0.199 -0.037 -0.034 0.1268851469 350 -0.003 0.103 -0.275 0.199 -0.037 -0.034 0.1268851387 355 -0.003 0.103 -0.275 0.199 -0.037 -0.034 0.1268851321 356 -0.003 0.103 -0.275 0.199 -0.037 -0.034 0.1268851311 402 -0.003 0.103 -0.275 0.199 -0.036 -0.034 0.1268851099 404 -0.003 0.103 -0.275 0.199 -0.036 -0.034 0.1268850452 413 -0.003 0.103 -0.275 0.199 -0.036 -0.034 0.1268850423 414 -0.003 0.103 -0.275 0.199 -0.036 -0.034 0.1268850316 418 -0.003 0.103 -0.275 0.199 -0.036 -0.034 0.1268850312 474 -0.003 0.103 -0.275 0.199 -0.036 -0.034 0.1268850109 530 -0.003 0.103 -0.275 0.199 -0.036 -0.034 0.1268850104 531 -0.003 0.103 -0.275 0.199 -0.036 -0.034 0.1268850093 Powell done niters = 7 Computing relative cost 0 -25.0 -25.0 -25.0 1.012531 1 -25.0 -25.0 25.0 1.011168 2 -25.0 25.0 -25.0 1.013170 3 -25.0 25.0 25.0 1.026299 4 25.0 -25.0 -25.0 1.036595 5 25.0 -25.0 25.0 1.032410 6 25.0 25.0 -25.0 1.028059 7 25.0 25.0 25.0 1.032638 REL: 8 0.126885 8.192870 1.024109 rel = 0.123898 Number of iterations 7 Min cost was 0.126885 Number of FunctionCalls 534 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 62.002000 sec Parameters at optimum (transmm) -0.00261 0.10287 -0.27464 Parameters at optimum (rotdeg) 0.19921 -0.03618 -0.03386 Final costs ---------------- Number of surface hits 240423 WM Intensity 64.9338 +/- 11.2144 Ctx Intensity 79.7146 +/- 12.8242 Pct Contrast 20.4261 +/- 13.7529 Cost 0.1269 RelCost 0.1304 Reg at min cost was 0.998 0.052 -0.029 0.073; 0.028 0.016 0.999 0.513; 0.052 -0.999 0.015 -0.164; 0.000 0.000 0.000 1.000; Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/T2raw.dat, type = 14 Original Reg 0.998 0.051 -0.029 0.075; 0.029 0.013 1.000 0.411; 0.051 -0.999 0.011 0.109; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg 0.000 -0.001 -0.001 0.002; 0.001 -0.003 0.000 -0.102; -0.001 -0.000 -0.003 0.273; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.217297 Computing change in rh position Surface RMS Diff (mm) 0.199717 0.396121 mri_segreg done tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/T2raw.dat --noedit --ltaout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/mri/orig/T2raw.mgz reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/T2raw.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- 0.998 0.052 -0.029 0.073; 0.028 0.016 0.999 0.513; 0.052 -0.999 0.015 -0.164; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- INFO: loading target /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/mri/orig/T2raw.mgz Tmov: -------------------- -0.700 0.000 0.000 95.894; 0.000 0.000 0.667 -128.000; 0.000 -0.667 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 0.998 0.052 -0.029 0.073; 0.028 0.016 0.999 0.513; 0.052 -0.999 0.015 -0.164; 0.000 0.000 0.000 1.000; Determinant 1 subject = sub003 RegMat --------------------------- 0.998 0.052 -0.029 0.073; 0.028 0.016 0.999 0.513; 0.052 -0.999 0.015 -0.164; 0.000 0.000 0.000 1.000; transformed matrix: 1.000 -0.001 -0.002 -0.083; 0.001 1.000 0.003 -0.144; 0.002 -0.003 1.000 -0.430; 0.000 0.000 0.000 1.000; transformed matrix: 0.699 0.035 -0.019 29.283; -0.020 0.010 -0.666 257.303; -0.036 0.666 0.011 2.863; 0.000 0.000 0.000 1.000; Cleaning up Started at Thu Aug 8 21:35:33 CEST 2013 Ended at Thu Aug 8 21:49:20 CEST 2013 BBR-Run-Time-Sec 827 bbregister Done To check results, run: tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/T2raw.dat --surf mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/T2.mgz mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/mri/orig/T2raw.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.99822, -0.0508489, 0.0311494) j_ras = (-0.0512259, 0.998622, -0.0114243) k_ras = (0.0305256, 0.0129996, 0.999449) INFO: Reading transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/T2raw.lta... Reading transform with LTAreadEx() reading extra input line subject sub003 reading extra input line fscale 0.150000 reading template info from volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/orig.mgz... INFO: Applying transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/T2raw.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 1.000 -0.001 -0.002 -0.083; 0.001 1.000 0.003 -0.144; 0.002 -0.003 1.000 -0.430; 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/sub003/mri/T2.mgz... mri_normalize -aseg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/aseg.mgz -sigma 4 -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.white identity.nofile -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.white identity.nofile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/T2.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/mri/T2.mgz... computing distance transform computing distance transform computing nonmaximum suppression 7298 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/sub003/mri/T2.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.woT2.pial `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.woT2.pial' mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub003 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/sub003/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/wm.mgz... 15061 bright wm thresholded. 302 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.orig... computing class statistics... border white: 229356 voxels (1.37%) border gray 266114 voxels (1.59%) WM (92.0): 92.8 +- 10.6 [70.0 --> 110.0] GM (74.0) : 72.1 +- 13.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 43.9 (was 70) setting MAX_BORDER_WHITE to 115.6 (was 105) setting MIN_BORDER_WHITE to 57.0 (was 85) setting MAX_CSF to 30.8 (was 40) setting MAX_GRAY to 94.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 50.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 17.6 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=57 mean inside = 92.8, mean outside = 67.3 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/sub003/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.90 +- 0.26 (0.03-->4.88) (max @ vno 61076 --> 128641) face area 0.33 +- 0.16 (0.00-->2.76) averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 82 points - only 0.00% unknown deleting segment 1 with 6 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown deleting segment 5 with 5 points - only 0.00% unknown deleting segment 6 with 10 points - only 0.00% unknown deleting segment 8 with 7 points - only 0.00% unknown deleting segment 9 with 14 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 10 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 11 with 2 points - only 0.00% unknown deleting segment 12 with 21 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 13 with 2 points - only 0.00% unknown deleting segment 14 with 7 points - only 0.00% unknown deleting segment 15 with 7 points - only 0.00% unknown tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.90 +- 0.25 (0.03-->4.88) (max @ vno 128641 --> 61076) face area 0.33 +- 0.16 (0.00-->2.76) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4386998.0, rms=0.00 rms = 2.14, time step reduction 1 of 3 to 0.250... rms = 0.53, time step reduction 2 of 3 to 0.125... rms = 0.07, time step reduction 3 of 3 to 0.062... 001: dt: 0.1250, sse=4386998.0, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 82 points - only 0.00% unknown deleting segment 1 with 6 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown deleting segment 4 with 10 points - only 0.00% unknown deleting segment 5 with 7 points - only 0.00% unknown deleting segment 6 with 14 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 7 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown deleting segment 9 with 21 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 10 with 2 points - only 0.00% unknown deleting segment 11 with 7 points - only 0.00% unknown deleting segment 12 with 7 points - only 0.00% unknown tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.03-->4.88) (max @ vno 128641 --> 61076) face area 0.33 +- 0.16 (0.00-->2.76) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4386998.0, rms=0.00 rms = 2.14, time step reduction 1 of 3 to 0.250... rms = 0.53, time step reduction 2 of 3 to 0.125... rms = 0.07, time step reduction 3 of 3 to 0.062... 002: dt: 0.1250, sse=4386998.0, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 82 points - only 0.00% unknown deleting segment 1 with 6 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown deleting segment 4 with 10 points - only 0.00% unknown deleting segment 5 with 7 points - only 0.00% unknown deleting segment 6 with 14 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 7 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown deleting segment 9 with 21 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 10 with 2 points - only 0.00% unknown deleting segment 11 with 7 points - only 0.00% unknown deleting segment 12 with 7 points - only 0.00% unknown tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.25 (0.03-->4.88) (max @ vno 128641 --> 61076) face area 0.33 +- 0.16 (0.00-->2.76) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4386998.0, rms=0.00 rms = 2.14, time step reduction 1 of 3 to 0.250... rms = 0.53, time step reduction 2 of 3 to 0.125... rms = 0.07, time step reduction 3 of 3 to 0.062... 003: dt: 0.1250, sse=4386998.0, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 82 points - only 0.00% unknown deleting segment 1 with 6 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown deleting segment 4 with 10 points - only 0.00% unknown deleting segment 5 with 7 points - only 0.00% unknown deleting segment 6 with 14 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 7 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown deleting segment 9 with 21 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 10 with 2 points - only 0.00% unknown deleting segment 11 with 7 points - only 0.00% unknown deleting segment 12 with 7 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=4386998.0, rms=0.00 rms = 2.14, time step reduction 1 of 3 to 0.250... rms = 0.53, time step reduction 2 of 3 to 0.125... rms = 0.07, time step reduction 3 of 3 to 0.062... 004: dt: 0.1250, sse=4386998.0, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... 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 [90.30 215.70], gm=153.00+-20.90, and vertices in regions > 142.5 32807 surface locations found to contain inconsistent values (2310 in, 30497 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=477812.7, rms=0.22 001: dt: 0.5000, sse=449355.5, rms=0.218 (0.000%) 002: dt: 0.5000, sse=432252.6, rms=0.205 (0.000%) 003: dt: 0.5000, sse=421216.9, rms=0.196 (0.000%) 004: dt: 0.5000, sse=412802.5, rms=0.187 (0.000%) 005: dt: 0.5000, sse=406688.1, rms=0.180 (0.000%) 006: dt: 0.5000, sse=402262.4, rms=0.174 (0.000%) 007: dt: 0.5000, sse=398851.8, rms=0.168 (0.000%) 008: dt: 0.5000, sse=396372.0, rms=0.164 (0.000%) 009: dt: 0.5000, sse=394094.9, rms=0.160 (0.000%) 010: dt: 0.5000, sse=392314.0, rms=0.157 (0.000%) 011: dt: 0.5000, sse=390760.2, rms=0.154 (0.000%) 012: dt: 0.5000, sse=389267.7, rms=0.151 (0.000%) 013: dt: 0.5000, sse=387842.2, rms=0.150 (0.000%) 014: dt: 0.5000, sse=386798.8, rms=0.148 (0.000%) 015: dt: 0.5000, sse=385312.5, rms=0.147 (0.000%) 016: dt: 0.5000, sse=384137.6, rms=0.146 (0.000%) 017: dt: 0.5000, sse=383178.7, rms=0.145 (0.000%) 018: dt: 0.5000, sse=381952.5, rms=0.144 (0.000%) 019: dt: 0.5000, sse=380576.8, rms=0.144 (0.000%) 020: dt: 0.5000, sse=379593.5, rms=0.143 (0.000%) 021: dt: 0.5000, sse=378391.9, rms=0.143 (0.000%) 022: dt: 0.5000, sse=377621.7, rms=0.143 (0.000%) 023: dt: 0.5000, sse=376297.8, rms=0.143 (0.000%) 024: dt: 0.5000, sse=375100.4, rms=0.143 (0.000%) 025: dt: 0.5000, sse=374101.6, rms=0.144 (0.000%) 026: dt: 0.5000, sse=373066.3, rms=0.144 (0.000%) 027: dt: 0.5000, sse=372314.5, rms=0.144 (0.000%) 028: dt: 0.5000, sse=371561.9, rms=0.144 (0.000%) 029: dt: 0.5000, sse=370353.1, rms=0.145 (0.000%) 030: dt: 0.5000, sse=369477.8, rms=0.145 (0.000%) positioning took 3.5 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [89.50 218.50], gm=154.00+-21.50, and vertices in regions > 143.2 27943 surface locations found to contain inconsistent values (809 in, 27134 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=38378.2, rms=0.12 031: dt: 0.5000, sse=38135.8, rms=0.120 (0.000%) 032: dt: 0.5000, sse=39009.0, rms=0.110 (0.000%) 033: dt: 0.5000, sse=40026.8, rms=0.102 (0.000%) 034: dt: 0.5000, sse=40911.9, rms=0.097 (0.000%) 035: dt: 0.5000, sse=41665.4, rms=0.091 (0.000%) 036: dt: 0.5000, sse=42385.6, rms=0.087 (0.000%) 037: dt: 0.5000, sse=43072.5, rms=0.082 (0.000%) 038: dt: 0.5000, sse=43729.2, rms=0.078 (0.000%) 039: dt: 0.5000, sse=44369.7, rms=0.075 (0.000%) 040: dt: 0.5000, sse=44999.9, rms=0.071 (0.000%) 041: dt: 0.5000, sse=45601.4, rms=0.068 (0.000%) 042: dt: 0.5000, sse=46167.7, rms=0.065 (0.000%) 043: dt: 0.5000, sse=46702.2, rms=0.062 (0.000%) 044: dt: 0.5000, sse=47200.3, rms=0.060 (0.000%) 045: dt: 0.5000, sse=47676.0, rms=0.057 (0.000%) 046: dt: 0.5000, sse=48146.5, rms=0.055 (0.000%) 047: dt: 0.5000, sse=48575.5, rms=0.053 (0.000%) 048: dt: 0.5000, sse=48998.5, rms=0.051 (0.000%) 049: dt: 0.5000, sse=49365.2, rms=0.050 (0.000%) 050: dt: 0.5000, sse=49735.8, rms=0.048 (0.000%) 051: dt: 0.5000, sse=50066.8, rms=0.047 (0.000%) 052: dt: 0.5000, sse=50379.9, rms=0.046 (0.000%) 053: dt: 0.5000, sse=50670.9, rms=0.045 (0.000%) 054: dt: 0.5000, sse=50904.4, rms=0.044 (0.000%) 055: dt: 0.5000, sse=51164.3, rms=0.043 (0.000%) 056: dt: 0.5000, sse=51377.6, rms=0.042 (0.000%) 057: dt: 0.5000, sse=51585.4, rms=0.041 (0.000%) 058: dt: 0.5000, sse=51787.5, rms=0.040 (0.000%) 059: dt: 0.5000, sse=51969.9, rms=0.040 (0.000%) 060: dt: 0.5000, sse=52121.2, rms=0.039 (0.000%) positioning took 3.4 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [108.70 199.30], gm=154.00+-15.10, and vertices in regions > 146.4 19570 surface locations found to contain inconsistent values (9132 in, 10438 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=11476.4, rms=0.23 061: dt: 0.5000, sse=11187.8, rms=0.220 (0.000%) 062: dt: 0.5000, sse=10539.7, rms=0.209 (0.000%) 063: dt: 0.5000, sse=10026.6, rms=0.198 (0.000%) 064: dt: 0.5000, sse=9615.5, rms=0.189 (0.000%) 065: dt: 0.5000, sse=9293.1, rms=0.180 (0.000%) 066: dt: 0.5000, sse=9042.6, rms=0.173 (0.000%) 067: dt: 0.5000, sse=8818.6, rms=0.166 (0.000%) 068: dt: 0.5000, sse=8612.3, rms=0.160 (0.000%) 069: dt: 0.5000, sse=8428.4, rms=0.153 (0.000%) 070: dt: 0.5000, sse=8277.6, rms=0.147 (0.000%) 071: dt: 0.5000, sse=8152.2, rms=0.141 (0.000%) 072: dt: 0.5000, sse=8046.2, rms=0.135 (0.000%) 073: dt: 0.5000, sse=7952.0, rms=0.130 (0.000%) 074: dt: 0.5000, sse=7872.8, rms=0.124 (0.000%) 075: dt: 0.5000, sse=7806.1, rms=0.119 (0.000%) 076: dt: 0.5000, sse=7751.3, rms=0.114 (0.000%) 077: dt: 0.5000, sse=7706.8, rms=0.110 (0.000%) 078: dt: 0.5000, sse=7672.5, rms=0.105 (0.000%) 079: dt: 0.5000, sse=7645.5, rms=0.100 (0.000%) 080: dt: 0.5000, sse=7627.4, rms=0.096 (0.000%) 081: dt: 0.5000, sse=7613.3, rms=0.092 (0.000%) 082: dt: 0.5000, sse=7607.2, rms=0.088 (0.000%) 083: dt: 0.5000, sse=7605.6, rms=0.084 (0.000%) 084: dt: 0.5000, sse=7604.2, rms=0.080 (0.000%) 085: dt: 0.5000, sse=7608.4, rms=0.077 (0.000%) 086: dt: 0.5000, sse=7614.9, rms=0.073 (0.000%) 087: dt: 0.5000, sse=7622.4, rms=0.070 (0.000%) 088: dt: 0.5000, sse=7628.2, rms=0.067 (0.000%) 089: dt: 0.5000, sse=7640.1, rms=0.064 (0.000%) 090: dt: 0.5000, sse=7649.8, rms=0.062 (0.000%) positioning took 3.5 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [87.40 220.60], gm=154.00+-22.20, and vertices in regions > 142.9 29719 surface locations found to contain inconsistent values (21 in, 29698 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/sub003/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1238.4, rms=0.06 091: dt: 0.5000, sse=1204.5, rms=0.063 (0.000%) 092: dt: 0.5000, sse=1125.0, rms=0.056 (0.000%) 093: dt: 0.5000, sse=1081.8, rms=0.052 (0.000%) 094: dt: 0.5000, sse=1051.0, rms=0.048 (0.000%) 095: dt: 0.5000, sse=1025.0, rms=0.045 (0.000%) 096: dt: 0.5000, sse=1007.5, rms=0.043 (0.000%) 097: dt: 0.5000, sse=993.6, rms=0.041 (0.000%) 098: dt: 0.5000, sse=982.4, rms=0.039 (0.000%) 099: dt: 0.5000, sse=971.8, rms=0.038 (0.000%) 100: dt: 0.5000, sse=963.0, rms=0.036 (0.000%) 101: dt: 0.5000, sse=955.3, rms=0.035 (0.000%) 102: dt: 0.5000, sse=948.3, rms=0.034 (0.000%) 103: dt: 0.5000, sse=943.1, rms=0.033 (0.000%) 104: dt: 0.5000, sse=938.0, rms=0.032 (0.000%) 105: dt: 0.5000, sse=934.2, rms=0.031 (0.000%) 106: dt: 0.5000, sse=930.5, rms=0.030 (0.000%) 107: dt: 0.5000, sse=927.6, rms=0.030 (0.000%) 108: dt: 0.5000, sse=924.8, rms=0.029 (0.000%) 109: dt: 0.5000, sse=923.0, rms=0.029 (0.000%) 110: dt: 0.5000, sse=921.2, rms=0.028 (0.000%) 111: dt: 0.5000, sse=919.6, rms=0.028 (0.000%) 112: dt: 0.5000, sse=918.5, rms=0.028 (0.000%) 113: dt: 0.5000, sse=917.8, rms=0.027 (0.000%) 114: dt: 0.5000, sse=917.3, rms=0.027 (0.000%) 115: dt: 0.5000, sse=916.8, rms=0.027 (0.000%) 116: dt: 0.5000, sse=916.2, rms=0.027 (0.000%) 117: dt: 0.5000, sse=915.7, rms=0.027 (0.000%) 118: dt: 0.5000, sse=915.5, rms=0.027 (0.000%) 119: dt: 0.5000, sse=915.3, rms=0.026 (0.000%) 120: dt: 0.5000, sse=915.3, rms=0.026 (0.000%) positioning took 3.4 minutes writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.area.pial vertex spacing 1.05 +- 0.45 (0.05-->8.33) (max @ vno 102151 --> 101354) face area 0.43 +- 0.33 (0.00-->6.26) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 128814 vertices processed 25000 of 128814 vertices processed 50000 of 128814 vertices processed 75000 of 128814 vertices processed 100000 of 128814 vertices processed 125000 of 128814 vertices processed 0 of 128814 vertices processed 25000 of 128814 vertices processed 50000 of 128814 vertices processed 75000 of 128814 vertices processed 100000 of 128814 vertices processed 125000 of 128814 vertices processed thickness calculation complete, 399:1099 truncations. 29395 vertices at 0 distance 87072 vertices at 1 distance 83101 vertices at 2 distance 34346 vertices at 3 distance 9174 vertices at 4 distance 2323 vertices at 5 distance 761 vertices at 6 distance 211 vertices at 7 distance 75 vertices at 8 distance 40 vertices at 9 distance 32 vertices at 10 distance 22 vertices at 11 distance 19 vertices at 12 distance 14 vertices at 13 distance 7 vertices at 14 distance 12 vertices at 15 distance 16 vertices at 16 distance 8 vertices at 17 distance 5 vertices at 18 distance 4 vertices at 19 distance 21 vertices at 20 distance writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.thickness positioning took 17.7 minutes /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.woT2.pial `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.woT2.pial' mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub003 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/sub003/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/wm.mgz... 14678 bright wm thresholded. 302 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.orig... computing class statistics... border white: 229356 voxels (1.37%) border gray 266114 voxels (1.59%) WM (92.0): 92.8 +- 10.5 [70.0 --> 110.0] GM (74.0) : 72.0 +- 13.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 42.7 (was 70) setting MAX_BORDER_WHITE to 115.5 (was 105) setting MIN_BORDER_WHITE to 56.0 (was 85) setting MAX_CSF to 29.3 (was 40) setting MAX_GRAY to 94.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 49.3 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 16.0 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=56 mean inside = 92.5, 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/sub003/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.90 +- 0.26 (0.02-->4.00) (max @ vno 95998 --> 96851) face area 0.34 +- 0.16 (0.00-->2.73) averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 1 with 4 points - only 0.00% unknown deleting segment 4 with 12 points - only 0.00% unknown deleting segment 6 with 460 points - only 2.61% unknown deleting segment 7 with 13 points - only 0.00% unknown deleting segment 8 with 64 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 10 with 11 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 11 with 2 points - only 0.00% unknown tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.90 +- 0.25 (0.04-->4.00) (max @ vno 96851 --> 95998) face area 0.34 +- 0.16 (0.00-->2.73) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4397407.0, rms=0.00 rms = 1.10, time step reduction 1 of 3 to 0.250... rms = 0.29, time step reduction 2 of 3 to 0.125... rms = 0.04, time step reduction 3 of 3 to 0.062... 001: dt: 0.1250, sse=4397407.0, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 0 with 4 points - only 0.00% unknown deleting segment 1 with 12 points - only 0.00% unknown deleting segment 2 with 460 points - only 2.61% unknown deleting segment 3 with 13 points - only 0.00% unknown deleting segment 4 with 64 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 6 with 11 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.04-->4.00) (max @ vno 96851 --> 95998) face area 0.34 +- 0.16 (0.00-->2.73) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4397407.0, rms=0.00 rms = 1.13, time step reduction 1 of 3 to 0.250... rms = 0.29, time step reduction 2 of 3 to 0.125... rms = 0.04, time step reduction 3 of 3 to 0.062... 002: dt: 0.1250, sse=4397407.0, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 0 with 4 points - only 0.00% unknown deleting segment 1 with 12 points - only 0.00% unknown deleting segment 2 with 460 points - only 2.61% unknown deleting segment 3 with 13 points - only 0.00% unknown deleting segment 4 with 64 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 6 with 11 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.25 (0.04-->4.00) (max @ vno 96851 --> 95998) face area 0.34 +- 0.16 (0.00-->2.73) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4397407.0, rms=0.00 rms = 1.10, time step reduction 1 of 3 to 0.250... rms = 0.29, time step reduction 2 of 3 to 0.125... rms = 0.04, time step reduction 3 of 3 to 0.062... 003: dt: 0.1250, sse=4397407.0, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 0 with 4 points - only 0.00% unknown deleting segment 1 with 12 points - only 0.00% unknown deleting segment 2 with 460 points - only 2.61% unknown deleting segment 3 with 13 points - only 0.00% unknown deleting segment 4 with 64 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 6 with 11 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4397407.0, rms=0.00 rms = 1.13, time step reduction 1 of 3 to 0.250... rms = 0.29, time step reduction 2 of 3 to 0.125... rms = 0.04, time step reduction 3 of 3 to 0.062... 004: dt: 0.1250, sse=4397407.0, rms=0.000 (1.000%) positioning took 0.3 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 [88.60 219.40], gm=154.00+-21.80, and vertices in regions > 143.1 34217 surface locations found to contain inconsistent values (2516 in, 31701 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=482860.4, rms=0.22 001: dt: 0.5000, sse=453568.3, rms=0.213 (0.000%) 002: dt: 0.5000, sse=435436.9, rms=0.201 (0.000%) 003: dt: 0.5000, sse=424307.9, rms=0.191 (0.000%) 004: dt: 0.5000, sse=415493.0, rms=0.182 (0.000%) 005: dt: 0.5000, sse=409468.9, rms=0.175 (0.000%) 006: dt: 0.5000, sse=404844.1, rms=0.169 (0.000%) 007: dt: 0.5000, sse=401477.8, rms=0.164 (0.000%) 008: dt: 0.5000, sse=398681.3, rms=0.160 (0.000%) 009: dt: 0.5000, sse=396681.0, rms=0.156 (0.000%) 010: dt: 0.5000, sse=394722.8, rms=0.153 (0.000%) 011: dt: 0.5000, sse=393133.6, rms=0.151 (0.000%) 012: dt: 0.5000, sse=391517.3, rms=0.149 (0.000%) 013: dt: 0.5000, sse=389977.8, rms=0.147 (0.000%) 014: dt: 0.5000, sse=388417.8, rms=0.146 (0.000%) 015: dt: 0.5000, sse=387054.7, rms=0.145 (0.000%) 016: dt: 0.5000, sse=385886.7, rms=0.145 (0.000%) 017: dt: 0.5000, sse=384518.3, rms=0.144 (0.000%) 018: dt: 0.5000, sse=383164.8, rms=0.144 (0.000%) 019: dt: 0.5000, sse=381827.3, rms=0.144 (0.000%) 020: dt: 0.5000, sse=380372.8, rms=0.144 (0.000%) 021: dt: 0.5000, sse=379264.2, rms=0.144 (0.000%) 022: dt: 0.5000, sse=377852.0, rms=0.144 (0.000%) 023: dt: 0.5000, sse=376810.3, rms=0.144 (0.000%) 024: dt: 0.5000, sse=375525.6, rms=0.144 (0.000%) 025: dt: 0.5000, sse=374336.8, rms=0.144 (0.000%) 026: dt: 0.5000, sse=373390.2, rms=0.145 (0.000%) 027: dt: 0.5000, sse=372069.3, rms=0.145 (0.000%) 028: dt: 0.5000, sse=371236.5, rms=0.146 (0.000%) 029: dt: 0.5000, sse=370461.8, rms=0.146 (0.000%) 030: dt: 0.5000, sse=369661.6, rms=0.146 (0.000%) positioning took 3.7 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [105.50 204.50], gm=155.00+-16.50, and vertices in regions > 146.7 25355 surface locations found to contain inconsistent values (7809 in, 17546 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=42535.0, rms=0.22 031: dt: 0.5000, sse=42114.6, rms=0.217 (0.000%) 032: dt: 0.5000, sse=41659.8, rms=0.205 (0.000%) 033: dt: 0.5000, sse=41729.4, rms=0.194 (0.000%) 034: dt: 0.5000, sse=42056.3, rms=0.186 (0.000%) 035: dt: 0.5000, sse=42418.2, rms=0.179 (0.000%) 036: dt: 0.5000, sse=42838.1, rms=0.171 (0.000%) 037: dt: 0.5000, sse=43298.3, rms=0.165 (0.000%) 038: dt: 0.5000, sse=43806.6, rms=0.158 (0.000%) 039: dt: 0.5000, sse=44370.1, rms=0.152 (0.000%) 040: dt: 0.5000, sse=44980.9, rms=0.146 (0.000%) 041: dt: 0.5000, sse=45632.4, rms=0.141 (0.000%) 042: dt: 0.5000, sse=46265.5, rms=0.136 (0.000%) 043: dt: 0.5000, sse=46913.8, rms=0.131 (0.000%) 044: dt: 0.5000, sse=47565.2, rms=0.126 (0.000%) 045: dt: 0.5000, sse=48197.7, rms=0.122 (0.000%) 046: dt: 0.5000, sse=48805.5, rms=0.117 (0.000%) 047: dt: 0.5000, sse=49411.1, rms=0.113 (0.000%) 048: dt: 0.5000, sse=49999.7, rms=0.109 (0.000%) 049: dt: 0.5000, sse=50571.0, rms=0.106 (0.000%) 050: dt: 0.5000, sse=51117.0, rms=0.102 (0.000%) 051: dt: 0.5000, sse=51633.1, rms=0.099 (0.000%) 052: dt: 0.5000, sse=52135.4, rms=0.095 (0.000%) 053: dt: 0.5000, sse=52612.7, rms=0.092 (0.000%) 054: dt: 0.5000, sse=53058.0, rms=0.089 (0.000%) 055: dt: 0.5000, sse=53490.7, rms=0.086 (0.000%) 056: dt: 0.5000, sse=53917.7, rms=0.083 (0.000%) 057: dt: 0.5000, sse=54323.5, rms=0.080 (0.000%) 058: dt: 0.5000, sse=54708.8, rms=0.077 (0.000%) 059: dt: 0.5000, sse=55063.3, rms=0.074 (0.000%) 060: dt: 0.5000, sse=55436.0, rms=0.072 (0.000%) positioning took 3.5 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [108.90 197.10], gm=153.00+-14.70, and vertices in regions > 145.6 21451 surface locations found to contain inconsistent values (12924 in, 8527 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=10524.7, rms=0.20 061: dt: 0.5000, sse=10284.0, rms=0.198 (0.000%) 062: dt: 0.5000, sse=9826.4, rms=0.188 (0.000%) 063: dt: 0.5000, sse=9480.1, rms=0.179 (0.000%) 064: dt: 0.5000, sse=9200.0, rms=0.171 (0.000%) 065: dt: 0.5000, sse=8970.0, rms=0.164 (0.000%) 066: dt: 0.5000, sse=8783.6, rms=0.158 (0.000%) 067: dt: 0.5000, sse=8611.4, rms=0.152 (0.000%) 068: dt: 0.5000, sse=8447.4, rms=0.146 (0.000%) 069: dt: 0.5000, sse=8299.6, rms=0.141 (0.000%) 070: dt: 0.5000, sse=8167.2, rms=0.135 (0.000%) 071: dt: 0.5000, sse=8054.4, rms=0.130 (0.000%) 072: dt: 0.5000, sse=7957.4, rms=0.125 (0.000%) 073: dt: 0.5000, sse=7872.5, rms=0.120 (0.000%) 074: dt: 0.5000, sse=7797.2, rms=0.115 (0.000%) 075: dt: 0.5000, sse=7731.2, rms=0.110 (0.000%) 076: dt: 0.5000, sse=7674.8, rms=0.106 (0.000%) 077: dt: 0.5000, sse=7625.3, rms=0.102 (0.000%) 078: dt: 0.5000, sse=7585.4, rms=0.097 (0.000%) 079: dt: 0.5000, sse=7550.1, rms=0.093 (0.000%) 080: dt: 0.5000, sse=7529.5, rms=0.090 (0.000%) 081: dt: 0.5000, sse=7506.7, rms=0.086 (0.000%) 082: dt: 0.5000, sse=7489.7, rms=0.083 (0.000%) 083: dt: 0.5000, sse=7478.4, rms=0.079 (0.000%) 084: dt: 0.5000, sse=7473.8, rms=0.076 (0.000%) 085: dt: 0.5000, sse=7465.4, rms=0.073 (0.000%) 086: dt: 0.5000, sse=7462.3, rms=0.070 (0.000%) 087: dt: 0.5000, sse=7465.9, rms=0.068 (0.000%) 088: dt: 0.5000, sse=7467.3, rms=0.065 (0.000%) 089: dt: 0.5000, sse=7472.5, rms=0.063 (0.000%) 090: dt: 0.5000, sse=7471.7, rms=0.061 (0.000%) positioning took 3.4 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [85.00 223.00], gm=154.00+-23.00, and vertices in regions > 142.5 37706 surface locations found to contain inconsistent values (8 in, 37698 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/sub003/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=1885.8, rms=0.10 091: dt: 0.5000, sse=1749.3, rms=0.093 (0.000%) 092: dt: 0.5000, sse=1521.6, rms=0.081 (0.000%) 093: dt: 0.5000, sse=1384.6, rms=0.073 (0.000%) 094: dt: 0.5000, sse=1291.3, rms=0.066 (0.000%) 095: dt: 0.5000, sse=1221.4, rms=0.060 (0.000%) 096: dt: 0.5000, sse=1178.9, rms=0.057 (0.000%) 097: dt: 0.5000, sse=1145.6, rms=0.053 (0.000%) 098: dt: 0.5000, sse=1118.7, rms=0.051 (0.000%) 099: dt: 0.5000, sse=1095.2, rms=0.048 (0.000%) 100: dt: 0.5000, sse=1077.4, rms=0.045 (0.000%) 101: dt: 0.5000, sse=1062.5, rms=0.043 (0.000%) 102: dt: 0.5000, sse=1050.8, rms=0.042 (0.000%) 103: dt: 0.5000, sse=1040.5, rms=0.040 (0.000%) 104: dt: 0.5000, sse=1032.4, rms=0.038 (0.000%) 105: dt: 0.5000, sse=1026.7, rms=0.037 (0.000%) 106: dt: 0.5000, sse=1021.3, rms=0.036 (0.000%) 107: dt: 0.5000, sse=1017.7, rms=0.035 (0.000%) 108: dt: 0.5000, sse=1014.3, rms=0.035 (0.000%) 109: dt: 0.5000, sse=1011.2, rms=0.034 (0.000%) 110: dt: 0.5000, sse=1008.9, rms=0.034 (0.000%) 111: dt: 0.5000, sse=1006.8, rms=0.033 (0.000%) 112: dt: 0.5000, sse=1005.6, rms=0.033 (0.000%) 113: dt: 0.5000, sse=1005.0, rms=0.032 (0.000%) 114: dt: 0.5000, sse=1004.1, rms=0.032 (0.000%) 115: dt: 0.5000, sse=1004.1, rms=0.032 (0.000%) 116: dt: 0.5000, sse=1003.4, rms=0.032 (0.000%) 117: dt: 0.5000, sse=1002.9, rms=0.032 (0.000%) 118: dt: 0.5000, sse=1002.3, rms=0.031 (0.000%) 119: dt: 0.5000, sse=1001.9, rms=0.031 (0.000%) 120: dt: 0.5000, sse=1001.3, rms=0.031 (0.000%) positioning took 3.4 minutes writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.area.pial vertex spacing 1.06 +- 0.46 (0.09-->6.06) (max @ vno 83570 --> 83557) face area 0.43 +- 0.33 (0.00-->5.92) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 127449 vertices processed 25000 of 127449 vertices processed 50000 of 127449 vertices processed 75000 of 127449 vertices processed 100000 of 127449 vertices processed 125000 of 127449 vertices processed 0 of 127449 vertices processed 25000 of 127449 vertices processed 50000 of 127449 vertices processed 75000 of 127449 vertices processed 100000 of 127449 vertices processed 125000 of 127449 vertices processed thickness calculation complete, 367:766 truncations. 29366 vertices at 0 distance 84591 vertices at 1 distance 82829 vertices at 2 distance 33888 vertices at 3 distance 8892 vertices at 4 distance 2439 vertices at 5 distance 696 vertices at 6 distance 252 vertices at 7 distance 125 vertices at 8 distance 62 vertices at 9 distance 36 vertices at 10 distance 49 vertices at 11 distance 43 vertices at 12 distance 37 vertices at 13 distance 21 vertices at 14 distance 16 vertices at 15 distance 8 vertices at 16 distance 10 vertices at 17 distance 15 vertices at 18 distance 16 vertices at 19 distance 7 vertices at 20 distance writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.thickness positioning took 18.2 minutes #-------------------------------------------- #@# Surf Volume lh Thu Aug 8 22:26:50 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 22:26:50 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 22:26:51 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon sub003 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 = 19 writing volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/ribbon.mgz writing ribbon files #-------------------------------------------- #@# ASeg Stats Thu Aug 8 22:50:35 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003 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 sub003 $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 sub003 sysname Linux hostname snake5 machine x86_64 user fkaule UseRobust 0 atlas_icv (eTIV) = 1018934 mm^3 (det: 1.911905 ) Computing euler number orig.nofix lheno = -16, rheno = -24 orig.nofix lhholes = 9, rhholes = 13 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 236673.500 235684.000 diff= 989.5 pctdiff= 0.418 rhCtxGM: 236677.165 235302.000 diff= 1375.2 pctdiff= 0.581 lhCtxWM: 188062.518 188277.500 diff= -215.0 pctdiff=-0.114 rhCtxWM: 190680.655 190057.500 diff= 623.2 pctdiff= 0.327 SubCortGMVol 59365.000 SupraTentVol 920678.838 (917222.000) diff=3456.838 pctdiff=0.375 SupraTentVolNotVent 912477.838 (909021.000) diff=3456.838 pctdiff=0.379 BrainSegVol 1042313.000 (1040328.000) diff=1985.000 pctdiff=0.190 BrainSegVolNotVent 1031549.000 (1034086.838) diff=-2537.838 pctdiff=-0.246 BrainSegVolNotVent 1031549.000 CerebellumVol 122293.000 VentChorVol 8201.000 3rd4th5thCSF 2563.000 CSFVol 597.000, OptChiasmVol 216.000 MaskVol 1465683.000 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 3174 3174.281 4 5 Left-Inf-Lat-Vent 341 340.772 5 7 Left-Cerebellum-White-Matter 12687 12687.178 6 8 Left-Cerebellum-Cortex 48130 48129.738 7 10 Left-Thalamus-Proper 7080 7079.920 8 11 Left-Caudate 3482 3482.067 9 12 Left-Putamen 6615 6615.351 10 13 Left-Pallidum 1985 1984.917 11 14 3rd-Ventricle 858 858.224 12 15 4th-Ventricle 1310 1309.628 13 16 Brain-Stem 18583 18583.396 14 17 Left-Hippocampus 3974 3974.137 15 18 Left-Amygdala 1426 1426.304 16 24 CSF 600 600.095 17 26 Left-Accumbens-area 727 726.984 18 28 Left-VentralDC 3496 3495.827 19 30 Left-vessel 198 197.954 20 31 Left-choroid-plexus 964 964.113 23 43 Right-Lateral-Ventricle 2276 2276.475 24 44 Right-Inf-Lat-Vent 215 214.511 25 46 Right-Cerebellum-White-Matter 13616 13616.034 26 47 Right-Cerebellum-Cortex 50097 50096.945 27 49 Right-Thalamus-Proper 7254 7254.009 28 50 Right-Caudate 3359 3359.181 29 51 Right-Putamen 6317 6317.163 30 52 Right-Pallidum 1790 1790.350 31 53 Right-Hippocampus 3896 3895.694 32 54 Right-Amygdala 1726 1726.466 33 58 Right-Accumbens-area 761 760.781 34 60 Right-VentralDC 3476 3476.094 35 62 Right-vessel 111 110.917 36 63 Right-choroid-plexus 1384 1384.161 37 72 5th-Ventricle 0 0.000 38 77 WM-hypointensities 1460 1460.332 39 78 Left-WM-hypointensities 0 0.000 40 79 Right-WM-hypointensities 0 0.000 41 80 non-WM-hypointensities 13 12.577 42 81 Left-non-WM-hypointensities 0 0.000 43 82 Right-non-WM-hypointensities 0 0.000 44 85 Optic-Chiasm 227 226.940 45 251 CC_Posterior 717 717.405 46 252 CC_Mid_Posterior 331 331.448 47 253 CC_Central 360 359.750 48 254 CC_Mid_Anterior 392 392.465 49 255 CC_Anterior 752 752.399 Reporting on 45 segmentations mri_segstats done #----------------------------------------- #@# AParc-to-ASeg Thu Aug 8 22:56:05 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003 mri_aparc2aseg --s sub003 --volmask SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer subject sub003 outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.white Reading lh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.pial Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/surf/rh.white Reading rh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.pial Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/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/sub003/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 = 468608 Used brute-force search on 0 voxels Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/aparc+aseg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003 mri_aparc2aseg --s sub003 --volmask --a2009s SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer subject sub003 outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.white Reading lh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.pial Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/surf/rh.white Reading rh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.pial Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/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/sub003/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 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baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/aparc+aseg.mgz Reading lh white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.white Reading lh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.pial Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/surf/rh.white Reading rh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.pial Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/mri/ribbon.mgz Loading filled from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/filled.mgz Ripping vertices labeled as unkown Ripped 7455 vertices from left hemi Ripped 8385 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/sub003/mri/aseg.mgz Loading Ctx Seg File /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 = 846670 Used brute-force search on 382 voxels Fixing Parahip LH WM Found 11 clusters 0 k 1.000000 1 k 6.000000 2 k 1322.000000 3 k 1.000000 4 k 1.000000 5 k 1.000000 6 k 1.000000 7 k 1.000000 8 k 2.000000 9 k 2.000000 10 k 1.000000 Fixing Parahip RH WM Found 14 clusters 0 k 1589.000000 1 k 1.000000 2 k 2.000000 3 k 1.000000 4 k 2.000000 5 k 1.000000 6 k 2.000000 7 k 1.000000 8 k 1.000000 9 k 11.000000 10 k 1.000000 11 k 1.000000 12 k 1.000000 13 k 1.000000 Writing output aseg to mri/wmparc.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003 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 sub003 --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 sub003 --surf-wm-vol --ctab /opt/freesurfer/5.3.0/WMParcStatsLUT.txt --etiv sysname Linux hostname snake5 machine x86_64 user fkaule UseRobust 0 atlas_icv (eTIV) = 1018934 mm^3 (det: 1.911905 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 236673.500 235684.000 diff= 989.5 pctdiff= 0.418 rhCtxGM: 236677.165 235302.000 diff= 1375.2 pctdiff= 0.581 lhCtxWM: 188062.518 188277.500 diff= -215.0 pctdiff=-0.114 rhCtxWM: 190680.655 190057.500 diff= 623.2 pctdiff= 0.327 SubCortGMVol 59365.000 SupraTentVol 920678.838 (917222.000) diff=3456.838 pctdiff=0.375 SupraTentVolNotVent 912477.838 (909021.000) diff=3456.838 pctdiff=0.379 BrainSegVol 1042313.000 (1040328.000) diff=1985.000 pctdiff=0.190 BrainSegVolNotVent 1031549.000 (1034086.838) diff=-2537.838 pctdiff=-0.246 BrainSegVolNotVent 1031549.000 CerebellumVol 122293.000 VentChorVol 8201.000 3rd4th5thCSF 2563.000 CSFVol 597.000, OptChiasmVol 216.000 MaskVol 1465683.000 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 2144 2143.738 2 3002 wm-lh-caudalanteriorcingulate 2810 2809.829 3 3003 wm-lh-caudalmiddlefrontal 5684 5684.414 4 3004 wm-lh-corpuscallosum 0 0.000 5 3005 wm-lh-cuneus 2013 2013.271 6 3006 wm-lh-entorhinal 916 916.275 7 3007 wm-lh-fusiform 5595 5594.664 8 3008 wm-lh-inferiorparietal 10709 10708.769 9 3009 wm-lh-inferiortemporal 5080 5079.736 10 3010 wm-lh-isthmuscingulate 3211 3210.994 11 3011 wm-lh-lateraloccipital 8140 8140.225 12 3012 wm-lh-lateralorbitofrontal 5232 5231.973 13 3013 wm-lh-lingual 5275 5275.343 14 3014 wm-lh-medialorbitofrontal 3112 3112.314 15 3015 wm-lh-middletemporal 4170 4169.850 16 3016 wm-lh-parahippocampal 1356 1355.829 17 3017 wm-lh-paracentral 2891 2890.717 18 3018 wm-lh-parsopercularis 3151 3150.771 19 3019 wm-lh-parsorbitalis 755 754.968 20 3020 wm-lh-parstriangularis 2848 2848.275 21 3021 wm-lh-pericalcarine 3337 3336.769 22 3022 wm-lh-postcentral 6306 6305.770 23 3023 wm-lh-posteriorcingulate 4348 4348.173 24 3024 wm-lh-precentral 9854 9853.964 25 3025 wm-lh-precuneus 8168 8168.355 26 3026 wm-lh-rostralanteriorcingulate 2574 2573.539 27 3027 wm-lh-rostralmiddlefrontal 10352 10351.646 28 3028 wm-lh-superiorfrontal 14322 14321.698 29 3029 wm-lh-superiorparietal 11486 11485.747 30 3030 wm-lh-superiortemporal 6842 6842.421 31 3031 wm-lh-supramarginal 6737 6737.016 32 3032 wm-lh-frontalpole 185 185.201 33 3033 wm-lh-temporalpole 533 532.920 34 3034 wm-lh-transversetemporal 564 563.637 35 3035 wm-lh-insula 6653 6652.805 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 2840 2840.422 120 4002 wm-rh-caudalanteriorcingulate 2610 2609.644 121 4003 wm-rh-caudalmiddlefrontal 4047 4046.623 122 4004 wm-rh-corpuscallosum 0 0.000 123 4005 wm-rh-cuneus 2033 2033.063 124 4006 wm-rh-entorhinal 551 550.972 125 4007 wm-rh-fusiform 5449 5448.645 126 4008 wm-rh-inferiorparietal 12357 12357.479 127 4009 wm-rh-inferiortemporal 4950 4949.798 128 4010 wm-rh-isthmuscingulate 2789 2788.676 129 4011 wm-rh-lateraloccipital 7763 7762.572 130 4012 wm-rh-lateralorbitofrontal 6147 6146.587 131 4013 wm-rh-lingual 5198 5197.819 132 4014 wm-rh-medialorbitofrontal 3322 3321.590 133 4015 wm-rh-middletemporal 4994 4993.922 134 4016 wm-rh-parahippocampal 1632 1632.081 135 4017 wm-rh-paracentral 4249 4248.789 136 4018 wm-rh-parsopercularis 2588 2588.202 137 4019 wm-rh-parsorbitalis 1054 1053.704 138 4020 wm-rh-parstriangularis 3209 3209.153 139 4021 wm-rh-pericalcarine 3090 3090.221 140 4022 wm-rh-postcentral 5844 5843.754 141 4023 wm-rh-posteriorcingulate 3819 3818.954 142 4024 wm-rh-precentral 10313 10313.099 143 4025 wm-rh-precuneus 9477 9477.032 144 4026 wm-rh-rostralanteriorcingulate 1585 1585.142 145 4027 wm-rh-rostralmiddlefrontal 10613 10613.044 146 4028 wm-rh-superiorfrontal 14713 14712.778 147 4029 wm-rh-superiorparietal 10255 10255.189 148 4030 wm-rh-superiortemporal 5277 5277.438 149 4031 wm-rh-supramarginal 7641 7640.863 150 4032 wm-rh-frontalpole 295 294.753 151 4033 wm-rh-temporalpole 524 523.643 152 4034 wm-rh-transversetemporal 399 399.371 153 4035 wm-rh-insula 6709 6709.368 154 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 21614 21613.861 237 5002 Right-UnsegmentedWhiteMatter 21556 21555.986 238 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/sub003/label #-------------------------------------------- #@# BA Labels lh Thu Aug 8 23:13:13 CEST 2013 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.label --trgsubject sub003 --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 = sub003 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/sub003/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814 Number of reverse mapping hits = 208 Checking for and removing duplicates Writing label file ./lh.BA1.label 4337 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.label --trgsubject sub003 --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 = sub003 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/sub003/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814 Number of reverse mapping hits = 390 Checking for and removing duplicates Writing label file ./lh.BA2.label 8299 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.label --trgsubject sub003 --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 = sub003 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/sub003/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814 Number of reverse mapping hits = 61 Checking for and removing duplicates Writing label file ./lh.BA3a.label 4138 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.label --trgsubject sub003 --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 = sub003 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/sub003/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814 Number of reverse mapping hits = 199 Checking for and removing duplicates Writing label file ./lh.BA3b.label 6182 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.label --trgsubject sub003 --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 = sub003 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/sub003/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814 Number of reverse mapping hits = 147 Checking for and removing duplicates Writing label file ./lh.BA4a.label 5931 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.label --trgsubject sub003 --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 = sub003 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/sub003/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814 Number of reverse mapping hits = 89 Checking for and removing duplicates Writing label file ./lh.BA4p.label 4159 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.label --trgsubject sub003 --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 = sub003 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/sub003/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814 Number of reverse mapping hits = 679 Checking for and removing duplicates Writing label file ./lh.BA6.label 14268 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.label --trgsubject sub003 --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 = sub003 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/sub003/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814 Number of reverse mapping hits = 210 Checking for and removing duplicates Writing label file ./lh.BA44.label 4391 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.label --trgsubject sub003 --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 = sub003 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/sub003/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814 Number of reverse mapping hits = 793 Checking for and removing duplicates Writing label file ./lh.BA45.label 4215 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.label --trgsubject sub003 --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 = sub003 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/sub003/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814 Number of reverse mapping hits = 1884 Checking for and removing duplicates Writing label file ./lh.V1.label 6525 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.label --trgsubject sub003 --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 = sub003 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/sub003/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814 Number of reverse mapping hits = 3494 Checking for and removing duplicates Writing label file ./lh.V2.label 11608 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.label --trgsubject sub003 --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 = sub003 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/sub003/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814 Number of reverse mapping hits = 371 Checking for and removing duplicates Writing label file ./lh.MT.label 2389 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.perirhinal.label --trgsubject sub003 --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 = sub003 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/sub003/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814 Number of reverse mapping hits = 154 Checking for and removing duplicates Writing label file ./lh.perirhinal.label 1353 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.thresh.label --trgsubject sub003 --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 = sub003 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/sub003/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814 Number of reverse mapping hits = 21 Checking for and removing duplicates Writing label file ./lh.BA1.thresh.label 1035 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.thresh.label --trgsubject sub003 --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 = sub003 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/sub003/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814 Number of reverse mapping hits = 165 Checking for and removing duplicates Writing label file ./lh.BA2.thresh.label 2257 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.thresh.label --trgsubject sub003 --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 = sub003 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/sub003/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814 Number of reverse mapping hits = 13 Checking for and removing duplicates Writing label file ./lh.BA3a.thresh.label 1517 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.thresh.label --trgsubject sub003 --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 = sub003 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/sub003/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814 Number of reverse mapping hits = 41 Checking for and removing duplicates Writing label file ./lh.BA3b.thresh.label 2037 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.thresh.label --trgsubject sub003 --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 = sub003 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/sub003/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814 Number of reverse mapping hits = 90 Checking for and removing duplicates Writing label file ./lh.BA4a.thresh.label 2409 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.thresh.label --trgsubject sub003 --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 = sub003 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/sub003/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814 Number of reverse mapping hits = 50 Checking for and removing duplicates Writing label file ./lh.BA4p.thresh.label 1599 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.thresh.label --trgsubject sub003 --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 = sub003 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/sub003/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814 Number of reverse mapping hits = 200 Checking for and removing duplicates Writing label file ./lh.BA6.thresh.label 7235 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.thresh.label --trgsubject sub003 --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 = sub003 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/sub003/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814 Number of reverse mapping hits = 100 Checking for and removing duplicates Writing label file ./lh.BA44.thresh.label 2012 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.thresh.label --trgsubject sub003 --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 = sub003 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/sub003/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814 Number of reverse mapping hits = 268 Checking for and removing duplicates Writing label file ./lh.BA45.thresh.label 1419 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.thresh.label --trgsubject sub003 --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 = sub003 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/sub003/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814 Number of reverse mapping hits = 1378 Checking for and removing duplicates Writing label file ./lh.V1.thresh.label 4783 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.thresh.label --trgsubject sub003 --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 = sub003 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/sub003/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814 Number of reverse mapping hits = 1676 Checking for and removing duplicates Writing label file ./lh.V2.thresh.label 5010 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.thresh.label --trgsubject sub003 --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 = sub003 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/sub003/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814 Number of reverse mapping hits = 74 Checking for and removing duplicates Writing label file ./lh.MT.thresh.label 587 mri_label2label: Done mris_label2annot --s sub003 --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/sub003/label cmdline mris_label2annot --s sub003 --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 snake5 machine x86_64 user fkaule subject sub003 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/sub003/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 89823 unhit vertices Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/label/lh.BA.annot mris_label2annot --s sub003 --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/sub003/label cmdline mris_label2annot --s sub003 --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 snake5 machine x86_64 user fkaule subject sub003 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/sub003/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 106666 unhit vertices Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/label/lh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab sub003 lh white computing statistics for each annotation in ./lh.BA.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 952 575 1632 1.886 0.639 0.172 0.094 29 3.0 BA1 3592 2423 6069 2.241 0.499 0.135 0.043 51 6.0 BA2 856 570 860 1.905 0.375 0.125 0.030 6 1.1 BA3a 2063 1404 3567 2.104 0.624 0.125 0.036 23 2.9 BA3b 1361 880 3200 2.694 0.520 0.120 0.030 15 1.7 BA4a 1133 756 2245 2.728 0.498 0.099 0.021 6 1.0 BA4p 7559 5146 18810 2.770 0.577 0.143 0.046 133 14.4 BA6 2101 1463 5099 2.879 0.453 0.131 0.040 33 3.4 BA44 3195 2137 6468 2.490 0.520 0.145 0.045 52 5.9 BA45 4154 2757 5619 1.936 0.496 0.144 0.069 72 11.5 V1 9099 5935 13860 2.093 0.511 0.167 0.069 187 23.7 V2 1926 1292 3502 2.450 0.426 0.152 0.049 31 3.9 MT 1000 672 2594 3.029 0.773 0.158 0.071 27 3.2 perirhinal mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab sub003 lh white computing statistics for each annotation in ./lh.BA.thresh.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 543 298 823 1.690 0.552 0.187 0.118 21 2.1 BA1 1445 945 2354 2.154 0.481 0.124 0.034 16 2.2 BA2 690 460 677 1.902 0.383 0.132 0.033 5 0.9 BA3a 1195 846 1749 1.816 0.480 0.097 0.023 8 1.1 BA3b 1379 898 3151 2.710 0.555 0.107 0.024 9 1.5 BA4a 931 623 1784 2.690 0.487 0.100 0.022 5 0.8 BA4p 3793 2541 9540 2.788 0.634 0.142 0.047 73 7.7 BA6 1334 932 3366 2.924 0.407 0.137 0.046 26 2.4 BA44 1220 819 3107 2.696 0.521 0.159 0.049 26 2.5 BA45 4425 2925 5993 1.934 0.498 0.146 0.067 79 11.6 V1 4693 3059 6728 1.943 0.501 0.173 0.082 102 15.0 V2 500 338 774 2.291 0.381 0.132 0.037 5 0.8 MT #-------------------------------------------- #@# BA Labels rh Thu Aug 8 23:18:12 CEST 2013 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.label --trgsubject sub003 --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 = sub003 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/sub003/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 127449 Number of reverse mapping hits = 157 Checking for and removing duplicates Writing label file ./rh.BA1.label 4119 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.label --trgsubject sub003 --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 = sub003 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/sub003/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 127449 Number of reverse mapping hits = 313 Checking for and removing duplicates Writing label file ./rh.BA2.label 7000 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.label --trgsubject sub003 --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 = sub003 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/sub003/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 127449 Number of reverse mapping hits = 57 Checking for and removing duplicates Writing label file ./rh.BA3a.label 4037 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.label --trgsubject sub003 --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 = sub003 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/sub003/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 127449 Number of reverse mapping hits = 109 Checking for and removing duplicates Writing label file ./rh.BA3b.label 4631 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.label --trgsubject sub003 --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 = sub003 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/sub003/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 127449 Number of reverse mapping hits = 184 Checking for and removing duplicates Writing label file ./rh.BA4a.label 5931 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.label --trgsubject sub003 --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 = sub003 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/sub003/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 127449 Number of reverse mapping hits = 107 Checking for and removing duplicates Writing label file ./rh.BA4p.label 4580 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.label --trgsubject sub003 --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 = sub003 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/sub003/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 127449 Number of reverse mapping hits = 620 Checking for and removing duplicates Writing label file ./rh.BA6.label 12876 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.label --trgsubject sub003 --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 = sub003 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/sub003/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 127449 Number of reverse mapping hits = 758 Checking for and removing duplicates Writing label file ./rh.BA44.label 7670 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.label --trgsubject sub003 --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 = sub003 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/sub003/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 127449 Number of reverse mapping hits = 1058 Checking for and removing duplicates Writing label file ./rh.BA45.label 6413 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.label --trgsubject sub003 --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 = sub003 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/sub003/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 127449 Number of reverse mapping hits = 1888 Checking for and removing duplicates Writing label file ./rh.V1.label 6615 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.label --trgsubject sub003 --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 = sub003 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/sub003/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 127449 Number of reverse mapping hits = 3220 Checking for and removing duplicates Writing label file ./rh.V2.label 11236 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.label --trgsubject sub003 --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 = sub003 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/sub003/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 127449 Number of reverse mapping hits = 303 Checking for and removing duplicates Writing label file ./rh.MT.label 2235 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.perirhinal.label --trgsubject sub003 --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 = sub003 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/sub003/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 127449 Number of reverse mapping hits = 41 Checking for and removing duplicates Writing label file ./rh.perirhinal.label 793 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.thresh.label --trgsubject sub003 --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 = sub003 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/sub003/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 127449 Number of reverse mapping hits = 49 Checking for and removing duplicates Writing label file ./rh.BA1.thresh.label 925 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.thresh.label --trgsubject sub003 --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 = sub003 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/sub003/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 127449 Number of reverse mapping hits = 88 Checking for and removing duplicates Writing label file ./rh.BA2.thresh.label 2776 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.thresh.label --trgsubject sub003 --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 = sub003 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/sub003/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 127449 Number of reverse mapping hits = 21 Checking for and removing duplicates Writing label file ./rh.BA3a.thresh.label 1719 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.thresh.label --trgsubject sub003 --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 = sub003 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/sub003/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 127449 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 sub003 --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 = sub003 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/sub003/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 127449 Number of reverse mapping hits = 18 Checking for and removing duplicates Writing label file ./rh.BA4a.thresh.label 1406 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.thresh.label --trgsubject sub003 --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 = sub003 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/sub003/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 127449 Number of reverse mapping hits = 65 Checking for and removing duplicates Writing label file ./rh.BA4p.thresh.label 1554 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.thresh.label --trgsubject sub003 --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 = sub003 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/sub003/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 127449 Number of reverse mapping hits = 339 Checking for and removing duplicates Writing label file ./rh.BA6.thresh.label 7298 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.thresh.label --trgsubject sub003 --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 = sub003 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/sub003/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 127449 Number of reverse mapping hits = 58 Checking for and removing duplicates Writing label file ./rh.BA44.thresh.label 1070 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.thresh.label --trgsubject sub003 --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 = sub003 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/sub003/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 127449 Number of reverse mapping hits = 204 Checking for and removing duplicates Writing label file ./rh.BA45.thresh.label 1382 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.thresh.label --trgsubject sub003 --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 = sub003 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/sub003/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 127449 Number of reverse mapping hits = 1244 Checking for and removing duplicates Writing label file ./rh.V1.thresh.label 4476 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.thresh.label --trgsubject sub003 --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 = sub003 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/sub003/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 127449 Number of reverse mapping hits = 1639 Checking for and removing duplicates Writing label file ./rh.V2.thresh.label 5076 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.thresh.label --trgsubject sub003 --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 = sub003 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/sub003/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 127449 Number of reverse mapping hits = 21 Checking for and removing duplicates Writing label file ./rh.MT.thresh.label 289 mri_label2label: Done mris_label2annot --s sub003 --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/sub003/label cmdline mris_label2annot --s sub003 --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 snake5 machine x86_64 user fkaule subject sub003 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/sub003/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 88818 unhit vertices Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/label/rh.BA.annot mris_label2annot --s sub003 --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/sub003/label cmdline mris_label2annot --s sub003 --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 snake5 machine x86_64 user fkaule subject sub003 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/sub003/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 106521 unhit vertices Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/label/rh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab sub003 rh white computing statistics for each annotation in ./rh.BA.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 812 500 1581 2.048 0.676 0.171 0.059 20 2.0 BA1 3056 2077 4963 2.102 0.532 0.126 0.040 37 4.2 BA2 852 553 882 1.985 0.480 0.122 0.032 6 1.1 BA3a 1641 1125 2735 1.919 0.563 0.114 0.037 19 2.8 BA3b 1165 778 2563 2.606 0.594 0.117 0.028 11 1.4 BA4a 1050 681 1916 2.595 0.495 0.112 0.028 8 1.3 BA4p 6867 4714 17154 2.800 0.589 0.137 0.042 91 11.5 BA6 3307 2273 6666 2.615 0.392 0.122 0.034 41 4.6 BA44 4552 3085 10200 2.641 0.492 0.156 0.058 95 9.6 BA45 4286 3014 6239 1.921 0.581 0.166 0.081 105 13.3 V1 8716 5752 13223 2.091 0.510 0.175 0.070 200 23.6 V2 1817 1259 2863 2.108 0.383 0.140 0.150 72 2.9 MT 510 352 1660 3.308 0.706 0.161 0.083 14 1.5 perirhinal mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab sub003 rh white computing statistics for each annotation in ./rh.BA.thresh.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 518 314 1029 2.054 0.654 0.182 0.067 13 1.3 BA1 1571 1080 2530 2.070 0.521 0.111 0.038 17 1.9 BA2 734 468 659 1.908 0.387 0.120 0.033 5 1.0 BA3a 1352 943 1998 1.815 0.459 0.102 0.030 12 2.1 BA3b 631 424 1408 2.480 0.704 0.125 0.030 7 0.8 BA4a 878 585 1682 2.616 0.461 0.108 0.026 5 1.1 BA4p 4361 2981 11297 2.816 0.596 0.141 0.043 63 7.5 BA6 719 529 1806 2.718 0.369 0.139 0.043 13 1.2 BA44 1108 778 2918 2.754 0.473 0.172 0.067 31 2.8 BA45 4109 2884 5847 1.905 0.605 0.164 0.078 98 12.6 V1 4724 3108 6777 1.985 0.489 0.183 0.078 118 14.1 V2 223 169 547 2.335 0.390 0.132 0.036 2 0.4 MT /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label lh Thu Aug 8 23:22:46 CEST 2013 mris_spherical_average -erode 1 -orig white -t 0.4 -o sub003 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject sub003. processing subject lh.EC_average... reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 929 points to lh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label sub003 lh white limiting computations to label ./lh.entorhinal_exvivo.label. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 343 214 902 2.738 0.688 0.126 0.038 3 0.6 ./lh.entorhinal_exvivo.label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label rh Thu Aug 8 23:23:02 CEST 2013 mris_spherical_average -erode 1 -orig white -t 0.4 -o sub003 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label painting output onto subject sub003. processing subject rh.EC_average... reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 667 points to rh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label sub003 rh white limiting computations to label ./rh.entorhinal_exvivo.label. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 280 175 891 3.051 0.725 0.141 0.053 3 0.7 ./rh.entorhinal_exvivo.label #------------------------------------------ Started at Thu Aug 8 10:53:55 CEST 2013 Ended at Thu Aug 8 23:23:17 CEST 2013 #@#%# recon-all-run-time-hours 12.489 recon-all -s sub003 finished without error at Thu Aug 8 23:23:17 CEST 2013