Thu Aug 8 10:53:55 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006 /opt/freesurfer/5.3.0/bin/recon-all -i /home/data/exppsy/forrest_gump/openfmri.org/sub006/anatomy/highres001.nii.gz -cw256 -all -T2 /home/data/exppsy/forrest_gump/openfmri.org/sub006/anatomy/other/t2w001.nii.gz -T2pial -subjid sub006 -sd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer subjid sub006 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/sub006 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub006/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/001.mgz mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub006/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/anatomy/highres001.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998757, 0.0408089, 0.02861) j_ras = (0.0441177, 0.99097, 0.126615) k_ras = (0.0231846, -0.12772, 0.991539) writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/001.mgz... #-------------------------------------------- #@# T2/FLAIR Input Thu Aug 8 10:54:17 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub006/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub006/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/anatomy/other/t2w001.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998757, 0.0408089, 0.02861) j_ras = (0.0441177, 0.99097, 0.126615) k_ras = (0.0231846, -0.12772, 0.991539) writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz... #-------------------------------------------- #@# MotionCor Thu Aug 8 10:54:33 CEST 2013 Found 1 runs /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/mri/orig/001.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig.mgz --conform --cw256 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998757, 0.0408089, 0.02861) j_ras = (0.0441177, 0.99097, 0.126615) k_ras = (0.0231846, -0.12772, 0.991539) Original Data has (0.699921, 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/sub006/mri/orig.mgz... mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/talairach.xfm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Aug 8 10:55:14 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Thu Aug 8 10:58:10 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6592, pval=0.3663 >= threshold=0.0050) awk -f /opt/freesurfer/5.3.0/bin/extract_talairach_avi_QA.awk /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/talairach_avi.log tal_QC_AZS /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/talairach_avi.log TalAviQA: 0.96493 z-score: -2 #-------------------------------------------- #@# Nu Intensity Correction Thu Aug 8 10:58:11 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/sub006/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 10:58:11 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.12861 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.12861/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.12861/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.16415e-09, 1.86265e-09) j_ras = (-1.86265e-09, 1.49012e-08, -1) k_ras = (9.31323e-10, 1, -1.49012e-08) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.12861/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Aug 8 10:58:14 CEST 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.12861/nu0.mnc ./tmp.mri_nu_correct.mni.12861/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.12861/0/ [fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/] [2013-08-08 10:58:14] 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.12861/0/ ./tmp.mri_nu_correct.mni.12861/nu0.mnc ./tmp.mri_nu_correct.mni.12861/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done 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Processing:.................................................................Done Number of iterations: 25 CV of field change: 0.000992595 [fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/] [2013-08-08 10:58:53] running: /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.12861/nu0.mnc ./tmp.mri_nu_correct.mni.12861/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Thu Aug 8 10:59:01 CEST 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.12861/nu1.mnc ./tmp.mri_nu_correct.mni.12861/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.12861/1/ [fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/] [2013-08-08 10:59:01] 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.12861/1/ ./tmp.mri_nu_correct.mni.12861/nu1.mnc ./tmp.mri_nu_correct.mni.12861/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done 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Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 22 CV of field change: 0.000982201 [fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/] [2013-08-08 10:59:39] running: /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.12861/nu1.mnc ./tmp.mri_nu_correct.mni.12861/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.12861/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.12861/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/sub006/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.12861/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.12861/ones.mgz sysname Linux hostname snake5 machine x86_64 user fkaule input ./tmp.mri_nu_correct.mni.12861/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.12861/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.12861/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.12861/sum.junk --avgwf ./tmp.mri_nu_correct.mni.12861/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.12861/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.12861/sum.junk --avgwf ./tmp.mri_nu_correct.mni.12861/input.mean.dat sysname Linux hostname snake5 machine x86_64 user fkaule UseRobust 0 Loading ./tmp.mri_nu_correct.mni.12861/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.12861/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.12861/ones.mgz --i ./tmp.mri_nu_correct.mni.12861/nu2.mnc --sum ./tmp.mri_nu_correct.mni.12861/sum.junk --avgwf ./tmp.mri_nu_correct.mni.12861/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.12861/ones.mgz --i ./tmp.mri_nu_correct.mni.12861/nu2.mnc --sum ./tmp.mri_nu_correct.mni.12861/sum.junk --avgwf ./tmp.mri_nu_correct.mni.12861/output.mean.dat sysname Linux hostname snake5 machine x86_64 user fkaule UseRobust 0 Loading ./tmp.mri_nu_correct.mni.12861/ones.mgz Loading ./tmp.mri_nu_correct.mni.12861/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.12861/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.12861/nu2.mnc ./tmp.mri_nu_correct.mni.12861/nu2.mnc mul .95246908919991135291 Saving result to './tmp.mri_nu_correct.mni.12861/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.12861/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.12861/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.12861/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.16415e-09, 1.86265e-09) j_ras = (-1.86265e-09, 1.49012e-08, -1) k_ras = (9.31323e-10, 1, -1.49012e-08) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 8 seconds. mapping (12, 169) to ( 3, 110) Thu Aug 8 11:00:31 CEST 2013 mri_nu_correct.mni done mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Thu Aug 8 11:00:33 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.130 -0.028 0.007 3.552; 0.019 0.978 0.305 -29.156; -0.010 -0.429 1.099 -5.547; 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 = 19 Starting OpenSpline(): npoints = 19 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 108 gm peak at 48 (48), valley at 37 (37) csf peak at 12, setting threshold to 36 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 49 (49), valley at 38 (38) csf peak at 12, setting threshold to 36 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 52 seconds. #-------------------------------------------- #@# Skull Stripping Thu Aug 8 11:03:25 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri mri_em_register -skull nu.mgz /opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta ======= NUMBER OF OPENMP THREADS = 1 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=8.0 skull bounding box = (49, 0, 9) --> (203, 255, 206) using (100, 85, 108) as brain centroid... mean wm in atlas = 126, using box (81,53,84) --> (118, 116,132) to find MRI wm before smoothing, mri peak at 110 after smoothing, mri peak at 110, scaling input intensities by 1.145 scaling channel 0 by 1.14545 initial log_p = -4.8 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.579503 @ (-9.091, 27.273, -9.091) max log p = -4.430745 @ (4.545, -4.545, -4.545) max log p = -4.333447 @ (2.273, 2.273, 2.273) max log p = -4.291113 @ (1.136, -3.409, 3.409) max log p = -4.289512 @ (0.568, 0.568, -0.568) max log p = -4.289512 @ (0.000, 0.000, 0.000) Found translation: (-0.6, 22.2, -8.5): log p = -4.290 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.3 (thresh=-4.3) 1.150 0.000 0.000 -19.518; 0.000 1.111 0.298 -22.904; 0.000 -0.220 0.821 33.748; 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) 1.150 0.000 0.000 -19.518; 0.000 1.148 0.450 -36.545; 0.000 -0.426 0.965 37.642; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.150 0.000 0.000 -19.518; 0.000 1.148 0.450 -36.545; 0.000 -0.426 0.965 37.642; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.1 (thresh=-4.1) 1.150 0.000 0.000 -19.518; 0.000 1.195 0.393 -36.297; 0.000 -0.343 0.973 28.950; 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) 1.150 0.000 0.000 -19.518; 0.000 1.195 0.393 -36.297; 0.000 -0.343 0.973 28.950; 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) 1.152 -0.014 -0.022 -16.911; 0.019 1.193 0.401 -40.410; 0.019 -0.352 0.968 27.618; 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) 1.150 -0.014 -0.022 -16.577; 0.019 1.196 0.402 -40.788; 0.019 -0.351 0.967 27.711; 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) 1.150 -0.014 -0.022 -16.577; 0.019 1.196 0.402 -40.788; 0.019 -0.351 0.967 27.711; 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 1.14969 -0.01394 -0.02235 -16.57664; 0.01903 1.19625 0.40165 -40.78821; 0.01860 -0.35144 0.96652 27.71052; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.14969 -0.01394 -0.02235 -16.57664; 0.01903 1.19625 0.40165 -40.78821; 0.01860 -0.35144 0.96652 27.71052; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 4 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.150 -0.014 -0.022 -16.577; 0.019 1.196 0.402 -40.788; 0.019 -0.351 0.967 27.711; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -4.0 (old=-4.8) transform before final EM align: 1.150 -0.014 -0.022 -16.577; 0.019 1.196 0.402 -40.788; 0.019 -0.351 0.967 27.711; 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 1.14969 -0.01394 -0.02235 -16.57664; 0.01903 1.19625 0.40165 -40.78821; 0.01860 -0.35144 0.96652 27.71052; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.14969 -0.01394 -0.02235 -16.57664; 0.01903 1.19625 0.40165 -40.78821; 0.01860 -0.35144 0.96652 27.71052; 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: 1.150 -0.014 -0.022 -16.577; 0.019 1.196 0.402 -40.788; 0.019 -0.351 0.967 27.711; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 40 minutes and 23 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=128 y=85 z=117 r=94 first estimation of the main basin volume: 3486435 voxels Looking for seedpoints 2 found in the cerebellum 16 found in the rest of the brain global maximum in x=147, y=83, z=76, Imax=255 CSF=13, 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=20180669030 voxels, voxel volume =1.000 = 20180669030 mmm3 = 20180668.416 cm3 done. PostAnalyze...Basin Prior 129 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=94, z=110, r=11272 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 45874 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1031766979 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1091834324 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1073225896 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1082017464 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=24 , nb = 1069711904 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 4, 5, 24, 49 after analyzing : 4, 18, 25, 25 RIGHT_CER before analyzing : 4, 4, 19, 50 after analyzing : 4, 18, 25, 26 LEFT_CER before analyzing : 4, 4, 20, 51 after analyzing : 4, 18, 25, 26 RIGHT_BRAIN before analyzing : 4, 5, 24, 49 after analyzing : 4, 18, 25, 25 LEFT_BRAIN before analyzing : 4, 5, 24, 45 after analyzing : 4, 18, 25, 24 OTHER before analyzing : 24, 55, 79, 95 after analyzing : 24, 71, 79, 77 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...70 iterations *********************VALIDATION********************* curvature mean = -0.012, std = 0.011 curvature mean = 74.901, std = 9.916 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 1.94, sigma = 3.55 after rotation: sse = 1.94, sigma = 3.55 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 2.15, its var is 3.63 before Erosion-Dilatation 0.50% 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...47 iterations mri_strip_skull: done peeling brain Brain Size = 2061870 voxels, voxel volume = 1.000 mm3 = 2061870 mmm3 = 2061.870 cm3 ****************************** Saving brainmask.auto.mgz done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Thu Aug 8 11:44:20 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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=20.0 skull bounding box = (58, 30, 25) --> (194, 179, 204) using (103, 80, 115) as brain centroid... mean wm in atlas = 107, using box (86,62,93) --> (119, 98,137) to find MRI wm before smoothing, mri peak at 108 after smoothing, mri peak at 109, scaling input intensities by 0.982 scaling channel 0 by 0.981651 initial log_p = -4.5 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.122993 @ (-9.091, 27.273, -9.091) max log p = -3.901602 @ (4.545, -4.545, 4.545) max log p = -3.831934 @ (2.273, -2.273, -2.273) max log p = -3.790007 @ (-1.136, 1.136, -1.136) max log p = -3.768490 @ (0.568, -0.568, -0.568) max log p = -3.768490 @ (0.000, 0.000, 0.000) Found translation: (-2.8, 21.0, -8.5): log p = -3.768 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.4, old_max_log_p =-3.8 (thresh=-3.8) 1.075 0.000 0.000 -12.565; 0.000 1.028 0.275 -5.513; 0.000 -0.236 0.883 27.980; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4) 1.075 0.000 0.000 -12.565; 0.000 1.028 0.275 -5.513; 0.000 -0.236 0.883 27.980; 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 =-3.4 (thresh=-3.4) 1.074 0.026 0.039 -17.352; -0.034 1.038 0.307 -9.231; -0.035 -0.266 0.856 40.123; 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) 1.054 0.025 0.038 -14.649; -0.034 1.038 0.307 -9.231; -0.035 -0.266 0.856 40.123; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.3 (thresh=-3.3) 1.057 0.021 0.022 -13.719; -0.025 1.045 0.279 -8.970; -0.018 -0.231 0.863 32.977; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2) 1.057 0.021 0.022 -13.719; -0.025 1.044 0.279 -8.820; -0.018 -0.231 0.863 32.977; 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) 1.057 0.021 0.022 -13.719; -0.025 1.044 0.279 -8.820; -0.018 -0.231 0.863 32.977; 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 1.05686 0.02056 0.02170 -13.71878; -0.02464 1.04352 0.27875 -8.82042; -0.01831 -0.23067 0.86304 32.97652; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 1.05686 0.02056 0.02170 -13.71878; -0.02464 1.04352 0.27875 -8.82042; -0.01831 -0.23067 0.86304 32.97652; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.057 0.021 0.022 -13.719; -0.025 1.044 0.279 -8.820; -0.018 -0.231 0.863 32.977; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.2 (old=-4.5) transform before final EM align: 1.057 0.021 0.022 -13.719; -0.025 1.044 0.279 -8.820; -0.018 -0.231 0.863 32.977; 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 1.05686 0.02056 0.02170 -13.71878; -0.02464 1.04352 0.27875 -8.82042; -0.01831 -0.23067 0.86304 32.97652; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 1.05686 0.02056 0.02170 -13.71878; -0.02464 1.04352 0.27875 -8.82042; -0.01831 -0.23067 0.86304 32.97652; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = 3.9 tol 0.000000 final transform: 1.057 0.021 0.022 -13.719; -0.025 1.044 0.279 -8.820; -0.018 -0.231 0.863 32.977; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 27 minutes and 20 seconds. #-------------------------------------- #@# CA Normalize Thu Aug 8 12:11:40 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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=20.0 skull bounding box = (57, 30, 25) --> (194, 179, 204) using (103, 80, 115) as brain centroid... mean wm in atlas = 107, using box (86,62,93) --> (119, 98,137) to find MRI wm before smoothing, mri peak at 108 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 1.057 0.021 0.022 -13.719; -0.025 1.044 0.279 -8.820; -0.018 -0.231 0.863 32.977; 0.000 0.000 0.000 1.000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (127, 33, 28) --> (190, 145, 210) Left_Cerebral_White_Matter: limiting intensities to 94.0 --> 160.0 0 of 71 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (67, 33, 27) --> (129, 136, 211) Right_Cerebral_White_Matter: limiting intensities to 98.0 --> 160.0 0 of 72 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (130, 118, 60) --> (175, 161, 119) Left_Cerebellum_White_Matter: limiting intensities to 82.0 --> 160.0 0 of 19 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (84, 118, 56) --> (128, 159, 119) Right_Cerebellum_White_Matter: limiting intensities to 84.0 --> 160.0 0 of 10 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (112, 106, 98) --> (143, 172, 131) Brain_Stem: limiting intensities to 80.0 --> 160.0 0 of 12 (0.0%) samples deleted using 184 total control points for intensity normalization... bias field = 1.002 +- 0.050 0 of 184 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (127, 33, 28) --> (190, 145, 210) Left_Cerebral_White_Matter: limiting intensities to 94.0 --> 154.0 0 of 116 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (67, 33, 27) --> (129, 136, 211) Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 154.0 0 of 112 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (130, 118, 60) --> (175, 161, 119) Left_Cerebellum_White_Matter: limiting intensities to 83.0 --> 154.0 0 of 33 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (84, 118, 56) --> (128, 159, 119) Right_Cerebellum_White_Matter: limiting intensities to 94.0 --> 154.0 21 of 44 (47.7%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (112, 106, 98) --> (143, 172, 131) Brain_Stem: limiting intensities to 74.0 --> 154.0 0 of 74 (0.0%) samples deleted using 379 total control points for intensity normalization... bias field = 0.990 +- 0.054 0 of 358 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (127, 33, 28) --> (190, 145, 210) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 152.0 0 of 200 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (67, 33, 27) --> (129, 136, 211) Right_Cerebral_White_Matter: limiting intensities to 94.0 --> 152.0 0 of 204 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (130, 118, 60) --> (175, 161, 119) Left_Cerebellum_White_Matter: limiting intensities to 80.0 --> 152.0 0 of 40 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (84, 118, 56) --> (128, 159, 119) Right_Cerebellum_White_Matter: limiting intensities to 74.0 --> 152.0 0 of 42 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (112, 106, 98) --> (143, 172, 131) Brain_Stem: limiting intensities to 70.0 --> 152.0 0 of 82 (0.0%) samples deleted using 568 total control points for intensity normalization... bias field = 1.010 +- 0.046 1 of 568 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 2 minutes and 3 seconds. #-------------------------------------- #@# CA Reg Thu Aug 8 12:13:44 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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) = 1.02 (predicted orig area = 7.8) 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=0.920, neg=0, invalid=96777 0001: dt=129.472000, rms=0.826 (10.230%), neg=0, invalid=96777 0002: dt=129.472000, rms=0.804 (2.702%), neg=0, invalid=96777 0003: dt=295.936000, rms=0.789 (1.859%), neg=0, invalid=96777 0004: dt=129.472000, rms=0.785 (0.456%), neg=0, invalid=96777 0005: dt=295.936000, rms=0.779 (0.775%), neg=0, invalid=96777 0006: dt=73.984000, rms=0.777 (0.346%), neg=0, invalid=96777 0007: dt=1479.680000, rms=0.765 (1.525%), neg=0, invalid=96777 0008: dt=92.480000, rms=0.762 (0.317%), neg=0, invalid=96777 0009: dt=443.904000, rms=0.759 (0.363%), neg=0, invalid=96777 0010: dt=55.488000, rms=0.758 (0.139%), neg=0, invalid=96777 0011: dt=55.488000, rms=0.758 (0.040%), neg=0, invalid=96777 0012: dt=55.488000, rms=0.758 (0.051%), neg=0, invalid=96777 0013: dt=55.488000, rms=0.757 (0.090%), neg=0, invalid=96777 0014: dt=55.488000, rms=0.756 (0.142%), neg=0, invalid=96777 0015: dt=55.488000, rms=0.755 (0.155%), neg=0, invalid=96777 0016: dt=55.488000, rms=0.754 (0.153%), neg=0, invalid=96777 0017: dt=55.488000, rms=0.752 (0.154%), neg=0, invalid=96777 0018: dt=55.488000, rms=0.751 (0.154%), neg=0, invalid=96777 0019: dt=55.488000, rms=0.750 (0.150%), neg=0, invalid=96777 0020: dt=55.488000, rms=0.749 (0.166%), neg=0, invalid=96777 0021: dt=55.488000, rms=0.748 (0.167%), neg=0, invalid=96777 0022: dt=55.488000, rms=0.747 (0.155%), neg=0, invalid=96777 0023: dt=55.488000, rms=0.746 (0.139%), neg=0, invalid=96777 0024: dt=55.488000, rms=0.745 (0.126%), neg=0, invalid=96777 0025: dt=55.488000, rms=0.744 (0.123%), neg=0, invalid=96777 0026: dt=55.488000, rms=0.743 (0.126%), neg=0, invalid=96777 0027: dt=55.488000, rms=0.742 (0.149%), neg=0, invalid=96777 0028: dt=55.488000, rms=0.741 (0.142%), neg=0, invalid=96777 0029: dt=55.488000, rms=0.740 (0.131%), neg=0, invalid=96777 0030: dt=55.488000, rms=0.739 (0.113%), neg=0, invalid=96777 0031: dt=55.488000, rms=0.738 (0.101%), neg=0, invalid=96777 0032: dt=517.888000, rms=0.737 (0.159%), neg=0, invalid=96777 0033: dt=27.744000, rms=0.737 (0.001%), neg=0, invalid=96777 0034: dt=27.744000, rms=0.737 (0.001%), neg=0, invalid=96777 0035: dt=27.744000, rms=0.737 (-0.011%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.737, neg=0, invalid=96777 0036: dt=92.480000, rms=0.736 (0.052%), neg=0, invalid=96777 0037: dt=369.920000, rms=0.735 (0.237%), neg=0, invalid=96777 0038: dt=32.368000, rms=0.735 (0.006%), neg=0, invalid=96777 0039: dt=32.368000, rms=0.735 (0.010%), neg=0, invalid=96777 0040: dt=32.368000, rms=0.735 (0.002%), neg=0, invalid=96777 0041: dt=32.368000, rms=0.735 (-0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.739, neg=0, invalid=96777 0042: dt=145.152000, rms=0.722 (2.270%), neg=0, invalid=96777 0043: dt=124.416000, rms=0.716 (0.928%), neg=0, invalid=96777 0044: dt=36.288000, rms=0.708 (1.005%), neg=0, invalid=96777 0045: dt=20.736000, rms=0.707 (0.170%), neg=0, invalid=96777 0046: dt=20.736000, rms=0.706 (0.181%), neg=0, invalid=96777 0047: dt=20.736000, rms=0.704 (0.308%), neg=0, invalid=96777 0048: dt=20.736000, rms=0.701 (0.414%), neg=0, invalid=96777 0049: dt=20.736000, rms=0.697 (0.491%), neg=0, invalid=96777 0050: dt=20.736000, rms=0.694 (0.558%), neg=0, invalid=96777 0051: dt=20.736000, rms=0.689 (0.592%), neg=0, invalid=96777 0052: dt=20.736000, rms=0.685 (0.576%), neg=0, invalid=96777 0053: dt=20.736000, rms=0.682 (0.555%), neg=0, invalid=96777 0054: dt=20.736000, rms=0.678 (0.513%), neg=0, invalid=96777 0055: dt=20.736000, rms=0.675 (0.476%), neg=0, invalid=96777 0056: dt=20.736000, rms=0.672 (0.425%), neg=0, invalid=96777 0057: dt=20.736000, rms=0.670 (0.376%), neg=0, invalid=96777 0058: dt=20.736000, rms=0.667 (0.334%), neg=0, invalid=96777 0059: dt=20.736000, rms=0.665 (0.280%), neg=0, invalid=96777 0060: dt=20.736000, rms=0.664 (0.249%), neg=0, invalid=96777 0061: dt=20.736000, rms=0.662 (0.238%), neg=0, invalid=96777 0062: dt=20.736000, rms=0.661 (0.236%), neg=0, invalid=96777 0063: dt=20.736000, rms=0.659 (0.200%), neg=0, invalid=96777 0064: dt=20.736000, rms=0.658 (0.155%), neg=0, invalid=96777 0065: dt=20.736000, rms=0.658 (0.110%), neg=0, invalid=96777 0066: dt=20.736000, rms=0.657 (0.098%), neg=0, invalid=96777 0067: dt=145.152000, rms=0.656 (0.130%), neg=0, invalid=96777 0068: dt=6.480000, rms=0.656 (0.000%), neg=0, invalid=96777 0069: dt=6.480000, rms=0.656 (0.003%), neg=0, invalid=96777 0070: dt=6.480000, rms=0.656 (-0.011%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.656, neg=0, invalid=96777 0071: dt=15.552000, rms=0.656 (0.025%), neg=0, invalid=96777 0072: dt=20.736000, rms=0.656 (0.019%), neg=0, invalid=96777 0073: dt=20.736000, rms=0.656 (0.017%), neg=0, invalid=96777 0074: dt=20.736000, rms=0.656 (-0.005%), neg=0, invalid=96777 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.681, neg=0, invalid=96777 0075: dt=7.157895, rms=0.681 (0.097%), neg=0, invalid=96777 0076: dt=2.800000, rms=0.681 (0.015%), neg=0, invalid=96777 0077: dt=2.800000, rms=0.681 (0.006%), neg=0, invalid=96777 0078: dt=2.800000, rms=0.681 (-0.022%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.681, neg=0, invalid=96777 0079: dt=0.000000, rms=0.681 (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=0.747, neg=0, invalid=96777 0080: dt=5.676259, rms=0.730 (2.311%), neg=0, invalid=96777 0081: dt=2.880000, rms=0.729 (0.101%), neg=0, invalid=96777 0082: dt=2.880000, rms=0.729 (-0.020%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.729, neg=0, invalid=96777 0083: dt=0.000000, rms=0.729 (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=0.798, neg=0, invalid=96777 0084: dt=0.877108, rms=0.795 (0.311%), neg=0, invalid=96777 0085: dt=2.204082, rms=0.790 (0.711%), neg=0, invalid=96777 0086: dt=1.280000, rms=0.788 (0.144%), neg=0, invalid=96777 0087: dt=1.280000, rms=0.787 (0.204%), neg=0, invalid=96777 0088: dt=1.280000, rms=0.786 (0.053%), neg=0, invalid=96777 0089: dt=1.280000, rms=0.786 (-0.358%), neg=0, invalid=96777 0090: dt=0.000000, rms=0.786 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.786, neg=0, invalid=96777 0091: dt=0.500000, rms=0.786 (0.058%), neg=0, invalid=96777 0092: dt=0.448000, rms=0.786 (0.007%), neg=0, invalid=96777 0093: dt=0.448000, rms=0.786 (-0.001%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.742, neg=0, invalid=96777 0094: dt=0.384000, rms=0.723 (2.622%), neg=0, invalid=96777 0095: dt=0.000000, rms=0.722 (0.005%), neg=0, invalid=96777 0096: dt=0.050000, rms=0.722 (-0.461%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.722, neg=0, invalid=96777 0097: dt=0.000000, rms=0.722 (0.000%), neg=0, invalid=96777 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.07898 ( 6) Left_Lateral_Ventricle (4): linear fit = 0.20 x + 0.0 (2036 voxels, overlap=0.082) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (2036 voxels, peak = 5), gca=9.6 gca peak = 0.14022 (22) mri peak = 0.14083 ( 8) Right_Lateral_Ventricle (43): linear fit = 0.32 x + 0.0 (1080 voxels, overlap=0.007) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (1080 voxels, peak = 7), gca=8.8 gca peak = 0.24234 (100) mri peak = 0.07527 (83) Right_Pallidum (52): linear fit = 0.83 x + 0.0 (426 voxels, overlap=0.049) Right_Pallidum (52): linear fit = 0.83 x + 0.0 (426 voxels, peak = 84), gca=83.5 gca peak = 0.19192 (97) mri peak = 0.12903 (77) Left_Pallidum (13): linear fit = 0.79 x + 0.0 (305 voxels, overlap=0.031) Left_Pallidum (13): linear fit = 0.79 x + 0.0 (305 voxels, peak = 76), gca=76.1 gca peak = 0.24007 (63) mri peak = 0.06263 (52) Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (495 voxels, overlap=0.567) Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (495 voxels, peak = 55), gca=55.1 gca peak = 0.29892 (64) mri peak = 0.07822 (59) Left_Hippocampus (17): linear fit = 0.90 x + 0.0 (594 voxels, overlap=0.712) Left_Hippocampus (17): linear fit = 0.90 x + 0.0 (594 voxels, peak = 58), gca=57.9 gca peak = 0.12541 (104) mri peak = 0.09221 (106) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (76693 voxels, overlap=0.760) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (76693 voxels, peak = 108), gca=107.6 gca peak = 0.13686 (104) mri peak = 0.08402 (106) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (81954 voxels, overlap=0.713) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (81954 voxels, peak = 109), gca=108.7 gca peak = 0.11691 (63) mri peak = 0.05463 (50) Left_Cerebral_Cortex (3): linear fit = 0.75 x + 0.0 (23299 voxels, overlap=0.013) Left_Cerebral_Cortex (3): linear fit = 0.75 x + 0.0 (23299 voxels, peak = 47), gca=46.9 gca peak = 0.13270 (63) mri peak = 0.06566 (52) Right_Cerebral_Cortex (42): linear fit = 0.77 x + 0.0 (23129 voxels, overlap=0.030) Right_Cerebral_Cortex (42): linear fit = 0.77 x + 0.0 (23129 voxels, peak = 49), gca=48.8 gca peak = 0.15182 (70) mri peak = 0.08707 (61) Right_Caudate (50): linear fit = 0.82 x + 0.0 (496 voxels, overlap=0.060) Right_Caudate (50): linear fit = 0.82 x + 0.0 (496 voxels, peak = 58), gca=57.8 gca peak = 0.14251 (76) mri peak = 0.07843 (62) Left_Caudate (11): linear fit = 0.81 x + 0.0 (658 voxels, overlap=0.019) Left_Caudate (11): linear fit = 0.81 x + 0.0 (658 voxels, peak = 61), gca=61.2 gca peak = 0.12116 (60) mri peak = 0.04924 (52) Left_Cerebellum_Cortex (8): linear fit = 0.86 x + 0.0 (8972 voxels, overlap=0.393) Left_Cerebellum_Cortex (8): linear fit = 0.86 x + 0.0 (8972 voxels, peak = 51), gca=51.3 gca peak = 0.12723 (61) mri peak = 0.03541 (54) Right_Cerebellum_Cortex (47): linear fit = 0.92 x + 0.0 (10365 voxels, overlap=0.602) Right_Cerebellum_Cortex (47): linear fit = 0.92 x + 0.0 (10365 voxels, peak = 56), gca=55.8 gca peak = 0.22684 (88) mri peak = 0.07428 (89) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (7794 voxels, overlap=0.948) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (7794 voxels, peak = 90), gca=90.2 gca peak = 0.21067 (87) mri peak = 0.07354 (87) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (7053 voxels, overlap=0.965) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (7053 voxels, peak = 88), gca=88.3 gca peak = 0.25455 (62) mri peak = 0.06376 (61) Left_Amygdala (18): linear fit = 0.93 x + 0.0 (338 voxels, overlap=0.325) Left_Amygdala (18): linear fit = 0.93 x + 0.0 (338 voxels, peak = 57), gca=57.4 gca peak = 0.39668 (62) mri peak = 0.11341 (52) Right_Amygdala (54): linear fit = 0.86 x + 0.0 (358 voxels, overlap=0.244) Right_Amygdala (54): linear fit = 0.86 x + 0.0 (358 voxels, peak = 53), gca=53.0 gca peak = 0.10129 (93) mri peak = 0.04493 (97) Left_Thalamus_Proper (10): linear fit = 1.05 x + 0.0 (6114 voxels, overlap=0.934) Left_Thalamus_Proper (10): linear fit = 1.05 x + 0.0 (6114 voxels, peak = 98), gca=98.1 gca peak = 0.12071 (89) mri peak = 0.05059 (91) Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (4304 voxels, overlap=0.986) Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (4304 voxels, peak = 91), gca=91.2 gca peak = 0.13716 (82) mri peak = 0.04188 (73) Left_Putamen (12): linear fit = 0.92 x + 0.0 (1836 voxels, overlap=0.536) Left_Putamen (12): linear fit = 0.92 x + 0.0 (1836 voxels, peak = 75), gca=75.0 gca peak = 0.15214 (84) mri peak = 0.05570 (69) Right_Putamen (51): linear fit = 0.83 x + 0.0 (2150 voxels, overlap=0.023) Right_Putamen (51): linear fit = 0.83 x + 0.0 (2150 voxels, peak = 70), gca=70.1 gca peak = 0.08983 (85) mri peak = 0.07156 (87) Brain_Stem (16): linear fit = 1.03 x + 0.0 (11745 voxels, overlap=0.778) Brain_Stem (16): linear fit = 1.03 x + 0.0 (11745 voxels, peak = 88), gca=88.0 gca peak = 0.11809 (92) mri peak = 0.05832 (89) Right_VentralDC (60): linear fit = 1.04 x + 0.0 (830 voxels, overlap=0.841) Right_VentralDC (60): linear fit = 1.04 x + 0.0 (830 voxels, peak = 96), gca=96.1 gca peak = 0.12914 (94) mri peak = 0.06610 (96) Left_VentralDC (28): linear fit = 1.01 x + 0.0 (887 voxels, overlap=0.860) Left_VentralDC (28): linear fit = 1.01 x + 0.0 (887 voxels, peak = 95), gca=95.4 gca peak = 0.21100 (36) mri peak = 0.50000 (54) Third_Ventricle (14): linear fit = 1.49 x + 0.0 (61 voxels, overlap=2.064) Third_Ventricle (14): linear fit = 1.49 x + 0.0 (61 voxels, peak = 53), gca=53.5 gca peak = 0.13542 (27) mri peak = 0.12434 (11) Fourth_Ventricle (15): linear fit = 0.37 x + 0.0 (399 voxels, overlap=0.024) Fourth_Ventricle (15): linear fit = 0.37 x + 0.0 (399 voxels, peak = 10), gca=9.9 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak Fourth_Ventricle = 0.13542 (27) gca peak CSF = 0.17123 (45) gca peak Left_Accumbens_area = 0.25875 (69) gca peak Left_undetermined = 0.96240 (36) gca peak Left_vessel = 0.33262 (65) gca peak Left_choroid_plexus = 0.09846 (46) gca peak Right_Inf_Lat_Vent = 0.28113 (34) gca peak Right_Accumbens_area = 0.27120 (72) gca peak Right_vessel = 0.61915 (60) gca peak Right_choroid_plexus = 0.12775 (51) gca peak Fifth_Ventricle = 0.45329 (44) gca peak WM_hypointensities = 0.11729 (81) gca peak non_WM_hypointensities = 0.10912 (56) gca peak Optic_Chiasm = 0.33287 (75) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 0.85 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 0.76 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=0.762, neg=0, invalid=96777 0098: dt=129.472000, rms=0.758 (0.578%), neg=0, invalid=96777 0099: dt=129.472000, rms=0.756 (0.302%), neg=0, invalid=96777 0100: dt=129.472000, rms=0.754 (0.225%), neg=0, invalid=96777 0101: dt=129.472000, rms=0.753 (0.132%), neg=0, invalid=96777 0102: dt=129.472000, rms=0.751 (0.185%), neg=0, invalid=96777 0103: dt=73.984000, rms=0.751 (0.046%), neg=0, invalid=96777 0104: dt=73.984000, rms=0.750 (0.088%), neg=0, invalid=96777 0105: dt=73.984000, rms=0.750 (0.119%), neg=0, invalid=96777 0106: dt=73.984000, rms=0.749 (0.130%), neg=0, invalid=96777 0107: dt=73.984000, rms=0.748 (0.132%), neg=0, invalid=96777 0108: dt=73.984000, rms=0.747 (0.149%), neg=0, invalid=96777 0109: dt=73.984000, rms=0.745 (0.142%), neg=0, invalid=96777 0110: dt=73.984000, rms=0.745 (0.119%), neg=0, invalid=96777 0111: dt=73.984000, rms=0.744 (0.094%), neg=0, invalid=96777 0112: dt=73.984000, rms=0.743 (0.092%), neg=0, invalid=96777 0113: dt=73.984000, rms=0.742 (0.112%), neg=0, invalid=96777 0114: dt=73.984000, rms=0.742 (0.092%), neg=0, invalid=96777 0115: dt=73.984000, rms=0.741 (0.084%), neg=0, invalid=96777 0116: dt=73.984000, rms=0.740 (0.079%), neg=0, invalid=96777 0117: dt=73.984000, rms=0.740 (0.070%), neg=0, invalid=96777 0118: dt=73.984000, rms=0.739 (0.078%), neg=0, invalid=96777 0119: dt=73.984000, rms=0.739 (0.084%), neg=0, invalid=96777 0120: dt=73.984000, rms=0.738 (0.076%), neg=0, invalid=96777 0121: dt=73.984000, rms=0.738 (0.077%), neg=0, invalid=96777 0122: dt=36.992000, rms=0.738 (0.009%), neg=0, invalid=96777 0123: dt=36.992000, rms=0.738 (0.007%), neg=0, invalid=96777 0124: dt=0.505750, rms=0.738 (0.000%), neg=0, invalid=96777 0125: dt=0.505750, rms=0.738 (0.000%), neg=0, invalid=96777 0126: dt=0.252875, rms=0.738 (0.000%), neg=0, invalid=96777 0127: dt=0.126438, rms=0.738 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.738, neg=0, invalid=96777 0128: dt=0.000000, rms=0.738 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.738, neg=0, invalid=96777 0129: dt=0.000000, rms=0.738 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.738, neg=0, invalid=96777 0130: dt=0.000000, rms=0.738 (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=0.739, neg=0, invalid=96777 0131: dt=75.304540, rms=0.664 (10.116%), neg=0, invalid=96777 0132: dt=25.094225, rms=0.647 (2.551%), neg=0, invalid=96777 0133: dt=2.800000, rms=0.645 (0.371%), neg=0, invalid=96777 0134: dt=8.000000, rms=0.640 (0.722%), neg=0, invalid=96777 0135: dt=44.800000, rms=0.628 (1.826%), neg=0, invalid=96777 0136: dt=2.800000, rms=0.627 (0.187%), neg=0, invalid=96777 0137: dt=8.000000, rms=0.625 (0.339%), neg=0, invalid=96777 0138: dt=44.800000, rms=0.619 (1.042%), neg=0, invalid=96777 0139: dt=11.200000, rms=0.616 (0.356%), neg=0, invalid=96777 0140: dt=13.714286, rms=0.614 (0.336%), neg=0, invalid=96777 0141: dt=11.200000, rms=0.613 (0.213%), neg=0, invalid=96777 0142: dt=19.200000, rms=0.611 (0.301%), neg=0, invalid=96777 0143: dt=8.000000, rms=0.610 (0.229%), neg=0, invalid=96777 0144: dt=44.800000, rms=0.608 (0.358%), neg=0, invalid=96777 0145: dt=2.800000, rms=0.606 (0.255%), neg=0, invalid=96777 0146: dt=7.353535, rms=0.604 (0.294%), neg=0, invalid=96777 0147: dt=153.600000, rms=0.600 (0.650%), neg=0, invalid=96777 0148: dt=9.486339, rms=0.593 (1.163%), neg=0, invalid=96777 0149: dt=11.200000, rms=0.592 (0.300%), neg=0, invalid=96777 0150: dt=11.200000, rms=0.591 (0.129%), neg=0, invalid=96777 0151: dt=44.800000, rms=0.590 (0.185%), neg=0, invalid=96777 0152: dt=8.655738, rms=0.589 (0.166%), neg=0, invalid=96777 0153: dt=25.600000, rms=0.588 (0.103%), neg=0, invalid=96777 0154: dt=9.600000, rms=0.587 (0.113%), neg=0, invalid=96777 0155: dt=19.200000, rms=0.587 (0.077%), neg=0, invalid=96777 0156: dt=11.200000, rms=0.586 (0.093%), neg=0, invalid=96777 0157: dt=11.200000, rms=0.586 (0.070%), neg=0, invalid=96777 0158: dt=11.200000, rms=0.586 (0.068%), neg=0, invalid=96777 0159: dt=38.400000, rms=0.585 (0.117%), neg=0, invalid=96777 0160: dt=8.380952, rms=0.584 (0.122%), neg=0, invalid=96777 0161: dt=25.600000, rms=0.584 (0.089%), neg=0, invalid=96777 0162: dt=8.000000, rms=0.583 (0.084%), neg=0, invalid=96777 0163: dt=32.000000, rms=0.583 (0.090%), neg=0, invalid=96777 0164: dt=8.000000, rms=0.582 (0.095%), neg=0, invalid=96777 0165: dt=32.000000, rms=0.582 (0.100%), neg=0, invalid=96777 0166: dt=6.400000, rms=0.581 (0.065%), neg=0, invalid=96777 0167: dt=153.600000, rms=0.579 (0.438%), neg=0, invalid=96777 0168: dt=0.150000, rms=0.579 (0.002%), neg=0, invalid=96777 0169: dt=0.004687, rms=0.579 (0.001%), neg=0, invalid=96777 0170: dt=0.000586, rms=0.579 (0.000%), neg=0, invalid=96777 0171: dt=0.000293, rms=0.579 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.579, neg=0, invalid=96777 0172: dt=0.000488, rms=0.579 (0.000%), neg=0, invalid=96777 0173: dt=0.000000, rms=0.579 (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=0.601, neg=0, invalid=96777 0174: dt=2.305085, rms=0.600 (0.105%), neg=0, invalid=96777 0175: dt=0.252000, rms=0.600 (0.015%), neg=0, invalid=96777 0176: dt=0.252000, rms=0.600 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.600, neg=0, invalid=96777 0177: dt=2.304000, rms=0.600 (0.051%), neg=0, invalid=96777 0178: dt=1.008000, rms=0.600 (0.011%), neg=0, invalid=96777 0179: dt=1.008000, rms=0.600 (-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=0.637, neg=0, invalid=96777 0180: dt=1.536313, rms=0.634 (0.516%), neg=0, invalid=96777 0181: dt=0.384000, rms=0.634 (0.013%), neg=0, invalid=96777 0182: dt=0.384000, rms=0.634 (-0.006%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.634, neg=0, invalid=96777 0183: dt=1.536000, rms=0.633 (0.203%), neg=0, invalid=96777 0184: dt=0.448000, rms=0.633 (0.015%), neg=0, invalid=96777 0185: dt=0.448000, rms=0.633 (-0.001%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.595, neg=0, invalid=96777 0186: dt=0.384000, rms=0.575 (3.369%), neg=0, invalid=96777 0187: dt=0.007000, rms=0.574 (0.014%), neg=0, invalid=96777 0188: dt=0.007000, rms=0.574 (0.019%), neg=0, invalid=96777 0189: dt=0.007000, rms=0.574 (0.036%), neg=0, invalid=96777 0190: dt=0.007000, rms=0.574 (0.053%), neg=0, invalid=96777 0191: dt=0.007000, rms=0.573 (0.064%), neg=0, invalid=96777 0192: dt=0.007000, rms=0.573 (0.075%), neg=0, invalid=96777 0193: dt=0.007000, rms=0.573 (0.085%), neg=0, invalid=96777 0194: dt=0.007000, rms=0.572 (0.094%), neg=0, invalid=96777 0195: dt=0.007000, rms=0.571 (0.099%), neg=0, invalid=96777 0196: dt=0.007000, rms=0.571 (0.102%), neg=0, invalid=96777 0197: dt=0.007000, rms=0.570 (0.106%), neg=0, invalid=96777 0198: dt=0.007000, rms=0.570 (0.107%), neg=0, invalid=96777 0199: dt=0.007000, rms=0.569 (0.111%), neg=0, invalid=96777 0200: dt=0.007000, rms=0.568 (0.110%), neg=0, invalid=96777 0201: dt=0.007000, rms=0.568 (0.108%), neg=0, invalid=96777 0202: dt=0.007000, rms=0.567 (0.107%), neg=0, invalid=96777 0203: dt=0.007000, rms=0.567 (0.104%), neg=0, invalid=96777 0204: dt=0.007000, rms=0.566 (0.101%), neg=0, invalid=96777 0205: dt=0.007000, rms=0.565 (0.096%), neg=0, invalid=96777 0206: dt=0.007000, rms=0.565 (0.093%), neg=0, invalid=96777 0207: dt=0.007000, rms=0.564 (0.090%), neg=0, invalid=96777 0208: dt=0.007000, rms=0.564 (0.086%), neg=0, invalid=96777 0209: dt=0.007000, rms=0.563 (0.080%), neg=0, invalid=96777 0210: dt=0.007000, rms=0.563 (0.078%), neg=0, invalid=96777 0211: dt=0.007000, rms=0.563 (0.074%), neg=0, invalid=96777 0212: dt=0.007000, rms=0.562 (0.068%), neg=0, invalid=96777 0213: dt=0.007000, rms=0.562 (0.063%), neg=0, invalid=96777 0214: dt=0.007000, rms=0.562 (0.058%), neg=0, invalid=96777 0215: dt=0.007000, rms=0.561 (0.057%), neg=0, invalid=96777 0216: dt=0.007000, rms=0.561 (0.053%), neg=0, invalid=96777 0217: dt=0.007000, rms=0.561 (0.046%), neg=0, invalid=96777 0218: dt=0.007000, rms=0.560 (0.043%), neg=0, invalid=96777 0219: dt=0.007000, rms=0.560 (0.041%), neg=0, invalid=96777 0220: dt=0.007000, rms=0.560 (0.039%), neg=0, invalid=96777 0221: dt=0.007000, rms=0.560 (0.035%), neg=0, invalid=96777 0222: dt=0.007000, rms=0.560 (0.035%), neg=0, invalid=96777 0223: dt=0.007000, rms=0.559 (0.026%), neg=0, invalid=96777 0224: dt=0.007000, rms=0.559 (0.026%), neg=0, invalid=96777 0225: dt=0.007000, rms=0.559 (0.027%), neg=0, invalid=96777 0226: dt=0.007000, rms=0.559 (0.021%), neg=0, invalid=96777 0227: dt=0.007000, rms=0.559 (0.019%), neg=0, invalid=96777 0228: dt=0.112000, rms=0.559 (0.011%), neg=0, invalid=96777 0229: dt=0.014000, rms=0.559 (0.005%), neg=0, invalid=96777 0230: dt=0.014000, rms=0.559 (0.003%), neg=0, invalid=96777 0231: dt=0.014000, rms=0.559 (0.005%), neg=0, invalid=96777 0232: dt=0.014000, rms=0.559 (0.004%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.559, neg=0, invalid=96777 0233: dt=0.112000, rms=0.557 (0.316%), neg=0, invalid=96777 0234: dt=0.112000, rms=0.556 (0.244%), neg=0, invalid=96777 0235: dt=0.028000, rms=0.555 (0.042%), neg=0, invalid=96777 0236: dt=0.028000, rms=0.555 (0.044%), neg=0, invalid=96777 0237: dt=0.028000, rms=0.555 (0.080%), neg=0, invalid=96777 0238: dt=0.028000, rms=0.554 (0.109%), neg=0, invalid=96777 0239: dt=0.028000, rms=0.553 (0.129%), neg=0, invalid=96777 0240: dt=0.007000, rms=0.553 (0.004%), neg=0, invalid=96777 0241: dt=0.007000, rms=0.553 (0.007%), neg=0, invalid=96777 0242: dt=0.007000, rms=0.553 (0.008%), neg=0, invalid=96777 0243: dt=0.007000, rms=0.553 (0.015%), neg=0, invalid=96777 0244: dt=0.007000, rms=0.553 (0.021%), neg=0, invalid=96777 0245: dt=0.007000, rms=0.553 (0.020%), neg=0, invalid=96777 0246: dt=0.112000, rms=0.553 (0.075%), neg=0, invalid=96777 0247: dt=0.112000, rms=0.552 (0.061%), neg=0, invalid=96777 0248: dt=0.007000, rms=0.552 (-0.000%), neg=0, invalid=96777 0249: dt=0.007000, rms=0.552 (0.003%), neg=0, invalid=96777 0250: dt=0.007000, rms=0.552 (0.006%), neg=0, invalid=96777 0251: dt=0.003500, rms=0.552 (0.001%), neg=0, invalid=96777 0252: dt=0.003500, rms=0.552 (0.003%), neg=0, invalid=96777 0253: dt=0.003500, rms=0.552 (0.004%), neg=0, invalid=96777 0254: dt=0.003500, rms=0.552 (0.007%), neg=0, invalid=96777 0255: dt=0.003500, rms=0.552 (0.004%), 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=0.550, neg=0, invalid=96777 0256: dt=129.472000, rms=0.550 (0.028%), neg=0, invalid=96777 0257: dt=73.984000, rms=0.550 (0.007%), neg=0, invalid=96777 0258: dt=73.984000, rms=0.550 (0.002%), neg=0, invalid=96777 0259: dt=73.984000, rms=0.549 (0.011%), neg=0, invalid=96777 0260: dt=73.984000, rms=0.549 (0.007%), neg=0, invalid=96777 0261: dt=73.984000, rms=0.549 (0.005%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.549, neg=0, invalid=96777 0262: dt=129.472000, rms=0.549 (0.109%), neg=0, invalid=96777 0263: dt=129.472000, rms=0.549 (0.046%), neg=0, invalid=96777 0264: dt=129.472000, rms=0.548 (0.034%), neg=0, invalid=96777 0265: dt=129.472000, rms=0.548 (0.048%), neg=0, invalid=96777 0266: dt=129.472000, rms=0.548 (0.034%), neg=0, invalid=96777 0267: dt=129.472000, rms=0.548 (0.041%), neg=0, invalid=96777 0268: dt=129.472000, rms=0.548 (0.033%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.548, neg=0, invalid=96777 0269: dt=36.288000, rms=0.547 (0.166%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0270: dt=82.944000, rms=0.546 (0.143%), neg=0, invalid=96777 0271: dt=82.944000, rms=0.545 (0.066%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0272: dt=82.944000, rms=0.546 (-0.534%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.546, neg=0, invalid=96777 0273: dt=20.736000, rms=0.544 (0.254%), neg=0, invalid=96777 0274: dt=103.680000, rms=0.542 (0.336%), neg=0, invalid=96777 0275: dt=15.552000, rms=0.542 (0.142%), neg=0, invalid=96777 0276: dt=15.552000, rms=0.541 (0.034%), neg=0, invalid=96777 0277: dt=15.552000, rms=0.541 (0.057%), neg=0, invalid=96777 0278: dt=15.552000, rms=0.541 (0.072%), neg=0, invalid=96777 0279: dt=15.552000, rms=0.540 (0.086%), neg=0, invalid=96777 0280: dt=15.552000, rms=0.540 (0.105%), neg=0, invalid=96777 0281: dt=15.552000, rms=0.539 (0.100%), neg=0, invalid=96777 0282: dt=15.552000, rms=0.539 (0.097%), neg=0, invalid=96777 0283: dt=145.152000, rms=0.538 (0.078%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.538, neg=0, invalid=96777 iter 0, gcam->neg = 21 after 10 iterations, nbhd size=1, neg = 0 0284: dt=44.800000, rms=0.532 (1.138%), neg=0, invalid=96777 0285: dt=8.292683, rms=0.530 (0.463%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 13 iterations, nbhd size=2, neg = 0 0286: dt=25.600000, rms=0.528 (0.368%), neg=0, invalid=96777 0287: dt=6.400000, rms=0.526 (0.327%), neg=0, invalid=96777 iter 0, gcam->neg = 24 after 46 iterations, nbhd size=3, neg = 0 0288: dt=44.800000, rms=0.523 (0.503%), neg=0, invalid=96777 0289: dt=6.774194, rms=0.522 (0.250%), neg=0, invalid=96777 0290: dt=6.774194, rms=0.522 (0.105%), neg=0, invalid=96777 0291: dt=6.774194, rms=0.521 (0.123%), neg=0, invalid=96777 iter 0, gcam->neg = 7 after 37 iterations, nbhd size=4, neg = 0 0292: dt=6.774194, rms=0.520 (0.130%), neg=0, invalid=96777 0293: dt=6.774194, rms=0.519 (0.206%), neg=0, invalid=96777 0294: dt=6.774194, rms=0.518 (0.219%), neg=0, invalid=96777 0295: dt=6.774194, rms=0.517 (0.240%), neg=0, invalid=96777 0296: dt=6.774194, rms=0.516 (0.229%), neg=0, invalid=96777 0297: dt=6.774194, rms=0.514 (0.235%), neg=0, invalid=96777 0298: dt=6.774194, rms=0.513 (0.207%), neg=0, invalid=96777 0299: dt=6.774194, rms=0.512 (0.192%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 43 iterations, nbhd size=4, neg = 0 0300: dt=6.774194, rms=0.512 (0.146%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0301: dt=6.774194, rms=0.511 (0.175%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0302: dt=6.774194, rms=0.510 (0.163%), neg=0, invalid=96777 0303: dt=6.774194, rms=0.509 (0.160%), neg=0, invalid=96777 0304: dt=6.774194, rms=0.508 (0.147%), neg=0, invalid=96777 0305: dt=6.774194, rms=0.508 (0.131%), neg=0, invalid=96777 0306: dt=6.774194, rms=0.507 (0.130%), neg=0, invalid=96777 0307: dt=6.774194, rms=0.506 (0.113%), neg=0, invalid=96777 0308: dt=6.774194, rms=0.506 (0.116%), neg=0, invalid=96777 0309: dt=6.774194, rms=0.505 (0.098%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 45 iterations, nbhd size=3, neg = 0 0310: dt=44.800000, rms=0.505 (-0.028%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.505, neg=0, invalid=96777 0311: dt=44.800000, rms=0.501 (0.785%), neg=0, invalid=96777 0312: dt=6.400000, rms=0.501 (0.066%), neg=0, invalid=96777 0313: dt=6.400000, rms=0.501 (0.060%), neg=0, invalid=96777 0314: dt=6.400000, rms=0.500 (0.091%), neg=0, invalid=96777 0315: dt=6.400000, rms=0.500 (0.095%), neg=0, invalid=96777 0316: dt=6.400000, rms=0.499 (0.092%), neg=0, invalid=96777 0317: dt=6.400000, rms=0.499 (0.090%), neg=0, invalid=96777 0318: dt=11.200000, rms=0.499 (0.052%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.506, neg=0, invalid=96777 iter 0, gcam->neg = 11 after 21 iterations, nbhd size=2, neg = 0 0319: dt=3.456000, rms=0.506 (0.081%), neg=0, invalid=96777 0320: dt=0.720000, rms=0.506 (-0.002%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.506, neg=0, invalid=96777 iter 0, gcam->neg = 12 after 3 iterations, nbhd size=0, neg = 0 0321: dt=1.826087, rms=0.506 (0.050%), neg=0, invalid=96777 iter 0, gcam->neg = 5 after 6 iterations, nbhd size=1, neg = 0 0322: dt=4.869565, rms=0.505 (0.128%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 5 iterations, nbhd size=1, neg = 0 0323: dt=4.032000, rms=0.505 (0.045%), neg=0, invalid=96777 iter 0, gcam->neg = 6 after 8 iterations, nbhd size=1, neg = 0 0324: dt=4.032000, rms=0.505 (0.031%), neg=0, invalid=96777 iter 0, gcam->neg = 36 after 9 iterations, nbhd size=1, neg = 0 0325: dt=4.032000, rms=0.505 (-0.033%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.513, neg=0, invalid=96777 0326: dt=0.000000, rms=0.513 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.513, neg=0, invalid=96777 0327: dt=0.000000, rms=0.513 (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=0.499, neg=0, invalid=96777 iter 0, gcam->neg = 1004 after 200 iterations, nbhd size=1, neg = 1 starting rms=0.006, neg=1, removing folds in lattice.... iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.006 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0328: dt=2.029326, 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 iter 0, gcam->neg = 1336 after 43 iterations, nbhd size=1, neg = 0 0329: dt=2.183805, rms=0.427 (14.344%), neg=0, invalid=96777 0330: dt=0.000016, rms=0.427 (0.005%), neg=0, invalid=96777 0331: dt=0.000016, rms=0.427 (0.000%), neg=0, invalid=96777 0332: dt=0.000016, rms=0.427 (0.000%), neg=0, invalid=96777 0333: dt=0.000016, rms=0.427 (0.000%), neg=0, invalid=96777 0334: dt=0.000016, rms=0.427 (0.000%), neg=0, invalid=96777 0335: dt=0.000050, rms=0.427 (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=0.399, neg=0, invalid=96777 0336: dt=0.000000, rms=0.400 (-0.319%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.400, neg=0, invalid=96777 0337: dt=32.368000, rms=0.400 (0.004%), neg=0, invalid=96777 0338: dt=8.092000, rms=0.400 (0.000%), neg=0, invalid=96777 0339: dt=8.092000, rms=0.400 (0.000%), neg=0, invalid=96777 0340: dt=8.092000, rms=0.400 (-0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.401, neg=0, invalid=96777 0341: dt=0.000000, rms=0.401 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.401, neg=0, invalid=96777 0342: dt=25.920000, rms=0.400 (0.011%), neg=0, invalid=96777 0343: dt=9.072000, rms=0.400 (0.001%), neg=0, invalid=96777 0344: dt=9.072000, rms=0.400 (0.001%), neg=0, invalid=96777 0345: dt=9.072000, rms=0.400 (0.000%), neg=0, invalid=96777 0346: dt=9.072000, rms=0.400 (-0.003%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.402, neg=0, invalid=96777 iter 0, gcam->neg = 5 after 200 iterations, nbhd size=3, neg = 1 starting rms=0.007, neg=1, removing folds in lattice.... iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.007 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0347: dt=6.400000, rms=0.402 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.402, neg=0, invalid=96777 iter 0, gcam->neg = 26 after 200 iterations, nbhd size=3, neg = 2 starting rms=0.008, neg=2, removing folds in lattice.... iter 1, dt=0.000000: new neg 2, old_neg 2, delta 0, rms=0.008 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0348: dt=32.000000, rms=0.402 (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=0.406, neg=0, invalid=96777 iter 0, gcam->neg = 41 after 200 iterations, nbhd size=2, neg = 1 starting rms=0.005, neg=1, removing folds in lattice.... iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.005 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0349: dt=3.456000, rms=0.406 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.406, neg=0, invalid=96777 iter 0, gcam->neg = 35 after 200 iterations, nbhd size=3, neg = 1 starting rms=0.004, neg=1, removing folds in lattice.... iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.004 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0350: dt=4.032000, rms=0.406 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.414, neg=0, invalid=96777 0351: dt=0.000000, rms=0.414 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.414, neg=0, invalid=96777 0352: dt=0.000000, rms=0.414 (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=0.400, neg=0, invalid=96777 iter 0, gcam->neg = 312 after 34 iterations, nbhd size=3, neg = 0 0353: dt=0.448000, rms=0.391 (2.148%), neg=0, invalid=96777 0354: dt=0.000027, rms=0.391 (0.002%), neg=0, invalid=96777 0355: dt=0.000027, rms=0.391 (0.000%), neg=0, invalid=96777 0356: dt=0.000027, rms=0.391 (0.000%), neg=0, invalid=96777 0357: dt=0.000027, rms=0.391 (0.000%), neg=0, invalid=96777 0358: dt=0.000027, rms=0.391 (0.000%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0359: dt=0.005000, rms=0.391 (0.002%), neg=0, invalid=96777 0360: dt=0.001250, rms=0.391 (0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.391, neg=0, invalid=96777 iter 0, gcam->neg = 12 after 14 iterations, nbhd size=2, neg = 0 0361: dt=0.028000, rms=0.391 (0.074%), neg=0, invalid=96777 0362: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777 0363: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777 0364: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777 0365: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777 0366: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777 0367: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777 0368: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777 0369: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777 0370: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777 0371: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777 0372: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777 0373: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777 0374: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777 0375: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777 0376: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777 0377: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777 0378: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777 0379: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777 0380: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777 0381: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777 0382: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777 0383: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777 0384: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777 0385: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777 0386: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777 0387: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777 0388: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777 0389: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777 0390: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777 0391: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777 0392: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777 0393: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777 0394: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777 writing output transformation to transforms/talairach.m3z... GCAMwrite registration took 3 hours, 46 minutes and 52 seconds. #-------------------------------------- #@# CA Reg Inv Thu Aug 8 16:00:36 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 16:02:02 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... 10449376 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 1 minutes and 31 seconds. #-------------------------------------- #@# SkullLTA Thu Aug 8 16:03:33 CEST 2013 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta ======= NUMBER OF OPENMP THREADS = 1 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 5 using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach_with_skull_2.log reading '/opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=9.0 skull bounding box = (43, 0, 0) --> (209, 205, 200) using (98, 68, 100) as brain centroid... mean wm in atlas = 126, using box (78,43,75) --> (118, 93,124) to find MRI wm before smoothing, mri peak at 110 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=-4.1, old_max_log_p =-4.2 (thresh=-4.2) 1.057 0.021 0.022 -13.719; -0.026 1.122 0.300 -18.565; -0.018 -0.231 0.863 32.977; 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) 1.057 0.021 0.022 -13.719; -0.026 1.122 0.300 -18.565; -0.018 -0.231 0.863 32.977; 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) 1.037 -0.015 0.012 -6.714; 0.009 1.080 0.289 -15.944; -0.019 -0.235 0.879 31.607; 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) 1.037 -0.007 -0.017 -4.208; 0.009 1.060 0.284 -15.249; 0.016 -0.240 0.896 25.836; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.041 -0.007 -0.017 -3.726; 0.009 1.047 0.312 -16.851; 0.015 -0.275 0.887 30.695; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.042 -0.007 -0.017 -3.878; 0.009 1.047 0.312 -16.851; 0.015 -0.275 0.887 30.695; 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 1.04224 -0.00684 -0.01683 -3.87823; 0.00940 1.04745 0.31168 -16.85081; 0.01530 -0.27454 0.88693 30.69490; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.04224 -0.00684 -0.01683 -3.87823; 0.00940 1.04745 0.31168 -16.85081; 0.01530 -0.27454 0.88693 30.69490; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 007: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.042 -0.007 -0.017 -3.878; 0.009 1.047 0.312 -16.851; 0.015 -0.275 0.887 30.695; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -4.0 (old=-4.2) transform before final EM align: 1.042 -0.007 -0.017 -3.878; 0.009 1.047 0.312 -16.851; 0.015 -0.275 0.887 30.695; 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 1.04224 -0.00684 -0.01683 -3.87823; 0.00940 1.04745 0.31168 -16.85081; 0.01530 -0.27454 0.88693 30.69490; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.04224 -0.00684 -0.01683 -3.87823; 0.00940 1.04745 0.31168 -16.85081; 0.01530 -0.27454 0.88693 30.69490; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = 4.4 tol 0.000000 final transform: 1.042 -0.007 -0.017 -3.878; 0.009 1.047 0.312 -16.851; 0.015 -0.275 0.887 30.695; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull_2.lta... registration took 38 minutes and 18 seconds. #-------------------------------------- #@# SubCort Seg Thu Aug 8 16:41:51 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/sub006/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 = 0.12487 ( 6) Left_Lateral_Ventricle (4): linear fit = 0.19 x + 0.0 (899 voxels, overlap=0.007) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (899 voxels, peak = 5), gca=10.8 gca peak = 0.14982 (20) mri peak = 0.13637 ( 8) Right_Lateral_Ventricle (43): linear fit = 0.32 x + 0.0 (1122 voxels, overlap=0.008) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (1122 voxels, peak = 6), gca=8.0 gca peak = 0.28003 (97) mri peak = 0.08549 (89) Right_Pallidum (52): linear fit = 0.88 x + 0.0 (505 voxels, overlap=0.058) Right_Pallidum (52): linear fit = 0.88 x + 0.0 (505 voxels, peak = 86), gca=85.8 gca peak = 0.18160 (96) mri peak = 0.09195 (85) Left_Pallidum (13): linear fit = 0.88 x + 0.0 (350 voxels, overlap=0.051) Left_Pallidum (13): linear fit = 0.88 x + 0.0 (350 voxels, peak = 84), gca=84.0 gca peak = 0.27536 (62) mri peak = 0.08812 (57) Right_Hippocampus (53): linear fit = 0.83 x + 0.0 (595 voxels, overlap=0.440) Right_Hippocampus (53): linear fit = 0.83 x + 0.0 (595 voxels, peak = 52), gca=51.8 gca peak = 0.32745 (63) mri peak = 0.08194 (59) Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (598 voxels, overlap=0.819) Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (598 voxels, peak = 58), gca=58.3 gca peak = 0.08597 (105) mri peak = 0.09455 (106) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (45864 voxels, overlap=0.701) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (45864 voxels, peak = 107), gca=106.6 gca peak = 0.09209 (106) mri peak = 0.08356 (109) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (47371 voxels, overlap=0.613) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (47371 voxels, peak = 110), gca=109.7 gca peak = 0.07826 (63) mri peak = 0.05887 (52) Left_Cerebral_Cortex (3): linear fit = 0.76 x + 0.0 (17471 voxels, overlap=0.107) Left_Cerebral_Cortex (3): linear fit = 0.76 x + 0.0 (17471 voxels, peak = 48), gca=48.2 gca peak = 0.08598 (64) mri peak = 0.07116 (52) Right_Cerebral_Cortex (42): linear fit = 0.75 x + 0.0 (16663 voxels, overlap=0.067) Right_Cerebral_Cortex (42): linear fit = 0.75 x + 0.0 (16663 voxels, peak = 48), gca=48.3 gca peak = 0.24164 (71) mri peak = 0.10545 (63) Right_Caudate (50): linear fit = 0.88 x + 0.0 (826 voxels, overlap=0.190) Right_Caudate (50): linear fit = 0.88 x + 0.0 (826 voxels, peak = 62), gca=62.1 gca peak = 0.18227 (75) mri peak = 0.08061 (65) Left_Caudate (11): linear fit = 0.86 x + 0.0 (1110 voxels, overlap=0.152) Left_Caudate (11): linear fit = 0.86 x + 0.0 (1110 voxels, peak = 64), gca=64.1 gca peak = 0.10629 (62) mri peak = 0.05314 (52) Left_Cerebellum_Cortex (8): linear fit = 0.88 x + 0.0 (6613 voxels, overlap=0.861) Left_Cerebellum_Cortex (8): linear fit = 0.88 x + 0.0 (6613 voxels, peak = 54), gca=54.2 gca peak = 0.11668 (59) mri peak = 0.05021 (53) Right_Cerebellum_Cortex (47): linear fit = 0.92 x + 0.0 (6203 voxels, overlap=0.768) Right_Cerebellum_Cortex (47): linear fit = 0.92 x + 0.0 (6203 voxels, peak = 54), gca=54.0 gca peak = 0.17849 (88) mri peak = 0.08202 (90) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (6058 voxels, overlap=0.980) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (6058 voxels, peak = 89), gca=89.3 gca peak = 0.16819 (86) mri peak = 0.07495 (87) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (6015 voxels, overlap=0.984) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (6015 voxels, peak = 87), gca=87.3 gca peak = 0.41688 (64) mri peak = 0.08299 (56) Left_Amygdala (18): linear fit = 0.86 x + 0.0 (264 voxels, overlap=0.768) Left_Amygdala (18): linear fit = 0.86 x + 0.0 (264 voxels, peak = 55), gca=54.7 gca peak = 0.42394 (62) mri peak = 0.10850 (52) Right_Amygdala (54): linear fit = 0.86 x + 0.0 (224 voxels, overlap=0.627) Right_Amygdala (54): linear fit = 0.86 x + 0.0 (224 voxels, peak = 53), gca=53.0 gca peak = 0.10041 (96) mri peak = 0.05823 (91) Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (3976 voxels, overlap=0.996) Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (3976 voxels, peak = 95), gca=94.6 gca peak = 0.13978 (88) mri peak = 0.06134 (90) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4124 voxels, overlap=0.984) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4124 voxels, peak = 88), gca=87.6 gca peak = 0.08514 (81) mri peak = 0.06002 (73) Left_Putamen (12): linear fit = 0.87 x + 0.0 (1705 voxels, overlap=0.271) Left_Putamen (12): linear fit = 0.87 x + 0.0 (1705 voxels, peak = 70), gca=70.1 gca peak = 0.09624 (82) mri peak = 0.07704 (69) Right_Putamen (51): linear fit = 0.85 x + 0.0 (1743 voxels, overlap=0.256) Right_Putamen (51): linear fit = 0.85 x + 0.0 (1743 voxels, peak = 69), gca=69.3 gca peak = 0.07543 (88) mri peak = 0.07082 (88) Brain_Stem (16): linear fit = 1.01 x + 0.0 (12039 voxels, overlap=0.765) Brain_Stem (16): linear fit = 1.01 x + 0.0 (12039 voxels, peak = 89), gca=89.3 gca peak = 0.12757 (95) mri peak = 0.07129 (89) Right_VentralDC (60): linear fit = 0.99 x + 0.0 (1045 voxels, overlap=0.834) Right_VentralDC (60): linear fit = 0.99 x + 0.0 (1045 voxels, peak = 94), gca=93.6 gca peak = 0.17004 (92) mri peak = 0.06245 (97) Left_VentralDC (28): linear fit = 1.03 x + 0.0 (1262 voxels, overlap=0.899) Left_VentralDC (28): linear fit = 1.03 x + 0.0 (1262 voxels, peak = 95), gca=95.2 gca peak = 0.21361 (36) mri peak = 0.07715 (11) gca peak = 0.26069 (23) mri peak = 0.11330 (12) Fourth_Ventricle (15): linear fit = 0.35 x + 0.0 (294 voxels, overlap=0.029) Fourth_Ventricle (15): linear fit = 0.35 x + 0.0 (294 voxels, peak = 8), gca=8.2 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak Third_Ventricle = 0.21361 (36) gca peak Fourth_Ventricle = 0.26069 (23) gca peak CSF = 0.14367 (38) gca peak Left_Accumbens_area = 0.57033 (70) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65201 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.31129 (32) gca peak Right_Accumbens_area = 0.30219 (72) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.72939 (42) gca peak WM_hypointensities = 0.14821 (82) gca peak non_WM_hypointensities = 0.10354 (53) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means estimating mean gm scale to be 0.83 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 0.40 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.31600 (11) mri peak = 0.12487 ( 6) Left_Lateral_Ventricle (4): linear fit = 0.52 x + 0.0 (899 voxels, overlap=0.781) Left_Lateral_Ventricle (4): linear fit = 0.52 x + 0.0 (899 voxels, peak = 6), gca=5.8 gca peak = 0.29325 ( 9) mri peak = 0.13637 ( 8) Right_Lateral_Ventricle (43): linear fit = 0.79 x + 0.0 (1122 voxels, overlap=0.940) Right_Lateral_Ventricle (43): linear fit = 0.79 x + 0.0 (1122 voxels, peak = 7), gca=7.1 gca peak = 0.27917 (88) mri peak = 0.08549 (89) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (505 voxels, overlap=1.022) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (505 voxels, peak = 88), gca=88.0 gca peak = 0.18877 (84) mri peak = 0.09195 (85) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (350 voxels, overlap=1.012) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (350 voxels, peak = 84), gca=83.6 gca peak = 0.32076 (52) mri peak = 0.08812 (57) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (595 voxels, overlap=1.008) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (595 voxels, peak = 52), gca=52.0 gca peak = 0.30493 (58) mri peak = 0.08194 (59) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (598 voxels, overlap=1.003) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (598 voxels, peak = 58), gca=58.0 gca peak = 0.08542 (107) mri peak = 0.09455 (106) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (45864 voxels, overlap=0.760) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (45864 voxels, peak = 108), gca=107.5 gca peak = 0.08544 (110) mri peak = 0.08356 (109) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (47371 voxels, overlap=0.744) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (47371 voxels, peak = 110), gca=110.0 gca peak = 0.09987 (48) mri peak = 0.05887 (52) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (17471 voxels, overlap=0.995) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (17471 voxels, peak = 48), gca=48.0 gca peak = 0.11781 (48) mri peak = 0.07116 (52) Right_Cerebral_Cortex (42): linear fit = 1.03 x + 0.0 (16663 voxels, overlap=0.995) Right_Cerebral_Cortex (42): linear fit = 1.03 x + 0.0 (16663 voxels, peak = 50), gca=49.7 gca peak = 0.24215 (64) mri peak = 0.10545 (63) Right_Caudate (50): linear fit = 0.99 x + 0.0 (826 voxels, overlap=1.006) Right_Caudate (50): linear fit = 0.99 x + 0.0 (826 voxels, peak = 63), gca=63.0 gca peak = 0.18458 (64) mri peak = 0.08061 (65) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1110 voxels, overlap=1.000) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1110 voxels, peak = 64), gca=64.0 gca peak = 0.12088 (53) mri peak = 0.05314 (52) Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (6613 voxels, overlap=0.995) Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (6613 voxels, peak = 55), gca=55.4 gca peak = 0.12940 (55) mri peak = 0.05021 (53) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (6203 voxels, overlap=1.000) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (6203 voxels, peak = 54), gca=54.2 gca peak = 0.17397 (89) mri peak = 0.08202 (90) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6058 voxels, overlap=0.992) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6058 voxels, peak = 89), gca=88.6 gca peak = 0.16063 (88) mri peak = 0.07495 (87) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6015 voxels, overlap=0.997) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6015 voxels, peak = 88), gca=87.6 gca peak = 0.32010 (55) mri peak = 0.08299 (56) Left_Amygdala (18): linear fit = 1.07 x + 0.0 (264 voxels, overlap=1.020) Left_Amygdala (18): linear fit = 1.07 x + 0.0 (264 voxels, peak = 59), gca=58.6 gca peak = 0.46062 (53) mri peak = 0.10850 (52) Right_Amygdala (54): linear fit = 1.07 x + 0.0 (224 voxels, overlap=1.023) Right_Amygdala (54): linear fit = 1.07 x + 0.0 (224 voxels, peak = 56), gca=56.4 gca peak = 0.10422 (93) mri peak = 0.05823 (91) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (3976 voxels, overlap=0.979) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (3976 voxels, peak = 94), gca=94.4 gca peak = 0.10935 (87) mri peak = 0.06134 (90) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4124 voxels, overlap=0.992) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4124 voxels, peak = 87), gca=86.6 gca peak = 0.09481 (74) mri peak = 0.06002 (73) Left_Putamen (12): linear fit = 0.98 x + 0.0 (1705 voxels, overlap=1.002) Left_Putamen (12): linear fit = 0.98 x + 0.0 (1705 voxels, peak = 72), gca=72.2 gca peak = 0.12360 (64) mri peak = 0.07704 (69) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1743 voxels, overlap=0.997) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1743 voxels, peak = 63), gca=63.0 gca peak = 0.07465 (87) mri peak = 0.07082 (88) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12039 voxels, overlap=0.799) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12039 voxels, peak = 87), gca=86.6 gca peak = 0.14053 (93) mri peak = 0.07129 (89) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1045 voxels, overlap=0.824) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1045 voxels, peak = 93), gca=92.5 gca peak = 0.15191 (95) mri peak = 0.06245 (97) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1262 voxels, overlap=0.923) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1262 voxels, peak = 95), gca=95.5 gca peak = 0.35640 (14) mri peak = 0.07715 (11) gca peak = 0.33827 ( 9) mri peak = 0.11330 (12) Fourth_Ventricle (15): linear fit = 1.05 x + 0.0 (294 voxels, overlap=0.965) Fourth_Ventricle (15): linear fit = 1.05 x + 0.0 (294 voxels, peak = 9), gca=9.5 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.24950 (33) 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 = 0.62149 (62) gca peak Left_choroid_plexus = 0.09108 (48) gca peak Right_Inf_Lat_Vent = 0.30433 (27) gca peak Right_Accumbens_area = 0.31102 (63) gca peak Right_vessel = 0.29571 (59) gca peak Right_choroid_plexus = 0.10219 (48) gca peak Fifth_Ventricle = 0.45329 (19) gca peak WM_hypointensities = 0.14093 (84) gca peak non_WM_hypointensities = 0.11402 (54) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.03 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.79 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 14369 gm and wm labels changed (%10 to gray, %90 to white out of all changed labels) 331 hippocampal voxels changed. 12 amygdala voxels changed. pass 1: 111271 changed. image ll: -2.298, PF=1.000 pass 2: 22081 changed. image ll: -2.296, PF=1.000 pass 3: 9319 changed. pass 4: 4519 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 20 minutes and 23 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/cc_up.lta sub006 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/sub006/mri/transforms/cc_up.lta reading aseg from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/aseg.auto_noCCseg.mgz reading norm from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/norm.mgz 16109 voxels in left wm, 22492 in right wm, xrange [125, 130] searching rotation angles z=[-8 6], y=[-5 9] searching scale 1 Z rot -7.8 searching scale 1 Z rot -7.6 searching scale 1 Z rot -7.3 searching scale 1 Z rot -7.1 searching scale 1 Z rot -6.8 searching scale 1 Z rot -6.6 searching scale 1 Z rot -6.3 searching scale 1 Z rot -6.1 searching scale 1 Z rot -5.8 searching scale 1 Z rot -5.6 searching scale 1 Z rot -5.3 searching scale 1 Z rot -5.1 searching scale 1 Z rot -4.8 searching scale 1 Z rot -4.6 searching scale 1 Z rot -4.3 searching scale 1 Z rot -4.1 searching scale 1 Z rot -3.8 searching scale 1 Z rot -3.6 searching scale 1 Z rot -3.3 searching scale 1 Z rot -3.1 searching scale 1 Z rot -2.8 searching scale 1 Z rot -2.6 searching scale 1 Z rot -2.3 searching scale 1 Z rot -2.1 searching scale 1 Z rot -1.8 searching scale 1 Z rot -1.6 searching scale 1 Z rot -1.3 searching scale 1 Z rot -1.1 searching scale 1 Z rot -0.8 searching scale 1 Z rot -0.6 searching scale 1 Z rot -0.3 searching scale 1 Z rot -0.1 searching scale 1 Z rot 0.2 searching scale 1 Z rot 0.4 searching scale 1 Z rot 0.7 searching scale 1 Z rot 0.9 searching scale 1 Z rot 1.2 searching scale 1 Z rot 1.4 searching scale 1 Z rot 1.7 searching scale 1 Z rot 1.9 searching scale 1 Z rot 2.2 searching scale 1 Z rot 2.4 searching scale 1 Z rot 2.7 searching scale 1 Z rot 2.9 searching scale 1 Z rot 3.2 searching scale 1 Z rot 3.4 searching scale 1 Z rot 3.7 searching scale 1 Z rot 3.9 searching scale 1 Z rot 4.2 searching scale 1 Z rot 4.4 searching scale 1 Z rot 4.7 searching scale 1 Z rot 4.9 searching scale 1 Z rot 5.2 searching scale 1 Z rot 5.4 searching scale 1 Z rot 5.7 searching scale 1 Z rot 5.9 global minimum found at slice 127.6, rotations (1.66, -0.84) final transformation (x=127.6, yr=1.660, zr=-0.844): 0.999 0.015 0.029 -3.518; -0.015 1.000 -0.000 47.929; -0.029 -0.000 1.000 34.736; 0.000 0.000 0.000 1.000; updating x range to be [127, 130] in xformed coordinates best xformed slice 129 cc center is found at 129 146 126 eigenvectors: -0.001 -0.004 1.000; -0.183 -0.983 -0.004; 0.983 -0.183 0.000; error in mid anterior detected - correcting... writing aseg with callosum to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/aseg.auto.mgz... corpus callosum matter segmentation took 0.6 minutes #-------------------------------------- #@# Merge ASeg Thu Aug 8 17:02:53 CEST 2013 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Thu Aug 8 17:02:53 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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... 4588 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 10, setting threshold to 40 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 31 (31) csf peak at 10, setting threshold to 40 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 4 minutes and 30 seconds. #-------------------------------------------- #@# Mask BFS Thu Aug 8 17:07:25 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1875800 voxels in mask (pct= 11.18) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Thu Aug 8 17:07:28 CEST 2013 mri_segment brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (108.0): 107.4 +- 4.6 [80.0 --> 125.0] GM (66.0) : 65.4 +- 9.8 [30.0 --> 96.0] setting bottom of white matter range to 75.2 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... 7560 sparsely connected voxels removed... thickening thin strands.... 20 segments, 6169 filled 374 bright non-wm voxels segmented. 4405 diagonally connected voxels added... white matter segmentation took 1.9 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 0.69 minutes reading wm segmentation from wm.seg.mgz... 45 voxels added to wm to prevent paths from MTL structures to cortex 1381 additional wm voxels added 0 additional wm voxels added SEG EDIT: 56233 voxels turned on, 47216 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+): 16 found - 16 modified | TOTAL: 16 pass 2 (xy+): 0 found - 16 modified | TOTAL: 16 pass 1 (xy-): 20 found - 20 modified | TOTAL: 36 pass 2 (xy-): 0 found - 20 modified | TOTAL: 36 pass 1 (yz+): 34 found - 34 modified | TOTAL: 70 pass 2 (yz+): 0 found - 34 modified | TOTAL: 70 pass 1 (yz-): 15 found - 15 modified | TOTAL: 85 pass 2 (yz-): 0 found - 15 modified | TOTAL: 85 pass 1 (xz+): 24 found - 24 modified | TOTAL: 109 pass 2 (xz+): 0 found - 24 modified | TOTAL: 109 pass 1 (xz-): 24 found - 24 modified | TOTAL: 133 pass 2 (xz-): 0 found - 24 modified | TOTAL: 133 Iteration Number : 1 pass 1 (+++): 25 found - 25 modified | TOTAL: 25 pass 2 (+++): 0 found - 25 modified | TOTAL: 25 pass 1 (+++): 10 found - 10 modified | TOTAL: 35 pass 2 (+++): 0 found - 10 modified | TOTAL: 35 pass 1 (+++): 10 found - 10 modified | TOTAL: 45 pass 2 (+++): 0 found - 10 modified | TOTAL: 45 pass 1 (+++): 19 found - 19 modified | TOTAL: 64 pass 2 (+++): 0 found - 19 modified | TOTAL: 64 Iteration Number : 1 pass 1 (++): 213 found - 213 modified | TOTAL: 213 pass 2 (++): 0 found - 213 modified | TOTAL: 213 pass 1 (+-): 173 found - 173 modified | TOTAL: 386 pass 2 (+-): 0 found - 173 modified | TOTAL: 386 pass 1 (--): 191 found - 191 modified | TOTAL: 577 pass 2 (--): 0 found - 191 modified | TOTAL: 577 pass 1 (-+): 190 found - 190 modified | TOTAL: 767 pass 2 (-+): 0 found - 190 modified | TOTAL: 767 Iteration Number : 2 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 5 found - 5 modified | TOTAL: 8 pass 2 (xy-): 0 found - 5 modified | TOTAL: 8 pass 1 (yz+): 1 found - 1 modified | TOTAL: 9 pass 2 (yz+): 0 found - 1 modified | TOTAL: 9 pass 1 (yz-): 1 found - 1 modified | TOTAL: 10 pass 2 (yz-): 0 found - 1 modified | TOTAL: 10 pass 1 (xz+): 3 found - 3 modified | TOTAL: 13 pass 2 (xz+): 0 found - 3 modified | TOTAL: 13 pass 1 (xz-): 4 found - 4 modified | TOTAL: 17 pass 2 (xz-): 0 found - 4 modified | TOTAL: 17 Iteration Number : 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 4 pass 2 (+++): 0 found - 2 modified | TOTAL: 4 pass 1 (+++): 2 found - 2 modified | TOTAL: 6 pass 2 (+++): 0 found - 2 modified | TOTAL: 6 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 1 found - 1 modified | TOTAL: 2 pass 2 (-+): 0 found - 1 modified | TOTAL: 2 Iteration Number : 3 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 0 found - 0 modified | TOTAL: 2 pass 1 (yz+): 0 found - 0 modified | TOTAL: 2 pass 1 (yz-): 1 found - 1 modified | TOTAL: 3 pass 2 (yz-): 0 found - 1 modified | TOTAL: 3 pass 1 (xz+): 1 found - 1 modified | TOTAL: 4 pass 2 (xz+): 0 found - 1 modified | TOTAL: 4 pass 1 (xz-): 0 found - 0 modified | TOTAL: 4 Iteration Number : 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 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 1 found - 1 modified | TOTAL: 1 pass 2 (xz-): 0 found - 1 modified | TOTAL: 1 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 5 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 : 5 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 : 5 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 = 995 (out of 667295: 0.149109) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Thu Aug 8 17:10:08 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 1.057 0.021 0.022 -13.719; -0.025 1.044 0.279 -8.820; -0.018 -0.231 0.863 32.977; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.057 0.021 0.022 -13.719; -0.025 1.044 0.279 -8.820; -0.018 -0.231 0.863 32.977; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 914 (min = 350, max = 1400), aspect = 0.45 (min = 0.10, max = 0.75) no need to search using seed (126, 115, 148), TAL = (2.0, 20.0, 13.0) talairach voxel to voxel transform 0.945 -0.022 -0.017 13.320; 0.016 0.894 -0.289 17.639; 0.024 0.238 1.081 -33.213; 0.000 0.000 0.000 1.000; segmentation indicates cc at (126, 115, 148) --> (2.0, 20.0, 13.0) done. writing output to filled.mgz... filling took 1.0 minutes talairach cc position changed to (2.00, 20.00, 13.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, 20.00, 13.00) SRC: (110.41, 79.37, 156.83) search lh wm seed point around talairach space (-16.00, 20.00, 13.00), SRC: (144.44, 79.94, 157.71) 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 17:11:07 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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-): 3 found - 3 modified | TOTAL: 5 pass 2 (xy-): 0 found - 3 modified | TOTAL: 5 pass 1 (yz+): 1 found - 1 modified | TOTAL: 6 pass 2 (yz+): 0 found - 1 modified | TOTAL: 6 pass 1 (yz-): 1 found - 1 modified | TOTAL: 7 pass 2 (yz-): 0 found - 1 modified | TOTAL: 7 pass 1 (xz+): 1 found - 1 modified | TOTAL: 8 pass 2 (xz+): 0 found - 1 modified | TOTAL: 8 pass 1 (xz-): 1 found - 1 modified | TOTAL: 9 pass 2 (xz-): 0 found - 1 modified | TOTAL: 9 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 1 found - 1 modified | TOTAL: 2 pass 2 (+-): 0 found - 1 modified | TOTAL: 2 pass 1 (--): 2 found - 2 modified | TOTAL: 4 pass 2 (--): 0 found - 2 modified | TOTAL: 4 pass 1 (-+): 0 found - 0 modified | TOTAL: 4 Iteration Number : 2 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 14 (out of 319770: 0.004378) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 30: 132 vertices, 158 faces slice 40: 5154 vertices, 5422 faces slice 50: 15090 vertices, 15484 faces slice 60: 27343 vertices, 27780 faces slice 70: 40146 vertices, 40596 faces slice 80: 52914 vertices, 53297 faces slice 90: 65174 vertices, 65598 faces slice 100: 78142 vertices, 78578 faces slice 110: 90088 vertices, 90497 faces slice 120: 102254 vertices, 102675 faces slice 130: 113707 vertices, 114156 faces slice 140: 125465 vertices, 125866 faces slice 150: 135787 vertices, 136156 faces slice 160: 145524 vertices, 145859 faces slice 170: 154037 vertices, 154323 faces slice 180: 161662 vertices, 161914 faces slice 190: 167381 vertices, 167600 faces slice 200: 171832 vertices, 171986 faces slice 210: 172752 vertices, 172782 faces slice 220: 172752 vertices, 172782 faces slice 230: 172752 vertices, 172782 faces slice 240: 172752 vertices, 172782 faces slice 250: 172752 vertices, 172782 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... 172752 voxel in cpt #1: X=-30 [v=172752,e=518346,f=345564] located at (-26.980938, -19.630371, 40.472919) For the whole surface: X=-30 [v=172752,e=518346,f=345564] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Thu Aug 8 17:11:17 CEST 2013 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 17:11:23 CEST 2013 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts avg radius = 52.1 mm, total surface area = 91668 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.7 minutes Not saving sulc step 000: RMS=0.098 (target=0.015) step 005: RMS=0.072 (target=0.015) step 010: RMS=0.052 (target=0.015) step 015: RMS=0.043 (target=0.015) step 020: RMS=0.036 (target=0.015) step 025: RMS=0.031 (target=0.015) step 030: RMS=0.028 (target=0.015) step 035: RMS=0.025 (target=0.015) step 040: RMS=0.022 (target=0.015) step 045: RMS=0.021 (target=0.015) step 050: RMS=0.020 (target=0.015) step 055: RMS=0.020 (target=0.015) step 060: RMS=0.019 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Thu Aug 8 17:12:06 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.88 +- 0.55 (0.00-->6.92) (max @ vno 79103 --> 79124) face area 0.02 +- 0.03 (-0.34-->0.86) scaling brain by 0.280... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.310, avgs=0 005/300: dt: 0.9000, rms radial error=176.051, avgs=0 010/300: dt: 0.9000, rms radial error=175.496, avgs=0 015/300: dt: 0.9000, rms radial error=174.766, avgs=0 020/300: dt: 0.9000, rms radial error=173.934, avgs=0 025/300: dt: 0.9000, rms radial error=173.044, avgs=0 030/300: dt: 0.9000, rms radial error=172.120, avgs=0 035/300: dt: 0.9000, rms radial error=171.178, avgs=0 040/300: dt: 0.9000, rms radial error=170.235, avgs=0 045/300: dt: 0.9000, rms radial error=169.288, avgs=0 050/300: dt: 0.9000, rms radial error=168.341, avgs=0 055/300: dt: 0.9000, rms radial error=167.397, avgs=0 060/300: dt: 0.9000, rms radial error=166.458, avgs=0 065/300: dt: 0.9000, rms radial error=165.528, avgs=0 070/300: dt: 0.9000, rms radial error=164.603, avgs=0 075/300: dt: 0.9000, rms radial error=163.682, avgs=0 080/300: dt: 0.9000, rms radial error=162.767, avgs=0 085/300: dt: 0.9000, rms radial error=161.856, avgs=0 090/300: dt: 0.9000, rms radial error=160.951, avgs=0 095/300: dt: 0.9000, rms radial error=160.050, avgs=0 100/300: dt: 0.9000, rms radial error=159.154, avgs=0 105/300: dt: 0.9000, rms radial error=158.264, avgs=0 110/300: dt: 0.9000, rms radial error=157.379, avgs=0 115/300: dt: 0.9000, rms radial error=156.499, avgs=0 120/300: dt: 0.9000, rms radial error=155.623, avgs=0 125/300: dt: 0.9000, rms radial error=154.752, avgs=0 130/300: dt: 0.9000, rms radial error=153.886, avgs=0 135/300: dt: 0.9000, rms radial error=153.024, avgs=0 140/300: dt: 0.9000, rms radial error=152.167, avgs=0 145/300: dt: 0.9000, rms radial error=151.315, avgs=0 150/300: dt: 0.9000, rms radial error=150.467, avgs=0 155/300: dt: 0.9000, rms radial error=149.624, avgs=0 160/300: dt: 0.9000, rms radial error=148.785, avgs=0 165/300: dt: 0.9000, rms radial error=147.951, avgs=0 170/300: dt: 0.9000, rms radial error=147.122, avgs=0 175/300: dt: 0.9000, rms radial error=146.296, avgs=0 180/300: dt: 0.9000, rms radial error=145.476, avgs=0 185/300: dt: 0.9000, rms radial error=144.660, avgs=0 190/300: dt: 0.9000, rms radial error=143.848, avgs=0 195/300: dt: 0.9000, rms radial error=143.041, avgs=0 200/300: dt: 0.9000, rms radial error=142.238, avgs=0 205/300: dt: 0.9000, rms radial error=141.439, avgs=0 210/300: dt: 0.9000, rms radial error=140.645, avgs=0 215/300: dt: 0.9000, rms radial error=139.855, avgs=0 220/300: dt: 0.9000, rms radial error=139.069, avgs=0 225/300: dt: 0.9000, rms radial error=138.288, avgs=0 230/300: dt: 0.9000, rms radial error=137.511, avgs=0 235/300: dt: 0.9000, rms radial error=136.738, avgs=0 240/300: dt: 0.9000, rms radial error=135.969, avgs=0 245/300: dt: 0.9000, rms radial error=135.205, avgs=0 250/300: dt: 0.9000, rms radial error=134.445, avgs=0 255/300: dt: 0.9000, rms radial error=133.689, avgs=0 260/300: dt: 0.9000, rms radial error=132.937, avgs=0 265/300: dt: 0.9000, rms radial error=132.190, avgs=0 270/300: dt: 0.9000, rms radial error=131.446, avgs=0 275/300: dt: 0.9000, rms radial error=130.707, avgs=0 280/300: dt: 0.9000, rms radial error=129.971, avgs=0 285/300: dt: 0.9000, rms radial error=129.240, avgs=0 290/300: dt: 0.9000, rms radial error=128.513, avgs=0 295/300: dt: 0.9000, rms radial error=127.790, avgs=0 300/300: dt: 0.9000, rms radial error=127.070, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 20881.80 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00012 epoch 2 (K=40.0), pass 1, starting sse = 3776.48 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00000 epoch 3 (K=160.0), pass 1, starting sse = 442.44 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/10 = 0.00462 epoch 4 (K=640.0), pass 1, starting sse = 29.50 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/12 = 0.00571 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.10 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Thu Aug 8 17:18:15 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/sub006/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub006 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=-30 (nv=172752, nf=345564, ne=518346, g=16) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 11 iterations marking ambiguous vertices... 2478 ambiguous faces found in tessellation segmenting defects... 25 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 6 into 4 -merging segment 8 into 7 -merging segment 11 into 7 22 defects to be corrected 0 vertices coincident reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.9378 (-4.9689) -vertex loglikelihood: -6.7130 (-3.3565) -normal dot loglikelihood: -3.6670 (-3.6670) -quad curv loglikelihood: -6.4196 (-3.2098) Total Loglikelihood : -26.7374 CORRECTING DEFECT 0 (vertices=10, convex hull=18) After retessellation of defect 0, euler #=-21 (171201,512909,341687) : difference with theory (-19) = 2 CORRECTING DEFECT 1 (vertices=90, convex hull=84) After retessellation of defect 1, euler #=-20 (171220,513001,341761) : difference with theory (-18) = 2 CORRECTING DEFECT 2 (vertices=101, convex hull=88) After retessellation of defect 2, euler #=-19 (171241,513104,341844) : difference with theory (-17) = 2 CORRECTING DEFECT 3 (vertices=33, convex hull=70) After retessellation of defect 3, euler #=-18 (171262,513194,341914) : difference with theory (-16) = 2 CORRECTING DEFECT 4 (vertices=228, convex hull=225) After retessellation of defect 4, euler #=-16 (171280,513353,342057) : difference with theory (-15) = 1 CORRECTING DEFECT 5 (vertices=213, convex hull=159) After retessellation of defect 5, euler #=-15 (171315,513528,342198) : difference with theory (-14) = 1 CORRECTING DEFECT 6 (vertices=342, convex hull=236) After retessellation of defect 6, euler #=-12 (171346,513753,342395) : difference with theory (-13) = -1 CORRECTING DEFECT 7 (vertices=6, convex hull=14) After retessellation of defect 7, euler #=-11 (171346,513757,342400) : difference with theory (-12) = -1 CORRECTING DEFECT 8 (vertices=26, convex hull=65) After retessellation of defect 8, euler #=-10 (171361,513830,342459) : difference with theory (-11) = -1 CORRECTING DEFECT 9 (vertices=47, convex hull=45) After retessellation of defect 9, euler #=-10 (171374,513891,342507) : difference with theory (-10) = 0 CORRECTING DEFECT 10 (vertices=25, convex hull=24) After retessellation of defect 10, euler #=-9 (171378,513911,342524) : difference with theory (-9) = 0 CORRECTING DEFECT 11 (vertices=57, convex hull=40) After retessellation of defect 11, euler #=-8 (171384,513944,342552) : difference with theory (-8) = 0 CORRECTING DEFECT 12 (vertices=21, convex hull=32) After retessellation of defect 12, euler #=-7 (171388,513967,342572) : difference with theory (-7) = 0 CORRECTING DEFECT 13 (vertices=12, convex hull=30) After retessellation of defect 13, euler #=-6 (171393,513994,342595) : difference with theory (-6) = 0 CORRECTING DEFECT 14 (vertices=51, convex hull=65) After retessellation of defect 14, euler #=-5 (171408,514062,342649) : difference with theory (-5) = 0 CORRECTING DEFECT 15 (vertices=70, convex hull=61) After retessellation of defect 15, euler #=-4 (171415,514107,342688) : difference with theory (-4) = 0 CORRECTING DEFECT 16 (vertices=23, convex hull=27) After retessellation of defect 16, euler #=-3 (171421,514133,342709) : difference with theory (-3) = 0 CORRECTING DEFECT 17 (vertices=9, convex hull=26) After retessellation of defect 17, euler #=-2 (171424,514150,342724) : difference with theory (-2) = 0 CORRECTING DEFECT 18 (vertices=55, convex hull=68) After retessellation of defect 18, euler #=-1 (171437,514214,342776) : difference with theory (-1) = 0 CORRECTING DEFECT 19 (vertices=34, convex hull=59) After retessellation of defect 19, euler #=0 (171445,514261,342816) : difference with theory (0) = 0 CORRECTING DEFECT 20 (vertices=45, convex hull=95) After retessellation of defect 20, euler #=1 (171462,514349,342888) : difference with theory (1) = 0 CORRECTING DEFECT 21 (vertices=49, convex hull=74) After retessellation of defect 21, euler #=2 (171478,514428,342952) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.23 (0.09-->11.19) (max @ vno 73397 --> 77073) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.23 (0.09-->11.19) (max @ vno 73397 --> 77073) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 81 mutations (34.6%), 153 crossovers (65.4%), 260 vertices were eliminated building final representation... 1274 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=171478, nf=342952, ne=514428, g=0) writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 29.8 minutes 0 defective edges removing intersecting faces 000: 202 intersecting 001: 2 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 171478 - 514428 + 342952 = 2 --> 0 holes F =2V-4: 342952 = 342956-4 (0) 2E=3F: 1028856 = 1028856 (0) total defect index = 0 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 19 intersecting 001: 3 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Thu Aug 8 17:48:10 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub006 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/sub006/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz... 24515 bright wm thresholded. 438 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.orig... computing class statistics... border white: 318128 voxels (1.90%) border gray 352780 voxels (2.10%) WM (93.0): 93.8 +- 10.2 [70.0 --> 110.0] GM (75.0) : 73.0 +- 13.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 43.3 (was 70) setting MAX_BORDER_WHITE to 116.2 (was 105) setting MIN_BORDER_WHITE to 57.0 (was 85) setting MAX_CSF to 29.7 (was 40) setting MAX_GRAY to 95.8 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 50.2 (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/sub006/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.03-->4.93) (max @ vno 73397 --> 77073) face area 0.28 +- 0.12 (0.00-->4.07) mean absolute distance = 0.66 +- 0.76 4605 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=106, GM=57 mean inside = 93.4, mean outside = 67.5 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=71.0, 74 (74) missing vertices, mean dist 0.4 [0.5 (%28.2)->0.7 (%71.8))] %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 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.26 (0.11-->7.80) (max @ vno 77073 --> 73397) face area 0.28 +- 0.13 (0.00-->6.15) mean absolute distance = 0.33 +- 0.46 4148 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=10027942.0, rms=14.60 001: dt: 0.5000, sse=9368935.0, rms=10.566 (0.000%) 002: dt: 0.5000, sse=9359829.0, rms=8.174 (0.000%) 003: dt: 0.5000, sse=9455504.0, rms=6.630 (0.000%) 004: dt: 0.5000, sse=9669029.0, rms=5.705 (0.000%) 005: dt: 0.5000, sse=9780128.0, rms=5.172 (0.000%) 006: dt: 0.5000, sse=9891815.0, rms=4.903 (0.000%) 007: dt: 0.5000, sse=9901317.0, rms=4.749 (0.000%) 008: dt: 0.5000, sse=9908980.0, rms=4.663 (0.000%) 009: dt: 0.5000, sse=9865048.0, rms=4.605 (0.000%) rms = 4.57, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=9860651.0, rms=4.565 (0.000%) 011: dt: 0.2500, sse=6112863.0, rms=3.143 (0.000%) 012: dt: 0.2500, sse=5634209.5, rms=2.705 (0.000%) 013: dt: 0.2500, sse=5322691.0, rms=2.631 (0.000%) 014: dt: 0.2500, sse=5252264.5, rms=2.570 (0.000%) rms = 2.56, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=5136448.5, rms=2.560 (0.000%) 016: dt: 0.1250, sse=4708750.5, rms=2.156 (0.000%) 017: dt: 0.1250, sse=4654870.0, rms=2.100 (0.000%) rms = 2.09, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=4617372.5, rms=2.093 (0.000%) positioning took 2.9 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=76.5, 49 (14) missing vertices, mean dist -0.2 [0.4 (%82.0)->0.2 (%18.0))] %84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.09-->8.01) (max @ vno 77073 --> 73397) face area 0.35 +- 0.17 (0.00-->8.31) mean absolute distance = 0.21 +- 0.28 4675 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=6305146.5, rms=7.16 019: dt: 0.5000, sse=6108556.5, rms=4.764 (0.000%) rms = 4.91, time step reduction 1 of 3 to 0.250... 020: dt: 0.2500, sse=5510872.5, rms=3.535 (0.000%) 021: dt: 0.2500, sse=5267443.5, rms=2.833 (0.000%) 022: dt: 0.2500, sse=5214090.5, rms=2.299 (0.000%) 023: dt: 0.2500, sse=5223199.5, rms=2.220 (0.000%) 024: dt: 0.2500, sse=5142760.5, rms=2.063 (0.000%) rms = 2.09, time step reduction 2 of 3 to 0.125... 025: dt: 0.1250, sse=5035590.5, rms=1.913 (0.000%) 026: dt: 0.1250, sse=4902379.0, rms=1.694 (0.000%) rms = 1.65, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=4851876.0, rms=1.651 (0.000%) positioning took 1.6 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=80.3, 35 (5) missing vertices, mean dist -0.1 [0.2 (%79.1)->0.2 (%20.9))] %91 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.25 (0.10-->8.21) (max @ vno 77073 --> 73397) face area 0.34 +- 0.16 (0.00-->8.32) mean absolute distance = 0.15 +- 0.22 3223 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5480494.5, rms=4.80 028: dt: 0.5000, sse=5843610.0, rms=4.653 (0.000%) 029: dt: 0.5000, sse=6094991.5, rms=4.548 (0.000%) rms = 4.91, time step reduction 1 of 3 to 0.250... 030: dt: 0.2500, sse=5307931.5, rms=2.755 (0.000%) 031: dt: 0.2500, sse=5336993.5, rms=2.063 (0.000%) rms = 2.07, time step reduction 2 of 3 to 0.125... 032: dt: 0.1250, sse=5213570.5, rms=1.842 (0.000%) 033: dt: 0.1250, sse=5036277.0, rms=1.485 (0.000%) 034: dt: 0.1250, sse=4985887.5, rms=1.407 (0.000%) rms = 1.41, time step reduction 3 of 3 to 0.062... 035: dt: 0.1250, sse=4985887.5, rms=1.407 (0.004%) positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=81.4, 30 (4) missing vertices, mean dist -0.0 [0.2 (%59.5)->0.1 (%40.5))] %93 local maxima, % 2 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=5031109.0, rms=1.92 rms = 3.04, time step reduction 1 of 3 to 0.250... 036: dt: 0.2500, sse=5082993.5, rms=1.249 (0.000%) 037: dt: 0.2500, sse=5214479.0, rms=1.069 (0.000%) rms = 1.06, time step reduction 2 of 3 to 0.125... 038: dt: 0.2500, sse=5316066.5, rms=1.065 (0.000%) rms = 1.03, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=5339791.5, rms=1.027 (0.000%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group generating cortex label... 22 non-cortical segments detected only using segment with 2212 vertices erasing segment 1 (vno[0] = 73466) erasing segment 2 (vno[0] = 78475) erasing segment 3 (vno[0] = 100956) erasing segment 4 (vno[0] = 112206) erasing segment 5 (vno[0] = 122789) erasing segment 6 (vno[0] = 123824) erasing segment 7 (vno[0] = 123835) erasing segment 8 (vno[0] = 123859) erasing segment 9 (vno[0] = 124890) erasing segment 10 (vno[0] = 127013) erasing segment 11 (vno[0] = 127062) erasing segment 12 (vno[0] = 127083) erasing segment 13 (vno[0] = 128190) erasing segment 14 (vno[0] = 129286) erasing segment 15 (vno[0] = 131208) erasing segment 16 (vno[0] = 131226) erasing segment 17 (vno[0] = 132184) erasing segment 18 (vno[0] = 133096) erasing segment 19 (vno[0] = 133105) erasing segment 20 (vno[0] = 133109) erasing segment 21 (vno[0] = 134078) writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/label/lh.cortex.label... writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.curv writing smoothed area to lh.area writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.area vertex spacing 0.89 +- 0.25 (0.09-->8.22) (max @ vno 77073 --> 73397) face area 0.34 +- 0.16 (0.00-->8.21) refinement took 9.4 minutes #-------------------------------------------- #@# Smooth2 lh Thu Aug 8 17:57:32 CEST 2013 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 17:57:37 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 52.3 mm, total surface area = 105174 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.113 (target=0.015) step 005: RMS=0.078 (target=0.015) step 010: RMS=0.056 (target=0.015) step 015: RMS=0.045 (target=0.015) step 020: RMS=0.038 (target=0.015) step 025: RMS=0.032 (target=0.015) step 030: RMS=0.026 (target=0.015) step 035: RMS=0.022 (target=0.015) step 040: RMS=0.019 (target=0.015) step 045: RMS=0.017 (target=0.015) step 050: RMS=0.015 (target=0.015) inflation complete. inflation took 0.6 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 242 vertices thresholded to be in k1 ~ [-0.25 0.92], k2 ~ [-0.17 0.07] total integrated curvature = 0.488*4pi (6.130) --> 1 handles ICI = 1.9, FI = 16.1, variation=257.292 156 vertices thresholded to be in [-0.03 0.01] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 128 vertices thresholded to be in [-0.13 0.17] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.015, std = 0.026 done. #----------------------------------------- #@# Curvature Stats lh Thu Aug 8 18:00:26 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub006 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 [ sub006/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 [ 311 ] Gb_filter = 0 WARN: S lookup min: -0.410253 WARN: S explicit min: 0.000000 vertex = 12 #-------------------------------------------- #@# Sphere lh Thu Aug 8 18:00:33 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 0.262... 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 %20.43 pass 1: epoch 2 of 3 starting distance error %20.34 unfolding complete - removing small folds... starting distance error %20.24 removing remaining folds... final distance error %20.25 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/lh.sphere spherical transformation took 1.28 hours #-------------------------------------------- #@# Surf Reg lh Thu Aug 8 19:17:36 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 = 0.579 curvature mean = 0.039, std = 0.935 curvature mean = 0.025, std = 0.829 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 0.00) sse = 379756.1, tmin=1.3897 d=32.00 min @ (8.00, 8.00, 0.00) sse = 336884.5, tmin=2.7776 d=16.00 min @ (0.00, -4.00, -4.00) sse = 296310.6, tmin=4.1916 d=8.00 min @ (-2.00, 0.00, 0.00) sse = 287756.1, tmin=5.6632 d=4.00 min @ (0.00, 0.00, 1.00) sse = 286234.4, tmin=7.1875 d=2.00 min @ (0.50, 1.00, -0.50) sse = 285496.2, tmin=8.7121 d=1.00 min @ (-0.25, -0.50, 0.25) sse = 285288.4, tmin=10.2292 d=0.50 min @ (0.00, 0.12, 0.00) sse = 285256.1, tmin=11.7381 tol=1.0e+00, sigma=0.5, host=snake, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 11.74 min curvature mean = 0.012, std = 0.938 curvature mean = 0.014, std = 0.924 curvature mean = 0.009, std = 0.948 curvature mean = 0.007, std = 0.963 curvature mean = 0.006, std = 0.946 curvature mean = 0.002, std = 0.983 2 Reading smoothwm curvature mean = -0.022, std = 0.292 curvature mean = 0.004, std = 0.066 curvature mean = 0.073, std = 0.308 curvature mean = 0.004, std = 0.077 curvature mean = 0.035, std = 0.494 curvature mean = 0.004, std = 0.083 curvature mean = 0.020, std = 0.639 curvature mean = 0.004, std = 0.085 curvature mean = 0.006, std = 0.758 MRISregister() return, current seed 0 writing registered surface to ../surf/lh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white lh Thu Aug 8 19:53:12 CEST 2013 mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Thu Aug 8 19:53:15 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts mrisp_paint -a 5 /opt/freesurfer/5.3.0/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /opt/freesurfer/5.3.0/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Thu Aug 8 19:53:18 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub006 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... 1813 labels changed using aseg relabeling using gibbs priors... 000: 3786 changed, 171478 examined... 001: 799 changed, 15881 examined... 002: 222 changed, 4452 examined... 003: 84 changed, 1319 examined... 004: 34 changed, 498 examined... 005: 14 changed, 217 examined... 006: 11 changed, 85 examined... 007: 2 changed, 46 examined... 008: 0 changed, 11 examined... 244 labels changed using aseg 000: 145 total segments, 102 labels (377 vertices) changed 001: 43 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 58 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1900 vertices marked for relabeling... 1900 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 1 minutes and 18 seconds. #-------------------------------------------- #@# Make Pial Surf lh Thu Aug 8 19:54:36 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub006 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/sub006/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz... 24515 bright wm thresholded. 438 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.orig... computing class statistics... border white: 318128 voxels (1.90%) border gray 352780 voxels (2.10%) WM (93.0): 93.8 +- 10.2 [70.0 --> 110.0] GM (75.0) : 73.0 +- 13.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 43.3 (was 70) setting MAX_BORDER_WHITE to 116.2 (was 105) setting MIN_BORDER_WHITE to 57.0 (was 85) setting MAX_CSF to 29.7 (was 40) setting MAX_GRAY to 95.8 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 50.2 (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=106, GM=57 mean inside = 93.4, mean outside = 67.5 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.03-->4.93) (max @ vno 73397 --> 77073) face area 0.28 +- 0.12 (0.00-->4.07) mean absolute distance = 0.66 +- 0.77 4633 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 193 points - only 7.25% unknown deleting segment 1 with 22 points - only 0.00% unknown deleting segment 2 with 14 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 3 with 2 points - only 0.00% unknown deleting segment 6 with 21 points - only 0.00% unknown deleting segment 7 with 741 points - only 0.00% unknown deleting segment 9 with 12 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 10 with 3 points - only 0.00% unknown deleting segment 12 with 16 points - only 0.00% unknown deleting segment 13 with 13 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 14 with 3 points - only 0.00% unknown deleting segment 15 with 5 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 16 with 3 points - only 0.00% unknown deleting segment 17 with 8 points - only 0.00% unknown mean border=71.0, 74 (74) missing vertices, mean dist 0.4 [0.5 (%28.4)->0.7 (%71.6))] %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 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.26 (0.11-->7.80) (max @ vno 77073 --> 73397) face area 0.28 +- 0.13 (0.00-->6.14) mean absolute distance = 0.33 +- 0.46 4164 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=10060111.0, rms=14.57 001: dt: 0.5000, sse=9420631.0, rms=10.543 (0.000%) 002: dt: 0.5000, sse=9418131.0, rms=8.156 (0.000%) 003: dt: 0.5000, sse=9519878.0, rms=6.618 (0.000%) 004: dt: 0.5000, sse=9735789.0, rms=5.693 (0.000%) 005: dt: 0.5000, sse=9850333.0, rms=5.165 (0.000%) 006: dt: 0.5000, sse=9963383.0, rms=4.895 (0.000%) 007: dt: 0.5000, sse=9970060.0, rms=4.742 (0.000%) 008: dt: 0.5000, sse=9981884.0, rms=4.655 (0.000%) 009: dt: 0.5000, sse=9935452.0, rms=4.600 (0.000%) rms = 4.56, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=9933331.0, rms=4.559 (0.000%) 011: dt: 0.2500, sse=6159862.0, rms=3.139 (0.000%) 012: dt: 0.2500, sse=5673852.5, rms=2.701 (0.000%) 013: dt: 0.2500, sse=5361696.0, rms=2.628 (0.000%) 014: dt: 0.2500, sse=5288730.5, rms=2.568 (0.000%) rms = 2.56, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=5172132.5, rms=2.558 (0.000%) 016: dt: 0.1250, sse=4745235.5, rms=2.156 (0.000%) 017: dt: 0.1250, sse=4692363.0, rms=2.101 (0.000%) rms = 2.09, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=4655493.5, rms=2.095 (0.000%) positioning took 2.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 244 points - only 8.61% unknown deleting segment 1 with 22 points - only 0.00% unknown deleting segment 2 with 17 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 1 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 19 points - only 0.00% unknown deleting segment 7 with 8 points - only 0.00% unknown deleting segment 8 with 660 points - only 0.00% unknown deleting segment 9 with 12 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 15 with 16 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 16 with 1 points - only 0.00% unknown deleting segment 17 with 6 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 18 with 3 points - only 0.00% unknown mean border=76.5, 54 (14) missing vertices, mean dist -0.2 [0.4 (%82.0)->0.2 (%18.0))] %85 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.09-->8.01) (max @ vno 77073 --> 73397) face area 0.35 +- 0.17 (0.00-->8.31) mean absolute distance = 0.21 +- 0.28 4693 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=6350666.5, rms=7.15 019: dt: 0.5000, sse=6157726.0, rms=4.757 (0.000%) rms = 4.90, time step reduction 1 of 3 to 0.250... 020: dt: 0.2500, sse=5554555.0, rms=3.530 (0.000%) 021: dt: 0.2500, sse=5309827.0, rms=2.830 (0.000%) 022: dt: 0.2500, sse=5256700.5, rms=2.297 (0.000%) 023: dt: 0.2500, sse=5266794.0, rms=2.219 (0.000%) 024: dt: 0.2500, sse=5183961.0, rms=2.063 (0.000%) rms = 2.09, time step reduction 2 of 3 to 0.125... 025: dt: 0.1250, sse=5076422.5, rms=1.914 (0.000%) 026: dt: 0.1250, sse=4942420.0, rms=1.695 (0.000%) rms = 1.65, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=4891604.5, rms=1.652 (0.000%) positioning took 1.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 216 points - only 6.48% unknown deleting segment 1 with 21 points - only 0.00% unknown deleting segment 2 with 17 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 1 points - only 0.00% unknown deleting segment 4 with 24 points - only 0.00% unknown deleting segment 5 with 700 points - only 0.00% unknown deleting segment 6 with 14 points - only 0.00% unknown deleting segment 9 with 5 points - only 0.00% unknown deleting segment 10 with 26 points - only 0.00% unknown deleting segment 12 with 18 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 13 with 4 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 14 with 4 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 15 with 3 points - only 0.00% unknown deleting segment 16 with 6 points - only 0.00% unknown mean border=80.2, 36 (5) missing vertices, mean dist -0.1 [0.2 (%79.0)->0.2 (%21.0))] %92 local maxima, % 4 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 +- 0.24 (0.10-->8.21) (max @ vno 77073 --> 73397) face area 0.34 +- 0.16 (0.00-->8.31) mean absolute distance = 0.15 +- 0.22 3263 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5522440.5, rms=4.79 028: dt: 0.5000, sse=5886809.0, rms=4.643 (0.000%) 029: dt: 0.5000, sse=6147410.0, rms=4.543 (0.000%) rms = 4.91, time step reduction 1 of 3 to 0.250... 030: dt: 0.2500, sse=5351452.0, rms=2.754 (0.000%) 031: dt: 0.2500, sse=5377083.0, rms=2.060 (0.000%) rms = 2.07, time step reduction 2 of 3 to 0.125... 032: dt: 0.1250, sse=5253498.0, rms=1.840 (0.000%) 033: dt: 0.1250, sse=5076645.5, rms=1.485 (0.000%) 034: dt: 0.1250, sse=5025209.0, rms=1.408 (0.000%) rms = 1.41, time step reduction 3 of 3 to 0.062... 035: dt: 0.1250, sse=5025209.0, rms=1.408 (0.004%) positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 215 points - only 5.58% unknown deleting segment 1 with 21 points - only 0.00% unknown deleting segment 2 with 17 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 1 points - only 0.00% unknown deleting segment 4 with 22 points - only 0.00% unknown deleting segment 5 with 707 points - only 0.00% unknown deleting segment 6 with 14 points - only 0.00% unknown deleting segment 7 with 5 points - only 0.00% unknown deleting segment 8 with 35 points - only 0.00% unknown deleting segment 9 with 20 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 10 with 4 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 11 with 4 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 12 with 3 points - only 0.00% unknown deleting segment 13 with 7 points - only 0.00% unknown mean border=81.3, 31 (4) missing vertices, mean dist -0.0 [0.2 (%59.4)->0.1 (%40.6))] %93 local maxima, % 2 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 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=5070727.0, rms=1.92 rms = 3.03, time step reduction 1 of 3 to 0.250... 036: dt: 0.2500, sse=5124402.0, rms=1.249 (0.000%) 037: dt: 0.2500, sse=5259710.5, rms=1.070 (0.000%) rms = 1.07, time step reduction 2 of 3 to 0.125... 038: dt: 0.2500, sse=5361433.0, rms=1.067 (0.000%) rms = 1.03, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=5386527.0, rms=1.029 (0.000%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... smoothing surface for 5 iterations... mean border=46.6, 37 (37) missing vertices, mean dist 1.8 [0.2 (%0.0)->2.3 (%100.0))] %14 local maxima, %62 large gradients and %20 min vals, 1854 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=41829020.0, rms=34.18 001: dt: 0.5000, sse=29729242.0, rms=28.287 (0.000%) 002: dt: 0.5000, sse=21449460.0, rms=23.444 (0.000%) 003: dt: 0.5000, sse=15982869.0, rms=19.550 (0.000%) 004: dt: 0.5000, sse=12582245.0, rms=16.460 (0.000%) 005: dt: 0.5000, sse=10589562.0, rms=14.062 (0.000%) 006: dt: 0.5000, sse=9451943.0, rms=12.170 (0.000%) 007: dt: 0.5000, sse=8684540.0, rms=10.517 (0.000%) 008: dt: 0.5000, sse=8174177.5, rms=9.004 (0.000%) 009: dt: 0.5000, sse=7824750.5, rms=7.641 (0.000%) 010: dt: 0.5000, sse=7654596.5, rms=6.437 (0.000%) 011: dt: 0.5000, sse=7620808.5, rms=5.478 (0.000%) 012: dt: 0.5000, sse=7788831.0, rms=4.808 (0.000%) 013: dt: 0.5000, sse=7917054.5, rms=4.418 (0.000%) 014: dt: 0.5000, sse=8059843.5, rms=4.191 (0.000%) 015: dt: 0.5000, sse=8142026.5, rms=4.081 (0.000%) 016: dt: 0.5000, sse=8267752.0, rms=3.996 (0.000%) rms = 3.95, time step reduction 1 of 3 to 0.250... 017: dt: 0.5000, sse=8282918.5, rms=3.953 (0.000%) 018: dt: 0.2500, sse=5694765.5, rms=3.099 (0.000%) 019: dt: 0.2500, sse=5496246.0, rms=2.870 (0.000%) rms = 2.84, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=5338956.0, rms=2.841 (0.000%) 021: dt: 0.1250, sse=5070952.5, rms=2.649 (0.000%) rms = 2.62, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=5036784.5, rms=2.623 (0.000%) positioning took 3.3 minutes mean border=43.9, 753 (5) missing vertices, mean dist 0.2 [0.2 (%48.8)->0.6 (%51.2))] %33 local maxima, %47 large gradients and %16 min vals, 476 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=5913994.5, rms=5.00 023: dt: 0.5000, sse=6323110.0, rms=4.222 (0.000%) 024: dt: 0.5000, sse=8048154.5, rms=4.157 (0.000%) rms = 4.14, time step reduction 1 of 3 to 0.250... 025: dt: 0.5000, sse=8038463.0, rms=4.141 (0.000%) 026: dt: 0.2500, sse=6275116.5, rms=3.104 (0.000%) 027: dt: 0.2500, sse=6170375.0, rms=2.796 (0.000%) rms = 2.79, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=5969225.5, rms=2.793 (0.000%) 029: dt: 0.1250, sse=5720778.5, rms=2.553 (0.000%) rms = 2.52, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=5693824.5, rms=2.518 (0.000%) positioning took 1.2 minutes mean border=40.9, 885 (3) missing vertices, mean dist 0.1 [0.2 (%35.5)->0.4 (%64.5))] %57 local maxima, %24 large gradients and %15 min vals, 602 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=6194776.0, rms=4.52 031: dt: 0.5000, sse=6317909.0, rms=4.116 (0.000%) rms = 4.10, time step reduction 1 of 3 to 0.250... 032: dt: 0.5000, sse=8341824.5, rms=4.101 (0.000%) 033: dt: 0.2500, sse=6203912.5, rms=3.015 (0.000%) 034: dt: 0.2500, sse=6381834.5, rms=2.697 (0.000%) rms = 2.72, time step reduction 2 of 3 to 0.125... 035: dt: 0.1250, sse=6219413.0, rms=2.580 (0.000%) 036: dt: 0.1250, sse=5955520.5, rms=2.417 (0.000%) rms = 2.39, time step reduction 3 of 3 to 0.062... 037: dt: 0.1250, sse=5891363.5, rms=2.393 (0.000%) positioning took 1.2 minutes mean border=39.4, 1880 (3) missing vertices, mean dist 0.1 [0.2 (%44.4)->0.3 (%55.6))] %61 local maxima, %19 large gradients and %15 min vals, 422 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/sub006/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=5991562.0, rms=2.98 rms = 3.99, time step reduction 1 of 3 to 0.250... 038: dt: 0.2500, sse=5783776.5, rms=2.557 (0.000%) 039: dt: 0.2500, sse=5942419.5, rms=2.448 (0.000%) rms = 2.42, time step reduction 2 of 3 to 0.125... 040: dt: 0.2500, sse=6016633.0, rms=2.420 (0.000%) 041: dt: 0.1250, sse=5899802.0, rms=2.287 (0.000%) rms = 2.27, time step reduction 3 of 3 to 0.062... 042: dt: 0.1250, sse=5903649.5, rms=2.271 (0.000%) positioning took 0.9 minutes writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.area.pial vertex spacing 1.01 +- 0.42 (0.07-->8.86) (max @ vno 77073 --> 73397) face area 0.41 +- 0.31 (0.00-->9.50) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 171478 vertices processed 25000 of 171478 vertices processed 50000 of 171478 vertices processed 75000 of 171478 vertices processed 100000 of 171478 vertices processed 125000 of 171478 vertices processed 150000 of 171478 vertices processed 0 of 171478 vertices processed 25000 of 171478 vertices processed 50000 of 171478 vertices processed 75000 of 171478 vertices processed 100000 of 171478 vertices processed 125000 of 171478 vertices processed 150000 of 171478 vertices processed thickness calculation complete, 240:598 truncations. 40441 vertices at 0 distance 120742 vertices at 1 distance 110846 vertices at 2 distance 42696 vertices at 3 distance 11082 vertices at 4 distance 2716 vertices at 5 distance 750 vertices at 6 distance 254 vertices at 7 distance 91 vertices at 8 distance 37 vertices at 9 distance 23 vertices at 10 distance 21 vertices at 11 distance 30 vertices at 12 distance 16 vertices at 13 distance 17 vertices at 14 distance 8 vertices at 15 distance 11 vertices at 16 distance 7 vertices at 17 distance 5 vertices at 18 distance 3 vertices at 19 distance 6 vertices at 20 distance writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.thickness positioning took 17.8 minutes #-------------------------------------------- #@# Surf Volume lh Thu Aug 8 20:12:24 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.volume lh.area.mid mul lh.thickness Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# WM/GM Contrast lh Thu Aug 8 20:12:24 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts pctsurfcon --s sub006 --lh-only Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts/pctsurfcon.log Thu Aug 8 20:12:24 CEST 2013 setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/tmp.pctsurfcon.2784/lh.wm.mgh --regheader sub006 --cortex srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/mri/orig.mgz as target reference. Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/label/lh.cortex.label Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 = 133568 Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/label/lh.cortex.label Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/tmp.pctsurfcon.2784/lh.wm.mgh Dim: 171478 1 1 mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/tmp.pctsurfcon.2784/lh.gm.mgh --projfrac 0.3 --regheader sub006 --cortex srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/mri/orig.mgz as target reference. Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/label/lh.cortex.label Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white Done reading source surface Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 = 153059 Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/label/lh.cortex.label Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/tmp.pctsurfcon.2784/lh.gm.mgh Dim: 171478 1 1 mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/tmp.pctsurfcon.2784/lh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/tmp.pctsurfcon.2784/lh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/surf/lh.w-g.pct.mgh mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.w-g.pct.mgh --annot sub006 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/surf/lh.w-g.pct.mgh --annot sub006 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/surf/lh.w-g.pct.mgh Vertex Area is 0.667218 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 1000 unknown 0 0.000 1 1001 bankssts 2087 1415.694 2 1002 caudalanteriorcingulate 1419 970.881 3 1003 caudalmiddlefrontal 3985 2657.052 4 1004 corpuscallosum 0 0.000 5 1005 cuneus 2537 1656.748 6 1006 entorhinal 575 407.499 7 1007 fusiform 5408 3712.237 8 1008 inferiorparietal 10252 6776.328 9 1009 inferiortemporal 6684 4582.200 10 1010 isthmuscingulate 2348 1537.153 11 1011 lateraloccipital 9326 5996.407 12 1012 lateralorbitofrontal 4511 3024.425 13 1013 lingual 4757 3296.165 14 1014 medialorbitofrontal 3425 2281.483 15 1015 middletemporal 5998 4283.024 16 1016 parahippocampal 1042 727.525 17 1017 paracentral 2679 1757.445 18 1018 parsopercularis 3585 2399.116 19 1019 parsorbitalis 1202 794.842 20 1020 parstriangularis 2543 1678.600 21 1021 pericalcarine 2257 1504.341 22 1022 postcentral 7698 4989.887 23 1023 posteriorcingulate 2513 1640.895 24 1024 precentral 8936 5689.858 25 1025 precuneus 7701 5090.480 26 1026 rostralanteriorcingulate 1900 1246.719 27 1027 rostralmiddlefrontal 10703 7305.083 28 1028 superiorfrontal 15137 10291.527 29 1029 superiorparietal 9869 6443.312 30 1030 superiortemporal 6608 4488.436 31 1031 supramarginal 8389 5600.073 32 1032 frontalpole 380 252.491 33 1033 temporalpole 784 570.839 34 1034 transversetemporal 845 525.919 35 1035 insula 4256 2755.293 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats lh Thu Aug 8 20:12:40 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 sub006 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 2087 1416 3779 2.712 0.419 0.119 0.030 17 2.6 bankssts 1419 971 3035 3.012 0.581 0.169 0.071 47 4.3 caudalanteriorcingulate 3985 2657 7761 2.670 0.495 0.128 0.053 57 7.2 caudalmiddlefrontal 2537 1657 3599 2.017 0.441 0.164 0.059 46 6.0 cuneus 575 407 2153 3.663 0.827 0.139 0.047 7 1.2 entorhinal 5408 3712 12135 2.805 0.544 0.142 0.048 98 11.7 fusiform 10252 6776 19259 2.508 0.468 0.131 0.041 141 16.7 inferiorparietal 6684 4582 14149 2.623 0.632 0.145 0.057 128 15.2 inferiortemporal 2348 1537 4343 2.576 0.845 0.155 0.063 53 5.6 isthmuscingulate 9326 5996 15104 2.248 0.461 0.148 0.051 155 19.0 lateraloccipital 4511 3024 9097 2.639 0.695 0.157 0.066 105 11.9 lateralorbitofrontal 4757 3296 7854 2.170 0.578 0.158 0.071 113 12.2 lingual 3425 2281 5652 2.116 0.698 0.146 0.071 96 10.7 medialorbitofrontal 5998 4283 14011 2.662 0.629 0.152 0.059 139 13.7 middletemporal 1042 728 2600 3.067 0.653 0.124 0.039 12 1.4 parahippocampal 2679 1757 5234 2.613 0.525 0.111 0.026 22 3.1 paracentral 3585 2399 7228 2.655 0.470 0.134 0.043 53 6.3 parsopercularis 1202 795 2720 2.697 0.541 0.169 0.060 27 2.9 parsorbitalis 2543 1679 4751 2.486 0.421 0.151 0.054 46 5.6 parstriangularis 2257 1504 2742 1.906 0.387 0.132 0.050 28 5.0 pericalcarine 7698 4990 12760 2.195 0.549 0.126 0.036 101 11.2 postcentral 2513 1641 4838 2.709 0.659 0.164 0.080 58 6.6 posteriorcingulate 8936 5690 17489 2.775 0.507 0.112 0.034 98 13.0 precentral 7701 5090 14236 2.560 0.508 0.137 0.046 130 13.8 precuneus 1900 1247 3957 2.678 0.653 0.157 0.079 62 5.0 rostralanteriorcingulate 10703 7305 19791 2.310 0.517 0.163 0.066 256 27.0 rostralmiddlefrontal 15137 10292 32166 2.685 0.544 0.136 0.042 221 25.9 superiorfrontal 9869 6443 16255 2.281 0.451 0.129 0.038 126 15.1 superiorparietal 6608 4488 15508 2.965 0.609 0.122 0.034 71 9.5 superiortemporal 8389 5600 16613 2.619 0.501 0.144 0.052 152 17.3 supramarginal 380 252 789 2.303 0.566 0.209 0.645 28 18.3 frontalpole 784 571 2976 3.741 0.581 0.155 0.060 16 1.8 temporalpole 845 526 1597 2.628 0.372 0.138 0.051 11 1.7 transversetemporal 4256 2755 8840 3.098 0.688 0.123 0.054 69 10.1 insula #----------------------------------------- #@# Cortical Parc 2 lh Thu Aug 8 20:13:16 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub006 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... 11 labels changed using aseg relabeling using gibbs priors... 000: 11640 changed, 171478 examined... 001: 2841 changed, 44597 examined... 002: 855 changed, 14481 examined... 003: 375 changed, 4767 examined... 004: 212 changed, 2161 examined... 005: 96 changed, 1161 examined... 006: 38 changed, 522 examined... 007: 23 changed, 235 examined... 008: 20 changed, 145 examined... 009: 11 changed, 106 examined... 010: 1 changed, 59 examined... 011: 2 changed, 7 examined... 012: 2 changed, 12 examined... 013: 0 changed, 6 examined... 2 labels changed using aseg 000: 336 total segments, 257 labels (3762 vertices) changed 001: 105 total segments, 26 labels (214 vertices) changed 002: 80 total segments, 1 labels (1 vertices) changed 003: 79 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 189 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1245 vertices marked for relabeling... 1245 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 1 minutes and 30 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Thu Aug 8 20:14:46 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 sub006 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 1737 1169 3047 2.147 0.633 0.169 0.069 40 4.7 G_and_S_frontomargin 1889 1237 3422 2.383 0.506 0.146 0.060 37 5.6 G_and_S_occipital_inf 1891 1142 3765 2.574 0.539 0.119 0.037 25 3.3 G_and_S_paracentral 1824 1243 3729 2.567 0.490 0.150 0.044 29 3.4 G_and_S_subcentral 852 595 1658 2.166 0.458 0.230 0.374 63 21.5 G_and_S_transv_frontopol 3193 2148 6376 2.589 0.589 0.143 0.063 75 7.5 G_and_S_cingul-Ant 2067 1418 4062 2.888 0.460 0.127 0.039 28 3.3 G_and_S_cingul-Mid-Ant 1797 1207 3398 2.709 0.515 0.126 0.063 27 3.0 G_and_S_cingul-Mid-Post 1115 716 2831 3.195 0.510 0.193 0.085 35 4.2 G_cingul-Post-dorsal 480 305 916 2.558 0.883 0.143 0.063 8 1.1 G_cingul-Post-ventral 2292 1503 3519 2.015 0.444 0.170 0.065 45 5.7 G_cuneus 2154 1428 5200 2.809 0.457 0.149 0.055 42 4.7 G_front_inf-Opercular 313 211 656 2.443 0.426 0.171 0.064 7 0.8 G_front_inf-Orbital 1592 1049 3519 2.610 0.414 0.162 0.059 37 3.9 G_front_inf-Triangul 5422 3699 12513 2.619 0.529 0.175 0.085 157 15.9 G_front_middle 10115 6825 23961 2.781 0.557 0.146 0.047 178 19.3 G_front_sup 754 461 1743 3.266 0.456 0.125 0.062 10 1.6 G_Ins_lg_and_S_cent_ins 991 620 2871 3.622 0.690 0.141 0.061 18 2.3 G_insular_short 3173 2021 6460 2.548 0.391 0.157 0.056 67 7.1 G_occipital_middle 1833 1159 3279 2.296 0.475 0.142 0.049 26 3.5 G_occipital_sup 2350 1511 5812 2.918 0.528 0.149 0.046 51 4.5 G_oc-temp_lat-fusifor 3136 2200 5725 2.155 0.589 0.177 0.089 100 9.4 G_oc-temp_med-Lingual 1291 889 3727 3.273 0.717 0.126 0.038 14 2.0 G_oc-temp_med-Parahip 3051 2056 7614 2.845 0.697 0.179 0.078 84 10.0 G_orbital 4175 2737 9599 2.737 0.517 0.144 0.050 75 8.6 G_pariet_inf-Angular 4269 2887 9859 2.740 0.498 0.151 0.057 87 10.1 G_pariet_inf-Supramar 3559 2334 6755 2.376 0.491 0.142 0.044 58 6.3 G_parietal_sup 3211 1999 6003 2.341 0.485 0.135 0.042 53 5.4 G_postcentral 3609 2190 8796 3.010 0.455 0.120 0.037 53 6.0 G_precentral 3348 2214 7711 2.720 0.504 0.152 0.053 82 6.8 G_precuneus 1113 734 2205 2.191 0.714 0.202 0.127 61 6.5 G_rectus 499 319 879 2.564 0.933 0.133 0.078 15 1.7 G_subcallosal 670 412 1433 2.742 0.366 0.146 0.051 11 1.5 G_temp_sup-G_T_transv 2497 1668 7760 3.253 0.579 0.144 0.044 37 4.5 G_temp_sup-Lateral 850 595 2382 3.593 0.552 0.113 0.041 6 1.3 G_temp_sup-Plan_polar 1029 709 2191 2.672 0.546 0.119 0.043 15 1.3 G_temp_sup-Plan_tempo 3537 2418 9164 2.797 0.696 0.173 0.079 103 11.4 G_temporal_inf 4024 2921 10745 2.734 0.616 0.174 0.076 123 11.6 G_temporal_middle 445 291 651 2.189 0.373 0.138 0.045 6 0.8 Lat_Fis-ant-Horizont 417 279 609 2.582 0.396 0.110 0.030 2 0.5 Lat_Fis-ant-Vertical 1217 820 1624 2.434 0.379 0.131 0.044 14 2.0 Lat_Fis-post 2975 1818 4538 2.099 0.443 0.153 0.059 61 7.2 Pole_occipital 2014 1430 6654 3.368 0.775 0.149 0.053 34 4.4 Pole_temporal 3300 2189 4297 2.155 0.608 0.128 0.049 37 6.8 S_calcarine 3623 2425 4628 2.134 0.652 0.100 0.023 19 3.7 S_central 1394 947 1970 2.403 0.452 0.108 0.028 8 1.6 S_cingul-Marginalis 736 481 1165 2.690 0.531 0.096 0.026 4 0.8 S_circular_insula_ant 1835 1226 3103 2.823 0.582 0.107 0.044 34 4.6 S_circular_insula_inf 2151 1456 3355 2.669 0.461 0.113 0.029 14 2.7 S_circular_insula_sup 1184 864 2131 2.609 0.442 0.110 0.026 8 1.3 S_collat_transv_ant 375 259 522 2.041 0.343 0.146 0.036 4 0.6 S_collat_transv_post 2928 1970 4637 2.352 0.440 0.133 0.039 37 4.8 S_front_inf 2089 1431 3099 2.169 0.396 0.122 0.037 22 2.9 S_front_middle 3628 2471 6259 2.484 0.415 0.115 0.034 38 4.8 S_front_sup 500 332 659 2.292 0.414 0.095 0.022 2 0.5 S_interm_prim-Jensen 4521 3004 6322 2.184 0.353 0.114 0.030 44 5.7 S_intrapariet_and_P_trans 1742 1163 2282 2.165 0.391 0.141 0.043 21 2.9 S_oc_middle_and_Lunatus 1724 1116 2290 2.197 0.364 0.123 0.030 16 2.2 S_oc_sup_and_transversal 606 421 779 2.107 0.358 0.112 0.024 3 0.7 S_occipital_ant 1021 720 1783 2.601 0.428 0.142 0.047 12 1.7 S_oc-temp_lat 2070 1466 3358 2.587 0.489 0.122 0.032 17 2.8 S_oc-temp_med_and_Lingual 590 389 855 2.173 0.415 0.150 0.051 12 1.1 S_orbital_lateral 835 560 1291 2.274 0.784 0.129 0.058 17 1.7 S_orbital_med-olfact 1564 1056 2608 2.381 0.579 0.147 0.051 29 2.9 S_orbital-H_Shaped 2740 1773 3830 2.311 0.511 0.125 0.038 30 4.5 S_parieto_occipital 2101 1369 2887 2.266 0.842 0.162 0.067 61 5.1 S_pericallosal 3223 2146 4469 2.279 0.436 0.119 0.033 31 4.2 S_postcentral 1958 1312 2909 2.481 0.365 0.104 0.026 13 2.0 S_precentral-inf-part 1773 1189 2591 2.489 0.448 0.107 0.026 12 1.8 S_precentral-sup-part 1103 736 1564 1.934 0.545 0.132 0.036 14 1.7 S_suborbital 1655 1123 2824 2.467 0.449 0.138 0.043 22 2.8 S_subparietal 2512 1717 3458 2.254 0.426 0.109 0.025 17 2.7 S_temporal_inf 7563 5109 12889 2.542 0.414 0.118 0.034 82 9.9 S_temporal_sup 525 349 851 2.728 0.377 0.130 0.034 6 0.8 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Thu Aug 8 20:15:16 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub006 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... 964 labels changed using aseg relabeling using gibbs priors... 000: 3465 changed, 171478 examined... 001: 815 changed, 14674 examined... 002: 221 changed, 4418 examined... 003: 70 changed, 1306 examined... 004: 38 changed, 425 examined... 005: 18 changed, 227 examined... 006: 6 changed, 97 examined... 007: 2 changed, 32 examined... 008: 0 changed, 12 examined... 42 labels changed using aseg 000: 82 total segments, 49 labels (370 vertices) changed 001: 35 total segments, 2 labels (2 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 44 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1232 vertices marked for relabeling... 1232 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas40.annot... classification took 1 minutes and 18 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Thu Aug 8 20:16:34 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 sub006 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 2585 1747 5532 2.995 0.549 0.144 0.052 58 5.7 caudalanteriorcingulate 4059 2709 7956 2.674 0.492 0.128 0.053 58 7.3 caudalmiddlefrontal 3609 2359 5415 2.123 0.452 0.151 0.051 56 7.4 cuneus 575 403 2011 3.578 0.875 0.137 0.045 7 1.1 entorhinal 4848 3312 10143 2.752 0.513 0.139 0.046 85 10.2 fusiform 9662 6365 18033 2.504 0.470 0.130 0.040 133 15.7 inferiorparietal 6594 4535 15065 2.685 0.677 0.150 0.059 135 15.7 inferiortemporal 2345 1531 4344 2.588 0.834 0.154 0.063 52 5.6 isthmuscingulate 9684 6216 15672 2.248 0.461 0.148 0.052 162 19.8 lateraloccipital 4809 3225 9957 2.622 0.741 0.161 0.071 118 13.4 lateralorbitofrontal 4776 3307 7882 2.171 0.576 0.158 0.071 113 12.2 lingual 2589 1731 4352 2.050 0.695 0.158 0.074 79 8.6 medialorbitofrontal 8191 5793 18327 2.668 0.591 0.147 0.054 164 17.2 middletemporal 1042 730 2607 3.066 0.657 0.123 0.039 12 1.3 parahippocampal 3151 2067 6041 2.584 0.519 0.110 0.028 25 4.0 paracentral 3200 2130 6516 2.700 0.441 0.136 0.045 48 5.9 parsopercularis 1305 859 2436 2.388 0.499 0.142 0.045 19 2.4 parsorbitalis 3386 2238 6226 2.480 0.464 0.151 0.053 61 7.2 parstriangularis 2301 1527 2775 1.898 0.392 0.134 0.051 29 5.2 pericalcarine 8522 5562 13931 2.198 0.542 0.126 0.035 108 12.2 postcentral 2674 1757 5051 2.701 0.663 0.161 0.077 59 6.7 posteriorcingulate 8839 5629 17249 2.772 0.514 0.113 0.033 97 12.5 precentral 7312 4870 13848 2.573 0.516 0.139 0.047 128 13.3 precuneus 2562 1677 4896 2.595 0.653 0.148 0.075 75 6.9 rostralanteriorcingulate 7048 4770 13361 2.359 0.526 0.155 0.056 144 15.3 rostralmiddlefrontal 16629 11399 34844 2.585 0.556 0.148 0.065 332 51.8 superiorfrontal 8053 5220 13213 2.290 0.444 0.128 0.037 103 12.1 superiorparietal 9265 6276 21747 2.991 0.647 0.127 0.043 137 17.4 superiortemporal 8092 5411 15950 2.613 0.505 0.143 0.051 140 16.7 supramarginal 790 493 1526 2.627 0.360 0.140 0.052 11 1.6 transversetemporal 3842 2501 8119 3.092 0.635 0.118 0.038 39 5.9 insula #-------------------------------------------- #@# Tessellate rh Thu Aug 8 20:17:01 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 1 found - 1 modified | TOTAL: 2 pass 2 (yz-): 0 found - 1 modified | TOTAL: 2 pass 1 (xz+): 1 found - 1 modified | TOTAL: 3 pass 2 (xz+): 0 found - 1 modified | TOTAL: 3 pass 1 (xz-): 3 found - 3 modified | TOTAL: 6 pass 2 (xz-): 0 found - 3 modified | TOTAL: 6 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 2 found - 2 modified | TOTAL: 3 pass 2 (-+): 0 found - 2 modified | TOTAL: 3 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 9 (out of 321357: 0.002801) 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 30: 847 vertices, 936 faces slice 40: 6079 vertices, 6323 faces slice 50: 15336 vertices, 15708 faces slice 60: 26939 vertices, 27348 faces slice 70: 39454 vertices, 39893 faces slice 80: 51385 vertices, 51797 faces slice 90: 63929 vertices, 64328 faces slice 100: 77185 vertices, 77639 faces slice 110: 88805 vertices, 89216 faces slice 120: 100731 vertices, 101178 faces slice 130: 112318 vertices, 112793 faces slice 140: 124196 vertices, 124580 faces slice 150: 134663 vertices, 135052 faces slice 160: 143514 vertices, 143849 faces slice 170: 152275 vertices, 152570 faces slice 180: 159355 vertices, 159609 faces slice 190: 165666 vertices, 165877 faces slice 200: 170251 vertices, 170436 faces slice 210: 171232 vertices, 171276 faces slice 220: 171232 vertices, 171276 faces slice 230: 171232 vertices, 171276 faces slice 240: 171232 vertices, 171276 faces slice 250: 171232 vertices, 171276 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... 171232 voxel in cpt #1: X=-44 [v=171232,e=513828,f=342552] located at (28.968430, -19.361048, 41.754677) For the whole surface: X=-44 [v=171232,e=513828,f=342552] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Thu Aug 8 20:17:11 CEST 2013 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 rh Thu Aug 8 20:17:17 CEST 2013 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts avg radius = 51.7 mm, total surface area = 91178 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.8 minutes Not saving sulc step 000: RMS=0.098 (target=0.015) step 005: RMS=0.072 (target=0.015) step 010: RMS=0.052 (target=0.015) step 015: RMS=0.043 (target=0.015) step 020: RMS=0.037 (target=0.015) step 025: RMS=0.033 (target=0.015) step 030: RMS=0.029 (target=0.015) step 035: RMS=0.026 (target=0.015) step 040: RMS=0.025 (target=0.015) step 045: RMS=0.023 (target=0.015) step 050: RMS=0.022 (target=0.015) step 055: RMS=0.022 (target=0.015) step 060: RMS=0.022 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Thu Aug 8 20:18:07 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.88 +- 0.54 (0.00-->6.40) (max @ vno 127943 --> 127944) face area 0.02 +- 0.03 (-0.12-->0.57) scaling brain by 0.274... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.945, avgs=0 005/300: dt: 0.9000, rms radial error=176.683, avgs=0 010/300: dt: 0.9000, rms radial error=176.120, avgs=0 015/300: dt: 0.9000, rms radial error=175.380, avgs=0 020/300: dt: 0.9000, rms radial error=174.537, avgs=0 025/300: dt: 0.9000, rms radial error=173.643, avgs=0 030/300: dt: 0.9000, rms radial error=172.720, avgs=0 035/300: dt: 0.9000, rms radial error=171.780, avgs=0 040/300: dt: 0.9000, rms radial error=170.832, avgs=0 045/300: dt: 0.9000, rms radial error=169.882, avgs=0 050/300: dt: 0.9000, rms radial error=168.932, avgs=0 055/300: dt: 0.9000, rms radial error=167.986, avgs=0 060/300: dt: 0.9000, rms radial error=167.043, avgs=0 065/300: dt: 0.9000, rms radial error=166.105, avgs=0 070/300: dt: 0.9000, rms radial error=165.172, avgs=0 075/300: dt: 0.9000, rms radial error=164.243, avgs=0 080/300: dt: 0.9000, rms radial error=163.320, avgs=0 085/300: dt: 0.9000, rms radial error=162.401, avgs=0 090/300: dt: 0.9000, rms radial error=161.488, avgs=0 095/300: dt: 0.9000, rms radial error=160.580, avgs=0 100/300: dt: 0.9000, rms radial error=159.678, avgs=0 105/300: dt: 0.9000, rms radial error=158.780, avgs=0 110/300: dt: 0.9000, rms radial error=157.888, avgs=0 115/300: dt: 0.9000, rms radial error=157.000, avgs=0 120/300: dt: 0.9000, rms radial error=156.118, avgs=0 125/300: dt: 0.9000, rms radial error=155.240, avgs=0 130/300: dt: 0.9000, rms radial error=154.367, avgs=0 135/300: dt: 0.9000, rms radial error=153.499, avgs=0 140/300: dt: 0.9000, rms radial error=152.636, avgs=0 145/300: dt: 0.9000, rms radial error=151.778, avgs=0 150/300: dt: 0.9000, rms radial error=150.924, avgs=0 155/300: dt: 0.9000, rms radial error=150.075, avgs=0 160/300: dt: 0.9000, rms radial error=149.230, avgs=0 165/300: dt: 0.9000, rms radial error=148.391, avgs=0 170/300: dt: 0.9000, rms radial error=147.555, avgs=0 175/300: dt: 0.9000, rms radial error=146.724, avgs=0 180/300: dt: 0.9000, rms radial error=145.898, avgs=0 185/300: dt: 0.9000, rms radial error=145.077, avgs=0 190/300: dt: 0.9000, rms radial error=144.260, avgs=0 195/300: dt: 0.9000, rms radial error=143.447, avgs=0 200/300: dt: 0.9000, rms radial error=142.639, avgs=0 205/300: dt: 0.9000, rms radial error=141.836, avgs=0 210/300: dt: 0.9000, rms radial error=141.037, avgs=0 215/300: dt: 0.9000, rms radial error=140.243, avgs=0 220/300: dt: 0.9000, rms radial error=139.453, avgs=0 225/300: dt: 0.9000, rms radial error=138.667, avgs=0 230/300: dt: 0.9000, rms radial error=137.887, avgs=0 235/300: dt: 0.9000, rms radial error=137.110, avgs=0 240/300: dt: 0.9000, rms radial error=136.338, avgs=0 245/300: dt: 0.9000, rms radial error=135.570, avgs=0 250/300: dt: 0.9000, rms radial error=134.806, avgs=0 255/300: dt: 0.9000, rms radial error=134.047, avgs=0 260/300: dt: 0.9000, rms radial error=133.292, avgs=0 265/300: dt: 0.9000, rms radial error=132.541, avgs=0 270/300: dt: 0.9000, rms radial error=131.794, avgs=0 275/300: dt: 0.9000, rms radial error=131.052, avgs=0 280/300: dt: 0.9000, rms radial error=130.314, avgs=0 285/300: dt: 0.9000, rms radial error=129.580, avgs=0 290/300: dt: 0.9000, rms radial error=128.850, avgs=0 295/300: dt: 0.9000, rms radial error=128.124, 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 = 20772.79 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00018 epoch 2 (K=40.0), pass 1, starting sse = 3745.31 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00001 epoch 3 (K=160.0), pass 1, starting sse = 451.40 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/11 = 0.00515 epoch 4 (K=640.0), pass 1, starting sse = 32.44 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.10/13 = 0.00754 final writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.10 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Thu Aug 8 20:24:21 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/sub006/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub006 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=-44 (nv=171232, nf=342552, ne=513828, g=23) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 11 iterations marking ambiguous vertices... 3594 ambiguous faces found in tessellation segmenting defects... 33 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 14 into 11 32 defects to be corrected 0 vertices coincident reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.9592 (-4.9796) -vertex loglikelihood: -6.6689 (-3.3344) -normal dot loglikelihood: -3.6129 (-3.6129) -quad curv loglikelihood: -6.2986 (-3.1493) Total Loglikelihood : -26.5396 CORRECTING DEFECT 0 (vertices=16, convex hull=50) After retessellation of defect 0, euler #=-28 (169043,506286,337215) : difference with theory (-29) = -1 CORRECTING DEFECT 1 (vertices=26, convex hull=56) After retessellation of defect 1, euler #=-27 (169052,506335,337256) : difference with theory (-28) = -1 CORRECTING DEFECT 2 (vertices=15, convex hull=21) After retessellation of defect 2, euler #=-26 (169056,506351,337269) : difference with theory (-27) = -1 CORRECTING DEFECT 3 (vertices=18, convex hull=49) After retessellation of defect 3, euler #=-25 (169058,506377,337294) : difference with theory (-26) = -1 CORRECTING DEFECT 4 (vertices=167, convex hull=117) After retessellation of defect 4, euler #=-24 (169095,506537,337418) : difference with theory (-25) = -1 CORRECTING DEFECT 5 (vertices=52, convex hull=78) After retessellation of defect 5, euler #=-23 (169107,506605,337475) : difference with theory (-24) = -1 CORRECTING DEFECT 6 (vertices=59, convex hull=81) After retessellation of defect 6, euler #=-22 (169137,506726,337567) : difference with theory (-23) = -1 CORRECTING DEFECT 7 (vertices=22, convex hull=30) After retessellation of defect 7, euler #=-21 (169140,506744,337583) : difference with theory (-22) = -1 CORRECTING DEFECT 8 (vertices=34, convex hull=84) After retessellation of defect 8, euler #=-20 (169158,506832,337654) : difference with theory (-21) = -1 CORRECTING DEFECT 9 (vertices=45, convex hull=80) After retessellation of defect 9, euler #=-19 (169186,506948,337743) : difference with theory (-20) = -1 CORRECTING DEFECT 10 (vertices=7, convex hull=22) After retessellation of defect 10, euler #=-18 (169189,506961,337754) : difference with theory (-19) = -1 CORRECTING DEFECT 11 (vertices=190, convex hull=202) normal vector of length zero at vertex 169579 with 3 faces normal vector of length zero at vertex 169579 with 3 faces normal vector of length zero at vertex 169579 with 3 faces normal vector of length zero at vertex 169579 with 3 faces After retessellation of defect 11, euler #=-16 (169240,507210,337954) : difference with theory (-18) = -2 CORRECTING DEFECT 12 (vertices=17, convex hull=33) After retessellation of defect 12, euler #=-15 (169247,507241,337979) : difference with theory (-17) = -2 CORRECTING DEFECT 13 (vertices=599, convex hull=272) After retessellation of defect 13, euler #=-16 (169424,507944,338504) : difference with theory (-16) = 0 CORRECTING DEFECT 14 (vertices=5, convex hull=15) Warning - incorrect dp selected!!!!(-143.980131 >= -143.980132 ) After retessellation of defect 14, euler #=-15 (169425,507949,338509) : difference with theory (-15) = 0 CORRECTING DEFECT 15 (vertices=9, convex hull=18) After retessellation of defect 15, euler #=-14 (169428,507960,338518) : difference with theory (-14) = 0 CORRECTING DEFECT 16 (vertices=11, convex hull=25) After retessellation of defect 16, euler #=-13 (169431,507975,338531) : difference with theory (-13) = 0 CORRECTING DEFECT 17 (vertices=60, convex hull=27) Warning - incorrect dp selected!!!!(-76.716434 >= -76.716439 ) After retessellation of defect 17, euler #=-12 (169436,508000,338552) : difference with theory (-12) = 0 CORRECTING DEFECT 18 (vertices=17, convex hull=36) After retessellation of defect 18, euler #=-11 (169448,508048,338589) : difference with theory (-11) = 0 CORRECTING DEFECT 19 (vertices=87, convex hull=39) After retessellation of defect 19, euler #=-10 (169457,508089,338622) : difference with theory (-10) = 0 CORRECTING DEFECT 20 (vertices=58, convex hull=50) After retessellation of defect 20, euler #=-9 (169466,508136,338661) : difference with theory (-9) = 0 CORRECTING DEFECT 21 (vertices=29, convex hull=51) After retessellation of defect 21, euler #=-8 (169475,508186,338703) : difference with theory (-8) = 0 CORRECTING DEFECT 22 (vertices=13, convex hull=28) After retessellation of defect 22, euler #=-7 (169480,508210,338723) : difference with theory (-7) = 0 CORRECTING DEFECT 23 (vertices=158, convex hull=52) After retessellation of defect 23, euler #=-6 (169491,508263,338766) : difference with theory (-6) = 0 CORRECTING DEFECT 24 (vertices=20, convex hull=71) After retessellation of defect 24, euler #=-5 (169505,508330,338820) : difference with theory (-5) = 0 CORRECTING DEFECT 25 (vertices=87, convex hull=60) After retessellation of defect 25, euler #=-4 (169527,508423,338892) : difference with theory (-4) = 0 CORRECTING DEFECT 26 (vertices=27, convex hull=26) After retessellation of defect 26, euler #=-3 (169530,508440,338907) : difference with theory (-3) = 0 CORRECTING DEFECT 27 (vertices=91, convex hull=77) After retessellation of defect 27, euler #=-2 (169559,508562,339001) : difference with theory (-2) = 0 CORRECTING DEFECT 28 (vertices=60, convex hull=64) After retessellation of defect 28, euler #=-1 (169583,508657,339073) : difference with theory (-1) = 0 CORRECTING DEFECT 29 (vertices=125, convex hull=102) After retessellation of defect 29, euler #=0 (169619,508810,339191) : difference with theory (0) = 0 CORRECTING DEFECT 30 (vertices=37, convex hull=50) After retessellation of defect 30, euler #=1 (169631,508865,339235) : difference with theory (1) = 0 CORRECTING DEFECT 31 (vertices=27, convex hull=60) After retessellation of defect 31, euler #=2 (169645,508929,339286) : 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-->7.64) (max @ vno 43725 --> 169136) 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-->7.64) (max @ vno 43725 --> 169136) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 106 mutations (34.8%), 199 crossovers (65.2%), 88 vertices were eliminated building final representation... 1587 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=169645, nf=339286, ne=508929, g=0) writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 22.0 minutes 0 defective edges removing intersecting faces 000: 199 intersecting 001: 15 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 169645 - 508929 + 339286 = 2 --> 0 holes F =2V-4: 339286 = 339290-4 (0) 2E=3F: 1017858 = 1017858 (0) total defect index = 0 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 30 intersecting 001: 2 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Thu Aug 8 20:46:30 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub006 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/sub006/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz... 25014 bright wm thresholded. 438 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.orig... computing class statistics... border white: 318128 voxels (1.90%) border gray 352780 voxels (2.10%) WM (93.0): 93.7 +- 10.3 [70.0 --> 110.0] GM (75.0) : 73.1 +- 13.4 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 43.6 (was 70) setting MAX_BORDER_WHITE to 116.3 (was 105) setting MIN_BORDER_WHITE to 57.0 (was 85) setting MAX_CSF to 30.2 (was 40) setting MAX_GRAY to 95.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 50.3 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 16.8 (was 40) repositioning cortical surface to gray/white boundary reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->5.00) (max @ vno 43725 --> 169070) face area 0.28 +- 0.12 (0.00-->2.22) mean absolute distance = 0.65 +- 0.73 5203 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=106, GM=57 mean inside = 93.6, mean outside = 67.7 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=71.2, 19 (19) missing vertices, mean dist 0.4 [0.4 (%28.5)->0.7 (%71.5))] %74 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.26 (0.07-->4.98) (max @ vno 43725 --> 169070) face area 0.28 +- 0.13 (0.00-->1.95) mean absolute distance = 0.33 +- 0.46 4503 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=9990156.0, rms=14.65 001: dt: 0.5000, sse=9387922.0, rms=10.573 (0.000%) 002: dt: 0.5000, sse=9285183.0, rms=8.140 (0.000%) 003: dt: 0.5000, sse=9331436.0, rms=6.565 (0.000%) 004: dt: 0.5000, sse=9548231.0, rms=5.626 (0.000%) 005: dt: 0.5000, sse=9633569.0, rms=5.075 (0.000%) 006: dt: 0.5000, sse=9750143.0, rms=4.811 (0.000%) 007: dt: 0.5000, sse=9731474.0, rms=4.648 (0.000%) 008: dt: 0.5000, sse=9764969.0, rms=4.577 (0.000%) 009: dt: 0.5000, sse=9673746.0, rms=4.507 (0.000%) rms = 4.48, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=9707184.0, rms=4.482 (0.000%) 011: dt: 0.2500, sse=5934601.0, rms=3.033 (0.000%) 012: dt: 0.2500, sse=5435345.0, rms=2.562 (0.000%) 013: dt: 0.2500, sse=5103281.0, rms=2.468 (0.000%) 014: dt: 0.2500, sse=5028657.0, rms=2.377 (0.000%) rms = 2.36, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=4909786.0, rms=2.356 (0.000%) 016: dt: 0.1250, sse=4550146.5, rms=1.988 (0.000%) 017: dt: 0.1250, sse=4497600.0, rms=1.937 (0.000%) rms = 1.93, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=4465426.5, rms=1.931 (0.000%) positioning took 2.9 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group mean border=76.9, 33 (1) missing vertices, mean dist -0.3 [0.3 (%83.0)->0.2 (%17.0))] %85 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.12-->4.65) (max @ vno 43725 --> 169070) face area 0.35 +- 0.16 (0.00-->2.52) mean absolute distance = 0.20 +- 0.27 5040 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=6179281.5, rms=7.16 019: dt: 0.5000, sse=5953634.5, rms=4.656 (0.000%) rms = 4.88, time step reduction 1 of 3 to 0.250... 020: dt: 0.2500, sse=5379315.0, rms=3.448 (0.000%) 021: dt: 0.2500, sse=5148878.5, rms=2.750 (0.000%) 022: dt: 0.2500, sse=5075867.5, rms=2.213 (0.000%) 023: dt: 0.2500, sse=5088533.5, rms=2.122 (0.000%) 024: dt: 0.2500, sse=5003672.0, rms=1.957 (0.000%) rms = 1.98, time step reduction 2 of 3 to 0.125... 025: dt: 0.1250, sse=4903640.0, rms=1.819 (0.000%) 026: dt: 0.1250, sse=4778593.0, rms=1.615 (0.000%) rms = 1.58, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=4730548.0, rms=1.577 (0.000%) positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group mean border=80.6, 28 (0) missing vertices, mean dist -0.1 [0.2 (%79.0)->0.2 (%21.0))] %91 local maxima, % 4 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 +- 0.24 (0.08-->4.51) (max @ vno 43725 --> 169070) face area 0.34 +- 0.16 (0.00-->2.53) mean absolute distance = 0.15 +- 0.21 2777 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5347951.5, rms=4.74 028: dt: 0.5000, sse=5737506.5, rms=4.523 (0.000%) rms = 4.52, time step reduction 1 of 3 to 0.250... 029: dt: 0.5000, sse=5971399.0, rms=4.523 (0.000%) 030: dt: 0.2500, sse=5333414.5, rms=2.476 (0.000%) 031: dt: 0.2500, sse=5356994.5, rms=2.198 (0.000%) 032: dt: 0.2500, sse=5267410.5, rms=2.040 (0.000%) rms = 2.08, time step reduction 2 of 3 to 0.125... 033: dt: 0.1250, sse=5128239.5, rms=1.809 (0.000%) 034: dt: 0.1250, sse=4969164.0, rms=1.449 (0.000%) 035: dt: 0.1250, sse=4908489.5, rms=1.381 (0.000%) rms = 1.39, time step reduction 3 of 3 to 0.062... 036: dt: 0.1250, sse=4908489.5, rms=1.381 (0.005%) positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group mean border=81.6, 37 (0) missing vertices, mean dist -0.0 [0.1 (%59.5)->0.1 (%40.5))] %93 local maxima, % 2 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=4953128.5, rms=1.90 rms = 3.03, time step reduction 1 of 3 to 0.250... 037: dt: 0.2500, sse=5013320.5, rms=1.213 (0.000%) 038: dt: 0.2500, sse=5143698.0, rms=1.045 (0.000%) rms = 1.04, time step reduction 2 of 3 to 0.125... 039: dt: 0.2500, sse=5229137.5, rms=1.042 (0.000%) rms = 1.01, time step reduction 3 of 3 to 0.062... 040: dt: 0.1250, sse=5254944.5, rms=1.006 (0.000%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group generating cortex label... 13 non-cortical segments detected only using segment with 1951 vertices erasing segment 1 (vno[0] = 107042) erasing segment 2 (vno[0] = 111864) erasing segment 3 (vno[0] = 116863) erasing segment 4 (vno[0] = 120328) erasing segment 5 (vno[0] = 121221) erasing segment 6 (vno[0] = 122277) erasing segment 7 (vno[0] = 122408) erasing segment 8 (vno[0] = 123167) erasing segment 9 (vno[0] = 123288) erasing segment 10 (vno[0] = 124218) erasing segment 11 (vno[0] = 130353) erasing segment 12 (vno[0] = 133485) writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/label/rh.cortex.label... writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.curv writing smoothed area to rh.area writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.area vertex spacing 0.89 +- 0.24 (0.09-->4.47) (max @ vno 43725 --> 169070) face area 0.34 +- 0.15 (0.00-->2.54) refinement took 9.5 minutes #-------------------------------------------- #@# Smooth2 rh Thu Aug 8 20:56:00 CEST 2013 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 rh Thu Aug 8 20:56:06 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 51.9 mm, total surface area = 104232 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.112 (target=0.015) step 005: RMS=0.078 (target=0.015) step 010: RMS=0.055 (target=0.015) step 015: RMS=0.045 (target=0.015) step 020: RMS=0.037 (target=0.015) step 025: RMS=0.031 (target=0.015) step 030: RMS=0.026 (target=0.015) step 035: RMS=0.022 (target=0.015) step 040: RMS=0.019 (target=0.015) step 045: RMS=0.017 (target=0.015) inflation complete. inflation took 0.7 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 200 vertices thresholded to be in k1 ~ [-0.41 0.19], k2 ~ [-0.13 0.06] total integrated curvature = 0.492*4pi (6.177) --> 1 handles ICI = 2.0, FI = 17.8, variation=283.367 152 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 164 vertices thresholded to be in [-0.19 0.10] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.015, std = 0.027 done. #----------------------------------------- #@# Curvature Stats rh Thu Aug 8 20:59:00 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub006 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 [ sub006/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 [ 322 ] Gb_filter = 0 WARN: S lookup min: -0.893362 WARN: S explicit min: 0.000000 vertex = 407 #-------------------------------------------- #@# Sphere rh Thu Aug 8 20:59:06 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 0.258... 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 %20.34 pass 1: epoch 2 of 3 starting distance error %20.31 unfolding complete - removing small folds... starting distance error %20.25 removing remaining folds... final distance error %20.26 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/rh.sphere spherical transformation took 1.19 hours #-------------------------------------------- #@# Surf Reg rh Thu Aug 8 22:10:14 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 = 0.581 curvature mean = 0.025, std = 0.936 curvature mean = 0.025, std = 0.831 Starting MRISrigidBodyAlignGlobal() d=32.00 min @ (0.00, -8.00, 0.00) sse = 349579.9, tmin=3.3531 d=16.00 min @ (4.00, 4.00, 0.00) sse = 342747.6, tmin=5.0340 d=8.00 min @ (-2.00, -2.00, 0.00) sse = 331556.2, tmin=6.7395 d=4.00 min @ (1.00, 0.00, 0.00) sse = 329772.9, tmin=8.4627 d=2.00 min @ (0.00, 0.00, 0.50) sse = 329564.4, tmin=10.2497 d=1.00 min @ (0.00, 0.00, -0.25) sse = 329553.1, tmin=11.9913 d=0.50 min @ (-0.12, 0.00, 0.12) sse = 329507.0, tmin=13.7184 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 13.72 min curvature mean = 0.010, std = 0.925 curvature mean = 0.013, std = 0.923 curvature mean = 0.006, std = 0.928 curvature mean = 0.006, std = 0.963 curvature mean = 0.004, std = 0.925 curvature mean = 0.002, std = 0.983 2 Reading smoothwm curvature mean = -0.023, std = 0.286 curvature mean = 0.006, std = 0.068 curvature mean = 0.070, std = 0.322 curvature mean = 0.006, std = 0.081 curvature mean = 0.035, std = 0.514 curvature mean = 0.006, std = 0.086 curvature mean = 0.018, std = 0.663 curvature mean = 0.007, std = 0.089 curvature mean = 0.006, std = 0.778 MRISregister() return, current seed 0 writing registered surface to ../surf/rh.sphere.reg... #-------------------------------------------- #@# Jacobian white rh Thu Aug 8 22:55:50 CEST 2013 mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv rh Thu Aug 8 22:55:55 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts mrisp_paint -a 5 /opt/freesurfer/5.3.0/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /opt/freesurfer/5.3.0/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Thu Aug 8 22:56:00 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub006 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... 1364 labels changed using aseg relabeling using gibbs priors... 000: 3470 changed, 169645 examined... 001: 819 changed, 14646 examined... 002: 187 changed, 4571 examined... 003: 61 changed, 1116 examined... 004: 21 changed, 387 examined... 005: 5 changed, 124 examined... 006: 1 changed, 32 examined... 007: 0 changed, 7 examined... 218 labels changed using aseg 000: 119 total segments, 80 labels (484 vertices) changed 001: 43 total segments, 4 labels (5 vertices) changed 002: 39 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 50 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1942 vertices marked for relabeling... 1942 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 1 minutes and 19 seconds. #-------------------------------------------- #@# Make Pial Surf rh Thu Aug 8 22:57:19 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub006 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/sub006/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz... 25014 bright wm thresholded. 438 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.orig... computing class statistics... border white: 318128 voxels (1.90%) border gray 352780 voxels (2.10%) WM (93.0): 93.7 +- 10.3 [70.0 --> 110.0] GM (75.0) : 73.1 +- 13.4 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 43.6 (was 70) setting MAX_BORDER_WHITE to 116.3 (was 105) setting MIN_BORDER_WHITE to 57.0 (was 85) setting MAX_CSF to 30.2 (was 40) setting MAX_GRAY to 95.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 50.3 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 16.8 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=106, GM=57 mean inside = 93.6, mean outside = 67.7 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/sub006/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->5.00) (max @ vno 43725 --> 169070) face area 0.28 +- 0.12 (0.00-->2.22) mean absolute distance = 0.65 +- 0.73 5230 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 19 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 2 with 4 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown deleting segment 5 with 380 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 11 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 8 points - only 0.00% unknown mean border=71.2, 19 (19) missing vertices, mean dist 0.4 [0.4 (%28.5)->0.7 (%71.5))] %74 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.26 (0.07-->4.98) (max @ vno 43725 --> 169070) face area 0.28 +- 0.13 (0.00-->1.95) mean absolute distance = 0.33 +- 0.46 4530 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=10003488.0, rms=14.64 001: dt: 0.5000, sse=9404758.0, rms=10.567 (0.000%) 002: dt: 0.5000, sse=9304696.0, rms=8.135 (0.000%) 003: dt: 0.5000, sse=9350051.0, rms=6.560 (0.000%) 004: dt: 0.5000, sse=9569986.0, rms=5.622 (0.000%) 005: dt: 0.5000, sse=9656816.0, rms=5.072 (0.000%) 006: dt: 0.5000, sse=9776060.0, rms=4.808 (0.000%) 007: dt: 0.5000, sse=9756018.0, rms=4.646 (0.000%) 008: dt: 0.5000, sse=9792059.0, rms=4.575 (0.000%) 009: dt: 0.5000, sse=9700319.0, rms=4.505 (0.000%) rms = 4.48, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=9735061.0, rms=4.481 (0.000%) 011: dt: 0.2500, sse=5951123.0, rms=3.033 (0.000%) 012: dt: 0.2500, sse=5449661.5, rms=2.563 (0.000%) 013: dt: 0.2500, sse=5117837.0, rms=2.469 (0.000%) 014: dt: 0.2500, sse=5043594.0, rms=2.378 (0.000%) rms = 2.36, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=4924040.5, rms=2.357 (0.000%) 016: dt: 0.1250, sse=4564908.5, rms=1.990 (0.000%) 017: dt: 0.1250, sse=4512501.0, rms=1.939 (0.000%) rms = 1.93, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=4479939.0, rms=1.934 (0.000%) positioning took 3.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 20 points - only 0.00% unknown deleting segment 1 with 5 points - only 0.00% unknown deleting segment 2 with 255 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 11 points - only 0.00% unknown deleting segment 5 with 25 points - only 44.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown deleting segment 7 with 19 points - only 0.00% unknown deleting segment 8 with 8 points - only 0.00% unknown mean border=76.8, 33 (1) missing vertices, mean dist -0.3 [0.3 (%82.9)->0.2 (%17.1))] %85 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.12-->4.65) (max @ vno 43725 --> 169070) face area 0.35 +- 0.16 (0.00-->2.52) mean absolute distance = 0.21 +- 0.27 5067 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=6199635.0, rms=7.16 019: dt: 0.5000, sse=5973438.0, rms=4.652 (0.000%) rms = 4.88, time step reduction 1 of 3 to 0.250... 020: dt: 0.2500, sse=5397965.5, rms=3.445 (0.000%) 021: dt: 0.2500, sse=5167652.5, rms=2.749 (0.000%) 022: dt: 0.2500, sse=5093224.0, rms=2.213 (0.000%) 023: dt: 0.2500, sse=5106467.0, rms=2.123 (0.000%) 024: dt: 0.2500, sse=5020157.5, rms=1.958 (0.000%) rms = 1.98, time step reduction 2 of 3 to 0.125... 025: dt: 0.1250, sse=4920171.0, rms=1.820 (0.000%) 026: dt: 0.1250, sse=4796014.0, rms=1.617 (0.000%) rms = 1.58, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=4747594.5, rms=1.580 (0.000%) positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 20 points - only 0.00% unknown deleting segment 1 with 10 points - only 0.00% unknown deleting segment 2 with 12 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 3 with 2 points - only 0.00% unknown deleting segment 4 with 300 points - only 0.00% unknown deleting segment 5 with 5 points - only 0.00% unknown deleting segment 6 with 18 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 7 with 4 points - only 0.00% unknown deleting segment 8 with 31 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown deleting segment 10 with 8 points - only 0.00% unknown mean border=80.5, 27 (0) missing vertices, mean dist -0.1 [0.2 (%78.9)->0.2 (%21.1))] %92 local maxima, % 4 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 +- 0.24 (0.06-->4.57) (max @ vno 43725 --> 169070) face area 0.34 +- 0.16 (0.00-->2.52) mean absolute distance = 0.15 +- 0.21 2870 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5364998.0, rms=4.74 028: dt: 0.5000, sse=5754745.0, rms=4.519 (0.000%) rms = 4.52, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=5142845.0, rms=2.842 (0.000%) 030: dt: 0.2500, sse=4988408.0, rms=2.323 (0.000%) 031: dt: 0.2500, sse=5072433.0, rms=1.909 (0.000%) rms = 1.99, time step reduction 2 of 3 to 0.125... 032: dt: 0.1250, sse=4977359.5, rms=1.707 (0.000%) 033: dt: 0.1250, sse=4858171.0, rms=1.407 (0.000%) 034: dt: 0.1250, sse=4822910.0, rms=1.357 (0.000%) rms = 1.37, time step reduction 3 of 3 to 0.062... 035: dt: 0.1250, sse=4822910.0, rms=1.357 (0.010%) positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 20 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 1 with 1 points - only 0.00% unknown deleting segment 2 with 16 points - only 0.00% unknown deleting segment 3 with 7 points - only 0.00% unknown deleting segment 4 with 12 points - only 0.00% unknown deleting segment 5 with 280 points - only 0.00% unknown deleting segment 6 with 8 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown deleting segment 8 with 5 points - only 0.00% unknown deleting segment 9 with 18 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 30 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 12 points - only 0.00% unknown mean border=81.6, 31 (0) missing vertices, mean dist -0.0 [0.1 (%59.4)->0.1 (%40.6))] %93 local maxima, % 2 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 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=4869947.5, rms=1.89 rms = 2.97, time step reduction 1 of 3 to 0.250... 036: dt: 0.2500, sse=4939095.5, rms=1.211 (0.000%) 037: dt: 0.2500, sse=5076491.0, rms=1.035 (0.000%) rms = 1.04, time step reduction 2 of 3 to 0.125... rms = 1.02, time step reduction 3 of 3 to 0.062... 038: dt: 0.1250, sse=5079325.0, rms=1.016 (0.000%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group smoothing surface for 5 iterations... mean border=46.6, 53 (53) missing vertices, mean dist 1.8 [0.2 (%0.0)->2.3 (%100.0))] %14 local maxima, %62 large gradients and %20 min vals, 1777 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=42034216.0, rms=34.46 001: dt: 0.5000, sse=29884576.0, rms=28.534 (0.000%) 002: dt: 0.5000, sse=21492024.0, rms=23.613 (0.000%) 003: dt: 0.5000, sse=15902650.0, rms=19.644 (0.000%) 004: dt: 0.5000, sse=12446432.0, rms=16.501 (0.000%) 005: dt: 0.5000, sse=10397814.0, rms=14.072 (0.000%) 006: dt: 0.5000, sse=9310842.0, rms=12.188 (0.000%) 007: dt: 0.5000, sse=8615309.0, rms=10.572 (0.000%) 008: dt: 0.5000, sse=8150395.5, rms=9.098 (0.000%) 009: dt: 0.5000, sse=7844656.5, rms=7.741 (0.000%) 010: dt: 0.5000, sse=7717932.0, rms=6.564 (0.000%) 011: dt: 0.5000, sse=7694301.5, rms=5.626 (0.000%) 012: dt: 0.5000, sse=7799948.5, rms=4.951 (0.000%) 013: dt: 0.5000, sse=7930760.0, rms=4.514 (0.000%) 014: dt: 0.5000, sse=8099019.5, rms=4.289 (0.000%) 015: dt: 0.5000, sse=8210826.0, rms=4.154 (0.000%) 016: dt: 0.5000, sse=8267964.5, rms=4.070 (0.000%) rms = 4.02, time step reduction 1 of 3 to 0.250... 017: dt: 0.5000, sse=8310543.5, rms=4.022 (0.000%) 018: dt: 0.2500, sse=5667292.0, rms=3.160 (0.000%) 019: dt: 0.2500, sse=5442487.5, rms=2.929 (0.000%) rms = 2.90, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=5284241.5, rms=2.899 (0.000%) 021: dt: 0.1250, sse=5025618.5, rms=2.716 (0.000%) rms = 2.69, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=4989413.5, rms=2.691 (0.000%) positioning took 3.2 minutes mean border=44.0, 754 (9) missing vertices, mean dist 0.2 [0.2 (%48.6)->0.5 (%51.4))] %34 local maxima, %46 large gradients and %16 min vals, 421 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=5811038.0, rms=4.88 023: dt: 0.5000, sse=6232976.0, rms=4.133 (0.000%) rms = 4.11, time step reduction 1 of 3 to 0.250... 024: dt: 0.5000, sse=7965109.0, rms=4.112 (0.000%) 025: dt: 0.2500, sse=6002721.5, rms=3.127 (0.000%) 026: dt: 0.2500, sse=6037564.5, rms=2.869 (0.000%) rms = 2.85, time step reduction 2 of 3 to 0.125... 027: dt: 0.2500, sse=5879275.5, rms=2.848 (0.000%) 028: dt: 0.1250, sse=5651194.0, rms=2.628 (0.000%) rms = 2.59, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=5624315.5, rms=2.588 (0.000%) positioning took 1.0 minutes mean border=41.2, 917 (8) missing vertices, mean dist 0.1 [0.2 (%36.6)->0.4 (%63.4))] %57 local maxima, %23 large gradients and %16 min vals, 581 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=6056351.0, rms=4.36 030: dt: 0.5000, sse=6282195.0, rms=4.138 (0.000%) rms = 4.13, time step reduction 1 of 3 to 0.250... 031: dt: 0.5000, sse=8222272.0, rms=4.128 (0.000%) 032: dt: 0.2500, sse=6136946.0, rms=3.043 (0.000%) 033: dt: 0.2500, sse=6323475.5, rms=2.712 (0.000%) rms = 2.74, time step reduction 2 of 3 to 0.125... 034: dt: 0.1250, sse=6165397.5, rms=2.598 (0.000%) 035: dt: 0.1250, sse=5898154.0, rms=2.439 (0.000%) rms = 2.41, time step reduction 3 of 3 to 0.062... 036: dt: 0.1250, sse=5838201.0, rms=2.414 (0.000%) positioning took 1.1 minutes mean border=39.9, 1803 (5) missing vertices, mean dist 0.1 [0.2 (%45.1)->0.3 (%54.9))] %61 local maxima, %18 large gradients and %16 min vals, 419 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/sub006/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=5926427.0, rms=2.93 rms = 3.94, time step reduction 1 of 3 to 0.250... 037: dt: 0.2500, sse=5730611.5, rms=2.536 (0.000%) 038: dt: 0.2500, sse=5896865.0, rms=2.457 (0.000%) rms = 2.44, time step reduction 2 of 3 to 0.125... 039: dt: 0.2500, sse=5980395.5, rms=2.440 (0.000%) 040: dt: 0.1250, sse=5854210.5, rms=2.301 (0.000%) rms = 2.28, time step reduction 3 of 3 to 0.062... 041: dt: 0.1250, sse=5855223.5, rms=2.279 (0.000%) positioning took 0.9 minutes writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.area.pial vertex spacing 1.01 +- 0.42 (0.05-->8.48) (max @ vno 120578 --> 119429) face area 0.41 +- 0.30 (0.00-->9.41) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 169645 vertices processed 25000 of 169645 vertices processed 50000 of 169645 vertices processed 75000 of 169645 vertices processed 100000 of 169645 vertices processed 125000 of 169645 vertices processed 150000 of 169645 vertices processed 0 of 169645 vertices processed 25000 of 169645 vertices processed 50000 of 169645 vertices processed 75000 of 169645 vertices processed 100000 of 169645 vertices processed 125000 of 169645 vertices processed 150000 of 169645 vertices processed thickness calculation complete, 164:643 truncations. 40505 vertices at 0 distance 121379 vertices at 1 distance 109370 vertices at 2 distance 40989 vertices at 3 distance 10693 vertices at 4 distance 2358 vertices at 5 distance 619 vertices at 6 distance 204 vertices at 7 distance 91 vertices at 8 distance 51 vertices at 9 distance 32 vertices at 10 distance 31 vertices at 11 distance 28 vertices at 12 distance 16 vertices at 13 distance 8 vertices at 14 distance 7 vertices at 15 distance 8 vertices at 16 distance 9 vertices at 17 distance 9 vertices at 18 distance 3 vertices at 19 distance 8 vertices at 20 distance writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.thickness positioning took 18.1 minutes #-------------------------------------------- #@# Surf Volume rh Thu Aug 8 23:15:26 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 23:15:30 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts pctsurfcon --s sub006 --rh-only Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts/pctsurfcon.log Thu Aug 8 23:15:31 CEST 2013 setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/tmp.pctsurfcon.18021/rh.wm.mgh --regheader sub006 --cortex srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/mri/orig.mgz as target reference. Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/label/rh.cortex.label Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 = 132232 Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/label/rh.cortex.label Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/tmp.pctsurfcon.18021/rh.wm.mgh Dim: 169645 1 1 mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/tmp.pctsurfcon.18021/rh.gm.mgh --projfrac 0.3 --regheader sub006 --cortex srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/mri/orig.mgz as target reference. Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/label/rh.cortex.label Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white Done reading source surface Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 = 151597 Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/label/rh.cortex.label Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/tmp.pctsurfcon.18021/rh.gm.mgh Dim: 169645 1 1 mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/tmp.pctsurfcon.18021/rh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/tmp.pctsurfcon.18021/rh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/surf/rh.w-g.pct.mgh mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.w-g.pct.mgh --annot sub006 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/surf/rh.w-g.pct.mgh --annot sub006 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/surf/rh.w-g.pct.mgh Vertex Area is 0.667852 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 2000 unknown 0 0.000 1 2001 bankssts 1610 1110.019 2 2002 caudalanteriorcingulate 1502 1063.116 3 2003 caudalmiddlefrontal 3799 2611.014 4 2004 corpuscallosum 0 0.000 5 2005 cuneus 2768 1817.631 6 2006 entorhinal 486 368.606 7 2007 fusiform 6320 4272.622 8 2008 inferiorparietal 11478 7683.567 9 2009 inferiortemporal 5811 3928.208 10 2010 isthmuscingulate 1736 1132.247 11 2011 lateraloccipital 9606 6132.968 12 2012 lateralorbitofrontal 4897 3264.001 13 2013 lingual 4996 3427.336 14 2014 medialorbitofrontal 2949 1973.371 15 2015 middletemporal 5856 4037.792 16 2016 parahippocampal 1110 765.764 17 2017 paracentral 3361 2175.972 18 2018 parsopercularis 2097 1417.664 19 2019 parsorbitalis 1361 918.504 20 2020 parstriangularis 2784 1843.752 21 2021 pericalcarine 2638 1805.453 22 2022 postcentral 7713 4966.229 23 2023 posteriorcingulate 2503 1716.131 24 2024 precentral 9841 6472.066 25 2025 precuneus 7647 5166.704 26 2026 rostralanteriorcingulate 1460 975.283 27 2027 rostralmiddlefrontal 11762 8062.871 28 2028 superiorfrontal 13951 9490.628 29 2029 superiorparietal 9841 6412.687 30 2030 superiortemporal 6693 4451.472 31 2031 supramarginal 6577 4376.953 32 2032 frontalpole 559 379.694 33 2033 temporalpole 754 536.237 34 2034 transversetemporal 591 366.553 35 2035 insula 3899 2599.391 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats rh Thu Aug 8 23:15:51 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 sub006 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 1610 1110 3092 2.880 0.441 0.118 0.027 14 1.8 bankssts 1502 1063 3240 2.787 0.712 0.158 0.065 39 4.7 caudalanteriorcingulate 3799 2611 7981 2.728 0.455 0.130 0.037 48 5.9 caudalmiddlefrontal 2768 1818 4177 2.055 0.434 0.164 0.058 49 6.7 cuneus 486 369 1741 3.642 0.638 0.143 0.050 4 1.0 entorhinal 6320 4273 13576 2.664 0.580 0.145 0.079 180 12.5 fusiform 11478 7684 21958 2.515 0.527 0.142 0.045 186 19.9 inferiorparietal 5811 3928 11520 2.455 0.710 0.149 0.063 125 14.8 inferiortemporal 1736 1132 3208 2.529 0.808 0.156 0.075 36 4.4 isthmuscingulate 9606 6133 15622 2.211 0.468 0.143 0.051 169 19.6 lateraloccipital 4897 3264 9898 2.687 0.698 0.149 0.061 89 12.1 lateralorbitofrontal 4996 3427 7828 2.146 0.516 0.158 0.072 92 11.8 lingual 2949 1973 5355 2.358 0.590 0.167 0.083 100 10.2 medialorbitofrontal 5856 4038 14461 2.879 0.637 0.135 0.044 98 10.1 middletemporal 1110 766 2406 2.744 0.618 0.138 0.053 15 2.4 parahippocampal 3361 2176 6071 2.540 0.533 0.122 0.033 33 4.6 paracentral 2097 1418 4645 2.841 0.438 0.124 0.036 23 3.0 parsopercularis 1361 919 3215 2.716 0.485 0.163 0.064 30 2.9 parsorbitalis 2784 1844 5152 2.508 0.388 0.132 0.040 40 4.6 parstriangularis 2638 1805 3496 2.021 0.392 0.129 0.036 28 3.7 pericalcarine 7713 4966 12208 2.182 0.563 0.117 0.033 79 11.3 postcentral 2503 1716 4944 2.554 0.696 0.154 0.051 53 4.9 posteriorcingulate 9841 6472 19598 2.729 0.564 0.117 0.033 99 13.4 precentral 7647 5167 13732 2.451 0.543 0.140 0.048 122 14.8 precuneus 1460 975 3341 2.920 0.624 0.149 0.087 31 3.1 rostralanteriorcingulate 11762 8063 22493 2.393 0.525 0.161 0.066 289 28.9 rostralmiddlefrontal 13951 9491 30200 2.750 0.524 0.139 0.043 210 24.0 superiorfrontal 9841 6413 16008 2.237 0.447 0.130 0.039 135 14.9 superiorparietal 6693 4451 15382 2.996 0.615 0.119 0.035 70 9.9 superiortemporal 6577 4377 12969 2.637 0.492 0.140 0.043 103 11.1 supramarginal 559 380 1318 2.561 0.551 0.194 0.074 16 1.7 frontalpole 754 536 2343 3.120 0.936 0.182 0.106 25 3.5 temporalpole 591 367 1191 2.796 0.341 0.131 0.038 7 0.9 transversetemporal 3899 2599 8105 2.984 0.698 0.133 0.059 84 9.1 insula #----------------------------------------- #@# Cortical Parc 2 rh Thu Aug 8 23:16:24 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub006 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... 2 labels changed using aseg relabeling using gibbs priors... 000: 11829 changed, 169645 examined... 001: 2876 changed, 45320 examined... 002: 908 changed, 14566 examined... 003: 403 changed, 5107 examined... 004: 203 changed, 2193 examined... 005: 109 changed, 1151 examined... 006: 64 changed, 629 examined... 007: 35 changed, 326 examined... 008: 13 changed, 174 examined... 009: 10 changed, 84 examined... 010: 10 changed, 57 examined... 011: 6 changed, 57 examined... 012: 2 changed, 30 examined... 013: 1 changed, 8 examined... 014: 2 changed, 8 examined... 015: 3 changed, 9 examined... 016: 0 changed, 12 examined... 1 labels changed using aseg 000: 351 total segments, 269 labels (3338 vertices) changed 001: 109 total segments, 27 labels (122 vertices) changed 002: 84 total segments, 2 labels (21 vertices) changed 003: 82 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 135 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1158 vertices marked for relabeling... 1158 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 1 minutes and 31 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Thu Aug 8 23:17:56 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 sub006 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 1199 831 2236 2.263 0.468 0.185 0.089 42 3.8 G_and_S_frontomargin 1656 1085 3232 2.411 0.561 0.147 0.044 25 3.0 G_and_S_occipital_inf 1833 1157 3543 2.487 0.591 0.119 0.041 18 3.7 G_and_S_paracentral 1730 1138 3512 2.629 0.514 0.132 0.038 23 2.8 G_and_S_subcentral 1574 1073 3401 2.415 0.579 0.206 0.107 59 6.1 G_and_S_transv_frontopol 3773 2524 7296 2.687 0.520 0.128 0.054 50 6.3 G_and_S_cingul-Ant 2081 1483 4625 2.905 0.459 0.135 0.037 32 3.2 G_and_S_cingul-Mid-Ant 2469 1657 4938 2.706 0.500 0.134 0.038 31 4.1 G_and_S_cingul-Mid-Post 863 584 2251 3.051 0.438 0.181 0.072 26 2.3 G_cingul-Post-dorsal 426 278 1075 2.945 0.541 0.204 0.149 16 2.2 G_cingul-Post-ventral 2491 1657 3713 1.996 0.442 0.167 0.061 46 6.1 G_cuneus 1211 820 3408 3.060 0.352 0.137 0.042 17 2.0 G_front_inf-Opercular 464 303 1078 2.642 0.402 0.154 0.051 11 1.0 G_front_inf-Orbital 1099 738 2650 2.725 0.312 0.157 0.055 24 2.5 G_front_inf-Triangul 5717 3978 14339 2.705 0.517 0.173 0.066 161 14.7 G_front_middle 9273 6277 22609 2.836 0.538 0.154 0.054 196 19.9 G_front_sup 766 497 1955 3.323 0.626 0.145 0.085 39 1.9 G_Ins_lg_and_S_cent_ins 898 609 2528 3.344 0.578 0.152 0.062 17 2.4 G_insular_short 3590 2264 7000 2.455 0.437 0.156 0.058 75 8.1 G_occipital_middle 2027 1268 3514 2.267 0.434 0.139 0.056 40 3.5 G_occipital_sup 2729 1779 6586 2.830 0.523 0.158 0.057 56 6.5 G_oc-temp_lat-fusifor 3008 2064 5328 2.206 0.566 0.179 0.091 73 8.7 G_oc-temp_med-Lingual 1454 1014 4481 3.391 0.722 0.156 0.067 23 3.8 G_oc-temp_med-Parahip 3246 2159 8014 2.839 0.695 0.173 0.075 85 10.3 G_orbital 4420 2968 10700 2.695 0.605 0.158 0.054 99 9.2 G_pariet_inf-Angular 3492 2323 8005 2.740 0.473 0.154 0.050 75 6.4 G_pariet_inf-Supramar 3233 2099 5997 2.299 0.434 0.138 0.039 54 5.1 G_parietal_sup 2762 1703 5058 2.335 0.456 0.127 0.035 35 4.0 G_postcentral 3697 2341 9230 3.045 0.461 0.123 0.037 49 5.1 G_precentral 2940 1987 6751 2.638 0.507 0.147 0.048 59 5.8 G_precuneus 579 403 1267 2.267 0.664 0.240 0.160 43 3.6 G_rectus 606 405 1196 2.541 0.870 0.105 0.053 8 1.5 G_subcallosal 480 291 1063 2.951 0.375 0.145 0.042 7 0.8 G_temp_sup-G_T_transv 2298 1478 6917 3.322 0.515 0.143 0.047 39 4.6 G_temp_sup-Lateral 1009 687 2589 3.153 0.703 0.122 0.052 19 2.6 G_temp_sup-Plan_polar 984 699 2168 2.802 0.487 0.117 0.026 7 1.1 G_temp_sup-Plan_tempo 3150 2099 7184 2.523 0.821 0.175 0.086 98 11.3 G_temporal_inf 3362 2298 10004 3.092 0.602 0.152 0.058 78 7.5 G_temporal_middle 578 380 899 2.421 0.401 0.102 0.021 4 0.6 Lat_Fis-ant-Horizont 219 155 373 2.633 0.479 0.096 0.026 1 0.2 Lat_Fis-ant-Vertical 1656 1102 2440 2.483 0.510 0.115 0.032 11 2.2 Lat_Fis-post 4572 2897 6639 1.997 0.418 0.151 0.059 90 11.4 Pole_occipital 1950 1380 5551 3.005 0.687 0.171 0.083 53 6.3 Pole_temporal 3051 2090 4282 2.247 0.565 0.133 0.047 37 5.4 S_calcarine 3677 2459 4755 2.107 0.705 0.107 0.030 24 4.8 S_central 1698 1147 2501 2.310 0.454 0.125 0.038 19 2.4 S_cingul-Marginalis 676 456 1194 2.725 0.553 0.104 0.024 3 0.7 S_circular_insula_ant 1466 971 2401 2.737 0.553 0.092 0.029 7 2.0 S_circular_insula_inf 1747 1163 2622 2.591 0.404 0.105 0.027 10 2.0 S_circular_insula_sup 1340 951 2179 2.361 0.483 0.115 0.030 12 1.8 S_collat_transv_ant 815 538 1150 2.232 0.371 0.126 0.037 7 1.2 S_collat_transv_post 2327 1584 3739 2.319 0.444 0.128 0.040 33 3.6 S_front_inf 3348 2232 4732 2.214 0.404 0.129 0.039 42 5.2 S_front_middle 2969 2074 5133 2.543 0.406 0.123 0.035 30 4.0 S_front_sup 1000 675 1282 2.163 0.386 0.112 0.025 6 1.1 S_interm_prim-Jensen 4107 2757 5883 2.263 0.439 0.128 0.042 49 6.0 S_intrapariet_and_P_trans 1628 1102 2199 2.127 0.382 0.135 0.032 15 2.2 S_oc_middle_and_Lunatus 1504 995 1987 2.046 0.379 0.107 0.023 11 1.4 S_oc_sup_and_transversal 915 608 1478 2.392 0.444 0.109 0.028 10 0.9 S_occipital_ant 1119 769 1819 2.321 0.494 0.135 0.211 93 1.8 S_oc-temp_lat 2333 1622 3685 2.414 0.386 0.108 0.028 15 2.5 S_oc-temp_med_and_Lingual 710 472 890 2.150 0.320 0.132 0.054 6 1.1 S_orbital_lateral 850 599 1306 2.320 0.791 0.115 0.042 9 0.9 S_orbital_med-olfact 1944 1290 3332 2.539 0.512 0.151 0.054 30 4.1 S_orbital-H_Shaped 3147 2075 4465 2.272 0.501 0.131 0.038 34 5.0 S_parieto_occipital 2093 1368 2621 2.156 0.865 0.149 0.067 46 6.1 S_pericallosal 2900 1919 4031 2.196 0.436 0.114 0.031 25 3.8 S_postcentral 1963 1307 3068 2.637 0.367 0.117 0.029 17 2.4 S_precentral-inf-part 2345 1586 3589 2.362 0.419 0.102 0.024 15 2.4 S_precentral-sup-part 402 265 542 2.059 0.517 0.165 0.055 7 0.9 S_suborbital 1593 1093 2476 2.302 0.331 0.128 0.037 18 2.4 S_subparietal 1807 1233 2434 2.221 0.531 0.107 0.023 11 1.8 S_temporal_inf 7570 5149 12736 2.654 0.511 0.118 0.030 68 9.3 S_temporal_sup 348 237 629 2.852 0.431 0.132 0.031 3 0.5 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 rh Thu Aug 8 23:18:25 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub006 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... 951 labels changed using aseg relabeling using gibbs priors... 000: 3255 changed, 169645 examined... 001: 750 changed, 13958 examined... 002: 161 changed, 4001 examined... 003: 62 changed, 952 examined... 004: 22 changed, 367 examined... 005: 10 changed, 126 examined... 006: 7 changed, 61 examined... 007: 4 changed, 45 examined... 008: 3 changed, 24 examined... 009: 1 changed, 19 examined... 010: 1 changed, 7 examined... 011: 1 changed, 9 examined... 012: 2 changed, 5 examined... 013: 3 changed, 10 examined... 014: 2 changed, 13 examined... 015: 2 changed, 14 examined... 016: 2 changed, 14 examined... 017: 2 changed, 13 examined... 018: 2 changed, 10 examined... 019: 2 changed, 15 examined... 020: 4 changed, 14 examined... 021: 1 changed, 16 examined... 022: 2 changed, 7 examined... 023: 3 changed, 8 examined... 024: 2 changed, 15 examined... 025: 2 changed, 11 examined... 026: 3 changed, 14 examined... 027: 0 changed, 11 examined... 132 labels changed using aseg 000: 70 total segments, 37 labels (189 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 46 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1079 vertices marked for relabeling... 1079 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas40.annot... classification took 1 minutes and 18 seconds. #----------------------------------------- #@# Parcellation Stats 3 rh Thu Aug 8 23:19:43 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 sub006 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 1508 1064 3233 2.777 0.723 0.158 0.065 39 4.7 caudalanteriorcingulate 4034 2755 8209 2.711 0.452 0.128 0.037 49 6.1 caudalmiddlefrontal 3476 2303 5187 2.072 0.415 0.156 0.052 55 7.6 cuneus 483 370 1752 3.672 0.631 0.145 0.051 5 1.0 entorhinal 5673 3810 12223 2.695 0.566 0.144 0.081 167 11.1 fusiform 10541 7050 20164 2.500 0.531 0.141 0.045 168 18.0 inferiorparietal 6462 4380 12924 2.462 0.705 0.150 0.063 143 16.3 inferiortemporal 1799 1173 3268 2.510 0.806 0.153 0.073 36 4.4 isthmuscingulate 10121 6449 16464 2.214 0.467 0.143 0.051 178 20.5 lateraloccipital 5262 3516 10471 2.630 0.714 0.160 0.068 111 14.6 lateralorbitofrontal 5011 3441 7881 2.148 0.516 0.157 0.071 91 11.7 lingual 2424 1646 4749 2.355 0.694 0.177 0.094 94 9.7 medialorbitofrontal 7140 4914 16799 2.874 0.616 0.133 0.042 111 11.9 middletemporal 1098 757 2352 2.708 0.609 0.138 0.052 15 2.3 parahippocampal 3515 2296 6431 2.539 0.529 0.124 0.033 35 4.8 paracentral 2144 1457 4679 2.827 0.437 0.122 0.035 23 3.1 parsopercularis 1472 990 3219 2.642 0.492 0.144 0.056 26 2.7 parsorbitalis 2990 1979 5362 2.466 0.416 0.134 0.040 42 5.2 parstriangularis 2641 1806 3515 2.027 0.390 0.131 0.038 29 3.9 pericalcarine 8196 5292 12923 2.180 0.562 0.117 0.034 84 11.9 postcentral 2669 1825 5537 2.622 0.691 0.155 0.052 56 5.5 posteriorcingulate 9377 6146 19002 2.753 0.561 0.119 0.034 97 13.1 precentral 7636 5155 13856 2.451 0.547 0.140 0.048 123 14.7 precuneus 1666 1103 3530 2.825 0.635 0.148 0.081 33 3.5 rostralanteriorcingulate 7457 5068 14428 2.450 0.508 0.155 0.058 162 16.6 rostralmiddlefrontal 18386 12561 38768 2.659 0.543 0.145 0.050 335 34.9 superiorfrontal 8370 5453 13730 2.253 0.453 0.131 0.040 118 12.9 superiorparietal 8815 5906 20569 2.989 0.636 0.127 0.043 119 16.5 superiortemporal 6446 4301 12618 2.630 0.491 0.141 0.043 103 10.8 supramarginal 584 361 1177 2.802 0.333 0.131 0.038 7 0.9 transversetemporal 3560 2397 7458 2.959 0.675 0.130 0.052 68 7.1 insula #-------------------------------------------- #@# Refine Pial Surfs w/ T2/FLAIR Thu Aug 8 23:20:09 CEST 2013 bbregister --s sub006 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.lta --init-fsl --T2 Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.dat.log Thu Aug 8 23:20:09 CEST 2013 setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts /opt/freesurfer/5.3.0/bin/bbregister --s sub006 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/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/sub006/mri/orig/T2raw.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998757, 0.0408089, 0.02861) j_ras = (0.0441177, 0.99097, 0.126615) k_ras = (0.0231846, -0.12772, 0.991539) writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii... fslregister --s sub006 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister --dof 6 --fsvol brainmask.mgz Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat.fslregister.log Thu Aug 8 23:20:14 CEST 2013 --s sub006 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/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/sub006/scripts mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/refvol.fslregister.nii mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/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/sub006/mri/brainmask.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.16415e-09, 1.86265e-09) j_ras = (-1.86265e-09, 1.49012e-08, -1) k_ras = (9.31323e-10, 1, -1.49012e-08) writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/refvol.fslregister.nii... -------------------------------------- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/movvol.fslregister.nii --frame 0 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/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/sub006/mri/transforms/tmp.bbregister.19132/template.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998757, 0.0408089, 0.02861) j_ras = (0.0441177, 0.99097, 0.126615) k_ras = (0.0231846, -0.12772, 0.991539) keeping frame 0 writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/movvol.fslregister.nii... Mov determinant is -0.311076 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/movvol.fslregister.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/reg0.19186.dat --regheader --fslregout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat.fsl.mat0 --s sub006 --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/sub006/mri/transforms/tmp.bbregister.19132/fslregister/movvol.fslregister.nii reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/reg0.19186.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/sub006/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/sub006/mri/transforms/tmp.bbregister.19132/fslregister/movvol.fslregister.nii Tmov: -------------------- -0.700 0.000 0.000 95.889; 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) -------- 0.999 -0.041 -0.029 -0.000; 0.023 -0.128 0.992 -0.000; -0.044 -0.991 -0.127 0.000; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 0.999 -0.041 -0.029 -0.000; 0.023 -0.128 0.992 -0.000; -0.044 -0.991 -0.127 0.000; 0.000 0.000 0.000 1.000; Determinant 1 subject = sub006 RegMat --------------------------- 0.999 -0.041 -0.029 -0.000; 0.023 -0.128 0.992 -0.000; -0.044 -0.991 -0.127 0.000; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -0.311076, ref det = -1 Thu Aug 8 23:20:22 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/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/sub006/mri/transforms/tmp.bbregister.19132/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat.fsl.mat0 Thu Aug 8 23:24:44 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/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/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat.fsl.mat -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/fslmat0.trans.mat -schedule /opt/freesurfer/5.3.0/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s sub006 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat --fslreg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat.fsl.mat --noedit tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl ---- FSL registration matrix -------- 0.999 -0.042 -0.020 40.136; -0.025 -0.120 -0.992 274.192; 0.039 0.992 -0.121 12.050; 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/sub006/mri/transforms/tmp.bbregister.19132/template.nii reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/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/sub006/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/sub006/mri/transforms/tmp.bbregister.19132/template.nii Tmov: -------------------- -0.700 0.000 0.000 95.889; 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 = -0.311076, ref det = -1 ---- Input registration matrix (computed) -------- 0.999 -0.039 -0.025 0.009; 0.020 -0.121 0.992 1.308; -0.042 -0.992 -0.120 -0.930; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 0.999 -0.039 -0.025 0.009; 0.020 -0.121 0.992 1.308; -0.042 -0.992 -0.120 -0.930; 0.000 0.000 0.000 1.000; Determinant 1 subject = sub006 RegMat --------------------------- 0.999 -0.039 -0.025 0.009; 0.020 -0.121 0.992 1.308; -0.042 -0.992 -0.120 -0.930; 0.000 0.000 0.000 1.000; Started at Thu Aug 8 23:20:14 CEST 2013 Ended at Thu Aug 8 23:31:25 CEST 2013 fslregister Done To check results, run: tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat --surf orig mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/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/sub006/scripts mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/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/sub006/mri/transforms/tmp.bbregister.19132/template.nii regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat subject sub006 dof 6 outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/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 1376052073 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.999 -0.039 -0.025 0.009; 0.020 -0.121 0.992 1.308; -0.042 -0.992 -0.120 -0.930; 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 0.990036 1 -25.0 -25.0 25.0 1.013869 2 -25.0 25.0 -25.0 1.045360 3 -25.0 25.0 25.0 1.003149 4 25.0 -25.0 -25.0 1.023281 5 25.0 -25.0 25.0 1.006686 6 25.0 25.0 -25.0 1.010024 7 25.0 25.0 25.0 1.048604 REL: 8 0.322576 8.141011 1.017626 rel = 0.316989 Initial costs ---------------- Number of surface hits 3238 WM Intensity 61.7561 +/- 11.7398 Ctx Intensity 77.7046 +/- 15.1309 Pct Contrast 22.3549 +/- 23.0208 Cost 0.3226 RelCost 0.3170 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9854 0.9854 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.9791 0.9791 0.0 3 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 -4.0000 0.9606 0.9606 0.0 6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.9556 0.9556 0.0 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.8671 0.8671 0.0 21 -4.0000 -4.0000 -4.0000 4.0000 0.0000 -4.0000 0.8189 0.8189 0.0 39 -4.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.7643 0.7643 0.0 120 -4.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.6566 0.6566 0.0 283 0.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.6078 0.6078 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.3226 0.3226 0.0 Brute Force -------------------------- Min cost was 0.322576 Number of iterations 729 Search time 2.528000 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 10 -0.006 0.000 0.000 0.000 0.000 0.000 0.3225513539 11 -0.005 0.000 0.000 0.000 0.000 0.000 0.3225499366 15 -0.005 -1.618 0.000 0.000 0.000 0.000 0.1223710691 20 -0.005 -1.431 0.000 0.000 0.000 0.000 0.1196453081 21 -0.005 -1.460 0.000 0.000 0.000 0.000 0.1190840389 22 -0.005 -1.491 0.000 0.000 0.000 0.000 0.1184857389 24 -0.005 -1.500 0.000 0.000 0.000 0.000 0.1184697786 25 -0.005 -1.498 0.000 0.000 0.000 0.000 0.1184583008 26 -0.005 -1.496 0.000 0.000 0.000 0.000 0.1184563610 29 -0.005 -1.496 1.000 0.000 0.000 0.000 0.1170204377 33 -0.005 -1.496 0.618 0.000 0.000 0.000 0.0877717013 35 -0.005 -1.496 0.524 0.000 0.000 0.000 0.0860064007 36 -0.005 -1.496 0.509 0.000 0.000 0.000 0.0859274583 38 -0.005 -1.496 0.507 0.000 0.000 0.000 0.0859264095 48 -0.005 -1.496 0.507 -0.064 0.000 0.000 0.0855856668 49 -0.005 -1.496 0.507 -0.038 0.000 0.000 0.0849571324 59 -0.005 -1.496 0.507 -0.038 -0.082 0.000 0.0845974589 60 -0.005 -1.496 0.507 -0.038 -0.052 0.000 0.0843965611 61 -0.005 -1.496 0.507 -0.038 -0.051 0.000 0.0843894536 62 -0.005 -1.496 0.507 -0.038 -0.032 0.000 0.0843761775 63 -0.005 -1.496 0.507 -0.038 -0.040 0.000 0.0843609554 64 -0.005 -1.496 0.507 -0.038 -0.039 0.000 0.0843584762 65 -0.005 -1.496 0.507 -0.038 -0.037 0.000 0.0843576955 74 -0.005 -1.496 0.507 -0.038 -0.037 0.119 0.0818356881 76 -0.005 -1.496 0.507 -0.038 -0.037 0.104 0.0817269000 79 -0.005 -1.496 0.507 -0.038 -0.037 0.098 0.0817165227 89 0.062 -1.496 0.507 -0.038 -0.037 0.098 0.0784200867 91 0.079 -1.496 0.507 -0.038 -0.037 0.098 0.0783580601 92 0.076 -1.496 0.507 -0.038 -0.037 0.098 0.0783375078 93 0.074 -1.496 0.507 -0.038 -0.037 0.098 0.0783332821 102 0.074 -1.500 0.507 -0.038 -0.037 0.098 0.0782613848 104 0.074 -1.532 0.507 -0.038 -0.037 0.098 0.0782124181 105 0.074 -1.518 0.507 -0.038 -0.037 0.098 0.0781260750 106 0.074 -1.519 0.507 -0.038 -0.037 0.098 0.0781256759 114 0.074 -1.519 0.518 -0.038 -0.037 0.098 0.0780031421 116 0.074 -1.519 0.528 -0.038 -0.037 0.098 0.0779685306 117 0.074 -1.519 0.530 -0.038 -0.037 0.098 0.0779660198 128 0.074 -1.519 0.530 -0.079 -0.037 0.098 0.0775032375 129 0.074 -1.519 0.530 -0.070 -0.037 0.098 0.0773934281 130 0.074 -1.519 0.530 -0.066 -0.037 0.098 0.0773850494 140 0.074 -1.519 0.530 -0.066 -0.045 0.098 0.0772513331 142 0.074 -1.519 0.530 -0.066 -0.049 0.098 0.0772355263 151 0.074 -1.519 0.530 -0.066 -0.049 0.153 0.0768815185 152 0.074 -1.519 0.530 -0.066 -0.049 0.144 0.0767667536 153 0.074 -1.519 0.530 -0.066 -0.049 0.133 0.0767352155 154 0.074 -1.519 0.530 -0.066 -0.049 0.136 0.0767350124 156 0.074 -1.519 0.530 -0.066 -0.049 0.135 0.0767345098 157 0.153 -1.542 0.554 -0.094 -0.061 0.171 0.0757315281 165 0.156 -1.543 0.555 -0.096 -0.062 0.173 0.0757278872 166 0.160 -1.544 0.556 -0.097 -0.062 0.175 0.0757259927 169 0.160 -1.544 0.556 -0.097 -0.062 0.175 0.0757256658 177 0.160 -1.544 0.556 -0.097 -0.062 0.204 0.0755171844 179 0.160 -1.544 0.556 -0.097 -0.062 0.196 0.0755028243 181 0.160 -1.544 0.556 -0.097 -0.062 0.199 0.0754996383 190 0.160 -1.513 0.556 -0.097 -0.062 0.199 0.0746624075 191 0.160 -1.464 0.556 -0.097 -0.062 0.199 0.0746055559 193 0.160 -1.487 0.556 -0.097 -0.062 0.199 0.0744588357 195 0.160 -1.489 0.556 -0.097 -0.062 0.199 0.0744576947 206 0.160 -1.489 0.566 -0.097 -0.062 0.199 0.0743555643 207 0.160 -1.489 0.571 -0.097 -0.062 0.199 0.0743416053 219 0.160 -1.489 0.571 -0.102 -0.062 0.199 0.0743244867 229 0.160 -1.489 0.571 -0.102 -0.054 0.199 0.0742840259 232 0.160 -1.489 0.571 -0.102 -0.055 0.199 0.0742834399 239 0.190 -1.498 0.580 -0.112 -0.059 0.213 0.0741403009 242 0.209 -1.503 0.586 -0.119 -0.062 0.221 0.0741398050 244 0.209 -1.503 0.586 -0.119 -0.062 0.221 0.0741395840 247 0.211 -1.504 0.586 -0.120 -0.063 0.222 0.0741395027 248 0.210 -1.503 0.586 -0.120 -0.062 0.222 0.0741393948 249 0.210 -1.503 0.586 -0.120 -0.062 0.222 0.0741393463 259 0.210 -1.503 0.586 -0.120 -0.062 0.233 0.0738855742 261 0.210 -1.503 0.586 -0.120 -0.062 0.248 0.0737759217 262 0.210 -1.503 0.586 -0.120 -0.062 0.246 0.0737721810 273 0.210 -1.490 0.586 -0.120 -0.062 0.246 0.0736963995 285 0.210 -1.490 0.587 -0.120 -0.062 0.246 0.0736915133 286 0.210 -1.490 0.592 -0.120 -0.062 0.246 0.0736834938 288 0.210 -1.490 0.591 -0.120 -0.062 0.246 0.0736833623 298 0.210 -1.490 0.591 -0.111 -0.062 0.246 0.0735968226 300 0.210 -1.490 0.591 -0.107 -0.062 0.246 0.0735963327 302 0.210 -1.490 0.591 -0.108 -0.062 0.246 0.0735944569 303 0.210 -1.490 0.591 -0.109 -0.062 0.246 0.0735940538 311 0.210 -1.490 0.591 -0.109 -0.070 0.246 0.0735228430 312 0.210 -1.490 0.591 -0.109 -0.074 0.246 0.0735080376 315 0.210 -1.490 0.591 -0.109 -0.075 0.246 0.0735077031 321 0.240 -1.498 0.599 -0.120 -0.080 0.260 0.0734949468 322 0.226 -1.494 0.595 -0.115 -0.078 0.254 0.0734300529 324 0.228 -1.495 0.596 -0.116 -0.078 0.255 0.0734286940 327 0.228 -1.495 0.596 -0.116 -0.078 0.255 0.0734286205 338 0.228 -1.495 0.596 -0.116 -0.078 0.253 0.0734281123 348 0.228 -1.479 0.596 -0.116 -0.078 0.253 0.0734006223 349 0.228 -1.482 0.596 -0.116 -0.078 0.253 0.0733844990 350 0.228 -1.486 0.596 -0.116 -0.078 0.253 0.0733790100 362 0.228 -1.486 0.592 -0.116 -0.078 0.253 0.0733697099 364 0.228 -1.486 0.593 -0.116 -0.078 0.253 0.0733696556 374 0.228 -1.486 0.593 -0.110 -0.078 0.253 0.0733206040 376 0.228 -1.486 0.593 -0.105 -0.078 0.253 0.0733125478 377 0.228 -1.486 0.593 -0.107 -0.078 0.253 0.0733110118 387 0.228 -1.486 0.593 -0.107 -0.083 0.253 0.0732951888 396 0.232 -1.487 0.595 -0.108 -0.083 0.255 0.0732732502 397 0.237 -1.488 0.596 -0.110 -0.084 0.257 0.0732630673 398 0.238 -1.488 0.596 -0.110 -0.084 0.258 0.0732627839 399 0.238 -1.488 0.596 -0.110 -0.084 0.257 0.0732624241 403 0.247 -1.482 0.597 -0.104 -0.090 0.260 0.0732474931 437 0.238 -1.483 0.592 -0.110 -0.084 0.259 0.0732438122 439 0.238 -1.483 0.590 -0.110 -0.084 0.259 0.0732404503 449 0.238 -1.483 0.590 -0.108 -0.084 0.259 0.0732309201 451 0.238 -1.483 0.590 -0.105 -0.084 0.259 0.0732277520 452 0.238 -1.483 0.590 -0.106 -0.084 0.259 0.0732268628 462 0.238 -1.483 0.590 -0.106 -0.083 0.259 0.0732261879 471 0.241 -1.484 0.590 -0.107 -0.084 0.260 0.0732203038 472 0.242 -1.484 0.591 -0.108 -0.084 0.260 0.0732202274 481 0.245 -1.480 0.585 -0.105 -0.083 0.263 0.0732121668 527 0.242 -1.483 0.588 -0.105 -0.084 0.260 0.0732108126 547 0.243 -1.483 0.589 -0.106 -0.084 0.261 0.0732097022 549 0.243 -1.483 0.589 -0.106 -0.084 0.261 0.0732096414 551 0.244 -1.482 0.587 -0.104 -0.084 0.262 0.0732042478 556 0.245 -1.481 0.586 -0.103 -0.084 0.262 0.0732030385 559 0.245 -1.481 0.585 -0.103 -0.084 0.262 0.0732029930 561 0.245 -1.481 0.585 -0.103 -0.084 0.262 0.0732029320 562 0.245 -1.481 0.585 -0.103 -0.084 0.262 0.0732029164 564 0.245 -1.481 0.585 -0.103 -0.084 0.262 0.0732028100 577 0.245 -1.481 0.585 -0.103 -0.084 0.264 0.0732018670 Powell done niters = 7 Computing relative cost 0 -25.0 -25.0 -25.0 1.013482 1 -25.0 -25.0 25.0 1.015559 2 -25.0 25.0 -25.0 1.034208 3 -25.0 25.0 25.0 1.000666 4 25.0 -25.0 -25.0 1.034182 5 25.0 -25.0 25.0 0.991798 6 25.0 25.0 -25.0 1.006023 7 25.0 25.0 25.0 1.034180 REL: 8 0.073202 8.130098 1.016262 rel = 0.0720305 Number of iterations 7 Min cost was 0.073202 Number of FunctionCalls 641 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 2.591000 sec Parameters at optimum (transmm) 0.24532 -1.48124 0.58539 Parameters at optimum (rotdeg) -0.10298 -0.08425 0.26413 Final costs ---------------- Number of surface hits 3238 WM Intensity 60.0746 +/- 10.5131 Ctx Intensity 78.1624 +/- 10.7433 Pct Contrast 26.4330 +/- 15.2985 Cost 0.0732 RelCost 0.3170 Reg at min cost was 0.999 -0.037 -0.029 0.250; 0.024 -0.123 0.992 -0.175; -0.040 -0.992 -0.122 -0.347; 0.000 0.000 0.000 1.000; Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/bbr.pass1.dat, type = 14 Original Reg 0.999 -0.039 -0.025 0.009; 0.020 -0.121 0.992 1.308; -0.042 -0.992 -0.120 -0.930; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg 0.000 -0.002 0.004 -0.241; -0.005 0.002 0.000 1.483; -0.001 -0.000 0.002 -0.583; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 1.655014 Computing change in rh position Surface RMS Diff (mm) 1.549561 1.872015 mri_segreg done mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/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/sub006/scripts mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/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/sub006/mri/transforms/tmp.bbregister.19132/template.nii regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/bbr.pass1.dat subject sub006 dof 6 outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 1376539157 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.999 -0.037 -0.029 0.250; 0.024 -0.123 0.992 -0.175; -0.040 -0.992 -0.122 -0.347; 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 1.000144 1 -25.0 -25.0 25.0 1.011963 2 -25.0 25.0 -25.0 1.028762 3 -25.0 25.0 25.0 1.017444 4 25.0 -25.0 -25.0 1.023030 5 25.0 -25.0 25.0 1.003200 6 25.0 25.0 -25.0 1.006099 7 25.0 25.0 25.0 1.018704 REL: 8 0.074000 8.109344 1.013668 rel = 0.0730019 Initial costs ---------------- Number of surface hits 323295 WM Intensity 60.0945 +/- 10.4129 Ctx Intensity 78.3960 +/- 10.7337 Pct Contrast 26.6644 +/- 15.2882 Cost 0.0740 RelCost 0.0730 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0884 0.0884 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.0860 0.0860 0.0 9 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 -0.1000 0.0824 0.0824 0.0 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.0789 0.0789 0.0 21 -0.1000 -0.1000 -0.1000 0.1000 0.0000 -0.1000 0.0775 0.0775 0.0 39 -0.1000 -0.1000 0.0000 0.0000 0.0000 -0.1000 0.0762 0.0762 0.0 120 -0.1000 0.0000 0.0000 0.0000 0.0000 -0.1000 0.0755 0.0755 0.0 121 -0.1000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0755 0.0755 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0732 0.0732 0.0 Brute Force -------------------------- Min cost was 0.073202 Number of iterations 729 Search time 2.842000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 7 -0.011 0.000 0.000 0.000 0.000 0.000 0.0739579968 8 -0.023 0.000 0.000 0.000 0.000 0.000 0.0739393766 10 -0.024 0.000 0.000 0.000 0.000 0.000 0.0739391684 18 -0.024 0.068 0.000 0.000 0.000 0.000 0.0736410288 19 -0.024 0.054 0.000 0.000 0.000 0.000 0.0736210929 28 -0.024 0.054 0.144 0.000 0.000 0.000 0.0712034427 29 -0.024 0.054 0.145 0.000 0.000 0.000 0.0712014029 30 -0.024 0.054 0.154 0.000 0.000 0.000 0.0711957153 32 -0.024 0.054 0.152 0.000 0.000 0.000 0.0711948811 42 -0.024 0.054 0.152 0.003 0.000 0.000 0.0711937157 51 -0.024 0.054 0.152 0.003 -0.021 0.000 0.0710840807 52 -0.024 0.054 0.152 0.003 -0.028 0.000 0.0710745386 55 -0.024 0.054 0.152 0.003 -0.029 0.000 0.0710742340 63 -0.024 0.054 0.152 0.003 -0.029 0.003 0.0710718816 65 -0.024 0.054 0.152 0.003 -0.029 0.005 0.0710714752 66 -0.024 0.054 0.152 0.003 -0.029 0.006 0.0710712416 77 -0.013 0.054 0.152 0.003 -0.029 0.006 0.0710605916 87 -0.013 0.055 0.152 0.003 -0.029 0.006 0.0710605245 96 -0.013 0.055 0.154 0.003 -0.029 0.006 0.0710602217 106 -0.013 0.055 0.154 0.004 -0.029 0.006 0.0710595122 115 -0.013 0.055 0.154 0.004 -0.031 0.006 0.0710593576 124 -0.013 0.055 0.154 0.004 -0.031 0.010 0.0710563353 126 -0.013 0.055 0.154 0.004 -0.031 0.011 0.0710561702 127 -0.013 0.055 0.154 0.004 -0.031 0.012 0.0710560869 130 -0.003 0.056 0.156 0.006 -0.032 0.018 0.0710552827 136 -0.007 0.056 0.155 0.005 -0.032 0.016 0.0710535106 137 -0.008 0.056 0.155 0.005 -0.031 0.015 0.0710534580 138 -0.008 0.056 0.155 0.005 -0.031 0.016 0.0710533858 162 -0.008 0.057 0.155 0.005 -0.031 0.016 0.0710532018 171 -0.008 0.057 0.152 0.005 -0.031 0.016 0.0710519125 198 -0.006 0.057 0.153 0.005 -0.032 0.016 0.0710517517 199 -0.006 0.057 0.153 0.005 -0.032 0.016 0.0710517061 200 -0.007 0.057 0.152 0.005 -0.032 0.016 0.0710517012 203 -0.007 0.057 0.152 0.005 -0.032 0.016 0.0710516797 217 -0.007 0.057 0.152 0.005 -0.032 0.017 0.0710516335 270 -0.007 0.057 0.152 0.005 -0.032 0.017 0.0710516217 Powell done niters = 4 Computing relative cost 0 -25.0 -25.0 -25.0 1.000527 1 -25.0 -25.0 25.0 1.012389 2 -25.0 25.0 -25.0 1.028572 3 -25.0 25.0 25.0 1.018441 4 25.0 -25.0 -25.0 1.022629 5 25.0 -25.0 25.0 1.001609 6 25.0 25.0 -25.0 1.005235 7 25.0 25.0 25.0 1.020102 REL: 8 0.071052 8.109503 1.013688 rel = 0.0700922 Number of iterations 4 Min cost was 0.071052 Number of FunctionCalls 333 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 51.287000 sec Parameters at optimum (transmm) -0.00683 0.05697 0.15243 Parameters at optimum (rotdeg) 0.00519 -0.03151 0.01697 Final costs ---------------- Number of surface hits 323295 WM Intensity 60.0684 +/- 10.3946 Ctx Intensity 78.3842 +/- 10.7444 Pct Contrast 26.6871 +/- 15.2674 Cost 0.0711 RelCost 0.0730 Reg at min cost was 0.999 -0.036 -0.029 0.243; 0.025 -0.123 0.992 -0.118; -0.040 -0.992 -0.122 -0.195; 0.000 0.000 0.000 1.000; Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.dat, type = 14 Original Reg 0.999 -0.037 -0.029 0.250; 0.024 -0.123 0.992 -0.175; -0.040 -0.992 -0.122 -0.347; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.000 -0.001 0.000 0.007; -0.000 -0.000 -0.000 -0.057; -0.001 0.000 -0.000 -0.153; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.153461 Computing change in rh position Surface RMS Diff (mm) 0.170445 0.209095 mri_segreg done tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.dat --noedit --ltaout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/mri/orig/T2raw.mgz reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 -------- 0.999 -0.036 -0.029 0.243; 0.025 -0.123 0.992 -0.118; -0.040 -0.992 -0.122 -0.195; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- INFO: loading target /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/mri/orig/T2raw.mgz Tmov: -------------------- -0.700 0.000 0.000 95.889; 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 -------- 0.999 -0.036 -0.029 0.243; 0.025 -0.123 0.992 -0.118; -0.040 -0.992 -0.122 -0.195; 0.000 0.000 0.000 1.000; Determinant 1 subject = sub006 RegMat --------------------------- 0.999 -0.036 -0.029 0.243; 0.025 -0.123 0.992 -0.118; -0.040 -0.992 -0.122 -0.195; 0.000 0.000 0.000 1.000; transformed matrix: 1.000 -0.005 0.001 -0.130; 0.005 1.000 0.005 -0.080; -0.001 -0.005 1.000 0.196; 0.000 0.000 0.000 1.000; transformed matrix: 0.699 -0.026 -0.016 40.677; -0.021 -0.081 -0.661 273.305; 0.025 0.661 -0.082 13.122; 0.000 0.000 0.000 1.000; Cleaning up Started at Thu Aug 8 23:20:09 CEST 2013 Ended at Thu Aug 8 23:33:28 CEST 2013 BBR-Run-Time-Sec 799 bbregister Done To check results, run: tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.dat --surf mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/T2.mgz mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/mri/orig/T2raw.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998757, 0.0408089, 0.02861) j_ras = (0.0441177, 0.99097, 0.126615) k_ras = (0.0231846, -0.12772, 0.991539) INFO: Reading transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.lta... Reading transform with LTAreadEx() reading extra input line subject sub006 reading extra input line fscale 0.150000 reading template info from volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig.mgz... INFO: Applying transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 1.000 -0.005 0.001 -0.129; 0.005 1.000 0.005 -0.080; -0.001 -0.005 1.000 0.196; 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/sub006/mri/T2.mgz... mri_normalize -aseg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/aseg.mgz -sigma 4 -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white identity.nofile -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white identity.nofile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/T2.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/mri/T2.mgz... computing distance transform computing distance transform computing nonmaximum suppression 14582 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/sub006/mri/T2.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.woT2.pial `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.woT2.pial' mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub006 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/sub006/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz... 24515 bright wm thresholded. 438 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.orig... computing class statistics... border white: 318128 voxels (1.90%) border gray 352780 voxels (2.10%) WM (93.0): 93.8 +- 10.2 [70.0 --> 110.0] GM (75.0) : 73.0 +- 13.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 43.3 (was 70) setting MAX_BORDER_WHITE to 116.2 (was 105) setting MIN_BORDER_WHITE to 57.0 (was 85) setting MAX_CSF to 29.7 (was 40) setting MAX_GRAY to 95.8 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 50.2 (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=106, GM=57 mean inside = 93.4, mean outside = 67.5 smoothing surface for 5 iterations... reading initial white vertex positions from white... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.89 +- 0.25 (0.03-->8.22) (max @ vno 73397 --> 77073) face area 0.33 +- 0.16 (0.00-->8.17) averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 0 with 2 points - only 0.00% unknown deleting segment 1 with 205 points - only 10.24% unknown deleting segment 2 with 22 points - only 0.00% unknown deleting segment 3 with 12 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 4 with 1 points - only 0.00% unknown deleting segment 7 with 21 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 9 with 742 points - only 0.00% unknown deleting segment 11 with 12 points - only 0.00% unknown deleting segment 13 with 5 points - only 0.00% unknown deleting segment 15 with 38 points - only 0.00% unknown deleting segment 16 with 15 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 17 with 4 points - only 0.00% unknown deleting segment 18 with 5 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 19 with 3 points - only 0.00% unknown deleting segment 20 with 8 points - only 0.00% unknown tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.89 +- 0.25 (0.09-->8.22) (max @ vno 77073 --> 73397) face area 0.33 +- 0.16 (0.00-->8.17) averaging target values for 5 iterations... 000: dt: 0.0000, sse=5338815.5, rms=0.00 rms = 1.34, time step reduction 1 of 3 to 0.250... rms = 0.34, 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=5338815.5, rms=0.000 (1.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 0 with 2 points - only 0.00% unknown deleting segment 1 with 205 points - only 10.24% unknown deleting segment 2 with 22 points - only 0.00% unknown deleting segment 3 with 12 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 4 with 1 points - only 0.00% unknown deleting segment 5 with 21 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 742 points - only 0.00% unknown deleting segment 8 with 12 points - only 0.00% unknown deleting segment 9 with 5 points - only 0.00% unknown deleting segment 10 with 38 points - only 0.00% unknown deleting segment 11 with 15 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 12 with 4 points - only 0.00% unknown deleting segment 13 with 5 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 14 with 3 points - only 0.00% unknown deleting segment 15 with 8 points - only 0.00% unknown tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.89 +- 0.25 (0.09-->8.22) (max @ vno 77073 --> 73397) face area 0.33 +- 0.16 (0.00-->8.17) averaging target values for 5 iterations... 000: dt: 0.0000, sse=5338815.5, rms=0.00 rms = 1.34, time step reduction 1 of 3 to 0.250... rms = 0.34, 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=5338815.5, rms=0.000 (1.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 0 with 2 points - only 0.00% unknown deleting segment 1 with 205 points - only 10.24% unknown deleting segment 2 with 22 points - only 0.00% unknown deleting segment 3 with 12 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 4 with 1 points - only 0.00% unknown deleting segment 5 with 21 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 742 points - only 0.00% unknown deleting segment 8 with 12 points - only 0.00% unknown deleting segment 9 with 5 points - only 0.00% unknown deleting segment 10 with 38 points - only 0.00% unknown deleting segment 11 with 15 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 12 with 4 points - only 0.00% unknown deleting segment 13 with 5 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 14 with 3 points - only 0.00% unknown deleting segment 15 with 8 points - only 0.00% unknown tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.09-->8.22) (max @ vno 77073 --> 73397) face area 0.33 +- 0.16 (0.00-->8.17) averaging target values for 5 iterations... 000: dt: 0.0000, sse=5338815.5, rms=0.00 rms = 1.34, time step reduction 1 of 3 to 0.250... rms = 0.34, 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=5338815.5, rms=0.000 (1.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 0 with 2 points - only 0.00% unknown deleting segment 1 with 205 points - only 10.24% unknown deleting segment 2 with 22 points - only 0.00% unknown deleting segment 3 with 12 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 4 with 1 points - only 0.00% unknown deleting segment 5 with 21 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 742 points - only 0.00% unknown deleting segment 8 with 12 points - only 0.00% unknown deleting segment 9 with 5 points - only 0.00% unknown deleting segment 10 with 38 points - only 0.00% unknown deleting segment 11 with 15 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 12 with 4 points - only 0.00% unknown deleting segment 13 with 5 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 14 with 3 points - only 0.00% unknown deleting segment 15 with 8 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=5338815.5, rms=0.00 rms = 1.34, time step reduction 1 of 3 to 0.250... rms = 0.34, 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=5338815.5, rms=0.000 (1.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 0 with 2 points - only 0.00% unknown removing 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 [101.60 232.40], gm=167.00+-21.80, and vertices in regions > 156.1 56865 surface locations found to contain inconsistent values (3318 in, 53547 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=585899.2, rms=0.24 001: dt: 0.5000, sse=552557.2, rms=0.233 (0.000%) 002: dt: 0.5000, sse=532313.9, rms=0.218 (0.000%) 003: dt: 0.5000, sse=520637.5, rms=0.207 (0.000%) 004: dt: 0.5000, sse=511675.7, rms=0.198 (0.000%) 005: dt: 0.5000, sse=505424.5, rms=0.189 (0.000%) 006: dt: 0.5000, sse=500991.1, rms=0.182 (0.000%) 007: dt: 0.5000, sse=498248.5, rms=0.175 (0.000%) 008: dt: 0.5000, sse=496290.6, rms=0.170 (0.000%) 009: dt: 0.5000, sse=494632.1, rms=0.165 (0.000%) 010: dt: 0.5000, sse=493524.8, rms=0.161 (0.000%) 011: dt: 0.5000, sse=492451.7, rms=0.158 (0.000%) 012: dt: 0.5000, sse=491455.6, rms=0.155 (0.000%) 013: dt: 0.5000, sse=490763.1, rms=0.153 (0.000%) 014: dt: 0.5000, sse=489956.1, rms=0.151 (0.000%) 015: dt: 0.5000, sse=489047.1, rms=0.149 (0.000%) 016: dt: 0.5000, sse=487979.8, rms=0.148 (0.000%) 017: dt: 0.5000, sse=486870.7, rms=0.146 (0.000%) 018: dt: 0.5000, sse=485633.1, rms=0.145 (0.000%) 019: dt: 0.5000, sse=484633.0, rms=0.145 (0.000%) 020: dt: 0.5000, sse=483442.2, rms=0.144 (0.000%) 021: dt: 0.5000, sse=482316.2, rms=0.144 (0.000%) 022: dt: 0.5000, sse=480975.9, rms=0.143 (0.000%) 023: dt: 0.5000, sse=479811.6, rms=0.143 (0.000%) 024: dt: 0.5000, sse=478604.6, rms=0.143 (0.000%) 025: dt: 0.5000, sse=477404.8, rms=0.143 (0.000%) 026: dt: 0.5000, sse=476307.0, rms=0.143 (0.000%) 027: dt: 0.5000, sse=475251.8, rms=0.143 (0.000%) 028: dt: 0.5000, sse=474003.1, rms=0.143 (0.000%) 029: dt: 0.5000, sse=472755.9, rms=0.144 (0.000%) 030: dt: 0.5000, sse=472009.8, rms=0.144 (0.000%) positioning took 4.9 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [102.80 231.20], gm=167.00+-21.40, and vertices in regions > 156.3 45313 surface locations found to contain inconsistent values (2095 in, 43218 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=49324.5, rms=0.13 031: dt: 0.5000, sse=49042.9, rms=0.124 (0.000%) 032: dt: 0.5000, sse=50265.4, rms=0.113 (0.000%) 033: dt: 0.5000, sse=51683.0, rms=0.105 (0.000%) 034: dt: 0.5000, sse=52895.4, rms=0.100 (0.000%) 035: dt: 0.5000, sse=53878.7, rms=0.095 (0.000%) 036: dt: 0.5000, sse=54822.2, rms=0.090 (0.000%) 037: dt: 0.5000, sse=55703.8, rms=0.085 (0.000%) 038: dt: 0.5000, sse=56564.3, rms=0.081 (0.000%) 039: dt: 0.5000, sse=57430.5, rms=0.077 (0.000%) 040: dt: 0.5000, sse=58277.3, rms=0.074 (0.000%) 041: dt: 0.5000, sse=59050.3, rms=0.071 (0.000%) 042: dt: 0.5000, sse=59801.1, rms=0.067 (0.000%) 043: dt: 0.5000, sse=60506.4, rms=0.065 (0.000%) 044: dt: 0.5000, sse=61189.5, rms=0.062 (0.000%) 045: dt: 0.5000, sse=61814.1, rms=0.060 (0.000%) 046: dt: 0.5000, sse=62407.8, rms=0.058 (0.000%) 047: dt: 0.5000, sse=62950.9, rms=0.055 (0.000%) 048: dt: 0.5000, sse=63444.4, rms=0.054 (0.000%) 049: dt: 0.5000, sse=63930.4, rms=0.052 (0.000%) 050: dt: 0.5000, sse=64379.0, rms=0.050 (0.000%) 051: dt: 0.5000, sse=64806.3, rms=0.049 (0.000%) 052: dt: 0.5000, sse=65179.3, rms=0.048 (0.000%) 053: dt: 0.5000, sse=65511.7, rms=0.046 (0.000%) 054: dt: 0.5000, sse=65844.9, rms=0.045 (0.000%) 055: dt: 0.5000, sse=66145.9, rms=0.044 (0.000%) 056: dt: 0.5000, sse=66411.4, rms=0.043 (0.000%) 057: dt: 0.5000, sse=66612.0, rms=0.042 (0.000%) 058: dt: 0.5000, sse=66851.4, rms=0.042 (0.000%) 059: dt: 0.5000, sse=67050.4, rms=0.041 (0.000%) 060: dt: 0.5000, sse=67243.6, rms=0.040 (0.000%) positioning took 5.2 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [63.40 268.60], gm=166.00+-34.20, and vertices in regions > 148.9 37661 surface locations found to contain inconsistent values (5 in, 37656 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=12155.9, rms=0.18 061: dt: 0.5000, sse=11530.2, rms=0.171 (0.000%) 062: dt: 0.5000, sse=10624.7, rms=0.153 (0.000%) 063: dt: 0.5000, sse=9952.6, rms=0.136 (0.000%) 064: dt: 0.5000, sse=9473.3, rms=0.121 (0.000%) 065: dt: 0.5000, sse=9178.2, rms=0.108 (0.000%) 066: dt: 0.5000, sse=9013.4, rms=0.098 (0.000%) 067: dt: 0.5000, sse=8920.9, rms=0.089 (0.000%) 068: dt: 0.5000, sse=8868.3, rms=0.083 (0.000%) 069: dt: 0.5000, sse=8861.6, rms=0.076 (0.000%) 070: dt: 0.5000, sse=8896.1, rms=0.071 (0.000%) 071: dt: 0.5000, sse=8960.4, rms=0.066 (0.000%) 072: dt: 0.5000, sse=9027.7, rms=0.062 (0.000%) 073: dt: 0.5000, sse=9092.5, rms=0.058 (0.000%) 074: dt: 0.5000, sse=9157.8, rms=0.054 (0.000%) 075: dt: 0.5000, sse=9223.9, rms=0.051 (0.000%) 076: dt: 0.5000, sse=9287.0, rms=0.048 (0.000%) 077: dt: 0.5000, sse=9349.0, rms=0.046 (0.000%) 078: dt: 0.5000, sse=9409.1, rms=0.044 (0.000%) 079: dt: 0.5000, sse=9464.9, rms=0.042 (0.000%) 080: dt: 0.5000, sse=9518.9, rms=0.040 (0.000%) 081: dt: 0.5000, sse=9571.4, rms=0.038 (0.000%) 082: dt: 0.5000, sse=9617.6, rms=0.037 (0.000%) 083: dt: 0.5000, sse=9662.5, rms=0.036 (0.000%) 084: dt: 0.5000, sse=9702.4, rms=0.035 (0.000%) 085: dt: 0.5000, sse=9738.6, rms=0.034 (0.000%) 086: dt: 0.5000, sse=9772.5, rms=0.033 (0.000%) 087: dt: 0.5000, sse=9803.9, rms=0.032 (0.000%) 088: dt: 0.5000, sse=9831.5, rms=0.032 (0.000%) 089: dt: 0.5000, sse=9856.0, rms=0.031 (0.000%) 090: dt: 0.5000, sse=9878.5, rms=0.031 (0.000%) positioning took 4.7 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [71.20 260.80], gm=166.00+-31.60, and vertices in regions > 150.2 10453 surface locations found to contain inconsistent values (10 in, 10443 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/sub006/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1900.5, rms=0.07 091: dt: 0.5000, sse=1866.7, rms=0.073 (0.000%) 092: dt: 0.5000, sse=1715.0, rms=0.067 (0.000%) 093: dt: 0.5000, sse=1589.9, rms=0.061 (0.000%) 094: dt: 0.5000, sse=1487.0, rms=0.056 (0.000%) 095: dt: 0.5000, sse=1408.0, rms=0.051 (0.000%) 096: dt: 0.5000, sse=1353.5, rms=0.048 (0.000%) 097: dt: 0.5000, sse=1316.5, rms=0.045 (0.000%) 098: dt: 0.5000, sse=1289.3, rms=0.043 (0.000%) 099: dt: 0.5000, sse=1264.8, rms=0.041 (0.000%) 100: dt: 0.5000, sse=1240.9, rms=0.039 (0.000%) 101: dt: 0.5000, sse=1219.6, rms=0.037 (0.000%) 102: dt: 0.5000, sse=1202.6, rms=0.035 (0.000%) 103: dt: 0.5000, sse=1188.9, rms=0.034 (0.000%) 104: dt: 0.5000, sse=1178.0, rms=0.033 (0.000%) 105: dt: 0.5000, sse=1169.0, rms=0.031 (0.000%) 106: dt: 0.5000, sse=1161.6, rms=0.030 (0.000%) 107: dt: 0.5000, sse=1155.5, rms=0.030 (0.000%) 108: dt: 0.5000, sse=1150.6, rms=0.029 (0.000%) 109: dt: 0.5000, sse=1147.0, rms=0.028 (0.000%) 110: dt: 0.5000, sse=1144.2, rms=0.028 (0.000%) 111: dt: 0.5000, sse=1141.2, rms=0.027 (0.000%) 112: dt: 0.5000, sse=1139.7, rms=0.027 (0.000%) 113: dt: 0.5000, sse=1138.0, rms=0.027 (0.000%) 114: dt: 0.5000, sse=1136.9, rms=0.026 (0.000%) 115: dt: 0.5000, sse=1135.8, rms=0.026 (0.000%) 116: dt: 0.5000, sse=1134.9, rms=0.026 (0.000%) 117: dt: 0.5000, sse=1134.2, rms=0.026 (0.000%) 118: dt: 0.5000, sse=1134.0, rms=0.026 (0.000%) 119: dt: 0.5000, sse=1133.7, rms=0.026 (0.000%) 120: dt: 0.5000, sse=1133.2, rms=0.026 (0.000%) positioning took 4.8 minutes writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.area.pial vertex spacing 1.04 +- 0.45 (0.06-->8.89) (max @ vno 77073 --> 73397) face area 0.42 +- 0.33 (0.00-->7.81) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 171478 vertices processed 25000 of 171478 vertices processed 50000 of 171478 vertices processed 75000 of 171478 vertices processed 100000 of 171478 vertices processed 125000 of 171478 vertices processed 150000 of 171478 vertices processed 0 of 171478 vertices processed 25000 of 171478 vertices processed 50000 of 171478 vertices processed 75000 of 171478 vertices processed 100000 of 171478 vertices processed 125000 of 171478 vertices processed 150000 of 171478 vertices processed thickness calculation complete, 260:847 truncations. 38131 vertices at 0 distance 119330 vertices at 1 distance 110616 vertices at 2 distance 44684 vertices at 3 distance 12417 vertices at 4 distance 3184 vertices at 5 distance 956 vertices at 6 distance 315 vertices at 7 distance 114 vertices at 8 distance 39 vertices at 9 distance 30 vertices at 10 distance 19 vertices at 11 distance 18 vertices at 12 distance 25 vertices at 13 distance 17 vertices at 14 distance 9 vertices at 15 distance 11 vertices at 16 distance 7 vertices at 17 distance 3 vertices at 18 distance 6 vertices at 19 distance 9 vertices at 20 distance writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.thickness positioning took 24.3 minutes /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.woT2.pial `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.woT2.pial' mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub006 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/sub006/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz... 25014 bright wm thresholded. 438 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.orig... computing class statistics... border white: 318128 voxels (1.90%) border gray 352780 voxels (2.10%) WM (93.0): 93.7 +- 10.3 [70.0 --> 110.0] GM (75.0) : 73.1 +- 13.4 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 43.6 (was 70) setting MAX_BORDER_WHITE to 116.3 (was 105) setting MIN_BORDER_WHITE to 57.0 (was 85) setting MAX_CSF to 30.2 (was 40) setting MAX_GRAY to 95.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 50.3 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 16.8 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=106, GM=57 mean inside = 93.6, mean outside = 67.7 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/sub006/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.89 +- 0.25 (0.03-->4.47) (max @ vno 43725 --> 169070) face area 0.33 +- 0.15 (0.00-->2.53) averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 19 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 1 with 1 points - only 0.00% unknown 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 4 with 2 points - only 0.00% unknown deleting segment 5 with 16 points - only 0.00% unknown deleting segment 6 with 7 points - only 0.00% unknown deleting segment 7 with 12 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 9 with 3 points - only 0.00% unknown deleting segment 10 with 12 points - only 0.00% unknown deleting segment 11 with 355 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 14 with 11 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 15 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 16 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 17 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 18 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 19 with 1 points - only 0.00% unknown deleting segment 20 with 8 points - only 0.00% unknown tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.89 +- 0.24 (0.09-->4.47) (max @ vno 43725 --> 169070) face area 0.33 +- 0.15 (0.00-->2.53) averaging target values for 5 iterations... 000: dt: 0.0000, sse=5232412.5, rms=0.00 rms = 1.52, time step reduction 1 of 3 to 0.250... rms = 0.40, time step reduction 2 of 3 to 0.125... rms = 0.05, time step reduction 3 of 3 to 0.062... 001: dt: 0.1250, sse=5232412.5, rms=0.000 (1.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 19 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 1 with 1 points - only 0.00% unknown 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 4 with 16 points - only 0.00% unknown deleting segment 5 with 7 points - only 0.00% unknown deleting segment 6 with 12 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown deleting segment 8 with 12 points - only 0.00% unknown deleting segment 9 with 355 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 11 with 11 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 12 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 13 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 14 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 15 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 16 with 1 points - only 0.00% unknown deleting segment 17 with 8 points - only 0.00% unknown tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.89 +- 0.24 (0.09-->4.47) (max @ vno 43725 --> 169070) face area 0.33 +- 0.15 (0.00-->2.53) averaging target values for 5 iterations... 000: dt: 0.0000, sse=5232412.5, rms=0.00 rms = 1.51, time step reduction 1 of 3 to 0.250... rms = 0.40, time step reduction 2 of 3 to 0.125... rms = 0.05, time step reduction 3 of 3 to 0.062... 002: dt: 0.1250, sse=5232412.5, rms=0.000 (1.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 19 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 1 with 1 points - only 0.00% unknown 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 4 with 16 points - only 0.00% unknown deleting segment 5 with 7 points - only 0.00% unknown deleting segment 6 with 12 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown deleting segment 8 with 12 points - only 0.00% unknown deleting segment 9 with 355 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 11 with 11 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 12 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 13 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 14 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 15 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 16 with 1 points - only 0.00% unknown deleting segment 17 with 8 points - only 0.00% unknown tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.24 (0.09-->4.47) (max @ vno 43725 --> 169070) face area 0.33 +- 0.15 (0.00-->2.53) averaging target values for 5 iterations... 000: dt: 0.0000, sse=5232412.5, rms=0.00 rms = 1.52, time step reduction 1 of 3 to 0.250... rms = 0.40, time step reduction 2 of 3 to 0.125... rms = 0.05, time step reduction 3 of 3 to 0.062... 003: dt: 0.1250, sse=5232412.5, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 19 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 1 with 1 points - only 0.00% unknown 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 4 with 16 points - only 0.00% unknown deleting segment 5 with 7 points - only 0.00% unknown deleting segment 6 with 12 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown deleting segment 8 with 12 points - only 0.00% unknown deleting segment 9 with 355 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 11 with 11 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 12 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 13 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 14 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 15 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 16 with 1 points - only 0.00% unknown deleting segment 17 with 8 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=5232412.5, rms=0.00 rms = 1.51, time step reduction 1 of 3 to 0.250... rms = 0.40, time step reduction 2 of 3 to 0.125... rms = 0.05, time step reduction 3 of 3 to 0.062... 004: dt: 0.1250, sse=5232412.5, rms=0.000 (1.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 2 vertex label from ripped group smoothing surface for 5 iterations... reading initial pial vertex positions from woT2.pial... repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [120.90 215.10], gm=168.00+-15.70, and vertices in regions > 160.1 66741 surface locations found to contain inconsistent values (16077 in, 50664 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=583937.5, rms=0.31 001: dt: 0.5000, sse=551291.9, rms=0.299 (0.000%) 002: dt: 0.5000, sse=531946.6, rms=0.285 (0.000%) 003: dt: 0.5000, sse=521613.3, rms=0.273 (0.000%) 004: dt: 0.5000, sse=513313.1, rms=0.264 (0.000%) 005: dt: 0.5000, sse=507816.8, rms=0.255 (0.000%) 006: dt: 0.5000, sse=504162.0, rms=0.247 (0.000%) 007: dt: 0.5000, sse=502088.8, rms=0.240 (0.000%) 008: dt: 0.5000, sse=500069.7, rms=0.234 (0.000%) 009: dt: 0.5000, sse=498060.4, rms=0.228 (0.000%) 010: dt: 0.5000, sse=497946.9, rms=0.223 (0.000%) 011: dt: 0.5000, sse=496109.5, rms=0.218 (0.000%) 012: dt: 0.5000, sse=495622.3, rms=0.214 (0.000%) 013: dt: 0.5000, sse=494527.0, rms=0.210 (0.000%) 014: dt: 0.5000, sse=493889.6, rms=0.206 (0.000%) 015: dt: 0.5000, sse=492955.4, rms=0.203 (0.000%) 016: dt: 0.5000, sse=491788.3, rms=0.200 (0.000%) 017: dt: 0.5000, sse=491022.9, rms=0.197 (0.000%) 018: dt: 0.5000, sse=490132.5, rms=0.194 (0.000%) 019: dt: 0.5000, sse=489833.7, rms=0.191 (0.000%) 020: dt: 0.5000, sse=488871.8, rms=0.189 (0.000%) 021: dt: 0.5000, sse=487999.1, rms=0.187 (0.000%) 022: dt: 0.5000, sse=487343.7, rms=0.185 (0.000%) 023: dt: 0.5000, sse=486283.6, rms=0.183 (0.000%) 024: dt: 0.5000, sse=485447.2, rms=0.181 (0.000%) 025: dt: 0.5000, sse=484462.7, rms=0.179 (0.000%) 026: dt: 0.5000, sse=483647.3, rms=0.178 (0.000%) 027: dt: 0.5000, sse=483251.5, rms=0.176 (0.000%) 028: dt: 0.5000, sse=482651.1, rms=0.175 (0.000%) 029: dt: 0.5000, sse=481343.0, rms=0.174 (0.000%) 030: dt: 0.5000, sse=480459.8, rms=0.173 (0.000%) positioning took 5.0 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [76.30 255.70], gm=166.00+-29.90, and vertices in regions > 151.0 49970 surface locations found to contain inconsistent values (100 in, 49870 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=54304.9, rms=0.21 031: dt: 0.5000, sse=53312.4, rms=0.196 (0.000%) 032: dt: 0.5000, sse=52236.9, rms=0.177 (0.000%) 033: dt: 0.5000, sse=51999.8, rms=0.161 (0.000%) 034: dt: 0.5000, sse=52344.8, rms=0.147 (0.000%) 035: dt: 0.5000, sse=53118.3, rms=0.135 (0.000%) 036: dt: 0.5000, sse=53940.3, rms=0.125 (0.000%) 037: dt: 0.5000, sse=54820.1, rms=0.116 (0.000%) 038: dt: 0.5000, sse=55713.6, rms=0.108 (0.000%) 039: dt: 0.5000, sse=56747.7, rms=0.102 (0.000%) 040: dt: 0.5000, sse=57823.4, rms=0.096 (0.000%) 041: dt: 0.5000, sse=58912.9, rms=0.091 (0.000%) 042: dt: 0.5000, sse=60000.9, rms=0.086 (0.000%) 043: dt: 0.5000, sse=61020.5, rms=0.082 (0.000%) 044: dt: 0.5000, sse=61998.4, rms=0.078 (0.000%) 045: dt: 0.5000, sse=62877.1, rms=0.075 (0.000%) 046: dt: 0.5000, sse=63736.4, rms=0.072 (0.000%) 047: dt: 0.5000, sse=64541.3, rms=0.069 (0.000%) 048: dt: 0.5000, sse=65293.5, rms=0.066 (0.000%) 049: dt: 0.5000, sse=65989.3, rms=0.064 (0.000%) 050: dt: 0.5000, sse=66664.4, rms=0.062 (0.000%) 051: dt: 0.5000, sse=67276.1, rms=0.060 (0.000%) 052: dt: 0.5000, sse=67850.1, rms=0.058 (0.000%) 053: dt: 0.5000, sse=68409.1, rms=0.056 (0.000%) 054: dt: 0.5000, sse=68891.1, rms=0.054 (0.000%) 055: dt: 0.5000, sse=69357.8, rms=0.053 (0.000%) 056: dt: 0.5000, sse=69782.3, rms=0.051 (0.000%) 057: dt: 0.5000, sse=70202.2, rms=0.050 (0.000%) 058: dt: 0.5000, sse=70580.1, rms=0.049 (0.000%) 059: dt: 0.5000, sse=70922.8, rms=0.047 (0.000%) 060: dt: 0.5000, sse=71252.9, rms=0.046 (0.000%) positioning took 4.6 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [114.00 222.00], gm=168.00+-18.00, and vertices in regions > 159.0 37039 surface locations found to contain inconsistent values (15337 in, 21702 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=10268.8, rms=0.14 061: dt: 0.5000, sse=10068.2, rms=0.135 (0.000%) 062: dt: 0.5000, sse=9596.7, rms=0.125 (0.000%) 063: dt: 0.5000, sse=9328.5, rms=0.118 (0.000%) 064: dt: 0.5000, sse=9147.7, rms=0.111 (0.000%) 065: dt: 0.5000, sse=9011.6, rms=0.106 (0.000%) 066: dt: 0.5000, sse=8905.1, rms=0.101 (0.000%) 067: dt: 0.5000, sse=8808.3, rms=0.097 (0.000%) 068: dt: 0.5000, sse=8732.1, rms=0.093 (0.000%) 069: dt: 0.5000, sse=8673.0, rms=0.089 (0.000%) 070: dt: 0.5000, sse=8628.8, rms=0.085 (0.000%) 071: dt: 0.5000, sse=8600.9, rms=0.081 (0.000%) 072: dt: 0.5000, sse=8578.6, rms=0.077 (0.000%) 073: dt: 0.5000, sse=8558.2, rms=0.074 (0.000%) 074: dt: 0.5000, sse=8545.4, rms=0.071 (0.000%) 075: dt: 0.5000, sse=8538.6, rms=0.068 (0.000%) 076: dt: 0.5000, sse=8539.4, rms=0.065 (0.000%) 077: dt: 0.5000, sse=8544.7, rms=0.062 (0.000%) 078: dt: 0.5000, sse=8548.4, rms=0.060 (0.000%) 079: dt: 0.5000, sse=8557.6, rms=0.058 (0.000%) 080: dt: 0.5000, sse=8572.7, rms=0.055 (0.000%) 081: dt: 0.5000, sse=8582.5, rms=0.053 (0.000%) 082: dt: 0.5000, sse=8600.0, rms=0.051 (0.000%) 083: dt: 0.5000, sse=8613.9, rms=0.049 (0.000%) 084: dt: 0.5000, sse=8633.2, rms=0.048 (0.000%) 085: dt: 0.5000, sse=8649.9, rms=0.046 (0.000%) 086: dt: 0.5000, sse=8660.2, rms=0.045 (0.000%) 087: dt: 0.5000, sse=8676.0, rms=0.043 (0.000%) 088: dt: 0.5000, sse=8688.7, rms=0.042 (0.000%) 089: dt: 0.5000, sse=8703.5, rms=0.041 (0.000%) 090: dt: 0.5000, sse=8719.0, rms=0.040 (0.000%) positioning took 4.6 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [91.20 244.80], gm=168.00+-25.60, and vertices in regions > 155.2 13872 surface locations found to contain inconsistent values (48 in, 13824 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/sub006/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=2027.1, rms=0.09 091: dt: 0.5000, sse=1969.7, rms=0.083 (0.000%) 092: dt: 0.5000, sse=1765.6, rms=0.075 (0.000%) 093: dt: 0.5000, sse=1605.0, rms=0.068 (0.000%) 094: dt: 0.5000, sse=1477.9, rms=0.061 (0.000%) 095: dt: 0.5000, sse=1383.8, rms=0.056 (0.000%) 096: dt: 0.5000, sse=1322.9, rms=0.052 (0.000%) 097: dt: 0.5000, sse=1277.8, rms=0.049 (0.000%) 098: dt: 0.5000, sse=1243.1, rms=0.046 (0.000%) 099: dt: 0.5000, sse=1214.2, rms=0.044 (0.000%) 100: dt: 0.5000, sse=1186.9, rms=0.042 (0.000%) 101: dt: 0.5000, sse=1165.8, rms=0.040 (0.000%) 102: dt: 0.5000, sse=1148.6, rms=0.038 (0.000%) 103: dt: 0.5000, sse=1134.2, rms=0.036 (0.000%) 104: dt: 0.5000, sse=1122.8, rms=0.035 (0.000%) 105: dt: 0.5000, sse=1113.8, rms=0.034 (0.000%) 106: dt: 0.5000, sse=1107.0, rms=0.033 (0.000%) 107: dt: 0.5000, sse=1101.6, rms=0.032 (0.000%) 108: dt: 0.5000, sse=1096.5, rms=0.031 (0.000%) 109: dt: 0.5000, sse=1092.6, rms=0.031 (0.000%) 110: dt: 0.5000, sse=1089.5, rms=0.030 (0.000%) 111: dt: 0.5000, sse=1087.5, rms=0.030 (0.000%) 112: dt: 0.5000, sse=1084.6, rms=0.030 (0.000%) 113: dt: 0.5000, sse=1082.9, rms=0.029 (0.000%) 114: dt: 0.5000, sse=1081.3, rms=0.029 (0.000%) 115: dt: 0.5000, sse=1079.9, rms=0.029 (0.000%) 116: dt: 0.5000, sse=1079.9, rms=0.029 (0.000%) 117: dt: 0.5000, sse=1079.1, rms=0.029 (0.000%) 118: dt: 0.5000, sse=1079.3, rms=0.028 (0.000%) 119: dt: 0.5000, sse=1078.9, rms=0.028 (0.000%) 120: dt: 0.5000, sse=1078.6, rms=0.028 (0.000%) positioning took 4.6 minutes writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.area.pial vertex spacing 1.04 +- 0.45 (0.09-->8.56) (max @ vno 120578 --> 119429) face area 0.42 +- 0.32 (0.00-->9.00) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 169645 vertices processed 25000 of 169645 vertices processed 50000 of 169645 vertices processed 75000 of 169645 vertices processed 100000 of 169645 vertices processed 125000 of 169645 vertices processed 150000 of 169645 vertices processed 0 of 169645 vertices processed 25000 of 169645 vertices processed 50000 of 169645 vertices processed 75000 of 169645 vertices processed 100000 of 169645 vertices processed 125000 of 169645 vertices processed 150000 of 169645 vertices processed thickness calculation complete, 257:851 truncations. 39532 vertices at 0 distance 119234 vertices at 1 distance 109115 vertices at 2 distance 42502 vertices at 3 distance 11691 vertices at 4 distance 2940 vertices at 5 distance 812 vertices at 6 distance 270 vertices at 7 distance 102 vertices at 8 distance 56 vertices at 9 distance 41 vertices at 10 distance 34 vertices at 11 distance 23 vertices at 12 distance 18 vertices at 13 distance 13 vertices at 14 distance 12 vertices at 15 distance 11 vertices at 16 distance 10 vertices at 17 distance 12 vertices at 18 distance 6 vertices at 19 distance 10 vertices at 20 distance writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.thickness positioning took 23.5 minutes #-------------------------------------------- #@# Surf Volume lh Fri Aug 9 00:23:44 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 Fri Aug 9 00:23:45 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 Fri Aug 9 00:23:45 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon sub006 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 = 10 writing volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/ribbon.mgz writing ribbon files #-------------------------------------------- #@# ASeg Stats Fri Aug 9 00:58:03 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006 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 sub006 $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 sub006 sysname Linux hostname snake5 machine x86_64 user fkaule UseRobust 0 atlas_icv (eTIV) = 1428534 mm^3 (det: 1.363710 ) Computing euler number orig.nofix lheno = -30, rheno = -44 orig.nofix lhholes = 16, rhholes = 23 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 336212.563 332461.000 diff= 3751.6 pctdiff= 1.116 rhCtxGM: 328476.300 325187.000 diff= 3289.3 pctdiff= 1.001 lhCtxWM: 277850.585 277588.500 diff= 262.1 pctdiff= 0.094 rhCtxWM: 278985.206 278975.500 diff= 9.7 pctdiff= 0.003 SubCortGMVol 73421.000 SupraTentVol 1315795.655 (1307464.000) diff=8331.655 pctdiff=0.633 SupraTentVolNotVent 1296172.655 (1287841.000) diff=8331.655 pctdiff=0.643 BrainSegVol 1456908.000 (1453971.000) diff=2937.000 pctdiff=0.202 BrainSegVolNotVent 1433208.000 (1440132.655) diff=-6924.655 pctdiff=-0.483 BrainSegVolNotVent 1433208.000 CerebellumVol 144979.000 VentChorVol 19623.000 3rd4th5thCSF 4077.000 CSFVol 1172.000, OptChiasmVol 356.000 MaskVol 1955327.000 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 7330 7330.012 4 5 Left-Inf-Lat-Vent 485 485.404 5 7 Left-Cerebellum-White-Matter 19126 19126.078 6 8 Left-Cerebellum-Cortex 54076 54075.738 7 10 Left-Thalamus-Proper 9801 9800.789 8 11 Left-Caudate 4593 4592.850 9 12 Left-Putamen 6882 6882.185 10 13 Left-Pallidum 2582 2581.743 11 14 3rd-Ventricle 1031 1030.534 12 15 4th-Ventricle 2076 2076.042 13 16 Brain-Stem 28015 28015.285 14 17 Left-Hippocampus 4356 4355.679 15 18 Left-Amygdala 1830 1830.003 16 24 CSF 1168 1167.957 17 26 Left-Accumbens-area 1138 1137.688 18 28 Left-VentralDC 4830 4829.687 19 30 Left-vessel 89 88.732 20 31 Left-choroid-plexus 1089 1088.721 23 43 Right-Lateral-Ventricle 8169 8168.733 24 44 Right-Inf-Lat-Vent 835 834.640 25 46 Right-Cerebellum-White-Matter 19688 19687.779 26 47 Right-Cerebellum-Cortex 54426 54426.105 27 49 Right-Thalamus-Proper 8898 8898.092 28 50 Right-Caudate 5030 5030.434 29 51 Right-Putamen 6987 6987.416 30 52 Right-Pallidum 2747 2746.605 31 53 Right-Hippocampus 4251 4250.944 32 54 Right-Amygdala 1875 1875.328 33 58 Right-Accumbens-area 902 901.986 34 60 Right-VentralDC 4849 4848.833 35 62 Right-vessel 98 97.882 36 63 Right-choroid-plexus 1666 1665.774 37 72 5th-Ventricle 0 0.000 38 77 WM-hypointensities 1291 1290.874 39 78 Left-WM-hypointensities 0 0.000 40 79 Right-WM-hypointensities 0 0.000 41 80 non-WM-hypointensities 30 29.574 42 81 Left-non-WM-hypointensities 0 0.000 43 82 Right-non-WM-hypointensities 0 0.000 44 85 Optic-Chiasm 360 359.910 45 251 CC_Posterior 733 732.649 46 252 CC_Mid_Posterior 381 380.823 47 253 CC_Central 374 373.556 48 254 CC_Mid_Anterior 392 392.228 49 255 CC_Anterior 867 866.925 Reporting on 45 segmentations mri_segstats done #----------------------------------------- #@# AParc-to-ASeg Fri Aug 9 01:02:15 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006 mri_aparc2aseg --s sub006 --volmask SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer subject sub006 outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white Reading lh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.pial Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/surf/rh.white Reading rh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.pial Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/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/sub006/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 = 655708 Used brute-force search on 0 voxels Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/aparc+aseg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006 mri_aparc2aseg --s sub006 --volmask --a2009s SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer subject sub006 outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white Reading lh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.pial Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/surf/rh.white Reading rh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.pial Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/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/sub006/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 = 655708 Used brute-force search on 0 voxels Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# WMParc Fri Aug 9 01:08:27 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006 mri_aparc2aseg --s sub006 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer subject sub006 outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/aparc+aseg.mgz Reading lh white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white Reading lh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.pial Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/surf/rh.white Reading rh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.pial Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/sub006/mri/ribbon.mgz Loading filled from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/filled.mgz Ripping vertices labeled as unkown Ripped 9139 vertices from left hemi Ripped 8689 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/sub006/mri/aseg.mgz Loading Ctx Seg File /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 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--brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject sub006 --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 sub006 --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) = 1428534 mm^3 (det: 1.363710 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 336212.563 332461.000 diff= 3751.6 pctdiff= 1.116 rhCtxGM: 328476.300 325187.000 diff= 3289.3 pctdiff= 1.001 lhCtxWM: 277850.585 277588.500 diff= 262.1 pctdiff= 0.094 rhCtxWM: 278985.206 278975.500 diff= 9.7 pctdiff= 0.003 SubCortGMVol 73421.000 SupraTentVol 1315795.655 (1307464.000) diff=8331.655 pctdiff=0.633 SupraTentVolNotVent 1296172.655 (1287841.000) diff=8331.655 pctdiff=0.643 BrainSegVol 1456908.000 (1453971.000) diff=2937.000 pctdiff=0.202 BrainSegVolNotVent 1433208.000 (1440132.655) diff=-6924.655 pctdiff=-0.483 BrainSegVolNotVent 1433208.000 CerebellumVol 144979.000 VentChorVol 19623.000 3rd4th5thCSF 4077.000 CSFVol 1172.000, OptChiasmVol 356.000 MaskVol 1955327.000 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 4418 4417.723 2 3002 wm-lh-caudalanteriorcingulate 3864 3864.340 3 3003 wm-lh-caudalmiddlefrontal 7755 7755.121 4 3004 wm-lh-corpuscallosum 0 0.000 5 3005 wm-lh-cuneus 2922 2922.244 6 3006 wm-lh-entorhinal 866 865.680 7 3007 wm-lh-fusiform 7879 7879.229 8 3008 wm-lh-inferiorparietal 13874 13874.421 9 3009 wm-lh-inferiortemporal 8577 8576.690 10 3010 wm-lh-isthmuscingulate 5079 5079.076 11 3011 wm-lh-lateraloccipital 11434 11433.657 12 3012 wm-lh-lateralorbitofrontal 7590 7590.018 13 3013 wm-lh-lingual 5167 5166.894 14 3014 wm-lh-medialorbitofrontal 4050 4049.541 15 3015 wm-lh-middletemporal 6849 6848.841 16 3016 wm-lh-parahippocampal 1745 1745.474 17 3017 wm-lh-paracentral 4994 4993.876 18 3018 wm-lh-parsopercularis 5347 5347.052 19 3019 wm-lh-parsorbitalis 1058 1058.097 20 3020 wm-lh-parstriangularis 3877 3876.976 21 3021 wm-lh-pericalcarine 3776 3775.736 22 3022 wm-lh-postcentral 9375 9375.486 23 3023 wm-lh-posteriorcingulate 5697 5696.546 24 3024 wm-lh-precentral 15315 15314.828 25 3025 wm-lh-precuneus 12411 12410.523 26 3026 wm-lh-rostralanteriorcingulate 3254 3253.774 27 3027 wm-lh-rostralmiddlefrontal 14948 14948.436 28 3028 wm-lh-superiorfrontal 24509 24508.672 29 3029 wm-lh-superiorparietal 14397 14396.718 30 3030 wm-lh-superiortemporal 8630 8630.139 31 3031 wm-lh-supramarginal 12144 12143.636 32 3032 wm-lh-frontalpole 242 241.895 33 3033 wm-lh-temporalpole 663 662.969 34 3034 wm-lh-transversetemporal 896 895.882 35 3035 wm-lh-insula 11996 11995.933 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 3372 3371.896 120 4002 wm-rh-caudalanteriorcingulate 3721 3721.009 121 4003 wm-rh-caudalmiddlefrontal 7093 7092.917 122 4004 wm-rh-corpuscallosum 0 0.000 123 4005 wm-rh-cuneus 2876 2875.500 124 4006 wm-rh-entorhinal 742 741.779 125 4007 wm-rh-fusiform 8916 8916.202 126 4008 wm-rh-inferiorparietal 16859 16858.648 127 4009 wm-rh-inferiortemporal 6662 6662.298 128 4010 wm-rh-isthmuscingulate 3680 3679.761 129 4011 wm-rh-lateraloccipital 11668 11668.020 130 4012 wm-rh-lateralorbitofrontal 8058 8058.475 131 4013 wm-rh-lingual 5615 5615.262 132 4014 wm-rh-medialorbitofrontal 4398 4398.331 133 4015 wm-rh-middletemporal 7127 7127.338 134 4016 wm-rh-parahippocampal 1785 1785.232 135 4017 wm-rh-paracentral 7082 7082.070 136 4018 wm-rh-parsopercularis 3396 3396.415 137 4019 wm-rh-parsorbitalis 1044 1044.153 138 4020 wm-rh-parstriangularis 4546 4545.789 139 4021 wm-rh-pericalcarine 4072 4071.632 140 4022 wm-rh-postcentral 9982 9982.438 141 4023 wm-rh-posteriorcingulate 5548 5548.213 142 4024 wm-rh-precentral 17896 17895.854 143 4025 wm-rh-precuneus 12276 12276.496 144 4026 wm-rh-rostralanteriorcingulate 2472 2471.522 145 4027 wm-rh-rostralmiddlefrontal 17153 17153.137 146 4028 wm-rh-superiorfrontal 22915 22914.824 147 4029 wm-rh-superiorparietal 13379 13379.062 148 4030 wm-rh-superiortemporal 8384 8383.724 149 4031 wm-rh-supramarginal 10440 10439.874 150 4032 wm-rh-frontalpole 371 370.807 151 4033 wm-rh-temporalpole 824 823.720 152 4034 wm-rh-transversetemporal 747 746.819 153 4035 wm-rh-insula 10663 10662.812 154 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 35030 35030.414 237 5002 Right-UnsegmentedWhiteMatter 35614 35613.559 238 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/sub006/label #-------------------------------------------- #@# BA Labels lh Fri Aug 9 01:20:29 CEST 2013 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.label --trgsubject sub006 --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 = sub006 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/sub006/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478 Number of reverse mapping hits = 550 Checking for and removing duplicates Writing label file ./lh.BA1.label 4679 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.label --trgsubject sub006 --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 = sub006 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/sub006/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478 Number of reverse mapping hits = 965 Checking for and removing duplicates Writing label file ./lh.BA2.label 8874 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.label --trgsubject sub006 --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 = sub006 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/sub006/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478 Number of reverse mapping hits = 323 Checking for and removing duplicates Writing label file ./lh.BA3a.label 4400 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.label --trgsubject sub006 --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 = sub006 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/sub006/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478 Number of reverse mapping hits = 716 Checking for and removing duplicates Writing label file ./lh.BA3b.label 6699 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.label --trgsubject sub006 --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 = sub006 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/sub006/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478 Number of reverse mapping hits = 915 Checking for and removing duplicates Writing label file ./lh.BA4a.label 6699 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.label --trgsubject sub006 --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 = sub006 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/sub006/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478 Number of reverse mapping hits = 541 Checking for and removing duplicates Writing label file ./lh.BA4p.label 4611 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.label --trgsubject sub006 --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 = sub006 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/sub006/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478 Number of reverse mapping hits = 3216 Checking for and removing duplicates Writing label file ./lh.BA6.label 16805 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.label --trgsubject sub006 --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 = sub006 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/sub006/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478 Number of reverse mapping hits = 1125 Checking for and removing duplicates Writing label file ./lh.BA44.label 5306 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.label --trgsubject sub006 --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 = sub006 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/sub006/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478 Number of reverse mapping hits = 1858 Checking for and removing duplicates Writing label file ./lh.BA45.label 5280 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.label --trgsubject sub006 --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 = sub006 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/sub006/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478 Number of reverse mapping hits = 1794 Checking for and removing duplicates Writing label file ./lh.V1.label 6435 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.label --trgsubject sub006 --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 = sub006 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/sub006/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478 Number of reverse mapping hits = 3925 Checking for and removing duplicates Writing label file ./lh.V2.label 12039 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.label --trgsubject sub006 --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 = sub006 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/sub006/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478 Number of reverse mapping hits = 721 Checking for and removing duplicates Writing label file ./lh.MT.label 2739 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.perirhinal.label --trgsubject sub006 --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 = sub006 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/sub006/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478 Number of reverse mapping hits = 133 Checking for and removing duplicates Writing label file ./lh.perirhinal.label 1332 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.thresh.label --trgsubject sub006 --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 = sub006 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/sub006/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478 Number of reverse mapping hits = 194 Checking for and removing duplicates Writing label file ./lh.BA1.thresh.label 1208 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.thresh.label --trgsubject sub006 --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 = sub006 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/sub006/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478 Number of reverse mapping hits = 273 Checking for and removing duplicates Writing label file ./lh.BA2.thresh.label 2365 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.thresh.label --trgsubject sub006 --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 = sub006 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/sub006/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478 Number of reverse mapping hits = 63 Checking for and removing duplicates Writing label file ./lh.BA3a.thresh.label 1567 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.thresh.label --trgsubject sub006 --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 = sub006 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/sub006/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478 Number of reverse mapping hits = 338 Checking for and removing duplicates Writing label file ./lh.BA3b.thresh.label 2334 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.thresh.label --trgsubject sub006 --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 = sub006 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/sub006/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478 Number of reverse mapping hits = 414 Checking for and removing duplicates Writing label file ./lh.BA4a.thresh.label 2733 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.thresh.label --trgsubject sub006 --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 = sub006 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/sub006/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478 Number of reverse mapping hits = 203 Checking for and removing duplicates Writing label file ./lh.BA4p.thresh.label 1752 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.thresh.label --trgsubject sub006 --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 = sub006 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/sub006/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478 Number of reverse mapping hits = 1544 Checking for and removing duplicates Writing label file ./lh.BA6.thresh.label 8579 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.thresh.label --trgsubject sub006 --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 = sub006 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/sub006/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478 Number of reverse mapping hits = 610 Checking for and removing duplicates Writing label file ./lh.BA44.thresh.label 2522 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.thresh.label --trgsubject sub006 --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 = sub006 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/sub006/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478 Number of reverse mapping hits = 787 Checking for and removing duplicates Writing label file ./lh.BA45.thresh.label 1938 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.thresh.label --trgsubject sub006 --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 = sub006 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/sub006/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478 Number of reverse mapping hits = 1254 Checking for and removing duplicates Writing label file ./lh.V1.thresh.label 4659 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.thresh.label --trgsubject sub006 --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 = sub006 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/sub006/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478 Number of reverse mapping hits = 1742 Checking for and removing duplicates Writing label file ./lh.V2.thresh.label 5076 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.thresh.label --trgsubject sub006 --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 = sub006 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/sub006/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478 Number of reverse mapping hits = 105 Checking for and removing duplicates Writing label file ./lh.MT.thresh.label 618 mri_label2label: Done mris_label2annot --s sub006 --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/sub006/label cmdline mris_label2annot --s sub006 --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 sub006 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/sub006/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 119564 unhit vertices Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/label/lh.BA.annot mris_label2annot --s sub006 --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/sub006/label cmdline mris_label2annot --s sub006 --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 sub006 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/sub006/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 141481 unhit vertices Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/label/lh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab sub006 lh white computing statistics for each annotation in ./lh.BA.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 1378 807 3306 2.741 0.426 0.156 0.056 31 2.8 BA1 4430 2985 8490 2.575 0.472 0.126 0.036 51 6.3 BA2 1063 731 1176 2.100 0.429 0.124 0.032 7 1.4 BA3a 2986 1952 4892 2.120 0.531 0.115 0.030 33 3.7 BA3b 2212 1327 5542 3.143 0.534 0.108 0.037 33 3.8 BA4a 1633 990 3294 3.204 0.511 0.087 0.028 10 2.2 BA4p 12933 8663 33247 2.976 0.590 0.127 0.036 155 19.9 BA6 3462 2296 7744 2.848 0.477 0.131 0.040 50 5.7 BA44 4517 2998 9386 2.593 0.519 0.150 0.052 81 9.7 BA45 4068 2705 6033 2.041 0.453 0.143 0.060 70 9.9 V1 9771 6406 15502 2.210 0.529 0.161 0.069 215 26.7 V2 2425 1628 4352 2.448 0.436 0.141 0.044 34 4.1 MT 1036 740 3633 3.547 0.666 0.143 0.047 15 2.2 perirhinal mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab sub006 lh white computing statistics for each annotation in ./lh.BA.thresh.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 916 498 2199 2.777 0.451 0.161 0.063 24 2.2 BA1 1751 1201 3672 2.621 0.441 0.118 0.029 18 2.0 BA2 888 608 917 2.063 0.437 0.127 0.032 6 1.3 BA3a 1918 1249 2800 1.992 0.439 0.095 0.021 13 1.6 BA3b 2123 1298 5281 3.195 0.550 0.096 0.024 18 2.4 BA4a 1272 785 2439 3.106 0.523 0.090 0.027 9 1.4 BA4p 7237 4829 18409 2.940 0.595 0.124 0.034 86 10.7 BA6 2322 1552 5408 2.887 0.475 0.137 0.042 35 3.9 BA44 1901 1245 4596 2.785 0.482 0.168 0.066 48 5.2 BA45 4307 2867 6459 2.040 0.454 0.144 0.061 78 10.5 V1 4819 3198 6972 2.041 0.499 0.172 0.078 116 14.3 V2 543 373 907 2.204 0.405 0.120 0.027 5 0.6 MT #-------------------------------------------- #@# BA Labels rh Fri Aug 9 01:25:46 CEST 2013 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.label --trgsubject sub006 --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 = sub006 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/sub006/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3962 nlabel points Performing mapping from target back to the source label 169645 Number of reverse mapping hits = 497 Checking for and removing duplicates Writing label file ./rh.BA1.label 4459 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.label --trgsubject sub006 --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 = sub006 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/sub006/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6687 nlabel points Performing mapping from target back to the source label 169645 Number of reverse mapping hits = 818 Checking for and removing duplicates Writing label file ./rh.BA2.label 7505 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.label --trgsubject sub006 --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 = sub006 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/sub006/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3980 nlabel points Performing mapping from target back to the source label 169645 Number of reverse mapping hits = 367 Checking for and removing duplicates Writing label file ./rh.BA3a.label 4347 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.label --trgsubject sub006 --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 = sub006 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/sub006/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4522 nlabel points Performing mapping from target back to the source label 169645 Number of reverse mapping hits = 564 Checking for and removing duplicates Writing label file ./rh.BA3b.label 5086 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.label --trgsubject sub006 --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 = sub006 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/sub006/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5747 nlabel points Performing mapping from target back to the source label 169645 Number of reverse mapping hits = 1117 Checking for and removing duplicates Writing label file ./rh.BA4a.label 6864 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.label --trgsubject sub006 --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 = sub006 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/sub006/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4473 nlabel points Performing mapping from target back to the source label 169645 Number of reverse mapping hits = 565 Checking for and removing duplicates Writing label file ./rh.BA4p.label 5038 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.label --trgsubject sub006 --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 = sub006 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/sub006/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 12256 nlabel points Performing mapping from target back to the source label 169645 Number of reverse mapping hits = 2990 Checking for and removing duplicates Writing label file ./rh.BA6.label 15246 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.label --trgsubject sub006 --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 = sub006 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/sub006/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6912 nlabel points Performing mapping from target back to the source label 169645 Number of reverse mapping hits = 1139 Checking for and removing duplicates Writing label file ./rh.BA44.label 8051 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.label --trgsubject sub006 --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 = sub006 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/sub006/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5355 nlabel points Performing mapping from target back to the source label 169645 Number of reverse mapping hits = 1562 Checking for and removing duplicates Writing label file ./rh.BA45.label 6917 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.label --trgsubject sub006 --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 = sub006 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/sub006/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4727 nlabel points Performing mapping from target back to the source label 169645 Number of reverse mapping hits = 2392 Checking for and removing duplicates Writing label file ./rh.V1.label 7119 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.label --trgsubject sub006 --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 = sub006 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/sub006/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8016 nlabel points Performing mapping from target back to the source label 169645 Number of reverse mapping hits = 4535 Checking for and removing duplicates Writing label file ./rh.V2.label 12551 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.label --trgsubject sub006 --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 = sub006 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/sub006/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1932 nlabel points Performing mapping from target back to the source label 169645 Number of reverse mapping hits = 1008 Checking for and removing duplicates Writing label file ./rh.MT.label 2940 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.perirhinal.label --trgsubject sub006 --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 = sub006 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/sub006/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 752 nlabel points Performing mapping from target back to the source label 169645 Number of reverse mapping hits = 79 Checking for and removing duplicates Writing label file ./rh.perirhinal.label 831 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.thresh.label --trgsubject sub006 --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 = sub006 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/sub006/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 876 nlabel points Performing mapping from target back to the source label 169645 Number of reverse mapping hits = 160 Checking for and removing duplicates Writing label file ./rh.BA1.thresh.label 1036 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.thresh.label --trgsubject sub006 --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 = sub006 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/sub006/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2688 nlabel points Performing mapping from target back to the source label 169645 Number of reverse mapping hits = 317 Checking for and removing duplicates Writing label file ./rh.BA2.thresh.label 3005 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.thresh.label --trgsubject sub006 --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 = sub006 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/sub006/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1698 nlabel points Performing mapping from target back to the source label 169645 Number of reverse mapping hits = 98 Checking for and removing duplicates Writing label file ./rh.BA3a.thresh.label 1796 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.thresh.label --trgsubject sub006 --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 = sub006 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/sub006/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2183 nlabel points Performing mapping from target back to the source label 169645 Number of reverse mapping hits = 332 Checking for and removing duplicates Writing label file ./rh.BA3b.thresh.label 2515 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.thresh.label --trgsubject sub006 --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 = sub006 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/sub006/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1388 nlabel points Performing mapping from target back to the source label 169645 Number of reverse mapping hits = 177 Checking for and removing duplicates Writing label file ./rh.BA4a.thresh.label 1565 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.thresh.label --trgsubject sub006 --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 = sub006 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/sub006/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1489 nlabel points Performing mapping from target back to the source label 169645 Number of reverse mapping hits = 218 Checking for and removing duplicates Writing label file ./rh.BA4p.thresh.label 1707 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.thresh.label --trgsubject sub006 --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 = sub006 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/sub006/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6959 nlabel points Performing mapping from target back to the source label 169645 Number of reverse mapping hits = 1884 Checking for and removing duplicates Writing label file ./rh.BA6.thresh.label 8843 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.thresh.label --trgsubject sub006 --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 = sub006 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/sub006/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1012 nlabel points Performing mapping from target back to the source label 169645 Number of reverse mapping hits = 161 Checking for and removing duplicates Writing label file ./rh.BA44.thresh.label 1173 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.thresh.label --trgsubject sub006 --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 = sub006 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/sub006/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1178 nlabel points Performing mapping from target back to the source label 169645 Number of reverse mapping hits = 215 Checking for and removing duplicates Writing label file ./rh.BA45.thresh.label 1393 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.thresh.label --trgsubject sub006 --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 = sub006 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/sub006/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3232 nlabel points Performing mapping from target back to the source label 169645 Number of reverse mapping hits = 1582 Checking for and removing duplicates Writing label file ./rh.V1.thresh.label 4814 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.thresh.label --trgsubject sub006 --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 = sub006 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/sub006/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3437 nlabel points Performing mapping from target back to the source label 169645 Number of reverse mapping hits = 1924 Checking for and removing duplicates Writing label file ./rh.V2.thresh.label 5361 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.thresh.label --trgsubject sub006 --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 = sub006 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/sub006/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 268 nlabel points Performing mapping from target back to the source label 169645 Number of reverse mapping hits = 157 Checking for and removing duplicates Writing label file ./rh.MT.thresh.label 425 mri_label2label: Done mris_label2annot --s sub006 --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/sub006/label cmdline mris_label2annot --s sub006 --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 sub006 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/sub006/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 118049 unhit vertices Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/label/rh.BA.annot mris_label2annot --s sub006 --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/sub006/label cmdline mris_label2annot --s sub006 --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 sub006 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/sub006/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 141116 unhit vertices Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/label/rh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab sub006 rh white computing statistics for each annotation in ./rh.BA.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 1105 660 2688 2.770 0.422 0.143 0.040 17 1.9 BA1 3922 2579 6929 2.511 0.470 0.110 0.028 34 4.6 BA2 1273 831 1327 2.040 0.505 0.122 0.035 10 1.8 BA3a 2457 1582 3835 2.036 0.491 0.112 0.036 23 4.3 BA3b 2087 1284 4635 2.870 0.719 0.107 0.029 18 2.8 BA4a 1453 941 2898 2.968 0.584 0.105 0.030 9 1.9 BA4p 11589 7829 29107 2.978 0.623 0.125 0.035 133 16.2 BA6 4073 2738 8712 2.858 0.456 0.123 0.032 43 5.7 BA44 5202 3488 11692 2.693 0.482 0.145 0.051 92 10.0 BA45 4782 3197 7009 2.051 0.442 0.146 0.059 93 12.0 V1 10170 6679 16461 2.231 0.498 0.155 0.063 177 21.8 V2 2839 1860 4901 2.463 0.467 0.135 0.040 41 4.5 MT 644 476 1946 3.377 0.629 0.144 0.047 7 1.3 perirhinal mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab sub006 rh white computing statistics for each annotation in ./rh.BA.thresh.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 789 452 1909 2.817 0.358 0.137 0.041 12 1.2 BA1 2254 1479 4014 2.489 0.475 0.103 0.024 16 2.4 BA2 1075 699 1063 2.043 0.493 0.123 0.036 7 1.6 BA3a 2021 1352 2836 1.912 0.421 0.102 0.024 14 2.1 BA3b 1150 712 2500 2.590 0.737 0.118 0.033 12 1.4 BA4a 1226 784 2518 3.157 0.527 0.104 0.030 8 1.6 BA4p 7764 5223 18944 2.911 0.643 0.125 0.035 91 10.9 BA6 954 667 2456 2.956 0.493 0.135 0.038 13 1.6 BA44 1186 821 3175 2.892 0.374 0.142 0.049 21 2.2 BA45 4570 3064 6629 2.052 0.441 0.143 0.057 84 11.5 V1 5134 3415 7778 2.088 0.498 0.171 0.075 100 12.6 V2 406 245 837 2.678 0.306 0.149 0.048 8 0.8 MT /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label lh Fri Aug 9 01:31:00 CEST 2013 mris_spherical_average -erode 1 -orig white -t 0.4 -o sub006 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject sub006. processing subject lh.EC_average... reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 1003 points to lh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label sub006 lh white limiting computations to label ./lh.entorhinal_exvivo.label. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 368 242 1509 3.742 0.513 0.126 0.051 5 0.9 ./lh.entorhinal_exvivo.label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label rh Fri Aug 9 01:31:17 CEST 2013 mris_spherical_average -erode 1 -orig white -t 0.4 -o sub006 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label painting output onto subject sub006. processing subject rh.EC_average... reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 789 points to rh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label sub006 rh white limiting computations to label ./rh.entorhinal_exvivo.label. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 283 193 947 3.346 0.579 0.139 0.039 3 0.5 ./rh.entorhinal_exvivo.label #------------------------------------------ Started at Thu Aug 8 10:53:55 CEST 2013 Ended at Fri Aug 9 01:31:34 CEST 2013 #@#%# recon-all-run-time-hours 14.627 recon-all -s sub006 finished without error at Fri Aug 9 01:31:34 CEST 2013