Thu Aug 8 10:54:16 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011 /opt/freesurfer/5.3.0/bin/recon-all -i /home/data/exppsy/forrest_gump/openfmri.org/sub011/anatomy/highres001.nii.gz -cw256 -all -T2 /home/data/exppsy/forrest_gump/openfmri.org/sub011/anatomy/other/t2w001.nii.gz -T2pial -subjid sub011 -sd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer subjid sub011 setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Actual FREESURFER_HOME /opt/freesurfer/5.3.0 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux snake6 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc unlimited maxlocks unlimited maxsignal 16382 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 99201692 96979616 2222076 0 118440 94733892 -/+ buffers/cache: 2127284 97074408 Swap: 25165780 2780 25163000 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/freesurfer/5.3.0/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /opt/freesurfer/5.3.0/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### -cw256 option is now persistent (remove with -clean-cw256) /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub011/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/orig/001.mgz mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub011/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/anatomy/highres001.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998102, -0.0611237, 0.00753358) j_ras = (-0.0606425, 0.996759, 0.0528636) k_ras = (0.0107404, -0.0523064, 0.998573) writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/orig/001.mgz... #-------------------------------------------- #@# T2/FLAIR Input Thu Aug 8 10:54:37 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub011/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/orig/T2raw.mgz mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub011/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/anatomy/other/t2w001.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998102, -0.0611237, 0.00753358) j_ras = (-0.0606425, 0.996759, 0.0528636) k_ras = (0.0107404, -0.0523064, 0.998573) writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/orig/T2raw.mgz... #-------------------------------------------- #@# MotionCor Thu Aug 8 10:54:54 CEST 2013 Found 1 runs /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/mri/orig/001.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/orig.mgz --conform --cw256 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998102, -0.0611237, 0.00753358) j_ras = (-0.0606425, 0.996759, 0.0528636) k_ras = (0.0107404, -0.0523064, 0.998573) Original Data has (0.699913, 0.666667, 0.666667) mm size and (274, 384, 384) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/orig.mgz... mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/talairach.xfm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Aug 8 10:55:34 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 10:58:13 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6269, 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/sub011/mri/transforms/talairach_avi.log tal_QC_AZS /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/talairach_avi.log TalAviQA: 0.96663 z-score: -2 #-------------------------------------------- #@# Nu Intensity Correction Thu Aug 8 10:58:14 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/sub011/mri /opt/freesurfer/5.3.0/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux snake6 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux Thu Aug 8 10:58:14 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.24474 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.24474/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.24474/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, 1.31549e-08, 0) j_ras = (0, -1.11759e-08, -1) k_ras = (5.47152e-09, 1, -3.72529e-09) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.24474/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Aug 8 10:58:17 CEST 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.24474/nu0.mnc ./tmp.mri_nu_correct.mni.24474/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.24474/0/ [fkaule@snake6:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/] [2013-08-08 10:58:18] running: /opt/freesurfer/5.3.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.24474/0/ ./tmp.mri_nu_correct.mni.24474/nu0.mnc ./tmp.mri_nu_correct.mni.24474/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done 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Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 32 CV of field change: 0.000995292 [fkaule@snake6:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/] [2013-08-08 10:58:58] running: /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.24474/nu0.mnc ./tmp.mri_nu_correct.mni.24474/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Thu Aug 8 10:59:06 CEST 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.24474/nu1.mnc ./tmp.mri_nu_correct.mni.24474/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.24474/1/ [fkaule@snake6:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/] [2013-08-08 10:59:06] 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.24474/1/ ./tmp.mri_nu_correct.mni.24474/nu1.mnc ./tmp.mri_nu_correct.mni.24474/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done 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Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 32 CV of field change: 0.000992195 [fkaule@snake6:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/] [2013-08-08 10:59:45] running: /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.24474/nu1.mnc ./tmp.mri_nu_correct.mni.24474/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.24474/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.24474/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/sub011/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.24474/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.24474/ones.mgz sysname Linux hostname snake6 machine x86_64 user fkaule input ./tmp.mri_nu_correct.mni.24474/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.24474/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.24474/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.24474/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24474/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.24474/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.24474/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24474/input.mean.dat sysname Linux hostname snake6 machine x86_64 user fkaule UseRobust 0 Loading ./tmp.mri_nu_correct.mni.24474/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.24474/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.24474/ones.mgz --i ./tmp.mri_nu_correct.mni.24474/nu2.mnc --sum ./tmp.mri_nu_correct.mni.24474/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24474/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.24474/ones.mgz --i ./tmp.mri_nu_correct.mni.24474/nu2.mnc --sum ./tmp.mri_nu_correct.mni.24474/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24474/output.mean.dat sysname Linux hostname snake6 machine x86_64 user fkaule UseRobust 0 Loading ./tmp.mri_nu_correct.mni.24474/ones.mgz Loading ./tmp.mri_nu_correct.mni.24474/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.24474/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.24474/nu2.mnc ./tmp.mri_nu_correct.mni.24474/nu2.mnc mul .93847485184404357313 Saving result to './tmp.mri_nu_correct.mni.24474/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.24474/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.24474/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.24474/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.31549e-08, 0) j_ras = (0, -1.11759e-08, -1) k_ras = (5.47152e-09, 1, -3.72529e-09) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 7 seconds. mapping ( 7, 150) 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/sub011/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Thu Aug 8 11:00:32 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.096 0.129 0.014 2.157; -0.159 1.026 0.259 -40.388; 0.042 -0.399 1.140 2.207; 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 109 gm peak at 54 (54), valley at 43 (43) csf peak at 11, setting threshold to 39 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 77 (77), valley at 0 (-1) csf peak at 38, setting threshold to 64 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 48 seconds. #-------------------------------------------- #@# Skull Stripping Thu Aug 8 11:03:21 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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, 16, 0) --> (210, 255, 194) using (103, 96, 97) as brain centroid... mean wm in atlas = 126, using box (83,66,73) --> (122, 125,120) 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 initial log_p = -4.7 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.447860 @ (-9.091, 27.273, -9.091) max log p = -4.353130 @ (4.545, -4.545, 4.545) max log p = -4.298753 @ (2.273, -2.273, 2.273) max log p = -4.271574 @ (1.136, -1.136, 3.409) max log p = -4.270184 @ (0.568, 0.568, -0.568) max log p = -4.245293 @ (0.284, -1.989, -1.989) Found translation: (-0.3, 17.9, -1.4): log p = -4.245 **************************************** 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) 1.140 0.057 -0.139 -11.174; 0.000 1.142 0.473 -33.728; 0.139 -0.404 0.974 33.423; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.1 (thresh=-4.0) 1.055 0.053 -0.128 -0.904; -0.017 1.096 0.316 -19.623; 0.127 -0.232 0.951 13.249; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.055 0.053 -0.128 -0.904; -0.017 1.096 0.316 -19.623; 0.127 -0.232 0.951 13.249; 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=-3.9, old_max_log_p =-4.0 (thresh=-4.0) 1.019 0.008 -0.100 5.060; 0.012 1.084 0.275 -14.089; 0.096 -0.203 0.981 13.069; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.000 0.043 -0.088 2.950; -0.019 1.096 0.316 -17.426; 0.094 -0.234 0.953 19.202; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.000 0.043 -0.088 2.950; -0.019 1.096 0.316 -17.426; 0.094 -0.234 0.953 19.202; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.002 0.043 -0.088 2.663; -0.017 1.094 0.333 -19.156; 0.095 -0.252 0.949 20.443; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.002 0.043 -0.088 2.663; -0.017 1.094 0.333 -19.156; 0.095 -0.252 0.949 20.443; 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 1.00219 0.04278 -0.08846 2.66256; -0.01700 1.09433 0.33261 -19.15604; 0.09452 -0.25172 0.94899 20.44276; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.00219 0.04278 -0.08846 2.66256; -0.01700 1.09433 0.33261 -19.15604; 0.09452 -0.25172 0.94899 20.44276; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.002 0.043 -0.088 2.663; -0.017 1.094 0.333 -19.156; 0.095 -0.252 0.949 20.443; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.9 (old=-4.7) transform before final EM align: 1.002 0.043 -0.088 2.663; -0.017 1.094 0.333 -19.156; 0.095 -0.252 0.949 20.443; 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 1.00219 0.04278 -0.08846 2.66256; -0.01700 1.09433 0.33261 -19.15604; 0.09452 -0.25172 0.94899 20.44276; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.00219 0.04278 -0.08846 2.66256; -0.01700 1.09433 0.33261 -19.15604; 0.09452 -0.25172 0.94899 20.44276; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 011: -log(p) = 4.3 after pass:transform: ( 1.00, 0.04, -0.09, 2.66) ( -0.02, 1.09, 0.33, -19.16) ( 0.09, -0.25, 0.95, 20.44) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 013: -log(p) = 4.3 tol 0.000000 final transform: 1.002 0.043 -0.088 2.663; -0.017 1.094 0.333 -19.156; 0.095 -0.252 0.949 20.443; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 38 minutes and 36 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=129 y=84 z=107 r=95 first estimation of the main basin volume: 3642261 voxels Looking for seedpoints 2 found in the cerebellum 18 found in the rest of the brain global maximum in x=145, y=88, z=62, 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=22614982755 voxels, voxel volume =1.000 = 22614982755 mmm3 = 22614982.656 cm3 done. PostAnalyze...Basin Prior 164 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=126,y=97, z=103, r=10360 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=9 , nb = 45460 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=19 , nb = -1031416867 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=20 , nb = 1100756446 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=8 , nb = -1071523831 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=8 , nb = 1083001950 OTHER CSF_MIN=0, CSF_intensity=10, CSF_MAX=41 , nb = 1063265510 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 9, 12, 25, 55 after analyzing : 9, 20, 25, 28 RIGHT_CER before analyzing : 19, 17, 15, 63 after analyzing : 17, 22, 25, 32 LEFT_CER before analyzing : 20, 21, 26, 64 after analyzing : 20, 24, 26, 34 RIGHT_BRAIN before analyzing : 8, 11, 26, 55 after analyzing : 8, 21, 26, 29 LEFT_BRAIN before analyzing : 8, 10, 24, 54 after analyzing : 8, 20, 25, 28 OTHER before analyzing : 41, 74, 85, 95 after analyzing : 41, 81, 85, 84 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...76 iterations *********************VALIDATION********************* curvature mean = -0.012, std = 0.012 curvature mean = 73.052, std = 9.262 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 3.05, sigma = 5.82 after rotation: sse = 3.05, sigma = 5.82 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 3.35, its var is 5.32 before Erosion-Dilatation 1.06% of inacurate vertices after Erosion-Dilatation 1.76% 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...42 iterations mri_strip_skull: done peeling brain Brain Size = 1940057 voxels, voxel volume = 1.000 mm3 = 1940057 mmm3 = 1940.057 cm3 ****************************** Saving brainmask.auto.mgz done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Thu Aug 8 11:42:26 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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=22.0 skull bounding box = (56, 33, 27) --> (192, 178, 196) using (101, 81, 112) as brain centroid... mean wm in atlas = 107, using box (84,63,91) --> (117, 98,132) to find MRI wm before smoothing, mri peak at 107 after smoothing, mri peak at 107, scaling input intensities by 1.000 scaling channel 0 by 1 initial log_p = -4.5 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.004340 @ (-9.091, 27.273, -9.091) max log p = -3.789185 @ (4.545, -4.545, 4.545) max log p = -3.770103 @ (2.273, -2.273, 2.273) max log p = -3.748410 @ (-1.136, 1.136, -1.136) max log p = -3.720674 @ (1.705, -0.568, 1.705) max log p = -3.720674 @ (0.000, 0.000, 0.000) Found translation: (-1.7, 21.0, -1.7): log p = -3.721 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.4, old_max_log_p =-3.7 (thresh=-3.7) 0.991 0.034 -0.126 9.584; 0.000 1.038 0.278 -12.511; 0.121 -0.237 0.886 18.222; 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) 0.991 0.034 -0.126 9.584; 0.000 1.038 0.278 -12.511; 0.121 -0.237 0.886 18.222; 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=-3.2, old_max_log_p =-3.4 (thresh=-3.4) 1.032 0.026 -0.102 2.669; 0.004 1.069 0.317 -16.343; 0.089 -0.279 0.896 28.969; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2) 1.032 0.026 -0.102 2.669; 0.004 1.069 0.317 -16.343; 0.089 -0.279 0.896 28.969; 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 =-3.2 (thresh=-3.2) 1.032 0.030 -0.117 3.863; 0.001 1.081 0.289 -14.239; 0.106 -0.243 0.904 22.566; 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) 1.032 0.030 -0.117 3.863; 0.001 1.081 0.289 -14.239; 0.106 -0.243 0.904 22.566; 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 1.03164 0.03013 -0.11703 3.86285; 0.00105 1.08130 0.28901 -14.23942; 0.10554 -0.24302 0.90434 22.56604; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 1.03164 0.03013 -0.11703 3.86285; 0.00105 1.08130 0.28901 -14.23942; 0.10554 -0.24302 0.90434 22.56604; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.032 0.030 -0.117 3.863; 0.001 1.081 0.289 -14.239; 0.106 -0.243 0.904 22.566; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.2 (old=-4.5) transform before final EM align: 1.032 0.030 -0.117 3.863; 0.001 1.081 0.289 -14.239; 0.106 -0.243 0.904 22.566; 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 1.03164 0.03013 -0.11703 3.86285; 0.00105 1.08130 0.28901 -14.23942; 0.10554 -0.24302 0.90434 22.56604; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 1.03164 0.03013 -0.11703 3.86285; 0.00105 1.08130 0.28901 -14.23942; 0.10554 -0.24302 0.90434 22.56604; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 009: -log(p) = 3.7 after pass:transform: ( 1.03, 0.03, -0.12, 3.86) ( 0.00, 1.08, 0.29, -14.24) ( 0.11, -0.24, 0.90, 22.57) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = 3.7 tol 0.000000 final transform: 1.032 0.030 -0.117 3.863; 0.001 1.081 0.289 -14.239; 0.106 -0.243 0.904 22.566; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 22 minutes and 56 seconds. #-------------------------------------- #@# CA Normalize Thu Aug 8 12:05:23 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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=22.0 skull bounding box = (56, 33, 27) --> (192, 178, 196) using (101, 81, 112) as brain centroid... mean wm in atlas = 107, using box (84,63,91) --> (117, 98,132) to find MRI wm before smoothing, mri peak at 107 after smoothing, mri peak at 107, scaling input intensities by 1.000 scaling channel 0 by 1 using 244171 sample points... INFO: compute sample coordinates transform 1.032 0.030 -0.117 3.863; 0.001 1.081 0.289 -14.239; 0.106 -0.243 0.904 22.566; 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 (116, 36, 22) --> (189, 144, 194) Left_Cerebral_White_Matter: limiting intensities to 100.0 --> 182.0 0 of 13 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (64, 35, 24) --> (134, 134, 197) Right_Cerebral_White_Matter: limiting intensities to 102.0 --> 182.0 0 of 11 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (123, 117, 51) --> (171, 159, 107) Left_Cerebellum_White_Matter: limiting intensities to 93.0 --> 182.0 0 of 7 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (79, 117, 52) --> (124, 156, 112) Right_Cerebellum_White_Matter: limiting intensities to 93.0 --> 182.0 0 of 19 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (112, 106, 89) --> (142, 169, 121) Brain_Stem: limiting intensities to 82.0 --> 182.0 1 of 9 (11.1%) samples deleted using 59 total control points for intensity normalization... bias field = 0.923 +- 0.074 0 of 58 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (116, 36, 22) --> (189, 144, 194) Left_Cerebral_White_Matter: limiting intensities to 93.0 --> 167.0 0 of 86 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (64, 35, 24) --> (134, 134, 197) Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 167.0 0 of 108 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (123, 117, 51) --> (171, 159, 107) Left_Cerebellum_White_Matter: limiting intensities to 76.0 --> 167.0 0 of 59 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (79, 117, 52) --> (124, 156, 112) Right_Cerebellum_White_Matter: limiting intensities to 81.0 --> 167.0 0 of 33 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (112, 106, 89) --> (142, 169, 121) Brain_Stem: limiting intensities to 73.0 --> 167.0 0 of 43 (0.0%) samples deleted using 329 total control points for intensity normalization... bias field = 1.003 +- 0.054 1 of 329 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (116, 36, 22) --> (189, 144, 194) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 165.0 0 of 212 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (64, 35, 24) --> (134, 134, 197) Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 165.0 0 of 188 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (123, 117, 51) --> (171, 159, 107) Left_Cerebellum_White_Matter: limiting intensities to 73.0 --> 165.0 0 of 50 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (79, 117, 52) --> (124, 156, 112) Right_Cerebellum_White_Matter: limiting intensities to 78.0 --> 165.0 0 of 24 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (112, 106, 89) --> (142, 169, 121) Brain_Stem: limiting intensities to 68.0 --> 165.0 0 of 82 (0.0%) samples deleted using 556 total control points for intensity normalization... bias field = 1.008 +- 0.050 1 of 556 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 2 minutes and 5 seconds. #-------------------------------------- #@# CA Reg Thu Aug 8 12:07:27 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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) = 1.10 (predicted orig area = 7.3) 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=0.831, neg=0, invalid=96777 0001: dt=129.472000, rms=0.776 (6.635%), neg=0, invalid=96777 0002: dt=129.472000, rms=0.763 (1.672%), neg=0, invalid=96777 0003: dt=129.472000, rms=0.757 (0.773%), neg=0, invalid=96777 0004: dt=221.952000, rms=0.750 (0.973%), neg=0, invalid=96777 0005: dt=92.480000, rms=0.746 (0.559%), neg=0, invalid=96777 0006: dt=295.936000, rms=0.741 (0.712%), neg=0, invalid=96777 0007: dt=73.984000, rms=0.737 (0.533%), neg=0, invalid=96777 0008: dt=517.888000, rms=0.730 (0.962%), neg=0, invalid=96777 0009: dt=73.984000, rms=0.727 (0.409%), neg=0, invalid=96777 0010: dt=887.808000, rms=0.721 (0.803%), neg=0, invalid=96777 0011: dt=110.976000, rms=0.717 (0.573%), neg=0, invalid=96777 0012: dt=221.952000, rms=0.715 (0.164%), neg=0, invalid=96777 0013: dt=221.952000, rms=0.714 (0.181%), neg=0, invalid=96777 0014: dt=221.952000, rms=0.711 (0.444%), neg=0, invalid=96777 0015: dt=221.952000, rms=0.709 (0.295%), neg=0, invalid=96777 0016: dt=221.952000, rms=0.705 (0.559%), neg=0, invalid=96777 0017: dt=221.952000, rms=0.701 (0.499%), neg=0, invalid=96777 0018: dt=221.952000, rms=0.699 (0.279%), neg=0, invalid=96777 0019: dt=221.952000, rms=0.695 (0.609%), neg=0, invalid=96777 0020: dt=221.952000, rms=0.693 (0.379%), neg=0, invalid=96777 0021: dt=221.952000, rms=0.691 (0.215%), neg=0, invalid=96777 0022: dt=221.952000, rms=0.688 (0.453%), neg=0, invalid=96777 0023: dt=221.952000, rms=0.686 (0.311%), neg=0, invalid=96777 0024: dt=221.952000, rms=0.684 (0.320%), neg=0, invalid=96777 0025: dt=221.952000, rms=0.682 (0.269%), neg=0, invalid=96777 0026: dt=221.952000, rms=0.680 (0.254%), neg=0, invalid=96777 0027: dt=221.952000, rms=0.678 (0.317%), neg=0, invalid=96777 0028: dt=221.952000, rms=0.676 (0.206%), neg=0, invalid=96777 0029: dt=221.952000, rms=0.676 (0.067%), neg=0, invalid=96777 0030: dt=221.952000, rms=0.674 (0.302%), neg=0, invalid=96777 0031: dt=221.952000, rms=0.673 (0.158%), neg=0, invalid=96777 0032: dt=221.952000, rms=0.673 (0.017%), neg=0, invalid=96777 0033: dt=221.952000, rms=0.671 (0.221%), neg=0, invalid=96777 0034: dt=221.952000, rms=0.671 (0.085%), neg=0, invalid=96777 0035: dt=221.952000, rms=0.670 (0.138%), neg=0, invalid=96777 0036: dt=221.952000, rms=0.669 (0.145%), neg=0, invalid=96777 0037: dt=221.952000, rms=0.669 (0.023%), neg=0, invalid=96777 0038: dt=221.952000, rms=0.667 (0.193%), neg=0, invalid=96777 0039: dt=221.952000, rms=0.667 (0.069%), neg=0, invalid=96777 0040: dt=221.952000, rms=0.667 (-0.004%), neg=0, invalid=96777 0041: dt=0.000000, rms=0.667 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.667, neg=0, invalid=96777 0042: dt=73.984000, rms=0.667 (0.023%), neg=0, invalid=96777 0043: dt=295.936000, rms=0.666 (0.115%), neg=0, invalid=96777 0044: dt=73.984000, rms=0.666 (0.006%), neg=0, invalid=96777 0045: dt=73.984000, rms=0.666 (0.007%), neg=0, invalid=96777 0046: dt=73.984000, rms=0.666 (0.000%), neg=0, invalid=96777 0047: dt=73.984000, rms=0.666 (-0.004%), neg=0, invalid=96777 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.674, neg=0, invalid=96777 0048: dt=145.152000, rms=0.665 (1.274%), neg=0, invalid=96777 0049: dt=82.944000, rms=0.661 (0.602%), neg=0, invalid=96777 0050: dt=36.288000, rms=0.658 (0.583%), neg=0, invalid=96777 0051: dt=62.208000, rms=0.656 (0.248%), neg=0, invalid=96777 0052: dt=62.208000, rms=0.653 (0.448%), neg=0, invalid=96777 0053: dt=62.208000, rms=0.649 (0.589%), neg=0, invalid=96777 0054: dt=62.208000, rms=0.643 (0.928%), neg=0, invalid=96777 0055: dt=62.208000, rms=0.637 (0.906%), neg=0, invalid=96777 0056: dt=62.208000, rms=0.632 (0.799%), neg=0, invalid=96777 0057: dt=62.208000, rms=0.627 (0.833%), neg=0, invalid=96777 0058: dt=62.208000, rms=0.623 (0.626%), neg=0, invalid=96777 0059: dt=62.208000, rms=0.620 (0.506%), neg=0, invalid=96777 0060: dt=62.208000, rms=0.617 (0.440%), neg=0, invalid=96777 0061: dt=62.208000, rms=0.614 (0.434%), neg=0, invalid=96777 0062: dt=62.208000, rms=0.612 (0.346%), neg=0, invalid=96777 0063: dt=62.208000, rms=0.611 (0.289%), neg=0, invalid=96777 0064: dt=62.208000, rms=0.609 (0.202%), neg=0, invalid=96777 0065: dt=62.208000, rms=0.608 (0.190%), neg=0, invalid=96777 0066: dt=62.208000, rms=0.607 (0.143%), neg=0, invalid=96777 0067: dt=62.208000, rms=0.606 (0.143%), neg=0, invalid=96777 0068: dt=62.208000, rms=0.606 (0.106%), neg=0, invalid=96777 0069: dt=62.208000, rms=0.605 (0.155%), neg=0, invalid=96777 0070: dt=62.208000, rms=0.604 (0.155%), neg=0, invalid=96777 0071: dt=62.208000, rms=0.603 (0.132%), neg=0, invalid=96777 0072: dt=62.208000, rms=0.602 (0.139%), neg=0, invalid=96777 0073: dt=62.208000, rms=0.601 (0.162%), neg=0, invalid=96777 0074: dt=62.208000, rms=0.601 (0.122%), neg=0, invalid=96777 0075: dt=62.208000, rms=0.600 (0.120%), neg=0, invalid=96777 0076: dt=62.208000, rms=0.600 (0.026%), neg=0, invalid=96777 0077: dt=62.208000, rms=0.600 (-0.039%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.600, neg=0, invalid=96777 0078: dt=31.104000, rms=0.600 (0.029%), neg=0, invalid=96777 0079: dt=36.288000, rms=0.599 (0.027%), neg=0, invalid=96777 0080: dt=36.288000, rms=0.599 (-0.027%), neg=0, invalid=96777 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.628, neg=0, invalid=96777 0081: dt=0.700000, rms=0.628 (0.002%), neg=0, invalid=96777 0082: dt=0.175000, rms=0.628 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.628, neg=0, invalid=96777 0083: dt=0.500000, rms=0.628 (0.001%), neg=0, invalid=96777 0084: dt=0.150000, rms=0.628 (0.001%), neg=0, invalid=96777 0085: dt=0.007812, rms=0.628 (-0.001%), neg=0, invalid=96777 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.712, neg=0, invalid=96777 0086: dt=4.998117, rms=0.686 (3.602%), neg=0, invalid=96777 0087: dt=3.159091, rms=0.684 (0.251%), neg=0, invalid=96777 0088: dt=0.864000, rms=0.684 (0.010%), neg=0, invalid=96777 0089: dt=0.864000, rms=0.684 (0.000%), neg=0, invalid=96777 0090: dt=0.864000, rms=0.684 (-0.040%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.684, neg=0, invalid=96777 0091: dt=0.000000, rms=0.684 (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=0.749, neg=0, invalid=96777 0092: dt=0.924883, rms=0.746 (0.378%), neg=0, invalid=96777 0093: dt=1.974522, rms=0.741 (0.645%), neg=0, invalid=96777 0094: dt=1.024000, rms=0.741 (0.097%), neg=0, invalid=96777 0095: dt=1.024000, rms=0.740 (0.165%), neg=0, invalid=96777 0096: dt=1.024000, rms=0.739 (0.089%), neg=0, invalid=96777 0097: dt=1.024000, rms=0.739 (-0.183%), neg=0, invalid=96777 0098: dt=0.112000, rms=0.739 (0.001%), neg=0, invalid=96777 0099: dt=0.112000, rms=0.739 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.739, neg=0, invalid=96777 0100: dt=1.024000, rms=0.738 (0.090%), neg=0, invalid=96777 0101: dt=0.000000, rms=0.738 (-0.003%), 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=0.697, neg=0, invalid=96777 0102: dt=0.157895, rms=0.689 (1.171%), neg=0, invalid=96777 0103: dt=0.000000, rms=0.689 (0.002%), neg=0, invalid=96777 0104: dt=0.050000, rms=0.689 (-0.034%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.689, neg=0, invalid=96777 0105: dt=0.250000, rms=0.687 (0.289%), neg=0, invalid=96777 0106: dt=0.096000, rms=0.686 (0.130%), neg=0, invalid=96777 0107: dt=0.096000, rms=0.686 (0.041%), neg=0, invalid=96777 0108: dt=0.096000, rms=0.686 (0.070%), neg=0, invalid=96777 0109: dt=0.096000, rms=0.685 (0.111%), neg=0, invalid=96777 0110: dt=0.096000, rms=0.684 (0.128%), neg=0, invalid=96777 0111: dt=0.096000, rms=0.683 (0.121%), neg=0, invalid=96777 0112: dt=0.096000, rms=0.682 (0.105%), neg=0, invalid=96777 0113: dt=0.000000, rms=0.682 (0.001%), neg=0, invalid=96777 0114: dt=0.050000, rms=0.682 (-0.001%), neg=0, invalid=96777 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.11688 ( 8) Left_Lateral_Ventricle (4): linear fit = 0.31 x + 0.0 (1727 voxels, overlap=0.006) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (1727 voxels, peak = 7), gca=9.6 gca peak = 0.14022 (22) mri peak = 0.13743 (10) Right_Lateral_Ventricle (43): linear fit = 0.41 x + 0.0 (1428 voxels, overlap=0.007) Right_Lateral_Ventricle (43): linear fit = 0.41 x + 0.0 (1428 voxels, peak = 9), gca=8.9 gca peak = 0.24234 (100) mri peak = 0.09243 (81) Right_Pallidum (52): linear fit = 0.81 x + 0.0 (472 voxels, overlap=0.049) Right_Pallidum (52): linear fit = 0.81 x + 0.0 (472 voxels, peak = 80), gca=80.5 gca peak = 0.19192 (97) mri peak = 0.10526 (77) Left_Pallidum (13): linear fit = 0.79 x + 0.0 (399 voxels, overlap=0.047) Left_Pallidum (13): linear fit = 0.79 x + 0.0 (399 voxels, peak = 76), gca=76.1 gca peak = 0.24007 (63) mri peak = 0.07313 (59) Right_Hippocampus (53): linear fit = 0.93 x + 0.0 (543 voxels, overlap=0.783) Right_Hippocampus (53): linear fit = 0.93 x + 0.0 (543 voxels, peak = 58), gca=58.3 gca peak = 0.29892 (64) mri peak = 0.06841 (59) Left_Hippocampus (17): linear fit = 0.90 x + 0.0 (581 voxels, overlap=0.710) Left_Hippocampus (17): linear fit = 0.90 x + 0.0 (581 voxels, peak = 58), gca=57.9 gca peak = 0.12541 (104) mri peak = 0.07006 (106) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (78113 voxels, overlap=0.812) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (78113 voxels, peak = 108), gca=107.6 gca peak = 0.13686 (104) mri peak = 0.07853 (107) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (80588 voxels, overlap=0.713) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (80588 voxels, peak = 109), gca=108.7 gca peak = 0.11691 (63) mri peak = 0.04927 (50) Left_Cerebral_Cortex (3): linear fit = 0.80 x + 0.0 (22125 voxels, overlap=0.067) Left_Cerebral_Cortex (3): linear fit = 0.80 x + 0.0 (22125 voxels, peak = 50), gca=50.1 gca peak = 0.13270 (63) mri peak = 0.05019 (54) Right_Cerebral_Cortex (42): linear fit = 0.83 x + 0.0 (20580 voxels, overlap=0.290) Right_Cerebral_Cortex (42): linear fit = 0.83 x + 0.0 (20580 voxels, peak = 53), gca=52.6 gca peak = 0.15182 (70) mri peak = 0.08925 (65) Right_Caudate (50): linear fit = 0.88 x + 0.0 (670 voxels, overlap=0.471) Right_Caudate (50): linear fit = 0.88 x + 0.0 (670 voxels, peak = 62), gca=62.0 gca peak = 0.14251 (76) mri peak = 0.07479 (66) Left_Caudate (11): linear fit = 0.85 x + 0.0 (813 voxels, overlap=0.091) Left_Caudate (11): linear fit = 0.85 x + 0.0 (813 voxels, peak = 64), gca=64.2 gca peak = 0.12116 (60) mri peak = 0.03908 (57) Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (15431 voxels, overlap=0.932) Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (15431 voxels, peak = 56), gca=56.1 gca peak = 0.12723 (61) mri peak = 0.03990 (56) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (13758 voxels, overlap=0.972) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (13758 voxels, peak = 59), gca=58.9 gca peak = 0.22684 (88) mri peak = 0.07232 (87) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (8311 voxels, overlap=0.976) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (8311 voxels, peak = 88), gca=87.6 gca peak = 0.21067 (87) mri peak = 0.06918 (86) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (7539 voxels, overlap=0.965) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (7539 voxels, peak = 89), gca=89.2 gca peak = 0.25455 (62) mri peak = 0.10207 (56) Left_Amygdala (18): linear fit = 0.88 x + 0.0 (379 voxels, overlap=0.619) Left_Amygdala (18): linear fit = 0.88 x + 0.0 (379 voxels, peak = 54), gca=54.2 gca peak = 0.39668 (62) mri peak = 0.11971 (53) Right_Amygdala (54): linear fit = 0.83 x + 0.0 (311 voxels, overlap=0.417) Right_Amygdala (54): linear fit = 0.83 x + 0.0 (311 voxels, peak = 52), gca=51.8 gca peak = 0.10129 (93) mri peak = 0.06025 (89) Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (5703 voxels, overlap=0.937) Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (5703 voxels, peak = 89), gca=88.8 gca peak = 0.12071 (89) mri peak = 0.05848 (87) Right_Thalamus_Proper (49): linear fit = 0.96 x + 0.0 (4707 voxels, overlap=0.972) Right_Thalamus_Proper (49): linear fit = 0.96 x + 0.0 (4707 voxels, peak = 86), gca=85.9 gca peak = 0.13716 (82) mri peak = 0.06062 (72) Left_Putamen (12): linear fit = 0.90 x + 0.0 (2119 voxels, overlap=0.788) Left_Putamen (12): linear fit = 0.90 x + 0.0 (2119 voxels, peak = 74), gca=74.2 gca peak = 0.15214 (84) mri peak = 0.06504 (75) Right_Putamen (51): linear fit = 0.92 x + 0.0 (2378 voxels, overlap=0.457) Right_Putamen (51): linear fit = 0.92 x + 0.0 (2378 voxels, peak = 77), gca=76.9 gca peak = 0.08983 (85) mri peak = 0.07193 (87) Brain_Stem (16): linear fit = 1.03 x + 0.0 (11713 voxels, overlap=0.778) Brain_Stem (16): linear fit = 1.03 x + 0.0 (11713 voxels, peak = 88), gca=88.0 gca peak = 0.11809 (92) mri peak = 0.06034 (88) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (862 voxels, overlap=0.905) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (862 voxels, peak = 93), gca=93.4 gca peak = 0.12914 (94) mri peak = 0.05874 (92) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (943 voxels, overlap=0.937) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (943 voxels, peak = 93), gca=92.6 gca peak = 0.21100 (36) mri peak = 0.05263 (53) gca peak = 0.13542 (27) mri peak = 0.12683 ( 8) Fourth_Ventricle (15): linear fit = 0.32 x + 0.0 (479 voxels, overlap=0.024) Fourth_Ventricle (15): linear fit = 0.32 x + 0.0 (479 voxels, peak = 9), gca=8.8 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak Third_Ventricle = 0.21100 (36) gca peak Fourth_Ventricle = 0.13542 (27) gca peak CSF = 0.17123 (45) gca peak Left_Accumbens_area = 0.25875 (69) gca peak Left_undetermined = 0.96240 (36) gca peak Left_vessel = 0.33262 (65) gca peak Left_choroid_plexus = 0.09846 (46) gca peak Right_Inf_Lat_Vent = 0.28113 (34) gca peak Right_Accumbens_area = 0.27120 (72) gca peak Right_vessel = 0.61915 (60) gca peak Right_choroid_plexus = 0.12775 (51) gca peak Fifth_Ventricle = 0.45329 (44) gca peak WM_hypointensities = 0.11729 (81) gca peak non_WM_hypointensities = 0.10912 (56) gca peak Optic_Chiasm = 0.33287 (75) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 0.86 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 0.40 x + 0.0 saving intensity scales to 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=0.724, neg=0, invalid=96777 0115: dt=129.472000, rms=0.719 (0.699%), neg=0, invalid=96777 0116: dt=295.936000, rms=0.714 (0.657%), neg=0, invalid=96777 0117: dt=110.976000, rms=0.712 (0.316%), neg=0, invalid=96777 0118: dt=129.472000, rms=0.711 (0.170%), neg=0, invalid=96777 0119: dt=295.936000, rms=0.708 (0.298%), neg=0, invalid=96777 0120: dt=73.984000, rms=0.707 (0.155%), neg=0, invalid=96777 0121: dt=517.888000, rms=0.705 (0.340%), neg=0, invalid=96777 0122: dt=73.984000, rms=0.704 (0.111%), neg=0, invalid=96777 0123: dt=295.936000, rms=0.704 (0.084%), neg=0, invalid=96777 0124: dt=55.488000, rms=0.703 (0.101%), neg=0, invalid=96777 0125: dt=1183.744000, rms=0.700 (0.345%), neg=0, invalid=96777 0126: dt=55.488000, rms=0.699 (0.183%), neg=0, invalid=96777 0127: dt=92.480000, rms=0.699 (0.041%), neg=0, invalid=96777 0128: dt=92.480000, rms=0.699 (0.024%), neg=0, invalid=96777 0129: dt=92.480000, rms=0.698 (0.041%), neg=0, invalid=96777 0130: dt=92.480000, rms=0.698 (0.075%), neg=0, invalid=96777 0131: dt=92.480000, rms=0.697 (0.104%), neg=0, invalid=96777 0132: dt=92.480000, rms=0.696 (0.119%), neg=0, invalid=96777 0133: dt=92.480000, rms=0.696 (0.116%), neg=0, invalid=96777 0134: dt=92.480000, rms=0.695 (0.110%), neg=0, invalid=96777 0135: dt=92.480000, rms=0.694 (0.119%), neg=0, invalid=96777 0136: dt=92.480000, rms=0.693 (0.118%), neg=0, invalid=96777 0137: dt=92.480000, rms=0.692 (0.116%), neg=0, invalid=96777 0138: dt=92.480000, rms=0.692 (0.100%), neg=0, invalid=96777 0139: dt=92.480000, rms=0.691 (0.091%), neg=0, invalid=96777 0140: dt=92.480000, rms=0.690 (0.096%), neg=0, invalid=96777 0141: dt=92.480000, rms=0.690 (0.103%), neg=0, invalid=96777 0142: dt=92.480000, rms=0.689 (0.103%), neg=0, invalid=96777 0143: dt=92.480000, rms=0.688 (0.091%), neg=0, invalid=96777 0144: dt=92.480000, rms=0.688 (0.085%), neg=0, invalid=96777 0145: dt=92.480000, rms=0.687 (0.081%), neg=0, invalid=96777 0146: dt=92.480000, rms=0.687 (0.091%), neg=0, invalid=96777 0147: dt=92.480000, rms=0.686 (0.081%), neg=0, invalid=96777 0148: dt=92.480000, rms=0.685 (0.075%), neg=0, invalid=96777 0149: dt=92.480000, rms=0.685 (0.067%), neg=0, invalid=96777 0150: dt=92.480000, rms=0.684 (0.071%), neg=0, invalid=96777 0151: dt=92.480000, rms=0.684 (0.085%), neg=0, invalid=96777 0152: dt=92.480000, rms=0.683 (0.082%), neg=0, invalid=96777 0153: dt=92.480000, rms=0.683 (0.067%), neg=0, invalid=96777 0154: dt=92.480000, rms=0.683 (0.055%), neg=0, invalid=96777 0155: dt=92.480000, rms=0.682 (0.052%), neg=0, invalid=96777 0156: dt=92.480000, rms=0.682 (0.062%), neg=0, invalid=96777 0157: dt=92.480000, rms=0.681 (0.064%), neg=0, invalid=96777 0158: dt=92.480000, rms=0.681 (0.050%), neg=0, invalid=96777 0159: dt=92.480000, rms=0.681 (0.043%), neg=0, invalid=96777 0160: dt=92.480000, rms=0.680 (0.041%), neg=0, invalid=96777 0161: dt=92.480000, rms=0.680 (0.048%), neg=0, invalid=96777 0162: dt=92.480000, rms=0.680 (0.052%), neg=0, invalid=96777 0163: dt=92.480000, rms=0.679 (0.051%), neg=0, invalid=96777 0164: dt=92.480000, rms=0.679 (0.049%), neg=0, invalid=96777 0165: dt=92.480000, rms=0.679 (0.044%), neg=0, invalid=96777 0166: dt=92.480000, rms=0.678 (0.042%), neg=0, invalid=96777 0167: dt=92.480000, rms=0.678 (0.034%), neg=0, invalid=96777 0168: dt=92.480000, rms=0.678 (0.038%), neg=0, invalid=96777 0169: dt=92.480000, rms=0.678 (0.039%), neg=0, invalid=96777 0170: dt=92.480000, rms=0.677 (0.042%), neg=0, invalid=96777 0171: dt=92.480000, rms=0.677 (0.033%), neg=0, invalid=96777 0172: dt=92.480000, rms=0.677 (0.031%), neg=0, invalid=96777 0173: dt=92.480000, rms=0.677 (0.031%), neg=0, invalid=96777 0174: dt=92.480000, rms=0.677 (0.035%), neg=0, invalid=96777 0175: dt=92.480000, rms=0.676 (0.036%), neg=0, invalid=96777 0176: dt=92.480000, rms=0.676 (0.039%), neg=0, invalid=96777 0177: dt=92.480000, rms=0.676 (0.034%), neg=0, invalid=96777 0178: dt=92.480000, rms=0.676 (0.028%), neg=0, invalid=96777 0179: dt=92.480000, rms=0.675 (0.032%), neg=0, invalid=96777 0180: dt=92.480000, rms=0.675 (0.034%), neg=0, invalid=96777 0181: dt=92.480000, rms=0.675 (0.024%), neg=0, invalid=96777 0182: dt=92.480000, rms=0.675 (0.023%), neg=0, invalid=96777 0183: dt=221.952000, rms=0.675 (0.004%), neg=0, invalid=96777 0184: dt=221.952000, rms=0.675 (0.009%), neg=0, invalid=96777 0185: dt=221.952000, rms=0.675 (-0.010%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.675, neg=0, invalid=96777 0186: dt=443.904000, rms=0.673 (0.200%), neg=0, invalid=96777 0187: dt=32.368000, rms=0.673 (-0.004%), neg=0, invalid=96777 0188: dt=32.368000, rms=0.673 (0.004%), neg=0, invalid=96777 0189: dt=32.368000, rms=0.673 (-0.006%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.674, neg=0, invalid=96777 0190: dt=124.416000, rms=0.670 (0.688%), neg=0, invalid=96777 0191: dt=82.944000, rms=0.662 (1.131%), neg=0, invalid=96777 0192: dt=25.920000, rms=0.661 (0.218%), neg=0, invalid=96777 0193: dt=145.152000, rms=0.657 (0.520%), neg=0, invalid=96777 0194: dt=36.288000, rms=0.654 (0.483%), neg=0, invalid=96777 0195: dt=331.776000, rms=0.648 (0.955%), neg=0, invalid=96777 0196: dt=20.736000, rms=0.644 (0.573%), neg=0, invalid=96777 0197: dt=145.152000, rms=0.642 (0.321%), neg=0, invalid=96777 0198: dt=36.288000, rms=0.640 (0.259%), neg=0, invalid=96777 0199: dt=62.208000, rms=0.640 (0.098%), neg=0, invalid=96777 0200: dt=36.288000, rms=0.639 (0.162%), neg=0, invalid=96777 0201: dt=103.680000, rms=0.638 (0.149%), neg=0, invalid=96777 0202: dt=25.920000, rms=0.637 (0.149%), neg=0, invalid=96777 0203: dt=145.152000, rms=0.635 (0.247%), neg=0, invalid=96777 0204: dt=20.736000, rms=0.634 (0.149%), neg=0, invalid=96777 0205: dt=580.608000, rms=0.627 (1.134%), neg=0, invalid=96777 0206: dt=36.288000, rms=0.627 (0.075%), neg=0, invalid=96777 0207: dt=82.944000, rms=0.626 (0.152%), neg=0, invalid=96777 0208: dt=20.736000, rms=0.625 (0.047%), neg=0, invalid=96777 0209: dt=20.736000, rms=0.625 (0.026%), neg=0, invalid=96777 0210: dt=20.736000, rms=0.625 (0.049%), neg=0, invalid=96777 0211: dt=20.736000, rms=0.624 (0.088%), neg=0, invalid=96777 0212: dt=20.736000, rms=0.624 (0.110%), neg=0, invalid=96777 0213: dt=20.736000, rms=0.623 (0.117%), neg=0, invalid=96777 0214: dt=20.736000, rms=0.622 (0.125%), neg=0, invalid=96777 0215: dt=20.736000, rms=0.621 (0.136%), neg=0, invalid=96777 0216: dt=20.736000, rms=0.621 (0.029%), neg=0, invalid=96777 0217: dt=20.736000, rms=0.621 (0.051%), neg=0, invalid=96777 0218: dt=10.368000, rms=0.621 (0.010%), neg=0, invalid=96777 0219: dt=5.184000, rms=0.621 (0.007%), neg=0, invalid=96777 0220: dt=1.620000, rms=0.621 (0.002%), neg=0, invalid=96777 0221: dt=0.202500, rms=0.621 (0.000%), neg=0, invalid=96777 0222: dt=0.025312, rms=0.621 (0.000%), neg=0, invalid=96777 0223: dt=0.003164, rms=0.621 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.621, neg=0, invalid=96777 0224: dt=145.152000, rms=0.618 (0.437%), neg=0, invalid=96777 0225: dt=36.288000, rms=0.617 (0.137%), neg=0, invalid=96777 0226: dt=103.680000, rms=0.616 (0.123%), neg=0, invalid=96777 0227: dt=36.288000, rms=0.616 (0.121%), neg=0, invalid=96777 0228: dt=36.288000, rms=0.615 (0.041%), neg=0, invalid=96777 0229: dt=36.288000, rms=0.615 (0.070%), neg=0, invalid=96777 0230: dt=36.288000, rms=0.615 (0.089%), neg=0, invalid=96777 0231: dt=36.288000, rms=0.614 (0.115%), neg=0, invalid=96777 0232: dt=36.288000, rms=0.613 (0.151%), neg=0, invalid=96777 0233: dt=36.288000, rms=0.612 (0.173%), neg=0, invalid=96777 0234: dt=36.288000, rms=0.611 (0.177%), neg=0, invalid=96777 0235: dt=36.288000, rms=0.610 (0.180%), neg=0, invalid=96777 0236: dt=36.288000, rms=0.609 (0.173%), neg=0, invalid=96777 0237: dt=36.288000, rms=0.607 (0.186%), neg=0, invalid=96777 0238: dt=36.288000, rms=0.606 (0.177%), neg=0, invalid=96777 0239: dt=36.288000, rms=0.605 (0.179%), neg=0, invalid=96777 0240: dt=36.288000, rms=0.604 (0.172%), neg=0, invalid=96777 0241: dt=36.288000, rms=0.603 (0.177%), neg=0, invalid=96777 0242: dt=36.288000, rms=0.602 (0.178%), neg=0, invalid=96777 0243: dt=36.288000, rms=0.601 (0.167%), neg=0, invalid=96777 0244: dt=36.288000, rms=0.600 (0.158%), neg=0, invalid=96777 0245: dt=36.288000, rms=0.599 (0.157%), neg=0, invalid=96777 0246: dt=36.288000, rms=0.598 (0.157%), neg=0, invalid=96777 0247: dt=36.288000, rms=0.597 (0.136%), neg=0, invalid=96777 0248: dt=36.288000, rms=0.597 (0.121%), neg=0, invalid=96777 0249: dt=36.288000, rms=0.596 (0.112%), neg=0, invalid=96777 0250: dt=36.288000, rms=0.595 (0.139%), neg=0, invalid=96777 0251: dt=36.288000, rms=0.594 (0.135%), neg=0, invalid=96777 0252: dt=36.288000, rms=0.594 (0.103%), neg=0, invalid=96777 0253: dt=18.144000, rms=0.594 (0.021%), neg=0, invalid=96777 0254: dt=18.144000, rms=0.594 (0.006%), neg=0, invalid=96777 0255: dt=36.288000, rms=0.594 (0.012%), neg=0, invalid=96777 0256: dt=9.072000, rms=0.594 (0.004%), neg=0, invalid=96777 0257: dt=9.072000, rms=0.594 (0.005%), neg=0, invalid=96777 0258: dt=4.536000, rms=0.594 (0.001%), neg=0, invalid=96777 0259: dt=2.268000, rms=0.594 (0.001%), neg=0, invalid=96777 0260: dt=0.567000, rms=0.594 (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=0.600, neg=0, invalid=96777 0261: dt=44.800000, rms=0.592 (1.295%), neg=0, invalid=96777 0262: dt=8.000000, rms=0.591 (0.259%), neg=0, invalid=96777 0263: dt=44.800000, rms=0.583 (1.221%), neg=0, invalid=96777 0264: dt=11.200000, rms=0.582 (0.224%), neg=0, invalid=96777 0265: dt=44.800000, rms=0.578 (0.784%), neg=0, invalid=96777 0266: dt=9.600000, rms=0.576 (0.206%), neg=0, invalid=96777 0267: dt=19.200000, rms=0.575 (0.249%), neg=0, invalid=96777 0268: dt=8.272109, rms=0.574 (0.201%), neg=0, invalid=96777 0269: dt=44.800000, rms=0.572 (0.304%), neg=0, invalid=96777 0270: dt=7.799544, rms=0.570 (0.383%), neg=0, invalid=96777 0271: dt=32.000000, rms=0.568 (0.363%), neg=0, invalid=96777 0272: dt=8.242424, rms=0.567 (0.128%), neg=0, invalid=96777 0273: dt=38.400000, rms=0.565 (0.301%), neg=0, invalid=96777 0274: dt=5.532710, rms=0.564 (0.153%), neg=0, invalid=96777 0275: dt=44.800000, rms=0.563 (0.286%), neg=0, invalid=96777 0276: dt=11.200000, rms=0.562 (0.208%), neg=0, invalid=96777 0277: dt=11.200000, rms=0.561 (0.097%), neg=0, invalid=96777 0278: dt=128.000000, rms=0.559 (0.411%), neg=0, invalid=96777 0279: dt=2.800000, rms=0.558 (0.199%), neg=0, invalid=96777 0280: dt=2.800000, rms=0.557 (0.180%), neg=0, invalid=96777 0281: dt=7.140187, rms=0.556 (0.192%), neg=0, invalid=96777 0282: dt=25.600000, rms=0.555 (0.147%), neg=0, invalid=96777 0283: dt=8.000000, rms=0.555 (0.046%), neg=0, invalid=96777 0284: dt=8.000000, rms=0.554 (0.068%), neg=0, invalid=96777 0285: dt=8.000000, rms=0.554 (0.075%), neg=0, invalid=96777 0286: dt=8.000000, rms=0.553 (0.107%), neg=0, invalid=96777 0287: dt=8.000000, rms=0.553 (0.117%), neg=0, invalid=96777 0288: dt=8.000000, rms=0.552 (0.153%), neg=0, invalid=96777 0289: dt=8.000000, rms=0.551 (0.175%), neg=0, invalid=96777 0290: dt=8.000000, rms=0.550 (0.178%), neg=0, invalid=96777 0291: dt=8.000000, rms=0.549 (0.177%), neg=0, invalid=96777 0292: dt=8.000000, rms=0.548 (0.175%), neg=0, invalid=96777 0293: dt=8.000000, rms=0.547 (0.197%), neg=0, invalid=96777 0294: dt=8.000000, rms=0.546 (0.205%), neg=0, invalid=96777 0295: dt=8.000000, rms=0.545 (0.188%), neg=0, invalid=96777 0296: dt=8.000000, rms=0.544 (0.168%), neg=0, invalid=96777 0297: dt=8.000000, rms=0.543 (0.154%), neg=0, invalid=96777 0298: dt=8.000000, rms=0.542 (0.145%), neg=0, invalid=96777 0299: dt=8.000000, rms=0.541 (0.140%), neg=0, invalid=96777 0300: dt=8.000000, rms=0.541 (0.134%), neg=0, invalid=96777 0301: dt=8.000000, rms=0.540 (0.139%), neg=0, invalid=96777 0302: dt=8.000000, rms=0.539 (0.122%), neg=0, invalid=96777 0303: dt=8.000000, rms=0.539 (0.120%), neg=0, invalid=96777 0304: dt=8.000000, rms=0.538 (0.113%), neg=0, invalid=96777 0305: dt=8.000000, rms=0.537 (0.099%), neg=0, invalid=96777 0306: dt=8.000000, rms=0.537 (0.097%), neg=0, invalid=96777 0307: dt=8.000000, rms=0.536 (0.094%), neg=0, invalid=96777 0308: dt=8.000000, rms=0.536 (0.086%), neg=0, invalid=96777 0309: dt=8.000000, rms=0.535 (0.089%), neg=0, invalid=96777 0310: dt=8.000000, rms=0.535 (0.076%), neg=0, invalid=96777 0311: dt=8.000000, rms=0.535 (0.067%), neg=0, invalid=96777 0312: dt=8.000000, rms=0.534 (0.056%), neg=0, invalid=96777 0313: dt=8.000000, rms=0.534 (0.060%), neg=0, invalid=96777 0314: dt=8.000000, rms=0.534 (0.059%), neg=0, invalid=96777 0315: dt=8.000000, rms=0.533 (0.064%), neg=0, invalid=96777 0316: dt=8.000000, rms=0.533 (0.054%), neg=0, invalid=96777 0317: dt=8.000000, rms=0.533 (0.053%), neg=0, invalid=96777 0318: dt=8.000000, rms=0.533 (0.040%), neg=0, invalid=96777 0319: dt=8.000000, rms=0.532 (0.037%), neg=0, invalid=96777 0320: dt=8.000000, rms=0.532 (0.050%), neg=0, invalid=96777 0321: dt=8.000000, rms=0.532 (0.050%), neg=0, invalid=96777 0322: dt=8.000000, rms=0.532 (0.043%), neg=0, invalid=96777 0323: dt=8.000000, rms=0.531 (0.041%), neg=0, invalid=96777 0324: dt=8.000000, rms=0.531 (0.041%), neg=0, invalid=96777 0325: dt=8.000000, rms=0.531 (0.036%), neg=0, invalid=96777 0326: dt=8.000000, rms=0.531 (0.038%), neg=0, invalid=96777 0327: dt=8.000000, rms=0.531 (0.034%), neg=0, invalid=96777 0328: dt=8.000000, rms=0.530 (0.037%), neg=0, invalid=96777 0329: dt=8.000000, rms=0.530 (0.044%), neg=0, invalid=96777 0330: dt=8.000000, rms=0.530 (0.042%), neg=0, invalid=96777 0331: dt=8.000000, rms=0.530 (0.036%), neg=0, invalid=96777 0332: dt=8.000000, rms=0.530 (0.038%), neg=0, invalid=96777 0333: dt=8.000000, rms=0.529 (0.033%), neg=0, invalid=96777 0334: dt=8.000000, rms=0.529 (0.025%), neg=0, invalid=96777 0335: dt=8.000000, rms=0.529 (0.026%), neg=0, invalid=96777 0336: dt=8.000000, rms=0.529 (0.027%), neg=0, invalid=96777 0337: dt=8.000000, rms=0.529 (0.032%), neg=0, invalid=96777 0338: dt=8.000000, rms=0.529 (0.034%), neg=0, invalid=96777 0339: dt=8.000000, rms=0.528 (0.031%), neg=0, invalid=96777 0340: dt=8.000000, rms=0.528 (0.032%), neg=0, invalid=96777 0341: dt=8.000000, rms=0.528 (0.027%), neg=0, invalid=96777 0342: dt=8.000000, rms=0.528 (0.020%), neg=0, invalid=96777 0343: dt=8.000000, rms=0.528 (0.023%), neg=0, invalid=96777 0344: dt=8.000000, rms=0.528 (0.021%), neg=0, invalid=96777 0345: dt=32.000000, rms=0.528 (0.017%), neg=0, invalid=96777 0346: dt=32.000000, rms=0.528 (-0.137%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.528, neg=0, invalid=96777 0347: dt=25.600000, rms=0.527 (0.159%), neg=0, invalid=96777 0348: dt=11.200000, rms=0.526 (0.115%), neg=0, invalid=96777 0349: dt=11.200000, rms=0.526 (0.052%), neg=0, invalid=96777 0350: dt=11.200000, rms=0.526 (0.037%), neg=0, invalid=96777 0351: dt=11.200000, rms=0.526 (0.027%), neg=0, invalid=96777 0352: dt=11.200000, rms=0.526 (0.042%), neg=0, invalid=96777 0353: dt=11.200000, rms=0.525 (0.042%), neg=0, invalid=96777 0354: dt=11.200000, rms=0.525 (0.041%), neg=0, invalid=96777 0355: dt=11.200000, rms=0.525 (0.020%), neg=0, invalid=96777 0356: dt=11.200000, rms=0.525 (0.007%), neg=0, invalid=96777 0357: dt=11.200000, rms=0.525 (0.011%), neg=0, invalid=96777 0358: dt=19.200000, rms=0.525 (0.033%), neg=0, invalid=96777 0359: dt=2.800000, rms=0.525 (0.005%), neg=0, invalid=96777 0360: dt=2.800000, rms=0.525 (-0.004%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.548, neg=0, invalid=96777 0361: dt=0.000000, rms=0.548 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.548, neg=0, invalid=96777 0362: dt=0.000000, rms=0.548 (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=0.594, neg=0, invalid=96777 0363: dt=1.436747, rms=0.588 (0.918%), neg=0, invalid=96777 0364: dt=0.320000, rms=0.588 (0.025%), neg=0, invalid=96777 0365: dt=0.320000, rms=0.588 (-0.010%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.588, neg=0, invalid=96777 0366: dt=0.500000, rms=0.588 (0.087%), neg=0, invalid=96777 0367: dt=0.384000, rms=0.588 (0.022%), neg=0, invalid=96777 0368: dt=0.384000, rms=0.588 (-0.006%), 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=0.540, neg=0, invalid=96777 0369: dt=0.170500, rms=0.532 (1.405%), neg=0, invalid=96777 0370: dt=0.143079, rms=0.528 (0.801%), neg=0, invalid=96777 0371: dt=0.126550, rms=0.525 (0.528%), neg=0, invalid=96777 0372: dt=0.118172, rms=0.523 (0.388%), neg=0, invalid=96777 0373: dt=0.112000, rms=0.522 (0.303%), neg=0, invalid=96777 0374: dt=0.112000, rms=0.521 (0.249%), neg=0, invalid=96777 0375: dt=0.112000, rms=0.519 (0.209%), neg=0, invalid=96777 0376: dt=0.320000, rms=0.517 (0.510%), neg=0, invalid=96777 0377: dt=0.005000, rms=0.517 (0.008%), neg=0, invalid=96777 0378: dt=0.005000, rms=0.517 (0.005%), neg=0, invalid=96777 0379: dt=0.005000, rms=0.517 (0.009%), neg=0, invalid=96777 0380: dt=0.005000, rms=0.517 (0.013%), neg=0, invalid=96777 0381: dt=0.005000, rms=0.517 (0.015%), neg=0, invalid=96777 0382: dt=0.005000, rms=0.516 (0.018%), neg=0, invalid=96777 0383: dt=0.005000, rms=0.516 (0.020%), neg=0, invalid=96777 0384: dt=0.005000, rms=0.516 (0.024%), neg=0, invalid=96777 0385: dt=0.005000, rms=0.516 (0.026%), neg=0, invalid=96777 0386: dt=0.005000, rms=0.516 (0.027%), neg=0, invalid=96777 0387: dt=0.005000, rms=0.516 (0.028%), neg=0, invalid=96777 0388: dt=0.005000, rms=0.516 (0.029%), neg=0, invalid=96777 0389: dt=0.005000, rms=0.515 (0.030%), neg=0, invalid=96777 0390: dt=0.005000, rms=0.515 (0.031%), neg=0, invalid=96777 0391: dt=0.005000, rms=0.515 (0.031%), neg=0, invalid=96777 0392: dt=0.005000, rms=0.515 (0.032%), neg=0, invalid=96777 0393: dt=0.005000, rms=0.515 (0.030%), neg=0, invalid=96777 0394: dt=0.005000, rms=0.515 (0.031%), neg=0, invalid=96777 0395: dt=0.005000, rms=0.515 (0.032%), neg=0, invalid=96777 0396: dt=0.005000, rms=0.514 (0.029%), neg=0, invalid=96777 0397: dt=0.005000, rms=0.514 (0.033%), neg=0, invalid=96777 0398: dt=0.005000, rms=0.514 (0.028%), neg=0, invalid=96777 0399: dt=0.005000, rms=0.514 (0.029%), neg=0, invalid=96777 0400: dt=0.005000, rms=0.514 (0.028%), neg=0, invalid=96777 0401: dt=0.005000, rms=0.514 (0.029%), neg=0, invalid=96777 0402: dt=0.005000, rms=0.513 (0.027%), neg=0, invalid=96777 0403: dt=0.005000, rms=0.513 (0.026%), neg=0, invalid=96777 0404: dt=0.005000, rms=0.513 (0.027%), neg=0, invalid=96777 0405: dt=0.005000, rms=0.513 (0.024%), neg=0, invalid=96777 0406: dt=0.005000, rms=0.513 (0.023%), neg=0, invalid=96777 0407: dt=0.112000, rms=0.513 (0.036%), neg=0, invalid=96777 0408: dt=0.112000, rms=0.513 (0.037%), neg=0, invalid=96777 0409: dt=0.112000, rms=0.512 (0.031%), neg=0, invalid=96777 0410: dt=0.014000, rms=0.512 (0.006%), neg=0, invalid=96777 0411: dt=0.014000, rms=0.512 (0.004%), neg=0, invalid=96777 0412: dt=0.014000, rms=0.512 (0.006%), neg=0, invalid=96777 0413: dt=0.014000, rms=0.512 (0.009%), neg=0, invalid=96777 0414: dt=0.014000, rms=0.512 (0.014%), neg=0, invalid=96777 0415: dt=0.014000, rms=0.512 (0.012%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.512, neg=0, invalid=96777 0416: dt=0.112000, rms=0.511 (0.316%), neg=0, invalid=96777 0417: dt=0.112000, rms=0.509 (0.243%), neg=0, invalid=96777 0418: dt=0.112000, rms=0.508 (0.177%), neg=0, invalid=96777 0419: dt=0.112000, rms=0.508 (0.144%), neg=0, invalid=96777 0420: dt=0.028000, rms=0.508 (0.033%), neg=0, invalid=96777 0421: dt=0.028000, rms=0.507 (0.023%), neg=0, invalid=96777 0422: dt=0.028000, rms=0.507 (0.047%), neg=0, invalid=96777 0423: dt=0.028000, rms=0.507 (0.068%), neg=0, invalid=96777 0424: dt=0.028000, rms=0.506 (0.077%), neg=0, invalid=96777 0425: dt=0.014000, rms=0.506 (0.006%), neg=0, invalid=96777 0426: dt=0.003500, rms=0.506 (0.003%), neg=0, invalid=96777 0427: dt=0.028000, rms=0.506 (0.015%), neg=0, invalid=96777 0428: dt=0.024000, rms=0.506 (0.012%), neg=0, invalid=96777 0429: dt=0.024000, rms=0.506 (0.011%), neg=0, invalid=96777 0430: dt=0.024000, rms=0.506 (0.012%), neg=0, invalid=96777 0431: dt=0.024000, rms=0.506 (0.022%), neg=0, invalid=96777 0432: dt=0.024000, rms=0.506 (0.024%), neg=0, invalid=96777 0433: dt=0.024000, rms=0.506 (0.033%), neg=0, invalid=96777 0434: dt=0.024000, rms=0.506 (0.039%), neg=0, invalid=96777 0435: dt=0.024000, rms=0.505 (0.044%), neg=0, invalid=96777 0436: dt=0.024000, rms=0.505 (0.037%), neg=0, invalid=96777 0437: dt=0.024000, rms=0.505 (0.040%), neg=0, invalid=96777 0438: dt=0.024000, rms=0.505 (0.040%), neg=0, invalid=96777 0439: dt=0.024000, rms=0.505 (0.032%), neg=0, invalid=96777 0440: dt=0.024000, rms=0.504 (0.031%), neg=0, invalid=96777 0441: dt=0.024000, rms=0.504 (0.030%), neg=0, invalid=96777 0442: dt=0.024000, rms=0.504 (0.028%), neg=0, invalid=96777 0443: dt=0.024000, rms=0.504 (0.013%), neg=0, invalid=96777 0444: dt=0.024000, rms=0.504 (0.014%), neg=0, invalid=96777 0445: dt=0.024000, rms=0.504 (0.012%), neg=0, invalid=96777 0446: dt=0.000000, rms=0.504 (0.002%), neg=0, invalid=96777 0447: dt=0.050000, rms=0.504 (-0.003%), neg=0, invalid=96777 label assignment complete, 0 changed (0.00%) ********************************************************************************************* ********************************************************************************************* ********************************************************************************************* ********************* ALLOWING NEGATIVE NODES IN DEFORMATION ******************************** ********************************************************************************************* ********************************************************************************************* ********************************************************************************************* **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.502, neg=0, invalid=96777 0448: dt=0.000000, rms=0.502 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.502, neg=0, invalid=96777 0449: dt=129.472000, rms=0.502 (0.051%), neg=0, invalid=96777 0450: dt=110.976000, rms=0.502 (0.014%), neg=0, invalid=96777 0451: dt=110.976000, rms=0.501 (0.006%), neg=0, invalid=96777 0452: dt=110.976000, rms=0.501 (0.043%), neg=0, invalid=96777 0453: dt=110.976000, rms=0.501 (0.015%), neg=0, invalid=96777 0454: dt=110.976000, rms=0.501 (0.003%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.501, neg=0, invalid=96777 0455: dt=36.288000, rms=0.500 (0.176%), neg=0, invalid=96777 0456: dt=36.288000, rms=0.500 (0.049%), neg=0, invalid=96777 0457: dt=36.288000, rms=0.500 (0.066%), neg=0, invalid=96777 0458: dt=36.288000, rms=0.500 (0.025%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0459: dt=36.288000, rms=0.500 (-0.060%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.500, neg=0, invalid=96777 0460: dt=103.680000, rms=0.498 (0.347%), neg=0, invalid=96777 0461: dt=36.288000, rms=0.497 (0.150%), neg=0, invalid=96777 0462: dt=36.288000, rms=0.497 (0.007%), neg=0, invalid=96777 0463: dt=36.288000, rms=0.497 (0.108%), neg=0, invalid=96777 0464: dt=36.288000, rms=0.496 (0.156%), neg=0, invalid=96777 0465: dt=36.288000, rms=0.495 (0.120%), neg=0, invalid=96777 0466: dt=36.288000, rms=0.495 (0.067%), neg=0, invalid=96777 0467: dt=25.920000, rms=0.495 (0.074%), neg=0, invalid=96777 0468: dt=15.552000, rms=0.495 (-0.002%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.495, neg=0, invalid=96777 iter 0, gcam->neg = 8 after 7 iterations, nbhd size=1, neg = 0 0469: dt=44.800000, rms=0.490 (0.886%), neg=0, invalid=96777 0470: dt=9.134752, rms=0.489 (0.310%), neg=0, invalid=96777 0471: dt=11.200000, rms=0.488 (0.204%), neg=0, invalid=96777 0472: dt=11.200000, rms=0.487 (0.183%), neg=0, invalid=96777 0473: dt=11.200000, rms=0.486 (0.292%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0474: dt=11.200000, rms=0.484 (0.306%), neg=0, invalid=96777 0475: dt=11.200000, rms=0.483 (0.316%), neg=0, invalid=96777 0476: dt=11.200000, rms=0.481 (0.300%), neg=0, invalid=96777 0477: dt=11.200000, rms=0.480 (0.251%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0478: dt=11.200000, rms=0.479 (0.193%), neg=0, invalid=96777 0479: dt=11.200000, rms=0.478 (0.202%), neg=0, invalid=96777 0480: dt=11.200000, rms=0.477 (0.201%), neg=0, invalid=96777 0481: dt=11.200000, rms=0.476 (0.179%), neg=0, invalid=96777 0482: dt=11.200000, rms=0.475 (0.190%), neg=0, invalid=96777 0483: dt=11.200000, rms=0.475 (0.158%), neg=0, invalid=96777 0484: dt=11.200000, rms=0.474 (0.167%), neg=0, invalid=96777 0485: dt=11.200000, rms=0.473 (0.145%), neg=0, invalid=96777 0486: dt=11.200000, rms=0.473 (0.118%), neg=0, invalid=96777 0487: dt=11.200000, rms=0.472 (0.088%), neg=0, invalid=96777 0488: dt=11.200000, rms=0.472 (0.025%), neg=0, invalid=96777 0489: dt=11.200000, rms=0.472 (0.035%), neg=0, invalid=96777 0490: dt=11.200000, rms=0.472 (0.025%), neg=0, invalid=96777 0491: dt=11.200000, rms=0.472 (0.040%), neg=0, invalid=96777 0492: dt=11.200000, rms=0.471 (0.033%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.471, neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0493: dt=44.800000, rms=0.469 (0.499%), neg=0, invalid=96777 0494: dt=7.306358, rms=0.468 (0.191%), neg=0, invalid=96777 0495: dt=7.306358, rms=0.468 (0.076%), neg=0, invalid=96777 0496: dt=7.306358, rms=0.467 (0.081%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0497: dt=7.306358, rms=0.467 (0.114%), neg=0, invalid=96777 iter 0, gcam->neg = 5 after 7 iterations, nbhd size=1, neg = 0 0498: dt=7.306358, rms=0.466 (0.101%), neg=0, invalid=96777 0499: dt=7.306358, rms=0.466 (0.093%), neg=0, invalid=96777 0500: dt=11.200000, rms=0.466 (0.033%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.472, neg=0, invalid=96777 iter 0, gcam->neg = 12 after 7 iterations, nbhd size=1, neg = 0 0501: dt=4.032000, rms=0.472 (0.096%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0502: dt=1.008000, rms=0.472 (0.008%), neg=0, invalid=96777 0503: dt=1.008000, rms=0.471 (0.016%), neg=0, invalid=96777 0504: dt=1.008000, rms=0.471 (0.020%), neg=0, invalid=96777 iter 0, gcam->neg = 6 after 7 iterations, nbhd size=1, neg = 0 0505: dt=1.008000, rms=0.471 (-0.005%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.471, neg=0, invalid=96777 iter 0, gcam->neg = 18 after 10 iterations, nbhd size=1, neg = 0 0506: dt=7.759657, rms=0.471 (0.171%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0507: dt=3.456000, rms=0.470 (0.026%), neg=0, invalid=96777 0508: dt=3.456000, rms=0.470 (0.074%), neg=0, invalid=96777 iter 0, gcam->neg = 24 after 16 iterations, nbhd size=2, neg = 0 0509: dt=3.456000, rms=0.470 (0.090%), neg=0, invalid=96777 iter 0, gcam->neg = 13 after 8 iterations, nbhd size=1, neg = 0 0510: dt=3.456000, rms=0.469 (0.075%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 7 iterations, nbhd size=1, neg = 0 0511: dt=3.456000, rms=0.469 (0.055%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.474, neg=0, invalid=96777 0512: dt=0.000000, rms=0.474 (-0.002%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.474, neg=0, invalid=96777 0513: dt=0.000000, rms=0.474 (0.000%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.466, neg=0, invalid=96777 iter 0, gcam->neg = 757 after 200 iterations, nbhd size=3, neg = 1 starting rms=0.006, neg=1, removing folds in lattice.... iter 1, dt=0.000039: new neg 0, old_neg 1, delta 1, rms=0.006 (10.584%) 0514: dt=2.001663, rms=0.422 (9.388%), neg=0, invalid=96777 0515: dt=0.000250, rms=0.422 (0.007%), neg=0, invalid=96777 0516: dt=0.000250, rms=0.422 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.422, neg=0, invalid=96777 0517: dt=0.000438, rms=0.422 (0.000%), neg=0, invalid=96777 0518: dt=0.000000, rms=0.422 (-0.000%), neg=0, invalid=96777 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.404, neg=0, invalid=96777 0519: dt=0.005645, rms=0.405 (-0.300%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.405, neg=0, invalid=96777 0520: dt=73.984000, rms=0.405 (0.014%), neg=0, invalid=96777 0521: dt=32.368000, rms=0.405 (0.001%), neg=0, invalid=96777 0522: dt=32.368000, rms=0.405 (0.000%), neg=0, invalid=96777 0523: dt=32.368000, rms=0.405 (-0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.405, neg=0, invalid=96777 0524: dt=0.972000, rms=0.405 (0.000%), neg=0, invalid=96777 0525: dt=0.002215, rms=0.405 (0.000%), neg=0, invalid=96777 0526: dt=0.002215, rms=0.405 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.405, neg=0, invalid=96777 0527: dt=36.288000, rms=0.405 (0.028%), neg=0, invalid=96777 0528: dt=82.944000, rms=0.405 (0.026%), neg=0, invalid=96777 0529: dt=82.944000, rms=0.405 (0.024%), neg=0, invalid=96777 0530: dt=82.944000, rms=0.405 (0.018%), neg=0, invalid=96777 0531: dt=82.944000, rms=0.405 (-0.006%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.405, neg=0, invalid=96777 iter 0, gcam->neg = 4 after 23 iterations, nbhd size=3, neg = 0 0532: dt=11.200000, rms=0.405 (0.075%), neg=0, invalid=96777 0533: dt=2.800000, rms=0.405 (0.006%), neg=0, invalid=96777 0534: dt=2.800000, rms=0.405 (0.016%), neg=0, invalid=96777 0535: dt=2.800000, rms=0.405 (0.024%), neg=0, invalid=96777 0536: dt=2.800000, rms=0.405 (0.020%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 26 iterations, nbhd size=4, neg = 0 0537: dt=2.800000, rms=0.405 (-0.022%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.405, neg=0, invalid=96777 iter 0, gcam->neg = 15 after 44 iterations, nbhd size=4, neg = 0 0538: dt=44.800000, rms=0.403 (0.349%), neg=0, invalid=96777 0539: dt=11.200000, rms=0.403 (0.042%), neg=0, invalid=96777 0540: dt=11.200000, rms=0.403 (0.106%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 200 iterations, nbhd size=1, neg = 1 starting rms=0.010, neg=1, removing folds in lattice.... iter 1, dt=0.000023: new neg 1, old_neg 1, delta 0, rms=0.003 (66.915%) iter 2, dt=0.000573: new neg 0, old_neg 1, delta 1, rms=0.003 (11.475%) 0541: dt=11.200000, rms=0.402 (0.138%), neg=0, invalid=96777 0542: dt=11.200000, rms=0.402 (0.057%), neg=0, invalid=96777 iter 0, gcam->neg = 5 after 200 iterations, nbhd size=1, neg = 1 starting rms=0.010, neg=1, removing folds in lattice.... iter 1, dt=0.000023: new neg 1, old_neg 1, delta 0, rms=0.003 (67.666%) iter 2, dt=0.000573: new neg 0, old_neg 1, delta 1, rms=0.003 (15.840%) 0543: dt=11.200000, rms=0.402 (0.091%), neg=0, invalid=96777 0544: dt=11.200000, rms=0.401 (0.052%), neg=0, invalid=96777 iter 0, gcam->neg = 18 after 200 iterations, nbhd size=2, neg = 2 starting rms=0.003, neg=2, removing folds in lattice.... iter 1, dt=0.000025: new neg 0, old_neg 2, delta 2, rms=0.003 (12.616%) 0545: dt=44.800000, rms=0.401 (0.138%), neg=0, invalid=96777 iter 0, gcam->neg = 26 after 200 iterations, nbhd size=1, neg = 2 starting rms=0.010, neg=2, removing folds in lattice.... iter 1, dt=0.000023: new neg 1, old_neg 2, delta 1, rms=0.004 (64.107%) iter 2, dt=0.000573: new neg 0, old_neg 1, delta 1, rms=0.003 (25.453%) 0546: dt=102.400000, rms=0.400 (0.105%), neg=0, invalid=96777 iter 0, gcam->neg = 210 after 200 iterations, nbhd size=2, neg = 6 starting rms=0.008, neg=6, removing folds in lattice.... iter 1, dt=0.000094: new neg 1, old_neg 6, delta 5, rms=0.004 (46.454%) iter 2, dt=0.000573: new neg 0, old_neg 1, delta 1, rms=0.004 (18.148%) 0547: dt=102.400000, rms=0.400 (-0.423%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.404, neg=0, invalid=96777 iter 0, gcam->neg = 18 after 21 iterations, nbhd size=2, neg = 0 0548: dt=4.032000, rms=0.403 (0.140%), neg=0, invalid=96777 0549: dt=0.063000, rms=0.403 (0.000%), neg=0, invalid=96777 0550: dt=0.063000, rms=0.403 (0.002%), neg=0, invalid=96777 0551: dt=0.063000, rms=0.403 (0.003%), neg=0, invalid=96777 0552: dt=0.063000, rms=0.403 (0.005%), neg=0, invalid=96777 0553: dt=0.063000, rms=0.403 (0.006%), neg=0, invalid=96777 0554: dt=0.063000, rms=0.403 (0.006%), neg=0, invalid=96777 0555: dt=0.063000, rms=0.403 (0.007%), neg=0, invalid=96777 0556: dt=0.063000, rms=0.403 (0.008%), neg=0, invalid=96777 0557: dt=0.063000, rms=0.403 (0.008%), neg=0, invalid=96777 0558: dt=0.063000, rms=0.403 (0.009%), neg=0, invalid=96777 0559: dt=0.063000, rms=0.403 (0.009%), neg=0, invalid=96777 0560: dt=0.063000, rms=0.403 (0.008%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.403, neg=0, invalid=96777 iter 0, gcam->neg = 35 after 31 iterations, nbhd size=3, neg = 0 0561: dt=9.216000, rms=0.402 (0.284%), neg=0, invalid=96777 0562: dt=0.009000, rms=0.402 (0.000%), neg=0, invalid=96777 0563: dt=0.009000, rms=0.402 (0.000%), neg=0, invalid=96777 0564: dt=0.009000, rms=0.402 (0.000%), neg=0, invalid=96777 0565: dt=0.009000, rms=0.402 (0.000%), neg=0, invalid=96777 0566: dt=0.009000, rms=0.402 (0.000%), neg=0, invalid=96777 0567: dt=0.009000, rms=0.402 (0.000%), neg=0, invalid=96777 0568: dt=0.009000, rms=0.402 (0.000%), neg=0, invalid=96777 0569: dt=0.009000, rms=0.402 (0.001%), neg=0, invalid=96777 0570: dt=0.009000, rms=0.402 (0.001%), neg=0, invalid=96777 0571: dt=0.009000, rms=0.402 (0.001%), neg=0, invalid=96777 0572: dt=0.009000, rms=0.402 (0.001%), neg=0, invalid=96777 0573: dt=0.009000, rms=0.402 (0.001%), neg=0, invalid=96777 0574: dt=0.009000, rms=0.402 (0.001%), neg=0, invalid=96777 0575: dt=0.009000, rms=0.402 (0.001%), neg=0, invalid=96777 0576: dt=0.009000, rms=0.402 (0.001%), neg=0, invalid=96777 0577: dt=0.009000, rms=0.402 (0.001%), neg=0, invalid=96777 0578: dt=0.009000, rms=0.402 (0.002%), neg=0, invalid=96777 0579: dt=0.009000, rms=0.402 (0.002%), neg=0, invalid=96777 0580: dt=0.009000, rms=0.402 (0.002%), neg=0, invalid=96777 0581: dt=0.009000, rms=0.402 (0.002%), neg=0, invalid=96777 0582: dt=0.009000, rms=0.402 (0.002%), neg=0, invalid=96777 0583: dt=0.009000, rms=0.402 (0.002%), neg=0, invalid=96777 0584: dt=0.009000, rms=0.402 (0.002%), neg=0, invalid=96777 0585: dt=0.009000, rms=0.402 (0.002%), neg=0, invalid=96777 0586: dt=0.009000, rms=0.402 (0.002%), neg=0, invalid=96777 0587: dt=0.009000, rms=0.402 (0.002%), neg=0, invalid=96777 0588: dt=0.009000, rms=0.402 (0.002%), neg=0, invalid=96777 0589: dt=0.009000, rms=0.402 (0.002%), neg=0, invalid=96777 0590: dt=0.009000, rms=0.402 (0.002%), neg=0, invalid=96777 0591: dt=0.009000, rms=0.402 (0.002%), neg=0, invalid=96777 0592: dt=0.009000, rms=0.402 (0.002%), neg=0, invalid=96777 0593: dt=0.009000, rms=0.402 (0.002%), neg=0, invalid=96777 0594: dt=0.009000, rms=0.402 (0.002%), neg=0, invalid=96777 0595: dt=0.009000, rms=0.402 (0.002%), neg=0, invalid=96777 0596: dt=0.009000, rms=0.402 (0.002%), neg=0, invalid=96777 0597: dt=0.009000, rms=0.402 (0.002%), neg=0, invalid=96777 0598: dt=0.009000, rms=0.402 (0.002%), neg=0, invalid=96777 iter 0, gcam->neg = 60 after 38 iterations, nbhd size=4, neg = 0 0599: dt=11.520000, rms=0.401 (0.128%), neg=0, invalid=96777 0600: dt=0.002250, rms=0.401 (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=0.408, neg=0, invalid=96777 0601: dt=0.000250, rms=0.408 (0.000%), neg=0, invalid=96777 0602: dt=0.000000, rms=0.408 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.408, neg=0, invalid=96777 0603: dt=0.000000, rms=0.408 (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=0.397, neg=0, invalid=96777 iter 0, gcam->neg = 442 after 46 iterations, nbhd size=4, neg = 0 0604: dt=0.768000, rms=0.384 (3.140%), neg=0, invalid=96777 0605: dt=0.000020, rms=0.384 (0.001%), neg=0, invalid=96777 0606: dt=0.000020, rms=0.384 (0.001%), neg=0, invalid=96777 0607: dt=0.000020, rms=0.384 (0.001%), neg=0, invalid=96777 0608: dt=0.000020, rms=0.384 (0.000%), neg=0, invalid=96777 0609: dt=0.000109, rms=0.384 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.384, neg=0, invalid=96777 0610: dt=0.000438, rms=0.384 (0.000%), neg=0, invalid=96777 0611: dt=0.001750, rms=0.384 (0.000%), neg=0, invalid=96777 0612: dt=0.001750, rms=0.384 (0.001%), neg=0, invalid=96777 0613: dt=0.001750, rms=0.384 (0.001%), neg=0, invalid=96777 0614: dt=0.001750, rms=0.384 (0.002%), neg=0, invalid=96777 0615: dt=0.001750, rms=0.384 (0.003%), neg=0, invalid=96777 0616: dt=0.001750, rms=0.384 (0.003%), neg=0, invalid=96777 0617: dt=0.001750, rms=0.384 (0.004%), neg=0, invalid=96777 0618: dt=0.001750, rms=0.384 (0.004%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0619: dt=0.001750, rms=0.384 (0.004%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0620: dt=0.001750, rms=0.384 (0.004%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0621: dt=0.001750, rms=0.384 (0.004%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0622: dt=0.001750, rms=0.384 (0.005%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 5 iterations, nbhd size=1, neg = 0 0623: dt=0.001750, rms=0.384 (0.005%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 5 iterations, nbhd size=1, neg = 0 0624: dt=0.001750, rms=0.384 (0.005%), neg=0, invalid=96777 writing output transformation to transforms/talairach.m3z... GCAMwrite registration took 4 hours, 15 minutes and 50 seconds. #-------------------------------------- #@# CA Reg Inv Thu Aug 8 16:23:18 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 16:24:42 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... 10751868 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 1 minutes and 26 seconds. #-------------------------------------- #@# SkullLTA Thu Aug 8 16:26:08 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=8.0 skull bounding box = (41, 16, 0) --> (210, 203, 194) using (97, 78, 97) as brain centroid... mean wm in atlas = 126, using box (76,55,73) --> (117, 101,120) to find MRI wm before smoothing, mri peak at 109 after smoothing, mri peak at 109, scaling input intensities by 1.156 scaling channel 0 by 1.15596 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.9, old_max_log_p =-4.1 (thresh=-4.0) 1.032 0.030 -0.117 3.863; 0.001 1.081 0.289 -14.239; 0.113 -0.261 0.972 16.306; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.032 0.030 -0.117 3.863; 0.001 1.081 0.289 -14.239; 0.113 -0.261 0.972 16.306; 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=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.032 0.030 -0.117 3.863; 0.001 1.041 0.278 -9.164; 0.113 -0.261 0.972 16.306; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.032 0.030 -0.117 3.863; 0.001 1.041 0.278 -9.164; 0.113 -0.261 0.972 16.306; 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=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.034 0.036 -0.107 1.460; -0.006 1.037 0.295 -9.760; 0.105 -0.278 0.965 19.749; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.034 0.036 -0.107 1.460; -0.006 1.036 0.295 -9.606; 0.105 -0.277 0.964 19.850; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.034 0.036 -0.107 1.460; -0.006 1.036 0.295 -9.606; 0.105 -0.277 0.964 19.850; 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 1.03373 0.03636 -0.10679 1.46017; -0.00558 1.03607 0.29492 -9.60604; 0.10453 -0.27718 0.96387 19.85009; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.03373 0.03636 -0.10679 1.46017; -0.00558 1.03607 0.29492 -9.60604; 0.10453 -0.27718 0.96387 19.85009; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.034 0.036 -0.107 1.460; -0.006 1.036 0.295 -9.606; 0.105 -0.277 0.964 19.850; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.9 (old=-4.1) transform before final EM align: 1.034 0.036 -0.107 1.460; -0.006 1.036 0.295 -9.606; 0.105 -0.277 0.964 19.850; 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 1.03373 0.03636 -0.10679 1.46017; -0.00558 1.03607 0.29492 -9.60604; 0.10453 -0.27718 0.96387 19.85009; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.03373 0.03636 -0.10679 1.46017; -0.00558 1.03607 0.29492 -9.60604; 0.10453 -0.27718 0.96387 19.85009; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = 4.3 tol 0.000000 final transform: 1.034 0.036 -0.107 1.460; -0.006 1.036 0.295 -9.606; 0.105 -0.277 0.964 19.850; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull_2.lta... registration took 37 minutes and 49 seconds. #-------------------------------------- #@# SubCort Seg Thu Aug 8 17:03:57 CEST 2013 mri_ca_label -align norm.mgz transforms/talairach.m3z /opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz sysname Linux hostname snake6 machine x86_64 setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 = 0.09989 (11) Left_Lateral_Ventricle (4): linear fit = 0.38 x + 0.0 (2756 voxels, overlap=0.007) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (2756 voxels, peak = 10), gca=10.8 gca peak = 0.14982 (20) mri peak = 0.12652 (10) Right_Lateral_Ventricle (43): linear fit = 0.35 x + 0.0 (1226 voxels, overlap=0.007) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (1226 voxels, peak = 7), gca=8.0 gca peak = 0.28003 (97) mri peak = 0.09471 (90) Right_Pallidum (52): linear fit = 0.88 x + 0.0 (353 voxels, overlap=0.049) Right_Pallidum (52): linear fit = 0.88 x + 0.0 (353 voxels, peak = 86), gca=85.8 gca peak = 0.18160 (96) mri peak = 0.08256 (87) Left_Pallidum (13): linear fit = 0.88 x + 0.0 (379 voxels, overlap=0.084) Left_Pallidum (13): linear fit = 0.88 x + 0.0 (379 voxels, peak = 84), gca=84.0 gca peak = 0.27536 (62) mri peak = 0.09570 (56) Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (578 voxels, overlap=0.631) Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (578 voxels, peak = 55), gca=54.9 gca peak = 0.32745 (63) mri peak = 0.07680 (59) Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (607 voxels, overlap=0.786) Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (607 voxels, peak = 58), gca=58.3 gca peak = 0.08597 (105) mri peak = 0.06944 (109) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (46078 voxels, overlap=0.701) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (46078 voxels, peak = 109), gca=108.7 gca peak = 0.09209 (106) mri peak = 0.07869 (109) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (48429 voxels, overlap=0.613) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (48429 voxels, peak = 111), gca=110.8 gca peak = 0.07826 (63) mri peak = 0.05008 (50) Left_Cerebral_Cortex (3): linear fit = 0.80 x + 0.0 (17863 voxels, overlap=0.236) Left_Cerebral_Cortex (3): linear fit = 0.80 x + 0.0 (17863 voxels, peak = 50), gca=50.1 gca peak = 0.08598 (64) mri peak = 0.05013 (51) Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (16328 voxels, overlap=0.347) Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (16328 voxels, peak = 53), gca=52.8 gca peak = 0.24164 (71) mri peak = 0.10371 (66) Right_Caudate (50): linear fit = 0.90 x + 0.0 (914 voxels, overlap=0.428) Right_Caudate (50): linear fit = 0.90 x + 0.0 (914 voxels, peak = 64), gca=64.3 gca peak = 0.18227 (75) mri peak = 0.08705 (68) Left_Caudate (11): linear fit = 0.87 x + 0.0 (966 voxels, overlap=0.149) Left_Caudate (11): linear fit = 0.87 x + 0.0 (966 voxels, peak = 65), gca=64.9 gca peak = 0.10629 (62) mri peak = 0.04937 (57) Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (11432 voxels, overlap=0.971) Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (11432 voxels, peak = 60), gca=59.8 gca peak = 0.11668 (59) mri peak = 0.04903 (57) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (8595 voxels, overlap=0.987) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (8595 voxels, peak = 57), gca=56.9 gca peak = 0.17849 (88) mri peak = 0.08428 (87) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5743 voxels, overlap=0.990) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5743 voxels, peak = 88), gca=87.6 gca peak = 0.16819 (86) mri peak = 0.07910 (89) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (5090 voxels, overlap=0.973) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (5090 voxels, peak = 88), gca=88.2 gca peak = 0.41688 (64) mri peak = 0.09510 (58) Left_Amygdala (18): linear fit = 0.88 x + 0.0 (350 voxels, overlap=1.040) Left_Amygdala (18): linear fit = 0.88 x + 0.0 (350 voxels, peak = 57), gca=56.6 gca peak = 0.42394 (62) mri peak = 0.08621 (57) Right_Amygdala (54): linear fit = 0.90 x + 0.0 (247 voxels, overlap=1.040) Right_Amygdala (54): linear fit = 0.90 x + 0.0 (247 voxels, peak = 56), gca=56.1 gca peak = 0.10041 (96) mri peak = 0.07499 (89) Left_Thalamus_Proper (10): linear fit = 0.94 x + 0.0 (3945 voxels, overlap=0.713) Left_Thalamus_Proper (10): linear fit = 0.94 x + 0.0 (3945 voxels, peak = 90), gca=89.8 gca peak = 0.13978 (88) mri peak = 0.07177 (87) Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (3802 voxels, overlap=0.887) Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (3802 voxels, peak = 86), gca=85.8 gca peak = 0.08514 (81) mri peak = 0.07651 (72) Left_Putamen (12): linear fit = 0.87 x + 0.0 (1749 voxels, overlap=0.342) Left_Putamen (12): linear fit = 0.87 x + 0.0 (1749 voxels, peak = 70), gca=70.1 gca peak = 0.09624 (82) mri peak = 0.07106 (75) Right_Putamen (51): linear fit = 0.87 x + 0.0 (1944 voxels, overlap=0.377) Right_Putamen (51): linear fit = 0.87 x + 0.0 (1944 voxels, peak = 71), gca=70.9 gca peak = 0.07543 (88) mri peak = 0.06908 (87) Brain_Stem (16): linear fit = 1.01 x + 0.0 (11648 voxels, overlap=0.765) Brain_Stem (16): linear fit = 1.01 x + 0.0 (11648 voxels, peak = 89), gca=89.3 gca peak = 0.12757 (95) mri peak = 0.06821 (93) Right_VentralDC (60): linear fit = 0.99 x + 0.0 (988 voxels, overlap=0.883) Right_VentralDC (60): linear fit = 0.99 x + 0.0 (988 voxels, peak = 94), gca=93.6 gca peak = 0.17004 (92) mri peak = 0.07131 (90) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1269 voxels, overlap=0.905) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1269 voxels, peak = 91), gca=90.6 gca peak = 0.21361 (36) mri peak = 0.08855 (12) gca peak = 0.26069 (23) mri peak = 0.12416 ( 8) Fourth_Ventricle (15): linear fit = 0.31 x + 0.0 (297 voxels, overlap=0.027) Fourth_Ventricle (15): linear fit = 0.31 x + 0.0 (297 voxels, peak = 7), gca=7.0 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak Third_Ventricle = 0.21361 (36) gca peak Fourth_Ventricle = 0.26069 (23) gca peak CSF = 0.14367 (38) gca peak Left_Accumbens_area = 0.57033 (70) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65201 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.31129 (32) gca peak Right_Accumbens_area = 0.30219 (72) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.72939 (42) gca peak WM_hypointensities = 0.14821 (82) gca peak non_WM_hypointensities = 0.10354 (53) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means estimating mean gm scale to be 0.87 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 0.40 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.31600 (11) mri peak = 0.09989 (11) Left_Lateral_Ventricle (4): linear fit = 1.04 x + 0.0 (2756 voxels, overlap=0.988) Left_Lateral_Ventricle (4): linear fit = 1.04 x + 0.0 (2756 voxels, peak = 11), gca=11.5 gca peak = 0.29325 ( 9) mri peak = 0.12652 (10) Right_Lateral_Ventricle (43): linear fit = 1.05 x + 0.0 (1226 voxels, overlap=0.968) Right_Lateral_Ventricle (43): linear fit = 1.05 x + 0.0 (1226 voxels, peak = 9), gca=9.5 gca peak = 0.26036 (86) mri peak = 0.09471 (90) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (353 voxels, overlap=1.015) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (353 voxels, peak = 85), gca=84.7 gca peak = 0.18878 (84) mri peak = 0.08256 (87) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (379 voxels, overlap=1.018) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (379 voxels, peak = 84), gca=84.0 gca peak = 0.31426 (55) mri peak = 0.09570 (56) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (578 voxels, overlap=1.008) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (578 voxels, peak = 55), gca=55.0 gca peak = 0.30737 (58) mri peak = 0.07680 (59) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (607 voxels, overlap=1.005) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (607 voxels, peak = 58), gca=58.0 gca peak = 0.08268 (109) mri peak = 0.06944 (109) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (46078 voxels, overlap=0.809) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (46078 voxels, peak = 109), gca=109.0 gca peak = 0.08584 (111) mri peak = 0.07869 (109) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (48429 voxels, overlap=0.753) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (48429 voxels, peak = 111), gca=111.0 gca peak = 0.09726 (50) mri peak = 0.05008 (50) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (17863 voxels, overlap=0.990) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (17863 voxels, peak = 49), gca=49.2 gca peak = 0.10559 (53) mri peak = 0.05013 (51) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (16328 voxels, overlap=0.986) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (16328 voxels, peak = 53), gca=53.0 gca peak = 0.24091 (64) mri peak = 0.10371 (66) Right_Caudate (50): linear fit = 1.00 x + 0.0 (914 voxels, overlap=1.004) Right_Caudate (50): linear fit = 1.00 x + 0.0 (914 voxels, peak = 64), gca=64.0 gca peak = 0.16577 (65) mri peak = 0.08705 (68) Left_Caudate (11): linear fit = 1.00 x + 0.0 (966 voxels, overlap=0.991) Left_Caudate (11): linear fit = 1.00 x + 0.0 (966 voxels, peak = 65), gca=65.0 gca peak = 0.10996 (60) mri peak = 0.04937 (57) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (11432 voxels, overlap=0.999) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (11432 voxels, peak = 59), gca=59.1 gca peak = 0.12346 (58) mri peak = 0.04903 (57) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (8595 voxels, overlap=1.000) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (8595 voxels, peak = 59), gca=59.4 gca peak = 0.18530 (87) mri peak = 0.08428 (87) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5743 voxels, overlap=0.987) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5743 voxels, peak = 87), gca=86.6 gca peak = 0.14595 (89) mri peak = 0.07910 (89) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5090 voxels, overlap=0.996) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5090 voxels, peak = 89), gca=88.6 gca peak = 0.31177 (57) mri peak = 0.09510 (58) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (350 voxels, overlap=1.032) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (350 voxels, peak = 57), gca=57.0 gca peak = 0.43549 (57) mri peak = 0.08621 (57) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (247 voxels, overlap=1.032) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (247 voxels, peak = 57), gca=57.0 gca peak = 0.11773 (90) mri peak = 0.07499 (89) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3945 voxels, overlap=0.968) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3945 voxels, peak = 90), gca=89.6 gca peak = 0.11840 (83) mri peak = 0.07177 (87) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3802 voxels, overlap=0.968) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3802 voxels, peak = 83), gca=82.6 gca peak = 0.09485 (74) mri peak = 0.07651 (72) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1749 voxels, overlap=1.001) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1749 voxels, peak = 74), gca=74.0 gca peak = 0.09818 (66) mri peak = 0.07106 (75) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1944 voxels, overlap=1.001) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1944 voxels, peak = 65), gca=65.0 gca peak = 0.07609 (87) mri peak = 0.06908 (87) Brain_Stem (16): linear fit = 1.00 x + 0.0 (11648 voxels, overlap=0.797) Brain_Stem (16): linear fit = 1.00 x + 0.0 (11648 voxels, peak = 87), gca=86.6 gca peak = 0.13957 (93) mri peak = 0.06821 (93) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (988 voxels, overlap=0.878) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (988 voxels, peak = 94), gca=94.4 gca peak = 0.16991 (91) mri peak = 0.07131 (90) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1269 voxels, overlap=0.921) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1269 voxels, peak = 91), gca=90.5 gca peak = 0.35640 (14) mri peak = 0.08855 (12) gca peak = 0.33827 ( 9) mri peak = 0.12416 ( 8) Fourth_Ventricle (15): linear fit = 1.05 x + 0.0 (297 voxels, overlap=0.932) Fourth_Ventricle (15): linear fit = 1.05 x + 0.0 (297 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 = 0.44858 (60) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.62149 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.33369 (28) gca peak Right_Accumbens_area = 0.35953 (65) gca peak Right_vessel = 0.57697 (60) gca peak Right_choroid_plexus = 0.10381 (48) gca peak Fifth_Ventricle = 0.45329 (19) gca peak WM_hypointensities = 0.16968 (85) gca peak non_WM_hypointensities = 0.11242 (55) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.05 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 14278 gm and wm labels changed (%10 to gray, %90 to white out of all changed labels) 284 hippocampal voxels changed. 6 amygdala voxels changed. pass 1: 98947 changed. image ll: -2.247, PF=1.000 pass 2: 18221 changed. image ll: -2.244, PF=1.000 pass 3: 6753 changed. pass 4: 3188 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 18 minutes and 11 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/cc_up.lta sub011 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/sub011/mri/transforms/cc_up.lta reading aseg from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/aseg.auto_noCCseg.mgz reading norm from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/norm.mgz 66835 voxels in left wm, 149031 in right wm, xrange [112, 135] searching rotation angles z=[-9 5], y=[-14 0] searching scale 1 Z rot -9.5 searching scale 1 Z rot -9.2 searching scale 1 Z rot -9.0 searching scale 1 Z rot -8.7 searching scale 1 Z rot -8.5 searching scale 1 Z rot -8.2 searching scale 1 Z rot -8.0 searching scale 1 Z rot -7.7 searching scale 1 Z rot -7.5 searching scale 1 Z rot -7.2 searching scale 1 Z rot -7.0 searching scale 1 Z rot -6.7 searching scale 1 Z rot -6.5 searching scale 1 Z rot -6.2 searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.7 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.2 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.2 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.2 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.2 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.2 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.0 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.3 searching scale 1 Z rot 4.5 searching scale 1 Z rot 4.8 global minimum found at slice 127.0, rotations (-7.01, -2.00) final transformation (x=127.0, yr=-7.012, zr=-1.998): 0.992 0.035 -0.122 11.106; -0.035 0.999 0.004 53.030; 0.122 0.000 0.993 16.222; 0.000 0.000 0.000 1.000; updating x range to be [125, 130] in xformed coordinates best xformed slice 128 cc center is found at 128 155 117 eigenvectors: 0.000 0.000 1.000; -0.179 -0.984 0.000; 0.984 -0.179 0.000; error in mid anterior detected - correcting... writing aseg with callosum to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/aseg.auto.mgz... corpus callosum matter segmentation took 3.3 minutes #-------------------------------------- #@# Merge ASeg Thu Aug 8 17:25:25 CEST 2013 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Thu Aug 8 17:25:25 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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... 1794 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 109 gm peak at 56 (56), valley at 23 (23) csf peak at 28, setting threshold to 46 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 58 (58), valley at 24 (24) csf peak at 29, setting threshold to 48 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 4 minutes and 18 seconds. #-------------------------------------------- #@# Mask BFS Thu Aug 8 17:29:44 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1798706 voxels in mask (pct= 10.72) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Thu Aug 8 17:29:46 CEST 2013 mri_segment brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (107.0): 107.2 +- 4.6 [80.0 --> 125.0] GM (68.0) : 66.7 +- 9.7 [30.0 --> 96.0] setting bottom of white matter range to 76.5 setting top of gray matter range to 86.2 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 6816 sparsely connected voxels removed... thickening thin strands.... 20 segments, 6489 filled 859 bright non-wm voxels segmented. 3959 diagonally connected voxels added... white matter segmentation took 1.8 minutes writing output to wm.seg.mgz... mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.64 minutes reading wm segmentation from wm.seg.mgz... 88 voxels added to wm to prevent paths from MTL structures to cortex 1313 additional wm voxels added 0 additional wm voxels added SEG EDIT: 63908 voxels turned on, 41859 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 0 new 0 115,126,128 old 0 new 0 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 17 found - 17 modified | TOTAL: 17 pass 2 (xy+): 0 found - 17 modified | TOTAL: 17 pass 1 (xy-): 17 found - 17 modified | TOTAL: 34 pass 2 (xy-): 0 found - 17 modified | TOTAL: 34 pass 1 (yz+): 26 found - 26 modified | TOTAL: 60 pass 2 (yz+): 0 found - 26 modified | TOTAL: 60 pass 1 (yz-): 23 found - 23 modified | TOTAL: 83 pass 2 (yz-): 0 found - 23 modified | TOTAL: 83 pass 1 (xz+): 26 found - 26 modified | TOTAL: 109 pass 2 (xz+): 0 found - 26 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 (+++): 8 found - 8 modified | TOTAL: 8 pass 2 (+++): 0 found - 8 modified | TOTAL: 8 pass 1 (+++): 21 found - 21 modified | TOTAL: 29 pass 2 (+++): 0 found - 21 modified | TOTAL: 29 pass 1 (+++): 10 found - 10 modified | TOTAL: 39 pass 2 (+++): 0 found - 10 modified | TOTAL: 39 pass 1 (+++): 19 found - 19 modified | TOTAL: 58 pass 2 (+++): 0 found - 19 modified | TOTAL: 58 Iteration Number : 1 pass 1 (++): 202 found - 202 modified | TOTAL: 202 pass 2 (++): 0 found - 202 modified | TOTAL: 202 pass 1 (+-): 157 found - 157 modified | TOTAL: 359 pass 2 (+-): 0 found - 157 modified | TOTAL: 359 pass 1 (--): 173 found - 173 modified | TOTAL: 532 pass 2 (--): 0 found - 173 modified | TOTAL: 532 pass 1 (-+): 157 found - 157 modified | TOTAL: 689 pass 2 (-+): 0 found - 157 modified | TOTAL: 689 Iteration Number : 2 pass 1 (xy+): 5 found - 5 modified | TOTAL: 5 pass 2 (xy+): 0 found - 5 modified | TOTAL: 5 pass 1 (xy-): 6 found - 6 modified | TOTAL: 11 pass 2 (xy-): 0 found - 6 modified | TOTAL: 11 pass 1 (yz+): 4 found - 4 modified | TOTAL: 15 pass 2 (yz+): 0 found - 4 modified | TOTAL: 15 pass 1 (yz-): 2 found - 2 modified | TOTAL: 17 pass 2 (yz-): 0 found - 2 modified | TOTAL: 17 pass 1 (xz+): 4 found - 4 modified | TOTAL: 21 pass 2 (xz+): 0 found - 4 modified | TOTAL: 21 pass 1 (xz-): 12 found - 12 modified | TOTAL: 33 pass 2 (xz-): 0 found - 12 modified | TOTAL: 33 Iteration Number : 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 4 pass 2 (+++): 0 found - 2 modified | TOTAL: 4 Iteration Number : 2 pass 1 (++): 2 found - 2 modified | TOTAL: 2 pass 2 (++): 0 found - 2 modified | TOTAL: 2 pass 1 (+-): 1 found - 1 modified | TOTAL: 3 pass 2 (+-): 0 found - 1 modified | TOTAL: 3 pass 1 (--): 5 found - 5 modified | TOTAL: 8 pass 2 (--): 0 found - 5 modified | TOTAL: 8 pass 1 (-+): 2 found - 2 modified | TOTAL: 10 pass 2 (-+): 0 found - 2 modified | TOTAL: 10 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-): 2 found - 2 modified | TOTAL: 2 pass 2 (yz-): 0 found - 2 modified | TOTAL: 2 pass 1 (xz+): 1 found - 1 modified | TOTAL: 3 pass 2 (xz+): 0 found - 1 modified | TOTAL: 3 pass 1 (xz-): 0 found - 0 modified | TOTAL: 3 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 (--): 3 found - 3 modified | TOTAL: 3 pass 2 (--): 0 found - 3 modified | TOTAL: 3 pass 1 (-+): 0 found - 0 modified | TOTAL: 3 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 933 (out of 649256: 0.143703) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Thu Aug 8 17:32:21 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 1.032 0.030 -0.117 3.863; 0.001 1.081 0.289 -14.239; 0.106 -0.243 0.904 22.566; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.032 0.030 -0.117 3.863; 0.001 1.081 0.289 -14.239; 0.106 -0.243 0.904 22.566; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1559 (min = 350, max = 1400), aspect = 0.47 (min = 0.10, max = 0.75) need search nearby using seed (127, 119, 155), TAL = (1.0, 27.0, 9.0) talairach voxel to voxel transform 0.957 0.001 0.123 -6.466; 0.027 0.863 -0.272 18.327; -0.104 0.232 1.018 -19.274; 0.000 0.000 0.000 1.000; segmentation indicates cc at (127, 119, 155) --> (1.0, 27.0, 9.0) done. writing output to filled.mgz... filling took 0.9 minutes talairach cc position changed to (1.00, 27.00, 9.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(19.00, 27.00, 9.00) SRC: (117.08, 81.75, 154.75) search lh wm seed point around talairach space (-17.00, 27.00, 9.00), SRC: (151.52, 82.72, 150.99) 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 17:33:17 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 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-): 5 found - 5 modified | TOTAL: 14 pass 2 (yz-): 0 found - 5 modified | TOTAL: 14 pass 1 (xz+): 0 found - 0 modified | TOTAL: 14 pass 1 (xz-): 3 found - 3 modified | TOTAL: 17 pass 2 (xz-): 0 found - 3 modified | TOTAL: 17 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 (++): 6 found - 6 modified | TOTAL: 6 pass 2 (++): 0 found - 6 modified | TOTAL: 6 pass 1 (+-): 1 found - 1 modified | TOTAL: 7 pass 2 (+-): 0 found - 1 modified | TOTAL: 7 pass 1 (--): 0 found - 0 modified | TOTAL: 7 pass 1 (-+): 1 found - 1 modified | TOTAL: 8 pass 2 (-+): 0 found - 1 modified | TOTAL: 8 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 = 25 (out of 315607: 0.007921) 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: 2005 vertices, 2154 faces slice 40: 11569 vertices, 11951 faces slice 50: 23411 vertices, 23864 faces slice 60: 36580 vertices, 36993 faces slice 70: 49105 vertices, 49506 faces slice 80: 61274 vertices, 61684 faces slice 90: 74008 vertices, 74419 faces slice 100: 85915 vertices, 86313 faces slice 110: 97610 vertices, 98021 faces slice 120: 108997 vertices, 109389 faces slice 130: 120046 vertices, 120460 faces slice 140: 129736 vertices, 130074 faces slice 150: 138007 vertices, 138311 faces slice 160: 144626 vertices, 144879 faces slice 170: 150573 vertices, 150787 faces slice 180: 155773 vertices, 155979 faces slice 190: 159365 vertices, 159483 faces slice 200: 159812 vertices, 159848 faces slice 210: 159812 vertices, 159848 faces slice 220: 159812 vertices, 159848 faces slice 230: 159812 vertices, 159848 faces slice 240: 159812 vertices, 159848 faces slice 250: 159812 vertices, 159848 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... 159812 voxel in cpt #1: X=-36 [v=159812,e=479544,f=319696] located at (-26.925438, -30.900133, 37.848133) For the whole surface: X=-36 [v=159812,e=479544,f=319696] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Thu Aug 8 17:33:24 CEST 2013 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 17:33:29 CEST 2013 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts avg radius = 51.1 mm, total surface area = 83945 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.6 minutes Not saving sulc step 000: RMS=0.100 (target=0.015) step 005: RMS=0.073 (target=0.015) step 010: RMS=0.053 (target=0.015) step 015: RMS=0.043 (target=0.015) step 020: RMS=0.037 (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=0.023 (target=0.015) step 045: RMS=0.022 (target=0.015) step 050: RMS=0.021 (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 17:34:07 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 0.90 +- 0.54 (0.00-->7.98) (max @ vno 110943 --> 110944) face area 0.02 +- 0.03 (-0.12-->0.52) scaling brain by 0.293... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.860, avgs=0 005/300: dt: 0.9000, rms radial error=175.611, avgs=0 010/300: dt: 0.9000, rms radial error=175.075, avgs=0 015/300: dt: 0.9000, rms radial error=174.368, avgs=0 020/300: dt: 0.9000, rms radial error=173.560, avgs=0 025/300: dt: 0.9000, rms radial error=172.693, avgs=0 030/300: dt: 0.9000, rms radial error=171.793, avgs=0 035/300: dt: 0.9000, rms radial error=170.857, avgs=0 040/300: dt: 0.9000, rms radial error=169.913, avgs=0 045/300: dt: 0.9000, rms radial error=168.967, avgs=0 050/300: dt: 0.9000, rms radial error=168.021, avgs=0 055/300: dt: 0.9000, rms radial error=167.080, avgs=0 060/300: dt: 0.9000, rms radial error=166.143, avgs=0 065/300: dt: 0.9000, rms radial error=165.211, avgs=0 070/300: dt: 0.9000, rms radial error=164.284, avgs=0 075/300: dt: 0.9000, rms radial error=163.362, avgs=0 080/300: dt: 0.9000, rms radial error=162.445, avgs=0 085/300: dt: 0.9000, rms radial error=161.533, avgs=0 090/300: dt: 0.9000, rms radial error=160.626, avgs=0 095/300: dt: 0.9000, rms radial error=159.723, avgs=0 100/300: dt: 0.9000, rms radial error=158.826, avgs=0 105/300: dt: 0.9000, rms radial error=157.933, avgs=0 110/300: dt: 0.9000, rms radial error=157.045, avgs=0 115/300: dt: 0.9000, rms radial error=156.162, avgs=0 120/300: dt: 0.9000, rms radial error=155.283, avgs=0 125/300: dt: 0.9000, rms radial error=154.410, avgs=0 130/300: dt: 0.9000, rms radial error=153.541, avgs=0 135/300: dt: 0.9000, rms radial error=152.677, avgs=0 140/300: dt: 0.9000, rms radial error=151.818, avgs=0 145/300: dt: 0.9000, rms radial error=150.963, avgs=0 150/300: dt: 0.9000, rms radial error=150.113, avgs=0 155/300: dt: 0.9000, rms radial error=149.268, avgs=0 160/300: dt: 0.9000, rms radial error=148.427, avgs=0 165/300: dt: 0.9000, rms radial error=147.591, avgs=0 170/300: dt: 0.9000, rms radial error=146.760, avgs=0 175/300: dt: 0.9000, rms radial error=145.934, avgs=0 180/300: dt: 0.9000, rms radial error=145.112, avgs=0 185/300: dt: 0.9000, rms radial error=144.294, avgs=0 190/300: dt: 0.9000, rms radial error=143.481, avgs=0 195/300: dt: 0.9000, rms radial error=142.673, avgs=0 200/300: dt: 0.9000, rms radial error=141.869, avgs=0 205/300: dt: 0.9000, rms radial error=141.069, avgs=0 210/300: dt: 0.9000, rms radial error=140.274, avgs=0 215/300: dt: 0.9000, rms radial error=139.483, avgs=0 220/300: dt: 0.9000, rms radial error=138.696, avgs=0 225/300: dt: 0.9000, rms radial error=137.914, avgs=0 230/300: dt: 0.9000, rms radial error=137.136, avgs=0 235/300: dt: 0.9000, rms radial error=136.362, avgs=0 240/300: dt: 0.9000, rms radial error=135.593, avgs=0 245/300: dt: 0.9000, rms radial error=134.828, avgs=0 250/300: dt: 0.9000, rms radial error=134.067, avgs=0 255/300: dt: 0.9000, rms radial error=133.311, avgs=0 260/300: dt: 0.9000, rms radial error=132.560, avgs=0 265/300: dt: 0.9000, rms radial error=131.813, avgs=0 270/300: dt: 0.9000, rms radial error=131.070, avgs=0 275/300: dt: 0.9000, rms radial error=130.332, avgs=0 280/300: dt: 0.9000, rms radial error=129.597, avgs=0 285/300: dt: 0.9000, rms radial error=128.867, avgs=0 290/300: dt: 0.9000, rms radial error=128.141, avgs=0 295/300: dt: 0.9000, rms radial error=127.419, avgs=0 300/300: dt: 0.9000, rms radial error=126.701, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 19093.60 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00007 epoch 2 (K=40.0), pass 1, starting sse = 3373.40 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 = 366.48 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.03/10 = 0.00288 epoch 4 (K=640.0), pass 1, starting sse = 22.40 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.02/10 = 0.00211 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.09 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Thu Aug 8 17:39:25 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/sub011/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub011 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=-36 (nv=159812, nf=319696, ne=479544, g=19) 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... 2626 ambiguous faces found in tessellation segmenting defects... 25 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 18 into 15 24 defects to be corrected 0 vertices coincident reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.7532 (-4.8766) -vertex loglikelihood: -6.6481 (-3.3240) -normal dot loglikelihood: -3.5987 (-3.5987) -quad curv loglikelihood: -6.5286 (-3.2643) Total Loglikelihood : -26.5286 CORRECTING DEFECT 0 (vertices=5, convex hull=25) After retessellation of defect 0, euler #=-22 (158178,473831,315631) : difference with theory (-21) = 1 CORRECTING DEFECT 1 (vertices=144, convex hull=93) After retessellation of defect 1, euler #=-21 (158217,473990,315752) : difference with theory (-20) = 1 CORRECTING DEFECT 2 (vertices=184, convex hull=105) After retessellation of defect 2, euler #=-20 (158243,474115,315852) : difference with theory (-19) = 1 CORRECTING DEFECT 3 (vertices=53, convex hull=79) After retessellation of defect 3, euler #=-19 (158269,474226,315938) : difference with theory (-18) = 1 CORRECTING DEFECT 4 (vertices=45, convex hull=66) After retessellation of defect 4, euler #=-18 (158286,474301,315997) : difference with theory (-17) = 1 CORRECTING DEFECT 5 (vertices=61, convex hull=63) After retessellation of defect 5, euler #=-17 (158311,474400,316072) : difference with theory (-16) = 1 CORRECTING DEFECT 6 (vertices=11, convex hull=19) After retessellation of defect 6, euler #=-16 (158312,474409,316081) : difference with theory (-15) = 1 CORRECTING DEFECT 7 (vertices=341, convex hull=252) normal vector of length zero at vertex 158902 with 4 faces normal vector of length zero at vertex 158902 with 4 faces normal vector of length zero at vertex 158836 with 3 faces normal vector of length zero at vertex 158836 with 3 faces normal vector of length zero at vertex 158836 with 3 faces After retessellation of defect 7, euler #=-15 (158325,474572,316232) : difference with theory (-14) = 1 CORRECTING DEFECT 8 (vertices=42, convex hull=40) After retessellation of defect 8, euler #=-14 (158340,474632,316278) : difference with theory (-13) = 1 CORRECTING DEFECT 9 (vertices=12, convex hull=22) After retessellation of defect 9, euler #=-13 (158341,474640,316286) : difference with theory (-12) = 1 CORRECTING DEFECT 10 (vertices=155, convex hull=185) After retessellation of defect 10, euler #=-12 (158379,474850,316459) : difference with theory (-11) = 1 CORRECTING DEFECT 11 (vertices=52, convex hull=45) After retessellation of defect 11, euler #=-11 (158384,474887,316492) : difference with theory (-10) = 1 CORRECTING DEFECT 12 (vertices=10, convex hull=27) After retessellation of defect 12, euler #=-10 (158387,474903,316506) : difference with theory (-9) = 1 CORRECTING DEFECT 13 (vertices=25, convex hull=59) After retessellation of defect 13, euler #=-9 (158400,474966,316557) : difference with theory (-8) = 1 CORRECTING DEFECT 14 (vertices=29, convex hull=57) After retessellation of defect 14, euler #=-8 (158410,475019,316601) : difference with theory (-7) = 1 CORRECTING DEFECT 15 (vertices=150, convex hull=121) After retessellation of defect 15, euler #=-6 (158435,475150,316709) : difference with theory (-6) = 0 CORRECTING DEFECT 16 (vertices=143, convex hull=64) After retessellation of defect 16, euler #=-5 (158446,475206,316755) : difference with theory (-5) = 0 CORRECTING DEFECT 17 (vertices=10, convex hull=20) After retessellation of defect 17, euler #=-4 (158450,475222,316768) : difference with theory (-4) = 0 CORRECTING DEFECT 18 (vertices=22, convex hull=55) After retessellation of defect 18, euler #=-3 (158460,475273,316810) : difference with theory (-3) = 0 CORRECTING DEFECT 19 (vertices=9, convex hull=15) After retessellation of defect 19, euler #=-2 (158460,475274,316812) : difference with theory (-2) = 0 CORRECTING DEFECT 20 (vertices=42, convex hull=55) After retessellation of defect 20, euler #=-1 (158463,475307,316843) : difference with theory (-1) = 0 CORRECTING DEFECT 21 (vertices=40, convex hull=79) After retessellation of defect 21, euler #=0 (158473,475369,316896) : difference with theory (0) = 0 CORRECTING DEFECT 22 (vertices=17, convex hull=44) After retessellation of defect 22, euler #=1 (158481,475409,316929) : difference with theory (1) = 0 CORRECTING DEFECT 23 (vertices=31, convex hull=74) After retessellation of defect 23, euler #=2 (158499,475491,316994) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.14-->8.09) (max @ vno 39825 --> 48461) 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 (0.14-->8.09) (max @ vno 39825 --> 48461) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 115 mutations (36.9%), 197 crossovers (63.1%), 265 vertices were eliminated building final representation... 1313 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=158499, nf=316994, ne=475491, g=0) writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 30.7 minutes 0 defective edges removing intersecting faces 000: 217 intersecting 001: 2 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 158499 - 475491 + 316994 = 2 --> 0 holes F =2V-4: 316994 = 316998-4 (0) 2E=3F: 950982 = 950982 (0) total defect index = 0 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 15 intersecting 001: 2 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Thu Aug 8 18:10:15 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub011 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/sub011/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/wm.mgz... 19648 bright wm thresholded. 948 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.orig... computing class statistics... border white: 292650 voxels (1.74%) border gray 329335 voxels (1.96%) WM (92.0): 93.5 +- 9.7 [70.0 --> 110.0] GM (76.0) : 74.2 +- 13.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 46.9 (was 70) setting MAX_BORDER_WHITE to 113.7 (was 105) setting MIN_BORDER_WHITE to 60.0 (was 85) setting MAX_CSF to 33.8 (was 40) setting MAX_GRAY to 94.3 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 53.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 20.6 (was 40) repositioning cortical surface to gray/white boundary reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.04-->3.88) (max @ vno 158222 --> 158228) face area 0.28 +- 0.12 (0.00-->2.78) mean absolute distance = 0.66 +- 0.80 3670 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104, GM=60 mean inside = 93.0, mean outside = 69.3 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=73.8, 21 (21) missing vertices, mean dist 0.3 [0.5 (%33.0)->0.7 (%67.0))] %71 local maxima, %24 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 (0.10-->4.35) (max @ vno 120419 --> 121336) face area 0.28 +- 0.13 (0.00-->2.15) mean absolute distance = 0.30 +- 0.49 2711 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=8318902.5, rms=13.42 001: dt: 0.5000, sse=8307937.0, rms=9.642 (0.000%) 002: dt: 0.5000, sse=8591579.0, rms=7.447 (0.000%) 003: dt: 0.5000, sse=8766030.0, rms=6.072 (0.000%) 004: dt: 0.5000, sse=9069262.0, rms=5.281 (0.000%) 005: dt: 0.5000, sse=9156258.0, rms=4.856 (0.000%) 006: dt: 0.5000, sse=9343889.0, rms=4.639 (0.000%) 007: dt: 0.5000, sse=9309365.0, rms=4.519 (0.000%) 008: dt: 0.5000, sse=9397955.0, rms=4.439 (0.000%) 009: dt: 0.5000, sse=9293000.0, rms=4.388 (0.000%) rms = 4.34, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=9352230.0, rms=4.341 (0.000%) 011: dt: 0.2500, sse=5813038.5, rms=3.017 (0.000%) 012: dt: 0.2500, sse=5305349.0, rms=2.553 (0.000%) 013: dt: 0.2500, sse=4999034.5, rms=2.457 (0.000%) 014: dt: 0.2500, sse=4903991.5, rms=2.364 (0.000%) rms = 2.34, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=4803816.5, rms=2.336 (0.000%) 016: dt: 0.1250, sse=4559721.0, rms=2.092 (0.000%) rms = 2.06, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=4510840.5, rms=2.059 (0.000%) positioning took 2.4 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group mean border=77.6, 38 (6) missing vertices, mean dist -0.2 [0.3 (%74.0)->0.2 (%26.0))] %79 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.25 (0.04-->3.86) (max @ vno 76660 --> 75430) face area 0.35 +- 0.16 (0.00-->2.74) mean absolute distance = 0.23 +- 0.34 3623 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5472760.5, rms=5.60 018: dt: 0.5000, sse=5867451.0, rms=3.879 (0.000%) rms = 4.33, time step reduction 1 of 3 to 0.250... 019: dt: 0.2500, sse=5308465.5, rms=2.790 (0.000%) 020: dt: 0.2500, sse=5096968.0, rms=2.229 (0.000%) 021: dt: 0.2500, sse=5010209.5, rms=1.895 (0.000%) rms = 1.86, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=4981557.0, rms=1.857 (0.000%) 023: dt: 0.1250, sse=4819734.5, rms=1.658 (0.000%) rms = 1.63, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=4769812.5, rms=1.629 (0.000%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group mean border=80.8, 21 (2) missing vertices, mean dist -0.1 [0.2 (%74.9)->0.2 (%25.1))] %87 local maxima, % 8 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 (0.07-->4.03) (max @ vno 76660 --> 75430) face area 0.34 +- 0.16 (0.00-->2.83) mean absolute distance = 0.18 +- 0.27 3431 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5183580.5, rms=4.14 025: dt: 0.5000, sse=5573927.5, rms=3.929 (0.000%) rms = 4.16, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=5074547.0, rms=2.517 (0.000%) 027: dt: 0.2500, sse=4948327.0, rms=2.015 (0.000%) 028: dt: 0.2500, sse=4992215.0, rms=1.684 (0.000%) rms = 1.72, time step reduction 2 of 3 to 0.125... 029: dt: 0.1250, sse=4927405.5, rms=1.571 (0.000%) 030: dt: 0.1250, sse=4839932.5, rms=1.416 (0.000%) rms = 1.40, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=4800880.5, rms=1.403 (0.000%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 4 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 mean border=81.9, 21 (0) missing vertices, mean dist -0.0 [0.2 (%58.8)->0.2 (%41.2))] %89 local maxima, % 5 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/sub011/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=4836710.5, rms=1.89 rms = 2.65, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=4933057.0, rms=1.250 (0.000%) 033: dt: 0.2500, sse=5104526.5, rms=1.050 (0.000%) rms = 1.06, time step reduction 2 of 3 to 0.125... rms = 1.04, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=5106081.0, rms=1.041 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group generating cortex label... 12 non-cortical segments detected only using segment with 2427 vertices erasing segment 1 (vno[0] = 95387) erasing segment 2 (vno[0] = 101027) erasing segment 3 (vno[0] = 106685) erasing segment 4 (vno[0] = 109983) erasing segment 5 (vno[0] = 110103) erasing segment 6 (vno[0] = 115282) erasing segment 7 (vno[0] = 119443) erasing segment 8 (vno[0] = 122296) erasing segment 9 (vno[0] = 125224) erasing segment 10 (vno[0] = 126154) erasing segment 11 (vno[0] = 127067) writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/label/lh.cortex.label... writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.curv writing smoothed area to lh.area writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.area vertex spacing 0.90 +- 0.25 (0.06-->4.35) (max @ vno 121336 --> 120419) face area 0.34 +- 0.16 (0.00-->2.87) refinement took 7.7 minutes #-------------------------------------------- #@# Smooth2 lh Thu Aug 8 18:17:56 CEST 2013 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 lh Thu Aug 8 18:18:01 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 51.4 mm, total surface area = 97210 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.117 (target=0.015) step 005: RMS=0.080 (target=0.015) step 010: RMS=0.058 (target=0.015) step 015: RMS=0.047 (target=0.015) step 020: RMS=0.038 (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) step 050: RMS=0.016 (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 207 vertices thresholded to be in k1 ~ [-0.65 0.43], k2 ~ [-0.19 0.17] total integrated curvature = 0.492*4pi (6.186) --> 1 handles ICI = 1.7, FI = 11.5, variation=194.498 173 vertices thresholded to be in [-0.06 0.01] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 128 vertices thresholded to be in [-0.21 0.15] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.015, std = 0.023 done. #----------------------------------------- #@# Curvature Stats lh Thu Aug 8 18:20:35 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub011 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 [ sub011/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 [ 299 ] Gb_filter = 0 WARN: S lookup min: -0.455109 WARN: S explicit min: 0.000000 vertex = 208 #-------------------------------------------- #@# Sphere lh Thu Aug 8 18:20:40 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 0.272... 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 %20.25 pass 1: epoch 2 of 3 starting distance error %20.17 unfolding complete - removing small folds... starting distance error %20.06 removing remaining folds... final distance error %20.07 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/lh.sphere spherical transformation took 1.09 hours #-------------------------------------------- #@# Surf Reg lh Thu Aug 8 19:26:18 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 = 0.577 curvature mean = 0.049, std = 0.947 curvature mean = 0.023, std = 0.838 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 0.00) sse = 374760.5, tmin=1.2742 d=32.00 min @ (8.00, 8.00, -8.00) sse = 301320.9, tmin=2.6405 d=16.00 min @ (0.00, -4.00, 4.00) sse = 270303.3, tmin=4.1247 d=8.00 min @ (0.00, 0.00, -2.00) sse = 265071.2, tmin=5.6329 d=4.00 min @ (-1.00, 0.00, 1.00) sse = 264140.4, tmin=7.1627 d=2.00 min @ (0.50, 0.50, -0.50) sse = 263578.5, tmin=8.7226 d=1.00 min @ (-0.25, -0.25, 0.00) sse = 263508.4, tmin=10.2998 d=0.50 min @ (0.00, 0.12, 0.00) sse = 263492.1, tmin=11.8797 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 11.88 min curvature mean = 0.024, std = 0.942 curvature mean = 0.012, std = 0.926 curvature mean = 0.024, std = 0.954 curvature mean = 0.006, std = 0.965 curvature mean = 0.021, std = 0.952 curvature mean = 0.002, std = 0.984 2 Reading smoothwm curvature mean = -0.022, std = 0.287 curvature mean = 0.005, std = 0.066 curvature mean = 0.071, std = 0.325 curvature mean = 0.005, std = 0.078 curvature mean = 0.037, std = 0.522 curvature mean = 0.005, std = 0.083 curvature mean = 0.020, std = 0.673 curvature mean = 0.005, std = 0.085 curvature mean = 0.005, std = 0.791 MRISregister() return, current seed 0 writing registered surface to ../surf/lh.sphere.reg... #-------------------------------------------- #@# Jacobian white lh Thu Aug 8 20:03:11 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 20:03:14 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 20:03:16 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub011 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... 1224 labels changed using aseg relabeling using gibbs priors... 000: 3407 changed, 158499 examined... 001: 794 changed, 14561 examined... 002: 187 changed, 4441 examined... 003: 68 changed, 1119 examined... 004: 31 changed, 394 examined... 005: 15 changed, 176 examined... 006: 6 changed, 96 examined... 007: 4 changed, 32 examined... 008: 3 changed, 24 examined... 009: 1 changed, 15 examined... 010: 1 changed, 7 examined... 011: 1 changed, 7 examined... 012: 2 changed, 7 examined... 013: 1 changed, 10 examined... 014: 2 changed, 9 examined... 015: 0 changed, 6 examined... 278 labels changed using aseg 000: 121 total segments, 75 labels (278 vertices) changed 001: 46 total segments, 1 labels (2 vertices) changed 002: 45 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 64 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1053 vertices marked for relabeling... 1053 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 1 minutes and 10 seconds. #-------------------------------------------- #@# Make Pial Surf lh Thu Aug 8 20:04:26 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub011 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/sub011/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/wm.mgz... 19648 bright wm thresholded. 948 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.orig... computing class statistics... border white: 292650 voxels (1.74%) border gray 329335 voxels (1.96%) WM (92.0): 93.5 +- 9.7 [70.0 --> 110.0] GM (76.0) : 74.2 +- 13.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 46.9 (was 70) setting MAX_BORDER_WHITE to 113.7 (was 105) setting MIN_BORDER_WHITE to 60.0 (was 85) setting MAX_CSF to 33.8 (was 40) setting MAX_GRAY to 94.3 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 53.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 20.6 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104, GM=60 mean inside = 93.0, mean outside = 69.3 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.04-->3.88) (max @ vno 158222 --> 158228) face area 0.28 +- 0.12 (0.00-->2.78) mean absolute distance = 0.66 +- 0.81 3708 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown deleting segment 3 with 12 points - only 0.00% unknown deleting segment 4 with 16 points - only 0.00% unknown deleting segment 5 with 816 points - only 0.00% unknown deleting segment 7 with 27 points - only 0.00% unknown deleting segment 8 with 6 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 deleting segment 11 with 5 points - only 0.00% unknown deleting segment 12 with 35 points - only 0.00% unknown deleting segment 13 with 7 points - only 0.00% unknown mean border=73.8, 21 (21) missing vertices, mean dist 0.3 [0.5 (%33.0)->0.7 (%67.0))] %71 local maxima, %24 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 (0.10-->4.35) (max @ vno 120419 --> 121336) face area 0.28 +- 0.13 (0.00-->2.15) mean absolute distance = 0.30 +- 0.49 2735 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=8344084.5, rms=13.40 001: dt: 0.5000, sse=8342708.5, rms=9.623 (0.000%) 002: dt: 0.5000, sse=8628524.0, rms=7.433 (0.000%) 003: dt: 0.5000, sse=8807791.0, rms=6.061 (0.000%) 004: dt: 0.5000, sse=9112575.0, rms=5.273 (0.000%) 005: dt: 0.5000, sse=9201597.0, rms=4.849 (0.000%) 006: dt: 0.5000, sse=9394261.0, rms=4.633 (0.000%) 007: dt: 0.5000, sse=9357459.0, rms=4.513 (0.000%) 008: dt: 0.5000, sse=9448341.0, rms=4.433 (0.000%) 009: dt: 0.5000, sse=9340989.0, rms=4.383 (0.000%) rms = 4.34, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=9404186.0, rms=4.337 (0.000%) 011: dt: 0.2500, sse=5838742.0, rms=3.013 (0.000%) 012: dt: 0.2500, sse=5329213.5, rms=2.550 (0.000%) 013: dt: 0.2500, sse=5020564.5, rms=2.454 (0.000%) 014: dt: 0.2500, sse=4924177.5, rms=2.361 (0.000%) rms = 2.33, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=4825814.0, rms=2.334 (0.000%) 016: dt: 0.1250, sse=4581110.0, rms=2.090 (0.000%) rms = 2.06, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=4532082.0, rms=2.057 (0.000%) positioning took 2.4 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 1 with 4 points - only 0.00% unknown deleting segment 2 with 7 points - only 0.00% unknown deleting segment 3 with 13 points - only 0.00% unknown deleting segment 5 with 659 points - only 0.00% unknown deleting segment 7 with 7 points - only 42.86% unknown deleting segment 8 with 37 points - only 0.00% unknown deleting segment 10 with 24 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 12 with 6 points - only 0.00% unknown deleting segment 13 with 6 points - only 0.00% unknown deleting segment 15 with 13 points - only 0.00% unknown deleting segment 16 with 7 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 17 with 3 points - only 0.00% unknown deleting segment 18 with 25 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 19 with 2 points - only 0.00% unknown deleting segment 20 with 10 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 21 with 1 points - only 0.00% unknown mean border=77.5, 34 (6) missing vertices, mean dist -0.2 [0.3 (%74.0)->0.2 (%26.0))] %80 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.25 (0.04-->3.86) (max @ vno 76660 --> 75430) face area 0.35 +- 0.16 (0.00-->2.74) mean absolute distance = 0.23 +- 0.34 3649 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5499196.5, rms=5.59 018: dt: 0.5000, sse=5902466.5, rms=3.872 (0.000%) rms = 4.32, time step reduction 1 of 3 to 0.250... 019: dt: 0.2500, sse=5341033.5, rms=2.785 (0.000%) 020: dt: 0.2500, sse=5125767.0, rms=2.226 (0.000%) 021: dt: 0.2500, sse=5039339.5, rms=1.892 (0.000%) rms = 1.86, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=5010136.5, rms=1.856 (0.000%) 023: dt: 0.1250, sse=4847970.0, rms=1.657 (0.000%) rms = 1.63, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=4798316.0, rms=1.629 (0.000%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown deleting segment 1 with 6 points - only 0.00% unknown deleting segment 2 with 7 points - only 0.00% unknown deleting segment 3 with 18 points - only 0.00% unknown deleting segment 4 with 701 points - only 0.00% unknown deleting segment 5 with 14 points - only 50.00% unknown deleting segment 6 with 37 points - only 0.00% unknown deleting segment 7 with 24 points - only 0.00% unknown removing 4 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 9 with 3 points - only 0.00% unknown deleting segment 10 with 6 points - only 0.00% unknown deleting segment 11 with 6 points - only 0.00% unknown deleting segment 12 with 13 points - only 0.00% unknown deleting segment 13 with 7 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 26 points - only 0.00% unknown deleting segment 16 with 5 points - only 0.00% unknown deleting segment 17 with 10 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 18 with 1 points - only 0.00% unknown mean border=80.8, 18 (2) missing vertices, mean dist -0.1 [0.2 (%74.8)->0.2 (%25.2))] %87 local maxima, % 8 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 (0.09-->4.03) (max @ vno 76660 --> 75430) face area 0.34 +- 0.16 (0.00-->2.83) mean absolute distance = 0.18 +- 0.27 3447 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5213834.5, rms=4.13 025: dt: 0.5000, sse=5606552.5, rms=3.922 (0.000%) rms = 4.15, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=5106193.5, rms=2.513 (0.000%) 027: dt: 0.2500, sse=4981098.5, rms=2.011 (0.000%) 028: dt: 0.2500, sse=5025713.0, rms=1.682 (0.000%) rms = 1.72, time step reduction 2 of 3 to 0.125... 029: dt: 0.1250, sse=4960682.0, rms=1.570 (0.000%) 030: dt: 0.1250, sse=4872179.5, rms=1.415 (0.000%) rms = 1.40, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=4832665.0, rms=1.402 (0.000%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown deleting segment 1 with 6 points - only 0.00% unknown deleting segment 2 with 9 points - only 0.00% unknown deleting segment 3 with 16 points - only 0.00% unknown deleting segment 4 with 695 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 5 with 4 points - only 0.00% unknown deleting segment 6 with 7 points - only 42.86% unknown deleting segment 7 with 38 points - only 0.00% unknown deleting segment 8 with 28 points - only 0.00% unknown removing 4 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 10 with 3 points - only 0.00% unknown deleting segment 11 with 6 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 12 with 2 points - only 0.00% unknown deleting segment 13 with 6 points - only 0.00% unknown deleting segment 14 with 11 points - only 0.00% unknown deleting segment 15 with 7 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 39 points - only 0.00% unknown deleting segment 18 with 10 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 19 with 1 points - only 0.00% unknown mean border=81.9, 16 (0) missing vertices, mean dist -0.0 [0.2 (%58.8)->0.2 (%41.2))] %90 local maxima, % 5 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=4868709.0, rms=1.89 rms = 2.65, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=4968167.5, rms=1.250 (0.000%) 033: dt: 0.2500, sse=5143750.5, rms=1.050 (0.000%) rms = 1.06, time step reduction 2 of 3 to 0.125... rms = 1.04, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=5145442.5, rms=1.041 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group smoothing surface for 5 iterations... mean border=49.7, 30 (30) missing vertices, mean dist 1.6 [0.1 (%0.0)->2.2 (%100.0))] %15 local maxima, %55 large gradients and %25 min vals, 2003 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=33518586.0, rms=31.61 001: dt: 0.5000, sse=24194100.0, rms=26.277 (0.000%) 002: dt: 0.5000, sse=17649570.0, rms=21.793 (0.000%) 003: dt: 0.5000, sse=13347920.0, rms=18.130 (0.000%) 004: dt: 0.5000, sse=10711668.0, rms=15.159 (0.000%) 005: dt: 0.5000, sse=9134480.0, rms=12.780 (0.000%) 006: dt: 0.5000, sse=8178029.5, rms=10.891 (0.000%) 007: dt: 0.5000, sse=7607395.0, rms=9.296 (0.000%) 008: dt: 0.5000, sse=7317464.5, rms=7.938 (0.000%) 009: dt: 0.5000, sse=7206807.0, rms=6.790 (0.000%) 010: dt: 0.5000, sse=7238428.5, rms=5.880 (0.000%) 011: dt: 0.5000, sse=7345923.5, rms=5.188 (0.000%) 012: dt: 0.5000, sse=7461944.5, rms=4.712 (0.000%) 013: dt: 0.5000, sse=7658667.5, rms=4.398 (0.000%) 014: dt: 0.5000, sse=7777544.5, rms=4.209 (0.000%) 015: dt: 0.5000, sse=7851391.5, rms=4.070 (0.000%) 016: dt: 0.5000, sse=7894189.5, rms=3.977 (0.000%) 017: dt: 0.5000, sse=7915245.5, rms=3.912 (0.000%) rms = 3.87, time step reduction 1 of 3 to 0.250... 018: dt: 0.5000, sse=7919688.5, rms=3.868 (0.000%) 019: dt: 0.2500, sse=5621893.0, rms=3.208 (0.000%) 020: dt: 0.2500, sse=5419712.0, rms=3.031 (0.000%) rms = 3.01, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=5272483.0, rms=3.008 (0.000%) 022: dt: 0.1250, sse=5063806.5, rms=2.909 (0.000%) rms = 2.90, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=5032504.5, rms=2.896 (0.000%) positioning took 3.2 minutes mean border=47.5, 849 (2) missing vertices, mean dist 0.2 [0.2 (%50.5)->0.6 (%49.5))] %32 local maxima, %42 large gradients and %21 min vals, 675 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=5802002.5, rms=5.03 024: dt: 0.5000, sse=6088457.5, rms=4.199 (0.000%) 025: dt: 0.5000, sse=7779875.5, rms=4.069 (0.000%) 026: dt: 0.5000, sse=7626329.0, rms=4.004 (0.000%) rms = 3.99, time step reduction 1 of 3 to 0.250... 027: dt: 0.5000, sse=8631633.0, rms=3.995 (0.000%) 028: dt: 0.2500, sse=6093355.0, rms=3.143 (0.000%) 029: dt: 0.2500, sse=6053249.5, rms=2.899 (0.000%) rms = 2.88, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=5870870.0, rms=2.876 (0.000%) 031: dt: 0.1250, sse=5674088.5, rms=2.735 (0.000%) rms = 2.71, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=5644993.5, rms=2.714 (0.000%) positioning took 1.2 minutes mean border=45.3, 1140 (2) missing vertices, mean dist 0.1 [0.2 (%40.2)->0.4 (%59.8))] %52 local maxima, %23 large gradients and %20 min vals, 874 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=5974194.5, rms=4.13 033: dt: 0.5000, sse=6191870.0, rms=3.798 (0.000%) rms = 3.89, time step reduction 1 of 3 to 0.250... 034: dt: 0.2500, sse=5836179.5, rms=3.152 (0.000%) 035: dt: 0.2500, sse=6059987.5, rms=2.858 (0.000%) 036: dt: 0.2500, sse=5971970.0, rms=2.794 (0.000%) rms = 2.76, time step reduction 2 of 3 to 0.125... 037: dt: 0.2500, sse=6033795.0, rms=2.761 (0.000%) 038: dt: 0.1250, sse=5836756.5, rms=2.639 (0.000%) rms = 2.62, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=5823511.5, rms=2.620 (0.000%) positioning took 1.1 minutes mean border=44.1, 2188 (2) missing vertices, mean dist 0.1 [0.2 (%45.0)->0.3 (%55.0))] %57 local maxima, %17 large gradients and %20 min vals, 629 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/sub011/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=5895207.0, rms=3.03 rms = 3.50, time step reduction 1 of 3 to 0.250... 040: dt: 0.2500, sse=5738429.0, rms=2.755 (0.000%) 041: dt: 0.2500, sse=5903055.5, rms=2.638 (0.000%) rms = 2.60, time step reduction 2 of 3 to 0.125... 042: dt: 0.2500, sse=5993334.0, rms=2.605 (0.000%) 043: dt: 0.1250, sse=5885290.5, rms=2.505 (0.000%) rms = 2.49, time step reduction 3 of 3 to 0.062... 044: dt: 0.1250, sse=5896572.0, rms=2.490 (0.000%) positioning took 0.9 minutes writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.area.pial vertex spacing 1.01 +- 0.42 (0.05-->8.06) (max @ vno 124187 --> 123190) face area 0.41 +- 0.30 (0.00-->6.08) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 158499 vertices processed 25000 of 158499 vertices processed 50000 of 158499 vertices processed 75000 of 158499 vertices processed 100000 of 158499 vertices processed 125000 of 158499 vertices processed 150000 of 158499 vertices processed 0 of 158499 vertices processed 25000 of 158499 vertices processed 50000 of 158499 vertices processed 75000 of 158499 vertices processed 100000 of 158499 vertices processed 125000 of 158499 vertices processed 150000 of 158499 vertices processed thickness calculation complete, 312:719 truncations. 34945 vertices at 0 distance 111349 vertices at 1 distance 101295 vertices at 2 distance 40385 vertices at 3 distance 10937 vertices at 4 distance 2991 vertices at 5 distance 915 vertices at 6 distance 319 vertices at 7 distance 111 vertices at 8 distance 44 vertices at 9 distance 33 vertices at 10 distance 22 vertices at 11 distance 21 vertices at 12 distance 12 vertices at 13 distance 12 vertices at 14 distance 9 vertices at 15 distance 9 vertices at 16 distance 3 vertices at 17 distance 1 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/sub011/surf/lh.thickness positioning took 15.6 minutes #-------------------------------------------- #@# Surf Volume lh Thu Aug 8 20:20:03 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 20:20:04 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts pctsurfcon --s sub011 --lh-only Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts/pctsurfcon.log Thu Aug 8 20:20:04 CEST 2013 setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts /opt/freesurfer/5.3.0/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux snake6 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux FREESURFER_HOME /opt/freesurfer/5.3.0 mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/tmp.pctsurfcon.9432/lh.wm.mgh --regheader sub011 --cortex srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/mri/orig.mgz as target reference. Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/label/lh.cortex.label Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 = 123232 Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/label/lh.cortex.label Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/tmp.pctsurfcon.9432/lh.wm.mgh Dim: 158499 1 1 mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/tmp.pctsurfcon.9432/lh.gm.mgh --projfrac 0.3 --regheader sub011 --cortex srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/mri/orig.mgz as target reference. Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/label/lh.cortex.label Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.white Done reading source surface Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 = 141256 Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/label/lh.cortex.label Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/tmp.pctsurfcon.9432/lh.gm.mgh Dim: 158499 1 1 mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/tmp.pctsurfcon.9432/lh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/tmp.pctsurfcon.9432/lh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/surf/lh.w-g.pct.mgh mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.w-g.pct.mgh --annot sub011 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/surf/lh.w-g.pct.mgh --annot sub011 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/stats/lh.w-g.pct.stats --snr sysname Linux hostname snake6 machine x86_64 user fkaule UseRobust 0 Constructing seg from annotation Reading annotation reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Seg base 1000 Loading /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.w-g.pct.mgh Vertex Area is 0.6705 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 1000 unknown 0 0.000 1 1001 bankssts 1878 1289.351 2 1002 caudalanteriorcingulate 1043 700.011 3 1003 caudalmiddlefrontal 4455 3031.344 4 1004 corpuscallosum 0 0.000 5 1005 cuneus 2390 1594.805 6 1006 entorhinal 561 401.584 7 1007 fusiform 5670 3840.466 8 1008 inferiorparietal 8553 5876.876 9 1009 inferiortemporal 5958 4031.534 10 1010 isthmuscingulate 1768 1187.077 11 1011 lateraloccipital 9014 5842.801 12 1012 lateralorbitofrontal 4512 2979.639 13 1013 lingual 4734 3210.272 14 1014 medialorbitofrontal 2356 1614.399 15 1015 middletemporal 5337 3682.813 16 1016 parahippocampal 1069 690.702 17 1017 paracentral 2077 1311.524 18 1018 parsopercularis 2582 1737.566 19 1019 parsorbitalis 1203 817.763 20 1020 parstriangularis 2302 1579.925 21 1021 pericalcarine 2110 1399.025 22 1022 postcentral 8318 5502.695 23 1023 posteriorcingulate 1974 1318.320 24 1024 precentral 8922 5912.194 25 1025 precuneus 6914 4614.999 26 1026 rostralanteriorcingulate 1620 1084.376 27 1027 rostralmiddlefrontal 10552 7285.981 28 1028 superiorfrontal 13157 8934.941 29 1029 superiorparietal 10453 6834.004 30 1030 superiortemporal 6228 4148.080 31 1031 supramarginal 5888 4015.426 32 1032 frontalpole 393 264.547 33 1033 temporalpole 614 443.185 34 1034 transversetemporal 786 486.986 35 1035 insula 3500 2312.378 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats lh Thu Aug 8 20:20:19 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 sub011 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 1878 1289 3342 2.643 0.393 0.114 0.027 14 2.1 bankssts 1043 700 1702 2.365 0.516 0.146 0.033 20 1.4 caudalanteriorcingulate 4455 3031 7998 2.379 0.499 0.131 0.037 56 6.6 caudalmiddlefrontal 2390 1595 3154 1.755 0.380 0.169 0.064 48 6.2 cuneus 561 402 1674 3.359 0.921 0.147 0.059 6 1.2 entorhinal 5670 3840 11847 2.693 0.598 0.154 0.066 123 12.8 fusiform 8553 5877 15416 2.363 0.466 0.141 0.052 139 15.8 inferiorparietal 5958 4032 11764 2.553 0.600 0.147 0.062 122 14.5 inferiortemporal 1768 1187 3317 2.664 0.689 0.168 0.066 42 4.6 isthmuscingulate 9014 5843 12474 1.940 0.433 0.149 0.050 135 18.5 lateraloccipital 4512 2980 8593 2.492 0.650 0.164 0.074 113 13.0 lateralorbitofrontal 4734 3210 7371 2.095 0.541 0.164 0.085 95 13.2 lingual 2356 1614 4165 2.117 0.613 0.170 0.124 88 7.7 medialorbitofrontal 5337 3683 12426 2.763 0.608 0.153 0.051 102 11.0 middletemporal 1069 691 2202 2.790 0.787 0.126 0.044 22 2.1 parahippocampal 2077 1312 3264 2.330 0.468 0.133 0.052 30 3.6 paracentral 2582 1738 4938 2.610 0.483 0.140 0.046 47 4.6 parsopercularis 1203 818 2875 2.587 0.563 0.159 0.060 27 2.7 parsorbitalis 2302 1580 4525 2.454 0.554 0.147 0.048 38 4.4 parstriangularis 2110 1399 2129 1.665 0.435 0.165 0.079 37 5.7 pericalcarine 8318 5503 11729 1.906 0.612 0.138 0.046 121 15.1 postcentral 1974 1318 3630 2.564 0.588 0.164 0.067 49 5.3 posteriorcingulate 8922 5912 15907 2.420 0.562 0.128 0.040 110 14.7 precentral 6914 4615 12540 2.491 0.519 0.147 0.057 125 16.0 precuneus 1620 1084 3426 2.590 0.653 0.172 0.138 49 5.6 rostralanteriorcingulate 10552 7286 18991 2.203 0.535 0.167 0.071 272 30.5 rostralmiddlefrontal 13157 8935 26591 2.563 0.585 0.140 0.049 248 25.4 superiorfrontal 10453 6834 16197 2.141 0.493 0.132 0.040 131 16.9 superiorparietal 6228 4148 12791 2.738 0.600 0.125 0.044 84 10.8 superiortemporal 5888 4015 11164 2.513 0.504 0.143 0.045 93 10.3 supramarginal 393 265 920 2.552 0.477 0.238 0.153 21 2.1 frontalpole 614 443 2173 3.580 0.760 0.161 0.120 13 1.9 temporalpole 786 487 1265 2.298 0.365 0.128 0.042 9 1.4 transversetemporal 3500 2312 7472 2.982 0.853 0.128 0.076 62 7.6 insula #----------------------------------------- #@# Cortical Parc 2 lh Thu Aug 8 20:20:42 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub011 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... 61 labels changed using aseg relabeling using gibbs priors... 000: 11151 changed, 158499 examined... 001: 2649 changed, 42437 examined... 002: 784 changed, 13494 examined... 003: 346 changed, 4453 examined... 004: 150 changed, 1867 examined... 005: 79 changed, 866 examined... 006: 39 changed, 457 examined... 007: 20 changed, 209 examined... 008: 6 changed, 112 examined... 009: 6 changed, 35 examined... 010: 3 changed, 27 examined... 011: 1 changed, 18 examined... 012: 0 changed, 7 examined... 28 labels changed using aseg 000: 369 total segments, 287 labels (4861 vertices) changed 001: 128 total segments, 47 labels (449 vertices) changed 002: 84 total segments, 3 labels (7 vertices) changed 003: 81 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 149 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 386 vertices marked for relabeling... 386 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 1 minutes and 21 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Thu Aug 8 20:22:03 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 sub011 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 1526 1047 2497 2.074 0.526 0.170 0.071 44 4.9 G_and_S_frontomargin 1844 1235 2709 1.996 0.416 0.149 0.049 28 3.6 G_and_S_occipital_inf 1703 1006 2720 2.268 0.514 0.130 0.059 24 3.7 G_and_S_paracentral 2009 1334 3827 2.591 0.533 0.152 0.054 37 4.1 G_and_S_subcentral 1082 746 2321 2.369 0.522 0.198 0.091 40 4.0 G_and_S_transv_frontopol 2553 1746 4811 2.396 0.614 0.156 0.104 59 6.9 G_and_S_cingul-Ant 2153 1471 4042 2.586 0.567 0.130 0.031 27 2.9 G_and_S_cingul-Mid-Ant 1603 1101 2943 2.625 0.453 0.147 0.058 31 3.8 G_and_S_cingul-Mid-Post 620 439 1612 2.958 0.446 0.188 0.072 19 1.8 G_cingul-Post-dorsal 303 199 532 2.399 0.760 0.163 0.071 6 0.8 G_cingul-Post-ventral 2079 1406 2844 1.754 0.371 0.181 0.075 48 6.3 G_cuneus 1699 1137 4069 2.816 0.459 0.165 0.067 49 4.3 G_front_inf-Opercular 460 311 1080 2.636 0.482 0.155 0.055 9 1.1 G_front_inf-Orbital 1310 895 3061 2.637 0.530 0.162 0.060 28 3.0 G_front_inf-Triangul 5103 3522 10829 2.434 0.548 0.169 0.071 133 14.3 G_front_middle 8485 5737 19109 2.650 0.581 0.152 0.061 214 20.1 G_front_sup 476 290 1079 2.894 0.604 0.150 0.091 11 1.9 G_Ins_lg_and_S_cent_ins 895 539 2799 3.668 0.846 0.140 0.156 34 2.6 G_insular_short 2786 1787 5097 2.228 0.504 0.156 0.063 57 6.5 G_occipital_middle 1682 1079 2708 2.149 0.541 0.149 0.049 27 3.1 G_occipital_sup 2415 1585 5539 2.860 0.550 0.171 0.087 79 6.5 G_oc-temp_lat-fusifor 3288 2202 5303 2.036 0.545 0.178 0.105 79 11.1 G_oc-temp_med-Lingual 1218 814 3010 2.983 0.893 0.137 0.056 25 2.8 G_oc-temp_med-Parahip 2875 1898 7144 2.741 0.562 0.184 0.090 88 10.6 G_orbital 3005 2039 6528 2.526 0.481 0.164 0.062 71 7.4 G_pariet_inf-Angular 2748 1897 6215 2.589 0.521 0.157 0.053 56 5.6 G_pariet_inf-Supramar 3645 2374 6921 2.320 0.542 0.136 0.043 53 6.3 G_parietal_sup 3352 2197 5095 1.919 0.567 0.147 0.057 64 7.4 G_postcentral 3534 2271 7646 2.614 0.550 0.129 0.039 51 5.4 G_precentral 3607 2374 7767 2.619 0.486 0.164 0.075 96 11.1 G_precuneus 1074 713 2325 2.378 0.589 0.225 0.233 82 5.7 G_rectus 324 221 691 2.753 0.477 0.179 0.089 9 1.0 G_subcallosal 552 338 995 2.325 0.277 0.130 0.044 8 1.0 G_temp_sup-G_T_transv 2403 1590 6567 2.966 0.542 0.152 0.065 52 5.8 G_temp_sup-Lateral 754 518 1921 3.376 0.910 0.108 0.036 6 1.0 G_temp_sup-Plan_polar 757 557 1533 2.447 0.427 0.112 0.030 7 0.8 G_temp_sup-Plan_tempo 3211 2165 7573 2.703 0.646 0.167 0.078 87 9.7 G_temporal_inf 3777 2590 9925 2.847 0.558 0.159 0.056 85 8.3 G_temporal_middle 441 310 766 2.324 0.407 0.145 0.037 6 0.8 Lat_Fis-ant-Horizont 332 221 518 2.392 0.526 0.142 0.039 4 0.6 Lat_Fis-ant-Vertical 1387 933 1851 2.293 0.531 0.127 0.037 12 2.2 Lat_Fis-post 2599 1636 3410 1.822 0.416 0.162 0.058 48 6.3 Pole_occipital 1822 1284 5448 3.155 0.792 0.175 0.097 42 6.0 Pole_temporal 2722 1829 3365 2.037 0.738 0.155 0.066 43 6.3 S_calcarine 3416 2315 3546 1.689 0.506 0.122 0.036 27 5.4 S_central 1194 815 1764 2.280 0.483 0.122 0.033 11 1.6 S_cingul-Marginalis 807 520 1134 2.665 0.543 0.115 0.031 6 1.1 S_circular_insula_ant 1561 1039 2369 2.600 0.540 0.092 0.026 9 1.8 S_circular_insula_inf 1907 1296 2969 2.560 0.512 0.115 0.032 13 2.6 S_circular_insula_sup 1064 784 1936 2.542 0.507 0.109 0.025 7 1.1 S_collat_transv_ant 300 198 451 2.080 0.376 0.122 0.039 2 0.4 S_collat_transv_post 2736 1883 3984 2.090 0.403 0.132 0.036 33 3.9 S_front_inf 2286 1602 3783 2.075 0.495 0.157 0.064 51 5.9 S_front_middle 3566 2402 5584 2.279 0.450 0.122 0.039 43 5.6 S_front_sup 349 230 580 2.347 0.495 0.130 0.038 6 0.6 S_interm_prim-Jensen 4149 2779 5514 2.096 0.415 0.117 0.029 35 5.0 S_intrapariet_and_P_trans 1903 1253 2158 1.917 0.354 0.150 0.050 24 4.0 S_oc_middle_and_Lunatus 1537 1017 1944 2.040 0.396 0.122 0.055 13 2.0 S_oc_sup_and_transversal 1296 858 1580 1.992 0.421 0.112 0.033 10 1.7 S_occipital_ant 1419 937 2069 2.558 0.413 0.126 0.039 14 2.1 S_oc-temp_lat 2189 1506 3485 2.413 0.515 0.128 0.038 22 3.3 S_oc-temp_med_and_Lingual 583 397 698 1.928 0.402 0.136 0.044 7 0.9 S_orbital_lateral 394 275 574 1.913 0.427 0.151 0.051 7 0.7 S_orbital_med-olfact 1584 1092 2568 2.137 0.642 0.156 0.060 29 3.5 S_orbital-H_Shaped 2193 1439 2973 2.241 0.591 0.131 0.039 23 3.2 S_parieto_occipital 1346 802 1522 2.219 0.742 0.150 0.053 30 2.8 S_pericallosal 4230 2816 5432 2.044 0.498 0.126 0.034 41 5.7 S_postcentral 1941 1362 2917 2.251 0.512 0.120 0.029 19 2.4 S_precentral-inf-part 1602 1105 2335 2.429 0.435 0.120 0.031 14 2.0 S_precentral-sup-part 782 543 957 1.729 0.379 0.113 0.024 5 0.8 S_suborbital 1611 1095 2494 2.348 0.440 0.135 0.043 16 2.8 S_subparietal 1627 1112 2296 2.176 0.515 0.134 0.043 23 2.8 S_temporal_inf 6746 4675 11155 2.511 0.482 0.127 0.036 71 10.0 S_temporal_sup 360 244 461 2.250 0.425 0.116 0.022 2 0.4 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Thu Aug 8 20:22:27 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub011 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... 1480 labels changed using aseg relabeling using gibbs priors... 000: 3330 changed, 158499 examined... 001: 830 changed, 13806 examined... 002: 200 changed, 4542 examined... 003: 86 changed, 1187 examined... 004: 40 changed, 496 examined... 005: 19 changed, 223 examined... 006: 6 changed, 98 examined... 007: 1 changed, 41 examined... 008: 1 changed, 7 examined... 009: 0 changed, 5 examined... 188 labels changed using aseg 000: 80 total segments, 47 labels (283 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 60 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 413 vertices marked for relabeling... 413 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas40.annot... classification took 1 minutes and 11 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Thu Aug 8 20:23:38 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 sub011 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 2002 1331 3919 2.649 0.619 0.143 0.039 34 3.2 caudalanteriorcingulate 4561 3096 8208 2.387 0.500 0.132 0.037 57 6.8 caudalmiddlefrontal 3203 2132 4202 1.829 0.437 0.161 0.057 58 7.4 cuneus 494 357 1352 3.228 0.898 0.146 0.053 5 1.1 entorhinal 5234 3530 10446 2.658 0.567 0.151 0.066 112 11.3 fusiform 8013 5463 14372 2.358 0.466 0.141 0.053 133 14.9 inferiorparietal 6023 4097 12725 2.619 0.644 0.151 0.064 125 14.8 inferiortemporal 1780 1197 3370 2.679 0.689 0.168 0.067 43 4.7 isthmuscingulate 9171 5937 12729 1.939 0.434 0.149 0.050 136 19.1 lateraloccipital 4419 2936 8699 2.437 0.689 0.170 0.078 120 13.5 lateralorbitofrontal 4721 3198 7346 2.089 0.539 0.164 0.085 95 13.2 lingual 1943 1330 3441 2.126 0.618 0.174 0.135 77 6.6 medialorbitofrontal 7371 5099 15912 2.661 0.588 0.144 0.047 124 14.1 middletemporal 1062 688 2195 2.789 0.788 0.126 0.044 21 2.1 parahippocampal 2338 1490 3747 2.364 0.469 0.131 0.050 32 3.9 paracentral 2299 1546 4486 2.660 0.460 0.141 0.045 42 4.3 parsopercularis 1308 875 2824 2.625 0.541 0.152 0.052 25 2.9 parsorbitalis 2964 2024 5375 2.338 0.540 0.145 0.049 53 5.5 parstriangularis 2116 1399 2129 1.664 0.431 0.166 0.079 38 5.8 pericalcarine 9342 6184 13311 1.933 0.616 0.138 0.046 136 16.9 postcentral 2121 1415 3793 2.560 0.576 0.159 0.064 49 5.4 posteriorcingulate 8899 5887 15827 2.423 0.562 0.128 0.040 110 14.8 precentral 6696 4467 12394 2.514 0.495 0.149 0.059 126 15.9 precuneus 2106 1404 4120 2.482 0.658 0.164 0.118 56 6.5 rostralanteriorcingulate 7274 5002 13153 2.219 0.566 0.167 0.073 188 21.1 rostralmiddlefrontal 14844 10198 29913 2.481 0.572 0.148 0.057 326 33.1 superiorfrontal 8525 5578 13243 2.151 0.485 0.130 0.039 104 13.5 superiorparietal 8298 5599 17770 2.819 0.650 0.129 0.049 114 15.0 superiortemporal 5652 3865 10707 2.510 0.510 0.142 0.044 85 9.8 supramarginal 784 487 1264 2.301 0.364 0.127 0.042 9 1.4 transversetemporal 3328 2169 7001 2.965 0.810 0.127 0.074 59 7.1 insula #-------------------------------------------- #@# Tessellate rh Thu Aug 8 20:24:00 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 1 found - 1 modified | TOTAL: 2 pass 2 (xz+): 0 found - 1 modified | TOTAL: 2 pass 1 (xz-): 2 found - 2 modified | TOTAL: 4 pass 2 (xz-): 0 found - 2 modified | TOTAL: 4 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 1 found - 1 modified | TOTAL: 1 pass 2 (-+): 0 found - 1 modified | TOTAL: 1 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 = 5 (out of 309686: 0.001615) 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: 92 vertices, 114 faces slice 40: 3456 vertices, 3664 faces slice 50: 11243 vertices, 11550 faces slice 60: 21962 vertices, 22395 faces slice 70: 34016 vertices, 34424 faces slice 80: 46310 vertices, 46739 faces slice 90: 58869 vertices, 59300 faces slice 100: 71468 vertices, 71890 faces slice 110: 83859 vertices, 84308 faces slice 120: 96212 vertices, 96680 faces slice 130: 108894 vertices, 109383 faces slice 140: 121013 vertices, 121423 faces slice 150: 131602 vertices, 131952 faces slice 160: 139935 vertices, 140221 faces slice 170: 146934 vertices, 147205 faces slice 180: 153698 vertices, 153904 faces slice 190: 159000 vertices, 159208 faces slice 200: 160904 vertices, 160934 faces slice 210: 160904 vertices, 160934 faces slice 220: 160904 vertices, 160934 faces slice 230: 160904 vertices, 160934 faces slice 240: 160904 vertices, 160934 faces slice 250: 160904 vertices, 160934 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... 160904 voxel in cpt #1: X=-30 [v=160904,e=482802,f=321868] located at (29.328512, -20.287563, 41.081017) For the whole surface: X=-30 [v=160904,e=482802,f=321868] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Thu Aug 8 20:24:08 CEST 2013 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 20:24:13 CEST 2013 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts avg radius = 49.0 mm, total surface area = 84350 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.6 minutes Not saving sulc step 000: RMS=0.100 (target=0.015) step 005: RMS=0.073 (target=0.015) step 010: RMS=0.053 (target=0.015) step 015: RMS=0.043 (target=0.015) step 020: RMS=0.037 (target=0.015) step 025: RMS=0.032 (target=0.015) step 030: RMS=0.029 (target=0.015) step 035: RMS=0.026 (target=0.015) step 040: RMS=0.024 (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 20:24:52 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 0.92 +- 0.53 (0.00-->5.59) (max @ vno 107171 --> 108458) face area 0.02 +- 0.03 (-0.22-->0.60) scaling brain by 0.295... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.393, avgs=0 005/300: dt: 0.9000, rms radial error=176.135, avgs=0 010/300: dt: 0.9000, rms radial error=175.581, avgs=0 015/300: dt: 0.9000, rms radial error=174.852, avgs=0 020/300: dt: 0.9000, rms radial error=174.020, avgs=0 025/300: dt: 0.9000, rms radial error=173.130, avgs=0 030/300: dt: 0.9000, rms radial error=172.207, avgs=0 035/300: dt: 0.9000, rms radial error=171.273, avgs=0 040/300: dt: 0.9000, rms radial error=170.331, avgs=0 045/300: dt: 0.9000, rms radial error=169.386, avgs=0 050/300: dt: 0.9000, rms radial error=168.441, avgs=0 055/300: dt: 0.9000, rms radial error=167.499, avgs=0 060/300: dt: 0.9000, rms radial error=166.561, avgs=0 065/300: dt: 0.9000, rms radial error=165.627, avgs=0 070/300: dt: 0.9000, rms radial error=164.698, avgs=0 075/300: dt: 0.9000, rms radial error=163.775, avgs=0 080/300: dt: 0.9000, rms radial error=162.856, avgs=0 085/300: dt: 0.9000, rms radial error=161.943, avgs=0 090/300: dt: 0.9000, rms radial error=161.035, avgs=0 095/300: dt: 0.9000, rms radial error=160.132, avgs=0 100/300: dt: 0.9000, rms radial error=159.233, avgs=0 105/300: dt: 0.9000, rms radial error=158.340, avgs=0 110/300: dt: 0.9000, rms radial error=157.452, avgs=0 115/300: dt: 0.9000, rms radial error=156.568, avgs=0 120/300: dt: 0.9000, rms radial error=155.690, avgs=0 125/300: dt: 0.9000, rms radial error=154.816, avgs=0 130/300: dt: 0.9000, rms radial error=153.947, avgs=0 135/300: dt: 0.9000, rms radial error=153.082, avgs=0 140/300: dt: 0.9000, rms radial error=152.223, avgs=0 145/300: dt: 0.9000, rms radial error=151.368, avgs=0 150/300: dt: 0.9000, rms radial error=150.517, avgs=0 155/300: dt: 0.9000, rms radial error=149.672, avgs=0 160/300: dt: 0.9000, rms radial error=148.830, avgs=0 165/300: dt: 0.9000, rms radial error=147.994, avgs=0 170/300: dt: 0.9000, rms radial error=147.162, avgs=0 175/300: dt: 0.9000, rms radial error=146.334, avgs=0 180/300: dt: 0.9000, rms radial error=145.511, avgs=0 185/300: dt: 0.9000, rms radial error=144.693, avgs=0 190/300: dt: 0.9000, rms radial error=143.879, avgs=0 195/300: dt: 0.9000, rms radial error=143.070, avgs=0 200/300: dt: 0.9000, rms radial error=142.265, avgs=0 205/300: dt: 0.9000, rms radial error=141.464, avgs=0 210/300: dt: 0.9000, rms radial error=140.668, avgs=0 215/300: dt: 0.9000, rms radial error=139.876, avgs=0 220/300: dt: 0.9000, rms radial error=139.089, avgs=0 225/300: dt: 0.9000, rms radial error=138.307, avgs=0 230/300: dt: 0.9000, rms radial error=137.528, avgs=0 235/300: dt: 0.9000, rms radial error=136.754, avgs=0 240/300: dt: 0.9000, rms radial error=135.984, avgs=0 245/300: dt: 0.9000, rms radial error=135.219, avgs=0 250/300: dt: 0.9000, rms radial error=134.458, avgs=0 255/300: dt: 0.9000, rms radial error=133.701, avgs=0 260/300: dt: 0.9000, rms radial error=132.949, avgs=0 265/300: dt: 0.9000, rms radial error=132.201, avgs=0 270/300: dt: 0.9000, rms radial error=131.457, avgs=0 275/300: dt: 0.9000, rms radial error=130.718, avgs=0 280/300: dt: 0.9000, rms radial error=129.982, avgs=0 285/300: dt: 0.9000, rms radial error=129.251, avgs=0 290/300: dt: 0.9000, rms radial error=128.523, avgs=0 295/300: dt: 0.9000, rms radial error=127.800, avgs=0 300/300: dt: 0.9000, rms radial error=127.081, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 19134.30 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00017 epoch 2 (K=40.0), pass 1, starting sse = 3289.60 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00003 epoch 3 (K=160.0), pass 1, starting sse = 350.71 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/11 = 0.00762 epoch 4 (K=640.0), pass 1, starting sse = 20.94 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.18/15 = 0.01187 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 20:30:34 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/sub011/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub011 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=-30 (nv=160904, nf=321868, ne=482802, 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 8 iterations marking ambiguous vertices... 2422 ambiguous faces found in tessellation segmenting defects... 15 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 15 defects to be corrected 0 vertices coincident reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.9098 (-4.9549) -vertex loglikelihood: -6.6368 (-3.3184) -normal dot loglikelihood: -3.5669 (-3.5669) -quad curv loglikelihood: -6.4444 (-3.2222) Total Loglikelihood : -26.5580 CORRECTING DEFECT 0 (vertices=551, convex hull=180) After retessellation of defect 0, euler #=-9 (159529,478130,318592) : difference with theory (-12) = -3 CORRECTING DEFECT 1 (vertices=31, convex hull=74) After retessellation of defect 1, euler #=-8 (159539,478190,318643) : difference with theory (-11) = -3 CORRECTING DEFECT 2 (vertices=33, convex hull=69) After retessellation of defect 2, euler #=-7 (159552,478253,318694) : difference with theory (-10) = -3 CORRECTING DEFECT 3 (vertices=49, convex hull=37) After retessellation of defect 3, euler #=-6 (159557,478282,318719) : difference with theory (-9) = -3 CORRECTING DEFECT 4 (vertices=9, convex hull=28) After retessellation of defect 4, euler #=-5 (159561,478301,318735) : difference with theory (-8) = -3 CORRECTING DEFECT 5 (vertices=56, convex hull=71) After retessellation of defect 5, euler #=-4 (159574,478375,318797) : difference with theory (-7) = -3 CORRECTING DEFECT 6 (vertices=438, convex hull=259) After retessellation of defect 6, euler #=-5 (159621,478668,319042) : difference with theory (-6) = -1 CORRECTING DEFECT 7 (vertices=53, convex hull=53) After retessellation of defect 7, euler #=-5 (159645,478765,319115) : difference with theory (-5) = 0 CORRECTING DEFECT 8 (vertices=27, convex hull=55) After retessellation of defect 8, euler #=-4 (159658,478822,319160) : difference with theory (-4) = 0 CORRECTING DEFECT 9 (vertices=6, convex hull=13) After retessellation of defect 9, euler #=-3 (159659,478828,319166) : difference with theory (-3) = 0 CORRECTING DEFECT 10 (vertices=55, convex hull=63) After retessellation of defect 10, euler #=-2 (159672,478895,319221) : difference with theory (-2) = 0 CORRECTING DEFECT 11 (vertices=33, convex hull=72) After retessellation of defect 11, euler #=-1 (159689,478973,319283) : difference with theory (-1) = 0 CORRECTING DEFECT 12 (vertices=57, convex hull=94) After retessellation of defect 12, euler #=0 (159702,479051,319349) : difference with theory (0) = 0 CORRECTING DEFECT 13 (vertices=33, convex hull=66) After retessellation of defect 13, euler #=1 (159714,479115,319402) : difference with theory (1) = 0 CORRECTING DEFECT 14 (vertices=29, convex hull=58) After retessellation of defect 14, euler #=2 (159726,479172,319448) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.06-->12.32) (max @ vno 45728 --> 48072) 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 (0.06-->12.32) (max @ vno 45728 --> 48072) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 54 mutations (36.5%), 94 crossovers (63.5%), 193 vertices were eliminated building final representation... 1178 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=159726, nf=319448, ne=479172, g=0) writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 20.2 minutes 0 defective edges removing intersecting faces 000: 187 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 159726 - 479172 + 319448 = 2 --> 0 holes F =2V-4: 319448 = 319452-4 (0) 2E=3F: 958344 = 958344 (0) total defect index = 0 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 43 intersecting 001: 2 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Thu Aug 8 20:50:54 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub011 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/sub011/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/wm.mgz... 20244 bright wm thresholded. 947 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.orig... computing class statistics... border white: 292650 voxels (1.74%) border gray 329335 voxels (1.96%) WM (92.0): 93.5 +- 10.0 [70.0 --> 110.0] GM (76.0) : 74.1 +- 12.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 46.1 (was 70) setting MAX_BORDER_WHITE to 115.0 (was 105) setting MIN_BORDER_WHITE to 59.0 (was 85) setting MAX_CSF to 33.2 (was 40) setting MAX_GRAY to 95.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 52.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 20.4 (was 40) repositioning cortical surface to gray/white boundary reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.04-->4.59) (max @ vno 159481 --> 159517) face area 0.28 +- 0.12 (0.00-->5.21) mean absolute distance = 0.65 +- 0.77 4463 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=59 mean inside = 93.3, mean outside = 69.4 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=73.6, 23 (23) missing vertices, mean dist 0.4 [0.5 (%31.7)->0.7 (%68.3))] %74 local maxima, %21 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 (0.11-->4.50) (max @ vno 159481 --> 159517) face area 0.28 +- 0.14 (0.00-->5.12) mean absolute distance = 0.31 +- 0.49 2837 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=8456153.0, rms=13.48 001: dt: 0.5000, sse=8474094.0, rms=9.726 (0.000%) 002: dt: 0.5000, sse=8757679.0, rms=7.574 (0.000%) 003: dt: 0.5000, sse=8942017.0, rms=6.208 (0.000%) 004: dt: 0.5000, sse=9234185.0, rms=5.389 (0.000%) 005: dt: 0.5000, sse=9309302.0, rms=4.899 (0.000%) 006: dt: 0.5000, sse=9489659.0, rms=4.653 (0.000%) 007: dt: 0.5000, sse=9469956.0, rms=4.485 (0.000%) 008: dt: 0.5000, sse=9528877.0, rms=4.413 (0.000%) 009: dt: 0.5000, sse=9441498.0, rms=4.340 (0.000%) rms = 4.31, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=9503375.0, rms=4.312 (0.000%) 011: dt: 0.2500, sse=5980742.5, rms=2.994 (0.000%) 012: dt: 0.2500, sse=5464564.5, rms=2.546 (0.000%) 013: dt: 0.2500, sse=5147420.5, rms=2.449 (0.000%) 014: dt: 0.2500, sse=5059029.5, rms=2.366 (0.000%) rms = 2.34, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=4957086.5, rms=2.341 (0.000%) 016: dt: 0.1250, sse=4739545.5, rms=2.156 (0.000%) rms = 2.14, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=4691896.0, rms=2.138 (0.000%) positioning took 2.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group mean border=77.6, 19 (3) missing vertices, mean dist -0.2 [0.3 (%74.8)->0.2 (%25.2))] %81 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.25 (0.06-->4.43) (max @ vno 45728 --> 159526) face area 0.35 +- 0.17 (0.00-->6.38) mean absolute distance = 0.23 +- 0.34 3605 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5716901.0, rms=5.75 018: dt: 0.5000, sse=6051761.5, rms=3.898 (0.000%) rms = 4.32, time step reduction 1 of 3 to 0.250... 019: dt: 0.2500, sse=5489718.5, rms=2.815 (0.000%) 020: dt: 0.2500, sse=5282124.0, rms=2.248 (0.000%) 021: dt: 0.2500, sse=5185390.5, rms=1.919 (0.000%) 022: dt: 0.2500, sse=5156414.5, rms=1.862 (0.000%) 023: dt: 0.2500, sse=5086782.5, rms=1.802 (0.000%) rms = 1.80, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=5098622.0, rms=1.796 (0.000%) 025: dt: 0.1250, sse=4955181.5, rms=1.651 (0.000%) rms = 1.64, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=4916362.0, rms=1.643 (0.000%) positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group mean border=81.1, 16 (3) missing vertices, mean dist -0.1 [0.2 (%76.6)->0.2 (%23.4))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.25 (0.10-->5.37) (max @ vno 159481 --> 159523) face area 0.34 +- 0.17 (0.00-->8.84) mean absolute distance = 0.18 +- 0.27 3338 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5399405.5, rms=4.41 027: dt: 0.5000, sse=5728430.0, rms=3.974 (0.000%) rms = 4.20, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=5210938.0, rms=2.556 (0.000%) 029: dt: 0.2500, sse=5081435.0, rms=2.055 (0.000%) 030: dt: 0.2500, sse=5132253.0, rms=1.704 (0.000%) rms = 1.73, time step reduction 2 of 3 to 0.125... 031: dt: 0.1250, sse=5065830.5, rms=1.594 (0.000%) 032: dt: 0.1250, sse=4977651.5, rms=1.442 (0.000%) rms = 1.43, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=4938956.5, rms=1.429 (0.000%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 1 vertex label from ripped group removing 1 vertex label from ripped group mean border=82.2, 15 (3) missing vertices, mean dist -0.0 [0.2 (%59.2)->0.2 (%40.8))] %91 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=4974679.5, rms=1.91 rms = 2.70, time step reduction 1 of 3 to 0.250... 034: dt: 0.2500, sse=5072500.0, rms=1.253 (0.000%) 035: dt: 0.2500, sse=5248130.0, rms=1.068 (0.000%) rms = 1.08, time step reduction 2 of 3 to 0.125... rms = 1.06, time step reduction 3 of 3 to 0.062... 036: dt: 0.1250, sse=5249605.5, rms=1.059 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 7 non-cortical segments detected only using segment with 1989 vertices erasing segment 1 (vno[0] = 96989) erasing segment 2 (vno[0] = 103184) erasing segment 3 (vno[0] = 109704) erasing segment 4 (vno[0] = 112267) erasing segment 5 (vno[0] = 117234) erasing segment 6 (vno[0] = 118242) writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/label/rh.cortex.label... writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.curv writing smoothed area to rh.area writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.area vertex spacing 0.90 +- 0.25 (0.05-->5.62) (max @ vno 159481 --> 159523) face area 0.34 +- 0.16 (0.00-->9.06) refinement took 8.2 minutes #-------------------------------------------- #@# Smooth2 rh Thu Aug 8 20:59:03 CEST 2013 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 20:59:09 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 49.2 mm, total surface area = 97696 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.117 (target=0.015) step 005: RMS=0.081 (target=0.015) step 010: RMS=0.058 (target=0.015) step 015: RMS=0.047 (target=0.015) step 020: RMS=0.039 (target=0.015) step 025: RMS=0.032 (target=0.015) step 030: RMS=0.028 (target=0.015) step 035: RMS=0.023 (target=0.015) step 040: RMS=0.020 (target=0.015) step 045: RMS=0.018 (target=0.015) step 050: RMS=0.016 (target=0.015) step 055: RMS=0.015 (target=0.015) inflation complete. inflation took 0.6 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 205 vertices thresholded to be in k1 ~ [-0.42 0.37], k2 ~ [-0.17 0.14] total integrated curvature = 0.527*4pi (6.626) --> 0 handles ICI = 1.7, FI = 12.1, variation=201.736 165 vertices thresholded to be in [-0.04 0.01] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 165 vertices thresholded to be in [-0.14 0.17] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.015, std = 0.024 done. #----------------------------------------- #@# Curvature Stats rh Thu Aug 8 21:01:47 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub011 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 [ sub011/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 [ 308 ] Gb_filter = 0 WARN: S lookup min: -0.857142 WARN: S explicit min: 0.000000 vertex = 464 #-------------------------------------------- #@# Sphere rh Thu Aug 8 21:01:53 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 0.274... 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 %20.02 pass 1: epoch 2 of 3 starting distance error %19.95 unfolding complete - removing small folds... starting distance error %19.82 removing remaining folds... final distance error %19.84 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/rh.sphere spherical transformation took 1.05 hours #-------------------------------------------- #@# Surf Reg rh Thu Aug 8 22:04:43 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 = 0.587 curvature mean = 0.029, std = 0.932 curvature mean = 0.025, std = 0.841 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 0.00) sse = 412018.2, tmin=1.3498 d=32.00 min @ (0.00, -8.00, 0.00) sse = 293392.5, tmin=2.8062 d=16.00 min @ (0.00, 0.00, 4.00) sse = 279558.9, tmin=4.1143 d=8.00 min @ (0.00, 2.00, -2.00) sse = 273814.4, tmin=5.4315 d=4.00 min @ (0.00, -1.00, 1.00) sse = 269481.1, tmin=6.7803 d=2.00 min @ (0.00, 0.00, -0.50) sse = 269029.4, tmin=8.1483 d=1.00 min @ (0.00, 0.00, 0.25) sse = 269027.5, tmin=9.5028 d=0.50 min @ (0.00, 0.00, -0.12) sse = 268967.0, tmin=10.8516 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 10.85 min curvature mean = -0.000, std = 0.937 curvature mean = 0.012, std = 0.929 curvature mean = -0.007, std = 0.944 curvature mean = 0.006, std = 0.966 curvature mean = -0.011, std = 0.941 curvature mean = 0.002, std = 0.984 2 Reading smoothwm curvature mean = -0.024, std = 0.291 curvature mean = 0.005, std = 0.069 curvature mean = 0.074, std = 0.317 curvature mean = 0.005, std = 0.082 curvature mean = 0.041, std = 0.510 curvature mean = 0.006, std = 0.088 curvature mean = 0.023, std = 0.660 curvature mean = 0.006, std = 0.090 curvature mean = 0.007, std = 0.780 MRISregister() return, current seed 0 writing registered surface to ../surf/rh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white rh Thu Aug 8 22:38:06 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 22:38:08 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 22:38:11 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub011 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... 1501 labels changed using aseg relabeling using gibbs priors... 000: 3392 changed, 159726 examined... 001: 735 changed, 14448 examined... 002: 190 changed, 4118 examined... 003: 70 changed, 1110 examined... 004: 35 changed, 395 examined... 005: 12 changed, 192 examined... 006: 5 changed, 75 examined... 007: 5 changed, 41 examined... 008: 3 changed, 31 examined... 009: 0 changed, 15 examined... 217 labels changed using aseg 000: 131 total segments, 91 labels (418 vertices) changed 001: 44 total segments, 4 labels (20 vertices) changed 002: 39 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 41 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1971 vertices marked for relabeling... 1971 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 1 minutes and 12 seconds. #-------------------------------------------- #@# Make Pial Surf rh Thu Aug 8 22:39:22 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub011 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/sub011/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/wm.mgz... 20244 bright wm thresholded. 947 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.orig... computing class statistics... border white: 292650 voxels (1.74%) border gray 329335 voxels (1.96%) WM (92.0): 93.5 +- 10.0 [70.0 --> 110.0] GM (76.0) : 74.1 +- 12.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 46.1 (was 70) setting MAX_BORDER_WHITE to 115.0 (was 105) setting MIN_BORDER_WHITE to 59.0 (was 85) setting MAX_CSF to 33.2 (was 40) setting MAX_GRAY to 95.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 52.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 20.4 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=59 mean inside = 93.3, mean outside = 69.4 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/sub011/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.04-->4.59) (max @ vno 159481 --> 159517) face area 0.28 +- 0.12 (0.00-->5.21) mean absolute distance = 0.66 +- 0.77 4512 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 6 points - only 0.00% unknown removing 4 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 4 with 4 points - only 0.00% unknown deleting segment 6 with 537 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 7 with 4 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 10 with 8 points - only 0.00% unknown deleting segment 11 with 6 points - only 0.00% unknown deleting segment 12 with 6 points - only 0.00% unknown deleting segment 13 with 16 points - only 0.00% unknown mean border=73.6, 23 (23) missing vertices, mean dist 0.4 [0.5 (%31.7)->0.7 (%68.3))] %75 local maxima, %21 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 (0.11-->4.50) (max @ vno 159481 --> 159517) face area 0.28 +- 0.13 (0.00-->5.11) mean absolute distance = 0.31 +- 0.49 2843 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=8473527.0, rms=13.47 001: dt: 0.5000, sse=8494065.0, rms=9.717 (0.000%) 002: dt: 0.5000, sse=8777156.0, rms=7.568 (0.000%) 003: dt: 0.5000, sse=8969415.0, rms=6.203 (0.000%) 004: dt: 0.5000, sse=9261748.0, rms=5.386 (0.000%) 005: dt: 0.5000, sse=9342896.0, rms=4.896 (0.000%) 006: dt: 0.5000, sse=9521777.0, rms=4.651 (0.000%) 007: dt: 0.5000, sse=9505386.0, rms=4.482 (0.000%) 008: dt: 0.5000, sse=9562392.0, rms=4.410 (0.000%) 009: dt: 0.5000, sse=9477041.0, rms=4.337 (0.000%) rms = 4.31, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=9537380.0, rms=4.309 (0.000%) 011: dt: 0.2500, sse=5998708.5, rms=2.992 (0.000%) 012: dt: 0.2500, sse=5481670.0, rms=2.545 (0.000%) 013: dt: 0.2500, sse=5163551.0, rms=2.448 (0.000%) 014: dt: 0.2500, sse=5076406.0, rms=2.365 (0.000%) rms = 2.34, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=4973673.0, rms=2.340 (0.000%) 016: dt: 0.1250, sse=4756675.0, rms=2.156 (0.000%) rms = 2.14, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=4708796.0, rms=2.138 (0.000%) positioning took 2.4 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 10 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 5 with 6 points - only 0.00% unknown deleting segment 6 with 266 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 7 with 4 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 8 with 1 points - only 0.00% unknown deleting segment 10 with 14 points - only 0.00% unknown removing 3 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 14 with 44 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 deleting segment 17 with 7 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 18 with 1 points - only 0.00% unknown deleting segment 19 with 17 points - only 0.00% unknown mean border=77.6, 19 (3) missing vertices, mean dist -0.2 [0.3 (%74.7)->0.2 (%25.3))] %81 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.25 (0.06-->4.43) (max @ vno 45728 --> 159526) face area 0.35 +- 0.17 (0.00-->6.38) mean absolute distance = 0.23 +- 0.34 3631 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5735269.5, rms=5.75 018: dt: 0.5000, sse=6073061.5, rms=3.893 (0.000%) rms = 4.32, time step reduction 1 of 3 to 0.250... 019: dt: 0.2500, sse=5509810.5, rms=2.812 (0.000%) 020: dt: 0.2500, sse=5302589.0, rms=2.247 (0.000%) 021: dt: 0.2500, sse=5205111.0, rms=1.919 (0.000%) 022: dt: 0.2500, sse=5175737.5, rms=1.862 (0.000%) 023: dt: 0.2500, sse=5106272.5, rms=1.802 (0.000%) rms = 1.80, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=5118582.0, rms=1.796 (0.000%) 025: dt: 0.1250, sse=4974942.5, rms=1.652 (0.000%) rms = 1.64, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=4935998.5, rms=1.644 (0.000%) positioning took 1.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 10 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown deleting segment 3 with 6 points - only 0.00% unknown deleting segment 4 with 263 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 5 with 4 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 6 with 1 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown deleting segment 8 with 11 points - only 0.00% unknown removing 3 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 11 with 64 points - only 0.00% unknown deleting segment 12 with 6 points - only 0.00% unknown deleting segment 13 with 5 points - only 0.00% unknown deleting segment 14 with 7 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 15 with 1 points - only 0.00% unknown deleting segment 16 with 19 points - only 0.00% unknown mean border=81.0, 17 (3) missing vertices, mean dist -0.1 [0.2 (%76.6)->0.2 (%23.4))] %89 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.25 (0.10-->5.37) (max @ vno 159481 --> 159523) face area 0.34 +- 0.16 (0.00-->8.83) mean absolute distance = 0.18 +- 0.27 3380 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5420578.0, rms=4.41 027: dt: 0.5000, sse=5748837.5, rms=3.969 (0.000%) rms = 4.20, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=5229811.5, rms=2.554 (0.000%) 029: dt: 0.2500, sse=5100590.0, rms=2.054 (0.000%) 030: dt: 0.2500, sse=5150585.5, rms=1.705 (0.000%) rms = 1.73, time step reduction 2 of 3 to 0.125... 031: dt: 0.1250, sse=5084212.0, rms=1.596 (0.000%) 032: dt: 0.1250, sse=4996539.0, rms=1.444 (0.000%) rms = 1.43, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=4958009.0, rms=1.431 (0.000%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 10 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown deleting segment 3 with 7 points - only 0.00% unknown deleting segment 4 with 272 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 5 with 4 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 6 with 1 points - only 0.00% unknown deleting segment 7 with 14 points - only 0.00% unknown deleting segment 9 with 64 points - only 0.00% unknown deleting segment 10 with 6 points - only 0.00% unknown deleting segment 11 with 5 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 7 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 14 with 1 points - only 0.00% unknown deleting segment 15 with 20 points - only 0.00% unknown mean border=82.2, 16 (3) missing vertices, mean dist -0.0 [0.2 (%59.2)->0.2 (%40.8))] %91 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4993643.0, rms=1.91 rms = 2.69, time step reduction 1 of 3 to 0.250... 034: dt: 0.2500, sse=5093207.0, rms=1.254 (0.000%) 035: dt: 0.2500, sse=5270818.0, rms=1.069 (0.000%) rms = 1.08, time step reduction 2 of 3 to 0.125... rms = 1.06, time step reduction 3 of 3 to 0.062... 036: dt: 0.1250, sse=5272450.5, rms=1.060 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... smoothing surface for 5 iterations... mean border=49.2, 17 (17) missing vertices, mean dist 1.7 [0.6 (%0.0)->2.3 (%100.0))] %14 local maxima, %56 large gradients and %26 min vals, 1614 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=35291056.0, rms=32.37 001: dt: 0.5000, sse=25554212.0, rms=26.991 (0.000%) 002: dt: 0.5000, sse=18703494.0, rms=22.476 (0.000%) 003: dt: 0.5000, sse=14080444.0, rms=18.788 (0.000%) 004: dt: 0.5000, sse=11205035.0, rms=15.804 (0.000%) 005: dt: 0.5000, sse=9506431.0, rms=13.410 (0.000%) 006: dt: 0.5000, sse=8555902.0, rms=11.498 (0.000%) 007: dt: 0.5000, sse=8009868.0, rms=9.870 (0.000%) 008: dt: 0.5000, sse=7710829.0, rms=8.476 (0.000%) 009: dt: 0.5000, sse=7555609.0, rms=7.273 (0.000%) 010: dt: 0.5000, sse=7583803.5, rms=6.330 (0.000%) 011: dt: 0.5000, sse=7692817.5, rms=5.586 (0.000%) 012: dt: 0.5000, sse=7841051.0, rms=5.065 (0.000%) 013: dt: 0.5000, sse=7985915.5, rms=4.690 (0.000%) 014: dt: 0.5000, sse=8164496.0, rms=4.486 (0.000%) 015: dt: 0.5000, sse=8183933.5, rms=4.315 (0.000%) 016: dt: 0.5000, sse=8308496.5, rms=4.216 (0.000%) 017: dt: 0.5000, sse=8267888.5, rms=4.126 (0.000%) rms = 4.10, time step reduction 1 of 3 to 0.250... 018: dt: 0.5000, sse=8374602.0, rms=4.099 (0.000%) 019: dt: 0.2500, sse=5795720.5, rms=3.372 (0.000%) 020: dt: 0.2500, sse=5567222.5, rms=3.178 (0.000%) rms = 3.16, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=5413352.0, rms=3.156 (0.000%) 022: dt: 0.1250, sse=5182234.0, rms=3.043 (0.000%) rms = 3.03, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=5153348.0, rms=3.031 (0.000%) positioning took 3.2 minutes mean border=47.2, 1057 (4) missing vertices, mean dist 0.1 [0.2 (%50.7)->0.6 (%49.3))] %32 local maxima, %41 large gradients and %21 min vals, 431 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=5823663.5, rms=4.74 024: dt: 0.5000, sse=6182866.0, rms=4.048 (0.000%) rms = 4.08, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=5768704.0, rms=3.505 (0.000%) 026: dt: 0.2500, sse=5884238.0, rms=3.256 (0.000%) 027: dt: 0.2500, sse=5806965.0, rms=3.143 (0.000%) 028: dt: 0.2500, sse=5854576.5, rms=3.078 (0.000%) rms = 3.04, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=5855774.0, rms=3.036 (0.000%) 030: dt: 0.1250, sse=5680723.5, rms=2.912 (0.000%) rms = 2.89, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=5671070.0, rms=2.886 (0.000%) positioning took 1.2 minutes mean border=45.0, 1285 (3) missing vertices, mean dist 0.1 [0.2 (%38.6)->0.4 (%61.4))] %54 local maxima, %20 large gradients and %21 min vals, 637 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=5984866.5, rms=4.21 032: dt: 0.5000, sse=6290843.0, rms=3.934 (0.000%) rms = 4.03, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=5918775.0, rms=3.224 (0.000%) 034: dt: 0.2500, sse=6174302.5, rms=2.942 (0.000%) 035: dt: 0.2500, sse=6104891.0, rms=2.882 (0.000%) rms = 2.85, time step reduction 2 of 3 to 0.125... 036: dt: 0.2500, sse=6180108.0, rms=2.848 (0.000%) 037: dt: 0.1250, sse=5965229.0, rms=2.722 (0.000%) rms = 2.70, time step reduction 3 of 3 to 0.062... 038: dt: 0.1250, sse=5953201.5, rms=2.702 (0.000%) positioning took 1.1 minutes mean border=43.8, 2543 (3) missing vertices, mean dist 0.1 [0.2 (%44.3)->0.3 (%55.7))] %58 local maxima, %15 large gradients and %21 min vals, 533 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/sub011/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=6021390.0, rms=3.07 rms = 3.71, time step reduction 1 of 3 to 0.250... 039: dt: 0.2500, sse=5856422.0, rms=2.786 (0.000%) 040: dt: 0.2500, sse=6058540.0, rms=2.704 (0.000%) rms = 2.67, time step reduction 2 of 3 to 0.125... 041: dt: 0.2500, sse=6139736.5, rms=2.673 (0.000%) 042: dt: 0.1250, sse=6035495.5, rms=2.572 (0.000%) rms = 2.56, time step reduction 3 of 3 to 0.062... 043: dt: 0.1250, sse=6047119.0, rms=2.556 (0.000%) positioning took 0.8 minutes writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.area.pial vertex spacing 1.01 +- 0.42 (0.04-->8.87) (max @ vno 111253 --> 109961) face area 0.41 +- 0.30 (0.00-->15.02) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 159726 vertices processed 25000 of 159726 vertices processed 50000 of 159726 vertices processed 75000 of 159726 vertices processed 100000 of 159726 vertices processed 125000 of 159726 vertices processed 150000 of 159726 vertices processed 0 of 159726 vertices processed 25000 of 159726 vertices processed 50000 of 159726 vertices processed 75000 of 159726 vertices processed 100000 of 159726 vertices processed 125000 of 159726 vertices processed 150000 of 159726 vertices processed thickness calculation complete, 283:749 truncations. 36993 vertices at 0 distance 111818 vertices at 1 distance 101992 vertices at 2 distance 39995 vertices at 3 distance 10838 vertices at 4 distance 2673 vertices at 5 distance 772 vertices at 6 distance 293 vertices at 7 distance 126 vertices at 8 distance 71 vertices at 9 distance 35 vertices at 10 distance 11 vertices at 11 distance 18 vertices at 12 distance 14 vertices at 13 distance 22 vertices at 14 distance 8 vertices at 15 distance 9 vertices at 16 distance 8 vertices at 17 distance 13 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/sub011/surf/rh.thickness positioning took 16.1 minutes #-------------------------------------------- #@# Surf Volume rh Thu Aug 8 22:55:28 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.volume rh.area.mid mul rh.thickness Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# WM/GM Contrast rh Thu Aug 8 22:55:31 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts pctsurfcon --s sub011 --rh-only Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts/pctsurfcon.log Thu Aug 8 22:55:31 CEST 2013 setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts /opt/freesurfer/5.3.0/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux snake6 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux FREESURFER_HOME /opt/freesurfer/5.3.0 mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/tmp.pctsurfcon.22373/rh.wm.mgh --regheader sub011 --cortex srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/mri/orig.mgz as target reference. Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/label/rh.cortex.label Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 = 123745 Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/label/rh.cortex.label Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/tmp.pctsurfcon.22373/rh.wm.mgh Dim: 159726 1 1 mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/tmp.pctsurfcon.22373/rh.gm.mgh --projfrac 0.3 --regheader sub011 --cortex srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/mri/orig.mgz as target reference. Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/label/rh.cortex.label Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.white Done reading source surface Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 = 142347 Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/label/rh.cortex.label Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/tmp.pctsurfcon.22373/rh.gm.mgh Dim: 159726 1 1 mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/tmp.pctsurfcon.22373/rh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/tmp.pctsurfcon.22373/rh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/surf/rh.w-g.pct.mgh mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.w-g.pct.mgh --annot sub011 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/surf/rh.w-g.pct.mgh --annot sub011 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/stats/rh.w-g.pct.stats --snr sysname Linux hostname snake6 machine x86_64 user fkaule UseRobust 0 Constructing seg from annotation Reading annotation reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Seg base 2000 Loading /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.w-g.pct.mgh Vertex Area is 0.669092 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 2000 unknown 0 0.000 1 2001 bankssts 1444 1006.144 2 2002 caudalanteriorcingulate 1713 1135.003 3 2003 caudalmiddlefrontal 3644 2389.215 4 2004 corpuscallosum 0 0.000 5 2005 cuneus 2396 1574.379 6 2006 entorhinal 572 421.194 7 2007 fusiform 5110 3446.380 8 2008 inferiorparietal 9379 6447.679 9 2009 inferiortemporal 5201 3558.020 10 2010 isthmuscingulate 1900 1247.385 11 2011 lateraloccipital 7738 5040.951 12 2012 lateralorbitofrontal 4217 2842.153 13 2013 lingual 4731 3373.175 14 2014 medialorbitofrontal 2926 1983.715 15 2015 middletemporal 5821 4035.433 16 2016 parahippocampal 1046 705.774 17 2017 paracentral 2912 1822.906 18 2018 parsopercularis 3475 2366.997 19 2019 parsorbitalis 1400 949.602 20 2020 parstriangularis 3276 2220.425 21 2021 pericalcarine 2260 1544.378 22 2022 postcentral 6873 4418.708 23 2023 posteriorcingulate 2288 1569.428 24 2024 precentral 9038 5721.352 25 2025 precuneus 7451 4972.561 26 2026 rostralanteriorcingulate 1597 1057.024 27 2027 rostralmiddlefrontal 10541 7216.732 28 2028 superiorfrontal 12639 8537.286 29 2029 superiorparietal 10631 6954.118 30 2030 superiortemporal 6297 4245.163 31 2031 supramarginal 6728 4451.228 32 2032 frontalpole 481 319.452 33 2033 temporalpole 527 400.592 34 2034 transversetemporal 676 430.078 35 2035 insula 3748 2465.553 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats rh Thu Aug 8 22:55:46 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 sub011 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 1444 1006 2504 2.461 0.433 0.129 0.038 19 2.5 bankssts 1713 1135 3201 2.510 0.624 0.134 0.030 28 2.2 caudalanteriorcingulate 3644 2389 6596 2.457 0.478 0.129 0.038 50 5.9 caudalmiddlefrontal 2396 1574 3204 1.850 0.453 0.176 0.069 44 6.9 cuneus 572 421 1865 3.317 0.877 0.150 0.063 8 1.3 entorhinal 5110 3446 10213 2.569 0.554 0.147 0.064 98 11.4 fusiform 9379 6448 17193 2.404 0.504 0.150 0.054 170 20.0 inferiorparietal 5201 3558 10531 2.379 0.680 0.165 0.079 124 14.8 inferiortemporal 1900 1247 3334 2.414 0.860 0.154 0.056 33 4.3 isthmuscingulate 7738 5041 11474 2.048 0.420 0.160 0.066 153 22.1 lateraloccipital 4217 2842 8516 2.656 0.617 0.157 0.069 85 12.0 lateralorbitofrontal 4731 3373 6910 1.935 0.535 0.181 0.080 107 15.3 lingual 2926 1984 5459 2.341 0.706 0.158 0.074 88 8.6 medialorbitofrontal 5821 4035 13614 2.741 0.634 0.149 0.059 122 15.4 middletemporal 1046 706 2379 2.942 0.587 0.129 0.041 12 1.7 parahippocampal 2912 1823 4560 2.336 0.455 0.125 0.045 35 5.8 paracentral 3475 2367 6522 2.474 0.395 0.133 0.046 55 6.5 parsopercularis 1400 950 3211 2.645 0.622 0.188 0.086 47 4.5 parsorbitalis 3276 2220 6186 2.388 0.520 0.146 0.053 63 6.6 parstriangularis 2260 1544 2143 1.494 0.320 0.156 0.063 31 5.8 pericalcarine 6873 4419 9459 1.919 0.622 0.125 0.042 88 12.3 postcentral 2288 1569 4287 2.440 0.809 0.169 0.065 58 6.3 posteriorcingulate 9038 5721 15299 2.452 0.483 0.122 0.056 99 26.7 precentral 7451 4973 12470 2.380 0.469 0.138 0.050 115 13.8 precuneus 1597 1057 3475 2.710 0.528 0.142 0.058 38 3.6 rostralanteriorcingulate 10541 7217 19853 2.382 0.539 0.175 0.099 403 33.1 rostralmiddlefrontal 12639 8537 26379 2.675 0.558 0.144 0.048 194 23.7 superiorfrontal 10631 6954 16075 2.115 0.396 0.130 0.041 147 17.5 superiorparietal 6297 4245 14153 2.856 0.657 0.138 0.054 111 14.5 superiortemporal 6728 4451 12177 2.443 0.494 0.137 0.046 109 12.5 supramarginal 481 319 1027 2.335 0.601 0.204 0.102 22 1.7 frontalpole 527 401 1932 3.618 0.759 0.203 0.103 16 1.9 temporalpole 676 430 993 2.142 0.459 0.145 0.054 10 1.4 transversetemporal 3748 2466 7690 2.880 0.851 0.138 0.071 72 10.8 insula #----------------------------------------- #@# Cortical Parc 2 rh Thu Aug 8 22:56:10 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub011 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... 20 labels changed using aseg relabeling using gibbs priors... 000: 11252 changed, 159726 examined... 001: 2787 changed, 43437 examined... 002: 904 changed, 14416 examined... 003: 421 changed, 5075 examined... 004: 199 changed, 2262 examined... 005: 94 changed, 1109 examined... 006: 56 changed, 507 examined... 007: 22 changed, 284 examined... 008: 14 changed, 116 examined... 009: 10 changed, 80 examined... 010: 10 changed, 58 examined... 011: 5 changed, 51 examined... 012: 3 changed, 31 examined... 013: 1 changed, 18 examined... 014: 1 changed, 7 examined... 015: 1 changed, 7 examined... 016: 0 changed, 7 examined... 10 labels changed using aseg 000: 342 total segments, 256 labels (3703 vertices) changed 001: 117 total segments, 32 labels (234 vertices) changed 002: 88 total segments, 3 labels (22 vertices) changed 003: 85 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 181 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1215 vertices marked for relabeling... 1215 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 1 minutes and 25 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Thu Aug 8 22:57:35 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 sub011 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 1089 718 1905 2.199 0.585 0.178 0.086 31 4.0 G_and_S_frontomargin 1532 1035 2721 2.322 0.431 0.147 0.045 25 2.8 G_and_S_occipital_inf 1508 888 2349 2.266 0.485 0.133 0.149 20 15.1 G_and_S_paracentral 1760 1169 3324 2.579 0.473 0.150 0.055 30 4.0 G_and_S_subcentral 1283 871 2491 2.224 0.528 0.190 0.088 50 4.2 G_and_S_transv_frontopol 3430 2279 6392 2.523 0.477 0.137 0.049 64 6.8 G_and_S_cingul-Ant 2187 1517 4475 2.715 0.531 0.138 0.040 31 3.4 G_and_S_cingul-Mid-Ant 1691 1196 3366 2.624 0.590 0.147 0.056 33 4.2 G_and_S_cingul-Mid-Post 817 545 1999 3.029 0.643 0.180 0.066 21 2.2 G_cingul-Post-dorsal 390 251 881 2.898 0.719 0.175 0.071 9 1.1 G_cingul-Post-ventral 2118 1404 2656 1.694 0.442 0.172 0.070 37 6.2 G_cuneus 2481 1687 5246 2.574 0.381 0.151 0.061 58 6.2 G_front_inf-Opercular 481 306 1226 2.905 0.365 0.185 0.094 18 1.5 G_front_inf-Orbital 1889 1287 3820 2.401 0.504 0.165 0.066 44 4.6 G_front_inf-Triangul 4290 2905 10090 2.690 0.503 0.184 0.125 240 14.8 G_front_middle 8225 5466 18847 2.750 0.582 0.156 0.056 156 17.2 G_front_sup 612 382 1398 3.174 0.720 0.138 0.103 19 2.5 G_Ins_lg_and_S_cent_ins 608 403 2091 3.592 0.746 0.161 0.084 15 1.8 G_insular_short 2423 1621 4717 2.388 0.464 0.170 0.081 65 7.7 G_occipital_middle 2231 1422 3644 2.168 0.347 0.153 0.055 43 4.8 G_occipital_sup 2233 1459 5090 2.720 0.457 0.162 0.078 57 5.5 G_oc-temp_lat-fusifor 3215 2167 4918 1.953 0.585 0.195 0.094 79 12.2 G_oc-temp_med-Lingual 1519 1021 4139 3.116 0.841 0.165 0.095 40 6.0 G_oc-temp_med-Parahip 3017 2030 7523 2.812 0.672 0.190 0.095 100 11.4 G_orbital 3650 2513 8384 2.595 0.539 0.165 0.060 88 8.8 G_pariet_inf-Angular 3133 2047 6435 2.554 0.486 0.144 0.051 60 6.4 G_pariet_inf-Supramar 3519 2273 6201 2.214 0.415 0.138 0.047 58 6.6 G_parietal_sup 2380 1480 3567 1.944 0.557 0.139 0.060 44 6.0 G_postcentral 3543 2097 7444 2.713 0.384 0.120 0.043 49 6.5 G_precentral 3592 2349 6902 2.386 0.485 0.155 0.061 82 8.6 G_precuneus 812 528 1739 2.334 0.654 0.197 0.134 47 4.5 G_rectus 516 329 1079 2.802 0.919 0.097 0.042 8 0.6 G_subcallosal 599 373 918 2.120 0.409 0.158 0.101 28 3.1 G_temp_sup-G_T_transv 2144 1448 6428 3.222 0.597 0.173 0.078 53 6.7 G_temp_sup-Lateral 687 477 2006 3.453 0.659 0.152 0.062 11 1.6 G_temp_sup-Plan_polar 1008 676 1983 2.668 0.411 0.115 0.035 11 1.3 G_temp_sup-Plan_tempo 3068 2120 7027 2.457 0.718 0.189 0.107 102 11.3 G_temporal_inf 3587 2490 9985 2.954 0.576 0.167 0.076 101 12.2 G_temporal_middle 486 319 644 2.185 0.355 0.096 0.023 2 0.4 Lat_Fis-ant-Horizont 373 252 687 2.582 0.370 0.139 0.041 6 0.6 Lat_Fis-ant-Vertical 1420 946 1775 2.177 0.507 0.120 0.042 13 2.2 Lat_Fis-post 3676 2335 4646 1.831 0.401 0.168 0.087 80 14.3 Pole_occipital 1845 1277 4874 2.828 0.819 0.169 0.081 43 5.6 Pole_temporal 2810 2074 3555 1.899 0.640 0.162 0.065 54 6.5 S_calcarine 3021 2013 3081 1.671 0.516 0.113 0.032 20 4.2 S_central 1649 1105 2257 2.142 0.338 0.114 0.031 12 2.1 S_cingul-Marginalis 746 503 1354 2.905 0.597 0.121 0.040 5 1.2 S_circular_insula_ant 1300 881 2198 2.693 0.623 0.097 0.027 6 1.5 S_circular_insula_inf 1931 1324 2829 2.342 0.437 0.117 0.035 13 3.0 S_circular_insula_sup 844 604 1469 2.482 0.497 0.108 0.035 8 1.0 S_collat_transv_ant 438 292 472 1.862 0.351 0.137 0.039 4 0.7 S_collat_transv_post 3180 2155 5125 2.256 0.435 0.133 0.042 44 5.3 S_front_inf 2533 1754 4325 2.294 0.483 0.164 0.084 68 6.6 S_front_middle 3429 2375 5822 2.417 0.407 0.131 0.044 44 6.5 S_front_sup 649 425 898 2.044 0.324 0.107 0.024 6 0.7 S_interm_prim-Jensen 4462 2969 5822 2.064 0.392 0.115 0.031 41 5.4 S_intrapariet_and_P_trans 1075 726 1259 1.849 0.394 0.155 0.048 13 2.1 S_oc_middle_and_Lunatus 1758 1169 2396 2.159 0.330 0.140 0.039 20 3.0 S_oc_sup_and_transversal 593 400 807 2.202 0.415 0.138 0.042 8 1.1 S_occipital_ant 1320 899 2042 2.186 0.477 0.131 0.036 13 2.1 S_oc-temp_lat 1906 1357 2953 2.419 0.550 0.116 0.030 12 2.3 S_oc-temp_med_and_Lingual 632 429 785 1.907 0.387 0.147 0.046 7 1.2 S_orbital_lateral 806 574 1396 2.304 0.807 0.119 0.034 7 1.0 S_orbital_med-olfact 1553 1070 2744 2.532 0.501 0.154 0.060 24 3.8 S_orbital-H_Shaped 2134 1448 3045 2.280 0.463 0.138 0.039 24 3.5 S_parieto_occipital 2333 1482 2788 2.008 0.765 0.139 0.042 38 4.0 S_pericallosal 3273 2158 3809 1.927 0.395 0.114 0.033 28 4.2 S_postcentral 2151 1397 3258 2.343 0.389 0.110 0.031 20 2.8 S_precentral-inf-part 1969 1285 2761 2.417 0.409 0.122 0.034 17 2.8 S_precentral-sup-part 292 208 364 1.796 0.805 0.150 0.030 3 0.4 S_suborbital 1722 1180 2679 2.379 0.482 0.121 0.036 15 2.5 S_subparietal 1430 977 1791 2.047 0.529 0.128 0.033 12 2.0 S_temporal_inf 7276 5009 12164 2.474 0.453 0.131 0.038 91 11.5 S_temporal_sup 394 268 606 2.567 0.451 0.124 0.030 3 0.5 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 rh Thu Aug 8 22:58:03 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub011 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... 1453 labels changed using aseg relabeling using gibbs priors... 000: 3236 changed, 159726 examined... 001: 766 changed, 13731 examined... 002: 198 changed, 4170 examined... 003: 82 changed, 1154 examined... 004: 36 changed, 486 examined... 005: 22 changed, 219 examined... 006: 5 changed, 128 examined... 007: 3 changed, 34 examined... 008: 2 changed, 21 examined... 009: 2 changed, 16 examined... 010: 1 changed, 10 examined... 011: 2 changed, 5 examined... 012: 0 changed, 12 examined... 147 labels changed using aseg 000: 72 total segments, 39 labels (204 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 59 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1100 vertices marked for relabeling... 1100 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas40.annot... classification took 1 minutes and 14 seconds. #----------------------------------------- #@# Parcellation Stats 3 rh Thu Aug 8 22:59:17 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 sub011 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 1775 1176 3484 2.559 0.638 0.138 0.032 31 2.4 caudalanteriorcingulate 3758 2456 6760 2.475 0.470 0.130 0.038 52 6.1 caudalmiddlefrontal 2863 1881 3767 1.857 0.438 0.171 0.066 51 7.7 cuneus 566 416 1854 3.322 0.892 0.151 0.064 8 1.3 entorhinal 4506 3053 8831 2.564 0.553 0.141 0.060 79 9.5 fusiform 8837 6076 16423 2.417 0.500 0.151 0.055 164 19.4 inferiorparietal 5751 3937 11827 2.404 0.680 0.166 0.081 140 16.6 inferiortemporal 1888 1242 3287 2.398 0.847 0.154 0.056 33 4.3 isthmuscingulate 8214 5347 12257 2.058 0.426 0.160 0.066 163 23.2 lateraloccipital 4667 3157 9620 2.604 0.678 0.169 0.080 114 15.4 lateralorbitofrontal 4699 3353 6875 1.937 0.535 0.180 0.079 106 14.8 lingual 2361 1586 4687 2.349 0.782 0.165 0.083 82 7.8 medialorbitofrontal 6800 4712 15334 2.709 0.616 0.148 0.057 135 16.9 middletemporal 1001 679 2310 2.920 0.590 0.131 0.042 12 1.7 parahippocampal 3035 1914 4699 2.321 0.461 0.125 0.044 35 6.0 paracentral 3744 2548 7261 2.502 0.403 0.138 0.049 66 7.4 parsopercularis 1507 1016 3232 2.635 0.507 0.161 0.066 38 3.6 parsorbitalis 3684 2500 6779 2.342 0.499 0.150 0.056 71 8.0 parstriangularis 2285 1559 2170 1.492 0.323 0.159 0.065 33 6.4 pericalcarine 7596 4886 10385 1.932 0.620 0.127 0.044 98 13.8 postcentral 2429 1671 4623 2.469 0.812 0.170 0.065 62 6.8 posteriorcingulate 8753 5516 14882 2.447 0.488 0.122 0.056 98 26.4 precentral 7548 5017 12810 2.388 0.459 0.139 0.052 125 14.6 precuneus 1752 1159 3663 2.697 0.520 0.141 0.056 39 3.9 rostralanteriorcingulate 6692 4601 12924 2.457 0.546 0.171 0.105 283 19.9 rostralmiddlefrontal 16079 10898 32236 2.582 0.564 0.150 0.056 296 34.2 superiorfrontal 9332 6119 14292 2.132 0.395 0.127 0.039 120 14.4 superiorparietal 8176 5542 18499 2.875 0.693 0.145 0.061 161 21.0 superiortemporal 6287 4171 11145 2.405 0.484 0.134 0.044 98 11.0 supramarginal 660 418 967 2.138 0.463 0.146 0.055 10 1.4 transversetemporal 3431 2265 7001 2.842 0.831 0.128 0.058 50 7.9 insula #-------------------------------------------- #@# Refine Pial Surfs w/ T2/FLAIR Thu Aug 8 22:59:45 CEST 2013 bbregister --s sub011 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/T2raw.lta --init-fsl --T2 Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/T2raw.dat.log Thu Aug 8 22:59:45 CEST 2013 setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts /opt/freesurfer/5.3.0/bin/bbregister --s sub011 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/T2raw.lta --init-fsl --T2 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ Linux snake6 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux FREESURFER_HOME /opt/freesurfer/5.3.0 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/template.nii mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/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/sub011/mri/orig/T2raw.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998102, -0.0611237, 0.00753358) j_ras = (-0.0606425, 0.996759, 0.0528636) k_ras = (0.0107404, -0.0523064, 0.998573) writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/template.nii... fslregister --s sub011 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/fslregister --dof 6 --fsvol brainmask.mgz Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/reg.init.dat.fslregister.log Thu Aug 8 22:59:51 CEST 2013 --s sub011 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/fslregister --dof 6 --fsvol brainmask.mgz $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ snake6 Linux snake6 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux nIters 1 -------------------------------------- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/fslregister/refvol.fslregister.nii mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/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/sub011/mri/brainmask.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.31549e-08, 0) j_ras = (0, -1.11759e-08, -1) k_ras = (5.47152e-09, 1, -3.72529e-09) writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/fslregister/refvol.fslregister.nii... -------------------------------------- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/fslregister/movvol.fslregister.nii --frame 0 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/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/sub011/mri/transforms/tmp.bbregister.22917/template.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998102, -0.0611237, 0.00753358) j_ras = (-0.0606425, 0.996759, 0.0528636) k_ras = (0.0107404, -0.0523064, 0.998573) keeping frame 0 writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/fslregister/movvol.fslregister.nii... Mov determinant is -0.311072 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/fslregister/movvol.fslregister.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/fslregister/reg0.22957.dat --regheader --fslregout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/reg.init.dat.fsl.mat0 --s sub011 --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/sub011/mri/transforms/tmp.bbregister.22917/fslregister/movvol.fslregister.nii reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/fslregister/reg0.22957.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/sub011/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/sub011/mri/transforms/tmp.bbregister.22917/fslregister/movvol.fslregister.nii Tmov: -------------------- -0.700 0.000 0.000 95.888; 0.000 0.000 0.667 -128.000; 0.000 -0.667 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 0.998 0.061 -0.008 0.000; 0.011 -0.052 0.999 -0.000; 0.061 -0.997 -0.053 -0.000; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 0.998 0.061 -0.008 0.000; 0.011 -0.052 0.999 -0.000; 0.061 -0.997 -0.053 -0.000; 0.000 0.000 0.000 1.000; Determinant 1 subject = sub011 RegMat --------------------------- 0.998 0.061 -0.008 0.000; 0.011 -0.052 0.999 -0.000; 0.061 -0.997 -0.053 -0.000; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -0.311072, ref det = -1 Thu Aug 8 22:59:59 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/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/sub011/mri/transforms/tmp.bbregister.22917/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/reg.init.dat.fsl.mat0 Thu Aug 8 23:04:29 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/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/sub011/mri/transforms/tmp.bbregister.22917/reg.init.dat.fsl.mat -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/fslregister/fslmat0.trans.mat -schedule /opt/freesurfer/5.3.0/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s sub011 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/reg.init.dat --fslreg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/reg.init.dat.fsl.mat --noedit tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl ---- FSL registration matrix -------- 0.998 0.056 -0.006 25.361; -0.003 -0.054 -0.999 262.100; -0.057 0.997 -0.053 11.865; 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/sub011/mri/transforms/tmp.bbregister.22917/template.nii reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/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/sub011/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/sub011/mri/transforms/tmp.bbregister.22917/template.nii Tmov: -------------------- -0.700 0.000 0.000 95.888; 0.000 0.000 0.667 -128.000; 0.000 -0.667 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 FSLOUTPUTTYPE NIFTI fsl2TkReg: mov det = -0.311072, ref det = -1 ---- Input registration matrix (computed) -------- 0.998 0.057 -0.003 -0.394; 0.006 -0.053 0.999 -0.884; 0.056 -0.997 -0.054 -0.749; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 0.998 0.057 -0.003 -0.394; 0.006 -0.053 0.999 -0.884; 0.056 -0.997 -0.054 -0.749; 0.000 0.000 0.000 1.000; Determinant 0.999999 subject = sub011 RegMat --------------------------- 0.998 0.057 -0.003 -0.394; 0.006 -0.053 0.999 -0.884; 0.056 -0.997 -0.054 -0.749; 0.000 0.000 0.000 1.000; Started at Thu Aug 8 22:59:51 CEST 2013 Ended at Thu Aug 8 23:10:51 CEST 2013 fslregister Done To check results, run: tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/reg.init.dat --surf orig mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/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/sub011/scripts mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Linux hostname snake6 machine x86_64 user fkaule movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/template.nii regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/reg.init.dat subject sub011 dof 6 outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/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 1376360729 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.998 0.057 -0.003 -0.394; 0.006 -0.053 0.999 -0.884; 0.056 -0.997 -0.054 -0.749; 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 1.057876 1 -25.0 -25.0 25.0 0.998681 2 -25.0 25.0 -25.0 1.013842 3 -25.0 25.0 25.0 1.042111 4 25.0 -25.0 -25.0 0.997035 5 25.0 -25.0 25.0 1.048967 6 25.0 25.0 -25.0 1.009851 7 25.0 25.0 25.0 1.018001 REL: 8 0.203528 8.186364 1.023295 rel = 0.198894 Initial costs ---------------- Number of surface hits 2995 WM Intensity 56.5723 +/- 9.2411 Ctx Intensity 70.8426 +/- 10.0568 Pct Contrast 22.4807 +/- 17.0063 Cost 0.2035 RelCost 0.1989 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9896 0.9896 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.9788 0.9788 0.0 3 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 -4.0000 0.9485 0.9485 0.0 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.8611 0.8611 0.0 39 -4.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.8176 0.8176 0.0 120 -4.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.6454 0.6454 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.2035 0.2035 0.0 Brute Force -------------------------- Min cost was 0.203528 Number of iterations 729 Search time 2.491000 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 0.130 0.000 0.000 0.000 0.000 0.000 0.2034642916 8 0.074 0.000 0.000 0.000 0.000 0.000 0.2031443284 10 0.085 0.000 0.000 0.000 0.000 0.000 0.2031342843 14 0.086 0.000 0.000 0.000 0.000 0.000 0.2031340495 22 0.086 -0.189 0.000 0.000 0.000 0.000 0.1983937281 24 0.086 -0.149 0.000 0.000 0.000 0.000 0.1980860239 28 0.086 -0.144 0.000 0.000 0.000 0.000 0.1980705380 32 0.086 -0.144 1.000 0.000 0.000 0.000 0.1577640908 36 0.086 -0.144 0.618 0.000 0.000 0.000 0.1438398302 37 0.086 -0.144 0.644 0.000 0.000 0.000 0.1426996156 38 0.086 -0.144 0.728 0.000 0.000 0.000 0.1407010084 42 0.086 -0.144 0.724 0.000 0.000 0.000 0.1406850420 44 0.086 -0.144 0.722 0.000 0.000 0.000 0.1406820771 45 0.086 -0.144 0.721 0.000 0.000 0.000 0.1406815801 53 0.086 -0.144 0.721 -0.152 0.000 0.000 0.1373417461 58 0.086 -0.144 0.721 -0.155 0.000 0.000 0.1373175690 59 0.086 -0.144 0.721 -0.158 0.000 0.000 0.1373110666 70 0.086 -0.144 0.721 -0.158 -0.014 0.000 0.1372380844 74 0.086 -0.144 0.721 -0.158 -0.018 0.000 0.1372318346 85 0.086 -0.144 0.721 -0.158 -0.018 0.011 0.1371067201 86 0.086 -0.144 0.721 -0.158 -0.018 0.014 0.1371022266 95 0.119 -0.199 0.997 -0.218 -0.025 0.019 0.1347986883 96 0.109 -0.181 0.908 -0.199 -0.023 0.018 0.1327542424 97 0.106 -0.177 0.884 -0.194 -0.022 0.017 0.1321923342 99 0.103 -0.172 0.861 -0.189 -0.022 0.017 0.1319468574 100 0.103 -0.172 0.859 -0.188 -0.022 0.017 0.1319444511 109 0.011 -0.172 0.859 -0.188 -0.022 0.017 0.1317341795 110 0.048 -0.172 0.859 -0.188 -0.022 0.017 0.1313706473 112 0.038 -0.172 0.859 -0.188 -0.022 0.017 0.1312968957 114 0.037 -0.172 0.859 -0.188 -0.022 0.017 0.1312965202 122 0.037 -0.138 0.859 -0.188 -0.022 0.017 0.1305159360 124 0.037 -0.132 0.859 -0.188 -0.022 0.017 0.1304955314 134 0.037 -0.132 0.859 -0.188 -0.022 0.000 0.1303771844 135 0.037 -0.132 0.859 -0.188 -0.022 -0.005 0.1303738252 136 0.037 -0.132 0.859 -0.188 -0.022 -0.004 0.1303726948 137 0.037 -0.132 0.859 -0.188 -0.022 -0.003 0.1303725804 147 0.037 -0.132 0.859 -0.182 -0.022 -0.003 0.1303205523 148 0.037 -0.132 0.859 -0.180 -0.022 -0.003 0.1303156177 149 0.037 -0.132 0.859 -0.179 -0.022 -0.003 0.1303153989 157 0.037 -0.132 0.859 -0.179 -0.095 -0.003 0.1287691551 160 0.037 -0.132 0.859 -0.179 -0.103 -0.003 0.1287197687 162 0.037 -0.132 0.859 -0.179 -0.107 -0.003 0.1287177795 172 0.046 -0.146 0.932 -0.195 -0.108 -0.001 0.1276837702 174 0.044 -0.142 0.912 -0.190 -0.108 -0.001 0.1275393465 175 0.044 -0.143 0.913 -0.191 -0.108 -0.001 0.1275355191 177 0.044 -0.143 0.914 -0.191 -0.108 -0.001 0.1275350705 187 0.032 -0.143 0.914 -0.191 -0.108 -0.001 0.1274689031 188 0.034 -0.143 0.914 -0.191 -0.108 -0.001 0.1274682212 198 0.034 -0.125 0.914 -0.191 -0.108 -0.001 0.1274375066 199 0.034 -0.133 0.914 -0.191 -0.108 -0.001 0.1273856814 200 0.034 -0.132 0.914 -0.191 -0.108 -0.001 0.1273855168 210 0.034 -0.132 0.914 -0.191 -0.108 0.005 0.1273372907 211 0.034 -0.132 0.914 -0.191 -0.108 0.007 0.1273334255 212 0.034 -0.132 0.914 -0.191 -0.108 0.006 0.1273333726 222 0.034 -0.132 0.914 -0.197 -0.108 0.006 0.1273089560 223 0.034 -0.132 0.914 -0.196 -0.108 0.006 0.1273074994 224 0.034 -0.132 0.914 -0.195 -0.108 0.006 0.1273073781 234 0.034 -0.132 0.914 -0.195 -0.087 0.006 0.1272798768 235 0.034 -0.132 0.914 -0.195 -0.097 0.006 0.1272034896 246 0.034 -0.132 0.915 -0.195 -0.097 0.006 0.1272033727 277 0.034 -0.132 0.915 -0.195 -0.097 0.008 0.1272005113 278 0.034 -0.132 0.915 -0.195 -0.097 0.009 0.1271987565 289 0.034 -0.132 0.915 -0.198 -0.097 0.009 0.1271953611 291 0.034 -0.132 0.915 -0.197 -0.097 0.009 0.1271936604 300 0.034 -0.132 0.915 -0.197 -0.095 0.009 0.1271935051 Powell done niters = 3 Computing relative cost 0 -25.0 -25.0 -25.0 1.037065 1 -25.0 -25.0 25.0 0.998962 2 -25.0 25.0 -25.0 1.011347 3 -25.0 25.0 25.0 1.042337 4 25.0 -25.0 -25.0 0.994005 5 25.0 -25.0 25.0 1.033060 6 25.0 25.0 -25.0 0.990798 7 25.0 25.0 25.0 1.017536 REL: 8 0.127194 8.125111 1.015639 rel = 0.125235 Number of iterations 3 Min cost was 0.127194 Number of FunctionCalls 312 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.987000 sec Parameters at optimum (transmm) 0.03368 -0.13187 0.91475 Parameters at optimum (rotdeg) -0.19683 -0.09497 0.00918 Final costs ---------------- Number of surface hits 2995 WM Intensity 56.3299 +/- 8.8332 Ctx Intensity 70.5509 +/- 9.3439 Pct Contrast 22.5565 +/- 15.1786 Cost 0.1272 RelCost 0.1989 Reg at min cost was 0.998 0.058 -0.003 -0.359; 0.006 -0.057 0.998 -1.018; 0.058 -0.997 -0.057 0.168; 0.000 0.000 0.000 1.000; Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/bbr.pass1.dat, type = 14 Original Reg 0.998 0.057 -0.003 -0.394; 0.006 -0.053 0.999 -0.884; 0.056 -0.997 -0.054 -0.749; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg 0.000 -0.002 0.000 -0.035; -0.000 0.003 0.000 0.135; -0.002 -0.000 0.003 -0.917; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.752483 Computing change in rh position Surface RMS Diff (mm) 0.794010 1.036774 mri_segreg done mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/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/sub011/scripts mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname snake6 machine x86_64 user fkaule movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/template.nii regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/bbr.pass1.dat subject sub011 dof 6 outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 1376192635 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.998 0.058 -0.003 -0.359; 0.006 -0.057 0.998 -1.018; 0.058 -0.997 -0.057 0.168; 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 1.018187 1 -25.0 -25.0 25.0 0.995931 2 -25.0 25.0 -25.0 1.003818 3 -25.0 25.0 25.0 1.024126 4 25.0 -25.0 -25.0 1.007993 5 25.0 -25.0 25.0 1.014129 6 25.0 25.0 -25.0 1.009329 7 25.0 25.0 25.0 1.009792 REL: 8 0.139924 8.083305 1.010413 rel = 0.138482 Initial costs ---------------- Number of surface hits 299567 WM Intensity 56.3035 +/- 8.8680 Ctx Intensity 70.8888 +/- 9.3725 Pct Contrast 23.0747 +/- 15.5948 Cost 0.1399 RelCost 0.1385 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1456 0.1456 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.1405 0.1405 0.0 6 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 0.1399 0.1399 0.0 9 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 -0.1000 0.1398 0.1398 0.0 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.1367 0.1367 0.0 21 -0.1000 -0.1000 -0.1000 0.1000 0.0000 -0.1000 0.1366 0.1366 0.0 30 -0.1000 -0.1000 0.0000 -0.1000 0.0000 -0.1000 0.1360 0.1360 0.0 36 -0.1000 -0.1000 0.0000 0.0000 -0.1000 -0.1000 0.1350 0.1350 0.0 39 -0.1000 -0.1000 0.0000 0.0000 0.0000 -0.1000 0.1325 0.1325 0.0 120 -0.1000 0.0000 0.0000 0.0000 0.0000 -0.1000 0.1295 0.1295 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1272 0.1272 0.0 Brute Force -------------------------- Min cost was 0.127194 Number of iterations 729 Search time 2.437000 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 8 0.003 0.000 0.000 0.000 0.000 0.000 0.1399238739 9 0.002 0.000 0.000 0.000 0.000 0.000 0.1399237850 18 0.001 -0.011 0.000 0.000 0.000 0.000 0.1399164532 19 0.001 -0.008 0.000 0.000 0.000 0.000 0.1399159395 28 0.001 -0.008 -0.025 0.000 0.000 0.000 0.1398514145 29 0.001 -0.008 -0.024 0.000 0.000 0.000 0.1398509487 30 0.001 -0.008 -0.023 0.000 0.000 0.000 0.1398503664 34 0.001 -0.008 -0.022 0.000 0.000 0.000 0.1398503202 42 0.001 -0.008 -0.022 -0.012 0.000 0.000 0.1398157908 43 0.001 -0.008 -0.022 -0.013 0.000 0.000 0.1398155572 51 0.001 -0.008 -0.022 -0.013 0.048 0.000 0.1396358289 54 0.001 -0.008 -0.022 -0.013 0.049 0.000 0.1396356576 62 0.001 -0.008 -0.022 -0.013 0.049 -0.043 0.1396089500 63 0.001 -0.008 -0.022 -0.013 0.049 -0.025 0.1395775731 64 0.001 -0.008 -0.022 -0.013 0.049 -0.026 0.1395773433 65 0.001 -0.008 -0.022 -0.013 0.049 -0.027 0.1395772903 76 0.004 -0.008 -0.022 -0.013 0.049 -0.027 0.1395741771 77 0.007 -0.008 -0.022 -0.013 0.049 -0.027 0.1395736245 87 0.007 -0.006 -0.022 -0.013 0.049 -0.027 0.1395723785 97 0.007 -0.006 -0.021 -0.013 0.049 -0.027 0.1395723097 106 0.007 -0.006 -0.021 -0.014 0.049 -0.027 0.1395709356 107 0.007 -0.006 -0.021 -0.016 0.049 -0.027 0.1395702076 117 0.007 -0.006 -0.021 -0.016 0.052 -0.027 0.1395691506 118 0.007 -0.006 -0.021 -0.016 0.051 -0.027 0.1395690480 126 0.007 -0.006 -0.021 -0.016 0.051 -0.019 0.1395681076 127 0.007 -0.006 -0.021 -0.016 0.051 -0.022 0.1395668976 130 0.012 -0.003 -0.020 -0.019 0.053 -0.018 0.1395662622 149 0.009 -0.007 -0.021 -0.016 0.051 -0.022 0.1395658813 158 0.009 -0.007 -0.018 -0.016 0.051 -0.022 0.1395655102 168 0.009 -0.007 -0.018 -0.017 0.051 -0.022 0.1395648956 169 0.009 -0.007 -0.018 -0.018 0.051 -0.022 0.1395645236 190 0.009 -0.007 -0.018 -0.018 0.051 -0.020 0.1395640269 192 0.012 -0.008 -0.016 -0.020 0.051 -0.019 0.1395621190 195 0.016 -0.010 -0.012 -0.023 0.051 -0.016 0.1395602555 199 0.017 -0.010 -0.011 -0.024 0.051 -0.015 0.1395601198 218 0.018 -0.010 -0.011 -0.024 0.051 -0.015 0.1395600548 229 0.018 -0.009 -0.011 -0.024 0.051 -0.015 0.1395600195 237 0.018 -0.009 -0.008 -0.024 0.051 -0.015 0.1395597334 248 0.018 -0.009 -0.008 -0.024 0.051 -0.016 0.1395596285 265 0.019 -0.010 -0.007 -0.025 0.051 -0.015 0.1395595386 266 0.019 -0.010 -0.007 -0.025 0.051 -0.015 0.1395595061 267 0.019 -0.009 -0.008 -0.025 0.051 -0.015 0.1395594792 313 0.018 -0.009 -0.008 -0.025 0.051 -0.016 0.1395594687 331 0.018 -0.010 -0.007 -0.025 0.051 -0.016 0.1395594184 334 0.018 -0.010 -0.007 -0.025 0.051 -0.016 0.1395594180 363 0.018 -0.010 -0.006 -0.025 0.051 -0.016 0.1395593736 402 0.018 -0.010 -0.006 -0.025 0.051 -0.016 0.1395593565 465 0.018 -0.010 -0.006 -0.025 0.051 -0.016 0.1395593556 Powell done niters = 6 Computing relative cost 0 -25.0 -25.0 -25.0 1.018320 1 -25.0 -25.0 25.0 0.995785 2 -25.0 25.0 -25.0 1.004295 3 -25.0 25.0 25.0 1.023517 4 25.0 -25.0 -25.0 1.007522 5 25.0 -25.0 25.0 1.014657 6 25.0 25.0 -25.0 1.009360 7 25.0 25.0 25.0 1.009739 REL: 8 0.139559 8.083193 1.010399 rel = 0.138123 Number of iterations 6 Min cost was 0.139559 Number of FunctionCalls 468 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 167.267000 sec Parameters at optimum (transmm) 0.01814 -0.00967 -0.00607 Parameters at optimum (rotdeg) -0.02500 0.05113 -0.01611 Final costs ---------------- Number of surface hits 299567 WM Intensity 56.3029 +/- 8.8562 Ctx Intensity 70.8842 +/- 9.3684 Pct Contrast 23.0685 +/- 15.5751 Cost 0.1396 RelCost 0.1385 Reg at min cost was 0.998 0.057 -0.003 -0.341; 0.006 -0.057 0.998 -1.028; 0.057 -0.997 -0.057 0.163; 0.000 0.000 0.000 1.000; Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/T2raw.dat, type = 14 Original Reg 0.998 0.058 -0.003 -0.359; 0.006 -0.057 0.998 -1.018; 0.058 -0.997 -0.057 0.168; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.000 0.001 -0.000 -0.018; 0.000 0.000 0.000 0.009; 0.001 0.000 0.000 0.005; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.064368 Computing change in rh position Surface RMS Diff (mm) 0.071316 0.123242 mri_segreg done tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/T2raw.dat --noedit --ltaout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/mri/orig/T2raw.mgz reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/T2raw.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- 0.998 0.057 -0.003 -0.341; 0.006 -0.057 0.998 -1.028; 0.057 -0.997 -0.057 0.163; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- INFO: loading target /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/mri/orig/T2raw.mgz Tmov: -------------------- -0.700 0.000 0.000 95.888; 0.000 0.000 0.667 -128.000; 0.000 -0.667 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 0.998 0.057 -0.003 -0.341; 0.006 -0.057 0.998 -1.028; 0.057 -0.997 -0.057 0.163; 0.000 0.000 0.000 1.000; Determinant 0.999999 subject = sub011 RegMat --------------------------- 0.998 0.057 -0.003 -0.341; 0.006 -0.057 0.998 -1.028; 0.057 -0.997 -0.057 0.163; 0.000 0.000 0.000 1.000; transformed matrix: 1.000 0.004 -0.005 0.079; -0.004 1.000 -0.005 -0.004; 0.005 0.005 1.000 0.861; 0.000 0.000 0.000 1.000; transformed matrix: 0.699 0.038 -0.004 25.386; -0.002 -0.038 -0.666 262.359; -0.040 0.664 -0.038 13.360; 0.000 0.000 0.000 1.000; Cleaning up Started at Thu Aug 8 22:59:45 CEST 2013 Ended at Thu Aug 8 23:15:42 CEST 2013 BBR-Run-Time-Sec 956 bbregister Done To check results, run: tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/T2raw.dat --surf mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/T2.mgz mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/mri/orig/T2raw.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998102, -0.0611237, 0.00753358) j_ras = (-0.0606425, 0.996759, 0.0528636) k_ras = (0.0107404, -0.0523064, 0.998573) INFO: Reading transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/T2raw.lta... Reading transform with LTAreadEx() reading extra input line subject sub011 reading extra input line fscale 0.150000 reading template info from volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/orig.mgz... INFO: Applying transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/T2raw.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 1.000 0.004 -0.005 0.079; -0.004 1.000 -0.005 -0.004; 0.005 0.005 1.000 0.861; 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/sub011/mri/T2.mgz... mri_normalize -aseg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/aseg.mgz -sigma 4 -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.white identity.nofile -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.white identity.nofile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/T2.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/mri/T2.mgz... computing distance transform computing distance transform computing nonmaximum suppression 18829 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/sub011/mri/T2.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.woT2.pial `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.woT2.pial' mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub011 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/sub011/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/wm.mgz... 19648 bright wm thresholded. 948 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.orig... computing class statistics... border white: 292650 voxels (1.74%) border gray 329335 voxels (1.96%) WM (92.0): 93.5 +- 9.7 [70.0 --> 110.0] GM (76.0) : 74.2 +- 13.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 46.9 (was 70) setting MAX_BORDER_WHITE to 113.7 (was 105) setting MIN_BORDER_WHITE to 60.0 (was 85) setting MAX_CSF to 33.8 (was 40) setting MAX_GRAY to 94.3 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 53.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 20.6 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104, GM=60 mean inside = 93.0, mean outside = 69.3 smoothing surface for 5 iterations... reading initial white vertex positions from white... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.90 +- 0.25 (0.04-->4.35) (max @ vno 120419 --> 121336) face area 0.34 +- 0.16 (0.00-->2.85) averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown deleting segment 1 with 6 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 16 points - only 0.00% unknown deleting segment 6 with 811 points - only 0.00% unknown deleting segment 8 with 31 points - only 0.00% unknown removing 1 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 10 with 3 points - only 0.00% unknown deleting segment 11 with 6 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 12 with 2 points - only 0.00% unknown deleting segment 13 with 6 points - only 0.00% unknown deleting segment 14 with 8 points - only 0.00% unknown deleting segment 15 with 5 points - only 0.00% unknown deleting segment 16 with 47 points - only 0.00% unknown deleting segment 17 with 7 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 18 with 1 points - only 0.00% unknown tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.90 +- 0.25 (0.06-->4.08) (max @ vno 76660 --> 75430) face area 0.34 +- 0.16 (0.00-->2.85) averaging target values for 5 iterations... 000: dt: 0.0000, sse=5097399.5, rms=0.00 rms = 1.34, time step reduction 1 of 3 to 0.250... rms = 0.35, 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=5097399.5, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown deleting segment 1 with 6 points - only 0.00% unknown deleting segment 2 with 12 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 16 points - only 0.00% unknown deleting segment 5 with 811 points - only 0.00% unknown deleting segment 6 with 31 points - only 0.00% unknown removing 1 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 8 with 3 points - only 0.00% unknown deleting segment 9 with 6 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 10 with 2 points - only 0.00% unknown deleting segment 11 with 6 points - only 0.00% unknown deleting segment 12 with 8 points - only 0.00% unknown deleting segment 13 with 5 points - only 0.00% unknown deleting segment 14 with 47 points - only 0.00% unknown deleting segment 15 with 7 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 16 with 1 points - only 0.00% unknown tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.06-->4.08) (max @ vno 76660 --> 75430) face area 0.34 +- 0.16 (0.00-->2.85) averaging target values for 5 iterations... 000: dt: 0.0000, sse=5097399.5, rms=0.00 rms = 1.34, time step reduction 1 of 3 to 0.250... rms = 0.35, 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=5097399.5, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown deleting segment 1 with 6 points - only 0.00% unknown deleting segment 2 with 12 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 16 points - only 0.00% unknown deleting segment 5 with 811 points - only 0.00% unknown deleting segment 6 with 31 points - only 0.00% unknown removing 1 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 8 with 3 points - only 0.00% unknown deleting segment 9 with 6 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 10 with 2 points - only 0.00% unknown deleting segment 11 with 6 points - only 0.00% unknown deleting segment 12 with 8 points - only 0.00% unknown deleting segment 13 with 5 points - only 0.00% unknown deleting segment 14 with 47 points - only 0.00% unknown deleting segment 15 with 7 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 16 with 1 points - only 0.00% unknown tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.25 (0.06-->4.08) (max @ vno 76660 --> 75430) face area 0.34 +- 0.16 (0.00-->2.85) averaging target values for 5 iterations... 000: dt: 0.0000, sse=5097399.5, rms=0.00 rms = 1.34, time step reduction 1 of 3 to 0.250... rms = 0.35, 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=5097399.5, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown deleting segment 1 with 6 points - only 0.00% unknown deleting segment 2 with 12 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 16 points - only 0.00% unknown deleting segment 5 with 811 points - only 0.00% unknown deleting segment 6 with 31 points - only 0.00% unknown removing 1 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 8 with 3 points - only 0.00% unknown deleting segment 9 with 6 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 10 with 2 points - only 0.00% unknown deleting segment 11 with 6 points - only 0.00% unknown deleting segment 12 with 8 points - only 0.00% unknown deleting segment 13 with 5 points - only 0.00% unknown deleting segment 14 with 47 points - only 0.00% unknown deleting segment 15 with 7 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 16 with 1 points - only 0.00% unknown tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=5097399.5, rms=0.00 rms = 1.34, time step reduction 1 of 3 to 0.250... rms = 0.35, 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=5097399.5, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group 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 [96.00 222.00], gm=159.00+-21.00, and vertices in regions > 148.5 33588 surface locations found to contain inconsistent values (4191 in, 29397 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=579143.0, rms=0.22 001: dt: 0.5000, sse=543734.5, rms=0.215 (0.000%) 002: dt: 0.5000, sse=522328.2, rms=0.203 (0.000%) 003: dt: 0.5000, sse=508482.0, rms=0.194 (0.000%) 004: dt: 0.5000, sse=498241.7, rms=0.187 (0.000%) 005: dt: 0.5000, sse=490733.8, rms=0.180 (0.000%) 006: dt: 0.5000, sse=485137.5, rms=0.174 (0.000%) 007: dt: 0.5000, sse=481224.1, rms=0.169 (0.000%) 008: dt: 0.5000, sse=478117.3, rms=0.164 (0.000%) 009: dt: 0.5000, sse=475359.8, rms=0.161 (0.000%) 010: dt: 0.5000, sse=473671.0, rms=0.157 (0.000%) 011: dt: 0.5000, sse=471807.7, rms=0.155 (0.000%) 012: dt: 0.5000, sse=469805.4, rms=0.153 (0.000%) 013: dt: 0.5000, sse=467931.1, rms=0.151 (0.000%) 014: dt: 0.5000, sse=465915.2, rms=0.149 (0.000%) 015: dt: 0.5000, sse=464230.7, rms=0.148 (0.000%) 016: dt: 0.5000, sse=462990.1, rms=0.147 (0.000%) 017: dt: 0.5000, sse=461627.8, rms=0.146 (0.000%) 018: dt: 0.5000, sse=460109.9, rms=0.146 (0.000%) 019: dt: 0.5000, sse=458580.4, rms=0.145 (0.000%) 020: dt: 0.5000, sse=457147.6, rms=0.145 (0.000%) 021: dt: 0.5000, sse=455719.2, rms=0.145 (0.000%) 022: dt: 0.5000, sse=454223.4, rms=0.144 (0.000%) 023: dt: 0.5000, sse=453087.3, rms=0.145 (0.000%) 024: dt: 0.5000, sse=451466.9, rms=0.145 (0.000%) 025: dt: 0.5000, sse=450565.6, rms=0.145 (0.000%) 026: dt: 0.5000, sse=449091.8, rms=0.145 (0.000%) 027: dt: 0.5000, sse=447970.5, rms=0.145 (0.000%) 028: dt: 0.5000, sse=446655.2, rms=0.145 (0.000%) 029: dt: 0.5000, sse=445560.3, rms=0.146 (0.000%) 030: dt: 0.5000, sse=444394.9, rms=0.146 (0.000%) positioning took 4.2 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [92.60 223.40], gm=158.00+-21.80, and vertices in regions > 147.1 26694 surface locations found to contain inconsistent values (1107 in, 25587 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=46144.3, rms=0.12 031: dt: 0.5000, sse=45886.8, rms=0.119 (0.000%) 032: dt: 0.5000, sse=46832.3, rms=0.109 (0.000%) 033: dt: 0.5000, sse=47972.2, rms=0.101 (0.000%) 034: dt: 0.5000, sse=48957.8, rms=0.096 (0.000%) 035: dt: 0.5000, sse=49832.3, rms=0.091 (0.000%) 036: dt: 0.5000, sse=50665.0, rms=0.087 (0.000%) 037: dt: 0.5000, sse=51462.3, rms=0.082 (0.000%) 038: dt: 0.5000, sse=52260.4, rms=0.078 (0.000%) 039: dt: 0.5000, sse=53058.8, rms=0.075 (0.000%) 040: dt: 0.5000, sse=53835.5, rms=0.071 (0.000%) 041: dt: 0.5000, sse=54601.3, rms=0.068 (0.000%) 042: dt: 0.5000, sse=55297.1, rms=0.065 (0.000%) 043: dt: 0.5000, sse=55947.0, rms=0.063 (0.000%) 044: dt: 0.5000, sse=56574.3, rms=0.060 (0.000%) 045: dt: 0.5000, sse=57183.2, rms=0.058 (0.000%) 046: dt: 0.5000, sse=57735.0, rms=0.056 (0.000%) 047: dt: 0.5000, sse=58241.3, rms=0.054 (0.000%) 048: dt: 0.5000, sse=58708.5, rms=0.052 (0.000%) 049: dt: 0.5000, sse=59163.7, rms=0.051 (0.000%) 050: dt: 0.5000, sse=59584.9, rms=0.049 (0.000%) 051: dt: 0.5000, sse=59956.4, rms=0.048 (0.000%) 052: dt: 0.5000, sse=60316.7, rms=0.047 (0.000%) 053: dt: 0.5000, sse=60633.4, rms=0.046 (0.000%) 054: dt: 0.5000, sse=60933.5, rms=0.045 (0.000%) 055: dt: 0.5000, sse=61227.5, rms=0.044 (0.000%) 056: dt: 0.5000, sse=61479.4, rms=0.043 (0.000%) 057: dt: 0.5000, sse=61720.0, rms=0.042 (0.000%) 058: dt: 0.5000, sse=61936.4, rms=0.041 (0.000%) 059: dt: 0.5000, sse=62120.2, rms=0.041 (0.000%) 060: dt: 0.5000, sse=62331.4, rms=0.040 (0.000%) positioning took 4.2 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [92.00 224.00], gm=158.00+-22.00, and vertices in regions > 147.0 25567 surface locations found to contain inconsistent values (247 in, 25320 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=6599.8, rms=0.05 061: dt: 0.5000, sse=6588.7, rms=0.048 (0.000%) 062: dt: 0.5000, sse=6661.1, rms=0.044 (0.000%) 063: dt: 0.5000, sse=6721.1, rms=0.041 (0.000%) 064: dt: 0.5000, sse=6770.9, rms=0.038 (0.000%) 065: dt: 0.5000, sse=6804.1, rms=0.037 (0.000%) 066: dt: 0.5000, sse=6822.4, rms=0.035 (0.000%) 067: dt: 0.5000, sse=6832.7, rms=0.034 (0.000%) 068: dt: 0.5000, sse=6839.2, rms=0.033 (0.000%) 069: dt: 0.5000, sse=6844.1, rms=0.032 (0.000%) 070: dt: 0.5000, sse=6849.5, rms=0.031 (0.000%) 071: dt: 0.5000, sse=6854.8, rms=0.030 (0.000%) 072: dt: 0.5000, sse=6860.6, rms=0.029 (0.000%) 073: dt: 0.5000, sse=6869.8, rms=0.028 (0.000%) 074: dt: 0.5000, sse=6877.9, rms=0.028 (0.000%) 075: dt: 0.5000, sse=6883.4, rms=0.027 (0.000%) 076: dt: 0.5000, sse=6885.9, rms=0.026 (0.000%) 077: dt: 0.5000, sse=6889.6, rms=0.026 (0.000%) 078: dt: 0.5000, sse=6894.8, rms=0.025 (0.000%) 079: dt: 0.5000, sse=6898.4, rms=0.025 (0.000%) 080: dt: 0.5000, sse=6904.9, rms=0.024 (0.000%) 081: dt: 0.5000, sse=6908.6, rms=0.024 (0.000%) 082: dt: 0.5000, sse=6912.8, rms=0.024 (0.000%) 083: dt: 0.5000, sse=6917.1, rms=0.023 (0.000%) 084: dt: 0.5000, sse=6920.4, rms=0.023 (0.000%) 085: dt: 0.5000, sse=6925.6, rms=0.023 (0.000%) 086: dt: 0.5000, sse=6927.1, rms=0.023 (0.000%) 087: dt: 0.5000, sse=6930.3, rms=0.022 (0.000%) 088: dt: 0.5000, sse=6932.2, rms=0.022 (0.000%) 089: dt: 0.5000, sse=6934.7, rms=0.022 (0.000%) 090: dt: 0.5000, sse=6938.1, rms=0.022 (0.000%) positioning took 4.2 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [92.00 224.00], gm=158.00+-22.00, and vertices in regions > 147.0 25331 surface locations found to contain inconsistent values (61 in, 25270 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/sub011/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=807.6, rms=0.03 091: dt: 0.5000, sse=806.8, rms=0.028 (0.000%) 092: dt: 0.5000, sse=798.8, rms=0.027 (0.000%) 093: dt: 0.5000, sse=792.7, rms=0.026 (0.000%) 094: dt: 0.5000, sse=787.4, rms=0.025 (0.000%) 095: dt: 0.5000, sse=782.6, rms=0.025 (0.000%) 096: dt: 0.5000, sse=778.9, rms=0.024 (0.000%) 097: dt: 0.5000, sse=776.2, rms=0.024 (0.000%) 098: dt: 0.5000, sse=774.1, rms=0.024 (0.000%) 099: dt: 0.5000, sse=772.4, rms=0.023 (0.000%) 100: dt: 0.5000, sse=770.2, rms=0.023 (0.000%) 101: dt: 0.5000, sse=769.0, rms=0.023 (0.000%) 102: dt: 0.5000, sse=766.5, rms=0.022 (0.000%) 103: dt: 0.5000, sse=764.3, rms=0.022 (0.000%) 104: dt: 0.5000, sse=762.4, rms=0.022 (0.000%) 105: dt: 0.5000, sse=760.7, rms=0.022 (0.000%) 106: dt: 0.5000, sse=759.3, rms=0.021 (0.000%) 107: dt: 0.5000, sse=758.7, rms=0.021 (0.000%) 108: dt: 0.5000, sse=757.9, rms=0.021 (0.000%) 109: dt: 0.5000, sse=757.2, rms=0.021 (0.000%) 110: dt: 0.5000, sse=756.8, rms=0.021 (0.000%) 111: dt: 0.5000, sse=756.1, rms=0.021 (0.000%) 112: dt: 0.5000, sse=755.2, rms=0.021 (0.000%) 113: dt: 0.5000, sse=754.5, rms=0.020 (0.000%) 114: dt: 0.5000, sse=753.9, rms=0.020 (0.000%) 115: dt: 0.5000, sse=753.4, rms=0.020 (0.000%) 116: dt: 0.5000, sse=753.6, rms=0.020 (0.000%) 117: dt: 0.5000, sse=753.3, rms=0.020 (0.000%) 118: dt: 0.5000, sse=753.2, rms=0.020 (0.000%) 119: dt: 0.5000, sse=752.8, rms=0.020 (0.000%) 120: dt: 0.5000, sse=752.6, rms=0.020 (0.000%) positioning took 4.1 minutes writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.area.pial vertex spacing 1.02 +- 0.43 (0.03-->8.04) (max @ vno 111042 --> 112201) face area 0.41 +- 0.31 (0.00-->6.37) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 158499 vertices processed 25000 of 158499 vertices processed 50000 of 158499 vertices processed 75000 of 158499 vertices processed 100000 of 158499 vertices processed 125000 of 158499 vertices processed 150000 of 158499 vertices processed 0 of 158499 vertices processed 25000 of 158499 vertices processed 50000 of 158499 vertices processed 75000 of 158499 vertices processed 100000 of 158499 vertices processed 125000 of 158499 vertices processed 150000 of 158499 vertices processed thickness calculation complete, 350:737 truncations. 34686 vertices at 0 distance 110927 vertices at 1 distance 101233 vertices at 2 distance 40584 vertices at 3 distance 11335 vertices at 4 distance 3143 vertices at 5 distance 996 vertices at 6 distance 328 vertices at 7 distance 124 vertices at 8 distance 54 vertices at 9 distance 31 vertices at 10 distance 14 vertices at 11 distance 13 vertices at 12 distance 7 vertices at 13 distance 10 vertices at 14 distance 7 vertices at 15 distance 5 vertices at 16 distance 4 vertices at 17 distance 0 vertices at 18 distance 4 vertices at 19 distance 9 vertices at 20 distance writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.thickness positioning took 20.6 minutes /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.woT2.pial `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.woT2.pial' mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub011 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/sub011/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/wm.mgz... 20244 bright wm thresholded. 947 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.orig... computing class statistics... border white: 292650 voxels (1.74%) border gray 329335 voxels (1.96%) WM (92.0): 93.5 +- 10.0 [70.0 --> 110.0] GM (76.0) : 74.1 +- 12.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 46.1 (was 70) setting MAX_BORDER_WHITE to 115.0 (was 105) setting MIN_BORDER_WHITE to 59.0 (was 85) setting MAX_CSF to 33.2 (was 40) setting MAX_GRAY to 95.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 52.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 20.4 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=59 mean inside = 93.3, mean outside = 69.4 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/sub011/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.90 +- 0.26 (0.04-->5.62) (max @ vno 159481 --> 159523) face area 0.33 +- 0.16 (0.00-->9.01) averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 6 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 3 with 2 points - only 0.00% unknown deleting segment 6 with 6 points - only 0.00% unknown deleting segment 8 with 533 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 9 with 4 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 11 with 1 points - only 0.00% unknown deleting segment 13 with 8 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 14 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 15 with 1 points - only 0.00% unknown deleting segment 16 with 7 points - only 0.00% unknown deleting segment 17 with 6 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 18 with 2 points - only 0.00% unknown deleting segment 19 with 16 points - only 0.00% unknown tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.90 +- 0.25 (0.05-->5.62) (max @ vno 159481 --> 159523) face area 0.33 +- 0.16 (0.00-->9.01) averaging target values for 5 iterations... 000: dt: 0.0000, sse=5228024.0, rms=0.00 rms = 1.17, time step reduction 1 of 3 to 0.250... rms = 0.30, time step reduction 2 of 3 to 0.125... rms = 0.04, time step reduction 3 of 3 to 0.062... 001: dt: 0.1250, sse=5228024.0, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 6 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown deleting segment 3 with 6 points - only 0.00% unknown deleting segment 4 with 533 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 5 with 4 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 6 with 1 points - only 0.00% unknown deleting segment 7 with 8 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 8 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 9 with 1 points - only 0.00% unknown deleting segment 10 with 7 points - only 0.00% unknown deleting segment 11 with 6 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 12 with 2 points - only 0.00% unknown deleting segment 13 with 16 points - only 0.00% unknown tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.05-->5.62) (max @ vno 159481 --> 159523) face area 0.33 +- 0.16 (0.00-->9.01) averaging target values for 5 iterations... 000: dt: 0.0000, sse=5228024.0, rms=0.00 rms = 1.17, time step reduction 1 of 3 to 0.250... rms = 0.30, time step reduction 2 of 3 to 0.125... rms = 0.04, time step reduction 3 of 3 to 0.062... 002: dt: 0.1250, sse=5228024.0, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 6 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown deleting segment 3 with 6 points - only 0.00% unknown deleting segment 4 with 533 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 5 with 4 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 6 with 1 points - only 0.00% unknown deleting segment 7 with 8 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 8 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 9 with 1 points - only 0.00% unknown deleting segment 10 with 7 points - only 0.00% unknown deleting segment 11 with 6 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 12 with 2 points - only 0.00% unknown deleting segment 13 with 16 points - only 0.00% unknown tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.25 (0.05-->5.62) (max @ vno 159481 --> 159523) face area 0.33 +- 0.16 (0.00-->9.01) averaging target values for 5 iterations... 000: dt: 0.0000, sse=5228024.0, rms=0.00 rms = 1.17, time step reduction 1 of 3 to 0.250... rms = 0.30, time step reduction 2 of 3 to 0.125... rms = 0.04, time step reduction 3 of 3 to 0.062... 003: dt: 0.1250, sse=5228024.0, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 6 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown deleting segment 3 with 6 points - only 0.00% unknown deleting segment 4 with 533 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 5 with 4 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 6 with 1 points - only 0.00% unknown deleting segment 7 with 8 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 8 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 9 with 1 points - only 0.00% unknown deleting segment 10 with 7 points - only 0.00% unknown deleting segment 11 with 6 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 12 with 2 points - only 0.00% unknown deleting segment 13 with 16 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=5228024.0, rms=0.00 rms = 1.17, time step reduction 1 of 3 to 0.250... rms = 0.30, time step reduction 2 of 3 to 0.125... rms = 0.04, time step reduction 3 of 3 to 0.062... 004: dt: 0.1250, sse=5228024.0, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... smoothing surface for 5 iterations... reading initial pial vertex positions from woT2.pial... repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [98.40 219.60], gm=159.00+-20.20, and vertices in regions > 148.9 37368 surface locations found to contain inconsistent values (6251 in, 31117 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=593587.2, rms=0.23 001: dt: 0.5000, sse=556116.8, rms=0.219 (0.000%) 002: dt: 0.5000, sse=534006.2, rms=0.206 (0.000%) 003: dt: 0.5000, sse=520517.3, rms=0.197 (0.000%) 004: dt: 0.5000, sse=510310.8, rms=0.189 (0.000%) 005: dt: 0.5000, sse=503439.6, rms=0.182 (0.000%) 006: dt: 0.5000, sse=498120.3, rms=0.176 (0.000%) 007: dt: 0.5000, sse=493928.0, rms=0.170 (0.000%) 008: dt: 0.5000, sse=490564.3, rms=0.166 (0.000%) 009: dt: 0.5000, sse=487583.5, rms=0.162 (0.000%) 010: dt: 0.5000, sse=485813.7, rms=0.158 (0.000%) 011: dt: 0.5000, sse=483978.0, rms=0.156 (0.000%) 012: dt: 0.5000, sse=482284.1, rms=0.153 (0.000%) 013: dt: 0.5000, sse=480515.2, rms=0.151 (0.000%) 014: dt: 0.5000, sse=479003.7, rms=0.150 (0.000%) 015: dt: 0.5000, sse=477497.9, rms=0.148 (0.000%) 016: dt: 0.5000, sse=476095.7, rms=0.147 (0.000%) 017: dt: 0.5000, sse=474579.2, rms=0.146 (0.000%) 018: dt: 0.5000, sse=473293.8, rms=0.145 (0.000%) 019: dt: 0.5000, sse=472160.0, rms=0.145 (0.000%) 020: dt: 0.5000, sse=470798.0, rms=0.144 (0.000%) 021: dt: 0.5000, sse=469630.6, rms=0.144 (0.000%) 022: dt: 0.5000, sse=468210.7, rms=0.144 (0.000%) 023: dt: 0.5000, sse=467027.4, rms=0.144 (0.000%) 024: dt: 0.5000, sse=465823.0, rms=0.144 (0.000%) 025: dt: 0.5000, sse=464833.6, rms=0.144 (0.000%) 026: dt: 0.5000, sse=463456.4, rms=0.144 (0.000%) 027: dt: 0.5000, sse=462114.9, rms=0.144 (0.000%) 028: dt: 0.5000, sse=461239.4, rms=0.144 (0.000%) 029: dt: 0.5000, sse=460058.2, rms=0.144 (0.000%) 030: dt: 0.5000, sse=459035.3, rms=0.145 (0.000%) positioning took 4.2 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [91.20 226.80], gm=159.00+-22.60, and vertices in regions > 147.7 28298 surface locations found to contain inconsistent values (845 in, 27453 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=47563.4, rms=0.12 031: dt: 0.5000, sse=47229.2, rms=0.117 (0.000%) 032: dt: 0.5000, sse=47999.2, rms=0.106 (0.000%) 033: dt: 0.5000, sse=49027.1, rms=0.099 (0.000%) 034: dt: 0.5000, sse=49949.0, rms=0.094 (0.000%) 035: dt: 0.5000, sse=50843.3, rms=0.089 (0.000%) 036: dt: 0.5000, sse=51689.9, rms=0.084 (0.000%) 037: dt: 0.5000, sse=52478.7, rms=0.080 (0.000%) 038: dt: 0.5000, sse=53272.0, rms=0.077 (0.000%) 039: dt: 0.5000, sse=54032.8, rms=0.073 (0.000%) 040: dt: 0.5000, sse=54793.0, rms=0.070 (0.000%) 041: dt: 0.5000, sse=55538.6, rms=0.067 (0.000%) 042: dt: 0.5000, sse=56232.8, rms=0.064 (0.000%) 043: dt: 0.5000, sse=56866.3, rms=0.061 (0.000%) 044: dt: 0.5000, sse=57474.3, rms=0.059 (0.000%) 045: dt: 0.5000, sse=58067.8, rms=0.056 (0.000%) 046: dt: 0.5000, sse=58601.0, rms=0.054 (0.000%) 047: dt: 0.5000, sse=59124.8, rms=0.052 (0.000%) 048: dt: 0.5000, sse=59599.1, rms=0.051 (0.000%) 049: dt: 0.5000, sse=60038.2, rms=0.049 (0.000%) 050: dt: 0.5000, sse=60433.9, rms=0.048 (0.000%) 051: dt: 0.5000, sse=60813.8, rms=0.046 (0.000%) 052: dt: 0.5000, sse=61167.3, rms=0.045 (0.000%) 053: dt: 0.5000, sse=61489.9, rms=0.044 (0.000%) 054: dt: 0.5000, sse=61770.3, rms=0.043 (0.000%) 055: dt: 0.5000, sse=62065.0, rms=0.042 (0.000%) 056: dt: 0.5000, sse=62325.3, rms=0.041 (0.000%) 057: dt: 0.5000, sse=62550.1, rms=0.040 (0.000%) 058: dt: 0.5000, sse=62766.7, rms=0.039 (0.000%) 059: dt: 0.5000, sse=62975.3, rms=0.039 (0.000%) 060: dt: 0.5000, sse=63176.6, rms=0.038 (0.000%) positioning took 4.1 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [93.00 231.00], gm=162.00+-23.00, and vertices in regions > 150.5 26978 surface locations found to contain inconsistent values (357 in, 26621 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=6931.5, rms=0.06 061: dt: 0.5000, sse=6866.3, rms=0.060 (0.000%) 062: dt: 0.5000, sse=6944.6, rms=0.052 (0.000%) 063: dt: 0.5000, sse=7049.0, rms=0.047 (0.000%) 064: dt: 0.5000, sse=7143.1, rms=0.044 (0.000%) 065: dt: 0.5000, sse=7214.7, rms=0.041 (0.000%) 066: dt: 0.5000, sse=7259.7, rms=0.039 (0.000%) 067: dt: 0.5000, sse=7291.5, rms=0.038 (0.000%) 068: dt: 0.5000, sse=7321.6, rms=0.036 (0.000%) 069: dt: 0.5000, sse=7350.6, rms=0.035 (0.000%) 070: dt: 0.5000, sse=7376.5, rms=0.034 (0.000%) 071: dt: 0.5000, sse=7400.0, rms=0.033 (0.000%) 072: dt: 0.5000, sse=7421.6, rms=0.032 (0.000%) 073: dt: 0.5000, sse=7441.7, rms=0.031 (0.000%) 074: dt: 0.5000, sse=7459.0, rms=0.030 (0.000%) 075: dt: 0.5000, sse=7473.4, rms=0.029 (0.000%) 076: dt: 0.5000, sse=7486.1, rms=0.028 (0.000%) 077: dt: 0.5000, sse=7497.7, rms=0.028 (0.000%) 078: dt: 0.5000, sse=7508.1, rms=0.027 (0.000%) 079: dt: 0.5000, sse=7517.2, rms=0.027 (0.000%) 080: dt: 0.5000, sse=7526.8, rms=0.026 (0.000%) 081: dt: 0.5000, sse=7535.2, rms=0.026 (0.000%) 082: dt: 0.5000, sse=7543.5, rms=0.025 (0.000%) 083: dt: 0.5000, sse=7550.9, rms=0.025 (0.000%) 084: dt: 0.5000, sse=7557.1, rms=0.025 (0.000%) 085: dt: 0.5000, sse=7563.5, rms=0.024 (0.000%) 086: dt: 0.5000, sse=7568.0, rms=0.024 (0.000%) 087: dt: 0.5000, sse=7571.8, rms=0.024 (0.000%) 088: dt: 0.5000, sse=7575.8, rms=0.024 (0.000%) 089: dt: 0.5000, sse=7579.0, rms=0.024 (0.000%) 090: dt: 0.5000, sse=7581.7, rms=0.023 (0.000%) positioning took 4.0 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [93.00 231.00], gm=162.00+-23.00, and vertices in regions > 150.5 26384 surface locations found to contain inconsistent values (73 in, 26311 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/sub011/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=861.3, rms=0.03 091: dt: 0.5000, sse=859.3, rms=0.027 (0.000%) 092: dt: 0.5000, sse=853.7, rms=0.026 (0.000%) 093: dt: 0.5000, sse=850.3, rms=0.025 (0.000%) 094: dt: 0.5000, sse=847.2, rms=0.025 (0.000%) 095: dt: 0.5000, sse=845.0, rms=0.024 (0.000%) 096: dt: 0.5000, sse=843.1, rms=0.024 (0.000%) 097: dt: 0.5000, sse=841.6, rms=0.024 (0.000%) 098: dt: 0.5000, sse=840.1, rms=0.023 (0.000%) 099: dt: 0.5000, sse=839.1, rms=0.023 (0.000%) 100: dt: 0.5000, sse=837.7, rms=0.023 (0.000%) 101: dt: 0.5000, sse=836.6, rms=0.023 (0.000%) 102: dt: 0.5000, sse=835.3, rms=0.023 (0.000%) 103: dt: 0.5000, sse=834.2, rms=0.022 (0.000%) 104: dt: 0.5000, sse=833.2, rms=0.022 (0.000%) 105: dt: 0.5000, sse=832.6, rms=0.022 (0.000%) 106: dt: 0.5000, sse=831.5, rms=0.022 (0.000%) 107: dt: 0.5000, sse=830.8, rms=0.022 (0.000%) 108: dt: 0.5000, sse=829.9, rms=0.022 (0.000%) 109: dt: 0.5000, sse=829.2, rms=0.022 (0.000%) 110: dt: 0.5000, sse=828.5, rms=0.022 (0.000%) 111: dt: 0.5000, sse=828.0, rms=0.022 (0.000%) 112: dt: 0.5000, sse=827.8, rms=0.021 (0.000%) 113: dt: 0.5000, sse=827.3, rms=0.021 (0.000%) 114: dt: 0.5000, sse=826.7, rms=0.021 (0.000%) 115: dt: 0.5000, sse=826.2, rms=0.021 (0.000%) 116: dt: 0.5000, sse=825.8, rms=0.021 (0.000%) 117: dt: 0.5000, sse=825.5, rms=0.021 (0.000%) 118: dt: 0.5000, sse=825.2, rms=0.021 (0.000%) 119: dt: 0.5000, sse=824.8, rms=0.021 (0.000%) 120: dt: 0.5000, sse=824.6, rms=0.021 (0.000%) positioning took 4.1 minutes writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.area.pial vertex spacing 1.02 +- 0.43 (0.02-->8.86) (max @ vno 111253 --> 109961) face area 0.41 +- 0.31 (0.00-->14.30) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 159726 vertices processed 25000 of 159726 vertices processed 50000 of 159726 vertices processed 75000 of 159726 vertices processed 100000 of 159726 vertices processed 125000 of 159726 vertices processed 150000 of 159726 vertices processed 0 of 159726 vertices processed 25000 of 159726 vertices processed 50000 of 159726 vertices processed 75000 of 159726 vertices processed 100000 of 159726 vertices processed 125000 of 159726 vertices processed 150000 of 159726 vertices processed thickness calculation complete, 408:849 truncations. 36239 vertices at 0 distance 111631 vertices at 1 distance 102370 vertices at 2 distance 40094 vertices at 3 distance 11130 vertices at 4 distance 2880 vertices at 5 distance 827 vertices at 6 distance 284 vertices at 7 distance 115 vertices at 8 distance 74 vertices at 9 distance 33 vertices at 10 distance 20 vertices at 11 distance 9 vertices at 12 distance 15 vertices at 13 distance 14 vertices at 14 distance 11 vertices at 15 distance 12 vertices at 16 distance 8 vertices at 17 distance 11 vertices at 18 distance 7 vertices at 19 distance 4 vertices at 20 distance writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.thickness positioning took 20.4 minutes #-------------------------------------------- #@# Surf Volume lh Thu Aug 8 23:58:42 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.volume lh.area.mid mul lh.thickness Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ] #-------------------------------------------- #@# Surf Volume rh Thu Aug 8 23:58:42 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.volume rh.area.mid mul rh.thickness Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ] #-------------------------------------------- #@# Cortical ribbon mask Thu Aug 8 23:58:43 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon sub011 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 = 15 writing volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/ribbon.mgz writing ribbon files #-------------------------------------------- #@# ASeg Stats Fri Aug 9 00:22:06 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011 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 sub011 $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 sub011 sysname Linux hostname snake6 machine x86_64 user fkaule UseRobust 0 atlas_icv (eTIV) = 1370643 mm^3 (det: 1.421308 ) Computing euler number orig.nofix lheno = -36, rheno = -30 orig.nofix lhholes = 19, rhholes = 16 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 277278.946 276423.000 diff= 855.9 pctdiff= 0.309 rhCtxGM: 280858.011 279721.000 diff= 1137.0 pctdiff= 0.405 lhCtxWM: 269869.337 269453.000 diff= 416.3 pctdiff= 0.154 rhCtxWM: 269533.409 269763.000 diff= -229.6 pctdiff=-0.085 SubCortGMVol 70375.000 SupraTentVol 1195183.703 (1191979.000) diff=3204.703 pctdiff=0.268 SupraTentVolNotVent 1169136.703 (1165932.000) diff=3204.703 pctdiff=0.274 BrainSegVol 1329620.000 (1325983.000) diff=3637.000 pctdiff=0.274 BrainSegVolNotVent 1298971.000 (1300821.703) diff=-1850.703 pctdiff=-0.142 BrainSegVolNotVent 1298971.000 CerebellumVol 132710.000 VentChorVol 26047.000 3rd4th5thCSF 4602.000 CSFVol 992.000, OptChiasmVol 302.000 MaskVol 1907947.000 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 13402 13402.228 4 5 Left-Inf-Lat-Vent 557 556.833 5 7 Left-Cerebellum-White-Matter 16888 16887.748 6 8 Left-Cerebellum-Cortex 51200 51199.930 7 10 Left-Thalamus-Proper 8908 8907.775 8 11 Left-Caudate 4195 4195.446 9 12 Left-Putamen 6838 6837.960 10 13 Left-Pallidum 2472 2472.189 11 14 3rd-Ventricle 1050 1050.020 12 15 4th-Ventricle 2785 2784.907 13 16 Brain-Stem 26255 26255.059 14 17 Left-Hippocampus 3823 3823.231 15 18 Left-Amygdala 1957 1957.385 16 24 CSF 995 995.296 17 26 Left-Accumbens-area 985 985.015 18 28 Left-VentralDC 4880 4880.312 19 30 Left-vessel 89 89.321 20 31 Left-choroid-plexus 1319 1319.028 23 43 Right-Lateral-Ventricle 8247 8246.752 24 44 Right-Inf-Lat-Vent 621 621.314 25 46 Right-Cerebellum-White-Matter 16640 16639.832 26 47 Right-Cerebellum-Cortex 50786 50786.008 27 49 Right-Thalamus-Proper 8448 8447.721 28 50 Right-Caudate 4647 4646.635 29 51 Right-Putamen 6611 6611.235 30 52 Right-Pallidum 2692 2692.193 31 53 Right-Hippocampus 4395 4394.645 32 54 Right-Amygdala 1787 1787.437 33 58 Right-Accumbens-area 842 842.284 34 60 Right-VentralDC 4547 4546.748 35 62 Right-vessel 93 93.224 36 63 Right-choroid-plexus 1749 1749.249 37 72 5th-Ventricle 0 0.000 38 77 WM-hypointensities 1693 1693.373 39 78 Left-WM-hypointensities 0 0.000 40 79 Right-WM-hypointensities 0 0.000 41 80 non-WM-hypointensities 23 22.659 42 81 Left-non-WM-hypointensities 0 0.000 43 82 Right-non-WM-hypointensities 0 0.000 44 85 Optic-Chiasm 309 309.220 45 251 CC_Posterior 1230 1230.396 46 252 CC_Mid_Posterior 596 595.513 47 253 CC_Central 557 557.162 48 254 CC_Mid_Anterior 552 552.144 49 255 CC_Anterior 1264 1263.762 Reporting on 45 segmentations mri_segstats done #----------------------------------------- #@# AParc-to-ASeg Fri Aug 9 00:25:20 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011 mri_aparc2aseg --s sub011 --volmask SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer subject sub011 outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.white Reading lh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.pial Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/surf/rh.white Reading rh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.pial Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/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/sub011/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 = 553178 Used brute-force search on 0 voxels Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/aparc+aseg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011 mri_aparc2aseg --s sub011 --volmask --a2009s SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer subject sub011 outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.white Reading lh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.pial Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/surf/rh.white Reading rh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.pial Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/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/sub011/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 = 553178 Used brute-force search on 0 voxels Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# WMParc Fri Aug 9 00:30:33 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011 mri_aparc2aseg --s sub011 --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 sub011 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/sub011/mri/aparc+aseg.mgz Reading lh white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.white Reading lh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.pial Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/surf/rh.white Reading rh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.pial Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/mri/ribbon.mgz Loading filled from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/filled.mgz Ripping vertices labeled as unkown Ripped 9608 vertices from left hemi Ripped 9050 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/sub011/mri/aseg.mgz Loading Ctx Seg File /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/aparc+aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 1090974 Used brute-force search on 421 voxels Fixing Parahip LH WM Found 7 clusters 0 k 11.000000 1 k 3.000000 2 k 2.000000 3 k 1.000000 4 k 1.000000 5 k 1557.000000 6 k 2.000000 Fixing Parahip RH WM Found 5 clusters 0 k 1.000000 1 k 1.000000 2 k 1.000000 3 k 1.000000 4 k 1745.000000 Writing output aseg to mri/wmparc.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011 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 sub011 --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 sub011 --surf-wm-vol --ctab /opt/freesurfer/5.3.0/WMParcStatsLUT.txt --etiv sysname Linux hostname snake6 machine x86_64 user fkaule UseRobust 0 atlas_icv (eTIV) = 1370643 mm^3 (det: 1.421308 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 277278.946 276423.000 diff= 855.9 pctdiff= 0.309 rhCtxGM: 280858.011 279721.000 diff= 1137.0 pctdiff= 0.405 lhCtxWM: 269869.337 269453.000 diff= 416.3 pctdiff= 0.154 rhCtxWM: 269533.409 269763.000 diff= -229.6 pctdiff=-0.085 SubCortGMVol 70375.000 SupraTentVol 1195183.703 (1191979.000) diff=3204.703 pctdiff=0.268 SupraTentVolNotVent 1169136.703 (1165932.000) diff=3204.703 pctdiff=0.274 BrainSegVol 1329620.000 (1325983.000) diff=3637.000 pctdiff=0.274 BrainSegVolNotVent 1298971.000 (1300821.703) diff=-1850.703 pctdiff=-0.142 BrainSegVolNotVent 1298971.000 CerebellumVol 132710.000 VentChorVol 26047.000 3rd4th5thCSF 4602.000 CSFVol 992.000, OptChiasmVol 302.000 MaskVol 1907947.000 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 3645 3644.832 2 3002 wm-lh-caudalanteriorcingulate 3672 3671.576 3 3003 wm-lh-caudalmiddlefrontal 7879 7878.777 4 3004 wm-lh-corpuscallosum 0 0.000 5 3005 wm-lh-cuneus 2393 2392.712 6 3006 wm-lh-entorhinal 965 964.953 7 3007 wm-lh-fusiform 8100 8100.317 8 3008 wm-lh-inferiorparietal 12255 12254.634 9 3009 wm-lh-inferiortemporal 7852 7852.207 10 3010 wm-lh-isthmuscingulate 4515 4515.104 11 3011 wm-lh-lateraloccipital 11248 11247.744 12 3012 wm-lh-lateralorbitofrontal 7404 7403.953 13 3013 wm-lh-lingual 5579 5579.343 14 3014 wm-lh-medialorbitofrontal 3285 3284.814 15 3015 wm-lh-middletemporal 6625 6624.548 16 3016 wm-lh-parahippocampal 1634 1633.566 17 3017 wm-lh-paracentral 3996 3996.251 18 3018 wm-lh-parsopercularis 4093 4093.467 19 3019 wm-lh-parsorbitalis 1129 1128.731 20 3020 wm-lh-parstriangularis 3488 3488.130 21 3021 wm-lh-pericalcarine 2795 2794.539 22 3022 wm-lh-postcentral 9876 9875.706 23 3023 wm-lh-posteriorcingulate 5082 5081.741 24 3024 wm-lh-precentral 15693 15693.481 25 3025 wm-lh-precuneus 11155 11155.121 26 3026 wm-lh-rostralanteriorcingulate 2905 2905.290 27 3027 wm-lh-rostralmiddlefrontal 15253 15252.552 28 3028 wm-lh-superiorfrontal 21260 21260.111 29 3029 wm-lh-superiorparietal 15877 15876.854 30 3030 wm-lh-superiortemporal 7807 7806.925 31 3031 wm-lh-supramarginal 9209 9209.423 32 3032 wm-lh-frontalpole 267 267.368 33 3033 wm-lh-temporalpole 570 569.530 34 3034 wm-lh-transversetemporal 738 738.356 35 3035 wm-lh-insula 9239 9238.698 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 3179 3179.003 120 4002 wm-rh-caudalanteriorcingulate 4736 4735.516 121 4003 wm-rh-caudalmiddlefrontal 6257 6257.334 122 4004 wm-rh-corpuscallosum 0 0.000 123 4005 wm-rh-cuneus 2379 2378.581 124 4006 wm-rh-entorhinal 943 943.463 125 4007 wm-rh-fusiform 7227 7226.715 126 4008 wm-rh-inferiorparietal 13632 13631.592 127 4009 wm-rh-inferiortemporal 7156 7156.098 128 4010 wm-rh-isthmuscingulate 4491 4490.825 129 4011 wm-rh-lateraloccipital 9463 9462.910 130 4012 wm-rh-lateralorbitofrontal 6939 6939.206 131 4013 wm-rh-lingual 6059 6058.833 132 4014 wm-rh-medialorbitofrontal 4376 4375.835 133 4015 wm-rh-middletemporal 7106 7106.391 134 4016 wm-rh-parahippocampal 1818 1817.799 135 4017 wm-rh-paracentral 5608 5608.405 136 4018 wm-rh-parsopercularis 5339 5338.899 137 4019 wm-rh-parsorbitalis 1471 1470.843 138 4020 wm-rh-parstriangularis 4540 4539.630 139 4021 wm-rh-pericalcarine 3282 3281.974 140 4022 wm-rh-postcentral 8250 8250.193 141 4023 wm-rh-posteriorcingulate 5564 5564.180 142 4024 wm-rh-precentral 15888 15888.439 143 4025 wm-rh-precuneus 11886 11886.087 144 4026 wm-rh-rostralanteriorcingulate 2360 2359.758 145 4027 wm-rh-rostralmiddlefrontal 15533 15533.347 146 4028 wm-rh-superiorfrontal 19765 19765.396 147 4029 wm-rh-superiorparietal 14394 14394.141 148 4030 wm-rh-superiortemporal 8042 8042.229 149 4031 wm-rh-supramarginal 10316 10315.623 150 4032 wm-rh-frontalpole 314 314.393 151 4033 wm-rh-temporalpole 654 653.988 152 4034 wm-rh-transversetemporal 707 707.230 153 4035 wm-rh-insula 9834 9833.537 154 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 41087 41086.664 237 5002 Right-UnsegmentedWhiteMatter 40709 40708.680 238 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/sub011/label #-------------------------------------------- #@# BA Labels lh Fri Aug 9 00:42:06 CEST 2013 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.label --trgsubject sub011 --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 = sub011 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/sub011/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499 Number of reverse mapping hits = 697 Checking for and removing duplicates Writing label file ./lh.BA1.label 4826 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.label --trgsubject sub011 --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 = sub011 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/sub011/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499 Number of reverse mapping hits = 1518 Checking for and removing duplicates Writing label file ./lh.BA2.label 9427 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.label --trgsubject sub011 --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 = sub011 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/sub011/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499 Number of reverse mapping hits = 234 Checking for and removing duplicates Writing label file ./lh.BA3a.label 4311 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.label --trgsubject sub011 --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 = sub011 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/sub011/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499 Number of reverse mapping hits = 506 Checking for and removing duplicates Writing label file ./lh.BA3b.label 6489 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.label --trgsubject sub011 --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 = sub011 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/sub011/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499 Number of reverse mapping hits = 694 Checking for and removing duplicates Writing label file ./lh.BA4a.label 6478 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.label --trgsubject sub011 --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 = sub011 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/sub011/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499 Number of reverse mapping hits = 403 Checking for and removing duplicates Writing label file ./lh.BA4p.label 4473 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.label --trgsubject sub011 --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 = sub011 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/sub011/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499 Number of reverse mapping hits = 2804 Checking for and removing duplicates Writing label file ./lh.BA6.label 16393 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.label --trgsubject sub011 --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 = sub011 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/sub011/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499 Number of reverse mapping hits = 587 Checking for and removing duplicates Writing label file ./lh.BA44.label 4768 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.label --trgsubject sub011 --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 = sub011 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/sub011/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499 Number of reverse mapping hits = 1465 Checking for and removing duplicates Writing label file ./lh.BA45.label 4887 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.label --trgsubject sub011 --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 = sub011 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/sub011/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499 Number of reverse mapping hits = 1722 Checking for and removing duplicates Writing label file ./lh.V1.label 6363 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.label --trgsubject sub011 --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 = sub011 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/sub011/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499 Number of reverse mapping hits = 3462 Checking for and removing duplicates Writing label file ./lh.V2.label 11576 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.label --trgsubject sub011 --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 = sub011 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/sub011/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499 Number of reverse mapping hits = 912 Checking for and removing duplicates Writing label file ./lh.MT.label 2930 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.perirhinal.label --trgsubject sub011 --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 = sub011 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/sub011/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499 Number of reverse mapping hits = 99 Checking for and removing duplicates Writing label file ./lh.perirhinal.label 1298 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.thresh.label --trgsubject sub011 --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 = sub011 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/sub011/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499 Number of reverse mapping hits = 153 Checking for and removing duplicates Writing label file ./lh.BA1.thresh.label 1167 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.thresh.label --trgsubject sub011 --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 = sub011 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/sub011/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499 Number of reverse mapping hits = 624 Checking for and removing duplicates Writing label file ./lh.BA2.thresh.label 2716 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.thresh.label --trgsubject sub011 --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 = sub011 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/sub011/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499 Number of reverse mapping hits = 69 Checking for and removing duplicates Writing label file ./lh.BA3a.thresh.label 1573 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.thresh.label --trgsubject sub011 --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 = sub011 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/sub011/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499 Number of reverse mapping hits = 207 Checking for and removing duplicates Writing label file ./lh.BA3b.thresh.label 2203 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.thresh.label --trgsubject sub011 --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 = sub011 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/sub011/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499 Number of reverse mapping hits = 392 Checking for and removing duplicates Writing label file ./lh.BA4a.thresh.label 2711 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.thresh.label --trgsubject sub011 --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 = sub011 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/sub011/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499 Number of reverse mapping hits = 104 Checking for and removing duplicates Writing label file ./lh.BA4p.thresh.label 1653 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.thresh.label --trgsubject sub011 --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 = sub011 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/sub011/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499 Number of reverse mapping hits = 1046 Checking for and removing duplicates Writing label file ./lh.BA6.thresh.label 8081 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.thresh.label --trgsubject sub011 --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 = sub011 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/sub011/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499 Number of reverse mapping hits = 280 Checking for and removing duplicates Writing label file ./lh.BA44.thresh.label 2192 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.thresh.label --trgsubject sub011 --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 = sub011 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/sub011/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499 Number of reverse mapping hits = 528 Checking for and removing duplicates Writing label file ./lh.BA45.thresh.label 1679 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.thresh.label --trgsubject sub011 --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 = sub011 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/sub011/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499 Number of reverse mapping hits = 1285 Checking for and removing duplicates Writing label file ./lh.V1.thresh.label 4690 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.thresh.label --trgsubject sub011 --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 = sub011 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/sub011/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499 Number of reverse mapping hits = 1485 Checking for and removing duplicates Writing label file ./lh.V2.thresh.label 4819 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.thresh.label --trgsubject sub011 --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 = sub011 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/sub011/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499 Number of reverse mapping hits = 272 Checking for and removing duplicates Writing label file ./lh.MT.thresh.label 785 mri_label2label: Done mris_label2annot --s sub011 --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/sub011/label cmdline mris_label2annot --s sub011 --hemi lh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --l lh.perirhinal.label --a BA --maxstatwinner --noverbose sysname Linux hostname snake6 machine x86_64 user fkaule subject sub011 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/sub011/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 109048 unhit vertices Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/label/lh.BA.annot mris_label2annot --s sub011 --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/sub011/label cmdline mris_label2annot --s sub011 --hemi lh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l lh.BA1.thresh.label --l lh.BA2.thresh.label --l lh.BA3a.thresh.label --l lh.BA3b.thresh.label --l lh.BA4a.thresh.label --l lh.BA4p.thresh.label --l lh.BA6.thresh.label --l lh.BA44.thresh.label --l lh.BA45.thresh.label --l lh.V1.thresh.label --l lh.V2.thresh.label --l lh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose sysname Linux hostname snake6 machine x86_64 user fkaule subject sub011 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/sub011/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 130961 unhit vertices Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/label/lh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab sub011 lh white computing statistics for each annotation in ./lh.BA.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 1385 876 2516 2.162 0.511 0.157 0.060 29 3.5 BA1 5659 3795 8768 2.169 0.554 0.132 0.039 67 8.8 BA2 1015 670 861 1.705 0.392 0.149 0.047 10 2.0 BA3a 2670 1784 3363 1.673 0.542 0.134 0.051 44 5.0 BA3b 1882 1100 3676 2.744 0.455 0.123 0.045 28 3.9 BA4a 1500 1025 2181 2.189 0.520 0.117 0.038 11 2.4 BA4p 12072 8156 26146 2.686 0.583 0.132 0.037 159 17.9 BA6 2778 1904 5938 2.697 0.500 0.141 0.044 52 5.0 BA44 3970 2705 7547 2.380 0.563 0.149 0.051 72 7.8 BA45 3890 2550 4493 1.713 0.424 0.166 0.078 76 11.6 V1 8987 5928 12659 1.992 0.466 0.163 0.067 165 21.9 V2 2733 1780 4007 2.136 0.467 0.135 0.046 35 4.8 MT 910 650 2695 3.351 0.884 0.147 0.051 11 1.8 perirhinal mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab sub011 lh white computing statistics for each annotation in ./lh.BA.thresh.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 821 491 1520 2.243 0.481 0.166 0.065 19 2.2 BA1 2398 1624 3805 2.090 0.537 0.126 0.034 26 3.3 BA2 884 578 678 1.648 0.353 0.156 0.052 10 1.9 BA3a 1660 1145 1848 1.446 0.378 0.118 0.032 17 2.2 BA3b 1928 1130 3670 2.667 0.489 0.116 0.044 28 3.8 BA4a 1146 824 1625 2.137 0.542 0.121 0.037 7 1.9 BA4p 6192 4186 13915 2.714 0.590 0.135 0.038 85 9.5 BA6 1751 1195 3875 2.755 0.434 0.149 0.049 38 3.7 BA44 1520 1054 3354 2.555 0.499 0.165 0.064 38 3.4 BA45 4131 2718 4876 1.717 0.418 0.166 0.078 81 12.5 V1 4348 2915 5878 1.899 0.436 0.171 0.081 87 11.7 V2 759 488 996 1.952 0.407 0.135 0.043 8 1.6 MT #-------------------------------------------- #@# BA Labels rh Fri Aug 9 00:47:03 CEST 2013 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.label --trgsubject sub011 --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 = sub011 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/sub011/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726 Number of reverse mapping hits = 415 Checking for and removing duplicates Writing label file ./rh.BA1.label 4377 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.label --trgsubject sub011 --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 = sub011 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/sub011/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726 Number of reverse mapping hits = 795 Checking for and removing duplicates Writing label file ./rh.BA2.label 7482 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.label --trgsubject sub011 --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 = sub011 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/sub011/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726 Number of reverse mapping hits = 152 Checking for and removing duplicates Writing label file ./rh.BA3a.label 4132 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.label --trgsubject sub011 --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 = sub011 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/sub011/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726 Number of reverse mapping hits = 330 Checking for and removing duplicates Writing label file ./rh.BA3b.label 4852 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.label --trgsubject sub011 --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 = sub011 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/sub011/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726 Number of reverse mapping hits = 722 Checking for and removing duplicates Writing label file ./rh.BA4a.label 6469 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.label --trgsubject sub011 --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 = sub011 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/sub011/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726 Number of reverse mapping hits = 285 Checking for and removing duplicates Writing label file ./rh.BA4p.label 4758 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.label --trgsubject sub011 --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 = sub011 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/sub011/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726 Number of reverse mapping hits = 2177 Checking for and removing duplicates Writing label file ./rh.BA6.label 14433 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.label --trgsubject sub011 --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 = sub011 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/sub011/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726 Number of reverse mapping hits = 3004 Checking for and removing duplicates Writing label file ./rh.BA44.label 9916 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.label --trgsubject sub011 --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 = sub011 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/sub011/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726 Number of reverse mapping hits = 3364 Checking for and removing duplicates Writing label file ./rh.BA45.label 8719 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.label --trgsubject sub011 --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 = sub011 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/sub011/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726 Number of reverse mapping hits = 2066 Checking for and removing duplicates Writing label file ./rh.V1.label 6793 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.label --trgsubject sub011 --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 = sub011 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/sub011/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726 Number of reverse mapping hits = 3411 Checking for and removing duplicates Writing label file ./rh.V2.label 11427 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.label --trgsubject sub011 --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 = sub011 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/sub011/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726 Number of reverse mapping hits = 404 Checking for and removing duplicates Writing label file ./rh.MT.label 2336 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.perirhinal.label --trgsubject sub011 --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 = sub011 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/sub011/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726 Number of reverse mapping hits = 68 Checking for and removing duplicates Writing label file ./rh.perirhinal.label 820 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.thresh.label --trgsubject sub011 --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 = sub011 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/sub011/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726 Number of reverse mapping hits = 88 Checking for and removing duplicates Writing label file ./rh.BA1.thresh.label 964 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.thresh.label --trgsubject sub011 --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 = sub011 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/sub011/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726 Number of reverse mapping hits = 283 Checking for and removing duplicates Writing label file ./rh.BA2.thresh.label 2971 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.thresh.label --trgsubject sub011 --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 = sub011 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/sub011/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726 Number of reverse mapping hits = 45 Checking for and removing duplicates Writing label file ./rh.BA3a.thresh.label 1743 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.thresh.label --trgsubject sub011 --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 = sub011 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/sub011/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726 Number of reverse mapping hits = 197 Checking for and removing duplicates Writing label file ./rh.BA3b.thresh.label 2380 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.thresh.label --trgsubject sub011 --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 = sub011 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/sub011/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726 Number of reverse mapping hits = 119 Checking for and removing duplicates Writing label file ./rh.BA4a.thresh.label 1507 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.thresh.label --trgsubject sub011 --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 = sub011 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/sub011/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726 Number of reverse mapping hits = 81 Checking for and removing duplicates Writing label file ./rh.BA4p.thresh.label 1570 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.thresh.label --trgsubject sub011 --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 = sub011 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/sub011/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726 Number of reverse mapping hits = 1396 Checking for and removing duplicates Writing label file ./rh.BA6.thresh.label 8355 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.thresh.label --trgsubject sub011 --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 = sub011 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/sub011/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726 Number of reverse mapping hits = 783 Checking for and removing duplicates Writing label file ./rh.BA44.thresh.label 1795 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.thresh.label --trgsubject sub011 --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 = sub011 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/sub011/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726 Number of reverse mapping hits = 772 Checking for and removing duplicates Writing label file ./rh.BA45.thresh.label 1950 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.thresh.label --trgsubject sub011 --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 = sub011 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/sub011/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726 Number of reverse mapping hits = 1379 Checking for and removing duplicates Writing label file ./rh.V1.thresh.label 4611 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.thresh.label --trgsubject sub011 --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 = sub011 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/sub011/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726 Number of reverse mapping hits = 1507 Checking for and removing duplicates Writing label file ./rh.V2.thresh.label 4944 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.thresh.label --trgsubject sub011 --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 = sub011 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/sub011/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726 Number of reverse mapping hits = 27 Checking for and removing duplicates Writing label file ./rh.MT.thresh.label 295 mri_label2label: Done mris_label2annot --s sub011 --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/sub011/label cmdline mris_label2annot --s sub011 --hemi rh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --l rh.perirhinal.label --a BA --maxstatwinner --noverbose sysname Linux hostname snake6 machine x86_64 user fkaule subject sub011 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/sub011/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 109967 unhit vertices Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/label/rh.BA.annot mris_label2annot --s sub011 --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/sub011/label cmdline mris_label2annot --s sub011 --hemi rh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l rh.BA1.thresh.label --l rh.BA2.thresh.label --l rh.BA3a.thresh.label --l rh.BA3b.thresh.label --l rh.BA4a.thresh.label --l rh.BA4p.thresh.label --l rh.BA6.thresh.label --l rh.BA44.thresh.label --l rh.BA45.thresh.label --l rh.V1.thresh.label --l rh.V2.thresh.label --l rh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose sysname Linux hostname snake6 machine x86_64 user fkaule subject sub011 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/sub011/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 132713 unhit vertices Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/label/rh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab sub011 rh white computing statistics for each annotation in ./rh.BA.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 982 585 1686 2.119 0.494 0.149 0.075 23 2.9 BA1 4065 2680 5956 2.111 0.452 0.119 0.036 42 6.4 BA2 979 634 898 1.743 0.455 0.140 0.047 10 1.9 BA3a 2098 1344 2504 1.604 0.538 0.118 0.035 24 3.0 BA3b 1740 1016 3091 2.613 0.444 0.107 0.118 13 13.9 BA4a 1245 817 1915 2.378 0.414 0.114 0.035 9 1.9 BA4p 10534 6864 23281 2.771 0.544 0.134 0.044 143 18.5 BA6 5399 3613 10416 2.553 0.427 0.123 0.039 72 8.8 BA44 6744 4539 13515 2.486 0.508 0.156 0.059 145 15.5 BA45 4438 3024 4935 1.626 0.407 0.174 0.093 91 17.8 V1 8903 5977 12445 1.974 0.476 0.175 0.072 193 25.6 V2 1989 1378 3268 2.248 0.468 0.156 0.057 37 4.6 MT 643 462 2166 3.363 0.654 0.150 0.062 10 1.5 perirhinal mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab sub011 rh white computing statistics for each annotation in ./rh.BA.thresh.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 670 376 946 1.899 0.482 0.150 0.079 18 2.4 BA1 2123 1407 3089 2.011 0.474 0.112 0.032 19 3.1 BA2 862 547 703 1.695 0.364 0.136 0.044 7 1.6 BA3a 1716 1123 1816 1.453 0.424 0.105 0.032 14 1.9 BA3b 1019 544 1941 2.759 0.499 0.113 0.181 9 13.1 BA4a 999 675 1499 2.359 0.398 0.117 0.038 7 1.6 BA4p 6955 4494 15037 2.739 0.526 0.133 0.047 95 12.8 BA6 1759 1195 3785 2.641 0.377 0.132 0.046 30 3.4 BA44 1886 1305 3972 2.472 0.474 0.157 0.059 42 4.4 BA45 4196 2887 4668 1.621 0.400 0.172 0.090 85 16.4 V1 4600 3131 6091 1.859 0.480 0.192 0.089 116 16.0 V2 228 161 443 2.359 0.343 0.156 0.067 4 0.6 MT /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label lh Fri Aug 9 00:52:09 CEST 2013 mris_spherical_average -erode 1 -orig white -t 0.4 -o sub011 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject sub011. processing subject lh.EC_average... reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 890 points to lh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label sub011 lh white limiting computations to label ./lh.entorhinal_exvivo.label. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 311 209 1068 3.180 0.748 0.138 0.057 5 0.8 ./lh.entorhinal_exvivo.label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label rh Fri Aug 9 00:52:26 CEST 2013 mris_spherical_average -erode 1 -orig white -t 0.4 -o sub011 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label painting output onto subject sub011. processing subject rh.EC_average... reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 801 points to rh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label sub011 rh white limiting computations to label ./rh.entorhinal_exvivo.label. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 306 202 1337 3.840 0.502 0.159 0.074 6 1.0 ./rh.entorhinal_exvivo.label #------------------------------------------ Started at Thu Aug 8 10:54:16 CEST 2013 Ended at Fri Aug 9 00:52:42 CEST 2013 #@#%# recon-all-run-time-hours 13.974 recon-all -s sub011 finished without error at Fri Aug 9 00:52:42 CEST 2013