Thu Aug 8 10:54:16 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016 /opt/freesurfer/5.3.0/bin/recon-all -i /home/data/exppsy/forrest_gump/openfmri.org/sub016/anatomy/highres001.nii.gz -cw256 -all -T2 /home/data/exppsy/forrest_gump/openfmri.org/sub016/anatomy/other/t2w001.nii.gz -T2pial -subjid sub016 -sd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer subjid sub016 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 96978996 2222696 0 118440 94733872 -/+ buffers/cache: 2126684 97075008 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/sub016 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub016/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig/001.mgz mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub016/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/anatomy/highres001.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999248, 0.0307568, 0.0236215) j_ras = (0.0317878, 0.9985, 0.0445881) k_ras = (0.0222147, -0.0453054, 0.998726) writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig/001.mgz... #-------------------------------------------- #@# T2/FLAIR Input Thu Aug 8 10:54:37 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub016/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig/T2raw.mgz mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub016/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/anatomy/other/t2w001.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999248, 0.0307568, 0.0236215) j_ras = (0.0317878, 0.9985, 0.0445881) k_ras = (0.0222147, -0.0453054, 0.998726) writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig/T2raw.mgz... #-------------------------------------------- #@# MotionCor Thu Aug 8 10:54:53 CEST 2013 Found 1 runs /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/mri/orig/001.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig.mgz --conform --cw256 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999248, 0.0307568, 0.0236215) j_ras = (0.0317878, 0.9985, 0.0445881) k_ras = (0.0222147, -0.0453054, 0.998726) Original Data has (0.699898, 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/sub016/mri/orig.mgz... mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/talairach.xfm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Aug 8 10:55:33 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 10:58:41 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7652, pval=0.6675 >= threshold=0.0050) awk -f /opt/freesurfer/5.3.0/bin/extract_talairach_avi_QA.awk /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/talairach_avi.log tal_QC_AZS /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/talairach_avi.log TalAviQA: 0.96776 z-score: -2 #-------------------------------------------- #@# Nu Intensity Correction Thu Aug 8 10:58:42 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/sub016/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 10:58:42 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.25504 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.25504/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.25504/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.86265e-09, 3.72529e-09) j_ras = (1.86265e-09, 0, -1) k_ras = (-1.97906e-09, 1, -3.72529e-09) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.25504/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Aug 8 10:58:46 CEST 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.25504/nu0.mnc ./tmp.mri_nu_correct.mni.25504/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.25504/0/ [fkaule@snake6:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/] [2013-08-08 10:58:46] 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.25504/0/ ./tmp.mri_nu_correct.mni.25504/nu0.mnc ./tmp.mri_nu_correct.mni.25504/nu1.imp 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Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 50 CV of field change: 0.00127909 [fkaule@snake6:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/] [2013-08-08 10:59:52] running: /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.25504/nu0.mnc ./tmp.mri_nu_correct.mni.25504/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Thu Aug 8 10:59:59 CEST 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.25504/nu1.mnc ./tmp.mri_nu_correct.mni.25504/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.25504/1/ [fkaule@snake6:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/] [2013-08-08 10:59:59] 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.25504/1/ ./tmp.mri_nu_correct.mni.25504/nu1.mnc ./tmp.mri_nu_correct.mni.25504/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done 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Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 36 CV of field change: 0.000992739 [fkaule@snake6:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/] [2013-08-08 11:00:35] running: /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.25504/nu1.mnc ./tmp.mri_nu_correct.mni.25504/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.25504/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.25504/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/sub016/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.25504/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.25504/ones.mgz sysname Linux hostname snake6 machine x86_64 user fkaule input ./tmp.mri_nu_correct.mni.25504/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.25504/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.25504/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.25504/sum.junk --avgwf ./tmp.mri_nu_correct.mni.25504/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.25504/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.25504/sum.junk --avgwf ./tmp.mri_nu_correct.mni.25504/input.mean.dat sysname Linux hostname snake6 machine x86_64 user fkaule UseRobust 0 Loading ./tmp.mri_nu_correct.mni.25504/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.25504/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.25504/ones.mgz --i ./tmp.mri_nu_correct.mni.25504/nu2.mnc --sum ./tmp.mri_nu_correct.mni.25504/sum.junk --avgwf ./tmp.mri_nu_correct.mni.25504/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.25504/ones.mgz --i ./tmp.mri_nu_correct.mni.25504/nu2.mnc --sum ./tmp.mri_nu_correct.mni.25504/sum.junk --avgwf ./tmp.mri_nu_correct.mni.25504/output.mean.dat sysname Linux hostname snake6 machine x86_64 user fkaule UseRobust 0 Loading ./tmp.mri_nu_correct.mni.25504/ones.mgz Loading ./tmp.mri_nu_correct.mni.25504/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.25504/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.25504/nu2.mnc ./tmp.mri_nu_correct.mni.25504/nu2.mnc mul .91902004648487725472 Saving result to './tmp.mri_nu_correct.mni.25504/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.25504/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.25504/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.25504/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.86264e-09, 3.72529e-09) j_ras = (1.86265e-09, 0, -1) k_ras = (-1.97906e-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 (11, 145) to ( 3, 110) Thu Aug 8 11:01:18 CEST 2013 mri_nu_correct.mni done mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Thu Aug 8 11:01:19 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.058 -0.012 -0.029 2.523; 0.001 1.053 0.291 -44.522; 0.050 -0.333 1.154 -5.882; 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 = 18 Starting OpenSpline(): npoints = 18 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 108 gm peak at 56 (56), valley at 38 (38) 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 57 (57), valley at 37 (37) csf peak at 28, setting threshold to 47 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 46 seconds. #-------------------------------------------- #@# Skull Stripping Thu Aug 8 11:04:06 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri mri_em_register -skull nu.mgz /opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta ======= NUMBER OF OPENMP THREADS = 1 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=10.0 skull bounding box = (48, 13, 15) --> (205, 255, 204) using (100, 94, 110) as brain centroid... mean wm in atlas = 126, using box (81,64,87) --> (119, 123,133) to find MRI wm before smoothing, mri peak at 108 after smoothing, mri peak at 108, scaling input intensities by 1.167 scaling channel 0 by 1.16667 initial log_p = -4.7 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.486263 @ (-9.091, 27.273, -9.091) max log p = -4.316039 @ (4.545, -4.545, -4.545) max log p = -4.208757 @ (2.273, -2.273, 6.818) max log p = -4.208757 @ (0.000, 0.000, 0.000) max log p = -4.208757 @ (0.000, 0.000, 0.000) max log p = -4.208757 @ (0.000, 0.000, 0.000) Found translation: (-2.3, 20.5, -6.8): log p = -4.209 **************************************** 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) 1.000 0.000 0.000 -2.273; 0.000 1.194 0.320 -35.195; 0.000 -0.239 0.893 29.301; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.000 0.000 0.000 -2.273; 0.000 1.194 0.320 -35.195; 0.000 -0.239 0.893 29.301; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.1 (thresh=-4.1) 0.962 -0.003 0.027 -0.106; -0.002 1.201 0.292 -28.668; -0.037 -0.210 0.955 24.058; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 0.962 -0.003 0.027 -0.106; -0.002 1.201 0.292 -28.668; -0.037 -0.210 0.955 24.058; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 0.966 -0.003 0.027 -0.575; -0.002 1.198 0.291 -28.306; -0.037 -0.210 0.958 24.199; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 0.966 -0.003 0.027 -0.575; -0.002 1.203 0.292 -28.832; -0.037 -0.210 0.957 24.295; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 0.966 -0.003 0.027 -0.575; -0.002 1.205 0.292 -29.183; -0.037 -0.210 0.956 24.391; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 0.966 -0.003 0.027 -0.575; -0.002 1.205 0.292 -29.183; -0.037 -0.210 0.956 24.391; 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 0.96553 -0.00330 0.02692 -0.57520; -0.00214 1.20541 0.29238 -29.18299; -0.03709 -0.20989 0.95579 24.39078; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 0.96553 -0.00330 0.02692 -0.57520; -0.00214 1.20541 0.29238 -29.18299; -0.03709 -0.20989 0.95579 24.39078; 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: 0.966 -0.003 0.027 -0.575; -0.002 1.205 0.292 -29.183; -0.037 -0.210 0.956 24.391; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -4.0 (old=-4.7) transform before final EM align: 0.966 -0.003 0.027 -0.575; -0.002 1.205 0.292 -29.183; -0.037 -0.210 0.956 24.391; 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 0.96553 -0.00330 0.02692 -0.57520; -0.00214 1.20541 0.29238 -29.18299; -0.03709 -0.20989 0.95579 24.39078; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 0.96553 -0.00330 0.02692 -0.57520; -0.00214 1.20541 0.29238 -29.18299; -0.03709 -0.20989 0.95579 24.39078; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 012: -log(p) = 4.4 tol 0.000000 final transform: 0.966 -0.003 0.027 -0.575; -0.002 1.205 0.292 -29.183; -0.037 -0.210 0.956 24.391; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 40 minutes and 24 seconds. mri_watershed -T1 -brain_atlas /opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=128 y=86 z=118 r=96 first estimation of the main basin volume: 3810863 voxels Looking for seedpoints 2 found in the cerebellum 18 found in the rest of the brain global maximum in x=165, y=88, z=85, 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=22582056777 voxels, voxel volume =1.000 = 22582056777 mmm3 = 22582056.960 cm3 done. PostAnalyze...Basin Prior 214 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=127,y=97, z=111, r=9970 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 45424 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=12 , nb = -1033853503 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = 1101477547 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1079460279 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1082319012 OTHER CSF_MIN=0, CSF_intensity=9, CSF_MAX=32 , nb = 1066689784 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 4, 6, 36, 57 after analyzing : 4, 26, 36, 33 RIGHT_CER before analyzing : 12, 20, 39, 61 after analyzing : 12, 32, 39, 39 LEFT_CER before analyzing : 5, 7, 36, 70 after analyzing : 5, 26, 36, 37 RIGHT_BRAIN before analyzing : 4, 6, 35, 56 after analyzing : 4, 25, 35, 32 LEFT_BRAIN before analyzing : 4, 6, 36, 57 after analyzing : 4, 26, 36, 33 OTHER before analyzing : 32, 66, 80, 89 after analyzing : 32, 75, 80, 78 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...66 iterations *********************VALIDATION********************* curvature mean = -0.012, std = 0.011 curvature mean = 73.306, std = 8.785 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 2.07, sigma = 3.40 after rotation: sse = 2.07, sigma = 3.40 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 2.13, its var is 2.71 before Erosion-Dilatation 0.01% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...52 iterations mri_strip_skull: done peeling brain Brain Size = 1932674 voxels, voxel volume = 1.000 mm3 = 1932674 mmm3 = 1932.674 cm3 ****************************** Saving brainmask.auto.mgz done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Thu Aug 8 11:45:00 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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, 37, 33) --> (198, 176, 203) using (103, 83, 118) as brain centroid... mean wm in atlas = 107, using box (86,66,97) --> (120, 100,138) to find MRI wm before smoothing, mri peak at 106 after smoothing, mri peak at 106, scaling input intensities by 1.009 scaling channel 0 by 1.00943 initial log_p = -4.5 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.052590 @ (-9.091, 27.273, -9.091) max log p = -3.920415 @ (4.545, -4.545, 4.545) max log p = -3.806407 @ (2.273, 2.273, -6.818) max log p = -3.742288 @ (1.136, -3.409, 3.409) max log p = -3.716874 @ (-1.705, -1.705, -0.568) max log p = -3.716874 @ (0.000, 0.000, 0.000) Found translation: (-2.8, 19.9, -8.5): log p = -3.717 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.6, old_max_log_p =-3.7 (thresh=-3.7) 1.000 0.000 0.000 -2.841; 0.000 1.050 0.156 -2.858; 0.000 -0.112 0.997 2.922; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.6, old_max_log_p =-3.6 (thresh=-3.6) 1.000 0.000 0.000 -2.841; 0.000 1.050 0.156 -2.858; 0.000 -0.112 0.997 2.922; 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=-3.5, old_max_log_p =-3.6 (thresh=-3.6) 0.998 -0.045 0.052 -3.782; 0.036 1.092 0.268 -20.552; -0.063 -0.199 0.940 28.185; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.4, old_max_log_p =-3.5 (thresh=-3.5) 0.980 -0.039 0.020 3.232; 0.039 1.119 0.241 -22.394; -0.030 -0.167 0.967 15.950; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4) 0.980 -0.039 0.020 3.232; 0.039 1.119 0.241 -22.394; -0.030 -0.167 0.967 15.950; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4) 0.981 -0.039 0.020 2.619; 0.039 1.121 0.242 -23.193; -0.030 -0.167 0.963 16.264; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4) 0.983 -0.021 0.024 0.151; 0.022 1.119 0.249 -21.700; -0.030 -0.176 0.960 17.535; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4) 0.983 -0.021 0.024 0.151; 0.022 1.116 0.249 -21.370; -0.030 -0.176 0.960 17.535; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 8 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4) 0.983 -0.021 0.024 0.151; 0.022 1.116 0.249 -21.370; -0.030 -0.176 0.960 17.535; 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 0.98311 -0.02089 0.02425 0.15113; 0.02232 1.11629 0.24862 -21.37015; -0.02989 -0.17573 0.96035 17.53523; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 0.98311 -0.02089 0.02425 0.15113; 0.02232 1.11629 0.24862 -21.37015; -0.02989 -0.17573 0.96035 17.53523; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.983 -0.021 0.024 0.151; 0.022 1.116 0.249 -21.370; -0.030 -0.176 0.960 17.535; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.4 (old=-4.5) transform before final EM align: 0.983 -0.021 0.024 0.151; 0.022 1.116 0.249 -21.370; -0.030 -0.176 0.960 17.535; 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 0.98311 -0.02089 0.02425 0.15113; 0.02232 1.11629 0.24862 -21.37015; -0.02989 -0.17573 0.96035 17.53523; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 0.98311 -0.02089 0.02425 0.15113; 0.02232 1.11629 0.24862 -21.37015; -0.02989 -0.17573 0.96035 17.53523; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 012: -log(p) = 3.9 after pass:transform: ( 0.98, -0.02, 0.02, 0.15) ( 0.02, 1.12, 0.25, -21.37) ( -0.03, -0.18, 0.96, 17.54) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 014: -log(p) = 3.9 tol 0.000000 final transform: 0.983 -0.021 0.024 0.151; 0.022 1.116 0.249 -21.370; -0.030 -0.176 0.960 17.535; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 34 minutes and 25 seconds. #-------------------------------------- #@# CA Normalize Thu Aug 8 12:19:24 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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, 37, 33) --> (198, 176, 203) using (103, 83, 118) as brain centroid... mean wm in atlas = 107, using box (86,66,97) --> (120, 100,138) to find MRI wm before smoothing, mri peak at 106 after smoothing, mri peak at 106, scaling input intensities by 1.009 scaling channel 0 by 1.00943 using 244171 sample points... INFO: compute sample coordinates transform 0.983 -0.021 0.024 0.151; 0.022 1.116 0.249 -21.370; -0.030 -0.176 0.960 17.535; 0.000 0.000 0.000 1.000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (127, 38, 35) --> (195, 141, 204) Left_Cerebral_White_Matter: limiting intensities to 106.0 --> 177.0 0 of 11 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (62, 39, 34) --> (128, 139, 203) Right_Cerebral_White_Matter: limiting intensities to 101.0 --> 177.0 0 of 8 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (130, 118, 63) --> (180, 157, 117) Left_Cerebellum_White_Matter: limiting intensities to 91.0 --> 177.0 0 of 7 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (82, 118, 59) --> (129, 158, 117) Right_Cerebellum_White_Matter: limiting intensities to 103.0 --> 177.0 2 of 7 (28.6%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (111, 108, 97) --> (144, 170, 128) Brain_Stem: limiting intensities to 79.0 --> 177.0 0 of 13 (0.0%) samples deleted using 46 total control points for intensity normalization... bias field = 0.956 +- 0.064 0 of 44 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (127, 38, 35) --> (195, 141, 204) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 169.0 0 of 91 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (62, 39, 34) --> (128, 139, 203) Right_Cerebral_White_Matter: limiting intensities to 99.0 --> 169.0 0 of 103 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (130, 118, 63) --> (180, 157, 117) Left_Cerebellum_White_Matter: limiting intensities to 99.0 --> 169.0 26 of 39 (66.7%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (82, 118, 59) --> (129, 158, 117) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 169.0 0 of 35 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (111, 108, 97) --> (144, 170, 128) Brain_Stem: limiting intensities to 89.0 --> 169.0 28 of 58 (48.3%) samples deleted using 326 total control points for intensity normalization... bias field = 0.957 +- 0.070 0 of 272 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (127, 38, 35) --> (195, 141, 204) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 154.0 3 of 220 (1.4%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (62, 39, 34) --> (128, 139, 203) Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 154.0 0 of 222 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (130, 118, 63) --> (180, 157, 117) Left_Cerebellum_White_Matter: limiting intensities to 75.0 --> 154.0 0 of 41 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (82, 118, 59) --> (129, 158, 117) Right_Cerebellum_White_Matter: limiting intensities to 81.0 --> 154.0 3 of 38 (7.9%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (111, 108, 97) --> (144, 170, 128) Brain_Stem: limiting intensities to 64.0 --> 154.0 0 of 58 (0.0%) samples deleted using 579 total control points for intensity normalization... bias field = 1.027 +- 0.060 0 of 573 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 2 minutes and 3 seconds. #-------------------------------------- #@# CA Reg Thu Aug 8 12:21:28 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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=0.863, neg=0, invalid=96777 0001: dt=129.472000, rms=0.793 (8.133%), neg=0, invalid=96777 0002: dt=129.472000, rms=0.779 (1.805%), neg=0, invalid=96777 0003: dt=129.472000, rms=0.765 (1.709%), neg=0, invalid=96777 0004: dt=110.976000, rms=0.761 (0.564%), neg=0, invalid=96777 0005: dt=129.472000, rms=0.754 (0.867%), neg=0, invalid=96777 0006: dt=92.480000, rms=0.752 (0.262%), neg=0, invalid=96777 0007: dt=369.920000, rms=0.745 (1.036%), neg=0, invalid=96777 0008: dt=55.488000, rms=0.742 (0.371%), neg=0, invalid=96777 0009: dt=129.472000, rms=0.740 (0.210%), neg=0, invalid=96777 0010: dt=129.472000, rms=0.738 (0.377%), neg=0, invalid=96777 0011: dt=129.472000, rms=0.734 (0.468%), neg=0, invalid=96777 0012: dt=129.472000, rms=0.731 (0.457%), neg=0, invalid=96777 0013: dt=129.472000, rms=0.726 (0.656%), neg=0, invalid=96777 0014: dt=129.472000, rms=0.721 (0.643%), neg=0, invalid=96777 0015: dt=129.472000, rms=0.718 (0.499%), neg=0, invalid=96777 0016: dt=129.472000, rms=0.715 (0.405%), neg=0, invalid=96777 0017: dt=129.472000, rms=0.712 (0.450%), neg=0, invalid=96777 0018: dt=129.472000, rms=0.709 (0.398%), neg=0, invalid=96777 0019: dt=129.472000, rms=0.707 (0.305%), neg=0, invalid=96777 0020: dt=129.472000, rms=0.705 (0.276%), neg=0, invalid=96777 0021: dt=129.472000, rms=0.703 (0.283%), neg=0, invalid=96777 0022: dt=129.472000, rms=0.701 (0.246%), neg=0, invalid=96777 0023: dt=129.472000, rms=0.699 (0.222%), neg=0, invalid=96777 0024: dt=129.472000, rms=0.698 (0.223%), neg=0, invalid=96777 0025: dt=129.472000, rms=0.696 (0.235%), neg=0, invalid=96777 0026: dt=129.472000, rms=0.694 (0.254%), neg=0, invalid=96777 0027: dt=129.472000, rms=0.693 (0.228%), neg=0, invalid=96777 0028: dt=129.472000, rms=0.691 (0.190%), neg=0, invalid=96777 0029: dt=129.472000, rms=0.690 (0.216%), neg=0, invalid=96777 0030: dt=129.472000, rms=0.689 (0.202%), neg=0, invalid=96777 0031: dt=129.472000, rms=0.687 (0.192%), neg=0, invalid=96777 0032: dt=129.472000, rms=0.686 (0.154%), neg=0, invalid=96777 0033: dt=129.472000, rms=0.685 (0.132%), neg=0, invalid=96777 0034: dt=129.472000, rms=0.684 (0.162%), neg=0, invalid=96777 0035: dt=129.472000, rms=0.683 (0.136%), neg=0, invalid=96777 0036: dt=129.472000, rms=0.683 (0.108%), neg=0, invalid=96777 0037: dt=129.472000, rms=0.682 (0.141%), neg=0, invalid=96777 0038: dt=129.472000, rms=0.680 (0.167%), neg=0, invalid=96777 0039: dt=129.472000, rms=0.679 (0.143%), neg=0, invalid=96777 0040: dt=129.472000, rms=0.679 (0.109%), neg=0, invalid=96777 0041: dt=129.472000, rms=0.678 (0.150%), neg=0, invalid=96777 0042: dt=129.472000, rms=0.677 (0.167%), neg=0, invalid=96777 0043: dt=129.472000, rms=0.676 (0.107%), neg=0, invalid=96777 0044: dt=129.472000, rms=0.675 (0.065%), neg=0, invalid=96777 0045: dt=295.936000, rms=0.675 (0.069%), neg=0, invalid=96777 0046: dt=4.624000, rms=0.675 (-0.006%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.675, neg=0, invalid=96777 0047: dt=27.744000, rms=0.675 (0.009%), neg=0, invalid=96777 0048: dt=18.496000, rms=0.675 (0.005%), neg=0, invalid=96777 0049: dt=18.496000, rms=0.675 (0.006%), neg=0, invalid=96777 0050: dt=18.496000, rms=0.675 (0.001%), neg=0, invalid=96777 0051: dt=18.496000, rms=0.675 (-0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.684, neg=0, invalid=96777 0052: dt=331.776000, rms=0.666 (2.583%), neg=0, invalid=96777 0053: dt=36.288000, rms=0.663 (0.424%), neg=0, invalid=96777 0054: dt=145.152000, rms=0.656 (1.150%), neg=0, invalid=96777 0055: dt=20.736000, rms=0.654 (0.263%), neg=0, invalid=96777 0056: dt=36.288000, rms=0.653 (0.116%), neg=0, invalid=96777 0057: dt=36.288000, rms=0.652 (0.227%), neg=0, invalid=96777 0058: dt=36.288000, rms=0.650 (0.299%), neg=0, invalid=96777 0059: dt=36.288000, rms=0.647 (0.341%), neg=0, invalid=96777 0060: dt=36.288000, rms=0.645 (0.435%), neg=0, invalid=96777 0061: dt=36.288000, rms=0.641 (0.555%), neg=0, invalid=96777 0062: dt=36.288000, rms=0.637 (0.575%), neg=0, invalid=96777 0063: dt=36.288000, rms=0.634 (0.491%), neg=0, invalid=96777 0064: dt=36.288000, rms=0.631 (0.437%), neg=0, invalid=96777 0065: dt=36.288000, rms=0.629 (0.393%), neg=0, invalid=96777 0066: dt=36.288000, rms=0.626 (0.403%), neg=0, invalid=96777 0067: dt=36.288000, rms=0.624 (0.368%), neg=0, invalid=96777 0068: dt=36.288000, rms=0.622 (0.297%), neg=0, invalid=96777 0069: dt=36.288000, rms=0.621 (0.261%), neg=0, invalid=96777 0070: dt=36.288000, rms=0.619 (0.301%), neg=0, invalid=96777 0071: dt=36.288000, rms=0.617 (0.291%), neg=0, invalid=96777 0072: dt=36.288000, rms=0.615 (0.239%), neg=0, invalid=96777 0073: dt=36.288000, rms=0.614 (0.186%), neg=0, invalid=96777 0074: dt=36.288000, rms=0.613 (0.163%), neg=0, invalid=96777 0075: dt=36.288000, rms=0.612 (0.169%), neg=0, invalid=96777 0076: dt=36.288000, rms=0.611 (0.149%), neg=0, invalid=96777 0077: dt=36.288000, rms=0.611 (0.104%), neg=0, invalid=96777 0078: dt=36.288000, rms=0.610 (0.063%), neg=0, invalid=96777 0079: dt=145.152000, rms=0.610 (0.082%), neg=0, invalid=96777 0080: dt=0.000000, rms=0.610 (-0.005%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.610, neg=0, invalid=96777 0081: dt=15.552000, rms=0.610 (0.015%), neg=0, invalid=96777 0082: dt=31.104000, rms=0.610 (0.019%), neg=0, invalid=96777 0083: dt=25.920000, rms=0.610 (0.013%), neg=0, invalid=96777 0084: dt=25.920000, rms=0.610 (-0.005%), neg=0, invalid=96777 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.640, neg=0, invalid=96777 0085: dt=2.800000, rms=0.640 (0.023%), neg=0, invalid=96777 0086: dt=0.700000, rms=0.640 (0.001%), neg=0, invalid=96777 0087: dt=0.700000, rms=0.640 (0.001%), neg=0, invalid=96777 0088: dt=0.700000, rms=0.640 (-0.003%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.640, neg=0, invalid=96777 0089: dt=0.000000, rms=0.640 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.725, neg=0, invalid=96777 0090: dt=5.393665, rms=0.700 (3.417%), neg=0, invalid=96777 0091: dt=3.456000, rms=0.699 (0.216%), neg=0, invalid=96777 0092: dt=3.456000, rms=0.699 (-0.021%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.699, neg=0, invalid=96777 0093: dt=0.000000, rms=0.699 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.774, neg=0, invalid=96777 0094: dt=1.290672, rms=0.768 (0.749%), neg=0, invalid=96777 0095: dt=1.536000, rms=0.760 (0.999%), neg=0, invalid=96777 0096: dt=0.816964, rms=0.759 (0.172%), neg=0, invalid=96777 0097: dt=0.816964, rms=0.758 (0.146%), neg=0, invalid=96777 0098: dt=0.816964, rms=0.757 (0.157%), neg=0, invalid=96777 0099: dt=0.816964, rms=0.757 (0.021%), neg=0, invalid=96777 0100: dt=0.816964, rms=0.757 (-0.282%), neg=0, invalid=96777 0101: dt=1.024000, rms=0.757 (0.018%), neg=0, invalid=96777 0102: dt=1.792000, rms=0.756 (0.071%), neg=0, invalid=96777 0103: dt=0.384000, rms=0.756 (0.005%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.756, neg=0, invalid=96777 0104: dt=1.166667, rms=0.755 (0.103%), neg=0, invalid=96777 0105: dt=0.000000, rms=0.755 (0.003%), neg=0, invalid=96777 0106: dt=0.100000, rms=0.755 (-0.004%), 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=0.719, neg=0, invalid=96777 0107: dt=0.155548, rms=0.711 (1.144%), neg=0, invalid=96777 0108: dt=0.000000, rms=0.711 (0.002%), neg=0, invalid=96777 0109: dt=0.050000, rms=0.711 (-0.029%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.711, neg=0, invalid=96777 0110: dt=0.278195, rms=0.709 (0.339%), neg=0, invalid=96777 0111: dt=0.081926, rms=0.708 (0.125%), neg=0, invalid=96777 0112: dt=0.081926, rms=0.708 (0.024%), neg=0, invalid=96777 0113: dt=0.081926, rms=0.707 (0.049%), neg=0, invalid=96777 0114: dt=0.081926, rms=0.707 (0.086%), neg=0, invalid=96777 0115: dt=0.081926, rms=0.706 (0.117%), neg=0, invalid=96777 0116: dt=0.081926, rms=0.705 (0.125%), neg=0, invalid=96777 0117: dt=0.081926, rms=0.704 (0.115%), neg=0, invalid=96777 0118: dt=0.081926, rms=0.703 (0.098%), neg=0, invalid=96777 0119: dt=0.000000, rms=0.703 (-0.000%), neg=0, invalid=96777 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.12699 ( 8) Left_Lateral_Ventricle (4): linear fit = 0.28 x + 0.0 (1441 voxels, overlap=0.154) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (1441 voxels, peak = 7), gca=9.6 gca peak = 0.14022 (22) mri peak = 0.16230 (10) Right_Lateral_Ventricle (43): linear fit = 0.28 x + 0.0 (1121 voxels, overlap=0.005) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (1121 voxels, peak = 6), gca=8.8 gca peak = 0.24234 (100) mri peak = 0.10576 (78) Right_Pallidum (52): linear fit = 0.81 x + 0.0 (420 voxels, overlap=0.039) Right_Pallidum (52): linear fit = 0.81 x + 0.0 (420 voxels, peak = 80), gca=80.5 gca peak = 0.19192 (97) mri peak = 0.12456 (75) Left_Pallidum (13): linear fit = 0.77 x + 0.0 (275 voxels, overlap=0.036) Left_Pallidum (13): linear fit = 0.77 x + 0.0 (275 voxels, peak = 75), gca=75.2 gca peak = 0.24007 (63) mri peak = 0.06338 (56) Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (563 voxels, overlap=0.562) Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (563 voxels, peak = 55), gca=55.1 gca peak = 0.29892 (64) mri peak = 0.08085 (61) Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (753 voxels, overlap=0.931) Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (753 voxels, peak = 59), gca=59.2 gca peak = 0.12541 (104) mri peak = 0.06872 (105) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (71044 voxels, overlap=0.897) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (71044 voxels, peak = 106), gca=105.6 gca peak = 0.13686 (104) mri peak = 0.07761 (105) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (73417 voxels, overlap=0.866) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (73417 voxels, peak = 106), gca=105.6 gca peak = 0.11691 (63) mri peak = 0.05348 (55) Left_Cerebral_Cortex (3): linear fit = 0.85 x + 0.0 (24106 voxels, overlap=0.379) Left_Cerebral_Cortex (3): linear fit = 0.85 x + 0.0 (24106 voxels, peak = 53), gca=53.2 gca peak = 0.13270 (63) mri peak = 0.05168 (54) Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (24760 voxels, overlap=0.382) Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (24760 voxels, peak = 52), gca=52.0 gca peak = 0.15182 (70) mri peak = 0.08942 (63) Right_Caudate (50): linear fit = 0.86 x + 0.0 (569 voxels, overlap=0.135) Right_Caudate (50): linear fit = 0.86 x + 0.0 (569 voxels, peak = 60), gca=59.9 gca peak = 0.14251 (76) mri peak = 0.08017 (63) Left_Caudate (11): linear fit = 0.79 x + 0.0 (718 voxels, overlap=0.017) Left_Caudate (11): linear fit = 0.79 x + 0.0 (718 voxels, peak = 60), gca=59.7 gca peak = 0.12116 (60) mri peak = 0.04645 (62) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (10675 voxels, overlap=0.948) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (10675 voxels, peak = 62), gca=61.5 gca peak = 0.12723 (61) mri peak = 0.05533 (58) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (12758 voxels, overlap=0.986) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (12758 voxels, peak = 60), gca=60.1 gca peak = 0.22684 (88) mri peak = 0.05304 (94) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (7086 voxels, overlap=0.844) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (7086 voxels, peak = 95), gca=95.5 gca peak = 0.21067 (87) mri peak = 0.06032 (89) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (6944 voxels, overlap=0.924) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (6944 voxels, peak = 94), gca=93.5 gca peak = 0.25455 (62) mri peak = 0.09078 (58) Left_Amygdala (18): linear fit = 0.88 x + 0.0 (357 voxels, overlap=0.846) Left_Amygdala (18): linear fit = 0.88 x + 0.0 (357 voxels, peak = 54), gca=54.2 gca peak = 0.39668 (62) mri peak = 0.10542 (57) Right_Amygdala (54): linear fit = 0.90 x + 0.0 (359 voxels, overlap=0.771) Right_Amygdala (54): linear fit = 0.90 x + 0.0 (359 voxels, peak = 56), gca=56.1 gca peak = 0.10129 (93) mri peak = 0.05544 (88) Left_Thalamus_Proper (10): linear fit = 0.94 x + 0.0 (5742 voxels, overlap=0.918) Left_Thalamus_Proper (10): linear fit = 0.94 x + 0.0 (5742 voxels, peak = 88), gca=87.9 gca peak = 0.12071 (89) mri peak = 0.06385 (80) Right_Thalamus_Proper (49): linear fit = 0.94 x + 0.0 (4190 voxels, overlap=0.796) Right_Thalamus_Proper (49): linear fit = 0.94 x + 0.0 (4190 voxels, peak = 83), gca=83.2 gca peak = 0.13716 (82) mri peak = 0.06132 (70) Left_Putamen (12): linear fit = 0.85 x + 0.0 (2017 voxels, overlap=0.082) Left_Putamen (12): linear fit = 0.85 x + 0.0 (2017 voxels, peak = 69), gca=69.3 gca peak = 0.15214 (84) mri peak = 0.06152 (68) Right_Putamen (51): linear fit = 0.81 x + 0.0 (2255 voxels, overlap=0.096) Right_Putamen (51): linear fit = 0.81 x + 0.0 (2255 voxels, peak = 68), gca=67.6 gca peak = 0.08983 (85) mri peak = 0.07352 (88) Brain_Stem (16): linear fit = 1.03 x + 0.0 (12104 voxels, overlap=0.777) Brain_Stem (16): linear fit = 1.03 x + 0.0 (12104 voxels, peak = 88), gca=88.0 gca peak = 0.11809 (92) mri peak = 0.07851 (92) Right_VentralDC (60): linear fit = 0.96 x + 0.0 (922 voxels, overlap=0.901) Right_VentralDC (60): linear fit = 0.96 x + 0.0 (922 voxels, peak = 89), gca=88.8 gca peak = 0.12914 (94) mri peak = 0.07596 (87) Left_VentralDC (28): linear fit = 0.95 x + 0.0 (1094 voxels, overlap=0.925) Left_VentralDC (28): linear fit = 0.95 x + 0.0 (1094 voxels, peak = 90), gca=89.8 gca peak = 0.21100 (36) mri peak = 0.15915 (55) Third_Ventricle (14): linear fit = 1.50 x + 0.0 (68 voxels, overlap=0.039) Third_Ventricle (14): linear fit = 1.50 x + 0.0 (68 voxels, peak = 54), gca=53.8 gca peak = 0.13542 (27) mri peak = 0.12095 ( 8) Fourth_Ventricle (15): linear fit = 0.32 x + 0.0 (239 voxels, overlap=0.022) Fourth_Ventricle (15): linear fit = 0.32 x + 0.0 (239 voxels, peak = 9), gca=8.8 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak Fourth_Ventricle = 0.13542 (27) gca peak CSF = 0.17123 (45) gca peak Left_Accumbens_area = 0.25875 (69) gca peak Left_undetermined = 0.96240 (36) gca peak Left_vessel = 0.33262 (65) gca peak Left_choroid_plexus = 0.09846 (46) gca peak Right_Inf_Lat_Vent = 0.28113 (34) gca peak Right_Accumbens_area = 0.27120 (72) gca peak Right_vessel = 0.61915 (60) gca peak Right_choroid_plexus = 0.12775 (51) gca peak Fifth_Ventricle = 0.45329 (44) gca peak WM_hypointensities = 0.11729 (81) gca peak non_WM_hypointensities = 0.10912 (56) gca peak Optic_Chiasm = 0.33287 (75) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 0.88 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 0.77 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=0.731, neg=0, invalid=96777 0120: dt=129.472000, rms=0.722 (1.153%), neg=0, invalid=96777 0121: dt=295.936000, rms=0.717 (0.792%), neg=0, invalid=96777 0122: dt=110.976000, rms=0.715 (0.267%), neg=0, invalid=96777 0123: dt=129.472000, rms=0.713 (0.248%), neg=0, invalid=96777 0124: dt=129.472000, rms=0.712 (0.150%), neg=0, invalid=96777 0125: dt=129.472000, rms=0.711 (0.163%), neg=0, invalid=96777 0126: dt=110.976000, rms=0.710 (0.112%), neg=0, invalid=96777 0127: dt=129.472000, rms=0.709 (0.126%), neg=0, invalid=96777 0128: dt=129.472000, rms=0.708 (0.083%), neg=0, invalid=96777 0129: dt=129.472000, rms=0.708 (0.110%), neg=0, invalid=96777 0130: dt=110.976000, rms=0.707 (0.074%), neg=0, invalid=96777 0131: dt=129.472000, rms=0.707 (0.093%), neg=0, invalid=96777 0132: dt=129.472000, rms=0.706 (0.069%), neg=0, invalid=96777 0133: dt=129.472000, rms=0.705 (0.080%), neg=0, invalid=96777 0134: dt=129.472000, rms=0.705 (0.064%), neg=0, invalid=96777 0135: dt=129.472000, rms=0.704 (0.075%), neg=0, invalid=96777 0136: dt=110.976000, rms=0.704 (0.047%), neg=0, invalid=96777 0137: dt=110.976000, rms=0.704 (0.063%), neg=0, invalid=96777 0138: dt=110.976000, rms=0.703 (0.085%), neg=0, invalid=96777 0139: dt=110.976000, rms=0.702 (0.118%), neg=0, invalid=96777 0140: dt=110.976000, rms=0.701 (0.121%), neg=0, invalid=96777 0141: dt=110.976000, rms=0.700 (0.158%), neg=0, invalid=96777 0142: dt=110.976000, rms=0.699 (0.145%), neg=0, invalid=96777 0143: dt=110.976000, rms=0.698 (0.165%), neg=0, invalid=96777 0144: dt=110.976000, rms=0.697 (0.131%), neg=0, invalid=96777 0145: dt=110.976000, rms=0.696 (0.130%), neg=0, invalid=96777 0146: dt=110.976000, rms=0.696 (0.090%), neg=0, invalid=96777 0147: dt=110.976000, rms=0.695 (0.109%), neg=0, invalid=96777 0148: dt=110.976000, rms=0.694 (0.080%), neg=0, invalid=96777 0149: dt=110.976000, rms=0.694 (0.105%), neg=0, invalid=96777 0150: dt=110.976000, rms=0.693 (0.091%), neg=0, invalid=96777 0151: dt=110.976000, rms=0.692 (0.097%), neg=0, invalid=96777 0152: dt=110.976000, rms=0.692 (0.103%), neg=0, invalid=96777 0153: dt=110.976000, rms=0.691 (0.083%), neg=0, invalid=96777 0154: dt=110.976000, rms=0.690 (0.102%), neg=0, invalid=96777 0155: dt=110.976000, rms=0.690 (0.095%), neg=0, invalid=96777 0156: dt=110.976000, rms=0.689 (0.096%), neg=0, invalid=96777 0157: dt=110.976000, rms=0.688 (0.082%), neg=0, invalid=96777 0158: dt=110.976000, rms=0.688 (0.100%), neg=0, invalid=96777 0159: dt=110.976000, rms=0.687 (0.096%), neg=0, invalid=96777 0160: dt=110.976000, rms=0.686 (0.099%), neg=0, invalid=96777 0161: dt=110.976000, rms=0.686 (0.078%), neg=0, invalid=96777 0162: dt=110.976000, rms=0.685 (0.106%), neg=0, invalid=96777 0163: dt=110.976000, rms=0.685 (0.095%), neg=0, invalid=96777 0164: dt=110.976000, rms=0.684 (0.079%), neg=0, invalid=96777 0165: dt=110.976000, rms=0.684 (0.067%), neg=0, invalid=96777 0166: dt=110.976000, rms=0.683 (0.090%), neg=0, invalid=96777 0167: dt=110.976000, rms=0.682 (0.079%), neg=0, invalid=96777 0168: dt=110.976000, rms=0.682 (0.068%), neg=0, invalid=96777 0169: dt=110.976000, rms=0.682 (0.057%), neg=0, invalid=96777 0170: dt=110.976000, rms=0.681 (0.069%), neg=0, invalid=96777 0171: dt=110.976000, rms=0.680 (0.084%), neg=0, invalid=96777 0172: dt=110.976000, rms=0.680 (0.073%), neg=0, invalid=96777 0173: dt=110.976000, rms=0.680 (0.059%), neg=0, invalid=96777 0174: dt=110.976000, rms=0.679 (0.049%), neg=0, invalid=96777 0175: dt=110.976000, rms=0.679 (0.062%), neg=0, invalid=96777 0176: dt=110.976000, rms=0.678 (0.065%), neg=0, invalid=96777 0177: dt=110.976000, rms=0.678 (0.054%), neg=0, invalid=96777 0178: dt=110.976000, rms=0.678 (0.040%), neg=0, invalid=96777 0179: dt=110.976000, rms=0.677 (0.054%), neg=0, invalid=96777 0180: dt=110.976000, rms=0.677 (0.055%), neg=0, invalid=96777 0181: dt=110.976000, rms=0.677 (0.059%), neg=0, invalid=96777 0182: dt=110.976000, rms=0.676 (0.048%), neg=0, invalid=96777 0183: dt=110.976000, rms=0.676 (0.044%), neg=0, invalid=96777 0184: dt=110.976000, rms=0.676 (0.037%), neg=0, invalid=96777 0185: dt=110.976000, rms=0.676 (0.027%), neg=0, invalid=96777 0186: dt=110.976000, rms=0.675 (0.037%), neg=0, invalid=96777 0187: dt=110.976000, rms=0.675 (0.038%), neg=0, invalid=96777 0188: dt=110.976000, rms=0.675 (0.052%), neg=0, invalid=96777 0189: dt=110.976000, rms=0.674 (0.042%), neg=0, invalid=96777 0190: dt=110.976000, rms=0.674 (0.028%), neg=0, invalid=96777 0191: dt=110.976000, rms=0.674 (0.029%), neg=0, invalid=96777 0192: dt=110.976000, rms=0.674 (0.031%), neg=0, invalid=96777 0193: dt=110.976000, rms=0.674 (0.033%), neg=0, invalid=96777 0194: dt=110.976000, rms=0.673 (0.036%), neg=0, invalid=96777 0195: dt=110.976000, rms=0.673 (0.032%), neg=0, invalid=96777 0196: dt=110.976000, rms=0.673 (0.022%), neg=0, invalid=96777 0197: dt=110.976000, rms=0.673 (0.020%), neg=0, invalid=96777 0198: dt=517.888000, rms=0.673 (0.045%), neg=0, invalid=96777 0199: dt=27.744000, rms=0.673 (0.003%), neg=0, invalid=96777 0200: dt=27.744000, rms=0.673 (-0.002%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.673, neg=0, invalid=96777 0201: dt=73.984000, rms=0.672 (0.035%), neg=0, invalid=96777 0202: dt=129.472000, rms=0.672 (0.056%), neg=0, invalid=96777 0203: dt=517.888000, rms=0.671 (0.128%), neg=0, invalid=96777 0204: dt=221.952000, rms=0.671 (0.070%), neg=0, invalid=96777 0205: dt=92.480000, rms=0.670 (0.019%), neg=0, invalid=96777 0206: dt=92.480000, rms=0.670 (0.015%), neg=0, invalid=96777 0207: dt=92.480000, rms=0.670 (0.019%), neg=0, invalid=96777 0208: dt=92.480000, rms=0.670 (0.028%), neg=0, invalid=96777 0209: dt=92.480000, rms=0.670 (0.035%), neg=0, invalid=96777 0210: dt=92.480000, rms=0.670 (0.038%), neg=0, invalid=96777 0211: dt=92.480000, rms=0.669 (0.039%), neg=0, invalid=96777 0212: dt=92.480000, rms=0.669 (0.037%), neg=0, invalid=96777 0213: dt=92.480000, rms=0.669 (0.028%), neg=0, invalid=96777 0214: dt=92.480000, rms=0.669 (0.021%), neg=0, invalid=96777 0215: dt=92.480000, rms=0.669 (0.023%), neg=0, invalid=96777 0216: dt=92.480000, rms=0.668 (0.023%), neg=0, invalid=96777 0217: dt=221.952000, rms=0.668 (0.011%), neg=0, invalid=96777 0218: dt=221.952000, rms=0.668 (-0.017%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.670, neg=0, invalid=96777 0219: dt=124.416000, rms=0.665 (0.803%), neg=0, invalid=96777 0220: dt=36.288000, rms=0.663 (0.199%), neg=0, invalid=96777 0221: dt=103.680000, rms=0.659 (0.685%), neg=0, invalid=96777 0222: dt=15.552000, rms=0.657 (0.221%), neg=0, invalid=96777 0223: dt=82.944000, rms=0.656 (0.265%), neg=0, invalid=96777 0224: dt=36.288000, rms=0.653 (0.434%), neg=0, invalid=96777 0225: dt=36.288000, rms=0.652 (0.098%), neg=0, invalid=96777 0226: dt=145.152000, rms=0.647 (0.697%), neg=0, invalid=96777 0227: dt=15.552000, rms=0.647 (0.136%), neg=0, invalid=96777 0228: dt=36.288000, rms=0.646 (0.108%), neg=0, invalid=96777 0229: dt=331.776000, rms=0.641 (0.822%), neg=0, invalid=96777 0230: dt=25.920000, rms=0.637 (0.561%), neg=0, invalid=96777 0231: dt=248.832000, rms=0.634 (0.468%), neg=0, invalid=96777 0232: dt=36.288000, rms=0.632 (0.367%), neg=0, invalid=96777 0233: dt=25.920000, rms=0.631 (0.101%), neg=0, invalid=96777 0234: dt=580.608000, rms=0.626 (0.761%), neg=0, invalid=96777 0235: dt=20.736000, rms=0.624 (0.438%), neg=0, invalid=96777 0236: dt=25.920000, rms=0.623 (0.093%), neg=0, invalid=96777 0237: dt=124.416000, rms=0.621 (0.265%), neg=0, invalid=96777 0238: dt=15.552000, rms=0.621 (0.069%), neg=0, invalid=96777 0239: dt=62.208000, rms=0.620 (0.061%), neg=0, invalid=96777 0240: dt=103.680000, rms=0.619 (0.188%), neg=0, invalid=96777 0241: dt=9.072000, rms=0.619 (0.037%), neg=0, invalid=96777 0242: dt=9.072000, rms=0.619 (0.020%), neg=0, invalid=96777 0243: dt=9.072000, rms=0.619 (0.001%), neg=0, invalid=96777 0244: dt=9.072000, rms=0.619 (0.010%), neg=0, invalid=96777 0245: dt=9.072000, rms=0.619 (0.025%), neg=0, invalid=96777 0246: dt=9.072000, rms=0.618 (0.063%), neg=0, invalid=96777 0247: dt=9.072000, rms=0.618 (0.089%), neg=0, invalid=96777 0248: dt=9.072000, rms=0.617 (0.088%), neg=0, invalid=96777 0249: dt=9.072000, rms=0.617 (0.075%), neg=0, invalid=96777 0250: dt=9.072000, rms=0.616 (0.071%), neg=0, invalid=96777 0251: dt=9.072000, rms=0.616 (0.076%), neg=0, invalid=96777 0252: dt=9.072000, rms=0.615 (0.067%), neg=0, invalid=96777 0253: dt=9.072000, rms=0.615 (0.068%), neg=0, invalid=96777 0254: dt=9.072000, rms=0.615 (0.078%), neg=0, invalid=96777 0255: dt=9.072000, rms=0.614 (0.086%), neg=0, invalid=96777 0256: dt=9.072000, rms=0.613 (0.097%), neg=0, invalid=96777 0257: dt=9.072000, rms=0.613 (0.012%), neg=0, invalid=96777 0258: dt=9.072000, rms=0.613 (0.027%), neg=0, invalid=96777 0259: dt=9.072000, rms=0.613 (0.034%), neg=0, invalid=96777 0260: dt=9.072000, rms=0.613 (0.033%), neg=0, invalid=96777 0261: dt=9.072000, rms=0.613 (0.042%), neg=0, invalid=96777 0262: dt=9.072000, rms=0.612 (0.043%), neg=0, invalid=96777 0263: dt=9.072000, rms=0.612 (0.049%), neg=0, invalid=96777 0264: dt=9.072000, rms=0.612 (0.053%), neg=0, invalid=96777 0265: dt=9.072000, rms=0.611 (0.057%), neg=0, invalid=96777 0266: dt=9.072000, rms=0.611 (0.060%), neg=0, invalid=96777 0267: dt=9.072000, rms=0.611 (0.065%), neg=0, invalid=96777 0268: dt=9.072000, rms=0.610 (0.068%), neg=0, invalid=96777 0269: dt=9.072000, rms=0.610 (0.010%), neg=0, invalid=96777 0270: dt=9.072000, rms=0.610 (0.017%), neg=0, invalid=96777 0271: dt=9.072000, rms=0.610 (0.021%), neg=0, invalid=96777 0272: dt=1.134000, rms=0.610 (0.000%), neg=0, invalid=96777 0273: dt=0.567000, rms=0.610 (0.001%), neg=0, invalid=96777 0274: dt=0.567000, rms=0.610 (0.001%), neg=0, invalid=96777 0275: dt=0.035437, rms=0.610 (0.000%), neg=0, invalid=96777 0276: dt=0.001107, rms=0.610 (0.000%), neg=0, invalid=96777 0277: dt=0.000277, rms=0.610 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.610, neg=0, invalid=96777 0278: dt=124.416000, rms=0.608 (0.325%), neg=0, invalid=96777 0279: dt=103.680000, rms=0.606 (0.324%), neg=0, invalid=96777 0280: dt=15.552000, rms=0.606 (0.051%), neg=0, invalid=96777 0281: dt=25.920000, rms=0.605 (0.029%), neg=0, invalid=96777 0282: dt=25.920000, rms=0.605 (0.028%), neg=0, invalid=96777 0283: dt=25.920000, rms=0.605 (0.052%), neg=0, invalid=96777 0284: dt=25.920000, rms=0.604 (0.087%), neg=0, invalid=96777 0285: dt=25.920000, rms=0.604 (0.116%), neg=0, invalid=96777 0286: dt=25.920000, rms=0.603 (0.139%), neg=0, invalid=96777 0287: dt=25.920000, rms=0.602 (0.137%), neg=0, invalid=96777 0288: dt=25.920000, rms=0.601 (0.132%), neg=0, invalid=96777 0289: dt=25.920000, rms=0.600 (0.127%), neg=0, invalid=96777 0290: dt=25.920000, rms=0.600 (0.124%), neg=0, invalid=96777 0291: dt=25.920000, rms=0.599 (0.118%), neg=0, invalid=96777 0292: dt=25.920000, rms=0.598 (0.126%), neg=0, invalid=96777 0293: dt=25.920000, rms=0.597 (0.130%), neg=0, invalid=96777 0294: dt=25.920000, rms=0.597 (0.131%), neg=0, invalid=96777 0295: dt=25.920000, rms=0.596 (0.121%), neg=0, invalid=96777 0296: dt=25.920000, rms=0.595 (0.121%), neg=0, invalid=96777 0297: dt=25.920000, rms=0.595 (0.121%), neg=0, invalid=96777 0298: dt=25.920000, rms=0.594 (0.123%), neg=0, invalid=96777 0299: dt=25.920000, rms=0.593 (0.130%), neg=0, invalid=96777 0300: dt=25.920000, rms=0.592 (0.115%), neg=0, invalid=96777 0301: dt=25.920000, rms=0.592 (0.109%), neg=0, invalid=96777 0302: dt=25.920000, rms=0.591 (0.109%), neg=0, invalid=96777 0303: dt=25.920000, rms=0.590 (0.113%), neg=0, invalid=96777 0304: dt=25.920000, rms=0.590 (0.114%), neg=0, invalid=96777 0305: dt=25.920000, rms=0.589 (0.107%), neg=0, invalid=96777 0306: dt=25.920000, rms=0.588 (0.110%), neg=0, invalid=96777 0307: dt=25.920000, rms=0.588 (0.095%), neg=0, invalid=96777 0308: dt=25.920000, rms=0.587 (0.091%), neg=0, invalid=96777 0309: dt=25.920000, rms=0.587 (0.091%), neg=0, invalid=96777 0310: dt=25.920000, rms=0.586 (0.092%), neg=0, invalid=96777 0311: dt=25.920000, rms=0.586 (0.095%), neg=0, invalid=96777 0312: dt=25.920000, rms=0.585 (0.084%), neg=0, invalid=96777 0313: dt=25.920000, rms=0.585 (0.088%), neg=0, invalid=96777 0314: dt=25.920000, rms=0.584 (0.069%), neg=0, invalid=96777 0315: dt=25.920000, rms=0.584 (0.068%), neg=0, invalid=96777 0316: dt=25.920000, rms=0.583 (0.078%), neg=0, invalid=96777 0317: dt=25.920000, rms=0.583 (0.080%), neg=0, invalid=96777 0318: dt=25.920000, rms=0.583 (0.068%), neg=0, invalid=96777 0319: dt=25.920000, rms=0.582 (0.063%), neg=0, invalid=96777 0320: dt=25.920000, rms=0.582 (0.066%), neg=0, invalid=96777 0321: dt=25.920000, rms=0.582 (0.052%), neg=0, invalid=96777 0322: dt=25.920000, rms=0.581 (0.061%), neg=0, invalid=96777 0323: dt=25.920000, rms=0.581 (0.059%), neg=0, invalid=96777 0324: dt=25.920000, rms=0.580 (0.057%), neg=0, invalid=96777 0325: dt=25.920000, rms=0.580 (0.059%), neg=0, invalid=96777 0326: dt=25.920000, rms=0.580 (0.058%), neg=0, invalid=96777 0327: dt=25.920000, rms=0.580 (0.053%), neg=0, invalid=96777 0328: dt=25.920000, rms=0.579 (0.050%), neg=0, invalid=96777 0329: dt=25.920000, rms=0.579 (0.046%), neg=0, invalid=96777 0330: dt=25.920000, rms=0.579 (0.045%), neg=0, invalid=96777 0331: dt=25.920000, rms=0.578 (0.045%), neg=0, invalid=96777 0332: dt=25.920000, rms=0.578 (0.044%), neg=0, invalid=96777 0333: dt=25.920000, rms=0.578 (0.048%), neg=0, invalid=96777 0334: dt=25.920000, rms=0.578 (0.042%), neg=0, invalid=96777 0335: dt=25.920000, rms=0.577 (0.037%), neg=0, invalid=96777 0336: dt=25.920000, rms=0.577 (0.036%), neg=0, invalid=96777 0337: dt=25.920000, rms=0.577 (0.041%), neg=0, invalid=96777 0338: dt=25.920000, rms=0.577 (0.042%), neg=0, invalid=96777 0339: dt=25.920000, rms=0.576 (0.045%), neg=0, invalid=96777 0340: dt=25.920000, rms=0.576 (0.038%), neg=0, invalid=96777 0341: dt=25.920000, rms=0.576 (0.037%), neg=0, invalid=96777 0342: dt=25.920000, rms=0.576 (0.032%), neg=0, invalid=96777 0343: dt=25.920000, rms=0.576 (0.035%), neg=0, invalid=96777 0344: dt=25.920000, rms=0.575 (0.034%), neg=0, invalid=96777 0345: dt=25.920000, rms=0.575 (0.034%), neg=0, invalid=96777 0346: dt=25.920000, rms=0.575 (0.034%), neg=0, invalid=96777 0347: dt=25.920000, rms=0.575 (0.032%), neg=0, invalid=96777 0348: dt=25.920000, rms=0.575 (0.035%), neg=0, invalid=96777 0349: dt=25.920000, rms=0.575 (0.033%), neg=0, invalid=96777 0350: dt=25.920000, rms=0.574 (0.029%), neg=0, invalid=96777 0351: dt=25.920000, rms=0.574 (0.026%), neg=0, invalid=96777 0352: dt=25.920000, rms=0.574 (0.028%), neg=0, invalid=96777 0353: dt=25.920000, rms=0.574 (0.033%), neg=0, invalid=96777 0354: dt=25.920000, rms=0.574 (0.029%), neg=0, invalid=96777 0355: dt=25.920000, rms=0.574 (0.027%), neg=0, invalid=96777 0356: dt=25.920000, rms=0.573 (0.029%), neg=0, invalid=96777 0357: dt=25.920000, rms=0.573 (0.024%), neg=0, invalid=96777 0358: dt=25.920000, rms=0.573 (0.027%), neg=0, invalid=96777 0359: dt=25.920000, rms=0.573 (0.031%), neg=0, invalid=96777 0360: dt=25.920000, rms=0.573 (0.029%), neg=0, invalid=96777 0361: dt=25.920000, rms=0.573 (0.036%), neg=0, invalid=96777 0362: dt=25.920000, rms=0.572 (0.024%), neg=0, invalid=96777 0363: dt=25.920000, rms=0.572 (0.030%), neg=0, invalid=96777 0364: dt=25.920000, rms=0.572 (0.018%), neg=0, invalid=96777 0365: dt=25.920000, rms=0.572 (0.029%), neg=0, invalid=96777 0366: dt=25.920000, rms=0.572 (0.027%), neg=0, invalid=96777 0367: dt=25.920000, rms=0.572 (0.026%), neg=0, invalid=96777 0368: dt=25.920000, rms=0.571 (0.027%), neg=0, invalid=96777 0369: dt=25.920000, rms=0.571 (0.025%), neg=0, invalid=96777 0370: dt=25.920000, rms=0.571 (0.023%), neg=0, invalid=96777 0371: dt=25.920000, rms=0.571 (0.022%), neg=0, invalid=96777 0372: dt=31.104000, rms=0.571 (0.003%), neg=0, invalid=96777 0373: dt=31.104000, rms=0.571 (0.006%), neg=0, invalid=96777 0374: dt=31.104000, rms=0.571 (0.005%), neg=0, invalid=96777 0375: dt=31.104000, rms=0.571 (0.003%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.580, neg=0, invalid=96777 0376: dt=32.000000, rms=0.577 (0.526%), neg=0, invalid=96777 0377: dt=11.200000, rms=0.576 (0.180%), neg=0, invalid=96777 0378: dt=102.400000, rms=0.572 (0.734%), neg=0, invalid=96777 0379: dt=7.463259, rms=0.570 (0.303%), neg=0, invalid=96777 0380: dt=44.800000, rms=0.566 (0.646%), neg=0, invalid=96777 0381: dt=8.000000, rms=0.565 (0.206%), neg=0, invalid=96777 0382: dt=76.800000, rms=0.562 (0.546%), neg=0, invalid=96777 0383: dt=2.800000, rms=0.561 (0.150%), neg=0, invalid=96777 0384: dt=2.800000, rms=0.561 (0.107%), neg=0, invalid=96777 0385: dt=2.800000, rms=0.560 (0.056%), neg=0, invalid=96777 0386: dt=19.200000, rms=0.559 (0.134%), neg=0, invalid=96777 0387: dt=11.200000, rms=0.559 (0.147%), neg=0, invalid=96777 0388: dt=11.200000, rms=0.558 (0.049%), neg=0, invalid=96777 0389: dt=11.200000, rms=0.558 (0.114%), neg=0, invalid=96777 0390: dt=11.200000, rms=0.557 (0.147%), neg=0, invalid=96777 0391: dt=11.200000, rms=0.556 (0.203%), neg=0, invalid=96777 0392: dt=11.200000, rms=0.554 (0.249%), neg=0, invalid=96777 0393: dt=11.200000, rms=0.553 (0.304%), neg=0, invalid=96777 0394: dt=11.200000, rms=0.551 (0.307%), neg=0, invalid=96777 0395: dt=11.200000, rms=0.549 (0.301%), neg=0, invalid=96777 0396: dt=11.200000, rms=0.548 (0.296%), neg=0, invalid=96777 0397: dt=11.200000, rms=0.546 (0.309%), neg=0, invalid=96777 0398: dt=11.200000, rms=0.544 (0.283%), neg=0, invalid=96777 0399: dt=11.200000, rms=0.543 (0.262%), neg=0, invalid=96777 0400: dt=11.200000, rms=0.542 (0.236%), neg=0, invalid=96777 0401: dt=11.200000, rms=0.541 (0.231%), neg=0, invalid=96777 0402: dt=11.200000, rms=0.539 (0.213%), neg=0, invalid=96777 0403: dt=11.200000, rms=0.538 (0.186%), neg=0, invalid=96777 0404: dt=11.200000, rms=0.537 (0.170%), neg=0, invalid=96777 0405: dt=11.200000, rms=0.537 (0.151%), neg=0, invalid=96777 0406: dt=11.200000, rms=0.536 (0.163%), neg=0, invalid=96777 0407: dt=11.200000, rms=0.535 (0.132%), neg=0, invalid=96777 0408: dt=11.200000, rms=0.534 (0.122%), neg=0, invalid=96777 0409: dt=11.200000, rms=0.534 (0.115%), neg=0, invalid=96777 0410: dt=11.200000, rms=0.533 (0.126%), neg=0, invalid=96777 0411: dt=11.200000, rms=0.533 (0.106%), neg=0, invalid=96777 0412: dt=11.200000, rms=0.532 (0.102%), neg=0, invalid=96777 0413: dt=11.200000, rms=0.532 (0.093%), neg=0, invalid=96777 0414: dt=11.200000, rms=0.531 (0.098%), neg=0, invalid=96777 0415: dt=11.200000, rms=0.531 (0.093%), neg=0, invalid=96777 0416: dt=11.200000, rms=0.530 (0.081%), neg=0, invalid=96777 0417: dt=11.200000, rms=0.530 (0.067%), neg=0, invalid=96777 0418: dt=11.200000, rms=0.529 (0.064%), neg=0, invalid=96777 0419: dt=11.200000, rms=0.529 (0.079%), neg=0, invalid=96777 0420: dt=11.200000, rms=0.529 (0.065%), neg=0, invalid=96777 0421: dt=11.200000, rms=0.528 (0.050%), neg=0, invalid=96777 0422: dt=11.200000, rms=0.528 (0.058%), neg=0, invalid=96777 0423: dt=11.200000, rms=0.528 (0.066%), neg=0, invalid=96777 0424: dt=11.200000, rms=0.527 (0.058%), neg=0, invalid=96777 0425: dt=11.200000, rms=0.527 (0.050%), neg=0, invalid=96777 0426: dt=11.200000, rms=0.527 (0.042%), neg=0, invalid=96777 0427: dt=11.200000, rms=0.527 (0.068%), neg=0, invalid=96777 0428: dt=11.200000, rms=0.526 (0.058%), neg=0, invalid=96777 0429: dt=11.200000, rms=0.526 (0.047%), neg=0, invalid=96777 0430: dt=11.200000, rms=0.526 (0.045%), neg=0, invalid=96777 0431: dt=11.200000, rms=0.526 (0.053%), neg=0, invalid=96777 0432: dt=11.200000, rms=0.525 (0.046%), neg=0, invalid=96777 0433: dt=11.200000, rms=0.525 (0.037%), neg=0, invalid=96777 0434: dt=11.200000, rms=0.525 (0.034%), neg=0, invalid=96777 0435: dt=11.200000, rms=0.525 (0.036%), neg=0, invalid=96777 0436: dt=11.200000, rms=0.524 (0.040%), neg=0, invalid=96777 0437: dt=11.200000, rms=0.524 (0.042%), neg=0, invalid=96777 0438: dt=11.200000, rms=0.524 (0.042%), neg=0, invalid=96777 0439: dt=11.200000, rms=0.524 (0.038%), neg=0, invalid=96777 0440: dt=11.200000, rms=0.524 (0.038%), neg=0, invalid=96777 0441: dt=11.200000, rms=0.523 (0.045%), neg=0, invalid=96777 0442: dt=11.200000, rms=0.523 (0.036%), neg=0, invalid=96777 0443: dt=11.200000, rms=0.523 (0.017%), neg=0, invalid=96777 0444: dt=11.200000, rms=0.523 (0.031%), neg=0, invalid=96777 0445: dt=11.200000, rms=0.523 (0.034%), neg=0, invalid=96777 0446: dt=11.200000, rms=0.523 (0.028%), neg=0, invalid=96777 0447: dt=11.200000, rms=0.523 (0.023%), neg=0, invalid=96777 0448: dt=11.200000, rms=0.522 (0.020%), neg=0, invalid=96777 0449: dt=11.200000, rms=0.522 (0.014%), neg=0, invalid=96777 0450: dt=11.200000, rms=0.522 (-0.004%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.522, neg=0, invalid=96777 0451: dt=32.000000, rms=0.521 (0.240%), neg=0, invalid=96777 0452: dt=19.200000, rms=0.520 (0.140%), neg=0, invalid=96777 0453: dt=2.800000, rms=0.520 (0.002%), neg=0, invalid=96777 0454: dt=2.800000, rms=0.520 (0.012%), neg=0, invalid=96777 0455: dt=2.800000, rms=0.520 (0.005%), neg=0, invalid=96777 0456: dt=2.800000, rms=0.520 (0.006%), neg=0, invalid=96777 0457: dt=2.800000, rms=0.520 (0.012%), neg=0, invalid=96777 0458: dt=2.800000, rms=0.520 (0.016%), neg=0, invalid=96777 0459: dt=2.800000, rms=0.520 (0.026%), neg=0, invalid=96777 0460: dt=2.800000, rms=0.520 (0.019%), neg=0, invalid=96777 0461: dt=2.800000, rms=0.520 (0.004%), neg=0, invalid=96777 0462: dt=2.800000, rms=0.520 (0.005%), neg=0, invalid=96777 0463: dt=6.400000, rms=0.520 (-0.003%), 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 0464: 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 0465: 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=0.604, neg=0, invalid=96777 0466: dt=1.454774, rms=0.597 (1.103%), neg=0, invalid=96777 0467: dt=0.384000, rms=0.597 (0.030%), neg=0, invalid=96777 0468: dt=0.384000, rms=0.597 (-0.013%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.597, neg=0, invalid=96777 0469: dt=0.527778, rms=0.596 (0.090%), neg=0, invalid=96777 0470: dt=0.384000, rms=0.596 (0.020%), neg=0, invalid=96777 0471: dt=0.384000, rms=0.596 (-0.015%), 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 0472: dt=0.171000, rms=0.532 (1.388%), neg=0, invalid=96777 0473: dt=0.142562, rms=0.528 (0.791%), neg=0, invalid=96777 0474: dt=0.127083, rms=0.525 (0.529%), neg=0, invalid=96777 0475: dt=0.116667, rms=0.523 (0.384%), neg=0, invalid=96777 0476: dt=0.112069, rms=0.522 (0.307%), neg=0, invalid=96777 0477: dt=0.448000, rms=0.516 (1.006%), neg=0, invalid=96777 0478: dt=0.028000, rms=0.516 (0.025%), neg=0, invalid=96777 0479: dt=0.028000, rms=0.516 (0.026%), neg=0, invalid=96777 0480: dt=0.028000, rms=0.516 (0.046%), neg=0, invalid=96777 0481: dt=0.028000, rms=0.516 (0.066%), neg=0, invalid=96777 0482: dt=0.028000, rms=0.515 (0.077%), neg=0, invalid=96777 0483: dt=0.028000, rms=0.515 (0.088%), neg=0, invalid=96777 0484: dt=0.028000, rms=0.514 (0.100%), neg=0, invalid=96777 0485: dt=0.028000, rms=0.514 (0.105%), neg=0, invalid=96777 0486: dt=0.028000, rms=0.513 (0.109%), neg=0, invalid=96777 0487: dt=0.028000, rms=0.513 (0.109%), neg=0, invalid=96777 0488: dt=0.028000, rms=0.512 (0.112%), neg=0, invalid=96777 0489: dt=0.028000, rms=0.511 (0.107%), neg=0, invalid=96777 0490: dt=0.028000, rms=0.511 (0.099%), neg=0, invalid=96777 0491: dt=0.028000, rms=0.510 (0.098%), neg=0, invalid=96777 0492: dt=0.028000, rms=0.510 (0.004%), neg=0, invalid=96777 0493: dt=0.028000, rms=0.510 (0.009%), neg=0, invalid=96777 0494: dt=0.028000, rms=0.510 (0.009%), neg=0, invalid=96777 0495: dt=0.448000, rms=0.510 (0.065%), neg=0, invalid=96777 0496: dt=0.007000, rms=0.510 (-0.003%), neg=0, invalid=96777 0497: dt=0.007000, rms=0.510 (0.001%), neg=0, invalid=96777 0498: dt=0.007000, rms=0.510 (0.002%), neg=0, invalid=96777 0499: dt=0.007000, rms=0.510 (0.004%), neg=0, invalid=96777 0500: dt=0.007000, rms=0.510 (0.003%), neg=0, invalid=96777 0501: dt=0.007000, rms=0.510 (0.004%), neg=0, invalid=96777 0502: dt=0.007000, rms=0.510 (0.007%), neg=0, invalid=96777 0503: dt=0.007000, rms=0.510 (0.004%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.510, neg=0, invalid=96777 0504: dt=0.112000, rms=0.508 (0.289%), neg=0, invalid=96777 0505: dt=0.112000, rms=0.507 (0.217%), neg=0, invalid=96777 0506: dt=0.112000, rms=0.506 (0.166%), neg=0, invalid=96777 0507: dt=0.112000, rms=0.506 (0.129%), neg=0, invalid=96777 0508: dt=0.384000, rms=0.504 (0.333%), neg=0, invalid=96777 0509: dt=0.112000, rms=0.504 (0.017%), neg=0, invalid=96777 0510: dt=0.112000, rms=0.504 (0.028%), neg=0, invalid=96777 0511: dt=0.112000, rms=0.504 (0.034%), neg=0, invalid=96777 0512: dt=0.007000, rms=0.504 (0.003%), neg=0, invalid=96777 0513: dt=0.007000, rms=0.504 (0.002%), neg=0, invalid=96777 0514: dt=0.020000, rms=0.504 (0.002%), neg=0, invalid=96777 0515: dt=0.020000, rms=0.504 (0.004%), neg=0, invalid=96777 0516: dt=0.020000, rms=0.504 (0.004%), neg=0, invalid=96777 0517: dt=0.020000, rms=0.504 (0.001%), neg=0, invalid=96777 0518: dt=0.020000, rms=0.504 (0.006%), neg=0, invalid=96777 0519: dt=0.020000, rms=0.504 (0.007%), neg=0, invalid=96777 0520: dt=0.020000, rms=0.504 (0.010%), neg=0, invalid=96777 0521: dt=0.020000, rms=0.503 (0.009%), 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=0.501, neg=0, invalid=96777 0522: dt=73.984000, rms=0.501 (0.013%), neg=0, invalid=96777 0523: dt=73.984000, rms=0.501 (-0.002%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.501, neg=0, invalid=96777 0524: dt=129.472000, rms=0.501 (0.116%), neg=0, invalid=96777 0525: dt=32.368000, rms=0.501 (0.019%), neg=0, invalid=96777 0526: dt=32.368000, rms=0.501 (0.002%), neg=0, invalid=96777 0527: dt=32.368000, rms=0.501 (0.015%), neg=0, invalid=96777 0528: dt=32.368000, rms=0.500 (0.022%), neg=0, invalid=96777 0529: dt=32.368000, rms=0.500 (0.029%), neg=0, invalid=96777 0530: dt=32.368000, rms=0.500 (0.029%), neg=0, invalid=96777 0531: dt=32.368000, rms=0.500 (0.026%), neg=0, invalid=96777 0532: dt=32.368000, rms=0.500 (0.027%), neg=0, invalid=96777 0533: dt=32.368000, rms=0.500 (0.027%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.500, neg=0, invalid=96777 0534: dt=36.288000, rms=0.499 (0.186%), neg=0, invalid=96777 0535: dt=36.288000, rms=0.498 (0.083%), neg=0, invalid=96777 0536: dt=36.288000, rms=0.498 (0.070%), neg=0, invalid=96777 0537: dt=36.288000, rms=0.498 (0.052%), neg=0, invalid=96777 0538: dt=36.288000, rms=0.498 (-0.027%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.498, neg=0, invalid=96777 0539: dt=82.944000, rms=0.496 (0.368%), neg=0, invalid=96777 0540: dt=36.288000, rms=0.495 (0.153%), neg=0, invalid=96777 0541: dt=36.288000, rms=0.495 (0.085%), neg=0, invalid=96777 0542: dt=36.288000, rms=0.494 (0.127%), neg=0, invalid=96777 0543: dt=36.288000, rms=0.493 (0.170%), neg=0, invalid=96777 0544: dt=36.288000, rms=0.493 (0.161%), neg=0, invalid=96777 0545: dt=36.288000, rms=0.492 (0.146%), neg=0, invalid=96777 0546: dt=36.288000, rms=0.491 (0.141%), neg=0, invalid=96777 0547: dt=36.288000, rms=0.491 (0.113%), neg=0, invalid=96777 0548: dt=36.288000, rms=0.490 (0.103%), neg=0, invalid=96777 0549: dt=25.920000, rms=0.490 (0.025%), neg=0, invalid=96777 0550: dt=25.920000, rms=0.490 (0.014%), neg=0, invalid=96777 0551: dt=25.920000, rms=0.490 (0.014%), neg=0, invalid=96777 0552: dt=25.920000, rms=0.490 (0.029%), neg=0, invalid=96777 0553: dt=25.920000, rms=0.490 (0.034%), neg=0, invalid=96777 0554: dt=25.920000, rms=0.489 (0.043%), neg=0, invalid=96777 0555: dt=25.920000, rms=0.489 (0.041%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.489, neg=0, invalid=96777 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0556: dt=44.800000, rms=0.485 (0.830%), neg=0, invalid=96777 iter 0, gcam->neg = 8 after 8 iterations, nbhd size=1, neg = 0 0557: dt=25.600000, rms=0.484 (0.306%), neg=0, invalid=96777 0558: dt=8.000000, rms=0.483 (0.249%), neg=0, invalid=96777 0559: dt=8.000000, rms=0.482 (0.124%), neg=0, invalid=96777 0560: dt=8.000000, rms=0.481 (0.162%), neg=0, invalid=96777 0561: dt=8.000000, rms=0.480 (0.234%), neg=0, invalid=96777 0562: dt=8.000000, rms=0.479 (0.240%), neg=0, invalid=96777 0563: dt=8.000000, rms=0.478 (0.236%), neg=0, invalid=96777 0564: dt=8.000000, rms=0.477 (0.239%), neg=0, invalid=96777 0565: dt=8.000000, rms=0.476 (0.200%), neg=0, invalid=96777 0566: dt=8.000000, rms=0.475 (0.193%), neg=0, invalid=96777 0567: dt=8.000000, rms=0.474 (0.174%), neg=0, invalid=96777 0568: dt=8.000000, rms=0.473 (0.164%), neg=0, invalid=96777 0569: dt=8.000000, rms=0.473 (0.157%), neg=0, invalid=96777 0570: dt=8.000000, rms=0.472 (0.128%), neg=0, invalid=96777 0571: dt=8.000000, rms=0.471 (0.144%), neg=0, invalid=96777 0572: dt=8.000000, rms=0.471 (0.156%), neg=0, invalid=96777 0573: dt=8.000000, rms=0.470 (0.132%), neg=0, invalid=96777 0574: dt=8.000000, rms=0.469 (0.125%), neg=0, invalid=96777 0575: dt=8.000000, rms=0.469 (0.109%), neg=0, invalid=96777 0576: dt=11.200000, rms=0.469 (0.030%), neg=0, invalid=96777 0577: dt=11.200000, rms=0.469 (0.012%), neg=0, invalid=96777 0578: dt=11.200000, rms=0.468 (0.033%), neg=0, invalid=96777 0579: dt=11.200000, rms=0.468 (0.040%), neg=0, invalid=96777 0580: dt=11.200000, rms=0.468 (0.041%), neg=0, invalid=96777 0581: dt=11.200000, rms=0.468 (0.035%), neg=0, invalid=96777 0582: dt=11.200000, rms=0.468 (0.051%), neg=0, invalid=96777 0583: dt=11.200000, rms=0.467 (0.052%), neg=0, invalid=96777 0584: dt=11.200000, rms=0.467 (0.050%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.467, neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0585: dt=44.800000, rms=0.464 (0.584%), neg=0, invalid=96777 0586: dt=11.200000, rms=0.464 (0.195%), neg=0, invalid=96777 0587: dt=11.200000, rms=0.463 (0.078%), neg=0, invalid=96777 0588: dt=11.200000, rms=0.463 (0.108%), neg=0, invalid=96777 0589: dt=11.200000, rms=0.462 (0.163%), neg=0, invalid=96777 0590: dt=11.200000, rms=0.461 (0.118%), neg=0, invalid=96777 0591: dt=11.200000, rms=0.461 (0.089%), neg=0, invalid=96777 0592: dt=32.000000, rms=0.461 (0.046%), neg=0, invalid=96777 0593: dt=32.000000, rms=0.461 (-0.269%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.467, neg=0, invalid=96777 0594: dt=2.304000, rms=0.466 (0.032%), neg=0, invalid=96777 0595: dt=1.008000, rms=0.466 (0.008%), neg=0, invalid=96777 0596: dt=1.008000, rms=0.466 (0.006%), neg=0, invalid=96777 0597: dt=1.008000, rms=0.466 (-0.011%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.466, neg=0, invalid=96777 0598: dt=4.032000, rms=0.466 (0.045%), neg=0, invalid=96777 0599: dt=4.032000, rms=0.466 (0.024%), neg=0, invalid=96777 0600: dt=4.032000, rms=0.466 (0.009%), neg=0, invalid=96777 0601: dt=4.032000, rms=0.466 (-0.022%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.473, neg=0, invalid=96777 0602: dt=0.000000, rms=0.473 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.473, neg=0, invalid=96777 0603: dt=0.064000, rms=0.473 (0.000%), neg=0, invalid=96777 0604: dt=0.064000, rms=0.473 (0.001%), neg=0, invalid=96777 0605: dt=0.020000, rms=0.473 (0.002%), neg=0, invalid=96777 0606: dt=0.016000, rms=0.473 (-0.001%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.461, neg=0, invalid=96777 iter 0, gcam->neg = 751 after 19 iterations, nbhd size=2, neg = 0 0607: dt=1.925076, rms=0.419 (9.275%), neg=0, invalid=96777 0608: dt=0.000109, rms=0.419 (0.003%), neg=0, invalid=96777 0609: dt=0.000109, rms=0.419 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.419, neg=0, invalid=96777 0610: dt=0.000375, rms=0.419 (0.000%), neg=0, invalid=96777 0611: dt=0.000000, rms=0.419 (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=0.401, neg=0, invalid=96777 0612: dt=0.000000, rms=0.402 (-0.257%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.402, neg=0, invalid=96777 0613: dt=18.496000, rms=0.402 (0.001%), neg=0, invalid=96777 0614: dt=0.022578, rms=0.402 (0.000%), neg=0, invalid=96777 0615: dt=0.022578, rms=0.402 (-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=0.403, neg=0, invalid=96777 0616: dt=0.000000, rms=0.403 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.403, neg=0, invalid=96777 0617: dt=25.920000, rms=0.403 (0.015%), neg=0, invalid=96777 0618: dt=20.736000, rms=0.403 (0.003%), neg=0, invalid=96777 0619: dt=20.736000, rms=0.403 (0.001%), neg=0, invalid=96777 0620: dt=20.736000, rms=0.403 (-0.003%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.403, neg=0, invalid=96777 0621: dt=11.200000, rms=0.403 (0.085%), neg=0, invalid=96777 0622: dt=6.400000, rms=0.403 (0.013%), neg=0, invalid=96777 0623: dt=6.400000, rms=0.403 (0.012%), neg=0, invalid=96777 0624: dt=6.400000, rms=0.403 (-0.007%), 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 = 1 after 0 iterations, nbhd size=0, neg = 0 0625: dt=38.400000, rms=0.402 (0.326%), neg=0, invalid=96777 0626: dt=11.200000, rms=0.401 (0.048%), neg=0, invalid=96777 0627: dt=11.200000, rms=0.401 (0.086%), neg=0, invalid=96777 0628: dt=11.200000, rms=0.400 (0.128%), neg=0, invalid=96777 0629: dt=11.200000, rms=0.400 (0.134%), neg=0, invalid=96777 iter 0, gcam->neg = 11 after 15 iterations, nbhd size=2, neg = 0 0630: dt=11.200000, rms=0.399 (0.124%), neg=0, invalid=96777 0631: dt=11.200000, rms=0.399 (0.073%), neg=0, invalid=96777 iter 0, gcam->neg = 14 after 17 iterations, nbhd size=2, neg = 0 0632: dt=76.800000, rms=0.399 (0.140%), neg=0, invalid=96777 0633: dt=2.800000, rms=0.399 (0.004%), neg=0, invalid=96777 0634: dt=2.800000, rms=0.399 (0.010%), neg=0, invalid=96777 0635: dt=2.800000, rms=0.398 (0.017%), neg=0, invalid=96777 0636: dt=2.800000, rms=0.398 (0.022%), neg=0, invalid=96777 0637: dt=2.800000, rms=0.398 (0.023%), neg=0, invalid=96777 0638: dt=2.800000, rms=0.398 (0.024%), neg=0, invalid=96777 0639: dt=2.800000, rms=0.398 (0.024%), neg=0, invalid=96777 0640: dt=2.800000, rms=0.398 (0.024%), neg=0, invalid=96777 0641: dt=2.800000, rms=0.398 (0.025%), neg=0, invalid=96777 0642: dt=2.800000, rms=0.398 (0.025%), neg=0, invalid=96777 0643: dt=2.800000, rms=0.398 (0.025%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.401, neg=0, invalid=96777 iter 0, gcam->neg = 11 after 9 iterations, nbhd size=1, neg = 0 0644: dt=4.032000, rms=0.401 (0.061%), neg=0, invalid=96777 0645: dt=0.006750, rms=0.401 (0.000%), neg=0, invalid=96777 0646: dt=0.006750, rms=0.401 (0.000%), neg=0, invalid=96777 0647: dt=0.006750, rms=0.401 (0.000%), neg=0, invalid=96777 0648: dt=0.006750, rms=0.401 (0.000%), neg=0, invalid=96777 0649: dt=0.006750, rms=0.401 (0.000%), neg=0, invalid=96777 0650: dt=0.006750, rms=0.401 (0.000%), neg=0, invalid=96777 0651: dt=0.006750, rms=0.401 (0.000%), neg=0, invalid=96777 0652: dt=0.006750, rms=0.401 (0.000%), neg=0, invalid=96777 0653: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777 0654: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777 0655: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777 0656: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777 0657: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777 0658: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777 0659: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777 0660: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777 0661: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777 0662: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777 0663: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777 0664: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777 0665: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777 0666: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777 0667: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777 0668: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777 0669: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777 0670: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777 0671: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777 0672: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777 0673: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.401, neg=0, invalid=96777 iter 0, gcam->neg = 83 after 38 iterations, nbhd size=3, neg = 0 0674: dt=16.128000, rms=0.399 (0.351%), neg=0, invalid=96777 0675: dt=0.003938, rms=0.399 (0.000%), neg=0, invalid=96777 0676: dt=0.003938, rms=0.399 (0.000%), neg=0, invalid=96777 0677: dt=0.003938, rms=0.399 (-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=0.405, neg=0, invalid=96777 0678: dt=0.000000, rms=0.405 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.405, neg=0, invalid=96777 0679: dt=0.000000, rms=0.405 (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=0.395, neg=0, invalid=96777 iter 0, gcam->neg = 565 after 34 iterations, nbhd size=3, neg = 0 0680: dt=0.910140, rms=0.380 (3.668%), neg=0, invalid=96777 0681: dt=0.000000, rms=0.380 (0.000%), neg=0, invalid=96777 iter 0, gcam->neg = 693 after 11 iterations, nbhd size=1, neg = 0 0682: dt=0.050000, rms=0.380 (-0.343%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.380, neg=0, invalid=96777 0683: dt=0.000000, rms=0.380 (-0.000%), neg=0, invalid=96777 writing output transformation to transforms/talairach.m3z... GCAMwrite registration took 4 hours, 5 minutes and 53 seconds. #-------------------------------------- #@# CA Reg Inv Thu Aug 8 16:27:21 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 16:28:41 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... 10717596 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 1 minutes and 23 seconds. #-------------------------------------- #@# SkullLTA Thu Aug 8 16:30:04 CEST 2013 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta ======= NUMBER OF OPENMP THREADS = 1 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 5 using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach_with_skull_2.log reading '/opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=11.0 skull bounding box = (41, 13, 12) --> (213, 203, 219) using (98, 76, 116) as brain centroid... mean wm in atlas = 126, using box (77,53,90) --> (119, 99,141) to find MRI wm before smoothing, mri peak at 108 after smoothing, mri peak at 108, scaling input intensities by 1.167 scaling channel 0 by 1.16667 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.1 (thresh=-4.1) 0.983 -0.021 0.024 0.151; 0.024 1.200 0.267 -32.056; -0.030 -0.176 0.960 17.535; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 0.983 -0.021 0.024 0.151; 0.022 1.110 0.247 -20.569; -0.030 -0.176 0.960 17.535; 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) 0.983 -0.021 0.024 0.151; 0.022 1.110 0.247 -20.569; -0.030 -0.176 0.960 17.535; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 0.983 -0.021 0.024 0.151; 0.022 1.124 0.282 -24.015; -0.031 -0.213 0.951 24.267; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 0.983 -0.021 0.024 0.151; 0.022 1.124 0.282 -24.015; -0.031 -0.213 0.951 24.267; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 0.981 -0.023 0.032 -0.221; 0.022 1.125 0.283 -24.185; -0.039 -0.213 0.952 25.667; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 0.981 -0.023 0.032 -0.221; 0.022 1.122 0.282 -23.844; -0.039 -0.213 0.950 25.855; 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 0.98052 -0.02259 0.03199 -0.22081; 0.02160 1.12247 0.28205 -23.84424; -0.03859 -0.21289 0.95010 25.85537; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 0.98052 -0.02259 0.03199 -0.22081; 0.02160 1.12247 0.28205 -23.84424; -0.03859 -0.21289 0.95010 25.85537; 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: 0.981 -0.023 0.032 -0.221; 0.022 1.122 0.282 -23.844; -0.039 -0.213 0.950 25.855; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -4.0 (old=-4.1) transform before final EM align: 0.981 -0.023 0.032 -0.221; 0.022 1.122 0.282 -23.844; -0.039 -0.213 0.950 25.855; 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 0.98052 -0.02259 0.03199 -0.22081; 0.02160 1.12247 0.28205 -23.84424; -0.03859 -0.21289 0.95010 25.85537; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 0.98052 -0.02259 0.03199 -0.22081; 0.02160 1.12247 0.28205 -23.84424; -0.03859 -0.21289 0.95010 25.85537; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = 4.4 tol 0.000000 final transform: 0.981 -0.023 0.032 -0.221; 0.022 1.122 0.282 -23.844; -0.039 -0.213 0.950 25.855; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull_2.lta... registration took 36 minutes and 21 seconds. #-------------------------------------- #@# SubCort Seg Thu Aug 8 17:06:25 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/sub016/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 = 0.09683 ( 8) Left_Lateral_Ventricle (4): linear fit = 0.25 x + 0.0 (650 voxels, overlap=0.008) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (650 voxels, peak = 7), gca=10.8 gca peak = 0.14982 (20) mri peak = 0.10375 (10) Right_Lateral_Ventricle (43): linear fit = 0.31 x + 0.0 (1059 voxels, overlap=0.010) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (1059 voxels, peak = 6), gca=8.0 gca peak = 0.28003 (97) mri peak = 0.10452 (80) Right_Pallidum (52): linear fit = 0.81 x + 0.0 (366 voxels, overlap=0.052) Right_Pallidum (52): linear fit = 0.81 x + 0.0 (366 voxels, peak = 79), gca=79.1 gca peak = 0.18160 (96) mri peak = 0.08193 (80) Left_Pallidum (13): linear fit = 0.83 x + 0.0 (446 voxels, overlap=0.054) Left_Pallidum (13): linear fit = 0.83 x + 0.0 (446 voxels, peak = 80), gca=80.2 gca peak = 0.27536 (62) mri peak = 0.07808 (56) Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (626 voxels, overlap=0.354) Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (626 voxels, peak = 54), gca=54.2 gca peak = 0.32745 (63) mri peak = 0.07985 (60) Left_Hippocampus (17): linear fit = 0.89 x + 0.0 (798 voxels, overlap=0.998) Left_Hippocampus (17): linear fit = 0.89 x + 0.0 (798 voxels, peak = 56), gca=56.4 gca peak = 0.08597 (105) mri peak = 0.06779 (107) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (42590 voxels, overlap=0.786) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (42590 voxels, peak = 107), gca=106.6 gca peak = 0.09209 (106) mri peak = 0.07226 (107) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (41902 voxels, overlap=0.750) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (41902 voxels, peak = 109), gca=108.6 gca peak = 0.07826 (63) mri peak = 0.05031 (56) Left_Cerebral_Cortex (3): linear fit = 0.86 x + 0.0 (19158 voxels, overlap=0.523) Left_Cerebral_Cortex (3): linear fit = 0.86 x + 0.0 (19158 voxels, peak = 54), gca=53.9 gca peak = 0.08598 (64) mri peak = 0.05205 (51) Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (19561 voxels, overlap=0.343) Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (19561 voxels, peak = 53), gca=52.8 gca peak = 0.24164 (71) mri peak = 0.09348 (63) Right_Caudate (50): linear fit = 0.88 x + 0.0 (921 voxels, overlap=0.027) Right_Caudate (50): linear fit = 0.88 x + 0.0 (921 voxels, peak = 62), gca=62.1 gca peak = 0.18227 (75) mri peak = 0.09183 (63) Left_Caudate (11): linear fit = 0.81 x + 0.0 (1188 voxels, overlap=0.028) Left_Caudate (11): linear fit = 0.81 x + 0.0 (1188 voxels, peak = 61), gca=61.1 gca peak = 0.10629 (62) mri peak = 0.05931 (62) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (9466 voxels, overlap=0.988) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (9466 voxels, peak = 64), gca=63.5 gca peak = 0.11668 (59) mri peak = 0.06138 (61) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (10220 voxels, overlap=0.998) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (10220 voxels, peak = 58), gca=58.1 gca peak = 0.17849 (88) mri peak = 0.06123 (94) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (4512 voxels, overlap=0.922) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (4512 voxels, peak = 95), gca=94.6 gca peak = 0.16819 (86) mri peak = 0.06784 (93) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (4332 voxels, overlap=0.945) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (4332 voxels, peak = 92), gca=91.6 gca peak = 0.41688 (64) mri peak = 0.08973 (59) Left_Amygdala (18): linear fit = 0.90 x + 0.0 (434 voxels, overlap=1.037) Left_Amygdala (18): linear fit = 0.90 x + 0.0 (434 voxels, peak = 58), gca=57.9 gca peak = 0.42394 (62) mri peak = 0.09194 (61) Right_Amygdala (54): linear fit = 0.88 x + 0.0 (450 voxels, overlap=1.041) Right_Amygdala (54): linear fit = 0.88 x + 0.0 (450 voxels, peak = 55), gca=54.9 gca peak = 0.10041 (96) mri peak = 0.07166 (85) Left_Thalamus_Proper (10): linear fit = 0.90 x + 0.0 (3745 voxels, overlap=0.469) Left_Thalamus_Proper (10): linear fit = 0.90 x + 0.0 (3745 voxels, peak = 87), gca=86.9 gca peak = 0.13978 (88) mri peak = 0.07968 (81) Right_Thalamus_Proper (49): linear fit = 0.93 x + 0.0 (3812 voxels, overlap=0.625) Right_Thalamus_Proper (49): linear fit = 0.93 x + 0.0 (3812 voxels, peak = 81), gca=81.4 gca peak = 0.08514 (81) mri peak = 0.07115 (70) Left_Putamen (12): linear fit = 0.81 x + 0.0 (1920 voxels, overlap=0.234) Left_Putamen (12): linear fit = 0.81 x + 0.0 (1920 voxels, peak = 66), gca=66.0 gca peak = 0.09624 (82) mri peak = 0.07615 (71) Right_Putamen (51): linear fit = 0.82 x + 0.0 (1787 voxels, overlap=0.023) Right_Putamen (51): linear fit = 0.82 x + 0.0 (1787 voxels, peak = 68), gca=67.7 gca peak = 0.07543 (88) mri peak = 0.07619 (88) Brain_Stem (16): linear fit = 1.01 x + 0.0 (11427 voxels, overlap=0.765) Brain_Stem (16): linear fit = 1.01 x + 0.0 (11427 voxels, peak = 89), gca=89.3 gca peak = 0.12757 (95) mri peak = 0.07479 (89) Right_VentralDC (60): linear fit = 0.94 x + 0.0 (936 voxels, overlap=0.827) Right_VentralDC (60): linear fit = 0.94 x + 0.0 (936 voxels, peak = 90), gca=89.8 gca peak = 0.17004 (92) mri peak = 0.07026 (87) Left_VentralDC (28): linear fit = 0.95 x + 0.0 (918 voxels, overlap=0.804) Left_VentralDC (28): linear fit = 0.95 x + 0.0 (918 voxels, peak = 88), gca=87.9 gca peak = 0.21361 (36) mri peak = 0.08496 (15) gca peak = 0.26069 (23) mri peak = 0.13778 (11) Fourth_Ventricle (15): linear fit = 0.44 x + 0.0 (98 voxels, overlap=0.031) Fourth_Ventricle (15): linear fit = 0.44 x + 0.0 (98 voxels, peak = 10), gca=10.0 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 1.02 x + 0.0 estimating mean csf scale to be 0.40 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.31600 (11) mri peak = 0.09683 ( 8) Left_Lateral_Ventricle (4): linear fit = 0.70 x + 0.0 (650 voxels, overlap=0.989) Left_Lateral_Ventricle (4): linear fit = 0.70 x + 0.0 (650 voxels, peak = 8), gca=7.8 gca peak = 0.29325 ( 9) mri peak = 0.10375 (10) Right_Lateral_Ventricle (43): linear fit = 0.79 x + 0.0 (1059 voxels, overlap=1.001) Right_Lateral_Ventricle (43): linear fit = 0.79 x + 0.0 (1059 voxels, peak = 7), gca=7.1 gca peak = 0.26534 (80) mri peak = 0.10452 (80) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (366 voxels, overlap=1.012) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (366 voxels, peak = 80), gca=80.0 gca peak = 0.20119 (80) mri peak = 0.08193 (80) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (446 voxels, overlap=1.013) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (446 voxels, peak = 80), gca=80.0 gca peak = 0.31053 (54) mri peak = 0.07808 (56) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (626 voxels, overlap=1.005) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (626 voxels, peak = 53), gca=53.2 gca peak = 0.26447 (56) mri peak = 0.07985 (60) Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (798 voxels, overlap=1.010) Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (798 voxels, peak = 57), gca=57.4 gca peak = 0.08540 (107) mri peak = 0.06779 (107) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (42590 voxels, overlap=0.834) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (42590 voxels, peak = 107), gca=107.0 gca peak = 0.08534 (108) mri peak = 0.07226 (107) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (41902 voxels, overlap=0.796) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (41902 voxels, peak = 107), gca=107.5 gca peak = 0.09232 (54) mri peak = 0.05031 (56) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (19158 voxels, overlap=0.991) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (19158 voxels, peak = 54), gca=54.0 gca peak = 0.10550 (53) mri peak = 0.05205 (51) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (19561 voxels, overlap=0.984) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (19561 voxels, peak = 53), gca=53.0 gca peak = 0.23948 (64) mri peak = 0.09348 (63) Right_Caudate (50): linear fit = 1.00 x + 0.0 (921 voxels, overlap=1.004) Right_Caudate (50): linear fit = 1.00 x + 0.0 (921 voxels, peak = 64), gca=64.0 gca peak = 0.18470 (61) mri peak = 0.09183 (63) Left_Caudate (11): linear fit = 0.99 x + 0.0 (1188 voxels, overlap=0.998) Left_Caudate (11): linear fit = 0.99 x + 0.0 (1188 voxels, peak = 60), gca=60.1 gca peak = 0.10027 (62) mri peak = 0.05931 (62) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (9466 voxels, overlap=0.997) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (9466 voxels, peak = 61), gca=61.1 gca peak = 0.12025 (59) mri peak = 0.06138 (61) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (10220 voxels, overlap=0.997) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (10220 voxels, peak = 60), gca=60.5 gca peak = 0.17137 (94) mri peak = 0.06123 (94) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4512 voxels, overlap=1.000) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4512 voxels, peak = 94), gca=93.5 gca peak = 0.16068 (92) mri peak = 0.06784 (93) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (4332 voxels, overlap=1.000) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (4332 voxels, peak = 91), gca=90.6 gca peak = 0.40361 (58) mri peak = 0.08973 (59) Left_Amygdala (18): linear fit = 1.04 x + 0.0 (434 voxels, overlap=1.027) Left_Amygdala (18): linear fit = 1.04 x + 0.0 (434 voxels, peak = 61), gca=60.6 gca peak = 0.57399 (55) mri peak = 0.09194 (61) Right_Amygdala (54): linear fit = 1.04 x + 0.0 (450 voxels, overlap=1.027) Right_Amygdala (54): linear fit = 1.04 x + 0.0 (450 voxels, peak = 57), gca=57.5 gca peak = 0.11982 (87) mri peak = 0.07166 (85) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3745 voxels, overlap=0.999) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3745 voxels, peak = 87), gca=86.6 gca peak = 0.11701 (81) mri peak = 0.07968 (81) Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (3812 voxels, overlap=0.980) Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (3812 voxels, peak = 80), gca=79.8 gca peak = 0.09700 (71) mri peak = 0.07115 (70) Left_Putamen (12): linear fit = 1.03 x + 0.0 (1920 voxels, overlap=1.000) Left_Putamen (12): linear fit = 1.03 x + 0.0 (1920 voxels, peak = 73), gca=73.5 gca peak = 0.10658 (68) mri peak = 0.07615 (71) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1787 voxels, overlap=0.991) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1787 voxels, peak = 67), gca=67.0 gca peak = 0.07507 (87) mri peak = 0.07619 (88) Brain_Stem (16): linear fit = 1.00 x + 0.0 (11427 voxels, overlap=0.798) Brain_Stem (16): linear fit = 1.00 x + 0.0 (11427 voxels, peak = 87), gca=86.6 gca peak = 0.12974 (86) mri peak = 0.07479 (89) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (936 voxels, overlap=0.817) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (936 voxels, peak = 88), gca=88.2 gca peak = 0.15097 (88) mri peak = 0.07026 (87) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (918 voxels, overlap=0.943) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (918 voxels, peak = 88), gca=87.6 gca peak = 0.35640 (14) mri peak = 0.08496 (15) gca peak = 0.33827 ( 9) mri peak = 0.13778 (11) Fourth_Ventricle (15): linear fit = 1.14 x + 0.0 (98 voxels, overlap=0.976) Fourth_Ventricle (15): linear fit = 1.14 x + 0.0 (98 voxels, peak = 10), gca=10.3 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.23697 (32) gca peak Third_Ventricle = 0.35640 (14) gca peak CSF = 0.30128 (18) gca peak Left_Accumbens_area = 0.68092 (57) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.42552 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.33086 (28) gca peak Right_Accumbens_area = 0.31091 (63) gca peak Right_vessel = 0.57322 (60) gca peak Right_choroid_plexus = 0.10278 (48) gca peak Fifth_Ventricle = 0.45329 (19) gca peak WM_hypointensities = 0.17567 (83) gca peak non_WM_hypointensities = 0.12171 (54) gca peak Optic_Chiasm = 0.34843 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.02 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.88 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 13374 gm and wm labels changed (%13 to gray, %87 to white out of all changed labels) 310 hippocampal voxels changed. 13 amygdala voxels changed. pass 1: 98944 changed. image ll: -2.251, PF=1.000 pass 2: 18094 changed. image ll: -2.249, PF=1.000 pass 3: 6959 changed. pass 4: 3144 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 18 minutes and 5 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/cc_up.lta sub016 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/sub016/mri/transforms/cc_up.lta reading aseg from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/aseg.auto_noCCseg.mgz reading norm from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/norm.mgz 24264 voxels in left wm, 26205 in right wm, xrange [124, 131] searching rotation angles z=[-6 8], y=[-6 8] searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.3 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.8 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.3 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.8 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.3 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.8 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.3 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.8 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.3 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.8 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.3 searching scale 1 Z rot -0.0 searching scale 1 Z rot 0.2 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.7 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.2 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.7 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.2 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.7 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.2 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.7 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.2 searching scale 1 Z rot 4.5 searching scale 1 Z rot 4.7 searching scale 1 Z rot 5.0 searching scale 1 Z rot 5.2 searching scale 1 Z rot 5.5 searching scale 1 Z rot 5.7 searching scale 1 Z rot 6.0 searching scale 1 Z rot 6.2 searching scale 1 Z rot 6.5 searching scale 1 Z rot 6.7 searching scale 1 Z rot 7.0 searching scale 1 Z rot 7.2 searching scale 1 Z rot 7.5 searching scale 1 Z rot 7.7 searching scale 1 Z rot 8.0 searching scale 1 Z rot 8.2 global minimum found at slice 127.2, rotations (0.87, 1.46) final transformation (x=127.2, yr=0.866, zr=1.458): 1.000 -0.025 0.015 1.292; 0.025 1.000 0.000 44.748; -0.015 -0.000 1.000 26.935; 0.000 0.000 0.000 1.000; updating x range to be [125, 131] in xformed coordinates best xformed slice 128 cc center is found at 128 147 116 eigenvectors: -0.000 0.001 1.000; -0.073 -0.997 0.001; 0.997 -0.073 0.001; error in mid anterior detected - correcting... writing aseg with callosum to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/aseg.auto.mgz... corpus callosum matter segmentation took 0.7 minutes #-------------------------------------- #@# Merge ASeg Thu Aug 8 17:25:11 CEST 2013 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Thu Aug 8 17:25:11 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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... 3712 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 57 (57), valley at 30 (30) csf peak at 28, setting threshold to 47 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 30 (30) 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 10 seconds. #-------------------------------------------- #@# Mask BFS Thu Aug 8 17:29:23 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1767582 voxels in mask (pct= 10.54) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Thu Aug 8 17:29:25 CEST 2013 mri_segment brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (107.0): 107.1 +- 5.1 [80.0 --> 125.0] GM (68.0) : 67.4 +- 9.2 [30.0 --> 96.0] setting bottom of white matter range to 76.6 setting top of gray matter range to 85.7 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... 10649 sparsely connected voxels removed... thickening thin strands.... 20 segments, 5279 filled 312 bright non-wm voxels segmented. 5168 diagonally connected voxels added... white matter segmentation took 1.9 minutes writing output to wm.seg.mgz... mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.65 minutes reading wm segmentation from wm.seg.mgz... 70 voxels added to wm to prevent paths from MTL structures to cortex 1160 additional wm voxels added 0 additional wm voxels added SEG EDIT: 51272 voxels turned on, 46916 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 86 new 86 115,126,128 old 86 new 86 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 28 found - 28 modified | TOTAL: 28 pass 2 (xy+): 0 found - 28 modified | TOTAL: 28 pass 1 (xy-): 25 found - 25 modified | TOTAL: 53 pass 2 (xy-): 0 found - 25 modified | TOTAL: 53 pass 1 (yz+): 32 found - 32 modified | TOTAL: 85 pass 2 (yz+): 0 found - 32 modified | TOTAL: 85 pass 1 (yz-): 23 found - 23 modified | TOTAL: 108 pass 2 (yz-): 0 found - 23 modified | TOTAL: 108 pass 1 (xz+): 18 found - 18 modified | TOTAL: 126 pass 2 (xz+): 0 found - 18 modified | TOTAL: 126 pass 1 (xz-): 23 found - 23 modified | TOTAL: 149 pass 2 (xz-): 0 found - 23 modified | TOTAL: 149 Iteration Number : 1 pass 1 (+++): 6 found - 6 modified | TOTAL: 6 pass 2 (+++): 0 found - 6 modified | TOTAL: 6 pass 1 (+++): 27 found - 27 modified | TOTAL: 33 pass 2 (+++): 0 found - 27 modified | TOTAL: 33 pass 1 (+++): 9 found - 9 modified | TOTAL: 42 pass 2 (+++): 0 found - 9 modified | TOTAL: 42 pass 1 (+++): 16 found - 16 modified | TOTAL: 58 pass 2 (+++): 0 found - 16 modified | TOTAL: 58 Iteration Number : 1 pass 1 (++): 204 found - 204 modified | TOTAL: 204 pass 2 (++): 0 found - 204 modified | TOTAL: 204 pass 1 (+-): 188 found - 188 modified | TOTAL: 392 pass 2 (+-): 0 found - 188 modified | TOTAL: 392 pass 1 (--): 178 found - 178 modified | TOTAL: 570 pass 2 (--): 0 found - 178 modified | TOTAL: 570 pass 1 (-+): 166 found - 166 modified | TOTAL: 736 pass 2 (-+): 0 found - 166 modified | TOTAL: 736 Iteration Number : 2 pass 1 (xy+): 9 found - 9 modified | TOTAL: 9 pass 2 (xy+): 0 found - 9 modified | TOTAL: 9 pass 1 (xy-): 7 found - 7 modified | TOTAL: 16 pass 2 (xy-): 0 found - 7 modified | TOTAL: 16 pass 1 (yz+): 2 found - 2 modified | TOTAL: 18 pass 2 (yz+): 0 found - 2 modified | TOTAL: 18 pass 1 (yz-): 8 found - 8 modified | TOTAL: 26 pass 2 (yz-): 0 found - 8 modified | TOTAL: 26 pass 1 (xz+): 3 found - 3 modified | TOTAL: 29 pass 2 (xz+): 0 found - 3 modified | TOTAL: 29 pass 1 (xz-): 2 found - 2 modified | TOTAL: 31 pass 2 (xz-): 0 found - 2 modified | TOTAL: 31 Iteration Number : 2 pass 1 (+++): 1 found - 1 modified | TOTAL: 1 pass 2 (+++): 0 found - 1 modified | TOTAL: 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 1 pass 1 (+++): 1 found - 1 modified | TOTAL: 2 pass 2 (+++): 0 found - 1 modified | TOTAL: 2 Iteration Number : 2 pass 1 (++): 3 found - 3 modified | TOTAL: 3 pass 2 (++): 0 found - 3 modified | TOTAL: 3 pass 1 (+-): 1 found - 1 modified | TOTAL: 4 pass 2 (+-): 0 found - 1 modified | TOTAL: 4 pass 1 (--): 2 found - 2 modified | TOTAL: 6 pass 2 (--): 0 found - 2 modified | TOTAL: 6 pass 1 (-+): 0 found - 0 modified | TOTAL: 6 Iteration Number : 3 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+): 1 found - 1 modified | TOTAL: 2 pass 2 (yz+): 0 found - 1 modified | TOTAL: 2 pass 1 (yz-): 0 found - 0 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 1 found - 1 modified | TOTAL: 1 pass 2 (+++): 0 found - 1 modified | TOTAL: 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 1 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 1 found - 1 modified | TOTAL: 2 pass 2 (-+): 0 found - 1 modified | TOTAL: 2 Iteration Number : 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 = 987 (out of 622745: 0.158492) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Thu Aug 8 17:32:05 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 0.983 -0.021 0.024 0.151; 0.022 1.116 0.249 -21.370; -0.030 -0.176 0.960 17.535; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 0.983 -0.021 0.024 0.151; 0.022 1.116 0.249 -21.370; -0.030 -0.176 0.960 17.535; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1119 (min = 350, max = 1400), aspect = 0.38 (min = 0.10, max = 0.75) no need to search using seed (126, 121, 149), TAL = (2.0, 21.0, 7.0) talairach voxel to voxel transform 1.016 0.014 -0.029 0.669; -0.026 0.860 -0.222 22.285; 0.027 0.158 1.000 -14.161; 0.000 0.000 0.000 1.000; segmentation indicates cc at (126, 121, 149) --> (2.0, 21.0, 7.0) done. writing output to filled.mgz... filling took 0.9 minutes talairach cc position changed to (2.00, 21.00, 7.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, 21.00, 7.00) SRC: (107.76, 90.46, 156.80) search lh wm seed point around talairach space (-16.00, 21.00, 7.00), SRC: (144.33, 89.52, 157.76) 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 17:33:00 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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-): 1 found - 1 modified | TOTAL: 4 pass 2 (xy-): 0 found - 1 modified | TOTAL: 4 pass 1 (yz+): 2 found - 2 modified | TOTAL: 6 pass 2 (yz+): 0 found - 2 modified | TOTAL: 6 pass 1 (yz-): 1 found - 1 modified | TOTAL: 7 pass 2 (yz-): 0 found - 1 modified | TOTAL: 7 pass 1 (xz+): 1 found - 1 modified | TOTAL: 8 pass 2 (xz+): 0 found - 1 modified | TOTAL: 8 pass 1 (xz-): 0 found - 0 modified | TOTAL: 8 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 2 found - 2 modified | TOTAL: 3 pass 2 (+-): 0 found - 2 modified | TOTAL: 3 pass 1 (--): 1 found - 1 modified | TOTAL: 4 pass 2 (--): 0 found - 1 modified | TOTAL: 4 pass 1 (-+): 0 found - 0 modified | TOTAL: 4 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 12 (out of 296303: 0.004050) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 40: 2247 vertices, 2412 faces slice 50: 10036 vertices, 10353 faces slice 60: 21453 vertices, 21827 faces slice 70: 33202 vertices, 33629 faces slice 80: 45185 vertices, 45605 faces slice 90: 57325 vertices, 57748 faces slice 100: 70349 vertices, 70817 faces slice 110: 83004 vertices, 83431 faces slice 120: 95002 vertices, 95456 faces slice 130: 107089 vertices, 107487 faces slice 140: 118705 vertices, 119157 faces slice 150: 129205 vertices, 129627 faces slice 160: 138040 vertices, 138350 faces slice 170: 146229 vertices, 146519 faces slice 180: 153318 vertices, 153599 faces slice 190: 158619 vertices, 158840 faces slice 200: 161732 vertices, 161843 faces slice 210: 161964 vertices, 162010 faces slice 220: 161964 vertices, 162010 faces slice 230: 161964 vertices, 162010 faces slice 240: 161964 vertices, 162010 faces slice 250: 161964 vertices, 162010 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... 161964 voxel in cpt #1: X=-46 [v=161964,e=486030,f=324020] located at (-28.711313, -18.458485, 37.919922) For the whole surface: X=-46 [v=161964,e=486030,f=324020] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Thu Aug 8 17:33:08 CEST 2013 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 17:33:13 CEST 2013 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts avg radius = 49.2 mm, total surface area = 86006 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.8 minutes Not saving sulc step 000: RMS=0.098 (target=0.015) step 005: RMS=0.072 (target=0.015) step 010: RMS=0.053 (target=0.015) step 015: RMS=0.044 (target=0.015) step 020: RMS=0.037 (target=0.015) step 025: RMS=0.033 (target=0.015) step 030: RMS=0.029 (target=0.015) step 035: RMS=0.026 (target=0.015) step 040: RMS=0.024 (target=0.015) step 045: RMS=0.022 (target=0.015) step 050: RMS=0.021 (target=0.015) step 055: RMS=0.021 (target=0.015) step 060: RMS=0.021 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Thu Aug 8 17:34:00 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 0.91 +- 0.54 (0.00-->6.75) (max @ vno 121685 --> 121686) face area 0.02 +- 0.03 (-0.18-->0.72) scaling brain by 0.291... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.656, avgs=0 005/300: dt: 0.9000, rms radial error=176.398, avgs=0 010/300: dt: 0.9000, rms radial error=175.843, avgs=0 015/300: dt: 0.9000, rms radial error=175.115, avgs=0 020/300: dt: 0.9000, rms radial error=174.285, avgs=0 025/300: dt: 0.9000, rms radial error=173.398, avgs=0 030/300: dt: 0.9000, rms radial error=172.480, avgs=0 035/300: dt: 0.9000, rms radial error=171.544, avgs=0 040/300: dt: 0.9000, rms radial error=170.601, avgs=0 045/300: dt: 0.9000, rms radial error=169.655, avgs=0 050/300: dt: 0.9000, rms radial error=168.709, avgs=0 055/300: dt: 0.9000, rms radial error=167.766, avgs=0 060/300: dt: 0.9000, rms radial error=166.826, avgs=0 065/300: dt: 0.9000, rms radial error=165.890, avgs=0 070/300: dt: 0.9000, rms radial error=164.959, avgs=0 075/300: dt: 0.9000, rms radial error=164.032, avgs=0 080/300: dt: 0.9000, rms radial error=163.111, avgs=0 085/300: dt: 0.9000, rms radial error=162.193, avgs=0 090/300: dt: 0.9000, rms radial error=161.281, avgs=0 095/300: dt: 0.9000, rms radial error=160.373, avgs=0 100/300: dt: 0.9000, rms radial error=159.471, avgs=0 105/300: dt: 0.9000, rms radial error=158.573, avgs=0 110/300: dt: 0.9000, rms radial error=157.680, avgs=0 115/300: dt: 0.9000, rms radial error=156.792, avgs=0 120/300: dt: 0.9000, rms radial error=155.909, avgs=0 125/300: dt: 0.9000, rms radial error=155.031, avgs=0 130/300: dt: 0.9000, rms radial error=154.157, avgs=0 135/300: dt: 0.9000, rms radial error=153.289, avgs=0 140/300: dt: 0.9000, rms radial error=152.425, avgs=0 145/300: dt: 0.9000, rms radial error=151.566, avgs=0 150/300: dt: 0.9000, rms radial error=150.711, avgs=0 155/300: dt: 0.9000, rms radial error=149.861, avgs=0 160/300: dt: 0.9000, rms radial error=149.016, avgs=0 165/300: dt: 0.9000, rms radial error=148.175, avgs=0 170/300: dt: 0.9000, rms radial error=147.339, avgs=0 175/300: dt: 0.9000, rms radial error=146.508, avgs=0 180/300: dt: 0.9000, rms radial error=145.681, avgs=0 185/300: dt: 0.9000, rms radial error=144.859, avgs=0 190/300: dt: 0.9000, rms radial error=144.042, avgs=0 195/300: dt: 0.9000, rms radial error=143.231, avgs=0 200/300: dt: 0.9000, rms radial error=142.425, avgs=0 205/300: dt: 0.9000, rms radial error=141.623, avgs=0 210/300: dt: 0.9000, rms radial error=140.825, avgs=0 215/300: dt: 0.9000, rms radial error=140.032, avgs=0 220/300: dt: 0.9000, rms radial error=139.244, avgs=0 225/300: dt: 0.9000, rms radial error=138.459, avgs=0 230/300: dt: 0.9000, rms radial error=137.679, avgs=0 235/300: dt: 0.9000, rms radial error=136.904, avgs=0 240/300: dt: 0.9000, rms radial error=136.132, avgs=0 245/300: dt: 0.9000, rms radial error=135.365, avgs=0 250/300: dt: 0.9000, rms radial error=134.602, avgs=0 255/300: dt: 0.9000, rms radial error=133.844, avgs=0 260/300: dt: 0.9000, rms radial error=133.090, avgs=0 265/300: dt: 0.9000, rms radial error=132.340, avgs=0 270/300: dt: 0.9000, rms radial error=131.595, avgs=0 275/300: dt: 0.9000, rms radial error=130.853, avgs=0 280/300: dt: 0.9000, rms radial error=130.116, avgs=0 285/300: dt: 0.9000, rms radial error=129.382, avgs=0 290/300: dt: 0.9000, rms radial error=128.653, avgs=0 295/300: dt: 0.9000, rms radial error=127.928, avgs=0 300/300: dt: 0.9000, rms radial error=127.207, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 19332.81 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00015 epoch 2 (K=40.0), pass 1, starting sse = 3371.47 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00004 epoch 3 (K=160.0), pass 1, starting sse = 367.24 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/11 = 0.00481 epoch 4 (K=640.0), pass 1, starting sse = 23.51 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.09/12 = 0.00726 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 17:39:17 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/sub016/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub016 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=-46 (nv=161964, nf=324020, ne=486030, g=24) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations marking ambiguous vertices... 3711 ambiguous faces found in tessellation segmenting defects... 26 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 26 defects to be corrected 0 vertices coincident reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.8304 (-4.9152) -vertex loglikelihood: -6.5729 (-3.2864) -normal dot loglikelihood: -3.6792 (-3.6792) -quad curv loglikelihood: -6.4542 (-3.2271) Total Loglikelihood : -26.5366 CORRECTING DEFECT 0 (vertices=25, convex hull=62) After retessellation of defect 0, euler #=-23 (159748,478470,318699) : difference with theory (-23) = 0 CORRECTING DEFECT 1 (vertices=694, convex hull=338) After retessellation of defect 1, euler #=-22 (160043,479516,319451) : difference with theory (-22) = 0 CORRECTING DEFECT 2 (vertices=33, convex hull=71) After retessellation of defect 2, euler #=-21 (160062,479601,319518) : difference with theory (-21) = 0 CORRECTING DEFECT 3 (vertices=5, convex hull=21) After retessellation of defect 3, euler #=-20 (160063,479608,319525) : difference with theory (-20) = 0 CORRECTING DEFECT 4 (vertices=40, convex hull=86) After retessellation of defect 4, euler #=-19 (160083,479704,319602) : difference with theory (-19) = 0 CORRECTING DEFECT 5 (vertices=6, convex hull=25) After retessellation of defect 5, euler #=-18 (160085,479718,319615) : difference with theory (-18) = 0 CORRECTING DEFECT 6 (vertices=152, convex hull=137) After retessellation of defect 6, euler #=-17 (160158,480004,319829) : difference with theory (-17) = 0 CORRECTING DEFECT 7 (vertices=238, convex hull=105) After retessellation of defect 7, euler #=-16 (160221,480241,320004) : difference with theory (-16) = 0 CORRECTING DEFECT 8 (vertices=31, convex hull=33) After retessellation of defect 8, euler #=-15 (160226,480266,320025) : difference with theory (-15) = 0 CORRECTING DEFECT 9 (vertices=30, convex hull=61) After retessellation of defect 9, euler #=-14 (160242,480344,320088) : difference with theory (-14) = 0 CORRECTING DEFECT 10 (vertices=179, convex hull=55) After retessellation of defect 10, euler #=-13 (160255,480404,320136) : difference with theory (-13) = 0 CORRECTING DEFECT 11 (vertices=75, convex hull=78) After retessellation of defect 11, euler #=-12 (160266,480472,320194) : difference with theory (-12) = 0 CORRECTING DEFECT 12 (vertices=12, convex hull=21) After retessellation of defect 12, euler #=-11 (160270,480488,320207) : difference with theory (-11) = 0 CORRECTING DEFECT 13 (vertices=34, convex hull=76) After retessellation of defect 13, euler #=-10 (160279,480545,320256) : difference with theory (-10) = 0 CORRECTING DEFECT 14 (vertices=5, convex hull=15) After retessellation of defect 14, euler #=-9 (160279,480548,320260) : difference with theory (-9) = 0 CORRECTING DEFECT 15 (vertices=46, convex hull=75) After retessellation of defect 15, euler #=-8 (160295,480626,320323) : difference with theory (-8) = 0 CORRECTING DEFECT 16 (vertices=175, convex hull=114) After retessellation of defect 16, euler #=-7 (160337,480802,320458) : difference with theory (-7) = 0 CORRECTING DEFECT 17 (vertices=125, convex hull=60) After retessellation of defect 17, euler #=-6 (160345,480860,320509) : difference with theory (-6) = 0 CORRECTING DEFECT 18 (vertices=123, convex hull=128) After retessellation of defect 18, euler #=-5 (160411,481113,320697) : difference with theory (-5) = 0 CORRECTING DEFECT 19 (vertices=40, convex hull=38) After retessellation of defect 19, euler #=-4 (160420,481152,320728) : difference with theory (-4) = 0 CORRECTING DEFECT 20 (vertices=34, convex hull=59) After retessellation of defect 20, euler #=-3 (160438,481227,320786) : difference with theory (-3) = 0 CORRECTING DEFECT 21 (vertices=10, convex hull=27) After retessellation of defect 21, euler #=-2 (160440,481240,320798) : difference with theory (-2) = 0 CORRECTING DEFECT 22 (vertices=22, convex hull=52) After retessellation of defect 22, euler #=-1 (160453,481299,320845) : difference with theory (-1) = 0 CORRECTING DEFECT 23 (vertices=16, convex hull=32) After retessellation of defect 23, euler #=0 (160460,481331,320871) : difference with theory (0) = 0 CORRECTING DEFECT 24 (vertices=42, convex hull=62) After retessellation of defect 24, euler #=1 (160469,481382,320914) : difference with theory (1) = 0 CORRECTING DEFECT 25 (vertices=25, convex hull=55) After retessellation of defect 25, euler #=2 (160479,481431,320954) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.05-->6.34) (max @ vno 116804 --> 122752) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.22 (0.05-->6.34) (max @ vno 116804 --> 122752) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 78 mutations (33.6%), 154 crossovers (66.4%), 79 vertices were eliminated building final representation... 1485 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=160479, nf=320954, ne=481431, g=0) writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 18.4 minutes 0 defective edges removing intersecting faces 000: 224 intersecting 001: 27 intersecting 002: 11 intersecting 003: 7 intersecting 004: 2 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 160479 - 481431 + 320954 = 2 --> 0 holes F =2V-4: 320954 = 320958-4 (0) 2E=3F: 962862 = 962862 (0) total defect index = 0 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 48 intersecting 001: 35 intersecting 002: 11 intersecting 003: 8 intersecting 004: 7 intersecting 005: 2 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Thu Aug 8 17:57:56 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub016 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/sub016/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz... 22234 bright wm thresholded. 384 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.orig... computing class statistics... border white: 298969 voxels (1.78%) border gray 333863 voxels (1.99%) WM (93.0): 93.9 +- 9.8 [70.0 --> 110.0] GM (77.0) : 75.0 +- 12.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 49.4 (was 70) setting MAX_BORDER_WHITE to 115.8 (was 105) setting MIN_BORDER_WHITE to 62.0 (was 85) setting MAX_CSF to 36.9 (was 40) setting MAX_GRAY to 96.2 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 55.7 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 24.3 (was 40) repositioning cortical surface to gray/white boundary reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.05-->3.95) (max @ vno 159822 --> 160009) face area 0.28 +- 0.12 (0.00-->5.04) mean absolute distance = 0.65 +- 0.78 4287 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=106, GM=62 mean inside = 93.8, mean outside = 70.2 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=74.3, 64 (64) missing vertices, mean dist 0.4 [0.5 (%30.4)->0.7 (%69.6))] %68 local maxima, %27 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 0.91 +- 0.26 (0.07-->5.11) (max @ vno 160099 --> 160100) face area 0.28 +- 0.13 (0.00-->4.98) mean absolute distance = 0.35 +- 0.49 4695 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=7818525.5, rms=12.80 001: dt: 0.5000, sse=7902479.5, rms=9.064 (0.000%) 002: dt: 0.5000, sse=8193120.5, rms=6.997 (0.000%) 003: dt: 0.5000, sse=8398064.0, rms=5.733 (0.000%) 004: dt: 0.5000, sse=8678498.0, rms=4.997 (0.000%) 005: dt: 0.5000, sse=8757485.0, rms=4.599 (0.000%) 006: dt: 0.5000, sse=8878632.0, rms=4.381 (0.000%) 007: dt: 0.5000, sse=8860942.0, rms=4.270 (0.000%) 008: dt: 0.5000, sse=8900009.0, rms=4.192 (0.000%) rms = 4.15, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=8836779.0, rms=4.152 (0.000%) 010: dt: 0.2500, sse=5476378.0, rms=2.827 (0.000%) 011: dt: 0.2500, sse=5013794.5, rms=2.398 (0.000%) 012: dt: 0.2500, sse=4718828.5, rms=2.294 (0.000%) 013: dt: 0.2500, sse=4647839.5, rms=2.209 (0.000%) rms = 2.18, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=4549292.0, rms=2.177 (0.000%) 015: dt: 0.1250, sse=4309767.5, rms=1.938 (0.000%) rms = 1.90, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=4266609.5, rms=1.905 (0.000%) positioning took 2.3 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=79.4, 72 (44) missing vertices, mean dist -0.3 [0.4 (%81.0)->0.2 (%19.0))] %83 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.11-->4.72) (max @ vno 160104 --> 70416) face area 0.35 +- 0.16 (0.00-->6.21) mean absolute distance = 0.22 +- 0.31 4347 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5623246.0, rms=6.60 017: dt: 0.5000, sse=5578929.0, rms=4.370 (0.000%) rms = 4.49, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=5083324.0, rms=3.327 (0.000%) 019: dt: 0.2500, sse=4849302.0, rms=2.589 (0.000%) 020: dt: 0.2500, sse=4754413.0, rms=2.103 (0.000%) 021: dt: 0.2500, sse=4719963.5, rms=1.946 (0.000%) 022: dt: 0.2500, sse=4634218.5, rms=1.791 (0.000%) rms = 1.75, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=4638862.0, rms=1.752 (0.000%) 024: dt: 0.1250, sse=4476490.5, rms=1.555 (0.000%) rms = 1.53, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=4435944.5, rms=1.528 (0.000%) positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=82.6, 61 (33) missing vertices, mean dist -0.1 [0.2 (%76.4)->0.2 (%23.6))] %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.10-->4.81) (max @ vno 160104 --> 70416) face area 0.33 +- 0.16 (0.00-->5.67) mean absolute distance = 0.16 +- 0.26 2934 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4852385.5, rms=4.12 026: dt: 0.5000, sse=5274197.5, rms=3.988 (0.000%) rms = 4.18, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=4756714.5, rms=2.523 (0.000%) 028: dt: 0.2500, sse=4627541.0, rms=1.989 (0.000%) 029: dt: 0.2500, sse=4676251.0, rms=1.663 (0.000%) rms = 1.68, time step reduction 2 of 3 to 0.125... 030: dt: 0.1250, sse=4608184.5, rms=1.537 (0.000%) 031: dt: 0.1250, sse=4516804.0, rms=1.356 (0.000%) rms = 1.34, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=4478627.0, rms=1.335 (0.000%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=83.5, 64 (27) missing vertices, mean dist -0.0 [0.2 (%57.9)->0.2 (%42.1))] %92 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=4507100.0, rms=1.72 rms = 2.50, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=4605772.0, rms=1.156 (0.000%) 034: dt: 0.2500, sse=4770604.0, rms=1.004 (0.000%) rms = 1.01, time step reduction 2 of 3 to 0.125... rms = 0.99, time step reduction 3 of 3 to 0.062... 035: dt: 0.1250, sse=4772717.5, rms=0.995 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group generating cortex label... 22 non-cortical segments detected only using segment with 2520 vertices erasing segment 1 (vno[0] = 73170) erasing segment 2 (vno[0] = 94623) erasing segment 3 (vno[0] = 99325) erasing segment 4 (vno[0] = 107577) erasing segment 5 (vno[0] = 110708) erasing segment 6 (vno[0] = 110734) erasing segment 7 (vno[0] = 112785) erasing segment 8 (vno[0] = 112886) erasing segment 9 (vno[0] = 114058) erasing segment 10 (vno[0] = 114341) erasing segment 11 (vno[0] = 115359) erasing segment 12 (vno[0] = 115383) erasing segment 13 (vno[0] = 116597) erasing segment 14 (vno[0] = 117688) erasing segment 15 (vno[0] = 117768) erasing segment 16 (vno[0] = 121659) erasing segment 17 (vno[0] = 122561) erasing segment 18 (vno[0] = 122612) erasing segment 19 (vno[0] = 124558) erasing segment 20 (vno[0] = 126720) erasing segment 21 (vno[0] = 128787) writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/label/lh.cortex.label... writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.curv writing smoothed area to lh.area writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.area vertex spacing 0.89 +- 0.25 (0.03-->4.83) (max @ vno 160104 --> 70416) face area 0.33 +- 0.16 (0.00-->5.70) refinement took 8.0 minutes #-------------------------------------------- #@# Smooth2 lh Thu Aug 8 18:05:54 CEST 2013 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 18:05:59 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 49.3 mm, total surface area = 97677 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.112 (target=0.015) step 005: RMS=0.078 (target=0.015) step 010: RMS=0.056 (target=0.015) step 015: RMS=0.046 (target=0.015) step 020: RMS=0.038 (target=0.015) step 025: RMS=0.032 (target=0.015) step 030: RMS=0.026 (target=0.015) step 035: RMS=0.022 (target=0.015) step 040: RMS=0.019 (target=0.015) step 045: RMS=0.017 (target=0.015) step 050: RMS=0.015 (target=0.015) inflation complete. inflation took 0.6 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 209 vertices thresholded to be in k1 ~ [-0.24 0.56], k2 ~ [-0.12 0.09] total integrated curvature = 0.392*4pi (4.931) --> 1 handles ICI = 1.8, FI = 13.8, variation=228.351 163 vertices thresholded to be in [-0.02 0.02] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 155 vertices thresholded to be in [-0.13 0.23] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.015, std = 0.025 done. #----------------------------------------- #@# Curvature Stats lh Thu Aug 8 18:08:39 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub016 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 [ sub016/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 [ 306 ] Gb_filter = 0 WARN: S lookup min: -0.080822 WARN: S explicit min: 0.000000 vertex = 1040 #-------------------------------------------- #@# Sphere lh Thu Aug 8 18:08:44 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 0.273... 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 %20.27 pass 1: epoch 2 of 3 starting distance error %20.21 unfolding complete - removing small folds... starting distance error %20.11 removing remaining folds... final distance error %20.12 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/lh.sphere spherical transformation took 1.24 hours #-------------------------------------------- #@# Surf Reg lh Thu Aug 8 19:23:03 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts mris_register -curv ../surf/lh.sphere /opt/freesurfer/5.3.0/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /opt/freesurfer/5.3.0/average/lh.average.curvature.filled.buckner40.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=snake, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 0 randomSeed 0 tol=5.0e-01, sigma=0.0, host=snake, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading lh.sulc curvature mean = -0.000, std = 0.579 curvature mean = 0.019, std = 0.933 curvature mean = 0.026, std = 0.836 Starting MRISrigidBodyAlignGlobal() d=32.00 min @ (0.00, -8.00, 0.00) sse = 346322.2, tmin=2.6324 d=16.00 min @ (4.00, 0.00, 0.00) sse = 340851.3, tmin=4.0946 d=8.00 min @ (-2.00, 0.00, 0.00) sse = 336519.5, tmin=5.5732 d=4.00 min @ (0.00, 0.00, -1.00) sse = 335921.1, tmin=7.0874 d=1.00 min @ (0.25, 0.00, 0.00) sse = 335842.9, tmin=10.1403 d=0.50 min @ (0.00, 0.12, 0.00) sse = 335828.7, tmin=11.6717 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 11.67 min curvature mean = 0.009, std = 0.939 curvature mean = 0.012, std = 0.923 curvature mean = 0.007, std = 0.950 curvature mean = 0.006, std = 0.963 curvature mean = 0.005, std = 0.950 curvature mean = 0.002, std = 0.983 2 Reading smoothwm curvature mean = -0.024, std = 0.291 curvature mean = 0.003, std = 0.066 curvature mean = 0.072, std = 0.316 curvature mean = 0.004, std = 0.078 curvature mean = 0.035, std = 0.506 curvature mean = 0.005, std = 0.084 curvature mean = 0.019, std = 0.650 curvature mean = 0.005, std = 0.086 curvature mean = 0.007, std = 0.765 MRISregister() return, current seed 0 writing registered surface to ../surf/lh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white lh Thu Aug 8 20:00:55 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 20:00:58 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 20:01:00 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub016 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... 1573 labels changed using aseg relabeling using gibbs priors... 000: 3403 changed, 160479 examined... 001: 803 changed, 14657 examined... 002: 213 changed, 4459 examined... 003: 72 changed, 1275 examined... 004: 23 changed, 437 examined... 005: 10 changed, 132 examined... 006: 3 changed, 65 examined... 007: 2 changed, 23 examined... 008: 2 changed, 11 examined... 009: 2 changed, 11 examined... 010: 1 changed, 10 examined... 011: 0 changed, 7 examined... 262 labels changed using aseg 000: 164 total segments, 119 labels (468 vertices) changed 001: 45 total segments, 4 labels (12 vertices) changed 002: 41 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 69 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1861 vertices marked for relabeling... 1861 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 20:02:11 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub016 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/sub016/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz... 22234 bright wm thresholded. 384 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.orig... computing class statistics... border white: 298969 voxels (1.78%) border gray 333863 voxels (1.99%) WM (93.0): 93.9 +- 9.8 [70.0 --> 110.0] GM (77.0) : 75.0 +- 12.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 49.4 (was 70) setting MAX_BORDER_WHITE to 115.8 (was 105) setting MIN_BORDER_WHITE to 62.0 (was 85) setting MAX_CSF to 36.9 (was 40) setting MAX_GRAY to 96.2 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 55.7 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 24.3 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=106, GM=62 mean inside = 93.8, mean outside = 70.2 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/sub016/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.05-->3.95) (max @ vno 159822 --> 160009) face area 0.28 +- 0.12 (0.00-->5.04) mean absolute distance = 0.65 +- 0.79 4390 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 247 points - only 4.05% unknown removing 4 vertex label from ripped group deleting segment 1 with 4 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown deleting segment 5 with 6 points - only 0.00% unknown deleting segment 6 with 840 points - only 0.00% unknown deleting segment 7 with 7 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 11 with 37 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 8 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 14 with 3 points - only 0.00% unknown deleting segment 15 with 5 points - only 0.00% unknown mean border=74.3, 66 (65) missing vertices, mean dist 0.4 [0.5 (%30.4)->0.7 (%69.6))] %69 local maxima, %27 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 0.91 +- 0.26 (0.07-->5.11) (max @ vno 160099 --> 160100) face area 0.28 +- 0.13 (0.00-->4.98) mean absolute distance = 0.35 +- 0.49 4775 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=7844055.5, rms=12.77 001: dt: 0.5000, sse=7941564.5, rms=9.040 (0.000%) 002: dt: 0.5000, sse=8239249.0, rms=6.981 (0.000%) 003: dt: 0.5000, sse=8449724.0, rms=5.724 (0.000%) 004: dt: 0.5000, sse=8730856.0, rms=4.991 (0.000%) 005: dt: 0.5000, sse=8813873.0, rms=4.595 (0.000%) 006: dt: 0.5000, sse=8934122.0, rms=4.376 (0.000%) 007: dt: 0.5000, sse=8914619.0, rms=4.266 (0.000%) 008: dt: 0.5000, sse=8955723.0, rms=4.187 (0.000%) rms = 4.15, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=8894941.0, rms=4.146 (0.000%) 010: dt: 0.2500, sse=5502699.5, rms=2.823 (0.000%) 011: dt: 0.2500, sse=5038612.0, rms=2.394 (0.000%) 012: dt: 0.2500, sse=4741387.5, rms=2.291 (0.000%) 013: dt: 0.2500, sse=4670505.5, rms=2.207 (0.000%) rms = 2.17, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=4573283.5, rms=2.175 (0.000%) 015: dt: 0.1250, sse=4333563.5, rms=1.938 (0.000%) rms = 1.91, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=4290018.5, rms=1.905 (0.000%) positioning took 2.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 276 points - only 3.62% unknown deleting segment 1 with 5 points - only 0.00% unknown deleting segment 2 with 9 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 3 with 2 points - only 0.00% unknown deleting segment 7 with 766 points - only 0.00% unknown deleting segment 11 with 14 points - only 7.14% unknown deleting segment 14 with 8 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 16 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 17 with 4 points - only 0.00% unknown mean border=79.4, 70 (43) missing vertices, mean dist -0.3 [0.4 (%80.9)->0.2 (%19.1))] %84 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.11-->4.72) (max @ vno 160104 --> 70416) face area 0.35 +- 0.16 (0.00-->6.21) mean absolute distance = 0.22 +- 0.31 4410 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5655265.0, rms=6.59 017: dt: 0.5000, sse=5613595.5, rms=4.364 (0.000%) rms = 4.49, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=5116181.5, rms=3.326 (0.000%) 019: dt: 0.2500, sse=4883240.5, rms=2.592 (0.000%) 020: dt: 0.2500, sse=4788981.5, rms=2.110 (0.000%) 021: dt: 0.2500, sse=4754010.0, rms=1.954 (0.000%) 022: dt: 0.2500, sse=4670228.5, rms=1.801 (0.000%) rms = 1.76, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=4675198.5, rms=1.763 (0.000%) 024: dt: 0.1250, sse=4512359.5, rms=1.569 (0.000%) rms = 1.54, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=4471475.0, rms=1.543 (0.000%) positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 264 points - only 3.79% unknown deleting segment 1 with 5 points - only 0.00% unknown deleting segment 2 with 9 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 3 with 2 points - only 0.00% unknown deleting segment 5 with 862 points - only 0.00% unknown deleting segment 6 with 11 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown deleting segment 10 with 10 points - only 10.00% unknown deleting segment 11 with 8 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 12 with 3 points - only 0.00% unknown deleting segment 13 with 5 points - only 0.00% unknown mean border=82.6, 68 (34) missing vertices, mean dist -0.1 [0.2 (%76.3)->0.2 (%23.7))] %91 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.10-->4.81) (max @ vno 160104 --> 70416) face area 0.33 +- 0.16 (0.00-->5.67) mean absolute distance = 0.16 +- 0.25 2994 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4889192.0, rms=4.12 026: dt: 0.5000, sse=5312165.5, rms=3.986 (0.000%) rms = 4.18, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=4792344.5, rms=2.529 (0.000%) 028: dt: 0.2500, sse=4666050.5, rms=2.000 (0.000%) 029: dt: 0.2500, sse=4714949.5, rms=1.677 (0.000%) rms = 1.70, time step reduction 2 of 3 to 0.125... 030: dt: 0.1250, sse=4647289.0, rms=1.554 (0.000%) 031: dt: 0.1250, sse=4557666.0, rms=1.376 (0.000%) rms = 1.36, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=4520176.0, rms=1.356 (0.000%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 281 points - only 3.56% unknown deleting segment 1 with 5 points - only 0.00% unknown deleting segment 2 with 9 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 3 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 4 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 870 points - only 0.00% unknown deleting segment 7 with 10 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown deleting segment 9 with 10 points - only 10.00% unknown deleting segment 10 with 8 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 11 with 3 points - only 0.00% unknown deleting segment 12 with 5 points - only 0.00% unknown mean border=83.5, 76 (27) missing vertices, mean dist -0.0 [0.2 (%57.8)->0.2 (%42.2))] %92 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 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=4548075.5, rms=1.73 rms = 2.49, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=4649222.5, rms=1.169 (0.000%) 034: dt: 0.2500, sse=4818127.0, rms=1.016 (0.000%) rms = 1.02, time step reduction 2 of 3 to 0.125... rms = 1.01, time step reduction 3 of 3 to 0.062... 035: dt: 0.1250, sse=4820042.5, rms=1.007 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 18 points - only 33.33% unknown smoothing surface for 5 iterations... mean border=51.7, 111 (111) missing vertices, mean dist 1.8 [0.2 (%0.0)->2.3 (%100.0))] %18 local maxima, %57 large gradients and %21 min vals, 1813 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=33252602.0, rms=31.32 001: dt: 0.5000, sse=23820164.0, rms=25.953 (0.000%) 002: dt: 0.5000, sse=17428042.0, rms=21.590 (0.000%) 003: dt: 0.5000, sse=13329135.0, rms=18.138 (0.000%) 004: dt: 0.5000, sse=10853808.0, rms=15.436 (0.000%) 005: dt: 0.5000, sse=9436409.0, rms=13.377 (0.000%) 006: dt: 0.5000, sse=8574854.0, rms=11.795 (0.000%) 007: dt: 0.5000, sse=8032852.0, rms=10.429 (0.000%) 008: dt: 0.5000, sse=7625669.5, rms=9.155 (0.000%) 009: dt: 0.5000, sse=7400627.5, rms=7.980 (0.000%) 010: dt: 0.5000, sse=7328718.5, rms=6.933 (0.000%) 011: dt: 0.5000, sse=7340751.0, rms=6.028 (0.000%) 012: dt: 0.5000, sse=7462176.0, rms=5.310 (0.000%) 013: dt: 0.5000, sse=7615104.5, rms=4.789 (0.000%) 014: dt: 0.5000, sse=7788750.5, rms=4.487 (0.000%) 015: dt: 0.5000, sse=7951089.5, rms=4.297 (0.000%) 016: dt: 0.5000, sse=8027350.0, rms=4.190 (0.000%) 017: dt: 0.5000, sse=8091952.0, rms=4.094 (0.000%) rms = 4.05, time step reduction 1 of 3 to 0.250... 018: dt: 0.5000, sse=8099899.0, rms=4.053 (0.000%) 019: dt: 0.2500, sse=5641960.0, rms=3.259 (0.000%) 020: dt: 0.2500, sse=5457684.5, rms=3.050 (0.000%) rms = 3.02, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=5298820.0, rms=3.016 (0.000%) 022: dt: 0.1250, sse=5029088.0, rms=2.837 (0.000%) rms = 2.81, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=5006962.5, rms=2.811 (0.000%) positioning took 3.3 minutes mean border=48.8, 993 (28) missing vertices, mean dist 0.2 [0.2 (%43.3)->0.5 (%56.7))] %37 local maxima, %41 large gradients and %18 min vals, 574 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=5916018.5, rms=5.31 024: dt: 0.5000, sse=6209243.5, rms=4.414 (0.000%) 025: dt: 0.5000, sse=7797205.5, rms=4.261 (0.000%) rms = 4.30, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=6394776.5, rms=3.436 (0.000%) 027: dt: 0.2500, sse=5863477.5, rms=3.090 (0.000%) 028: dt: 0.2500, sse=5800961.0, rms=2.998 (0.000%) 029: dt: 0.2500, sse=5753294.5, rms=2.948 (0.000%) rms = 2.93, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=5763284.0, rms=2.930 (0.000%) 031: dt: 0.1250, sse=5501244.5, rms=2.698 (0.000%) rms = 2.66, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=5479329.0, rms=2.658 (0.000%) positioning took 1.4 minutes mean border=46.1, 1229 (21) missing vertices, mean dist 0.1 [0.2 (%34.9)->0.4 (%65.1))] %56 local maxima, %22 large gradients and %17 min vals, 621 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=5883961.0, rms=4.40 033: dt: 0.5000, sse=6194537.5, rms=4.201 (0.000%) rms = 4.17, time step reduction 1 of 3 to 0.250... 034: dt: 0.5000, sse=8006900.0, rms=4.171 (0.000%) 035: dt: 0.2500, sse=6001242.5, rms=3.119 (0.000%) 036: dt: 0.2500, sse=6192814.5, rms=2.792 (0.000%) rms = 2.81, time step reduction 2 of 3 to 0.125... 037: dt: 0.1250, sse=6027948.5, rms=2.661 (0.000%) 038: dt: 0.1250, sse=5747886.5, rms=2.474 (0.000%) rms = 2.44, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=5683501.0, rms=2.439 (0.000%) positioning took 1.2 minutes mean border=44.9, 2472 (16) missing vertices, mean dist 0.0 [0.2 (%43.8)->0.2 (%56.2))] %58 local maxima, %20 large gradients and %17 min vals, 447 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/sub016/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=5745762.5, rms=2.86 rms = 3.79, time step reduction 1 of 3 to 0.250... 040: dt: 0.2500, sse=5579690.0, rms=2.540 (0.000%) 041: dt: 0.2500, sse=5757399.5, rms=2.466 (0.000%) rms = 2.48, time step reduction 2 of 3 to 0.125... rms = 2.42, time step reduction 3 of 3 to 0.062... 042: dt: 0.1250, sse=5697529.5, rms=2.425 (0.000%) positioning took 0.7 minutes writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.area.pial vertex spacing 1.01 +- 0.43 (0.05-->7.37) (max @ vno 109705 --> 108677) face area 0.41 +- 0.31 (0.00-->7.60) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 160479 vertices processed 25000 of 160479 vertices processed 50000 of 160479 vertices processed 75000 of 160479 vertices processed 100000 of 160479 vertices processed 125000 of 160479 vertices processed 150000 of 160479 vertices processed 0 of 160479 vertices processed 25000 of 160479 vertices processed 50000 of 160479 vertices processed 75000 of 160479 vertices processed 100000 of 160479 vertices processed 125000 of 160479 vertices processed 150000 of 160479 vertices processed thickness calculation complete, 283:849 truncations. 38541 vertices at 0 distance 110303 vertices at 1 distance 101984 vertices at 2 distance 41552 vertices at 3 distance 11775 vertices at 4 distance 3027 vertices at 5 distance 822 vertices at 6 distance 267 vertices at 7 distance 118 vertices at 8 distance 49 vertices at 9 distance 29 vertices at 10 distance 21 vertices at 11 distance 18 vertices at 12 distance 14 vertices at 13 distance 14 vertices at 14 distance 13 vertices at 15 distance 17 vertices at 16 distance 10 vertices at 17 distance 8 vertices at 18 distance 7 vertices at 19 distance 15 vertices at 20 distance writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.thickness positioning took 16.2 minutes #-------------------------------------------- #@# Surf Volume lh Thu Aug 8 20:18:20 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 20:18:21 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts pctsurfcon --s sub016 --lh-only Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts/pctsurfcon.log Thu Aug 8 20:18:21 CEST 2013 setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/tmp.pctsurfcon.9267/lh.wm.mgh --regheader sub016 --cortex srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/mri/orig.mgz as target reference. Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/label/lh.cortex.label Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 = 124623 Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/label/lh.cortex.label Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/tmp.pctsurfcon.9267/lh.wm.mgh Dim: 160479 1 1 mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/tmp.pctsurfcon.9267/lh.gm.mgh --projfrac 0.3 --regheader sub016 --cortex srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/mri/orig.mgz as target reference. Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/label/lh.cortex.label Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.white Done reading source surface Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 = 142718 Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/label/lh.cortex.label Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/tmp.pctsurfcon.9267/lh.gm.mgh Dim: 160479 1 1 mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/tmp.pctsurfcon.9267/lh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/tmp.pctsurfcon.9267/lh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/surf/lh.w-g.pct.mgh mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.w-g.pct.mgh --annot sub016 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/surf/lh.w-g.pct.mgh --annot sub016 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/surf/lh.w-g.pct.mgh Vertex Area is 0.660622 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 1000 unknown 0 0.000 1 1001 bankssts 1512 1056.612 2 1002 caudalanteriorcingulate 1250 846.357 3 1003 caudalmiddlefrontal 3443 2308.520 4 1004 corpuscallosum 0 0.000 5 1005 cuneus 2906 1843.261 6 1006 entorhinal 750 510.895 7 1007 fusiform 5411 3674.410 8 1008 inferiorparietal 8099 5476.500 9 1009 inferiortemporal 7888 5305.233 10 1010 isthmuscingulate 2079 1352.020 11 1011 lateraloccipital 8202 5319.603 12 1012 lateralorbitofrontal 4837 3217.664 13 1013 lingual 5239 3490.395 14 1014 medialorbitofrontal 3096 2007.213 15 1015 middletemporal 5955 4078.508 16 1016 parahippocampal 1473 959.961 17 1017 paracentral 2087 1225.595 18 1018 parsopercularis 3193 2112.798 19 1019 parsorbitalis 1216 781.607 20 1020 parstriangularis 2274 1526.439 21 1021 pericalcarine 2660 1943.400 22 1022 postcentral 7142 4493.574 23 1023 posteriorcingulate 2413 1614.474 24 1024 precentral 8460 5267.162 25 1025 precuneus 7244 4771.850 26 1026 rostralanteriorcingulate 1630 1076.536 27 1027 rostralmiddlefrontal 8850 6006.854 28 1028 superiorfrontal 12261 8237.140 29 1029 superiorparietal 10142 6578.766 30 1030 superiortemporal 6058 4059.571 31 1031 supramarginal 7259 4838.904 32 1032 frontalpole 293 200.763 33 1033 temporalpole 701 477.017 34 1034 transversetemporal 1015 612.610 35 1035 insula 4037 2649.110 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats lh Thu Aug 8 20:18:36 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 sub016 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 1512 1057 2788 2.484 0.577 0.109 0.030 16 1.9 bankssts 1250 846 2519 2.694 0.558 0.132 0.039 20 1.9 caudalanteriorcingulate 3443 2309 6884 2.643 0.506 0.124 0.038 42 5.3 caudalmiddlefrontal 2906 1843 4888 2.270 0.557 0.151 0.065 56 8.1 cuneus 750 511 1990 3.183 0.555 0.141 0.049 10 1.5 entorhinal 5411 3674 11873 2.829 0.552 0.145 0.064 104 12.7 fusiform 8099 5476 15082 2.452 0.454 0.136 0.048 147 15.8 inferiorparietal 7888 5305 17636 2.745 0.662 0.143 0.064 184 19.7 inferiortemporal 2079 1352 3419 2.358 0.806 0.147 0.068 58 5.9 isthmuscingulate 8202 5320 13729 2.285 0.508 0.154 0.062 165 20.3 lateraloccipital 4837 3218 9518 2.570 0.607 0.154 0.072 98 12.5 lateralorbitofrontal 5239 3490 8311 2.164 0.560 0.154 0.077 104 17.9 lingual 3096 2007 5386 2.231 0.752 0.164 0.091 112 10.3 medialorbitofrontal 5955 4078 14688 2.876 0.629 0.146 0.053 113 12.2 middletemporal 1473 960 3480 3.050 0.644 0.161 0.204 54 6.4 parahippocampal 2087 1226 3632 2.649 0.600 0.113 0.183 52 4.7 paracentral 3193 2113 6704 2.788 0.481 0.127 0.040 46 5.5 parsopercularis 1216 782 2883 2.875 0.687 0.148 0.053 24 2.5 parsorbitalis 2274 1526 4452 2.475 0.542 0.138 0.046 38 4.1 parstriangularis 2660 1943 3720 2.004 0.464 0.156 0.059 48 6.9 pericalcarine 7142 4494 11708 2.289 0.613 0.130 0.054 188 17.9 postcentral 2413 1614 4505 2.550 0.656 0.135 0.048 39 4.1 posteriorcingulate 8460 5267 16227 2.749 0.553 0.113 0.040 178 13.8 precentral 7244 4772 13273 2.573 0.506 0.139 0.050 113 14.9 precuneus 1630 1077 3658 2.643 0.838 0.156 0.058 30 3.8 rostralanteriorcingulate 8850 6007 16555 2.345 0.560 0.145 0.052 167 19.0 rostralmiddlefrontal 12261 8237 26422 2.723 0.604 0.130 0.040 150 20.3 superiorfrontal 10142 6579 17306 2.358 0.445 0.130 0.043 162 17.5 superiorparietal 6058 4060 14107 3.042 0.686 0.122 0.041 78 9.4 superiortemporal 7259 4839 14989 2.719 0.528 0.141 0.049 160 14.3 supramarginal 293 201 790 2.634 0.541 0.237 0.128 14 1.1 frontalpole 701 477 2545 3.779 0.688 0.160 0.063 13 1.9 temporalpole 1015 613 2006 2.729 0.354 0.150 0.130 37 6.9 transversetemporal 4037 2649 8630 3.118 0.753 0.118 0.076 80 11.0 insula #----------------------------------------- #@# Cortical Parc 2 lh Thu Aug 8 20:18:59 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub016 lh ../surf/lh.sphere.reg /opt/freesurfer/5.3.0/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /opt/freesurfer/5.3.0/average/lh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 3.9 0.2 using min determinant for regularization = 0.000 0 singular and 1066 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 27 labels changed using aseg relabeling using gibbs priors... 000: 11050 changed, 160479 examined... 001: 2709 changed, 41932 examined... 002: 839 changed, 13821 examined... 003: 359 changed, 4563 examined... 004: 198 changed, 1995 examined... 005: 85 changed, 1065 examined... 006: 45 changed, 501 examined... 007: 25 changed, 248 examined... 008: 15 changed, 139 examined... 009: 9 changed, 82 examined... 010: 4 changed, 50 examined... 011: 2 changed, 24 examined... 012: 0 changed, 12 examined... 1 labels changed using aseg 000: 326 total segments, 243 labels (2925 vertices) changed 001: 104 total segments, 22 labels (106 vertices) changed 002: 82 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 128 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1047 vertices marked for relabeling... 1047 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 1 minutes and 22 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Thu Aug 8 20:20:20 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 sub016 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 1398 965 2614 2.232 0.588 0.153 0.052 29 3.1 G_and_S_frontomargin 1188 747 1903 2.183 0.403 0.122 0.054 29 2.3 G_and_S_occipital_inf 1708 930 2996 2.566 0.594 0.121 0.058 57 4.0 G_and_S_paracentral 2065 1309 4502 2.929 0.542 0.147 0.052 37 4.4 G_and_S_subcentral 613 424 1429 2.417 0.542 0.185 0.096 23 2.0 G_and_S_transv_frontopol 3293 2209 6728 2.546 0.738 0.145 0.053 53 6.4 G_and_S_cingul-Ant 1399 982 2690 2.599 0.569 0.116 0.040 15 2.0 G_and_S_cingul-Mid-Ant 1557 1044 2801 2.580 0.491 0.108 0.033 13 2.2 G_and_S_cingul-Mid-Post 969 616 2176 3.017 0.624 0.162 0.068 22 2.2 G_cingul-Post-dorsal 459 275 659 2.140 0.767 0.148 0.074 8 1.3 G_cingul-Post-ventral 2693 1742 4781 2.164 0.562 0.165 0.073 62 8.6 G_cuneus 1741 1119 4314 2.985 0.434 0.143 0.053 35 4.0 G_front_inf-Opercular 318 193 833 3.056 0.457 0.161 0.065 8 0.8 G_front_inf-Orbital 1238 845 2870 2.667 0.472 0.161 0.056 30 2.8 G_front_inf-Triangul 4770 3234 11350 2.683 0.510 0.160 0.062 112 11.8 G_front_middle 8303 5409 19745 2.878 0.584 0.137 0.078 152 15.8 G_front_sup 585 383 1443 3.214 0.499 0.125 0.062 8 1.2 G_Ins_lg_and_S_cent_ins 936 587 3021 3.869 0.650 0.145 0.167 51 5.2 G_insular_short 2895 1870 6213 2.594 0.475 0.174 0.088 99 9.8 G_occipital_middle 1937 1278 3192 2.268 0.428 0.150 0.054 54 4.4 G_occipital_sup 1579 1020 4156 3.069 0.447 0.159 0.065 40 3.8 G_oc-temp_lat-fusifor 3433 2248 5849 2.169 0.597 0.175 0.100 92 15.6 G_oc-temp_med-Lingual 1862 1244 5210 3.285 0.548 0.165 0.180 61 7.5 G_oc-temp_med-Parahip 3134 2051 7575 2.779 0.609 0.172 0.094 92 10.2 G_orbital 2868 1900 6701 2.675 0.474 0.158 0.063 80 7.5 G_pariet_inf-Angular 3884 2581 9527 2.905 0.493 0.153 0.051 80 7.8 G_pariet_inf-Supramar 4289 2725 8589 2.487 0.475 0.137 0.048 76 7.9 G_parietal_sup 2584 1530 4729 2.368 0.475 0.139 0.077 133 10.3 G_postcentral 3137 1796 7414 3.066 0.425 0.117 0.050 102 6.0 G_precentral 3240 2129 7232 2.764 0.505 0.158 0.060 69 7.8 G_precuneus 1054 665 2367 2.432 0.724 0.185 0.106 41 4.6 G_rectus 528 336 942 2.619 0.925 0.201 0.167 42 2.7 G_subcallosal 806 476 1868 2.876 0.428 0.157 0.150 36 6.5 G_temp_sup-G_T_transv 2099 1376 6291 3.287 0.569 0.144 0.047 44 4.1 G_temp_sup-Lateral 797 546 2450 3.766 0.713 0.126 0.056 9 1.8 G_temp_sup-Plan_polar 1421 954 3002 2.826 0.481 0.111 0.036 14 2.0 G_temp_sup-Plan_tempo 4735 3150 12232 2.902 0.696 0.168 0.085 161 15.4 G_temporal_inf 4179 2835 11296 2.979 0.610 0.150 0.057 89 8.9 G_temporal_middle 601 392 970 2.301 0.556 0.122 0.037 6 0.9 Lat_Fis-ant-Horizont 405 278 716 2.510 0.515 0.108 0.027 3 0.5 Lat_Fis-ant-Vertical 1616 1063 2328 2.569 0.489 0.119 0.037 13 2.4 Lat_Fis-post 2348 1502 3846 2.180 0.536 0.168 0.075 51 7.6 Pole_occipital 2019 1388 5883 3.157 0.733 0.173 0.090 48 6.8 Pole_temporal 3836 2660 5170 2.087 0.521 0.135 0.049 53 8.1 S_calcarine 3491 2319 4297 2.050 0.529 0.113 0.030 25 4.6 S_central 1249 834 1902 2.301 0.389 0.108 0.028 11 1.4 S_cingul-Marginalis 635 424 1051 2.606 0.552 0.112 0.042 5 0.9 S_circular_insula_ant 1843 1225 3131 2.905 0.720 0.094 0.023 8 1.9 S_circular_insula_inf 2052 1380 3127 2.685 0.520 0.101 0.030 12 2.4 S_circular_insula_sup 1820 1250 3121 2.680 0.526 0.106 0.028 12 2.2 S_collat_transv_ant 372 259 470 2.203 0.330 0.125 0.030 3 0.5 S_collat_transv_post 2485 1659 3858 2.268 0.461 0.116 0.031 23 3.3 S_front_inf 1660 1114 2382 2.089 0.458 0.127 0.045 20 3.1 S_front_middle 3117 2120 5236 2.484 0.505 0.110 0.031 25 4.2 S_front_sup 270 183 415 2.394 0.436 0.148 0.056 3 0.8 S_interm_prim-Jensen 3972 2642 5744 2.295 0.389 0.114 0.032 34 5.3 S_intrapariet_and_P_trans 1315 888 1703 1.936 0.351 0.123 0.033 14 1.7 S_oc_middle_and_Lunatus 1148 802 1778 2.314 0.363 0.148 0.045 15 2.1 S_oc_sup_and_transversal 1147 777 1667 2.349 0.413 0.140 0.040 13 2.0 S_occipital_ant 1621 1128 2813 2.551 0.379 0.103 0.024 10 1.7 S_oc-temp_lat 2180 1493 3796 2.606 0.538 0.138 0.053 27 4.5 S_oc-temp_med_and_Lingual 500 338 636 2.086 0.492 0.101 0.024 2 0.6 S_orbital_lateral 783 545 1203 2.192 0.724 0.126 0.040 7 1.4 S_orbital_med-olfact 1897 1253 3345 2.495 0.628 0.147 0.056 31 4.5 S_orbital-H_Shaped 2790 1859 4345 2.493 0.510 0.124 0.040 28 4.6 S_parieto_occipital 1802 1186 2164 2.040 0.678 0.140 0.057 59 4.5 S_pericallosal 3177 2122 4456 2.276 0.407 0.119 0.037 62 4.5 S_postcentral 1723 1173 2589 2.390 0.429 0.106 0.026 11 2.0 S_precentral-inf-part 1504 1062 2365 2.535 0.502 0.096 0.023 6 1.5 S_precentral-sup-part 573 397 822 1.895 0.805 0.160 0.053 11 1.4 S_suborbital 1235 833 2058 2.471 0.397 0.133 0.044 16 2.3 S_subparietal 1969 1385 3100 2.384 0.510 0.111 0.027 13 2.4 S_temporal_inf 5778 3972 9464 2.394 0.469 0.113 0.034 64 7.8 S_temporal_sup 448 298 661 2.708 0.332 0.114 0.031 3 0.6 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Thu Aug 8 20:20:46 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub016 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... 1036 labels changed using aseg relabeling using gibbs priors... 000: 3290 changed, 160479 examined... 001: 797 changed, 13782 examined... 002: 203 changed, 4294 examined... 003: 71 changed, 1206 examined... 004: 42 changed, 397 examined... 005: 17 changed, 242 examined... 006: 9 changed, 105 examined... 007: 6 changed, 52 examined... 008: 3 changed, 34 examined... 009: 4 changed, 17 examined... 010: 1 changed, 15 examined... 011: 0 changed, 7 examined... 76 labels changed using aseg 000: 76 total segments, 43 labels (249 vertices) changed 001: 35 total segments, 2 labels (3 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 60 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 969 vertices marked for relabeling... 969 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas40.annot... classification took 1 minutes and 12 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Thu Aug 8 20:21:58 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 sub016 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 1893 1283 3926 2.752 0.604 0.132 0.040 27 2.9 caudalanteriorcingulate 3593 2400 7209 2.654 0.505 0.125 0.039 46 5.6 caudalmiddlefrontal 4013 2602 6428 2.246 0.530 0.146 0.058 69 10.0 cuneus 735 502 1959 3.204 0.559 0.135 0.043 8 1.3 entorhinal 4879 3297 10290 2.812 0.529 0.142 0.058 91 10.7 fusiform 7514 5088 13954 2.440 0.456 0.139 0.049 141 15.0 inferiorparietal 7834 5269 17861 2.771 0.671 0.144 0.065 181 19.7 inferiortemporal 2094 1351 3494 2.388 0.796 0.150 0.070 61 6.3 isthmuscingulate 8527 5521 14461 2.289 0.509 0.155 0.063 194 21.8 lateraloccipital 5148 3450 10650 2.605 0.623 0.165 0.094 131 17.8 lateralorbitofrontal 5174 3449 8220 2.165 0.560 0.154 0.077 102 17.8 lingual 2650 1728 4923 2.253 0.765 0.166 0.090 89 8.4 medialorbitofrontal 8067 5546 18703 2.774 0.632 0.144 0.052 148 16.7 middletemporal 1449 947 3427 3.051 0.641 0.161 0.206 54 6.4 parahippocampal 2469 1480 4347 2.661 0.575 0.111 0.159 55 5.2 paracentral 2851 1869 6007 2.818 0.479 0.126 0.041 41 5.0 parsopercularis 1239 795 2574 2.679 0.729 0.130 0.040 16 2.0 parsorbitalis 2842 1915 5509 2.464 0.537 0.140 0.045 50 5.3 parstriangularis 2666 1939 3741 2.016 0.474 0.155 0.059 47 6.9 pericalcarine 7942 5036 12997 2.297 0.607 0.129 0.051 194 18.6 postcentral 2570 1728 4662 2.520 0.661 0.132 0.046 39 4.2 posteriorcingulate 8474 5275 16160 2.748 0.551 0.114 0.041 178 13.9 precentral 6877 4527 12820 2.568 0.515 0.138 0.050 108 13.9 precuneus 2140 1408 4323 2.557 0.819 0.158 0.071 58 5.8 rostralanteriorcingulate 6215 4195 12007 2.418 0.597 0.142 0.049 106 12.6 rostralmiddlefrontal 13430 9036 28222 2.631 0.617 0.134 0.043 190 23.9 superiorfrontal 8234 5309 14237 2.393 0.433 0.129 0.042 118 13.7 superiorparietal 8005 5378 18976 3.041 0.720 0.123 0.043 104 13.3 superiortemporal 7050 4696 14499 2.709 0.539 0.142 0.049 157 13.9 supramarginal 1007 606 1995 2.729 0.354 0.150 0.131 37 6.9 transversetemporal 3494 2295 7719 3.170 0.723 0.109 0.052 62 6.3 insula #-------------------------------------------- #@# Tessellate rh Thu Aug 8 20:22:22 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 1 found - 1 modified | TOTAL: 2 pass 2 (xy-): 0 found - 1 modified | TOTAL: 2 pass 1 (yz+): 4 found - 4 modified | TOTAL: 6 pass 2 (yz+): 0 found - 4 modified | TOTAL: 6 pass 1 (yz-): 0 found - 0 modified | TOTAL: 6 pass 1 (xz+): 0 found - 0 modified | TOTAL: 6 pass 1 (xz-): 3 found - 3 modified | TOTAL: 9 pass 2 (xz-): 0 found - 3 modified | TOTAL: 9 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 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 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 = 12 (out of 303005: 0.003960) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 40: 1681 vertices, 1847 faces slice 50: 9012 vertices, 9345 faces slice 60: 19700 vertices, 20123 faces slice 70: 32179 vertices, 32646 faces slice 80: 44565 vertices, 45009 faces slice 90: 57262 vertices, 57668 faces slice 100: 70063 vertices, 70480 faces slice 110: 82614 vertices, 83037 faces slice 120: 94695 vertices, 95131 faces slice 130: 106511 vertices, 106941 faces slice 140: 118494 vertices, 118916 faces slice 150: 129325 vertices, 129675 faces slice 160: 138302 vertices, 138625 faces slice 170: 146915 vertices, 147215 faces slice 180: 154406 vertices, 154657 faces slice 190: 159885 vertices, 160074 faces slice 200: 163409 vertices, 163504 faces slice 210: 163856 vertices, 163888 faces slice 220: 163856 vertices, 163888 faces slice 230: 163856 vertices, 163888 faces slice 240: 163856 vertices, 163888 faces slice 250: 163856 vertices, 163888 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... 163856 voxel in cpt #1: X=-32 [v=163856,e=491664,f=327776] located at (30.498199, -17.300087, 36.784977) For the whole surface: X=-32 [v=163856,e=491664,f=327776] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Thu Aug 8 20:22:30 CEST 2013 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 20:22:36 CEST 2013 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts avg radius = 49.6 mm, total surface area = 86888 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.7 minutes Not saving sulc step 000: RMS=0.098 (target=0.015) step 005: RMS=0.072 (target=0.015) step 010: RMS=0.053 (target=0.015) step 015: RMS=0.044 (target=0.015) step 020: RMS=0.038 (target=0.015) step 025: RMS=0.033 (target=0.015) step 030: RMS=0.030 (target=0.015) step 035: RMS=0.028 (target=0.015) step 040: RMS=0.027 (target=0.015) step 045: RMS=0.025 (target=0.015) step 050: RMS=0.024 (target=0.015) step 055: RMS=0.024 (target=0.015) step 060: RMS=0.023 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Thu Aug 8 20:23:15 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 0.91 +- 0.54 (0.00-->8.07) (max @ vno 116886 --> 118105) face area 0.02 +- 0.03 (-0.28-->0.62) scaling brain by 0.290... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.534, avgs=0 005/300: dt: 0.9000, rms radial error=176.274, avgs=0 010/300: dt: 0.9000, rms radial error=175.718, avgs=0 015/300: dt: 0.9000, rms radial error=174.987, avgs=0 020/300: dt: 0.9000, rms radial error=174.154, avgs=0 025/300: dt: 0.9000, rms radial error=173.264, avgs=0 030/300: dt: 0.9000, rms radial error=172.342, avgs=0 035/300: dt: 0.9000, rms radial error=171.405, avgs=0 040/300: dt: 0.9000, rms radial error=170.459, avgs=0 045/300: dt: 0.9000, rms radial error=169.511, avgs=0 050/300: dt: 0.9000, rms radial error=168.565, avgs=0 055/300: dt: 0.9000, rms radial error=167.620, avgs=0 060/300: dt: 0.9000, rms radial error=166.680, avgs=0 065/300: dt: 0.9000, rms radial error=165.744, avgs=0 070/300: dt: 0.9000, rms radial error=164.813, avgs=0 075/300: dt: 0.9000, rms radial error=163.887, avgs=0 080/300: dt: 0.9000, rms radial error=162.965, avgs=0 085/300: dt: 0.9000, rms radial error=162.051, avgs=0 090/300: dt: 0.9000, rms radial error=161.141, avgs=0 095/300: dt: 0.9000, rms radial error=160.237, avgs=0 100/300: dt: 0.9000, rms radial error=159.337, avgs=0 105/300: dt: 0.9000, rms radial error=158.443, avgs=0 110/300: dt: 0.9000, rms radial error=157.553, avgs=0 115/300: dt: 0.9000, rms radial error=156.668, avgs=0 120/300: dt: 0.9000, rms radial error=155.788, avgs=0 125/300: dt: 0.9000, rms radial error=154.912, avgs=0 130/300: dt: 0.9000, rms radial error=154.042, avgs=0 135/300: dt: 0.9000, rms radial error=153.176, avgs=0 140/300: dt: 0.9000, rms radial error=152.315, avgs=0 145/300: dt: 0.9000, rms radial error=151.459, avgs=0 150/300: dt: 0.9000, rms radial error=150.607, avgs=0 155/300: dt: 0.9000, rms radial error=149.760, avgs=0 160/300: dt: 0.9000, rms radial error=148.918, avgs=0 165/300: dt: 0.9000, rms radial error=148.080, avgs=0 170/300: dt: 0.9000, rms radial error=147.247, avgs=0 175/300: dt: 0.9000, rms radial error=146.419, avgs=0 180/300: dt: 0.9000, rms radial error=145.595, avgs=0 185/300: dt: 0.9000, rms radial error=144.776, avgs=0 190/300: dt: 0.9000, rms radial error=143.961, avgs=0 195/300: dt: 0.9000, rms radial error=143.151, avgs=0 200/300: dt: 0.9000, rms radial error=142.345, avgs=0 205/300: dt: 0.9000, rms radial error=141.544, avgs=0 210/300: dt: 0.9000, rms radial error=140.747, avgs=0 215/300: dt: 0.9000, rms radial error=139.955, avgs=0 220/300: dt: 0.9000, rms radial error=139.167, avgs=0 225/300: dt: 0.9000, rms radial error=138.384, avgs=0 230/300: dt: 0.9000, rms radial error=137.605, avgs=0 235/300: dt: 0.9000, rms radial error=136.830, avgs=0 240/300: dt: 0.9000, rms radial error=136.060, avgs=0 245/300: dt: 0.9000, rms radial error=135.293, avgs=0 250/300: dt: 0.9000, rms radial error=134.532, avgs=0 255/300: dt: 0.9000, rms radial error=133.774, avgs=0 260/300: dt: 0.9000, rms radial error=133.021, avgs=0 265/300: dt: 0.9000, rms radial error=132.271, avgs=0 270/300: dt: 0.9000, rms radial error=131.526, avgs=0 275/300: dt: 0.9000, rms radial error=130.785, avgs=0 280/300: dt: 0.9000, rms radial error=130.049, avgs=0 285/300: dt: 0.9000, rms radial error=129.316, avgs=0 290/300: dt: 0.9000, rms radial error=128.588, avgs=0 295/300: dt: 0.9000, rms radial error=127.863, avgs=0 300/300: dt: 0.9000, rms radial error=127.143, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 19564.79 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00013 epoch 2 (K=40.0), pass 1, starting sse = 3392.89 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 = 370.22 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/11 = 0.00471 epoch 4 (K=640.0), pass 1, starting sse = 25.03 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/11 = 0.00562 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 20:29:05 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/sub016/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub016 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=-32 (nv=163856, nf=327776, ne=491664, g=17) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations marking ambiguous vertices... 3558 ambiguous faces found in tessellation segmenting defects... 34 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 34 defects to be corrected 0 vertices coincident reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.8298 (-4.9149) -vertex loglikelihood: -6.6052 (-3.3026) -normal dot loglikelihood: -3.6164 (-3.6164) -quad curv loglikelihood: -6.3230 (-3.1615) Total Loglikelihood : -26.3744 CORRECTING DEFECT 0 (vertices=51, convex hull=77) After retessellation of defect 0, euler #=-31 (161715,484343,322597) : difference with theory (-31) = 0 CORRECTING DEFECT 1 (vertices=8, convex hull=27) After retessellation of defect 1, euler #=-30 (161716,484353,322607) : difference with theory (-30) = 0 CORRECTING DEFECT 2 (vertices=8, convex hull=21) After retessellation of defect 2, euler #=-29 (161718,484364,322617) : difference with theory (-29) = 0 CORRECTING DEFECT 3 (vertices=9, convex hull=23) After retessellation of defect 3, euler #=-28 (161719,484374,322627) : difference with theory (-28) = 0 CORRECTING DEFECT 4 (vertices=25, convex hull=44) After retessellation of defect 4, euler #=-27 (161724,484404,322653) : difference with theory (-27) = 0 CORRECTING DEFECT 5 (vertices=36, convex hull=89) After retessellation of defect 5, euler #=-26 (161743,484497,322728) : difference with theory (-26) = 0 CORRECTING DEFECT 6 (vertices=44, convex hull=34) After retessellation of defect 6, euler #=-25 (161747,484522,322750) : difference with theory (-25) = 0 CORRECTING DEFECT 7 (vertices=32, convex hull=57) After retessellation of defect 7, euler #=-24 (161756,484567,322787) : difference with theory (-24) = 0 CORRECTING DEFECT 8 (vertices=448, convex hull=240) After retessellation of defect 8, euler #=-23 (161788,484784,322973) : difference with theory (-23) = 0 CORRECTING DEFECT 9 (vertices=33, convex hull=32) After retessellation of defect 9, euler #=-22 (161793,484809,322994) : difference with theory (-22) = 0 CORRECTING DEFECT 10 (vertices=15, convex hull=35) After retessellation of defect 10, euler #=-21 (161796,484831,323014) : difference with theory (-21) = 0 CORRECTING DEFECT 11 (vertices=25, convex hull=59) After retessellation of defect 11, euler #=-20 (161807,484886,323059) : difference with theory (-20) = 0 CORRECTING DEFECT 12 (vertices=58, convex hull=50) After retessellation of defect 12, euler #=-19 (161818,484939,323102) : difference with theory (-19) = 0 CORRECTING DEFECT 13 (vertices=25, convex hull=45) After retessellation of defect 13, euler #=-18 (161835,485005,323152) : difference with theory (-18) = 0 CORRECTING DEFECT 14 (vertices=88, convex hull=89) After retessellation of defect 14, euler #=-17 (161859,485121,323245) : difference with theory (-17) = 0 CORRECTING DEFECT 15 (vertices=16, convex hull=43) After retessellation of defect 15, euler #=-16 (161868,485163,323279) : difference with theory (-16) = 0 CORRECTING DEFECT 16 (vertices=437, convex hull=123) After retessellation of defect 16, euler #=-15 (161905,485336,323416) : difference with theory (-15) = 0 CORRECTING DEFECT 17 (vertices=16, convex hull=26) After retessellation of defect 17, euler #=-14 (161910,485359,323435) : difference with theory (-14) = 0 CORRECTING DEFECT 18 (vertices=21, convex hull=28) After retessellation of defect 18, euler #=-13 (161912,485378,323453) : difference with theory (-13) = 0 CORRECTING DEFECT 19 (vertices=15, convex hull=17) After retessellation of defect 19, euler #=-12 (161914,485390,323464) : difference with theory (-12) = 0 CORRECTING DEFECT 20 (vertices=81, convex hull=88) After retessellation of defect 20, euler #=-11 (161935,485483,323537) : difference with theory (-11) = 0 CORRECTING DEFECT 21 (vertices=17, convex hull=10) After retessellation of defect 21, euler #=-10 (161935,485485,323540) : difference with theory (-10) = 0 CORRECTING DEFECT 22 (vertices=33, convex hull=18) After retessellation of defect 22, euler #=-9 (161940,485504,323555) : difference with theory (-9) = 0 CORRECTING DEFECT 23 (vertices=117, convex hull=135) After retessellation of defect 23, euler #=-8 (161991,485716,323717) : difference with theory (-8) = 0 CORRECTING DEFECT 24 (vertices=90, convex hull=65) After retessellation of defect 24, euler #=-7 (162011,485798,323780) : difference with theory (-7) = 0 CORRECTING DEFECT 25 (vertices=113, convex hull=61) After retessellation of defect 25, euler #=-6 (162019,485846,323821) : difference with theory (-6) = 0 CORRECTING DEFECT 26 (vertices=6, convex hull=28) After retessellation of defect 26, euler #=-5 (162020,485857,323832) : difference with theory (-5) = 0 CORRECTING DEFECT 27 (vertices=16, convex hull=31) After retessellation of defect 27, euler #=-4 (162022,485872,323846) : difference with theory (-4) = 0 CORRECTING DEFECT 28 (vertices=93, convex hull=92) After retessellation of defect 28, euler #=-3 (162072,486063,323988) : difference with theory (-3) = 0 CORRECTING DEFECT 29 (vertices=54, convex hull=87) After retessellation of defect 29, euler #=-2 (162096,486177,324079) : difference with theory (-2) = 0 CORRECTING DEFECT 30 (vertices=55, convex hull=82) After retessellation of defect 30, euler #=-1 (162129,486310,324180) : difference with theory (-1) = 0 CORRECTING DEFECT 31 (vertices=25, convex hull=82) After retessellation of defect 31, euler #=0 (162142,486381,324239) : difference with theory (0) = 0 CORRECTING DEFECT 32 (vertices=8, convex hull=31) Warning - incorrect dp selected!!!!(-87.980212 >= -87.980213 ) After retessellation of defect 32, euler #=1 (162143,486393,324251) : difference with theory (1) = 0 CORRECTING DEFECT 33 (vertices=33, convex hull=78) After retessellation of defect 33, euler #=2 (162159,486471,324314) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.23 (0.10-->11.94) (max @ vno 66835 --> 69415) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.23 (0.10-->11.94) (max @ vno 66835 --> 69415) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 129 mutations (35.9%), 230 crossovers (64.1%), 190 vertices were eliminated building final representation... 1697 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=162159, nf=324314, ne=486471, g=0) writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 28.8 minutes 0 defective edges removing intersecting faces 000: 225 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 162159 - 486471 + 324314 = 2 --> 0 holes F =2V-4: 324314 = 324318-4 (0) 2E=3F: 972942 = 972942 (0) total defect index = 0 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 39 intersecting 001: 2 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Thu Aug 8 20:58:01 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub016 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/sub016/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz... 23684 bright wm thresholded. 383 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.orig... computing class statistics... border white: 298969 voxels (1.78%) border gray 333863 voxels (1.99%) WM (93.0): 94.0 +- 9.8 [70.0 --> 110.0] GM (76.0) : 74.9 +- 12.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 47.3 (was 70) setting MAX_BORDER_WHITE to 114.8 (was 105) setting MIN_BORDER_WHITE to 60.0 (was 85) setting MAX_CSF to 34.5 (was 40) setting MAX_GRAY to 95.2 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 53.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 21.8 (was 40) repositioning cortical surface to gray/white boundary reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.03-->5.50) (max @ vno 65573 --> 70451) face area 0.28 +- 0.12 (0.00-->5.65) mean absolute distance = 0.66 +- 0.79 5111 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=60 mean inside = 93.5, mean outside = 69.7 smoothing surface for 5 iterations... 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 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=73.5, 62 (62) missing vertices, mean dist 0.4 [0.5 (%29.6)->0.7 (%70.4))] %73 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.26 (0.11-->8.50) (max @ vno 70451 --> 68130) face area 0.28 +- 0.13 (0.00-->5.07) mean absolute distance = 0.36 +- 0.50 4632 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=8153363.5, rms=13.09 001: dt: 0.5000, sse=8206518.0, rms=9.369 (0.000%) 002: dt: 0.5000, sse=8371105.0, rms=7.213 (0.000%) 003: dt: 0.5000, sse=8617238.0, rms=5.862 (0.000%) 004: dt: 0.5000, sse=8847876.0, rms=5.082 (0.000%) 005: dt: 0.5000, sse=8998998.0, rms=4.631 (0.000%) 006: dt: 0.5000, sse=9049736.0, rms=4.420 (0.000%) 007: dt: 0.5000, sse=9107665.0, rms=4.280 (0.000%) 008: dt: 0.5000, sse=9068589.0, rms=4.220 (0.000%) 009: dt: 0.5000, sse=9084191.0, rms=4.148 (0.000%) rms = 4.13, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=9032769.0, rms=4.134 (0.000%) 011: dt: 0.2500, sse=5589936.0, rms=2.796 (0.000%) 012: dt: 0.2500, sse=5133850.5, rms=2.355 (0.000%) 013: dt: 0.2500, sse=4815090.0, rms=2.251 (0.000%) 014: dt: 0.2500, sse=4742968.5, rms=2.161 (0.000%) rms = 2.13, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=4631043.5, rms=2.131 (0.000%) 016: dt: 0.1250, sse=4418955.5, rms=1.928 (0.000%) rms = 1.90, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=4371228.5, rms=1.900 (0.000%) positioning took 2.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=78.9, 77 (16) missing vertices, mean dist -0.3 [0.4 (%82.3)->0.2 (%17.7))] %86 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.05-->9.31) (max @ vno 70451 --> 68130) face area 0.35 +- 0.17 (0.00-->6.95) mean absolute distance = 0.21 +- 0.29 3579 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5901340.5, rms=6.95 018: dt: 0.5000, sse=5746078.5, rms=4.582 (0.000%) rms = 4.63, time step reduction 1 of 3 to 0.250... 019: dt: 0.2500, sse=5250808.0, rms=3.566 (0.000%) 020: dt: 0.2500, sse=4974762.0, rms=2.789 (0.000%) 021: dt: 0.2500, sse=4867593.5, rms=2.265 (0.000%) 022: dt: 0.2500, sse=4830676.5, rms=2.073 (0.000%) 023: dt: 0.2500, sse=4749424.0, rms=1.885 (0.000%) 024: dt: 0.2500, sse=4768091.0, rms=1.810 (0.000%) 025: dt: 0.2500, sse=4708092.0, rms=1.748 (0.000%) rms = 1.72, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=4736196.0, rms=1.725 (0.000%) 027: dt: 0.1250, sse=4562554.5, rms=1.541 (0.000%) rms = 1.53, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=4521904.5, rms=1.529 (0.000%) positioning took 1.7 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 3 vertex label from ripped group mean border=82.1, 58 (7) missing vertices, mean dist -0.1 [0.2 (%76.9)->0.2 (%23.1))] %92 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.04-->9.68) (max @ vno 70451 --> 68130) face area 0.33 +- 0.16 (0.00-->6.87) mean absolute distance = 0.16 +- 0.23 3256 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4962088.0, rms=4.20 029: dt: 0.5000, sse=5376449.5, rms=4.009 (0.000%) rms = 4.18, time step reduction 1 of 3 to 0.250... 030: dt: 0.2500, sse=4837316.0, rms=2.522 (0.000%) 031: dt: 0.2500, sse=4704395.5, rms=1.988 (0.000%) 032: dt: 0.2500, sse=4748966.0, rms=1.651 (0.000%) rms = 1.68, time step reduction 2 of 3 to 0.125... 033: dt: 0.1250, sse=4679433.5, rms=1.528 (0.000%) 034: dt: 0.1250, sse=4588254.5, rms=1.352 (0.000%) rms = 1.33, time step reduction 3 of 3 to 0.062... 035: dt: 0.1250, sse=4547578.5, rms=1.333 (0.000%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=83.0, 51 (4) missing vertices, mean dist -0.0 [0.2 (%58.0)->0.2 (%42.0))] %93 local maxima, % 2 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=4576333.0, rms=1.72 rms = 2.52, time step reduction 1 of 3 to 0.250... 036: dt: 0.2500, sse=4675320.0, rms=1.142 (0.000%) 037: dt: 0.2500, sse=4840894.5, rms=1.004 (0.000%) rms = 1.01, time step reduction 2 of 3 to 0.125... rms = 1.00, time step reduction 3 of 3 to 0.062... 038: dt: 0.1250, sse=4841039.0, rms=0.995 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 20 non-cortical segments detected only using segment with 2323 vertices erasing segment 1 (vno[0] = 103811) erasing segment 2 (vno[0] = 106145) erasing segment 3 (vno[0] = 109699) erasing segment 4 (vno[0] = 110811) erasing segment 5 (vno[0] = 113952) erasing segment 6 (vno[0] = 113958) erasing segment 7 (vno[0] = 114058) erasing segment 8 (vno[0] = 114087) erasing segment 9 (vno[0] = 115145) erasing segment 10 (vno[0] = 116433) erasing segment 11 (vno[0] = 116525) erasing segment 12 (vno[0] = 120936) erasing segment 13 (vno[0] = 121020) erasing segment 14 (vno[0] = 124279) erasing segment 15 (vno[0] = 124302) erasing segment 16 (vno[0] = 125188) erasing segment 17 (vno[0] = 125211) erasing segment 18 (vno[0] = 127009) erasing segment 19 (vno[0] = 127902) writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/label/rh.cortex.label... writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.curv writing smoothed area to rh.area writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.area vertex spacing 0.89 +- 0.25 (0.05-->9.83) (max @ vno 70451 --> 68130) face area 0.33 +- 0.16 (0.00-->6.86) refinement took 8.6 minutes #-------------------------------------------- #@# Smooth2 rh Thu Aug 8 21:06:36 CEST 2013 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 21:06:41 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 49.8 mm, total surface area = 98579 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.112 (target=0.015) step 005: RMS=0.078 (target=0.015) step 010: RMS=0.056 (target=0.015) step 015: RMS=0.046 (target=0.015) step 020: RMS=0.037 (target=0.015) step 025: RMS=0.031 (target=0.015) step 030: RMS=0.027 (target=0.015) step 035: RMS=0.023 (target=0.015) step 040: RMS=0.019 (target=0.015) step 045: RMS=0.017 (target=0.015) step 050: RMS=0.016 (target=0.015) inflation complete. inflation took 0.6 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 212 vertices thresholded to be in k1 ~ [-0.61 0.39], k2 ~ [-0.21 0.11] total integrated curvature = 0.400*4pi (5.028) --> 1 handles ICI = 1.7, FI = 14.3, variation=232.796 169 vertices thresholded to be in [-0.03 0.02] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 134 vertices thresholded to be in [-0.18 0.19] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.015, std = 0.026 done. #----------------------------------------- #@# Curvature Stats rh Thu Aug 8 21:09:21 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub016 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 [ sub016/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 [ 318 ] Gb_filter = 0 #-------------------------------------------- #@# Sphere rh Thu Aug 8 21:09:27 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 0.271... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=snake, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.61 pass 1: epoch 2 of 3 starting distance error %19.56 unfolding complete - removing small folds... starting distance error %19.45 removing remaining folds... final distance error %19.46 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/rh.sphere spherical transformation took 1.24 hours #-------------------------------------------- #@# Surf Reg rh Thu Aug 8 22:23:50 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 = 0.583 curvature mean = 0.026, std = 0.944 curvature mean = 0.026, std = 0.838 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 0.00) sse = 442935.7, tmin=1.3303 d=32.00 min @ (-8.00, -8.00, 0.00) sse = 380528.0, tmin=2.6304 d=16.00 min @ (0.00, 4.00, 4.00) sse = 335983.4, tmin=3.9825 d=8.00 min @ (0.00, -2.00, 0.00) sse = 330664.6, tmin=5.3504 d=2.00 min @ (0.00, 0.50, -0.50) sse = 330548.4, tmin=8.1105 d=1.00 min @ (-0.25, -0.25, 0.25) sse = 330150.7, tmin=9.4755 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 10.87 min curvature mean = 0.002, std = 0.935 curvature mean = 0.011, std = 0.927 curvature mean = -0.004, std = 0.939 curvature mean = 0.006, std = 0.965 curvature mean = -0.007, std = 0.935 curvature mean = 0.001, std = 0.983 2 Reading smoothwm curvature mean = -0.023, std = 0.289 curvature mean = 0.004, std = 0.069 curvature mean = 0.073, std = 0.319 curvature mean = 0.005, std = 0.082 curvature mean = 0.036, std = 0.504 curvature mean = 0.005, std = 0.088 curvature mean = 0.020, std = 0.646 curvature mean = 0.006, std = 0.090 curvature mean = 0.007, std = 0.759 MRISregister() return, current seed 0 writing registered surface to ../surf/rh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white rh Thu Aug 8 22:59:28 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 22:59:32 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 22:59:35 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub016 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... 1118 labels changed using aseg relabeling using gibbs priors... 000: 3403 changed, 162159 examined... 001: 812 changed, 14508 examined... 002: 208 changed, 4507 examined... 003: 52 changed, 1249 examined... 004: 24 changed, 343 examined... 005: 12 changed, 145 examined... 006: 3 changed, 72 examined... 007: 1 changed, 19 examined... 008: 2 changed, 6 examined... 009: 1 changed, 10 examined... 010: 0 changed, 8 examined... 184 labels changed using aseg 000: 104 total segments, 64 labels (442 vertices) changed 001: 41 total segments, 1 labels (7 vertices) changed 002: 40 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... 2159 vertices marked for relabeling... 2159 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 1 minutes and 15 seconds. #-------------------------------------------- #@# Make Pial Surf rh Thu Aug 8 23:00:50 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub016 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/sub016/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz... 23684 bright wm thresholded. 383 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.orig... computing class statistics... border white: 298969 voxels (1.78%) border gray 333863 voxels (1.99%) WM (93.0): 94.0 +- 9.8 [70.0 --> 110.0] GM (76.0) : 74.9 +- 12.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 47.3 (was 70) setting MAX_BORDER_WHITE to 114.8 (was 105) setting MIN_BORDER_WHITE to 60.0 (was 85) setting MAX_CSF to 34.5 (was 40) setting MAX_GRAY to 95.2 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 53.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 21.8 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=60 mean inside = 93.5, mean outside = 69.7 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.03-->5.50) (max @ vno 65573 --> 70451) face area 0.28 +- 0.12 (0.00-->5.65) mean absolute distance = 0.66 +- 0.79 5220 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 12 points - only 0.00% unknown deleting segment 1 with 23 points - only 0.00% unknown deleting segment 2 with 14 points - only 0.00% unknown deleting segment 4 with 5 points - only 0.00% unknown deleting segment 5 with 19 points - only 0.00% unknown deleting segment 7 with 20 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 8 with 3 points - only 0.00% unknown deleting segment 9 with 40 points - only 0.00% unknown deleting segment 10 with 504 points - only 0.00% unknown deleting segment 11 with 6 points - only 0.00% unknown deleting segment 13 with 115 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 16 with 4 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 17 with 4 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 18 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 19 with 3 points - only 0.00% unknown mean border=73.4, 65 (64) missing vertices, mean dist 0.4 [0.5 (%29.6)->0.7 (%70.4))] %74 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.26 (0.11-->8.50) (max @ vno 70451 --> 68130) face area 0.28 +- 0.13 (0.00-->5.07) mean absolute distance = 0.36 +- 0.50 4697 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=8176584.0, rms=13.08 001: dt: 0.5000, sse=8234243.5, rms=9.358 (0.000%) 002: dt: 0.5000, sse=8408520.0, rms=7.207 (0.000%) 003: dt: 0.5000, sse=8659359.0, rms=5.858 (0.000%) 004: dt: 0.5000, sse=8894008.0, rms=5.080 (0.000%) 005: dt: 0.5000, sse=9050424.0, rms=4.630 (0.000%) 006: dt: 0.5000, sse=9104576.0, rms=4.419 (0.000%) 007: dt: 0.5000, sse=9161903.0, rms=4.280 (0.000%) 008: dt: 0.5000, sse=9124109.0, rms=4.218 (0.000%) 009: dt: 0.5000, sse=9137261.0, rms=4.148 (0.000%) rms = 4.13, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=9089501.0, rms=4.133 (0.000%) 011: dt: 0.2500, sse=5633577.5, rms=2.799 (0.000%) 012: dt: 0.2500, sse=5175912.0, rms=2.359 (0.000%) 013: dt: 0.2500, sse=4855685.0, rms=2.257 (0.000%) 014: dt: 0.2500, sse=4781068.5, rms=2.168 (0.000%) rms = 2.14, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=4670974.0, rms=2.137 (0.000%) 016: dt: 0.1250, sse=4458593.5, rms=1.936 (0.000%) rms = 1.91, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=4409677.5, rms=1.908 (0.000%) positioning took 2.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 19 points - only 0.00% unknown deleting segment 1 with 28 points - only 0.00% unknown deleting segment 2 with 18 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 3 with 2 points - only 0.00% unknown deleting segment 4 with 8 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 23 points - only 0.00% unknown deleting segment 7 with 16 points - only 0.00% unknown deleting segment 10 with 33 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 11 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 12 with 1 points - only 0.00% unknown deleting segment 14 with 329 points - only 0.00% unknown deleting segment 15 with 5 points - only 0.00% unknown deleting segment 19 with 24 points - only 0.00% unknown deleting segment 20 with 24 points - only 0.00% unknown deleting segment 21 with 9 points - only 33.33% unknown deleting segment 22 with 12 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 23 with 3 points - only 0.00% unknown mean border=78.9, 88 (18) missing vertices, mean dist -0.3 [0.4 (%82.2)->0.2 (%17.8))] %86 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.05-->9.31) (max @ vno 70451 --> 68130) face area 0.35 +- 0.17 (0.00-->6.95) mean absolute distance = 0.21 +- 0.30 3652 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5945504.5, rms=6.94 018: dt: 0.5000, sse=5791920.5, rms=4.578 (0.000%) rms = 4.62, time step reduction 1 of 3 to 0.250... 019: dt: 0.2500, sse=5293300.5, rms=3.565 (0.000%) 020: dt: 0.2500, sse=5015019.0, rms=2.790 (0.000%) 021: dt: 0.2500, sse=4908255.0, rms=2.268 (0.000%) 022: dt: 0.2500, sse=4870418.0, rms=2.077 (0.000%) 023: dt: 0.2500, sse=4789291.0, rms=1.889 (0.000%) 024: dt: 0.2500, sse=4807856.0, rms=1.815 (0.000%) 025: dt: 0.2500, sse=4749047.0, rms=1.753 (0.000%) rms = 1.73, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=4776147.5, rms=1.731 (0.000%) 027: dt: 0.1250, sse=4603768.0, rms=1.548 (0.000%) rms = 1.54, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=4562413.5, rms=1.536 (0.000%) positioning took 1.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 19 points - only 0.00% unknown deleting segment 1 with 28 points - only 0.00% unknown deleting segment 2 with 20 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 3 with 2 points - only 0.00% unknown deleting segment 4 with 8 points - only 0.00% unknown deleting segment 5 with 21 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 4 points - only 0.00% unknown deleting segment 7 with 18 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 9 with 32 points - only 0.00% unknown deleting segment 10 with 352 points - only 0.00% unknown deleting segment 11 with 5 points - only 0.00% unknown deleting segment 12 with 29 points - only 0.00% unknown deleting segment 14 with 24 points - only 0.00% unknown deleting segment 15 with 37 points - only 0.00% unknown deleting segment 16 with 8 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 17 with 4 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 18 with 3 points - only 0.00% unknown mean border=82.1, 68 (9) missing vertices, mean dist -0.1 [0.2 (%76.8)->0.2 (%23.2))] %92 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.04-->9.68) (max @ vno 70451 --> 68130) face area 0.33 +- 0.16 (0.00-->6.87) mean absolute distance = 0.16 +- 0.23 3372 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5002988.5, rms=4.19 029: dt: 0.5000, sse=5418778.5, rms=4.003 (0.000%) rms = 4.17, time step reduction 1 of 3 to 0.250... 030: dt: 0.2500, sse=4876998.0, rms=2.521 (0.000%) 031: dt: 0.2500, sse=4744753.5, rms=1.990 (0.000%) 032: dt: 0.2500, sse=4789559.5, rms=1.655 (0.000%) rms = 1.68, time step reduction 2 of 3 to 0.125... 033: dt: 0.1250, sse=4719764.5, rms=1.533 (0.000%) 034: dt: 0.1250, sse=4626804.5, rms=1.358 (0.000%) rms = 1.34, time step reduction 3 of 3 to 0.062... 035: dt: 0.1250, sse=4588271.5, rms=1.340 (0.000%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 18 points - only 0.00% unknown deleting segment 1 with 23 points - only 0.00% unknown deleting segment 2 with 19 points - only 0.00% unknown deleting segment 3 with 6 points - only 0.00% unknown deleting segment 4 with 21 points - only 0.00% unknown deleting segment 5 with 17 points - only 0.00% unknown deleting segment 6 with 38 points - only 0.00% unknown deleting segment 7 with 346 points - only 0.00% unknown deleting segment 8 with 5 points - only 0.00% unknown deleting segment 9 with 36 points - only 0.00% unknown deleting segment 10 with 24 points - only 0.00% unknown deleting segment 11 with 51 points - only 0.00% unknown deleting segment 12 with 8 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 13 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 14 with 4 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 15 with 3 points - only 0.00% unknown mean border=83.0, 64 (6) missing vertices, mean dist -0.0 [0.2 (%58.0)->0.2 (%42.0))] %94 local maxima, % 2 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4617414.0, rms=1.73 rms = 2.51, time step reduction 1 of 3 to 0.250... 036: dt: 0.2500, sse=4718826.5, rms=1.153 (0.000%) 037: dt: 0.2500, sse=4896739.0, rms=1.012 (0.000%) rms = 1.02, time step reduction 2 of 3 to 0.125... rms = 1.00, time step reduction 3 of 3 to 0.062... 038: dt: 0.1250, sse=4889615.5, rms=1.003 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... smoothing surface for 5 iterations... mean border=49.8, 100 (100) missing vertices, mean dist 1.8 [0.1 (%0.0)->2.4 (%100.0))] %15 local maxima, %57 large gradients and %24 min vals, 1971 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=36520256.0, rms=32.77 001: dt: 0.5000, sse=26287360.0, rms=27.276 (0.000%) 002: dt: 0.5000, sse=19262446.0, rms=22.771 (0.000%) 003: dt: 0.5000, sse=14590273.0, rms=19.190 (0.000%) 004: dt: 0.5000, sse=11692645.0, rms=16.407 (0.000%) 005: dt: 0.5000, sse=10083440.0, rms=14.299 (0.000%) 006: dt: 0.5000, sse=9162082.0, rms=12.662 (0.000%) 007: dt: 0.5000, sse=8570043.0, rms=11.251 (0.000%) 008: dt: 0.5000, sse=8137810.5, rms=9.926 (0.000%) 009: dt: 0.5000, sse=7807090.0, rms=8.653 (0.000%) 010: dt: 0.5000, sse=7590589.5, rms=7.412 (0.000%) 011: dt: 0.5000, sse=7568264.0, rms=6.315 (0.000%) 012: dt: 0.5000, sse=7606946.5, rms=5.423 (0.000%) 013: dt: 0.5000, sse=7820857.5, rms=4.870 (0.000%) 014: dt: 0.5000, sse=7968421.5, rms=4.535 (0.000%) 015: dt: 0.5000, sse=8149022.5, rms=4.367 (0.000%) 016: dt: 0.5000, sse=8199023.0, rms=4.246 (0.000%) rms = 4.21, time step reduction 1 of 3 to 0.250... 017: dt: 0.5000, sse=8339397.5, rms=4.210 (0.000%) 018: dt: 0.2500, sse=5771961.0, rms=3.380 (0.000%) 019: dt: 0.2500, sse=5591880.0, rms=3.164 (0.000%) rms = 3.15, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=5431412.5, rms=3.154 (0.000%) 021: dt: 0.1250, sse=5119481.0, rms=2.926 (0.000%) rms = 2.90, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=5087547.5, rms=2.895 (0.000%) positioning took 3.2 minutes mean border=47.4, 982 (23) missing vertices, mean dist 0.1 [0.2 (%47.6)->0.5 (%52.4))] %34 local maxima, %41 large gradients and %20 min vals, 595 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=5842710.5, rms=4.86 023: dt: 0.5000, sse=6254044.5, rms=4.286 (0.000%) rms = 4.24, time step reduction 1 of 3 to 0.250... 024: dt: 0.5000, sse=8056153.0, rms=4.242 (0.000%) 025: dt: 0.2500, sse=5984153.0, rms=3.279 (0.000%) 026: dt: 0.2500, sse=6065187.5, rms=3.020 (0.000%) rms = 3.00, time step reduction 2 of 3 to 0.125... 027: dt: 0.2500, sse=5908627.0, rms=2.998 (0.000%) 028: dt: 0.1250, sse=5647260.5, rms=2.720 (0.000%) rms = 2.68, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=5628531.0, rms=2.676 (0.000%) positioning took 1.0 minutes mean border=44.9, 1247 (6) missing vertices, mean dist 0.1 [0.2 (%36.8)->0.3 (%63.2))] %54 local maxima, %21 large gradients and %20 min vals, 785 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=5971874.0, rms=4.17 rms = 4.25, time step reduction 1 of 3 to 0.250... 030: dt: 0.2500, sse=5692742.0, rms=3.447 (0.000%) 031: dt: 0.2500, sse=5601804.0, rms=2.962 (0.000%) 032: dt: 0.2500, sse=5887626.0, rms=2.847 (0.000%) rms = 2.86, time step reduction 2 of 3 to 0.125... 033: dt: 0.1250, sse=5791303.0, rms=2.764 (0.000%) 034: dt: 0.1250, sse=5689471.0, rms=2.644 (0.000%) rms = 2.62, time step reduction 3 of 3 to 0.062... 035: dt: 0.1250, sse=5678918.0, rms=2.618 (0.000%) positioning took 1.1 minutes mean border=43.8, 2605 (4) missing vertices, mean dist 0.0 [0.2 (%45.3)->0.3 (%54.7))] %56 local maxima, %18 large gradients and %20 min vals, 612 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/sub016/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=5742438.0, rms=3.01 rms = 3.94, time step reduction 1 of 3 to 0.250... 036: dt: 0.2500, sse=5610674.5, rms=2.712 (0.000%) 037: dt: 0.2500, sse=5872142.0, rms=2.638 (0.000%) rms = 2.63, time step reduction 2 of 3 to 0.125... 038: dt: 0.2500, sse=5959964.5, rms=2.632 (0.000%) 039: dt: 0.1250, sse=5855301.0, rms=2.482 (0.000%) rms = 2.46, time step reduction 3 of 3 to 0.062... 040: dt: 0.1250, sse=5874691.5, rms=2.456 (0.000%) positioning took 0.9 minutes writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.area.pial vertex spacing 1.01 +- 0.42 (0.07-->10.54) (max @ vno 70451 --> 68130) face area 0.41 +- 0.30 (0.00-->8.44) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 162159 vertices processed 25000 of 162159 vertices processed 50000 of 162159 vertices processed 75000 of 162159 vertices processed 100000 of 162159 vertices processed 125000 of 162159 vertices processed 150000 of 162159 vertices processed 0 of 162159 vertices processed 25000 of 162159 vertices processed 50000 of 162159 vertices processed 75000 of 162159 vertices processed 100000 of 162159 vertices processed 125000 of 162159 vertices processed 150000 of 162159 vertices processed thickness calculation complete, 368:737 truncations. 38776 vertices at 0 distance 112698 vertices at 1 distance 103614 vertices at 2 distance 41260 vertices at 3 distance 11150 vertices at 4 distance 2941 vertices at 5 distance 936 vertices at 6 distance 295 vertices at 7 distance 133 vertices at 8 distance 81 vertices at 9 distance 42 vertices at 10 distance 24 vertices at 11 distance 18 vertices at 12 distance 13 vertices at 13 distance 13 vertices at 14 distance 14 vertices at 15 distance 14 vertices at 16 distance 7 vertices at 17 distance 7 vertices at 18 distance 17 vertices at 19 distance 15 vertices at 20 distance writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.thickness positioning took 16.8 minutes #-------------------------------------------- #@# Surf Volume rh Thu Aug 8 23:17:38 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.volume rh.area.mid mul rh.thickness Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# WM/GM Contrast rh Thu Aug 8 23:17:40 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts pctsurfcon --s sub016 --rh-only Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts/pctsurfcon.log Thu Aug 8 23:17:40 CEST 2013 setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/tmp.pctsurfcon.24216/rh.wm.mgh --regheader sub016 --cortex srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/mri/orig.mgz as target reference. Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/label/rh.cortex.label Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 = 125587 Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/label/rh.cortex.label Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/tmp.pctsurfcon.24216/rh.wm.mgh Dim: 162159 1 1 mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/tmp.pctsurfcon.24216/rh.gm.mgh --projfrac 0.3 --regheader sub016 --cortex srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/mri/orig.mgz as target reference. Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/label/rh.cortex.label Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.white Done reading source surface Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 = 144176 Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/label/rh.cortex.label Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/tmp.pctsurfcon.24216/rh.gm.mgh Dim: 162159 1 1 mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/tmp.pctsurfcon.24216/rh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/tmp.pctsurfcon.24216/rh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/surf/rh.w-g.pct.mgh mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.w-g.pct.mgh --annot sub016 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/surf/rh.w-g.pct.mgh --annot sub016 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/surf/rh.w-g.pct.mgh Vertex Area is 0.659965 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 2000 unknown 0 0.000 1 2001 bankssts 1538 1060.178 2 2002 caudalanteriorcingulate 744 498.773 3 2003 caudalmiddlefrontal 3373 2197.764 4 2004 corpuscallosum 0 0.000 5 2005 cuneus 2869 1883.642 6 2006 entorhinal 690 475.663 7 2007 fusiform 5435 3635.177 8 2008 inferiorparietal 10204 6793.776 9 2009 inferiortemporal 6788 4625.739 10 2010 isthmuscingulate 2352 1535.103 11 2011 lateraloccipital 8661 5648.796 12 2012 lateralorbitofrontal 4716 3174.235 13 2013 lingual 5406 3594.387 14 2014 medialorbitofrontal 3155 2060.892 15 2015 middletemporal 6473 4426.597 16 2016 parahippocampal 1241 845.652 17 2017 paracentral 3127 1926.372 18 2018 parsopercularis 3195 2085.679 19 2019 parsorbitalis 1295 920.021 20 2020 parstriangularis 2843 1916.146 21 2021 pericalcarine 2969 1987.918 22 2022 postcentral 7380 4679.101 23 2023 posteriorcingulate 2178 1427.377 24 2024 precentral 8535 5212.754 25 2025 precuneus 6617 4442.093 26 2026 rostralanteriorcingulate 957 615.840 27 2027 rostralmiddlefrontal 9516 6459.534 28 2028 superiorfrontal 13925 9212.408 29 2029 superiorparietal 9031 5771.498 30 2030 superiortemporal 5912 4041.441 31 2031 supramarginal 6201 4178.135 32 2032 frontalpole 435 286.539 33 2033 temporalpole 695 510.966 34 2034 transversetemporal 724 436.670 35 2035 insula 4226 2783.282 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats rh Thu Aug 8 23:17:54 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 sub016 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 1538 1060 2781 2.609 0.461 0.113 0.025 12 1.5 bankssts 744 499 1460 2.758 0.537 0.137 0.031 10 0.9 caudalanteriorcingulate 3373 2198 7148 2.880 0.490 0.131 0.085 61 6.6 caudalmiddlefrontal 2869 1884 4653 2.212 0.457 0.156 0.063 53 7.6 cuneus 690 476 1929 3.237 0.729 0.138 0.053 8 1.6 entorhinal 5435 3635 11899 2.707 0.545 0.146 0.066 107 15.3 fusiform 10204 6794 19774 2.558 0.499 0.143 0.053 188 20.3 inferiorparietal 6788 4626 15324 2.720 0.628 0.148 0.058 183 15.4 inferiortemporal 2352 1535 3946 2.362 0.936 0.160 0.084 70 8.9 isthmuscingulate 8661 5649 15111 2.353 0.485 0.153 0.059 174 20.3 lateraloccipital 4716 3174 10076 2.788 0.666 0.154 0.069 132 14.5 lateralorbitofrontal 5406 3594 8505 2.179 0.597 0.164 0.114 129 16.7 lingual 3155 2061 6074 2.505 0.732 0.155 0.089 95 12.8 medialorbitofrontal 6473 4427 15580 2.785 0.728 0.137 0.047 118 12.9 middletemporal 1241 846 2556 2.650 0.566 0.140 0.050 20 2.6 parahippocampal 3127 1926 5458 2.595 0.490 0.118 0.037 34 5.3 paracentral 3195 2086 6449 2.742 0.484 0.113 0.041 33 4.2 parsopercularis 1295 920 3171 2.710 0.557 0.179 0.075 34 3.5 parsorbitalis 2843 1916 5723 2.549 0.555 0.131 0.070 90 4.4 parstriangularis 2969 1988 3908 2.060 0.409 0.147 0.059 45 7.0 pericalcarine 7380 4679 12299 2.251 0.549 0.115 0.101 112 11.4 postcentral 2178 1427 4317 2.694 0.719 0.148 0.055 40 5.5 posteriorcingulate 8535 5213 15798 2.770 0.601 0.111 0.143 327 60.1 precentral 6617 4442 12727 2.601 0.539 0.143 0.051 117 13.4 precuneus 957 616 1784 2.977 0.788 0.122 0.150 131 5.9 rostralanteriorcingulate 9516 6460 18680 2.468 0.516 0.151 0.052 180 19.9 rostralmiddlefrontal 13925 9212 30286 2.842 0.528 0.130 0.046 234 26.0 superiorfrontal 9031 5771 14961 2.320 0.425 0.128 0.057 174 21.9 superiorparietal 5912 4041 14092 3.032 0.644 0.132 0.039 73 9.8 superiortemporal 6201 4178 12336 2.627 0.535 0.137 0.089 169 10.6 supramarginal 435 287 1023 2.472 0.637 0.208 0.100 20 2.1 frontalpole 695 511 2594 3.604 0.666 0.145 0.054 11 1.7 temporalpole 724 437 1532 2.915 0.317 0.122 0.046 8 1.2 transversetemporal 4226 2783 9058 3.049 0.957 0.131 0.065 70 9.6 insula #----------------------------------------- #@# Cortical Parc 2 rh Thu Aug 8 23:18:19 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub016 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... 7 labels changed using aseg relabeling using gibbs priors... 000: 11017 changed, 162159 examined... 001: 2717 changed, 42462 examined... 002: 854 changed, 13815 examined... 003: 385 changed, 4642 examined... 004: 167 changed, 2104 examined... 005: 83 changed, 924 examined... 006: 62 changed, 468 examined... 007: 36 changed, 333 examined... 008: 8 changed, 185 examined... 009: 8 changed, 51 examined... 010: 9 changed, 47 examined... 011: 5 changed, 47 examined... 012: 1 changed, 26 examined... 013: 0 changed, 6 examined... 8 labels changed using aseg 000: 314 total segments, 229 labels (3312 vertices) changed 001: 99 total segments, 14 labels (43 vertices) changed 002: 85 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 190 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1277 vertices marked for relabeling... 1277 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 1 minutes and 22 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Thu Aug 8 23:19:41 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 sub016 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 1096 752 2031 2.274 0.613 0.168 0.064 29 3.2 G_and_S_frontomargin 1490 988 2829 2.438 0.528 0.143 0.046 22 2.8 G_and_S_occipital_inf 1927 1097 3660 2.663 0.500 0.125 0.047 29 3.8 G_and_S_paracentral 1882 1226 3765 2.615 0.447 0.143 0.045 30 3.4 G_and_S_subcentral 1332 919 2841 2.470 0.516 0.172 0.062 34 3.6 G_and_S_transv_frontopol 3701 2483 7190 2.739 0.578 0.123 0.038 41 6.0 G_and_S_cingul-Ant 1779 1209 3639 2.736 0.465 0.130 0.052 23 3.1 G_and_S_cingul-Mid-Ant 1893 1251 3748 2.869 0.514 0.128 0.044 23 3.8 G_and_S_cingul-Mid-Post 889 575 2307 3.096 0.550 0.180 0.065 23 2.3 G_cingul-Post-dorsal 478 311 1199 2.950 0.740 0.164 0.082 12 1.4 G_cingul-Post-ventral 2709 1774 4465 2.141 0.435 0.165 0.076 59 8.4 G_cuneus 2036 1331 4855 2.855 0.442 0.133 0.052 32 3.3 G_front_inf-Opercular 420 286 1196 2.985 0.301 0.179 0.274 63 1.1 G_front_inf-Orbital 1567 1044 4008 2.840 0.506 0.149 0.050 30 3.1 G_front_inf-Triangul 4421 2987 11147 2.808 0.493 0.160 0.092 116 11.2 G_front_middle 8623 5535 20666 2.939 0.542 0.136 0.051 185 19.0 G_front_sup 693 447 1467 3.083 1.136 0.149 0.101 20 2.3 G_Ins_lg_and_S_cent_ins 630 409 2384 3.973 0.807 0.170 0.114 14 2.2 G_insular_short 2805 1773 6473 2.725 0.438 0.176 0.080 91 8.7 G_occipital_middle 2014 1254 3540 2.341 0.430 0.154 0.094 63 10.1 G_occipital_sup 1879 1203 4450 2.753 0.523 0.157 0.079 45 6.7 G_oc-temp_lat-fusifor 3604 2365 5923 2.141 0.611 0.176 0.144 106 12.6 G_oc-temp_med-Lingual 1831 1249 4931 3.056 0.754 0.159 0.078 38 5.4 G_oc-temp_med-Parahip 3321 2254 8708 2.942 0.633 0.180 0.077 90 10.7 G_orbital 3908 2565 8611 2.601 0.538 0.158 0.069 97 9.1 G_pariet_inf-Angular 3482 2356 8290 2.762 0.530 0.153 0.134 146 6.9 G_pariet_inf-Supramar 2579 1667 5060 2.473 0.462 0.132 0.043 40 4.5 G_parietal_sup 2697 1571 4949 2.408 0.503 0.115 0.221 64 5.1 G_postcentral 3108 1654 7103 3.209 0.474 0.107 0.339 285 52.9 G_precentral 2531 1707 6237 2.769 0.493 0.154 0.058 56 6.0 G_precuneus 831 534 1873 2.531 0.702 0.207 0.198 59 7.7 G_rectus 720 485 1550 2.850 0.877 0.175 0.233 146 6.8 G_subcallosal 668 408 1559 2.984 0.349 0.139 0.053 10 1.3 G_temp_sup-G_T_transv 2006 1348 6337 3.307 0.557 0.160 0.053 40 4.5 G_temp_sup-Lateral 848 615 2421 3.453 0.688 0.123 0.039 7 1.4 G_temp_sup-Plan_polar 1067 715 2144 2.849 0.491 0.117 0.034 11 1.6 G_temp_sup-Plan_tempo 3975 2690 10435 2.865 0.619 0.168 0.072 149 11.1 G_temporal_inf 3685 2521 10596 3.003 0.710 0.147 0.051 83 7.7 G_temporal_middle 630 411 847 2.232 0.444 0.093 0.019 3 0.5 Lat_Fis-ant-Horizont 395 263 547 2.533 0.383 0.096 0.023 2 0.4 Lat_Fis-ant-Vertical 1732 1151 2400 2.383 0.561 0.119 0.034 13 2.5 Lat_Fis-post 3856 2540 6340 2.205 0.478 0.157 0.067 75 10.0 Pole_occipital 2199 1555 6553 2.987 0.896 0.159 0.074 50 6.9 Pole_temporal 3545 2377 4758 2.182 0.586 0.137 0.049 46 7.1 S_calcarine 3502 2325 4313 2.047 0.580 0.104 0.029 19 4.5 S_central 1702 1132 2575 2.381 0.384 0.111 0.031 13 2.2 S_cingul-Marginalis 715 454 1395 3.296 0.629 0.124 0.062 8 1.3 S_circular_insula_ant 1422 946 2353 2.876 0.648 0.100 0.025 7 1.5 S_circular_insula_inf 1874 1269 3079 2.632 0.547 0.105 0.030 12 2.5 S_circular_insula_sup 1613 1099 2899 2.641 0.492 0.107 0.030 14 2.0 S_collat_transv_ant 487 325 780 2.491 0.456 0.159 0.055 8 1.2 S_collat_transv_post 2003 1348 3072 2.351 0.469 0.112 0.029 14 2.6 S_front_inf 2655 1772 4046 2.340 0.430 0.135 0.048 35 4.6 S_front_middle 3026 2041 5273 2.633 0.460 0.120 0.033 30 4.2 S_front_sup 363 245 556 2.499 0.510 0.132 0.032 3 0.5 S_interm_prim-Jensen 3607 2342 5253 2.233 0.381 0.110 0.032 38 4.7 S_intrapariet_and_P_trans 1529 1035 2207 2.262 0.419 0.124 0.036 15 2.1 S_oc_middle_and_Lunatus 1889 1247 2824 2.294 0.370 0.136 0.038 22 3.1 S_oc_sup_and_transversal 1026 689 1491 2.324 0.402 0.131 0.049 14 2.2 S_occipital_ant 1031 721 1710 2.572 0.471 0.108 0.029 5 1.3 S_oc-temp_lat 1926 1310 3304 2.645 0.453 0.131 0.042 23 3.6 S_oc-temp_med_and_Lingual 607 397 748 2.132 0.415 0.136 0.040 8 0.9 S_orbital_lateral 908 629 1432 2.399 0.729 0.117 0.080 51 4.1 S_orbital_med-olfact 1809 1235 3281 2.498 0.577 0.147 0.049 28 3.6 S_orbital-H_Shaped 3013 2007 4711 2.508 0.468 0.136 0.043 45 5.1 S_parieto_occipital 1788 1129 1989 1.998 0.976 0.154 0.077 53 6.8 S_pericallosal 2867 1919 3863 2.227 0.347 0.102 0.051 44 4.8 S_postcentral 1452 960 2390 2.687 0.386 0.109 0.030 12 1.6 S_precentral-inf-part 1761 1207 2737 2.457 0.492 0.111 0.026 12 2.0 S_precentral-sup-part 426 276 571 2.092 0.733 0.116 0.036 5 0.7 S_suborbital 1218 831 2140 2.524 0.485 0.133 0.047 16 2.4 S_subparietal 2137 1470 3119 2.265 0.558 0.130 0.045 31 3.7 S_temporal_inf 7180 4873 12323 2.568 0.482 0.117 0.031 68 9.1 S_temporal_sup 388 264 552 2.681 0.398 0.115 0.024 2 0.4 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 rh Thu Aug 8 23:20:05 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub016 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... 1104 labels changed using aseg relabeling using gibbs priors... 000: 3246 changed, 162159 examined... 001: 744 changed, 13762 examined... 002: 171 changed, 4059 examined... 003: 78 changed, 1021 examined... 004: 39 changed, 437 examined... 005: 18 changed, 219 examined... 006: 8 changed, 102 examined... 007: 9 changed, 52 examined... 008: 5 changed, 57 examined... 009: 5 changed, 33 examined... 010: 3 changed, 26 examined... 011: 3 changed, 21 examined... 012: 5 changed, 21 examined... 013: 6 changed, 29 examined... 014: 7 changed, 33 examined... 015: 6 changed, 39 examined... 016: 6 changed, 33 examined... 017: 4 changed, 30 examined... 018: 2 changed, 17 examined... 019: 3 changed, 10 examined... 020: 5 changed, 14 examined... 021: 2 changed, 19 examined... 022: 4 changed, 14 examined... 023: 5 changed, 19 examined... 024: 1 changed, 27 examined... 025: 1 changed, 8 examined... 026: 1 changed, 6 examined... 027: 1 changed, 7 examined... 028: 1 changed, 7 examined... 029: 1 changed, 7 examined... 030: 1 changed, 7 examined... 031: 0 changed, 7 examined... 223 labels changed using aseg 000: 72 total segments, 38 labels (218 vertices) changed 001: 34 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... 1230 vertices marked for relabeling... 1230 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas40.annot... classification took 1 minutes and 10 seconds. #----------------------------------------- #@# Parcellation Stats 3 rh Thu Aug 8 23:21:16 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 sub016 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 825 539 1678 2.803 0.558 0.143 0.058 13 1.1 caudalanteriorcingulate 3459 2269 7161 2.846 0.509 0.130 0.082 59 6.4 caudalmiddlefrontal 3488 2305 5757 2.268 0.457 0.149 0.057 58 8.4 cuneus 719 499 1968 3.209 0.724 0.138 0.051 8 1.6 entorhinal 4652 3113 10238 2.740 0.517 0.144 0.063 88 12.7 fusiform 9665 6411 18366 2.536 0.502 0.144 0.054 176 19.6 inferiorparietal 7469 5086 16763 2.696 0.637 0.149 0.061 201 17.9 inferiortemporal 2357 1539 3956 2.365 0.939 0.161 0.084 70 8.9 isthmuscingulate 9192 5987 16108 2.350 0.476 0.154 0.067 204 26.9 lateraloccipital 5244 3537 11285 2.718 0.679 0.160 0.072 159 16.9 lateralorbitofrontal 5477 3641 8694 2.183 0.605 0.163 0.113 130 16.8 lingual 2886 1874 5726 2.500 0.771 0.157 0.116 106 13.0 medialorbitofrontal 7553 5192 17626 2.749 0.691 0.133 0.044 130 14.0 middletemporal 1246 851 2573 2.668 0.562 0.140 0.051 20 2.6 parahippocampal 3214 1977 5663 2.609 0.492 0.118 0.037 34 5.4 paracentral 3328 2163 6592 2.723 0.477 0.114 0.041 36 4.4 parsopercularis 1436 1011 3342 2.708 0.569 0.159 0.063 29 3.2 parsorbitalis 2973 2006 5940 2.518 0.579 0.132 0.068 92 4.8 parstriangularis 2921 1957 3836 2.062 0.403 0.147 0.059 45 6.8 pericalcarine 8046 5091 13212 2.250 0.539 0.117 0.127 195 12.4 postcentral 2270 1487 4441 2.686 0.708 0.146 0.055 41 5.7 posteriorcingulate 8099 4949 15152 2.780 0.605 0.110 0.149 323 59.6 precentral 6594 4411 12746 2.591 0.537 0.142 0.051 118 13.4 precuneus 1018 656 1863 3.000 0.735 0.120 0.082 126 5.4 rostralanteriorcingulate 5927 3980 11386 2.484 0.480 0.146 0.049 104 12.1 rostralmiddlefrontal 17813 11902 38228 2.763 0.558 0.136 0.047 313 34.8 superiorfrontal 7643 4886 12640 2.319 0.436 0.125 0.040 108 12.1 superiorparietal 7917 5409 19364 3.068 0.662 0.135 0.042 102 13.8 superiortemporal 5709 3860 11375 2.638 0.534 0.136 0.063 113 11.4 supramarginal 719 434 1520 2.912 0.320 0.122 0.046 8 1.2 transversetemporal 3547 2326 7814 3.148 0.923 0.130 0.063 53 8.1 insula #-------------------------------------------- #@# Refine Pial Surfs w/ T2/FLAIR Thu Aug 8 23:21:39 CEST 2013 bbregister --s sub016 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/T2raw.lta --init-fsl --T2 Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/T2raw.dat.log Thu Aug 8 23:21:40 CEST 2013 setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts /opt/freesurfer/5.3.0/bin/bbregister --s sub016 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/template.nii mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/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/sub016/mri/orig/T2raw.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999248, 0.0307568, 0.0236215) j_ras = (0.0317878, 0.9985, 0.0445881) k_ras = (0.0222147, -0.0453054, 0.998726) writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/template.nii... fslregister --s sub016 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/fslregister --dof 6 --fsvol brainmask.mgz Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/reg.init.dat.fslregister.log Thu Aug 8 23:21:45 CEST 2013 --s sub016 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/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/sub016/scripts mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/fslregister/refvol.fslregister.nii mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/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/sub016/mri/brainmask.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.86265e-09, 3.72529e-09) j_ras = (1.86265e-09, 0, -1) k_ras = (-1.97906e-09, 1, -3.72529e-09) writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/fslregister/refvol.fslregister.nii... -------------------------------------- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/fslregister/movvol.fslregister.nii --frame 0 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/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/sub016/mri/transforms/tmp.bbregister.24421/template.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999248, 0.0307568, 0.0236215) j_ras = (0.0317878, 0.9985, 0.0445881) k_ras = (0.0222147, -0.0453054, 0.998726) keeping frame 0 writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/fslregister/movvol.fslregister.nii... Mov determinant is -0.311066 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/fslregister/movvol.fslregister.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/fslregister/reg0.24460.dat --regheader --fslregout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/reg.init.dat.fsl.mat0 --s sub016 --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/sub016/mri/transforms/tmp.bbregister.24421/fslregister/movvol.fslregister.nii reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/fslregister/reg0.24460.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/sub016/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/sub016/mri/transforms/tmp.bbregister.24421/fslregister/movvol.fslregister.nii Tmov: -------------------- -0.700 0.000 0.000 95.886; 0.000 0.000 0.667 -128.000; 0.000 -0.667 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 0.999 -0.031 -0.024 -0.000; 0.022 -0.045 0.999 -0.000; -0.032 -0.998 -0.045 -0.000; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 0.999 -0.031 -0.024 -0.000; 0.022 -0.045 0.999 -0.000; -0.032 -0.998 -0.045 -0.000; 0.000 0.000 0.000 1.000; Determinant 1 subject = sub016 RegMat --------------------------- 0.999 -0.031 -0.024 -0.000; 0.022 -0.045 0.999 -0.000; -0.032 -0.998 -0.045 -0.000; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -0.311066, ref det = -1 Thu Aug 8 23:21:54 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/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/sub016/mri/transforms/tmp.bbregister.24421/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/reg.init.dat.fsl.mat0 Thu Aug 8 23:26:14 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/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/sub016/mri/transforms/tmp.bbregister.24421/reg.init.dat.fsl.mat -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/fslregister/fslmat0.trans.mat -schedule /opt/freesurfer/5.3.0/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s sub016 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/reg.init.dat --fslreg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/reg.init.dat.fsl.mat --noedit tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl ---- FSL registration matrix -------- 0.999 -0.033 -0.022 39.132; -0.023 -0.039 -0.999 265.314; 0.032 0.999 -0.040 0.697; 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/sub016/mri/transforms/tmp.bbregister.24421/template.nii reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/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/sub016/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/sub016/mri/transforms/tmp.bbregister.24421/template.nii Tmov: -------------------- -0.700 0.000 0.000 95.886; 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 = -0.311066, ref det = -1 ---- Input registration matrix (computed) -------- 0.999 -0.032 -0.023 -0.073; 0.022 -0.040 0.999 2.189; -0.033 -0.999 -0.039 -1.621; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 0.999 -0.032 -0.023 -0.073; 0.022 -0.040 0.999 2.189; -0.033 -0.999 -0.039 -1.621; 0.000 0.000 0.000 1.000; Determinant 1 subject = sub016 RegMat --------------------------- 0.999 -0.032 -0.023 -0.073; 0.022 -0.040 0.999 2.189; -0.033 -0.999 -0.039 -1.621; 0.000 0.000 0.000 1.000; Started at Thu Aug 8 23:21:45 CEST 2013 Ended at Thu Aug 8 23:31:55 CEST 2013 fslregister Done To check results, run: tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/reg.init.dat --surf orig mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/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/sub016/scripts mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/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/sub016/mri/transforms/tmp.bbregister.24421/template.nii regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/reg.init.dat subject sub016 dof 6 outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/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 1376727398 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.999 -0.032 -0.023 -0.073; 0.022 -0.040 0.999 2.189; -0.033 -0.999 -0.039 -1.621; 0.000 0.000 0.000 1.000; Loading mov Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 0.991698 1 -25.0 -25.0 25.0 1.017919 2 -25.0 25.0 -25.0 1.014961 3 -25.0 25.0 25.0 1.012154 4 25.0 -25.0 -25.0 1.053511 5 25.0 -25.0 25.0 1.038265 6 25.0 25.0 -25.0 1.025332 7 25.0 25.0 25.0 1.040335 REL: 8 0.497330 8.194174 1.024272 rel = 0.485545 Initial costs ---------------- Number of surface hits 3047 WM Intensity 58.1412 +/- 8.4125 Ctx Intensity 68.1580 +/- 13.9941 Pct Contrast 14.7458 +/- 22.3937 Cost 0.4973 RelCost 0.4855 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9706 0.9706 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.9683 0.9683 0.0 3 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 -4.0000 0.9651 0.9651 0.0 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.8698 0.8698 0.0 21 -4.0000 -4.0000 -4.0000 4.0000 0.0000 -4.0000 0.8503 0.8503 0.0 39 -4.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.8111 0.8111 0.0 120 -4.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.7265 0.7265 0.0 346 0.0000 0.0000 -4.0000 4.0000 0.0000 0.0000 0.7237 0.7237 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.4973 0.4973 0.0 Brute Force -------------------------- Min cost was 0.497330 Number of iterations 729 Search time 2.336000 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 0.058 0.000 0.000 0.000 0.000 0.000 0.4962479741 8 0.173 0.000 0.000 0.000 0.000 0.000 0.4956493570 9 0.150 0.000 0.000 0.000 0.000 0.000 0.4954339777 11 0.148 0.000 0.000 0.000 0.000 0.000 0.4954213621 12 0.144 0.000 0.000 0.000 0.000 0.000 0.4954030878 18 0.144 -1.618 0.000 0.000 0.000 0.000 0.3123496406 23 0.144 -1.481 0.000 0.000 0.000 0.000 0.3072172974 24 0.144 -1.427 0.000 0.000 0.000 0.000 0.3064682236 26 0.144 -1.443 0.000 0.000 0.000 0.000 0.3063398337 27 0.144 -1.442 0.000 0.000 0.000 0.000 0.3063332070 28 0.144 -1.439 0.000 0.000 0.000 0.000 0.3063242057 33 0.144 -1.439 1.000 0.000 0.000 0.000 0.1447468946 38 0.144 -1.439 1.258 0.000 0.000 0.000 0.1406853989 39 0.144 -1.439 1.242 0.000 0.000 0.000 0.1403118087 40 0.144 -1.439 1.178 0.000 0.000 0.000 0.1399896185 42 0.144 -1.439 1.199 0.000 0.000 0.000 0.1397496399 44 0.144 -1.439 1.200 0.000 0.000 0.000 0.1397479461 57 0.144 -1.439 1.200 0.009 0.000 0.000 0.1395871869 58 0.144 -1.439 1.200 0.011 0.000 0.000 0.1395814210 67 0.144 -1.439 1.200 0.011 -0.164 0.000 0.1379313531 68 0.144 -1.439 1.200 0.011 -0.132 0.000 0.1376534846 69 0.144 -1.439 1.200 0.011 -0.118 0.000 0.1373763056 71 0.144 -1.439 1.200 0.011 -0.103 0.000 0.1372832564 80 0.144 -1.439 1.200 0.011 -0.103 0.119 0.1361960394 81 0.144 -1.439 1.200 0.011 -0.103 0.101 0.1360196246 82 0.144 -1.439 1.200 0.011 -0.103 0.083 0.1359179116 84 0.144 -1.439 1.200 0.011 -0.103 0.079 0.1359153918 85 0.144 -1.439 1.200 0.011 -0.103 0.080 0.1359150338 97 0.151 -1.439 1.200 0.011 -0.103 0.080 0.1359105495 98 0.149 -1.439 1.200 0.011 -0.103 0.080 0.1359064688 99 0.148 -1.439 1.200 0.011 -0.103 0.080 0.1359061504 107 0.148 -1.462 1.200 0.011 -0.103 0.080 0.1354371527 109 0.148 -1.526 1.200 0.011 -0.103 0.080 0.1348476725 110 0.148 -1.545 1.200 0.011 -0.103 0.080 0.1346955371 111 0.148 -1.577 1.200 0.011 -0.103 0.080 0.1345269131 113 0.148 -1.565 1.200 0.011 -0.103 0.080 0.1345157736 114 0.148 -1.570 1.200 0.011 -0.103 0.080 0.1345017495 115 0.148 -1.571 1.200 0.011 -0.103 0.080 0.1345011534 124 0.148 -1.571 1.153 0.011 -0.103 0.080 0.1344975072 125 0.148 -1.571 1.176 0.011 -0.103 0.080 0.1343772027 127 0.148 -1.571 1.171 0.011 -0.103 0.080 0.1343579904 129 0.148 -1.571 1.169 0.011 -0.103 0.080 0.1343552516 141 0.148 -1.571 1.169 0.010 -0.103 0.080 0.1343542902 150 0.148 -1.571 1.169 0.010 -0.131 0.080 0.1339936964 152 0.148 -1.571 1.169 0.010 -0.132 0.080 0.1339928523 162 0.148 -1.571 1.169 0.010 -0.132 0.045 0.1339816050 163 0.148 -1.571 1.169 0.010 -0.132 0.062 0.1338638798 166 0.148 -1.571 1.169 0.010 -0.132 0.064 0.1338620199 175 0.141 -1.571 1.169 0.010 -0.132 0.064 0.1337887306 179 0.138 -1.571 1.169 0.010 -0.132 0.064 0.1337767557 191 0.138 -1.582 1.169 0.010 -0.132 0.064 0.1337187231 193 0.138 -1.581 1.169 0.010 -0.132 0.064 0.1337185913 206 0.138 -1.581 1.164 0.010 -0.132 0.064 0.1336990090 208 0.138 -1.581 1.163 0.010 -0.132 0.064 0.1336987668 218 0.138 -1.581 1.163 0.012 -0.132 0.064 0.1336981293 241 0.138 -1.581 1.163 0.012 -0.132 0.048 0.1336249538 244 0.128 -1.592 1.156 0.014 -0.132 0.033 0.1335438535 251 0.129 -1.591 1.157 0.014 -0.132 0.034 0.1335415787 252 0.129 -1.590 1.157 0.014 -0.132 0.035 0.1335407690 257 0.129 -1.590 1.157 0.014 -0.132 0.035 0.1335407147 261 0.129 -1.590 1.157 0.014 -0.132 0.035 0.1335406048 270 0.129 -1.590 1.157 0.014 -0.132 0.038 0.1335310703 272 0.129 -1.590 1.157 0.014 -0.132 0.040 0.1335282673 273 0.129 -1.590 1.157 0.014 -0.132 0.041 0.1335277339 282 0.129 -1.581 1.157 0.014 -0.132 0.041 0.1334871275 283 0.129 -1.579 1.157 0.014 -0.132 0.041 0.1334814295 287 0.129 -1.577 1.157 0.014 -0.132 0.041 0.1334805825 301 0.129 -1.577 1.152 0.014 -0.132 0.041 0.1334726852 312 0.129 -1.577 1.152 0.015 -0.132 0.041 0.1334665716 313 0.129 -1.577 1.152 0.017 -0.132 0.041 0.1334652903 324 0.129 -1.577 1.152 0.017 -0.135 0.041 0.1334594948 328 0.120 -1.588 1.146 0.019 -0.135 0.026 0.1334288625 332 0.123 -1.584 1.149 0.018 -0.135 0.031 0.1334217989 334 0.123 -1.584 1.148 0.018 -0.135 0.031 0.1334216584 339 0.123 -1.584 1.149 0.018 -0.135 0.031 0.1334215674 341 0.123 -1.584 1.149 0.018 -0.135 0.031 0.1334214761 344 0.109 -1.587 1.134 0.024 -0.137 0.014 0.1333468299 351 0.107 -1.588 1.133 0.025 -0.138 0.012 0.1333424901 352 0.106 -1.588 1.132 0.026 -0.138 0.011 0.1333423748 353 0.106 -1.588 1.132 0.025 -0.138 0.011 0.1333422128 354 0.106 -1.588 1.132 0.025 -0.138 0.011 0.1333421542 374 0.112 -1.581 1.136 0.024 -0.138 0.021 0.1333064110 380 0.112 -1.581 1.136 0.024 -0.138 0.021 0.1333063697 411 0.112 -1.581 1.136 0.022 -0.138 0.021 0.1332996639 421 0.112 -1.581 1.136 0.022 -0.137 0.021 0.1332967946 422 0.112 -1.581 1.136 0.022 -0.135 0.021 0.1332967036 430 0.107 -1.582 1.131 0.025 -0.136 0.014 0.1332811809 431 0.106 -1.582 1.130 0.025 -0.136 0.013 0.1332794866 434 0.106 -1.582 1.130 0.025 -0.136 0.013 0.1332792467 451 0.106 -1.582 1.130 0.025 -0.136 0.011 0.1332780862 459 0.108 -1.579 1.131 0.025 -0.136 0.015 0.1332721868 460 0.108 -1.580 1.131 0.025 -0.136 0.015 0.1332718205 461 0.108 -1.580 1.131 0.025 -0.136 0.014 0.1332717118 470 0.108 -1.580 1.131 0.025 -0.136 0.014 0.1332716711 482 0.108 -1.580 1.139 0.025 -0.136 0.014 0.1332685167 483 0.108 -1.580 1.135 0.025 -0.136 0.014 0.1332621981 494 0.108 -1.580 1.135 0.022 -0.136 0.014 0.1332613604 496 0.108 -1.580 1.135 0.023 -0.136 0.014 0.1332588580 508 0.108 -1.580 1.135 0.023 -0.137 0.014 0.1332585011 514 0.102 -1.581 1.130 0.025 -0.138 0.008 0.1332576465 515 0.105 -1.581 1.133 0.024 -0.138 0.011 0.1332523634 516 0.105 -1.581 1.133 0.024 -0.138 0.011 0.1332522537 518 0.105 -1.581 1.133 0.024 -0.138 0.011 0.1332522008 526 0.105 -1.579 1.136 0.023 -0.139 0.009 0.1332483876 586 0.106 -1.580 1.136 0.023 -0.135 0.013 0.1332471225 587 0.106 -1.580 1.136 0.023 -0.136 0.013 0.1332467187 594 0.103 -1.581 1.133 0.024 -0.137 0.010 0.1332410557 Powell done niters = 6 Computing relative cost 0 -25.0 -25.0 -25.0 0.987108 1 -25.0 -25.0 25.0 1.009174 2 -25.0 25.0 -25.0 0.994077 3 -25.0 25.0 25.0 1.024224 4 25.0 -25.0 -25.0 1.032857 5 25.0 -25.0 25.0 1.005481 6 25.0 25.0 -25.0 0.980632 7 25.0 25.0 25.0 1.024402 REL: 8 0.133241 8.057954 1.007244 rel = 0.132283 Number of iterations 6 Min cost was 0.133241 Number of FunctionCalls 602 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 1.771000 sec Parameters at optimum (transmm) 0.10308 -1.58084 1.13322 Parameters at optimum (rotdeg) 0.02365 -0.13659 0.00979 Final costs ---------------- Number of surface hits 3047 WM Intensity 56.4536 +/- 7.1833 Ctx Intensity 67.5397 +/- 7.6173 Pct Contrast 17.8999 +/- 12.3774 Cost 0.1332 RelCost 0.4855 Reg at min cost was 0.999 -0.029 -0.023 0.034; 0.022 -0.039 0.999 0.608; -0.030 -0.999 -0.039 -0.487; 0.000 0.000 0.000 1.000; Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/bbr.pass1.dat, type = 14 Original Reg 0.999 -0.032 -0.023 -0.073; 0.022 -0.040 0.999 2.189; -0.033 -0.999 -0.039 -1.621; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.000 -0.002 0.000 -0.107; -0.000 -0.000 -0.000 1.580; -0.002 0.000 -0.000 -1.134; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 1.928128 Computing change in rh position Surface RMS Diff (mm) 1.965314 2.053568 mri_segreg done mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/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/sub016/scripts mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/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/sub016/mri/transforms/tmp.bbregister.24421/template.nii regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/bbr.pass1.dat subject sub016 dof 6 outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 1376990004 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.999 -0.029 -0.023 0.034; 0.022 -0.039 0.999 0.608; -0.030 -0.999 -0.039 -0.487; 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 1.013674 1 -25.0 -25.0 25.0 0.994273 2 -25.0 25.0 -25.0 0.995462 3 -25.0 25.0 25.0 1.013802 4 25.0 -25.0 -25.0 1.027246 5 25.0 -25.0 25.0 1.007479 6 25.0 25.0 -25.0 0.998557 7 25.0 25.0 25.0 1.024932 REL: 8 0.141688 8.075426 1.009428 rel = 0.140364 Initial costs ---------------- Number of surface hits 304481 WM Intensity 56.5409 +/- 7.1624 Ctx Intensity 67.6348 +/- 7.7629 Pct Contrast 17.8592 +/- 12.5660 Cost 0.1417 RelCost 0.1404 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1471 0.1471 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.1459 0.1459 0.0 9 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 -0.1000 0.1439 0.1439 0.0 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.1434 0.1434 0.0 13 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.1426 0.1426 0.0 22 -0.1000 -0.1000 -0.1000 0.1000 0.0000 0.0000 0.1399 0.1399 0.0 39 -0.1000 -0.1000 0.0000 0.0000 0.0000 -0.1000 0.1396 0.1396 0.0 40 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.0000 0.1377 0.1377 0.0 49 -0.1000 -0.1000 0.0000 0.1000 0.0000 0.0000 0.1362 0.1362 0.0 67 -0.1000 -0.1000 0.1000 0.0000 0.0000 0.0000 0.1344 0.1344 0.0 130 -0.1000 0.0000 0.0000 0.1000 0.0000 0.0000 0.1344 0.1344 0.0 148 -0.1000 0.0000 0.1000 0.0000 0.0000 0.0000 0.1342 0.1342 0.0 157 -0.1000 0.0000 0.1000 0.1000 0.0000 0.0000 0.1342 0.1342 0.0 211 -0.1000 0.1000 0.0000 0.1000 0.0000 0.0000 0.1332 0.1332 0.0 Brute Force -------------------------- Min cost was 0.133165 Number of iterations 729 Search time 2.128000 sec Parameters at best (transmm, rotdeg) -0.100 0.100 0.000 0.100 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 -0.1 1 0.1 2 0 3 0.1 4 0 5 0 7 -0.040 0.100 0.000 0.100 0.000 0.000 0.1383786066 8 -0.060 0.100 0.000 0.100 0.000 0.000 0.1383350291 10 -0.059 0.100 0.000 0.100 0.000 0.000 0.1383349480 19 -0.059 0.196 0.000 0.100 0.000 0.000 0.1372708911 28 -0.059 0.196 0.126 0.100 0.000 0.000 0.1360247476 29 -0.059 0.196 0.120 0.100 0.000 0.000 0.1360163550 30 -0.059 0.196 0.116 0.100 0.000 0.000 0.1360147204 39 -0.059 0.196 0.116 0.051 0.000 0.000 0.1354389563 40 -0.059 0.196 0.116 0.044 0.000 0.000 0.1354184637 41 -0.059 0.196 0.116 0.038 0.000 0.000 0.1354155472 42 -0.059 0.196 0.116 0.040 0.000 0.000 0.1354152911 50 -0.059 0.196 0.116 0.040 -0.061 0.000 0.1348322987 52 -0.059 0.196 0.116 0.040 -0.065 0.000 0.1348295650 53 -0.059 0.196 0.116 0.040 -0.064 0.000 0.1348295083 61 -0.059 0.196 0.116 0.040 -0.064 0.015 0.1348115263 62 -0.059 0.196 0.116 0.040 -0.064 0.013 0.1348100653 63 -0.059 0.196 0.116 0.040 -0.064 0.012 0.1348097944 72 -0.023 0.196 0.116 0.040 -0.064 0.012 0.1347987256 73 -0.039 0.196 0.116 0.040 -0.064 0.012 0.1347666581 83 -0.039 0.189 0.116 0.040 -0.064 0.012 0.1347613712 92 -0.039 0.189 0.182 0.040 -0.064 0.012 0.1345687690 93 -0.039 0.189 0.167 0.040 -0.064 0.012 0.1345484474 95 -0.039 0.189 0.162 0.040 -0.064 0.012 0.1345484171 97 -0.039 0.189 0.164 0.040 -0.064 0.012 0.1345479816 106 -0.039 0.189 0.164 0.026 -0.064 0.012 0.1344668773 107 -0.039 0.189 0.164 0.016 -0.064 0.012 0.1344402774 108 -0.039 0.189 0.164 0.012 -0.064 0.012 0.1344367260 117 -0.039 0.189 0.164 0.012 -0.067 0.012 0.1344335818 118 -0.039 0.189 0.164 0.012 -0.071 0.012 0.1344296615 120 -0.039 0.189 0.164 0.012 -0.076 0.012 0.1344282299 122 -0.039 0.189 0.164 0.012 -0.075 0.012 0.1344281565 130 -0.039 0.189 0.164 0.012 -0.075 0.026 0.1344084441 131 -0.039 0.189 0.164 0.012 -0.075 0.025 0.1344074875 132 -0.039 0.189 0.164 0.012 -0.075 0.023 0.1344071491 134 -0.019 0.182 0.212 -0.015 -0.085 0.035 0.1343182007 140 -0.027 0.185 0.194 -0.005 -0.081 0.030 0.1343139430 141 -0.024 0.184 0.201 -0.009 -0.083 0.032 0.1343115115 142 -0.024 0.184 0.201 -0.009 -0.082 0.032 0.1343114196 144 -0.024 0.184 0.200 -0.009 -0.082 0.032 0.1343114161 145 -0.024 0.184 0.201 -0.009 -0.082 0.032 0.1343113993 146 -0.024 0.184 0.201 -0.009 -0.082 0.032 0.1343113763 156 -0.023 0.184 0.201 -0.009 -0.082 0.032 0.1343113219 165 -0.023 0.168 0.201 -0.009 -0.082 0.032 0.1342921102 168 -0.023 0.169 0.201 -0.009 -0.082 0.032 0.1342919357 186 -0.023 0.169 0.201 -0.010 -0.082 0.032 0.1342918736 194 -0.023 0.169 0.201 -0.010 -0.077 0.032 0.1342895233 196 -0.023 0.169 0.201 -0.010 -0.076 0.032 0.1342893447 204 -0.016 0.167 0.219 -0.020 -0.080 0.036 0.1342801141 205 -0.017 0.167 0.215 -0.018 -0.079 0.035 0.1342795104 206 -0.017 0.167 0.215 -0.018 -0.079 0.035 0.1342794935 207 -0.017 0.167 0.215 -0.018 -0.079 0.035 0.1342794915 208 -0.017 0.167 0.215 -0.018 -0.079 0.035 0.1342794695 220 -0.018 0.167 0.215 -0.018 -0.079 0.035 0.1342793241 228 -0.018 0.166 0.215 -0.018 -0.079 0.035 0.1342780381 229 -0.018 0.163 0.215 -0.018 -0.079 0.035 0.1342773814 231 -0.018 0.164 0.215 -0.018 -0.079 0.035 0.1342773395 240 -0.018 0.164 0.215 -0.018 -0.079 0.034 0.1342769522 251 -0.018 0.164 0.215 -0.014 -0.079 0.034 0.1342747860 269 -0.017 0.163 0.219 -0.016 -0.080 0.035 0.1342731830 270 -0.016 0.163 0.220 -0.017 -0.080 0.035 0.1342730505 271 -0.016 0.163 0.220 -0.017 -0.080 0.035 0.1342730021 274 -0.016 0.163 0.221 -0.017 -0.080 0.036 0.1342729395 288 -0.018 0.163 0.221 -0.017 -0.080 0.036 0.1342724065 306 -0.018 0.163 0.221 -0.017 -0.080 0.034 0.1342722990 307 -0.018 0.163 0.221 -0.017 -0.080 0.033 0.1342721992 321 -0.018 0.163 0.221 -0.016 -0.080 0.033 0.1342720073 330 -0.018 0.163 0.221 -0.016 -0.078 0.033 0.1342712016 341 -0.018 0.163 0.222 -0.017 -0.078 0.033 0.1342711738 344 -0.018 0.163 0.222 -0.017 -0.078 0.033 0.1342711728 357 -0.020 0.163 0.222 -0.017 -0.078 0.033 0.1342708052 366 -0.020 0.164 0.222 -0.017 -0.078 0.033 0.1342707798 375 -0.020 0.164 0.222 -0.017 -0.078 0.032 0.1342707229 384 -0.020 0.164 0.222 -0.016 -0.078 0.032 0.1342706602 393 -0.020 0.164 0.222 -0.016 -0.077 0.032 0.1342704408 417 -0.021 0.164 0.222 -0.016 -0.077 0.032 0.1342703886 454 -0.021 0.164 0.222 -0.016 -0.076 0.032 0.1342703700 466 -0.021 0.164 0.222 -0.016 -0.076 0.032 0.1342703523 Powell done niters = 7 Computing relative cost 0 -25.0 -25.0 -25.0 1.014724 1 -25.0 -25.0 25.0 0.993885 2 -25.0 25.0 -25.0 0.993645 3 -25.0 25.0 25.0 1.012720 4 25.0 -25.0 -25.0 1.028029 5 25.0 -25.0 25.0 1.005782 6 25.0 25.0 -25.0 0.999341 7 25.0 25.0 25.0 1.024793 REL: 8 0.134270 8.072920 1.009115 rel = 0.133058 Number of iterations 7 Min cost was 0.134270 Number of FunctionCalls 527 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 69.051000 sec Parameters at optimum (transmm) -0.02074 0.16374 0.22181 Parameters at optimum (rotdeg) -0.01581 -0.07641 0.03234 Final costs ---------------- Number of surface hits 304481 WM Intensity 56.5318 +/- 7.1402 Ctx Intensity 67.5968 +/- 7.7119 Pct Contrast 17.8233 +/- 12.4061 Cost 0.1343 RelCost 0.1404 Reg at min cost was 0.999 -0.028 -0.023 0.013; 0.022 -0.040 0.999 0.772; -0.029 -0.999 -0.039 -0.265; 0.000 0.000 0.000 1.000; Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/T2raw.dat, type = 14 Original Reg 0.999 -0.029 -0.023 0.034; 0.022 -0.039 0.999 0.608; -0.030 -0.999 -0.039 -0.487; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.000 -0.001 0.001 0.020; -0.001 0.000 0.000 -0.164; -0.001 0.000 0.000 -0.222; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.244708 Computing change in rh position Surface RMS Diff (mm) 0.284066 0.379271 mri_segreg done tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/T2raw.dat --noedit --ltaout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/mri/orig/T2raw.mgz reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/T2raw.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- 0.999 -0.028 -0.023 0.013; 0.022 -0.040 0.999 0.772; -0.029 -0.999 -0.039 -0.265; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- INFO: loading target /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/mri/orig/T2raw.mgz Tmov: -------------------- -0.700 0.000 0.000 95.886; 0.000 0.000 0.667 -128.000; 0.000 -0.667 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 0.999 -0.028 -0.023 0.013; 0.022 -0.040 0.999 0.772; -0.029 -0.999 -0.039 -0.265; 0.000 0.000 0.000 1.000; Determinant 1 subject = sub016 RegMat --------------------------- 0.999 -0.028 -0.023 0.013; 0.022 -0.040 0.999 0.772; -0.029 -0.999 -0.039 -0.265; 0.000 0.000 0.000 1.000; transformed matrix: 1.000 -0.003 -0.000 0.059; 0.003 1.000 0.006 -0.142; 0.000 -0.006 1.000 -0.599; 0.000 0.000 0.000 1.000; transformed matrix: 0.699 -0.019 -0.015 38.752; -0.016 -0.026 -0.666 263.892; 0.020 0.666 -0.026 2.326; 0.000 0.000 0.000 1.000; Cleaning up Started at Thu Aug 8 23:21:39 CEST 2013 Ended at Thu Aug 8 23:33:58 CEST 2013 BBR-Run-Time-Sec 739 bbregister Done To check results, run: tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/T2raw.dat --surf mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/T2.mgz mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/mri/orig/T2raw.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999248, 0.0307568, 0.0236215) j_ras = (0.0317878, 0.9985, 0.0445881) k_ras = (0.0222147, -0.0453054, 0.998726) INFO: Reading transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/T2raw.lta... Reading transform with LTAreadEx() reading extra input line subject sub016 reading extra input line fscale 0.150000 reading template info from volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig.mgz... INFO: Applying transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/T2raw.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 1.000 -0.003 -0.000 0.059; 0.003 1.000 0.006 -0.142; 0.000 -0.006 1.000 -0.599; 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/sub016/mri/T2.mgz... mri_normalize -aseg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/aseg.mgz -sigma 4 -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.white identity.nofile -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.white identity.nofile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/T2.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/mri/T2.mgz... computing distance transform computing distance transform computing nonmaximum suppression 15456 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/sub016/mri/T2.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.woT2.pial `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.woT2.pial' mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub016 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/sub016/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz... 22234 bright wm thresholded. 384 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.orig... computing class statistics... border white: 298969 voxels (1.78%) border gray 333863 voxels (1.99%) WM (93.0): 93.9 +- 9.8 [70.0 --> 110.0] GM (77.0) : 75.0 +- 12.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 49.4 (was 70) setting MAX_BORDER_WHITE to 115.8 (was 105) setting MIN_BORDER_WHITE to 62.0 (was 85) setting MAX_CSF to 36.9 (was 40) setting MAX_GRAY to 96.2 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 55.7 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 24.3 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=106, GM=62 mean inside = 93.8, mean outside = 70.2 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/sub016/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.89 +- 0.26 (0.03-->5.11) (max @ vno 160099 --> 160100) face area 0.33 +- 0.16 (0.00-->5.68) averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 247 points - only 4.05% unknown deleting segment 1 with 5 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 3 with 2 points - only 0.00% unknown deleting segment 4 with 5 points - only 0.00% unknown deleting segment 6 with 6 points - only 0.00% unknown deleting segment 7 with 881 points - only 0.00% unknown deleting segment 8 with 7 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 12 with 37 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 2 vertex label from ripped group deleting segment 15 with 2 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 5 points - only 0.00% unknown tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.89 +- 0.25 (0.03-->4.83) (max @ vno 160104 --> 70416) face area 0.33 +- 0.16 (0.00-->5.68) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4771560.0, rms=0.00 rms = 1.14, time step reduction 1 of 3 to 0.250... rms = 0.29, time step reduction 2 of 3 to 0.125... rms = 0.04, time step reduction 3 of 3 to 0.062... 001: dt: 0.1250, sse=4771560.0, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 247 points - only 4.05% unknown deleting segment 1 with 5 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown deleting segment 4 with 6 points - only 0.00% unknown deleting segment 5 with 881 points - only 0.00% unknown deleting segment 6 with 7 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 9 with 37 points - only 0.00% unknown deleting segment 10 with 8 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 11 with 1 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 12 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 13 with 3 points - only 0.00% unknown deleting segment 14 with 5 points - only 0.00% unknown tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.89 +- 0.25 (0.03-->4.83) (max @ vno 160104 --> 70416) face area 0.33 +- 0.16 (0.00-->5.68) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4771560.0, rms=0.00 rms = 1.14, time step reduction 1 of 3 to 0.250... rms = 0.29, time step reduction 2 of 3 to 0.125... rms = 0.04, time step reduction 3 of 3 to 0.062... 002: dt: 0.1250, sse=4771560.0, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 247 points - only 4.05% unknown deleting segment 1 with 5 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown deleting segment 4 with 6 points - only 0.00% unknown deleting segment 5 with 881 points - only 0.00% unknown deleting segment 6 with 7 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 9 with 37 points - only 0.00% unknown deleting segment 10 with 8 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 11 with 1 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 12 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 13 with 3 points - only 0.00% unknown deleting segment 14 with 5 points - only 0.00% unknown tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.03-->4.83) (max @ vno 160104 --> 70416) face area 0.33 +- 0.16 (0.00-->5.68) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4771560.0, rms=0.00 rms = 1.14, time step reduction 1 of 3 to 0.250... rms = 0.29, time step reduction 2 of 3 to 0.125... rms = 0.04, time step reduction 3 of 3 to 0.062... 003: dt: 0.1250, sse=4771560.0, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 247 points - only 4.05% unknown deleting segment 1 with 5 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown deleting segment 4 with 6 points - only 0.00% unknown deleting segment 5 with 881 points - only 0.00% unknown deleting segment 6 with 7 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 9 with 37 points - only 0.00% unknown deleting segment 10 with 8 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 11 with 1 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 12 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 13 with 3 points - only 0.00% unknown deleting segment 14 with 5 points - only 0.00% unknown tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4771560.0, rms=0.00 rms = 1.14, time step reduction 1 of 3 to 0.250... rms = 0.29, time step reduction 2 of 3 to 0.125... rms = 0.04, time step reduction 3 of 3 to 0.062... 004: dt: 0.1250, sse=4771560.0, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 7 points - only 0.00% unknown removing 1 vertex label from ripped group smoothing surface for 5 iterations... reading initial pial vertex positions from woT2.pial... repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [90.50 201.50], gm=146.00+-18.50, and vertices in regions > 136.7 54026 surface locations found to contain inconsistent values (5139 in, 48887 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=562411.2, rms=0.25 001: dt: 0.5000, sse=527796.3, rms=0.244 (0.000%) 002: dt: 0.5000, sse=506658.5, rms=0.230 (0.000%) 003: dt: 0.5000, sse=493634.9, rms=0.220 (0.000%) 004: dt: 0.5000, sse=483524.0, rms=0.210 (0.000%) 005: dt: 0.5000, sse=476287.5, rms=0.202 (0.000%) 006: dt: 0.5000, sse=470805.8, rms=0.195 (0.000%) 007: dt: 0.5000, sse=466676.5, rms=0.188 (0.000%) 008: dt: 0.5000, sse=463023.4, rms=0.183 (0.000%) 009: dt: 0.5000, sse=460242.7, rms=0.178 (0.000%) 010: dt: 0.5000, sse=457962.3, rms=0.174 (0.000%) 011: dt: 0.5000, sse=456483.0, rms=0.170 (0.000%) 012: dt: 0.5000, sse=454198.5, rms=0.166 (0.000%) 013: dt: 0.5000, sse=452938.7, rms=0.163 (0.000%) 014: dt: 0.5000, sse=451551.8, rms=0.161 (0.000%) 015: dt: 0.5000, sse=450075.8, rms=0.158 (0.000%) 016: dt: 0.5000, sse=448673.4, rms=0.156 (0.000%) 017: dt: 0.5000, sse=447105.9, rms=0.154 (0.000%) 018: dt: 0.5000, sse=445862.4, rms=0.152 (0.000%) 019: dt: 0.5000, sse=444415.1, rms=0.151 (0.000%) 020: dt: 0.5000, sse=442952.5, rms=0.149 (0.000%) 021: dt: 0.5000, sse=442219.8, rms=0.148 (0.000%) 022: dt: 0.5000, sse=440692.2, rms=0.147 (0.000%) 023: dt: 0.5000, sse=439257.3, rms=0.146 (0.000%) 024: dt: 0.5000, sse=438124.2, rms=0.145 (0.000%) 025: dt: 0.5000, sse=436748.1, rms=0.144 (0.000%) 026: dt: 0.5000, sse=435682.4, rms=0.144 (0.000%) 027: dt: 0.5000, sse=434302.8, rms=0.143 (0.000%) 028: dt: 0.5000, sse=433407.2, rms=0.143 (0.000%) 029: dt: 0.5000, sse=432330.4, rms=0.142 (0.000%) 030: dt: 0.5000, sse=431423.0, rms=0.142 (0.000%) positioning took 4.3 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [89.00 203.00], gm=146.00+-19.00, and vertices in regions > 136.5 45632 surface locations found to contain inconsistent values (2102 in, 43530 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=45237.0, rms=0.13 031: dt: 0.5000, sse=44966.7, rms=0.127 (0.000%) 032: dt: 0.5000, sse=46114.0, rms=0.117 (0.000%) 033: dt: 0.5000, sse=47380.2, rms=0.110 (0.000%) 034: dt: 0.5000, sse=48373.9, rms=0.105 (0.000%) 035: dt: 0.5000, sse=49166.3, rms=0.100 (0.000%) 036: dt: 0.5000, sse=49909.8, rms=0.095 (0.000%) 037: dt: 0.5000, sse=50589.5, rms=0.091 (0.000%) 038: dt: 0.5000, sse=51284.1, rms=0.087 (0.000%) 039: dt: 0.5000, sse=51925.8, rms=0.084 (0.000%) 040: dt: 0.5000, sse=52511.0, rms=0.080 (0.000%) 041: dt: 0.5000, sse=53114.1, rms=0.077 (0.000%) 042: dt: 0.5000, sse=53633.8, rms=0.074 (0.000%) 043: dt: 0.5000, sse=54133.5, rms=0.071 (0.000%) 044: dt: 0.5000, sse=54613.6, rms=0.069 (0.000%) 045: dt: 0.5000, sse=55071.5, rms=0.066 (0.000%) 046: dt: 0.5000, sse=55508.4, rms=0.064 (0.000%) 047: dt: 0.5000, sse=55901.6, rms=0.062 (0.000%) 048: dt: 0.5000, sse=56286.2, rms=0.060 (0.000%) 049: dt: 0.5000, sse=56608.5, rms=0.058 (0.000%) 050: dt: 0.5000, sse=56914.4, rms=0.056 (0.000%) 051: dt: 0.5000, sse=57187.7, rms=0.054 (0.000%) 052: dt: 0.5000, sse=57457.3, rms=0.053 (0.000%) 053: dt: 0.5000, sse=57711.3, rms=0.051 (0.000%) 054: dt: 0.5000, sse=57931.1, rms=0.050 (0.000%) 055: dt: 0.5000, sse=58145.2, rms=0.049 (0.000%) 056: dt: 0.5000, sse=58316.2, rms=0.048 (0.000%) 057: dt: 0.5000, sse=58474.2, rms=0.047 (0.000%) 058: dt: 0.5000, sse=58636.4, rms=0.045 (0.000%) 059: dt: 0.5000, sse=58802.0, rms=0.045 (0.000%) 060: dt: 0.5000, sse=58943.7, rms=0.044 (0.000%) positioning took 4.2 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [87.50 204.50], gm=146.00+-19.50, and vertices in regions > 136.2 44528 surface locations found to contain inconsistent values (409 in, 44119 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=6391.9, rms=0.06 061: dt: 0.5000, sse=6374.1, rms=0.056 (0.000%) 062: dt: 0.5000, sse=6430.7, rms=0.050 (0.000%) 063: dt: 0.5000, sse=6488.5, rms=0.047 (0.000%) 064: dt: 0.5000, sse=6531.4, rms=0.045 (0.000%) 065: dt: 0.5000, sse=6554.4, rms=0.043 (0.000%) 066: dt: 0.5000, sse=6563.4, rms=0.041 (0.000%) 067: dt: 0.5000, sse=6572.1, rms=0.040 (0.000%) 068: dt: 0.5000, sse=6573.9, rms=0.039 (0.000%) 069: dt: 0.5000, sse=6574.2, rms=0.038 (0.000%) 070: dt: 0.5000, sse=6576.4, rms=0.036 (0.000%) 071: dt: 0.5000, sse=6576.7, rms=0.035 (0.000%) 072: dt: 0.5000, sse=6579.1, rms=0.035 (0.000%) 073: dt: 0.5000, sse=6580.4, rms=0.034 (0.000%) 074: dt: 0.5000, sse=6582.4, rms=0.033 (0.000%) 075: dt: 0.5000, sse=6582.9, rms=0.032 (0.000%) 076: dt: 0.5000, sse=6584.1, rms=0.031 (0.000%) 077: dt: 0.5000, sse=6586.4, rms=0.031 (0.000%) 078: dt: 0.5000, sse=6588.9, rms=0.030 (0.000%) 079: dt: 0.5000, sse=6589.1, rms=0.030 (0.000%) 080: dt: 0.5000, sse=6590.0, rms=0.029 (0.000%) 081: dt: 0.5000, sse=6594.9, rms=0.029 (0.000%) 082: dt: 0.5000, sse=6596.0, rms=0.028 (0.000%) 083: dt: 0.5000, sse=6596.7, rms=0.028 (0.000%) 084: dt: 0.5000, sse=6599.7, rms=0.028 (0.000%) 085: dt: 0.5000, sse=6600.9, rms=0.027 (0.000%) 086: dt: 0.5000, sse=6604.3, rms=0.027 (0.000%) 087: dt: 0.5000, sse=6604.2, rms=0.027 (0.000%) 088: dt: 0.5000, sse=6605.7, rms=0.027 (0.000%) 089: dt: 0.5000, sse=6606.5, rms=0.026 (0.000%) 090: dt: 0.5000, sse=6611.2, rms=0.026 (0.000%) positioning took 4.3 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [87.50 204.50], gm=146.00+-19.50, and vertices in regions > 136.2 44069 surface locations found to contain inconsistent values (113 in, 43956 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/sub016/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=814.6, rms=0.03 091: dt: 0.5000, sse=813.8, rms=0.032 (0.000%) 092: dt: 0.5000, sse=803.1, rms=0.031 (0.000%) 093: dt: 0.5000, sse=793.9, rms=0.030 (0.000%) 094: dt: 0.5000, sse=786.1, rms=0.029 (0.000%) 095: dt: 0.5000, sse=779.1, rms=0.028 (0.000%) 096: dt: 0.5000, sse=773.7, rms=0.028 (0.000%) 097: dt: 0.5000, sse=769.7, rms=0.027 (0.000%) 098: dt: 0.5000, sse=767.7, rms=0.027 (0.000%) 099: dt: 0.5000, sse=764.6, rms=0.027 (0.000%) 100: dt: 0.5000, sse=761.1, rms=0.026 (0.000%) 101: dt: 0.5000, sse=759.5, rms=0.026 (0.000%) 102: dt: 0.5000, sse=758.9, rms=0.026 (0.000%) 103: dt: 0.5000, sse=755.6, rms=0.025 (0.000%) 104: dt: 0.5000, sse=752.5, rms=0.025 (0.000%) 105: dt: 0.5000, sse=750.5, rms=0.025 (0.000%) 106: dt: 0.5000, sse=748.2, rms=0.024 (0.000%) 107: dt: 0.5000, sse=746.3, rms=0.024 (0.000%) 108: dt: 0.5000, sse=744.5, rms=0.024 (0.000%) 109: dt: 0.5000, sse=745.6, rms=0.024 (0.000%) 110: dt: 0.5000, sse=743.9, rms=0.024 (0.000%) 111: dt: 0.5000, sse=742.1, rms=0.024 (0.000%) 112: dt: 0.5000, sse=742.7, rms=0.024 (0.000%) 113: dt: 0.5000, sse=743.1, rms=0.024 (0.000%) 114: dt: 0.5000, sse=742.2, rms=0.024 (0.000%) 115: dt: 0.5000, sse=740.9, rms=0.023 (0.000%) 116: dt: 0.5000, sse=739.1, rms=0.023 (0.000%) 117: dt: 0.5000, sse=738.5, rms=0.023 (0.000%) 118: dt: 0.5000, sse=739.1, rms=0.023 (0.000%) 119: dt: 0.5000, sse=738.0, rms=0.023 (0.000%) 120: dt: 0.5000, sse=740.1, rms=0.023 (0.000%) positioning took 4.2 minutes writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.area.pial vertex spacing 1.02 +- 0.44 (0.05-->7.32) (max @ vno 103206 --> 104423) face area 0.41 +- 0.32 (0.00-->7.45) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 160479 vertices processed 25000 of 160479 vertices processed 50000 of 160479 vertices processed 75000 of 160479 vertices processed 100000 of 160479 vertices processed 125000 of 160479 vertices processed 150000 of 160479 vertices processed 0 of 160479 vertices processed 25000 of 160479 vertices processed 50000 of 160479 vertices processed 75000 of 160479 vertices processed 100000 of 160479 vertices processed 125000 of 160479 vertices processed 150000 of 160479 vertices processed thickness calculation complete, 355:897 truncations. 37984 vertices at 0 distance 109456 vertices at 1 distance 102099 vertices at 2 distance 42033 vertices at 3 distance 12152 vertices at 4 distance 3266 vertices at 5 distance 931 vertices at 6 distance 266 vertices at 7 distance 118 vertices at 8 distance 58 vertices at 9 distance 39 vertices at 10 distance 24 vertices at 11 distance 13 vertices at 12 distance 14 vertices at 13 distance 9 vertices at 14 distance 18 vertices at 15 distance 14 vertices at 16 distance 11 vertices at 17 distance 5 vertices at 18 distance 4 vertices at 19 distance 16 vertices at 20 distance writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.thickness positioning took 20.8 minutes /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.woT2.pial `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.woT2.pial' mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub016 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/sub016/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz... 23684 bright wm thresholded. 383 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.orig... computing class statistics... border white: 298969 voxels (1.78%) border gray 333863 voxels (1.99%) WM (93.0): 94.0 +- 9.8 [70.0 --> 110.0] GM (76.0) : 74.9 +- 12.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 47.3 (was 70) setting MAX_BORDER_WHITE to 114.8 (was 105) setting MIN_BORDER_WHITE to 60.0 (was 85) setting MAX_CSF to 34.5 (was 40) setting MAX_GRAY to 95.2 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 53.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 21.8 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=60 mean inside = 93.5, mean outside = 69.7 smoothing surface for 5 iterations... reading initial white vertex positions from white... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.89 +- 0.26 (0.03-->9.83) (max @ vno 68130 --> 70451) face area 0.33 +- 0.16 (0.00-->6.84) averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 12 points - only 0.00% unknown deleting segment 1 with 21 points - only 0.00% unknown deleting segment 2 with 14 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 5 points - only 0.00% unknown deleting segment 6 with 19 points - only 0.00% unknown deleting segment 8 with 20 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 10 with 3 points - only 0.00% unknown deleting segment 11 with 40 points - only 0.00% unknown deleting segment 12 with 487 points - only 0.00% unknown deleting segment 13 with 6 points - only 0.00% unknown deleting segment 15 with 105 points - only 0.00% unknown removing 2 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 18 with 4 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 19 with 1 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 20 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 21 with 2 points - only 0.00% unknown tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.89 +- 0.25 (0.05-->9.83) (max @ vno 70451 --> 68130) face area 0.33 +- 0.16 (0.00-->6.84) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4833013.5, rms=0.00 rms = 1.31, time step reduction 1 of 3 to 0.250... rms = 0.32, 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=4833013.5, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 12 points - only 0.00% unknown deleting segment 1 with 21 points - only 0.00% unknown deleting segment 2 with 14 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 5 points - only 0.00% unknown deleting segment 5 with 19 points - only 0.00% unknown deleting segment 6 with 20 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 40 points - only 0.00% unknown deleting segment 9 with 487 points - only 0.00% unknown deleting segment 10 with 6 points - only 0.00% unknown deleting segment 11 with 105 points - only 0.00% unknown removing 2 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 13 with 4 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 14 with 1 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 15 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 16 with 2 points - only 0.00% unknown tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.89 +- 0.25 (0.05-->9.83) (max @ vno 70451 --> 68130) face area 0.33 +- 0.16 (0.00-->6.84) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4833013.5, rms=0.00 rms = 1.33, time step reduction 1 of 3 to 0.250... rms = 0.33, 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=4833013.5, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 12 points - only 0.00% unknown deleting segment 1 with 21 points - only 0.00% unknown deleting segment 2 with 14 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 5 points - only 0.00% unknown deleting segment 5 with 19 points - only 0.00% unknown deleting segment 6 with 20 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 40 points - only 0.00% unknown deleting segment 9 with 487 points - only 0.00% unknown deleting segment 10 with 6 points - only 0.00% unknown deleting segment 11 with 105 points - only 0.00% unknown removing 2 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 13 with 4 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 14 with 1 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 15 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 16 with 2 points - only 0.00% unknown tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.05-->9.83) (max @ vno 70451 --> 68130) face area 0.33 +- 0.16 (0.00-->6.84) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4833013.5, rms=0.00 rms = 1.31, time step reduction 1 of 3 to 0.250... rms = 0.32, 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=4833013.5, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 12 points - only 0.00% unknown deleting segment 1 with 21 points - only 0.00% unknown deleting segment 2 with 14 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 5 points - only 0.00% unknown deleting segment 5 with 19 points - only 0.00% unknown deleting segment 6 with 20 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 40 points - only 0.00% unknown deleting segment 9 with 487 points - only 0.00% unknown deleting segment 10 with 6 points - only 0.00% unknown deleting segment 11 with 105 points - only 0.00% unknown removing 2 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 13 with 4 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 14 with 1 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 15 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 16 with 2 points - only 0.00% unknown tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4833013.5, rms=0.00 rms = 1.33, time step reduction 1 of 3 to 0.250... rms = 0.33, 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=4833013.5, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group smoothing surface for 5 iterations... reading initial pial vertex positions from woT2.pial... repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [92.30 205.70], gm=149.00+-18.90, and vertices in regions > 139.5 53781 surface locations found to contain inconsistent values (6053 in, 47728 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=577312.1, rms=0.22 001: dt: 0.5000, sse=540316.5, rms=0.215 (0.000%) 002: dt: 0.5000, sse=518240.6, rms=0.201 (0.000%) 003: dt: 0.5000, sse=504950.8, rms=0.190 (0.000%) 004: dt: 0.5000, sse=494329.2, rms=0.180 (0.000%) 005: dt: 0.5000, sse=487119.2, rms=0.172 (0.000%) 006: dt: 0.5000, sse=481500.6, rms=0.166 (0.000%) 007: dt: 0.5000, sse=476917.7, rms=0.160 (0.000%) 008: dt: 0.5000, sse=473099.1, rms=0.155 (0.000%) 009: dt: 0.5000, sse=470895.4, rms=0.151 (0.000%) 010: dt: 0.5000, sse=468088.1, rms=0.147 (0.000%) 011: dt: 0.5000, sse=466238.7, rms=0.144 (0.000%) 012: dt: 0.5000, sse=464480.7, rms=0.142 (0.000%) 013: dt: 0.5000, sse=463018.3, rms=0.140 (0.000%) 014: dt: 0.5000, sse=461407.7, rms=0.138 (0.000%) 015: dt: 0.5000, sse=460017.0, rms=0.137 (0.000%) 016: dt: 0.5000, sse=458620.0, rms=0.136 (0.000%) 017: dt: 0.5000, sse=457024.2, rms=0.135 (0.000%) 018: dt: 0.5000, sse=455395.4, rms=0.135 (0.000%) 019: dt: 0.5000, sse=453960.3, rms=0.135 (0.000%) 020: dt: 0.5000, sse=453225.4, rms=0.135 (0.000%) 021: dt: 0.5000, sse=452069.9, rms=0.135 (0.000%) 022: dt: 0.5000, sse=450405.6, rms=0.135 (0.000%) 023: dt: 0.5000, sse=449234.2, rms=0.135 (0.000%) 024: dt: 0.5000, sse=448341.0, rms=0.135 (0.000%) 025: dt: 0.5000, sse=446750.0, rms=0.135 (0.000%) 026: dt: 0.5000, sse=446009.4, rms=0.136 (0.000%) 027: dt: 0.5000, sse=444634.4, rms=0.136 (0.000%) 028: dt: 0.5000, sse=443450.3, rms=0.136 (0.000%) 029: dt: 0.5000, sse=442174.8, rms=0.137 (0.000%) 030: dt: 0.5000, sse=441035.6, rms=0.137 (0.000%) positioning took 4.3 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [89.80 206.20], gm=148.00+-19.40, and vertices in regions > 138.3 43282 surface locations found to contain inconsistent values (2125 in, 41157 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=45524.7, rms=0.11 031: dt: 0.5000, sse=45359.8, rms=0.109 (0.000%) 032: dt: 0.5000, sse=46338.8, rms=0.099 (0.000%) 033: dt: 0.5000, sse=47439.3, rms=0.093 (0.000%) 034: dt: 0.5000, sse=48338.7, rms=0.088 (0.000%) 035: dt: 0.5000, sse=49099.1, rms=0.084 (0.000%) 036: dt: 0.5000, sse=49763.9, rms=0.080 (0.000%) 037: dt: 0.5000, sse=50400.2, rms=0.076 (0.000%) 038: dt: 0.5000, sse=51024.8, rms=0.073 (0.000%) 039: dt: 0.5000, sse=51626.3, rms=0.069 (0.000%) 040: dt: 0.5000, sse=52250.5, rms=0.067 (0.000%) 041: dt: 0.5000, sse=52839.6, rms=0.064 (0.000%) 042: dt: 0.5000, sse=53378.6, rms=0.062 (0.000%) 043: dt: 0.5000, sse=53894.7, rms=0.059 (0.000%) 044: dt: 0.5000, sse=54327.8, rms=0.057 (0.000%) 045: dt: 0.5000, sse=54761.2, rms=0.056 (0.000%) 046: dt: 0.5000, sse=55220.6, rms=0.054 (0.000%) 047: dt: 0.5000, sse=55600.4, rms=0.052 (0.000%) 048: dt: 0.5000, sse=55980.4, rms=0.051 (0.000%) 049: dt: 0.5000, sse=56346.9, rms=0.050 (0.000%) 050: dt: 0.5000, sse=56656.5, rms=0.049 (0.000%) 051: dt: 0.5000, sse=56945.3, rms=0.047 (0.000%) 052: dt: 0.5000, sse=57205.8, rms=0.046 (0.000%) 053: dt: 0.5000, sse=57428.1, rms=0.045 (0.000%) 054: dt: 0.5000, sse=57662.9, rms=0.044 (0.000%) 055: dt: 0.5000, sse=57878.0, rms=0.044 (0.000%) 056: dt: 0.5000, sse=58036.0, rms=0.043 (0.000%) 057: dt: 0.5000, sse=58191.1, rms=0.042 (0.000%) 058: dt: 0.5000, sse=58353.2, rms=0.041 (0.000%) 059: dt: 0.5000, sse=58484.9, rms=0.041 (0.000%) 060: dt: 0.5000, sse=58627.5, rms=0.040 (0.000%) positioning took 4.3 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [89.50 206.50], gm=148.00+-19.50, and vertices in regions > 138.2 41413 surface locations found to contain inconsistent values (523 in, 40890 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=6252.5, rms=0.05 061: dt: 0.5000, sse=6250.9, rms=0.050 (0.000%) 062: dt: 0.5000, sse=6288.3, rms=0.046 (0.000%) 063: dt: 0.5000, sse=6318.4, rms=0.044 (0.000%) 064: dt: 0.5000, sse=6338.7, rms=0.042 (0.000%) 065: dt: 0.5000, sse=6347.6, rms=0.040 (0.000%) 066: dt: 0.5000, sse=6352.7, rms=0.038 (0.000%) 067: dt: 0.5000, sse=6353.5, rms=0.037 (0.000%) 068: dt: 0.5000, sse=6354.3, rms=0.036 (0.000%) 069: dt: 0.5000, sse=6355.8, rms=0.035 (0.000%) 070: dt: 0.5000, sse=6358.2, rms=0.034 (0.000%) 071: dt: 0.5000, sse=6364.1, rms=0.033 (0.000%) 072: dt: 0.5000, sse=6367.2, rms=0.033 (0.000%) 073: dt: 0.5000, sse=6371.2, rms=0.032 (0.000%) 074: dt: 0.5000, sse=6373.3, rms=0.031 (0.000%) 075: dt: 0.5000, sse=6375.0, rms=0.030 (0.000%) 076: dt: 0.5000, sse=6377.8, rms=0.030 (0.000%) 077: dt: 0.5000, sse=6379.8, rms=0.029 (0.000%) 078: dt: 0.5000, sse=6383.7, rms=0.028 (0.000%) 079: dt: 0.5000, sse=6387.8, rms=0.028 (0.000%) 080: dt: 0.5000, sse=6391.2, rms=0.028 (0.000%) 081: dt: 0.5000, sse=6395.9, rms=0.027 (0.000%) 082: dt: 0.5000, sse=6399.5, rms=0.027 (0.000%) 083: dt: 0.5000, sse=6405.0, rms=0.027 (0.000%) 084: dt: 0.5000, sse=6407.4, rms=0.027 (0.000%) 085: dt: 0.5000, sse=6411.0, rms=0.026 (0.000%) 086: dt: 0.5000, sse=6413.6, rms=0.026 (0.000%) 087: dt: 0.5000, sse=6416.7, rms=0.026 (0.000%) 088: dt: 0.5000, sse=6419.7, rms=0.026 (0.000%) 089: dt: 0.5000, sse=6420.7, rms=0.026 (0.000%) 090: dt: 0.5000, sse=6420.5, rms=0.026 (0.000%) positioning took 4.3 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [88.50 205.50], gm=147.00+-19.50, and vertices in regions > 137.2 34465 surface locations found to contain inconsistent values (509 in, 33956 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/sub016/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=924.1, rms=0.04 091: dt: 0.5000, sse=921.2, rms=0.043 (0.000%) 092: dt: 0.5000, sse=891.2, rms=0.041 (0.000%) 093: dt: 0.5000, sse=867.7, rms=0.039 (0.000%) 094: dt: 0.5000, sse=846.4, rms=0.037 (0.000%) 095: dt: 0.5000, sse=828.1, rms=0.035 (0.000%) 096: dt: 0.5000, sse=815.2, rms=0.034 (0.000%) 097: dt: 0.5000, sse=805.5, rms=0.033 (0.000%) 098: dt: 0.5000, sse=798.8, rms=0.032 (0.000%) 099: dt: 0.5000, sse=792.5, rms=0.032 (0.000%) 100: dt: 0.5000, sse=786.2, rms=0.031 (0.000%) 101: dt: 0.5000, sse=779.7, rms=0.030 (0.000%) 102: dt: 0.5000, sse=774.9, rms=0.030 (0.000%) 103: dt: 0.5000, sse=770.3, rms=0.029 (0.000%) 104: dt: 0.5000, sse=766.4, rms=0.029 (0.000%) 105: dt: 0.5000, sse=762.4, rms=0.028 (0.000%) 106: dt: 0.5000, sse=759.3, rms=0.028 (0.000%) 107: dt: 0.5000, sse=756.1, rms=0.027 (0.000%) 108: dt: 0.5000, sse=753.5, rms=0.027 (0.000%) 109: dt: 0.5000, sse=750.8, rms=0.026 (0.000%) 110: dt: 0.5000, sse=749.4, rms=0.026 (0.000%) 111: dt: 0.5000, sse=747.7, rms=0.026 (0.000%) 112: dt: 0.5000, sse=748.8, rms=0.026 (0.000%) 113: dt: 0.5000, sse=747.9, rms=0.026 (0.000%) 114: dt: 0.5000, sse=746.2, rms=0.026 (0.000%) 115: dt: 0.5000, sse=744.9, rms=0.025 (0.000%) 116: dt: 0.5000, sse=744.1, rms=0.025 (0.000%) 117: dt: 0.5000, sse=742.9, rms=0.025 (0.000%) 118: dt: 0.5000, sse=742.5, rms=0.025 (0.000%) 119: dt: 0.5000, sse=741.8, rms=0.025 (0.000%) 120: dt: 0.5000, sse=742.3, rms=0.025 (0.000%) positioning took 4.2 minutes writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.area.pial vertex spacing 1.02 +- 0.43 (0.05-->10.65) (max @ vno 70451 --> 68130) face area 0.41 +- 0.31 (0.00-->8.47) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 162159 vertices processed 25000 of 162159 vertices processed 50000 of 162159 vertices processed 75000 of 162159 vertices processed 100000 of 162159 vertices processed 125000 of 162159 vertices processed 150000 of 162159 vertices processed 0 of 162159 vertices processed 25000 of 162159 vertices processed 50000 of 162159 vertices processed 75000 of 162159 vertices processed 100000 of 162159 vertices processed 125000 of 162159 vertices processed 150000 of 162159 vertices processed thickness calculation complete, 487:848 truncations. 38169 vertices at 0 distance 112062 vertices at 1 distance 103989 vertices at 2 distance 41599 vertices at 3 distance 11472 vertices at 4 distance 3120 vertices at 5 distance 962 vertices at 6 distance 336 vertices at 7 distance 162 vertices at 8 distance 95 vertices at 9 distance 65 vertices at 10 distance 30 vertices at 11 distance 19 vertices at 12 distance 22 vertices at 13 distance 14 vertices at 14 distance 19 vertices at 15 distance 22 vertices at 16 distance 15 vertices at 17 distance 9 vertices at 18 distance 11 vertices at 19 distance 14 vertices at 20 distance writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.thickness positioning took 20.9 minutes #-------------------------------------------- #@# Surf Volume lh Fri Aug 9 00:17:18 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.volume lh.area.mid mul lh.thickness Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ] #-------------------------------------------- #@# Surf Volume rh Fri Aug 9 00:17:18 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.volume rh.area.mid mul rh.thickness Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ] #-------------------------------------------- #@# Cortical ribbon mask Fri Aug 9 00:17:19 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon sub016 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 = 37 writing volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/ribbon.mgz writing ribbon files #-------------------------------------------- #@# ASeg Stats Fri Aug 9 00:39:03 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016 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 sub016 $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 sub016 sysname Linux hostname snake6 machine x86_64 user fkaule UseRobust 0 atlas_icv (eTIV) = 1402840 mm^3 (det: 1.388687 ) Computing euler number orig.nofix lheno = -46, rheno = -32 orig.nofix lhholes = 24, rhholes = 17 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 306260.490 305489.000 diff= 771.5 pctdiff= 0.252 rhCtxGM: 309907.285 309138.000 diff= 769.3 pctdiff= 0.248 lhCtxWM: 253268.933 253103.500 diff= 165.4 pctdiff= 0.065 rhCtxWM: 258556.463 258667.500 diff= -111.0 pctdiff=-0.043 SubCortGMVol 75858.000 SupraTentVol 1220313.171 (1217624.000) diff=2689.171 pctdiff=0.220 SupraTentVolNotVent 1205373.171 (1202684.000) diff=2689.171 pctdiff=0.223 BrainSegVol 1369384.000 (1366874.000) diff=2510.000 pctdiff=0.183 BrainSegVolNotVent 1350669.000 (1351917.171) diff=-1248.171 pctdiff=-0.092 BrainSegVolNotVent 1350669.000 CerebellumVol 147638.000 VentChorVol 14940.000 3rd4th5thCSF 3775.000 CSFVol 1308.000, OptChiasmVol 304.000 MaskVol 1848686.000 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 5205 5204.545 4 5 Left-Inf-Lat-Vent 587 587.482 5 7 Left-Cerebellum-White-Matter 15848 15847.543 6 8 Left-Cerebellum-Cortex 57326 57326.152 7 10 Left-Thalamus-Proper 9388 9388.153 8 11 Left-Caudate 5055 5055.190 9 12 Left-Putamen 7345 7345.435 10 13 Left-Pallidum 2485 2484.961 11 14 3rd-Ventricle 878 878.457 12 15 4th-Ventricle 1789 1788.563 13 16 Brain-Stem 25619 25619.164 14 17 Left-Hippocampus 5163 5163.188 15 18 Left-Amygdala 1837 1837.226 16 24 CSF 1269 1268.591 17 26 Left-Accumbens-area 926 926.388 18 28 Left-VentralDC 4287 4287.005 19 30 Left-vessel 252 252.209 20 31 Left-choroid-plexus 1120 1119.660 23 43 Right-Lateral-Ventricle 6175 6175.496 24 44 Right-Inf-Lat-Vent 417 417.325 25 46 Right-Cerebellum-White-Matter 16511 16510.811 26 47 Right-Cerebellum-Cortex 60517 60517.289 27 49 Right-Thalamus-Proper 8712 8711.553 28 50 Right-Caudate 6116 6115.571 29 51 Right-Putamen 6870 6870.305 30 52 Right-Pallidum 2510 2509.738 31 53 Right-Hippocampus 4969 4968.664 32 54 Right-Amygdala 2274 2273.631 33 58 Right-Accumbens-area 1003 1003.480 34 60 Right-VentralDC 4570 4569.587 35 62 Right-vessel 123 123.374 36 63 Right-choroid-plexus 1462 1462.179 37 72 5th-Ventricle 0 0.000 38 77 WM-hypointensities 3867 3866.558 39 78 Left-WM-hypointensities 0 0.000 40 79 Right-WM-hypointensities 0 0.000 41 80 non-WM-hypointensities 39 39.195 42 81 Left-non-WM-hypointensities 0 0.000 43 82 Right-non-WM-hypointensities 0 0.000 44 85 Optic-Chiasm 301 300.605 45 251 CC_Posterior 857 856.593 46 252 CC_Mid_Posterior 412 411.740 47 253 CC_Central 428 427.937 48 254 CC_Mid_Anterior 500 499.593 49 255 CC_Anterior 905 904.610 Reporting on 45 segmentations mri_segstats done #----------------------------------------- #@# AParc-to-ASeg Fri Aug 9 00:41:45 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016 mri_aparc2aseg --s sub016 --volmask SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer subject sub016 outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.white Reading lh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.pial Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/surf/rh.white Reading rh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.pial Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/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/sub016/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 = 611610 Used brute-force search on 0 voxels Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/aparc+aseg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016 mri_aparc2aseg --s sub016 --volmask --a2009s SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer subject sub016 outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.white Reading lh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.pial Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/surf/rh.white Reading rh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.pial Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/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/sub016/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 = 611610 Used brute-force search on 0 voxels Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# WMParc Fri Aug 9 00:47:13 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016 mri_aparc2aseg --s sub016 --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 sub016 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/sub016/mri/aparc+aseg.mgz Reading lh white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.white Reading lh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.pial Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/surf/rh.white Reading rh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.pial Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/mri/ribbon.mgz Loading filled from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/filled.mgz Ripping vertices labeled as unkown Ripped 9404 vertices from left hemi Ripped 8753 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/sub016/mri/aseg.mgz Loading Ctx Seg File /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 = 1123151 Used brute-force search on 127 voxels Fixing Parahip LH WM Found 8 clusters 0 k 2078.000000 1 k 1.000000 2 k 1.000000 3 k 1.000000 4 k 1.000000 5 k 12.000000 6 k 1.000000 7 k 12.000000 Fixing Parahip RH WM Found 9 clusters 0 k 1.000000 1 k 1929.000000 2 k 1.000000 3 k 1.000000 4 k 1.000000 5 k 1.000000 6 k 1.000000 7 k 2.000000 8 k 1.000000 Writing output aseg to mri/wmparc.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016 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 sub016 --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 sub016 --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) = 1402840 mm^3 (det: 1.388687 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 306260.490 305489.000 diff= 771.5 pctdiff= 0.252 rhCtxGM: 309907.285 309138.000 diff= 769.3 pctdiff= 0.248 lhCtxWM: 253268.933 253103.500 diff= 165.4 pctdiff= 0.065 rhCtxWM: 258556.463 258667.500 diff= -111.0 pctdiff=-0.043 SubCortGMVol 75858.000 SupraTentVol 1220313.171 (1217624.000) diff=2689.171 pctdiff=0.220 SupraTentVolNotVent 1205373.171 (1202684.000) diff=2689.171 pctdiff=0.223 BrainSegVol 1369384.000 (1366874.000) diff=2510.000 pctdiff=0.183 BrainSegVolNotVent 1350669.000 (1351917.171) diff=-1248.171 pctdiff=-0.092 BrainSegVolNotVent 1350669.000 CerebellumVol 147638.000 VentChorVol 14940.000 3rd4th5thCSF 3775.000 CSFVol 1308.000, OptChiasmVol 304.000 MaskVol 1848686.000 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 2452 2451.532 2 3002 wm-lh-caudalanteriorcingulate 3946 3945.573 3 3003 wm-lh-caudalmiddlefrontal 6079 6078.784 4 3004 wm-lh-corpuscallosum 0 0.000 5 3005 wm-lh-cuneus 2961 2961.475 6 3006 wm-lh-entorhinal 1284 1284.438 7 3007 wm-lh-fusiform 7966 7965.979 8 3008 wm-lh-inferiorparietal 11257 11256.769 9 3009 wm-lh-inferiortemporal 9263 9262.991 10 3010 wm-lh-isthmuscingulate 4640 4639.525 11 3011 wm-lh-lateraloccipital 9338 9337.695 12 3012 wm-lh-lateralorbitofrontal 7724 7724.123 13 3013 wm-lh-lingual 6364 6364.017 14 3014 wm-lh-medialorbitofrontal 3724 3724.163 15 3015 wm-lh-middletemporal 7293 7293.097 16 3016 wm-lh-parahippocampal 2142 2141.513 17 3017 wm-lh-paracentral 3707 3707.155 18 3018 wm-lh-parsopercularis 4535 4534.863 19 3019 wm-lh-parsorbitalis 1171 1171.051 20 3020 wm-lh-parstriangularis 3172 3171.806 21 3021 wm-lh-pericalcarine 4592 4591.900 22 3022 wm-lh-postcentral 7609 7608.956 23 3023 wm-lh-posteriorcingulate 5355 5355.249 24 3024 wm-lh-precentral 14215 14214.800 25 3025 wm-lh-precuneus 11123 11122.730 26 3026 wm-lh-rostralanteriorcingulate 2619 2619.199 27 3027 wm-lh-rostralmiddlefrontal 12685 12685.373 28 3028 wm-lh-superiorfrontal 20937 20937.270 29 3029 wm-lh-superiorparietal 14351 14350.940 30 3030 wm-lh-superiortemporal 9641 9641.078 31 3031 wm-lh-supramarginal 10236 10236.092 32 3032 wm-lh-frontalpole 151 151.290 33 3033 wm-lh-temporalpole 731 730.634 34 3034 wm-lh-transversetemporal 929 928.537 35 3035 wm-lh-insula 10118 10118.451 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 2831 2831.255 120 4002 wm-rh-caudalanteriorcingulate 2638 2637.598 121 4003 wm-rh-caudalmiddlefrontal 5731 5730.535 122 4004 wm-rh-corpuscallosum 0 0.000 123 4005 wm-rh-cuneus 3045 3045.040 124 4006 wm-rh-entorhinal 1034 1033.776 125 4007 wm-rh-fusiform 7612 7611.993 126 4008 wm-rh-inferiorparietal 13814 13813.651 127 4009 wm-rh-inferiortemporal 8415 8414.678 128 4010 wm-rh-isthmuscingulate 5231 5230.636 129 4011 wm-rh-lateraloccipital 9901 9900.562 130 4012 wm-rh-lateralorbitofrontal 7480 7480.153 131 4013 wm-rh-lingual 6713 6712.950 132 4014 wm-rh-medialorbitofrontal 3751 3750.894 133 4015 wm-rh-middletemporal 7945 7944.837 134 4016 wm-rh-parahippocampal 1995 1995.037 135 4017 wm-rh-paracentral 6093 6093.256 136 4018 wm-rh-parsopercularis 5347 5346.578 137 4019 wm-rh-parsorbitalis 1301 1301.438 138 4020 wm-rh-parstriangularis 4404 4404.237 139 4021 wm-rh-pericalcarine 4362 4361.587 140 4022 wm-rh-postcentral 8380 8379.893 141 4023 wm-rh-posteriorcingulate 4716 4716.122 142 4024 wm-rh-precentral 14818 14817.553 143 4025 wm-rh-precuneus 10880 10879.696 144 4026 wm-rh-rostralanteriorcingulate 2748 2747.739 145 4027 wm-rh-rostralmiddlefrontal 12665 12665.396 146 4028 wm-rh-superiorfrontal 22764 22763.979 147 4029 wm-rh-superiorparietal 11638 11637.731 148 4030 wm-rh-superiortemporal 7994 7994.231 149 4031 wm-rh-supramarginal 9586 9586.322 150 4032 wm-rh-frontalpole 256 256.280 151 4033 wm-rh-temporalpole 654 653.627 152 4034 wm-rh-transversetemporal 747 747.147 153 4035 wm-rh-insula 10469 10468.917 154 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 30700 30700.072 237 5002 Right-UnsegmentedWhiteMatter 32089 32089.314 238 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/sub016/label #-------------------------------------------- #@# BA Labels lh Fri Aug 9 00:59:53 CEST 2013 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.label --trgsubject sub016 --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 = sub016 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/sub016/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479 Number of reverse mapping hits = 398 Checking for and removing duplicates Writing label file ./lh.BA1.label 4527 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.label --trgsubject sub016 --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 = sub016 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/sub016/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479 Number of reverse mapping hits = 926 Checking for and removing duplicates Writing label file ./lh.BA2.label 8835 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.label --trgsubject sub016 --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 = sub016 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/sub016/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479 Number of reverse mapping hits = 241 Checking for and removing duplicates Writing label file ./lh.BA3a.label 4318 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.label --trgsubject sub016 --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 = sub016 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/sub016/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479 Number of reverse mapping hits = 611 Checking for and removing duplicates Writing label file ./lh.BA3b.label 6594 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.label --trgsubject sub016 --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 = sub016 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/sub016/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479 Number of reverse mapping hits = 681 Checking for and removing duplicates Writing label file ./lh.BA4a.label 6465 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.label --trgsubject sub016 --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 = sub016 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/sub016/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479 Number of reverse mapping hits = 406 Checking for and removing duplicates Writing label file ./lh.BA4p.label 4476 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.label --trgsubject sub016 --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 = sub016 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/sub016/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479 Number of reverse mapping hits = 1787 Checking for and removing duplicates Writing label file ./lh.BA6.label 15376 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.label --trgsubject sub016 --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 = sub016 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/sub016/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479 Number of reverse mapping hits = 889 Checking for and removing duplicates Writing label file ./lh.BA44.label 5070 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.label --trgsubject sub016 --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 = sub016 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/sub016/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479 Number of reverse mapping hits = 1201 Checking for and removing duplicates Writing label file ./lh.BA45.label 4623 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.label --trgsubject sub016 --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 = sub016 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/sub016/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479 Number of reverse mapping hits = 2377 Checking for and removing duplicates Writing label file ./lh.V1.label 7018 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.label --trgsubject sub016 --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 = sub016 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/sub016/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479 Number of reverse mapping hits = 3898 Checking for and removing duplicates Writing label file ./lh.V2.label 12012 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.label --trgsubject sub016 --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 = sub016 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/sub016/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479 Number of reverse mapping hits = 833 Checking for and removing duplicates Writing label file ./lh.MT.label 2851 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.perirhinal.label --trgsubject sub016 --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 = sub016 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/sub016/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479 Number of reverse mapping hits = 351 Checking for and removing duplicates Writing label file ./lh.perirhinal.label 1550 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.thresh.label --trgsubject sub016 --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 = sub016 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/sub016/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479 Number of reverse mapping hits = 86 Checking for and removing duplicates Writing label file ./lh.BA1.thresh.label 1100 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.thresh.label --trgsubject sub016 --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 = sub016 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/sub016/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479 Number of reverse mapping hits = 166 Checking for and removing duplicates Writing label file ./lh.BA2.thresh.label 2258 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.thresh.label --trgsubject sub016 --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 = sub016 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/sub016/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479 Number of reverse mapping hits = 23 Checking for and removing duplicates Writing label file ./lh.BA3a.thresh.label 1527 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.thresh.label --trgsubject sub016 --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 = sub016 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/sub016/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479 Number of reverse mapping hits = 248 Checking for and removing duplicates Writing label file ./lh.BA3b.thresh.label 2244 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.thresh.label --trgsubject sub016 --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 = sub016 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/sub016/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479 Number of reverse mapping hits = 433 Checking for and removing duplicates Writing label file ./lh.BA4a.thresh.label 2752 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.thresh.label --trgsubject sub016 --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 = sub016 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/sub016/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479 Number of reverse mapping hits = 157 Checking for and removing duplicates Writing label file ./lh.BA4p.thresh.label 1706 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.thresh.label --trgsubject sub016 --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 = sub016 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/sub016/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479 Number of reverse mapping hits = 635 Checking for and removing duplicates Writing label file ./lh.BA6.thresh.label 7670 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.thresh.label --trgsubject sub016 --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 = sub016 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/sub016/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479 Number of reverse mapping hits = 512 Checking for and removing duplicates Writing label file ./lh.BA44.thresh.label 2424 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.thresh.label --trgsubject sub016 --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 = sub016 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/sub016/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479 Number of reverse mapping hits = 510 Checking for and removing duplicates Writing label file ./lh.BA45.thresh.label 1661 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.thresh.label --trgsubject sub016 --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 = sub016 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/sub016/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479 Number of reverse mapping hits = 1745 Checking for and removing duplicates Writing label file ./lh.V1.thresh.label 5150 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.thresh.label --trgsubject sub016 --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 = sub016 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/sub016/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479 Number of reverse mapping hits = 1781 Checking for and removing duplicates Writing label file ./lh.V2.thresh.label 5115 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.thresh.label --trgsubject sub016 --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 = sub016 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/sub016/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479 Number of reverse mapping hits = 271 Checking for and removing duplicates Writing label file ./lh.MT.thresh.label 784 mri_label2label: Done mris_label2annot --s sub016 --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/sub016/label cmdline mris_label2annot --s sub016 --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 sub016 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/sub016/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 112515 unhit vertices Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/label/lh.BA.annot mris_label2annot --s sub016 --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/sub016/label cmdline mris_label2annot --s sub016 --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 sub016 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/sub016/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 132861 unhit vertices Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/label/lh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab sub016 lh white computing statistics for each annotation in ./lh.BA.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 1149 613 2316 2.623 0.404 0.163 0.131 114 8.4 BA1 4525 2973 8268 2.566 0.464 0.121 0.034 50 6.3 BA2 983 673 962 1.921 0.366 0.143 0.049 10 2.0 BA3a 2836 1812 4720 2.242 0.614 0.120 0.037 35 4.4 BA3b 1949 1016 4013 3.077 0.491 0.110 0.210 60 5.3 BA4a 1569 944 2751 2.818 0.448 0.105 0.030 12 2.0 BA4p 10174 6679 25171 3.070 0.614 0.119 0.035 191 15.6 BA6 3033 1986 6744 2.844 0.490 0.120 0.038 40 5.0 BA44 3724 2528 7712 2.570 0.571 0.142 0.046 66 7.1 BA45 4613 3269 6851 2.042 0.462 0.156 0.067 92 13.4 V1 9425 6060 14706 2.214 0.545 0.158 0.071 208 29.0 V2 2623 1768 4380 2.381 0.448 0.140 0.049 43 4.9 MT 1361 949 3783 3.229 0.681 0.163 0.072 26 4.0 perirhinal mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab sub016 lh white computing statistics for each annotation in ./lh.BA.thresh.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 701 335 1409 2.627 0.332 0.181 0.181 105 7.5 BA1 1576 1045 2963 2.516 0.433 0.116 0.030 15 1.9 BA2 781 533 718 1.886 0.361 0.155 0.051 8 1.7 BA3a 1753 1164 2431 1.925 0.344 0.102 0.028 15 1.8 BA3b 2046 1043 4172 3.119 0.492 0.111 0.208 149 6.3 BA4a 1224 760 1963 2.666 0.406 0.102 0.027 8 1.3 BA4p 5405 3525 13798 3.144 0.580 0.117 0.035 56 8.0 BA6 2112 1377 4634 2.831 0.460 0.126 0.041 32 3.8 BA44 1587 1072 3832 2.814 0.450 0.163 0.058 38 3.7 BA45 4860 3446 7264 2.031 0.465 0.157 0.073 100 16.5 V1 4822 3104 7146 2.140 0.516 0.169 0.081 108 16.2 V2 751 475 1281 2.497 0.423 0.144 0.052 12 1.5 MT #-------------------------------------------- #@# BA Labels rh Fri Aug 9 01:04:52 CEST 2013 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.label --trgsubject sub016 --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 = sub016 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/sub016/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159 Number of reverse mapping hits = 604 Checking for and removing duplicates Writing label file ./rh.BA1.label 4566 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.label --trgsubject sub016 --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 = sub016 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/sub016/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159 Number of reverse mapping hits = 676 Checking for and removing duplicates Writing label file ./rh.BA2.label 7363 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.label --trgsubject sub016 --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 = sub016 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/sub016/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159 Number of reverse mapping hits = 228 Checking for and removing duplicates Writing label file ./rh.BA3a.label 4208 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.label --trgsubject sub016 --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 = sub016 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/sub016/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159 Number of reverse mapping hits = 555 Checking for and removing duplicates Writing label file ./rh.BA3b.label 5077 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.label --trgsubject sub016 --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 = sub016 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/sub016/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159 Number of reverse mapping hits = 895 Checking for and removing duplicates Writing label file ./rh.BA4a.label 6642 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.label --trgsubject sub016 --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 = sub016 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/sub016/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159 Number of reverse mapping hits = 447 Checking for and removing duplicates Writing label file ./rh.BA4p.label 4920 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.label --trgsubject sub016 --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 = sub016 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/sub016/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159 Number of reverse mapping hits = 2322 Checking for and removing duplicates Writing label file ./rh.BA6.label 14578 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.label --trgsubject sub016 --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 = sub016 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/sub016/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159 Number of reverse mapping hits = 1756 Checking for and removing duplicates Writing label file ./rh.BA44.label 8668 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.label --trgsubject sub016 --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 = sub016 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/sub016/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159 Number of reverse mapping hits = 1802 Checking for and removing duplicates Writing label file ./rh.BA45.label 7157 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.label --trgsubject sub016 --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 = sub016 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/sub016/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159 Number of reverse mapping hits = 2730 Checking for and removing duplicates Writing label file ./rh.V1.label 7457 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.label --trgsubject sub016 --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 = sub016 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/sub016/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159 Number of reverse mapping hits = 4422 Checking for and removing duplicates Writing label file ./rh.V2.label 12438 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.label --trgsubject sub016 --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 = sub016 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/sub016/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159 Number of reverse mapping hits = 925 Checking for and removing duplicates Writing label file ./rh.MT.label 2857 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.perirhinal.label --trgsubject sub016 --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 = sub016 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/sub016/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159 Number of reverse mapping hits = 192 Checking for and removing duplicates Writing label file ./rh.perirhinal.label 944 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.thresh.label --trgsubject sub016 --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 = sub016 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/sub016/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159 Number of reverse mapping hits = 272 Checking for and removing duplicates Writing label file ./rh.BA1.thresh.label 1148 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.thresh.label --trgsubject sub016 --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 = sub016 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/sub016/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159 Number of reverse mapping hits = 194 Checking for and removing duplicates Writing label file ./rh.BA2.thresh.label 2882 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.thresh.label --trgsubject sub016 --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 = sub016 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/sub016/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159 Number of reverse mapping hits = 59 Checking for and removing duplicates Writing label file ./rh.BA3a.thresh.label 1757 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.thresh.label --trgsubject sub016 --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 = sub016 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/sub016/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159 Number of reverse mapping hits = 347 Checking for and removing duplicates Writing label file ./rh.BA3b.thresh.label 2530 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.thresh.label --trgsubject sub016 --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 = sub016 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/sub016/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159 Number of reverse mapping hits = 238 Checking for and removing duplicates Writing label file ./rh.BA4a.thresh.label 1626 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.thresh.label --trgsubject sub016 --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 = sub016 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/sub016/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159 Number of reverse mapping hits = 152 Checking for and removing duplicates Writing label file ./rh.BA4p.thresh.label 1641 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.thresh.label --trgsubject sub016 --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 = sub016 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/sub016/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159 Number of reverse mapping hits = 1149 Checking for and removing duplicates Writing label file ./rh.BA6.thresh.label 8108 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.thresh.label --trgsubject sub016 --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 = sub016 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/sub016/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159 Number of reverse mapping hits = 471 Checking for and removing duplicates Writing label file ./rh.BA44.thresh.label 1483 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.thresh.label --trgsubject sub016 --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 = sub016 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/sub016/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159 Number of reverse mapping hits = 568 Checking for and removing duplicates Writing label file ./rh.BA45.thresh.label 1746 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.thresh.label --trgsubject sub016 --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 = sub016 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/sub016/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159 Number of reverse mapping hits = 1953 Checking for and removing duplicates Writing label file ./rh.V1.thresh.label 5185 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.thresh.label --trgsubject sub016 --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 = sub016 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/sub016/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159 Number of reverse mapping hits = 2003 Checking for and removing duplicates Writing label file ./rh.V2.thresh.label 5440 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.thresh.label --trgsubject sub016 --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 = sub016 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/sub016/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159 Number of reverse mapping hits = 127 Checking for and removing duplicates Writing label file ./rh.MT.thresh.label 395 mri_label2label: Done mris_label2annot --s sub016 --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/sub016/label cmdline mris_label2annot --s sub016 --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 sub016 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/sub016/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 111800 unhit vertices Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/label/rh.BA.annot mris_label2annot --s sub016 --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/sub016/label cmdline mris_label2annot --s sub016 --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 sub016 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/sub016/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 133862 unhit vertices Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/label/rh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab sub016 rh white computing statistics for each annotation in ./rh.BA.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 1234 622 2657 2.836 0.465 0.128 0.447 48 3.2 BA1 3411 2318 5760 2.412 0.397 0.101 0.026 26 3.6 BA2 1110 754 1172 1.983 0.380 0.131 0.038 9 1.8 BA3a 2380 1505 3726 2.079 0.543 0.106 0.031 23 3.0 BA3b 2154 1136 4370 3.141 0.553 0.104 0.294 211 47.9 BA4a 1389 887 2423 2.795 0.441 0.098 0.031 12 1.8 BA4p 10186 6414 23606 3.041 0.597 0.120 0.078 212 22.4 BA6 4529 2987 8799 2.749 0.447 0.113 0.036 42 5.6 BA44 5076 3432 11633 2.717 0.589 0.142 0.064 133 9.4 BA45 5217 3502 7631 2.067 0.413 0.155 0.071 97 15.4 V1 10109 6603 16061 2.250 0.529 0.161 0.092 238 31.4 V2 2738 1871 4700 2.415 0.459 0.142 0.055 51 5.9 MT 826 562 1993 3.049 0.765 0.149 0.064 11 2.1 perirhinal mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab sub016 rh white computing statistics for each annotation in ./rh.BA.thresh.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 939 455 1971 2.804 0.481 0.129 0.576 46 2.7 BA1 1971 1324 3546 2.430 0.392 0.092 0.023 13 1.9 BA2 951 644 912 1.977 0.367 0.132 0.036 7 1.5 BA3a 1988 1285 2678 1.914 0.438 0.096 0.026 14 2.3 BA3b 1224 601 2317 3.155 0.551 0.099 0.044 16 2.6 BA4a 1173 746 2044 2.887 0.495 0.098 0.032 10 1.6 BA4p 6353 3964 14626 3.011 0.600 0.116 0.101 169 16.1 BA6 1412 937 3367 2.868 0.383 0.112 0.043 15 1.7 BA44 1662 1115 4315 2.933 0.476 0.138 0.043 28 3.0 BA45 5008 3350 7193 2.063 0.420 0.153 0.070 90 14.5 V1 5235 3453 7829 2.089 0.483 0.174 0.075 111 15.5 V2 381 250 753 2.535 0.449 0.144 0.051 8 0.8 MT /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label lh Fri Aug 9 01:09:53 CEST 2013 mris_spherical_average -erode 1 -orig white -t 0.4 -o sub016 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject sub016. processing subject lh.EC_average... reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 1259 points to lh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label sub016 lh white limiting computations to label ./lh.entorhinal_exvivo.label. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 470 298 1375 3.150 0.616 0.126 0.042 4 0.9 ./lh.entorhinal_exvivo.label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label rh Fri Aug 9 01:10:09 CEST 2013 mris_spherical_average -erode 1 -orig white -t 0.4 -o sub016 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label painting output onto subject sub016. processing subject rh.EC_average... reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 1079 points to rh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label sub016 rh white limiting computations to label ./rh.entorhinal_exvivo.label. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 447 289 1300 3.259 0.643 0.131 0.064 5 1.1 ./rh.entorhinal_exvivo.label #------------------------------------------ Started at Thu Aug 8 10:54:16 CEST 2013 Ended at Fri Aug 9 01:10:26 CEST 2013 #@#%# recon-all-run-time-hours 14.269 recon-all -s sub016 finished without error at Fri Aug 9 01:10:26 CEST 2013