Thu Aug 8 10:53:55 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002 /opt/freesurfer/5.3.0/bin/recon-all -i /home/data/exppsy/forrest_gump/openfmri.org/sub002/anatomy/highres001.nii.gz -cw256 -all -T2 /home/data/exppsy/forrest_gump/openfmri.org/sub002/anatomy/other/t2w001.nii.gz -T2pial -subjid sub002 -sd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer subjid sub002 setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer FREESURFER_HOME /opt/freesurfer/5.3.0 Actual FREESURFER_HOME /opt/freesurfer/5.3.0 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux snake5 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc unlimited maxlocks unlimited maxsignal 16382 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 99201692 96466116 2735576 0 177872 94401912 -/+ buffers/cache: 1886332 97315360 Swap: 25165780 3620 25162160 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:56-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:56-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:56-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:56-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:56-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:56-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:56-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:56-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:58-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:58-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:58-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:58-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:58-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:58-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:58-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:58-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:58-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:58-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:59-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:59-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:59-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:59-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:59-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:59-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:59-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:59-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:59-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:59-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/freesurfer/5.3.0/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /opt/freesurfer/5.3.0/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### -cw256 option is now persistent (remove with -clean-cw256) /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub002/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig/001.mgz mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub002/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/anatomy/highres001.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999032, 0.0218052, 0.0381938) j_ras = (0.0265301, 0.991428, 0.127932) k_ras = (0.0350768, -0.128822, 0.991047) writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig/001.mgz... #-------------------------------------------- #@# T2/FLAIR Input Thu Aug 8 10:54:17 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub002/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig/T2raw.mgz mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub002/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/anatomy/other/t2w001.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999032, 0.0218052, 0.0381938) j_ras = (0.0265301, 0.991428, 0.127932) k_ras = (0.0350768, -0.128822, 0.991047) writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig/T2raw.mgz... #-------------------------------------------- #@# MotionCor Thu Aug 8 10:54:34 CEST 2013 Found 1 runs /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/mri/orig/001.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig.mgz --conform --cw256 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999032, 0.0218052, 0.0381938) j_ras = (0.0265301, 0.991428, 0.127932) k_ras = (0.0350768, -0.128822, 0.991047) Original Data has (0.69986, 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/sub002/mri/orig.mgz... mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/talairach.xfm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Aug 8 10:55:15 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 10:58:20 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6149, pval=0.2817 >= threshold=0.0050) awk -f /opt/freesurfer/5.3.0/bin/extract_talairach_avi_QA.awk /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/talairach_avi.log tal_QC_AZS /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/talairach_avi.log TalAviQA: 0.96536 z-score: -2 #-------------------------------------------- #@# Nu Intensity Correction Thu Aug 8 10:58:20 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/sub002/mri /opt/freesurfer/5.3.0/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux snake5 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux Thu Aug 8 10:58:20 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.13482 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.13482/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.13482/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 4.19095e-09, 0) j_ras = (0, 1.49012e-08, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.13482/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Aug 8 10:58:24 CEST 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.13482/nu0.mnc ./tmp.mri_nu_correct.mni.13482/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.13482/0/ [fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/] [2013-08-08 10:58:24] 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.13482/0/ ./tmp.mri_nu_correct.mni.13482/nu0.mnc ./tmp.mri_nu_correct.mni.13482/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 24 CV of field change: 0.000983369 [fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/] [2013-08-08 10:59:04] running: /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.13482/nu0.mnc ./tmp.mri_nu_correct.mni.13482/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Thu Aug 8 10:59:10 CEST 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.13482/nu1.mnc ./tmp.mri_nu_correct.mni.13482/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.13482/1/ [fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/] [2013-08-08 10:59:11] 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.13482/1/ ./tmp.mri_nu_correct.mni.13482/nu1.mnc ./tmp.mri_nu_correct.mni.13482/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 19 CV of field change: 0.000998983 [fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/] [2013-08-08 10:59:43] running: /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.13482/nu1.mnc ./tmp.mri_nu_correct.mni.13482/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.13482/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.13482/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/sub002/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.13482/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.13482/ones.mgz sysname Linux hostname snake5 machine x86_64 user fkaule input ./tmp.mri_nu_correct.mni.13482/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.13482/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.13482/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.13482/sum.junk --avgwf ./tmp.mri_nu_correct.mni.13482/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.13482/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.13482/sum.junk --avgwf ./tmp.mri_nu_correct.mni.13482/input.mean.dat sysname Linux hostname snake5 machine x86_64 user fkaule UseRobust 0 Loading ./tmp.mri_nu_correct.mni.13482/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.13482/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.13482/ones.mgz --i ./tmp.mri_nu_correct.mni.13482/nu2.mnc --sum ./tmp.mri_nu_correct.mni.13482/sum.junk --avgwf ./tmp.mri_nu_correct.mni.13482/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.13482/ones.mgz --i ./tmp.mri_nu_correct.mni.13482/nu2.mnc --sum ./tmp.mri_nu_correct.mni.13482/sum.junk --avgwf ./tmp.mri_nu_correct.mni.13482/output.mean.dat sysname Linux hostname snake5 machine x86_64 user fkaule UseRobust 0 Loading ./tmp.mri_nu_correct.mni.13482/ones.mgz Loading ./tmp.mri_nu_correct.mni.13482/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.13482/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.13482/nu2.mnc ./tmp.mri_nu_correct.mni.13482/nu2.mnc mul .95897357684828611735 Saving result to './tmp.mri_nu_correct.mni.13482/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.13482/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.13482/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.13482/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 4.19095e-09, 0) j_ras = (0, 1.49012e-08, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 8 seconds. mapping (12, 186) to ( 3, 110) Thu Aug 8 11:00:37 CEST 2013 mri_nu_correct.mni done mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Thu Aug 8 11:00:39 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.074 0.029 -0.002 1.673; -0.085 0.995 0.325 -24.310; 0.058 -0.436 1.080 3.275; 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 = 17 Starting OpenSpline(): npoints = 17 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 55 (55), valley at 44 (44) csf peak at 27, setting threshold to 45 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 58 (58), valley at 46 (46) csf peak at 10, setting threshold to 42 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 50 seconds. #-------------------------------------------- #@# Skull Stripping Thu Aug 8 11:03:30 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri mri_em_register -skull nu.mgz /opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta ======= NUMBER OF OPENMP THREADS = 1 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=8.0 skull bounding box = (48, 14, 9) --> (203, 255, 206) using (100, 94, 108) as brain centroid... mean wm in atlas = 126, using box (81,64,84) --> (119, 123,132) to find MRI wm before smoothing, mri peak at 109 after smoothing, mri peak at 110, scaling input intensities by 1.145 scaling channel 0 by 1.14545 initial log_p = -4.8 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.516131 @ (-9.091, 27.273, -9.091) max log p = -4.328604 @ (4.545, -4.545, -4.545) max log p = -4.280679 @ (6.818, 2.273, 2.273) max log p = -4.239203 @ (-3.409, -1.136, 3.409) max log p = -4.239203 @ (0.000, 0.000, 0.000) max log p = -4.239203 @ (0.000, 0.000, 0.000) Found translation: (-1.1, 23.9, -8.0): log p = -4.239 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.2 (thresh=-4.2) 1.000 0.000 0.000 -1.136; 0.000 1.111 0.298 -20.841; 0.000 -0.259 0.966 21.099; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.000 0.000 0.000 -1.136; 0.000 1.111 0.298 -20.841; 0.000 -0.259 0.966 21.099; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-4.0 (thresh=-4.0) 1.037 0.010 -0.031 -3.322; 0.000 1.081 0.323 -19.077; 0.033 -0.289 0.937 26.785; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.037 0.010 -0.031 -3.322; 0.000 1.081 0.323 -19.077; 0.033 -0.289 0.937 26.785; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.040 0.014 -0.013 -5.550; -0.008 1.074 0.338 -19.449; 0.016 -0.308 0.933 31.166; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.037 0.007 -0.024 -3.947; 0.001 1.072 0.337 -20.348; 0.025 -0.309 0.936 29.822; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.037 0.007 -0.024 -3.947; 0.001 1.072 0.337 -20.348; 0.025 -0.309 0.937 29.733; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3481 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.03718 0.00722 -0.02361 -3.94694; 0.00063 1.07237 0.33720 -20.34751; 0.02498 -0.30908 0.93747 29.73334; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.03718 0.00722 -0.02361 -3.94694; 0.00063 1.07237 0.33720 -20.34751; 0.02498 -0.30908 0.93747 29.73334; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.037 0.007 -0.024 -3.947; 0.001 1.072 0.337 -20.348; 0.025 -0.309 0.937 29.733; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.9 (old=-4.8) transform before final EM align: 1.037 0.007 -0.024 -3.947; 0.001 1.072 0.337 -20.348; 0.025 -0.309 0.937 29.733; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 382743 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.03718 0.00722 -0.02361 -3.94694; 0.00063 1.07237 0.33720 -20.34751; 0.02498 -0.30908 0.93747 29.73334; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.03718 0.00722 -0.02361 -3.94694; 0.00063 1.07237 0.33720 -20.34751; 0.02498 -0.30908 0.93747 29.73334; 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: 011: -log(p) = 4.3 tol 0.000000 final transform: 1.037 0.007 -0.024 -3.947; 0.001 1.072 0.337 -20.348; 0.025 -0.309 0.937 29.733; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 34 minutes and 35 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=127 y=82 z=115 r=95 first estimation of the main basin volume: 3669857 voxels Looking for seedpoints 2 found in the cerebellum 18 found in the rest of the brain global maximum in x=106, y=83, z=72, Imax=255 CSF=12, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done. Analyze... main basin size=22454927539 voxels, voxel volume =1.000 = 22454927539 mmm3 = 22454927.360 cm3 done. PostAnalyze...Basin Prior 101 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=126,y=96, z=109, r=10759 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = 45624 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=11 , nb = -1030081359 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = 1085671112 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1077613020 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1080297068 OTHER CSF_MIN=0, CSF_intensity=4, CSF_MAX=20 , nb = 1078030124 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 5, 6, 23, 57 after analyzing : 5, 18, 25, 27 RIGHT_CER before analyzing : 11, 14, 28, 61 after analyzing : 11, 23, 28, 32 LEFT_CER before analyzing : 5, 7, 31, 60 after analyzing : 5, 23, 31, 32 RIGHT_BRAIN before analyzing : 4, 4, 20, 56 after analyzing : 4, 18, 25, 27 LEFT_BRAIN before analyzing : 4, 4, 22, 57 after analyzing : 4, 18, 25, 27 OTHER before analyzing : 20, 56, 83, 95 after analyzing : 20, 74, 83, 79 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...73 iterations *********************VALIDATION********************* curvature mean = -0.012, std = 0.011 curvature mean = 74.768, std = 9.612 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 2.57, sigma = 4.37 after rotation: sse = 2.57, sigma = 4.37 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 2.70, its var is 4.15 before Erosion-Dilatation 0.61% 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...37 iterations mri_strip_skull: done peeling brain Brain Size = 2059915 voxels, voxel volume = 1.000 mm3 = 2059915 mmm3 = 2059.915 cm3 ****************************** Saving brainmask.auto.mgz done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Thu Aug 8 11:38:34 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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=19.0 skull bounding box = (58, 29, 30) --> (192, 180, 201) using (103, 79, 116) as brain centroid... mean wm in atlas = 107, using box (87,60,95) --> (119, 97,137) to find MRI wm before smoothing, mri peak at 109 after smoothing, mri peak at 109, scaling input intensities by 0.982 scaling channel 0 by 0.981651 initial log_p = -4.4 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.067876 @ (-9.091, 27.273, -9.091) max log p = -3.863126 @ (4.545, -4.545, -4.545) max log p = -3.785619 @ (2.273, -2.273, 6.818) max log p = -3.774508 @ (-1.136, 1.136, -3.409) max log p = -3.746221 @ (1.705, 0.568, 1.705) max log p = -3.746221 @ (0.000, 0.000, 0.000) Found translation: (-1.7, 22.2, -8.5): log p = -3.746 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.3, old_max_log_p =-3.7 (thresh=-3.7) 1.000 0.000 0.000 -1.705; 0.000 1.028 0.275 -11.845; 0.000 -0.236 0.883 27.712; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3) 1.000 0.000 0.000 -1.705; 0.000 1.028 0.275 -11.845; 0.000 -0.236 0.883 27.712; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.2, old_max_log_p =-3.3 (thresh=-3.3) 1.037 0.007 -0.030 -3.554; 0.002 1.038 0.311 -15.194; 0.034 -0.279 0.906 28.550; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2) 1.037 0.007 -0.030 -3.554; 0.002 1.038 0.311 -15.194; 0.034 -0.279 0.906 28.550; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2) 1.035 0.007 -0.030 -3.248; 0.002 1.039 0.311 -15.351; 0.034 -0.278 0.903 29.756; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.1) 1.035 0.007 -0.030 -3.248; 0.002 1.039 0.311 -15.351; 0.034 -0.278 0.903 29.756; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2772 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.03451 0.00692 -0.03020 -3.24805; 0.00226 1.03926 0.31115 -15.35058; 0.03379 -0.27772 0.90255 29.75585; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 1.03451 0.00692 -0.03020 -3.24805; 0.00226 1.03926 0.31115 -15.35058; 0.03379 -0.27772 0.90255 29.75585; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.035 0.007 -0.030 -3.248; 0.002 1.039 0.311 -15.351; 0.034 -0.278 0.903 29.756; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.2 (old=-4.4) transform before final EM align: 1.035 0.007 -0.030 -3.248; 0.002 1.039 0.311 -15.351; 0.034 -0.278 0.903 29.756; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 312841 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.03451 0.00692 -0.03020 -3.24805; 0.00226 1.03926 0.31115 -15.35058; 0.03379 -0.27772 0.90255 29.75585; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 1.03451 0.00692 -0.03020 -3.24805; 0.00226 1.03926 0.31115 -15.35058; 0.03379 -0.27772 0.90255 29.75585; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 009: -log(p) = 3.8 after pass:transform: ( 1.03, 0.01, -0.03, -3.25) ( 0.00, 1.04, 0.31, -15.35) ( 0.03, -0.28, 0.90, 29.76) dfp_em_step_func: 010: -log(p) = 3.8 after pass:transform: ( 1.03, 0.01, -0.03, -3.25) ( 0.00, 1.04, 0.31, -15.35) ( 0.03, -0.28, 0.90, 29.76) dfp_em_step_func: 011: -log(p) = 3.8 after pass:transform: ( 1.03, 0.01, -0.03, -3.25) ( 0.00, 1.04, 0.31, -15.35) ( 0.03, -0.28, 0.90, 29.76) dfp_em_step_func: 012: -log(p) = 3.8 after pass:transform: ( 1.03, 0.01, -0.03, -3.25) ( 0.00, 1.04, 0.31, -15.35) ( 0.03, -0.28, 0.90, 29.76) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 014: -log(p) = 3.8 tol 0.000000 final transform: 1.035 0.007 -0.030 -3.248; 0.002 1.039 0.311 -15.351; 0.034 -0.278 0.903 29.756; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 24 minutes and 39 seconds. #-------------------------------------- #@# CA Normalize Thu Aug 8 12:03:13 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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=19.0 skull bounding box = (58, 29, 30) --> (192, 180, 201) using (103, 79, 116) as brain centroid... mean wm in atlas = 107, using box (87,60,95) --> (119, 97,137) to find MRI wm before smoothing, mri peak at 109 after smoothing, mri peak at 109, scaling input intensities by 0.982 scaling channel 0 by 0.981651 using 244171 sample points... INFO: compute sample coordinates transform 1.035 0.007 -0.030 -3.248; 0.002 1.039 0.311 -15.351; 0.034 -0.278 0.903 29.756; 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 (123, 35, 29) --> (191, 147, 201) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 143.0 0 of 18 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (65, 34, 30) --> (129, 138, 203) Right_Cerebral_White_Matter: limiting intensities to 98.0 --> 143.0 0 of 18 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (128, 119, 61) --> (175, 162, 116) Left_Cerebellum_White_Matter: limiting intensities to 82.0 --> 143.0 0 of 9 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (82, 119, 59) --> (127, 160, 119) Right_Cerebellum_White_Matter: limiting intensities to 94.0 --> 143.0 3 of 9 (33.3%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (112, 107, 96) --> (143, 172, 128) Brain_Stem: limiting intensities to 91.0 --> 143.0 5 of 10 (50.0%) samples deleted using 64 total control points for intensity normalization... bias field = 0.990 +- 0.066 0 of 56 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (123, 35, 29) --> (191, 147, 201) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 136.0 0 of 112 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (65, 34, 30) --> (129, 138, 203) Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 136.0 0 of 77 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (128, 119, 61) --> (175, 162, 116) Left_Cerebellum_White_Matter: limiting intensities to 80.0 --> 136.0 0 of 28 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (82, 119, 59) --> (127, 160, 119) Right_Cerebellum_White_Matter: limiting intensities to 82.0 --> 136.0 0 of 42 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (112, 107, 96) --> (143, 172, 128) Brain_Stem: limiting intensities to 87.0 --> 136.0 21 of 66 (31.8%) samples deleted using 325 total control points for intensity normalization... bias field = 0.983 +- 0.048 0 of 304 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (123, 35, 29) --> (191, 147, 201) Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 134.0 1 of 201 (0.5%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (65, 34, 30) --> (129, 138, 203) Right_Cerebral_White_Matter: limiting intensities to 94.0 --> 134.0 0 of 213 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (128, 119, 61) --> (175, 162, 116) Left_Cerebellum_White_Matter: limiting intensities to 76.0 --> 134.0 0 of 43 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (82, 119, 59) --> (127, 160, 119) Right_Cerebellum_White_Matter: limiting intensities to 76.0 --> 134.0 0 of 43 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (112, 107, 96) --> (143, 172, 128) Brain_Stem: limiting intensities to 74.0 --> 134.0 0 of 80 (0.0%) samples deleted using 580 total control points for intensity normalization... bias field = 1.009 +- 0.045 1 of 579 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 2 minutes and 4 seconds. #-------------------------------------- #@# CA Reg Thu Aug 8 12:05:17 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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) = 1.06 (predicted orig area = 7.5) 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=0.869, neg=0, invalid=96777 0001: dt=129.472000, rms=0.799 (8.041%), neg=0, invalid=96777 0002: dt=110.976000, rms=0.791 (1.042%), neg=0, invalid=96777 0003: dt=129.472000, rms=0.780 (1.290%), neg=0, invalid=96777 0004: dt=129.472000, rms=0.778 (0.344%), neg=0, invalid=96777 0005: dt=221.952000, rms=0.770 (1.002%), neg=0, invalid=96777 0006: dt=32.368000, rms=0.768 (0.224%), neg=0, invalid=96777 0007: dt=32.368000, rms=0.767 (0.104%), neg=0, invalid=96777 0008: dt=32.368000, rms=0.767 (0.098%), neg=0, invalid=96777 0009: dt=32.368000, rms=0.766 (0.128%), neg=0, invalid=96777 0010: dt=32.368000, rms=0.764 (0.245%), neg=0, invalid=96777 0011: dt=32.368000, rms=0.761 (0.376%), neg=0, invalid=96777 0012: dt=32.368000, rms=0.758 (0.412%), neg=0, invalid=96777 0013: dt=32.368000, rms=0.755 (0.361%), neg=0, invalid=96777 0014: dt=32.368000, rms=0.753 (0.295%), neg=0, invalid=96777 0015: dt=32.368000, rms=0.751 (0.271%), neg=0, invalid=96777 0016: dt=32.368000, rms=0.749 (0.260%), neg=0, invalid=96777 0017: dt=32.368000, rms=0.747 (0.203%), neg=0, invalid=96777 0018: dt=32.368000, rms=0.746 (0.174%), neg=0, invalid=96777 0019: dt=32.368000, rms=0.744 (0.195%), neg=0, invalid=96777 0020: dt=32.368000, rms=0.743 (0.225%), neg=0, invalid=96777 0021: dt=32.368000, rms=0.741 (0.229%), neg=0, invalid=96777 0022: dt=32.368000, rms=0.740 (0.188%), neg=0, invalid=96777 0023: dt=32.368000, rms=0.738 (0.180%), neg=0, invalid=96777 0024: dt=32.368000, rms=0.737 (0.178%), neg=0, invalid=96777 0025: dt=32.368000, rms=0.736 (0.162%), neg=0, invalid=96777 0026: dt=32.368000, rms=0.735 (0.144%), neg=0, invalid=96777 0027: dt=32.368000, rms=0.734 (0.143%), neg=0, invalid=96777 0028: dt=32.368000, rms=0.733 (0.159%), neg=0, invalid=96777 0029: dt=32.368000, rms=0.731 (0.170%), neg=0, invalid=96777 0030: dt=32.368000, rms=0.730 (0.169%), neg=0, invalid=96777 0031: dt=32.368000, rms=0.729 (0.145%), neg=0, invalid=96777 0032: dt=32.368000, rms=0.728 (0.135%), neg=0, invalid=96777 0033: dt=32.368000, rms=0.727 (0.125%), neg=0, invalid=96777 0034: dt=32.368000, rms=0.726 (0.116%), neg=0, invalid=96777 0035: dt=32.368000, rms=0.726 (0.105%), neg=0, invalid=96777 0036: dt=1479.680000, rms=0.722 (0.481%), neg=0, invalid=96777 0037: dt=32.368000, rms=0.721 (0.141%), neg=0, invalid=96777 0038: dt=32.368000, rms=0.721 (0.036%), neg=0, invalid=96777 0039: dt=32.368000, rms=0.721 (-0.015%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.721, neg=0, invalid=96777 0040: dt=73.984000, rms=0.720 (0.075%), neg=0, invalid=96777 0041: dt=295.936000, rms=0.719 (0.186%), neg=0, invalid=96777 0042: dt=443.904000, rms=0.718 (0.153%), neg=0, invalid=96777 0043: dt=443.904000, rms=0.718 (-0.118%), neg=0, invalid=96777 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.722, neg=0, invalid=96777 0044: dt=145.152000, rms=0.704 (2.480%), neg=0, invalid=96777 0045: dt=124.416000, rms=0.694 (1.496%), neg=0, invalid=96777 0046: dt=25.920000, rms=0.688 (0.745%), neg=0, invalid=96777 0047: dt=145.152000, rms=0.681 (1.090%), neg=0, invalid=96777 0048: dt=36.288000, rms=0.678 (0.408%), neg=0, invalid=96777 0049: dt=145.152000, rms=0.672 (0.838%), neg=0, invalid=96777 0050: dt=15.552000, rms=0.671 (0.263%), neg=0, invalid=96777 0051: dt=36.288000, rms=0.670 (0.136%), neg=0, invalid=96777 0052: dt=36.288000, rms=0.668 (0.251%), neg=0, invalid=96777 0053: dt=36.288000, rms=0.666 (0.305%), neg=0, invalid=96777 0054: dt=36.288000, rms=0.664 (0.363%), neg=0, invalid=96777 0055: dt=36.288000, rms=0.660 (0.476%), neg=0, invalid=96777 0056: dt=36.288000, rms=0.657 (0.588%), neg=0, invalid=96777 0057: dt=36.288000, rms=0.653 (0.557%), neg=0, invalid=96777 0058: dt=36.288000, rms=0.650 (0.483%), neg=0, invalid=96777 0059: dt=36.288000, rms=0.647 (0.448%), neg=0, invalid=96777 0060: dt=36.288000, rms=0.644 (0.463%), neg=0, invalid=96777 0061: dt=36.288000, rms=0.641 (0.428%), neg=0, invalid=96777 0062: dt=36.288000, rms=0.639 (0.360%), neg=0, invalid=96777 0063: dt=36.288000, rms=0.637 (0.300%), neg=0, invalid=96777 0064: dt=36.288000, rms=0.635 (0.317%), neg=0, invalid=96777 0065: dt=36.288000, rms=0.633 (0.291%), neg=0, invalid=96777 0066: dt=36.288000, rms=0.631 (0.240%), neg=0, invalid=96777 0067: dt=36.288000, rms=0.630 (0.205%), neg=0, invalid=96777 0068: dt=36.288000, rms=0.629 (0.202%), neg=0, invalid=96777 0069: dt=36.288000, rms=0.628 (0.196%), neg=0, invalid=96777 0070: dt=36.288000, rms=0.627 (0.141%), neg=0, invalid=96777 0071: dt=36.288000, rms=0.626 (0.097%), neg=0, invalid=96777 0072: dt=36.288000, rms=0.625 (0.114%), neg=0, invalid=96777 0073: dt=36.288000, rms=0.625 (0.149%), neg=0, invalid=96777 0074: dt=36.288000, rms=0.624 (0.137%), neg=0, invalid=96777 0075: dt=36.288000, rms=0.623 (0.113%), neg=0, invalid=96777 0076: dt=36.288000, rms=0.622 (0.111%), neg=0, invalid=96777 0077: dt=36.288000, rms=0.622 (0.007%), neg=0, invalid=96777 0078: dt=36.288000, rms=0.622 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.622, neg=0, invalid=96777 0079: dt=36.288000, rms=0.622 (0.052%), neg=0, invalid=96777 0080: dt=25.920000, rms=0.622 (0.014%), neg=0, invalid=96777 0081: dt=25.920000, rms=0.622 (-0.011%), neg=0, invalid=96777 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.649, neg=0, invalid=96777 0082: dt=0.000000, rms=0.649 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.649, neg=0, invalid=96777 0083: dt=0.000000, rms=0.649 (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=0.730, neg=0, invalid=96777 0084: dt=4.939759, rms=0.707 (3.214%), neg=0, invalid=96777 0085: dt=2.880000, rms=0.705 (0.187%), neg=0, invalid=96777 0086: dt=2.880000, rms=0.705 (-0.047%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.705, neg=0, invalid=96777 0087: dt=0.000000, rms=0.705 (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=0.778, neg=0, invalid=96777 0088: dt=1.278926, rms=0.771 (0.800%), neg=0, invalid=96777 0089: dt=2.075117, rms=0.764 (0.918%), neg=0, invalid=96777 0090: dt=0.474138, rms=0.764 (0.108%), neg=0, invalid=96777 0091: dt=0.474138, rms=0.763 (0.037%), neg=0, invalid=96777 0092: dt=0.474138, rms=0.763 (0.032%), neg=0, invalid=96777 0093: dt=0.474138, rms=0.763 (0.001%), neg=0, invalid=96777 0094: dt=1.792000, rms=0.762 (0.137%), neg=0, invalid=96777 0095: dt=0.112000, rms=0.762 (0.005%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.762, neg=0, invalid=96777 0096: dt=0.448000, rms=0.762 (0.047%), neg=0, invalid=96777 0097: dt=0.112000, rms=0.762 (-0.003%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.723, neg=0, invalid=96777 0098: dt=0.448000, rms=0.700 (3.088%), neg=0, invalid=96777 0099: dt=0.000000, rms=0.700 (0.006%), neg=0, invalid=96777 0100: dt=0.050000, rms=0.700 (-0.558%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.700, neg=0, invalid=96777 0101: dt=0.000000, rms=0.700 (0.000%), neg=0, invalid=96777 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.13388 ( 9) Left_Lateral_Ventricle (4): linear fit = 0.28 x + 0.0 (1805 voxels, overlap=0.006) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (1805 voxels, peak = 7), gca=9.6 gca peak = 0.14022 (22) mri peak = 0.11438 ( 8) Right_Lateral_Ventricle (43): linear fit = 0.32 x + 0.0 (995 voxels, overlap=0.007) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (995 voxels, peak = 7), gca=8.8 gca peak = 0.24234 (100) mri peak = 0.07713 (89) Right_Pallidum (52): linear fit = 0.92 x + 0.0 (435 voxels, overlap=0.104) Right_Pallidum (52): linear fit = 0.92 x + 0.0 (435 voxels, peak = 92), gca=91.5 gca peak = 0.19192 (97) mri peak = 0.07113 (86) Left_Pallidum (13): linear fit = 0.88 x + 0.0 (268 voxels, overlap=0.558) Left_Pallidum (13): linear fit = 0.88 x + 0.0 (268 voxels, peak = 85), gca=84.9 gca peak = 0.24007 (63) mri peak = 0.06438 (63) Right_Hippocampus (53): linear fit = 0.90 x + 0.0 (548 voxels, overlap=0.725) Right_Hippocampus (53): linear fit = 0.90 x + 0.0 (548 voxels, peak = 57), gca=57.0 gca peak = 0.29892 (64) mri peak = 0.07181 (61) Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (633 voxels, overlap=0.930) Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (633 voxels, peak = 59), gca=59.2 gca peak = 0.12541 (104) mri peak = 0.08267 (106) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (76042 voxels, overlap=0.760) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (76042 voxels, peak = 108), gca=107.6 gca peak = 0.13686 (104) mri peak = 0.08044 (107) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (78479 voxels, overlap=0.713) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (78479 voxels, peak = 108), gca=107.6 gca peak = 0.11691 (63) mri peak = 0.05104 (54) Left_Cerebral_Cortex (3): linear fit = 0.85 x + 0.0 (21575 voxels, overlap=0.379) Left_Cerebral_Cortex (3): linear fit = 0.85 x + 0.0 (21575 voxels, peak = 53), gca=53.2 gca peak = 0.13270 (63) mri peak = 0.04791 (52) Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (21648 voxels, overlap=0.382) Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (21648 voxels, peak = 52), gca=52.0 gca peak = 0.15182 (70) mri peak = 0.09658 (64) Right_Caudate (50): linear fit = 0.89 x + 0.0 (470 voxels, overlap=0.363) Right_Caudate (50): linear fit = 0.89 x + 0.0 (470 voxels, peak = 63), gca=62.6 gca peak = 0.14251 (76) mri peak = 0.07769 (68) Left_Caudate (11): linear fit = 0.85 x + 0.0 (845 voxels, overlap=0.365) Left_Caudate (11): linear fit = 0.85 x + 0.0 (845 voxels, peak = 64), gca=64.2 gca peak = 0.12116 (60) mri peak = 0.04100 (51) Left_Cerebellum_Cortex (8): linear fit = 0.88 x + 0.0 (13216 voxels, overlap=0.498) Left_Cerebellum_Cortex (8): linear fit = 0.88 x + 0.0 (13216 voxels, peak = 53), gca=53.1 gca peak = 0.12723 (61) mri peak = 0.04605 (51) Right_Cerebellum_Cortex (47): linear fit = 0.92 x + 0.0 (14246 voxels, overlap=0.732) Right_Cerebellum_Cortex (47): linear fit = 0.92 x + 0.0 (14246 voxels, peak = 56), gca=55.8 gca peak = 0.22684 (88) mri peak = 0.07191 (90) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (7317 voxels, overlap=0.904) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (7317 voxels, peak = 91), gca=91.1 gca peak = 0.21067 (87) mri peak = 0.07444 (87) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (6810 voxels, overlap=0.923) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (6810 voxels, peak = 89), gca=89.2 gca peak = 0.25455 (62) mri peak = 0.09069 (63) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (413 voxels, overlap=0.999) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (413 voxels, peak = 62), gca=62.0 gca peak = 0.39668 (62) mri peak = 0.08782 (54) Right_Amygdala (54): linear fit = 0.88 x + 0.0 (364 voxels, overlap=0.997) Right_Amygdala (54): linear fit = 0.88 x + 0.0 (364 voxels, peak = 54), gca=54.2 gca peak = 0.10129 (93) mri peak = 0.05045 (95) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (5858 voxels, overlap=0.987) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (5858 voxels, peak = 94), gca=94.4 gca peak = 0.12071 (89) mri peak = 0.05184 (87) Right_Thalamus_Proper (49): linear fit = 0.96 x + 0.0 (3750 voxels, overlap=0.972) Right_Thalamus_Proper (49): linear fit = 0.96 x + 0.0 (3750 voxels, peak = 86), gca=85.9 gca peak = 0.13716 (82) mri peak = 0.05498 (79) Left_Putamen (12): linear fit = 0.95 x + 0.0 (2334 voxels, overlap=0.826) Left_Putamen (12): linear fit = 0.95 x + 0.0 (2334 voxels, peak = 78), gca=78.3 gca peak = 0.15214 (84) mri peak = 0.04022 (73) Right_Putamen (51): linear fit = 0.86 x + 0.0 (2222 voxels, overlap=0.338) Right_Putamen (51): linear fit = 0.86 x + 0.0 (2222 voxels, peak = 72), gca=71.8 gca peak = 0.08983 (85) mri peak = 0.06721 (86) Brain_Stem (16): linear fit = 1.04 x + 0.0 (11530 voxels, overlap=0.778) Brain_Stem (16): linear fit = 1.04 x + 0.0 (11530 voxels, peak = 89), gca=88.8 gca peak = 0.11809 (92) mri peak = 0.07593 (94) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (814 voxels, overlap=0.681) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (814 voxels, peak = 94), gca=94.3 gca peak = 0.12914 (94) mri peak = 0.06676 (94) Left_VentralDC (28): linear fit = 1.01 x + 0.0 (982 voxels, overlap=0.802) Left_VentralDC (28): linear fit = 1.01 x + 0.0 (982 voxels, peak = 95), gca=95.4 gca peak = 0.21100 (36) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13542 (27) mri peak = 0.11251 (10) Fourth_Ventricle (15): linear fit = 0.37 x + 0.0 (384 voxels, overlap=0.027) Fourth_Ventricle (15): linear fit = 0.37 x + 0.0 (384 voxels, peak = 10), gca=9.9 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak Third_Ventricle = 0.21100 (36) gca peak Fourth_Ventricle = 0.13542 (27) gca peak CSF = 0.17123 (45) gca peak Left_Accumbens_area = 0.25875 (69) gca peak Left_undetermined = 0.96240 (36) gca peak Left_vessel = 0.33262 (65) gca peak Left_choroid_plexus = 0.09846 (46) gca peak Right_Inf_Lat_Vent = 0.28113 (34) gca peak Right_Accumbens_area = 0.27120 (72) gca peak Right_vessel = 0.61915 (60) gca peak Right_choroid_plexus = 0.12775 (51) gca peak Fifth_Ventricle = 0.45329 (44) gca peak WM_hypointensities = 0.11729 (81) gca peak non_WM_hypointensities = 0.10912 (56) gca peak Optic_Chiasm = 0.33287 (75) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 0.90 x + 0.0 estimating mean wm scale to be 1.03 x + 0.0 estimating mean csf scale to be 0.40 x + 0.0 saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.723, neg=0, invalid=96777 0102: dt=129.472000, rms=0.717 (0.854%), neg=0, invalid=96777 0103: dt=129.472000, rms=0.714 (0.329%), neg=0, invalid=96777 0104: dt=295.936000, rms=0.710 (0.512%), neg=0, invalid=96777 0105: dt=32.368000, rms=0.710 (0.107%), neg=0, invalid=96777 0106: dt=73.984000, rms=0.709 (0.062%), neg=0, invalid=96777 0107: dt=517.888000, rms=0.706 (0.399%), neg=0, invalid=96777 0108: dt=32.368000, rms=0.706 (0.113%), neg=0, invalid=96777 0109: dt=32.368000, rms=0.705 (0.034%), neg=0, invalid=96777 0110: dt=32.368000, rms=0.705 (0.021%), neg=0, invalid=96777 0111: dt=32.368000, rms=0.705 (0.029%), neg=0, invalid=96777 0112: dt=32.368000, rms=0.705 (0.045%), neg=0, invalid=96777 0113: dt=32.368000, rms=0.704 (0.072%), neg=0, invalid=96777 0114: dt=32.368000, rms=0.704 (0.088%), neg=0, invalid=96777 0115: dt=32.368000, rms=0.703 (0.100%), neg=0, invalid=96777 0116: dt=32.368000, rms=0.702 (0.096%), neg=0, invalid=96777 0117: dt=32.368000, rms=0.702 (0.096%), neg=0, invalid=96777 0118: dt=32.368000, rms=0.701 (0.093%), neg=0, invalid=96777 0119: dt=32.368000, rms=0.700 (0.088%), neg=0, invalid=96777 0120: dt=32.368000, rms=0.700 (0.087%), neg=0, invalid=96777 0121: dt=32.368000, rms=0.699 (0.087%), neg=0, invalid=96777 0122: dt=32.368000, rms=0.699 (0.083%), neg=0, invalid=96777 0123: dt=32.368000, rms=0.698 (0.076%), neg=0, invalid=96777 0124: dt=32.368000, rms=0.697 (0.074%), neg=0, invalid=96777 0125: dt=32.368000, rms=0.697 (0.073%), neg=0, invalid=96777 0126: dt=32.368000, rms=0.696 (0.074%), neg=0, invalid=96777 0127: dt=32.368000, rms=0.696 (0.070%), neg=0, invalid=96777 0128: dt=32.368000, rms=0.695 (0.068%), neg=0, invalid=96777 0129: dt=32.368000, rms=0.695 (0.066%), neg=0, invalid=96777 0130: dt=32.368000, rms=0.695 (0.061%), neg=0, invalid=96777 0131: dt=32.368000, rms=0.694 (0.064%), neg=0, invalid=96777 0132: dt=32.368000, rms=0.694 (0.056%), neg=0, invalid=96777 0133: dt=32.368000, rms=0.693 (0.056%), neg=0, invalid=96777 0134: dt=32.368000, rms=0.693 (0.048%), neg=0, invalid=96777 0135: dt=32.368000, rms=0.693 (0.046%), neg=0, invalid=96777 0136: dt=32.368000, rms=0.692 (0.053%), neg=0, invalid=96777 0137: dt=32.368000, rms=0.692 (0.055%), neg=0, invalid=96777 0138: dt=32.368000, rms=0.692 (0.054%), neg=0, invalid=96777 0139: dt=32.368000, rms=0.691 (0.049%), neg=0, invalid=96777 0140: dt=32.368000, rms=0.691 (0.045%), neg=0, invalid=96777 0141: dt=32.368000, rms=0.691 (0.041%), neg=0, invalid=96777 0142: dt=32.368000, rms=0.690 (0.040%), neg=0, invalid=96777 0143: dt=32.368000, rms=0.690 (0.038%), neg=0, invalid=96777 0144: dt=32.368000, rms=0.690 (0.042%), neg=0, invalid=96777 0145: dt=32.368000, rms=0.690 (0.043%), neg=0, invalid=96777 0146: dt=32.368000, rms=0.689 (0.043%), neg=0, invalid=96777 0147: dt=32.368000, rms=0.689 (0.042%), neg=0, invalid=96777 0148: dt=32.368000, rms=0.689 (0.041%), neg=0, invalid=96777 0149: dt=32.368000, rms=0.688 (0.036%), neg=0, invalid=96777 0150: dt=32.368000, rms=0.688 (0.034%), neg=0, invalid=96777 0151: dt=32.368000, rms=0.688 (0.036%), neg=0, invalid=96777 0152: dt=32.368000, rms=0.688 (0.033%), neg=0, invalid=96777 0153: dt=32.368000, rms=0.687 (0.031%), neg=0, invalid=96777 0154: dt=32.368000, rms=0.687 (0.029%), neg=0, invalid=96777 0155: dt=32.368000, rms=0.687 (0.029%), neg=0, invalid=96777 0156: dt=32.368000, rms=0.687 (0.030%), neg=0, invalid=96777 0157: dt=32.368000, rms=0.687 (0.030%), neg=0, invalid=96777 0158: dt=32.368000, rms=0.686 (0.030%), neg=0, invalid=96777 0159: dt=32.368000, rms=0.686 (0.028%), neg=0, invalid=96777 0160: dt=32.368000, rms=0.686 (0.029%), neg=0, invalid=96777 0161: dt=32.368000, rms=0.686 (0.029%), neg=0, invalid=96777 0162: dt=32.368000, rms=0.686 (0.027%), neg=0, invalid=96777 0163: dt=32.368000, rms=0.686 (0.025%), neg=0, invalid=96777 0164: dt=32.368000, rms=0.685 (0.028%), neg=0, invalid=96777 0165: dt=32.368000, rms=0.685 (0.027%), neg=0, invalid=96777 0166: dt=32.368000, rms=0.685 (0.027%), neg=0, invalid=96777 0167: dt=32.368000, rms=0.685 (0.026%), neg=0, invalid=96777 0168: dt=32.368000, rms=0.685 (0.026%), neg=0, invalid=96777 0169: dt=32.368000, rms=0.684 (0.025%), neg=0, invalid=96777 0170: dt=32.368000, rms=0.684 (0.025%), neg=0, invalid=96777 0171: dt=129.472000, rms=0.684 (0.001%), neg=0, invalid=96777 0172: dt=129.472000, rms=0.684 (0.021%), neg=0, invalid=96777 0173: dt=129.472000, rms=0.684 (0.013%), neg=0, invalid=96777 0174: dt=129.472000, rms=0.684 (0.016%), neg=0, invalid=96777 0175: dt=129.472000, rms=0.684 (0.031%), neg=0, invalid=96777 0176: dt=129.472000, rms=0.683 (0.043%), neg=0, invalid=96777 0177: dt=129.472000, rms=0.683 (0.036%), neg=0, invalid=96777 0178: dt=129.472000, rms=0.683 (0.030%), neg=0, invalid=96777 0179: dt=129.472000, rms=0.683 (0.065%), neg=0, invalid=96777 0180: dt=129.472000, rms=0.682 (0.052%), neg=0, invalid=96777 0181: dt=129.472000, rms=0.682 (0.032%), neg=0, invalid=96777 0182: dt=129.472000, rms=0.682 (0.055%), neg=0, invalid=96777 0183: dt=129.472000, rms=0.681 (0.049%), neg=0, invalid=96777 0184: dt=129.472000, rms=0.681 (0.038%), neg=0, invalid=96777 0185: dt=129.472000, rms=0.681 (0.057%), neg=0, invalid=96777 0186: dt=129.472000, rms=0.680 (0.049%), neg=0, invalid=96777 0187: dt=129.472000, rms=0.680 (0.044%), neg=0, invalid=96777 0188: dt=129.472000, rms=0.680 (0.048%), neg=0, invalid=96777 0189: dt=129.472000, rms=0.679 (0.048%), neg=0, invalid=96777 0190: dt=129.472000, rms=0.679 (0.039%), neg=0, invalid=96777 0191: dt=129.472000, rms=0.679 (0.033%), neg=0, invalid=96777 0192: dt=129.472000, rms=0.678 (0.050%), neg=0, invalid=96777 0193: dt=129.472000, rms=0.678 (0.040%), neg=0, invalid=96777 0194: dt=129.472000, rms=0.678 (0.033%), neg=0, invalid=96777 0195: dt=129.472000, rms=0.678 (0.038%), neg=0, invalid=96777 0196: dt=129.472000, rms=0.677 (0.035%), neg=0, invalid=96777 0197: dt=129.472000, rms=0.677 (0.042%), neg=0, invalid=96777 0198: dt=129.472000, rms=0.677 (0.036%), neg=0, invalid=96777 0199: dt=129.472000, rms=0.677 (0.032%), neg=0, invalid=96777 0200: dt=129.472000, rms=0.676 (0.050%), neg=0, invalid=96777 0201: dt=129.472000, rms=0.676 (0.029%), neg=0, invalid=96777 0202: dt=129.472000, rms=0.676 (0.026%), neg=0, invalid=96777 0203: dt=129.472000, rms=0.676 (0.037%), neg=0, invalid=96777 0204: dt=129.472000, rms=0.676 (0.023%), neg=0, invalid=96777 0205: dt=129.472000, rms=0.675 (0.028%), neg=0, invalid=96777 0206: dt=129.472000, rms=0.675 (0.035%), neg=0, invalid=96777 0207: dt=129.472000, rms=0.675 (0.031%), neg=0, invalid=96777 0208: dt=129.472000, rms=0.675 (0.024%), neg=0, invalid=96777 0209: dt=129.472000, rms=0.675 (0.033%), neg=0, invalid=96777 0210: dt=129.472000, rms=0.674 (0.032%), neg=0, invalid=96777 0211: dt=129.472000, rms=0.674 (0.021%), neg=0, invalid=96777 0212: dt=129.472000, rms=0.674 (0.022%), neg=0, invalid=96777 0213: dt=129.472000, rms=0.674 (0.032%), neg=0, invalid=96777 0214: dt=129.472000, rms=0.674 (0.030%), neg=0, invalid=96777 0215: dt=129.472000, rms=0.674 (0.019%), neg=0, invalid=96777 0216: dt=129.472000, rms=0.673 (0.015%), neg=0, invalid=96777 0217: dt=295.936000, rms=0.673 (0.025%), neg=0, invalid=96777 0218: dt=6.936000, rms=0.673 (0.002%), neg=0, invalid=96777 0219: dt=6.936000, rms=0.673 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.673, neg=0, invalid=96777 0220: dt=73.984000, rms=0.673 (0.041%), neg=0, invalid=96777 0221: dt=369.920000, rms=0.672 (0.146%), neg=0, invalid=96777 0222: dt=6.936000, rms=0.672 (0.003%), neg=0, invalid=96777 0223: dt=6.936000, rms=0.672 (-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=0.673, neg=0, invalid=96777 0224: dt=103.680000, rms=0.669 (0.598%), neg=0, invalid=96777 0225: dt=62.208000, rms=0.664 (0.693%), neg=0, invalid=96777 0226: dt=15.552000, rms=0.663 (0.204%), neg=0, invalid=96777 0227: dt=124.416000, rms=0.661 (0.329%), neg=0, invalid=96777 0228: dt=31.104000, rms=0.656 (0.676%), neg=0, invalid=96777 0229: dt=25.920000, rms=0.656 (0.073%), neg=0, invalid=96777 0230: dt=145.152000, rms=0.652 (0.595%), neg=0, invalid=96777 0231: dt=15.552000, rms=0.650 (0.244%), neg=0, invalid=96777 0232: dt=36.288000, rms=0.650 (0.086%), neg=0, invalid=96777 0233: dt=82.944000, rms=0.648 (0.361%), neg=0, invalid=96777 0234: dt=9.072000, rms=0.647 (0.092%), neg=0, invalid=96777 0235: dt=9.072000, rms=0.647 (0.038%), neg=0, invalid=96777 0236: dt=9.072000, rms=0.647 (0.030%), neg=0, invalid=96777 0237: dt=9.072000, rms=0.646 (0.043%), neg=0, invalid=96777 0238: dt=9.072000, rms=0.646 (0.070%), neg=0, invalid=96777 0239: dt=9.072000, rms=0.645 (0.100%), neg=0, invalid=96777 0240: dt=9.072000, rms=0.644 (0.136%), neg=0, invalid=96777 0241: dt=9.072000, rms=0.643 (0.165%), neg=0, invalid=96777 0242: dt=9.072000, rms=0.642 (0.173%), neg=0, invalid=96777 0243: dt=9.072000, rms=0.641 (0.171%), neg=0, invalid=96777 0244: dt=9.072000, rms=0.640 (0.169%), neg=0, invalid=96777 0245: dt=9.072000, rms=0.639 (0.165%), neg=0, invalid=96777 0246: dt=9.072000, rms=0.638 (0.161%), neg=0, invalid=96777 0247: dt=9.072000, rms=0.637 (0.160%), neg=0, invalid=96777 0248: dt=9.072000, rms=0.636 (0.161%), neg=0, invalid=96777 0249: dt=9.072000, rms=0.635 (0.173%), neg=0, invalid=96777 0250: dt=9.072000, rms=0.634 (0.170%), neg=0, invalid=96777 0251: dt=9.072000, rms=0.633 (0.164%), neg=0, invalid=96777 0252: dt=9.072000, rms=0.632 (0.161%), neg=0, invalid=96777 0253: dt=9.072000, rms=0.631 (0.150%), neg=0, invalid=96777 0254: dt=9.072000, rms=0.630 (0.146%), neg=0, invalid=96777 0255: dt=9.072000, rms=0.629 (0.139%), neg=0, invalid=96777 0256: dt=9.072000, rms=0.628 (0.136%), neg=0, invalid=96777 0257: dt=9.072000, rms=0.627 (0.135%), neg=0, invalid=96777 0258: dt=9.072000, rms=0.626 (0.139%), neg=0, invalid=96777 0259: dt=9.072000, rms=0.625 (0.133%), neg=0, invalid=96777 0260: dt=9.072000, rms=0.625 (0.137%), neg=0, invalid=96777 0261: dt=9.072000, rms=0.624 (0.128%), neg=0, invalid=96777 0262: dt=9.072000, rms=0.623 (0.127%), neg=0, invalid=96777 0263: dt=9.072000, rms=0.622 (0.123%), neg=0, invalid=96777 0264: dt=9.072000, rms=0.621 (0.121%), neg=0, invalid=96777 0265: dt=9.072000, rms=0.621 (0.118%), neg=0, invalid=96777 0266: dt=9.072000, rms=0.620 (0.116%), neg=0, invalid=96777 0267: dt=9.072000, rms=0.619 (0.109%), neg=0, invalid=96777 0268: dt=9.072000, rms=0.619 (0.110%), neg=0, invalid=96777 0269: dt=9.072000, rms=0.618 (0.103%), neg=0, invalid=96777 0270: dt=9.072000, rms=0.617 (0.094%), neg=0, invalid=96777 0271: dt=9.072000, rms=0.617 (0.088%), neg=0, invalid=96777 0272: dt=9.072000, rms=0.616 (0.088%), neg=0, invalid=96777 0273: dt=9.072000, rms=0.616 (0.084%), neg=0, invalid=96777 0274: dt=9.072000, rms=0.615 (0.089%), neg=0, invalid=96777 0275: dt=9.072000, rms=0.615 (0.089%), neg=0, invalid=96777 0276: dt=9.072000, rms=0.614 (0.080%), neg=0, invalid=96777 0277: dt=9.072000, rms=0.614 (0.082%), neg=0, invalid=96777 0278: dt=9.072000, rms=0.613 (0.078%), neg=0, invalid=96777 0279: dt=9.072000, rms=0.613 (0.076%), neg=0, invalid=96777 0280: dt=9.072000, rms=0.612 (0.072%), neg=0, invalid=96777 0281: dt=9.072000, rms=0.612 (0.071%), neg=0, invalid=96777 0282: dt=9.072000, rms=0.611 (0.068%), neg=0, invalid=96777 0283: dt=9.072000, rms=0.611 (0.067%), neg=0, invalid=96777 0284: dt=9.072000, rms=0.611 (0.064%), neg=0, invalid=96777 0285: dt=9.072000, rms=0.610 (0.061%), neg=0, invalid=96777 0286: dt=9.072000, rms=0.610 (0.061%), neg=0, invalid=96777 0287: dt=9.072000, rms=0.610 (0.059%), neg=0, invalid=96777 0288: dt=9.072000, rms=0.609 (0.059%), neg=0, invalid=96777 0289: dt=9.072000, rms=0.609 (0.058%), neg=0, invalid=96777 0290: dt=9.072000, rms=0.609 (0.055%), neg=0, invalid=96777 0291: dt=9.072000, rms=0.608 (0.049%), neg=0, invalid=96777 0292: dt=9.072000, rms=0.608 (0.053%), neg=0, invalid=96777 0293: dt=9.072000, rms=0.608 (0.052%), neg=0, invalid=96777 0294: dt=9.072000, rms=0.607 (0.053%), neg=0, invalid=96777 0295: dt=9.072000, rms=0.607 (0.050%), neg=0, invalid=96777 0296: dt=9.072000, rms=0.607 (0.048%), neg=0, invalid=96777 0297: dt=9.072000, rms=0.606 (0.045%), neg=0, invalid=96777 0298: dt=9.072000, rms=0.606 (0.045%), neg=0, invalid=96777 0299: dt=9.072000, rms=0.606 (0.046%), neg=0, invalid=96777 0300: dt=9.072000, rms=0.606 (0.043%), neg=0, invalid=96777 0301: dt=9.072000, rms=0.605 (0.043%), neg=0, invalid=96777 0302: dt=9.072000, rms=0.605 (0.045%), neg=0, invalid=96777 0303: dt=9.072000, rms=0.605 (0.049%), neg=0, invalid=96777 0304: dt=9.072000, rms=0.604 (0.045%), neg=0, invalid=96777 0305: dt=9.072000, rms=0.604 (0.043%), neg=0, invalid=96777 0306: dt=9.072000, rms=0.604 (0.042%), neg=0, invalid=96777 0307: dt=9.072000, rms=0.604 (0.043%), neg=0, invalid=96777 0308: dt=9.072000, rms=0.603 (0.039%), neg=0, invalid=96777 0309: dt=9.072000, rms=0.603 (0.034%), neg=0, invalid=96777 0310: dt=9.072000, rms=0.603 (0.035%), neg=0, invalid=96777 0311: dt=9.072000, rms=0.603 (0.029%), neg=0, invalid=96777 0312: dt=9.072000, rms=0.603 (0.034%), neg=0, invalid=96777 0313: dt=9.072000, rms=0.602 (0.040%), neg=0, invalid=96777 0314: dt=9.072000, rms=0.602 (0.040%), neg=0, invalid=96777 0315: dt=9.072000, rms=0.602 (0.040%), neg=0, invalid=96777 0316: dt=9.072000, rms=0.602 (0.042%), neg=0, invalid=96777 0317: dt=9.072000, rms=0.602 (0.032%), neg=0, invalid=96777 0318: dt=9.072000, rms=0.601 (0.036%), neg=0, invalid=96777 0319: dt=9.072000, rms=0.601 (0.027%), neg=0, invalid=96777 0320: dt=9.072000, rms=0.601 (0.034%), neg=0, invalid=96777 0321: dt=9.072000, rms=0.601 (0.037%), neg=0, invalid=96777 0322: dt=9.072000, rms=0.600 (0.039%), neg=0, invalid=96777 0323: dt=9.072000, rms=0.600 (0.039%), neg=0, invalid=96777 0324: dt=9.072000, rms=0.600 (0.035%), neg=0, invalid=96777 0325: dt=9.072000, rms=0.600 (0.033%), neg=0, invalid=96777 0326: dt=9.072000, rms=0.600 (0.036%), neg=0, invalid=96777 0327: dt=9.072000, rms=0.599 (0.031%), neg=0, invalid=96777 0328: dt=9.072000, rms=0.599 (0.027%), neg=0, invalid=96777 0329: dt=9.072000, rms=0.599 (0.032%), neg=0, invalid=96777 0330: dt=9.072000, rms=0.599 (0.034%), neg=0, invalid=96777 0331: dt=9.072000, rms=0.599 (0.031%), neg=0, invalid=96777 0332: dt=9.072000, rms=0.599 (0.032%), neg=0, invalid=96777 0333: dt=9.072000, rms=0.598 (0.035%), neg=0, invalid=96777 0334: dt=9.072000, rms=0.598 (0.032%), neg=0, invalid=96777 0335: dt=9.072000, rms=0.598 (0.031%), neg=0, invalid=96777 0336: dt=9.072000, rms=0.598 (0.029%), neg=0, invalid=96777 0337: dt=9.072000, rms=0.598 (0.030%), neg=0, invalid=96777 0338: dt=9.072000, rms=0.597 (0.028%), neg=0, invalid=96777 0339: dt=9.072000, rms=0.597 (0.034%), neg=0, invalid=96777 0340: dt=9.072000, rms=0.597 (0.026%), neg=0, invalid=96777 0341: dt=9.072000, rms=0.597 (0.027%), neg=0, invalid=96777 0342: dt=9.072000, rms=0.597 (0.024%), neg=0, invalid=96777 0343: dt=9.072000, rms=0.597 (0.023%), neg=0, invalid=96777 0344: dt=580.608000, rms=0.596 (0.112%), neg=0, invalid=96777 0345: dt=15.552000, rms=0.596 (0.036%), neg=0, invalid=96777 0346: dt=15.552000, rms=0.596 (0.007%), neg=0, invalid=96777 0347: dt=15.552000, rms=0.596 (-0.008%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.596, neg=0, invalid=96777 0348: dt=82.944000, rms=0.594 (0.219%), neg=0, invalid=96777 0349: dt=36.288000, rms=0.594 (0.140%), neg=0, invalid=96777 0350: dt=103.680000, rms=0.593 (0.069%), neg=0, invalid=96777 0351: dt=36.288000, rms=0.593 (0.092%), neg=0, invalid=96777 0352: dt=36.288000, rms=0.592 (0.037%), neg=0, invalid=96777 0353: dt=36.288000, rms=0.592 (0.046%), neg=0, invalid=96777 0354: dt=36.288000, rms=0.592 (0.038%), neg=0, invalid=96777 0355: dt=36.288000, rms=0.592 (0.050%), neg=0, invalid=96777 0356: dt=36.288000, rms=0.591 (0.072%), neg=0, invalid=96777 0357: dt=36.288000, rms=0.591 (0.087%), neg=0, invalid=96777 0358: dt=36.288000, rms=0.590 (0.081%), neg=0, invalid=96777 0359: dt=36.288000, rms=0.590 (0.065%), neg=0, invalid=96777 0360: dt=36.288000, rms=0.589 (0.066%), neg=0, invalid=96777 0361: dt=36.288000, rms=0.589 (0.070%), neg=0, invalid=96777 0362: dt=36.288000, rms=0.589 (0.068%), neg=0, invalid=96777 0363: dt=36.288000, rms=0.588 (0.068%), neg=0, invalid=96777 0364: dt=36.288000, rms=0.588 (0.067%), neg=0, invalid=96777 0365: dt=36.288000, rms=0.587 (0.074%), neg=0, invalid=96777 0366: dt=36.288000, rms=0.587 (0.073%), neg=0, invalid=96777 0367: dt=36.288000, rms=0.586 (0.079%), neg=0, invalid=96777 0368: dt=36.288000, rms=0.586 (0.078%), neg=0, invalid=96777 0369: dt=36.288000, rms=0.586 (0.065%), neg=0, invalid=96777 0370: dt=36.288000, rms=0.585 (0.067%), neg=0, invalid=96777 0371: dt=36.288000, rms=0.585 (0.057%), neg=0, invalid=96777 0372: dt=36.288000, rms=0.585 (0.054%), neg=0, invalid=96777 0373: dt=36.288000, rms=0.584 (0.073%), neg=0, invalid=96777 0374: dt=36.288000, rms=0.584 (0.064%), neg=0, invalid=96777 0375: dt=36.288000, rms=0.583 (0.058%), neg=0, invalid=96777 0376: dt=36.288000, rms=0.583 (0.059%), neg=0, invalid=96777 0377: dt=36.288000, rms=0.583 (0.054%), neg=0, invalid=96777 0378: dt=36.288000, rms=0.582 (0.047%), neg=0, invalid=96777 0379: dt=36.288000, rms=0.582 (0.049%), neg=0, invalid=96777 0380: dt=36.288000, rms=0.582 (0.052%), neg=0, invalid=96777 0381: dt=36.288000, rms=0.582 (0.061%), neg=0, invalid=96777 0382: dt=36.288000, rms=0.581 (0.055%), neg=0, invalid=96777 0383: dt=36.288000, rms=0.581 (0.047%), neg=0, invalid=96777 0384: dt=36.288000, rms=0.581 (0.047%), neg=0, invalid=96777 0385: dt=36.288000, rms=0.580 (0.046%), neg=0, invalid=96777 0386: dt=36.288000, rms=0.580 (0.050%), neg=0, invalid=96777 0387: dt=36.288000, rms=0.580 (0.062%), neg=0, invalid=96777 0388: dt=36.288000, rms=0.579 (0.054%), neg=0, invalid=96777 0389: dt=36.288000, rms=0.579 (0.046%), neg=0, invalid=96777 0390: dt=36.288000, rms=0.579 (0.047%), neg=0, invalid=96777 0391: dt=36.288000, rms=0.579 (0.040%), neg=0, invalid=96777 0392: dt=36.288000, rms=0.578 (0.043%), neg=0, invalid=96777 0393: dt=36.288000, rms=0.578 (0.040%), neg=0, invalid=96777 0394: dt=36.288000, rms=0.578 (0.036%), neg=0, invalid=96777 0395: dt=36.288000, rms=0.578 (0.037%), neg=0, invalid=96777 0396: dt=36.288000, rms=0.578 (0.036%), neg=0, invalid=96777 0397: dt=36.288000, rms=0.577 (0.035%), neg=0, invalid=96777 0398: dt=36.288000, rms=0.577 (0.031%), neg=0, invalid=96777 0399: dt=36.288000, rms=0.577 (0.027%), neg=0, invalid=96777 0400: dt=36.288000, rms=0.577 (0.023%), neg=0, invalid=96777 0401: dt=36.288000, rms=0.577 (0.024%), neg=0, invalid=96777 0402: dt=36.288000, rms=0.577 (0.030%), neg=0, invalid=96777 0403: dt=36.288000, rms=0.576 (0.034%), neg=0, invalid=96777 0404: dt=36.288000, rms=0.576 (0.032%), neg=0, invalid=96777 0405: dt=36.288000, rms=0.576 (0.025%), neg=0, invalid=96777 0406: dt=36.288000, rms=0.576 (0.021%), neg=0, invalid=96777 0407: dt=36.288000, rms=0.576 (0.026%), neg=0, invalid=96777 0408: dt=36.288000, rms=0.576 (0.030%), neg=0, invalid=96777 0409: dt=36.288000, rms=0.575 (0.026%), neg=0, invalid=96777 0410: dt=36.288000, rms=0.575 (0.020%), neg=0, invalid=96777 0411: dt=36.288000, rms=0.575 (0.026%), neg=0, invalid=96777 0412: dt=36.288000, rms=0.575 (0.016%), neg=0, invalid=96777 0413: dt=36.288000, rms=0.575 (0.030%), neg=0, invalid=96777 0414: dt=36.288000, rms=0.575 (0.031%), neg=0, invalid=96777 0415: dt=36.288000, rms=0.575 (0.033%), neg=0, invalid=96777 0416: dt=36.288000, rms=0.574 (0.027%), neg=0, invalid=96777 0417: dt=36.288000, rms=0.574 (0.027%), neg=0, invalid=96777 0418: dt=36.288000, rms=0.574 (0.019%), neg=0, invalid=96777 0419: dt=36.288000, rms=0.574 (0.012%), neg=0, invalid=96777 0420: dt=103.680000, rms=0.574 (0.012%), neg=0, invalid=96777 0421: dt=103.680000, rms=0.574 (-0.060%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.582, neg=0, invalid=96777 0422: dt=25.600000, rms=0.580 (0.293%), neg=0, invalid=96777 0423: dt=38.400000, rms=0.578 (0.316%), neg=0, invalid=96777 0424: dt=5.908497, rms=0.578 (0.119%), neg=0, invalid=96777 0425: dt=44.800000, rms=0.575 (0.508%), neg=0, invalid=96777 0426: dt=8.000000, rms=0.574 (0.079%), neg=0, invalid=96777 0427: dt=44.800000, rms=0.571 (0.493%), neg=0, invalid=96777 0428: dt=6.400000, rms=0.571 (0.041%), neg=0, invalid=96777 0429: dt=6.400000, rms=0.571 (0.088%), neg=0, invalid=96777 0430: dt=6.400000, rms=0.570 (0.130%), neg=0, invalid=96777 0431: dt=6.400000, rms=0.569 (0.158%), neg=0, invalid=96777 0432: dt=6.400000, rms=0.568 (0.185%), neg=0, invalid=96777 0433: dt=6.400000, rms=0.567 (0.191%), neg=0, invalid=96777 0434: dt=6.400000, rms=0.565 (0.244%), neg=0, invalid=96777 0435: dt=6.400000, rms=0.564 (0.285%), neg=0, invalid=96777 0436: dt=6.400000, rms=0.562 (0.292%), neg=0, invalid=96777 0437: dt=6.400000, rms=0.561 (0.279%), neg=0, invalid=96777 0438: dt=6.400000, rms=0.559 (0.265%), neg=0, invalid=96777 0439: dt=6.400000, rms=0.558 (0.249%), neg=0, invalid=96777 0440: dt=6.400000, rms=0.556 (0.264%), neg=0, invalid=96777 0441: dt=6.400000, rms=0.555 (0.249%), neg=0, invalid=96777 0442: dt=6.400000, rms=0.553 (0.246%), neg=0, invalid=96777 0443: dt=6.400000, rms=0.552 (0.238%), neg=0, invalid=96777 0444: dt=6.400000, rms=0.551 (0.222%), neg=0, invalid=96777 0445: dt=6.400000, rms=0.550 (0.216%), neg=0, invalid=96777 0446: dt=6.400000, rms=0.549 (0.202%), neg=0, invalid=96777 0447: dt=6.400000, rms=0.548 (0.195%), neg=0, invalid=96777 0448: dt=6.400000, rms=0.547 (0.177%), neg=0, invalid=96777 0449: dt=6.400000, rms=0.546 (0.165%), neg=0, invalid=96777 0450: dt=6.400000, rms=0.545 (0.151%), neg=0, invalid=96777 0451: dt=6.400000, rms=0.544 (0.145%), neg=0, invalid=96777 0452: dt=6.400000, rms=0.543 (0.139%), neg=0, invalid=96777 0453: dt=6.400000, rms=0.543 (0.143%), neg=0, invalid=96777 0454: dt=6.400000, rms=0.542 (0.124%), neg=0, invalid=96777 0455: dt=6.400000, rms=0.541 (0.112%), neg=0, invalid=96777 0456: dt=6.400000, rms=0.541 (0.110%), neg=0, invalid=96777 0457: dt=6.400000, rms=0.540 (0.097%), neg=0, invalid=96777 0458: dt=6.400000, rms=0.540 (0.088%), neg=0, invalid=96777 0459: dt=6.400000, rms=0.539 (0.086%), neg=0, invalid=96777 0460: dt=6.400000, rms=0.539 (0.080%), neg=0, invalid=96777 0461: dt=6.400000, rms=0.538 (0.074%), neg=0, invalid=96777 0462: dt=6.400000, rms=0.538 (0.071%), neg=0, invalid=96777 0463: dt=6.400000, rms=0.538 (0.060%), neg=0, invalid=96777 0464: dt=6.400000, rms=0.537 (0.055%), neg=0, invalid=96777 0465: dt=6.400000, rms=0.537 (0.053%), neg=0, invalid=96777 0466: dt=6.400000, rms=0.537 (0.047%), neg=0, invalid=96777 0467: dt=6.400000, rms=0.537 (0.045%), neg=0, invalid=96777 0468: dt=6.400000, rms=0.536 (0.044%), neg=0, invalid=96777 0469: dt=6.400000, rms=0.536 (0.044%), neg=0, invalid=96777 0470: dt=6.400000, rms=0.536 (0.046%), neg=0, invalid=96777 0471: dt=6.400000, rms=0.536 (0.046%), neg=0, invalid=96777 0472: dt=6.400000, rms=0.535 (0.047%), neg=0, invalid=96777 0473: dt=6.400000, rms=0.535 (0.045%), neg=0, invalid=96777 0474: dt=6.400000, rms=0.535 (0.040%), neg=0, invalid=96777 0475: dt=6.400000, rms=0.535 (0.038%), neg=0, invalid=96777 0476: dt=6.400000, rms=0.535 (0.040%), neg=0, invalid=96777 0477: dt=6.400000, rms=0.534 (0.043%), neg=0, invalid=96777 0478: dt=6.400000, rms=0.534 (0.039%), neg=0, invalid=96777 0479: dt=6.400000, rms=0.534 (0.035%), neg=0, invalid=96777 0480: dt=6.400000, rms=0.534 (0.038%), neg=0, invalid=96777 0481: dt=6.400000, rms=0.533 (0.036%), neg=0, invalid=96777 0482: dt=6.400000, rms=0.533 (0.039%), neg=0, invalid=96777 0483: dt=6.400000, rms=0.533 (0.039%), neg=0, invalid=96777 0484: dt=6.400000, rms=0.533 (0.032%), neg=0, invalid=96777 0485: dt=6.400000, rms=0.533 (0.032%), neg=0, invalid=96777 0486: dt=6.400000, rms=0.533 (0.032%), neg=0, invalid=96777 0487: dt=6.400000, rms=0.532 (0.023%), neg=0, invalid=96777 0488: dt=6.400000, rms=0.532 (0.029%), neg=0, invalid=96777 0489: dt=6.400000, rms=0.532 (0.033%), neg=0, invalid=96777 0490: dt=6.400000, rms=0.532 (0.029%), neg=0, invalid=96777 0491: dt=6.400000, rms=0.532 (0.023%), neg=0, invalid=96777 0492: dt=6.400000, rms=0.532 (0.026%), neg=0, invalid=96777 0493: dt=6.400000, rms=0.532 (0.027%), neg=0, invalid=96777 0494: dt=6.400000, rms=0.531 (0.031%), neg=0, invalid=96777 0495: dt=6.400000, rms=0.531 (0.023%), neg=0, invalid=96777 0496: dt=6.400000, rms=0.531 (0.026%), neg=0, invalid=96777 0497: dt=6.400000, rms=0.531 (0.023%), neg=0, invalid=96777 0498: dt=6.400000, rms=0.531 (0.029%), neg=0, invalid=96777 0499: dt=6.400000, rms=0.531 (0.022%), neg=0, invalid=96777 0500: dt=6.400000, rms=0.531 (0.012%), neg=0, invalid=96777 0501: dt=9.600000, rms=0.531 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.531, neg=0, invalid=96777 0502: dt=38.400000, rms=0.529 (0.297%), neg=0, invalid=96777 0503: dt=9.600000, rms=0.529 (0.033%), neg=0, invalid=96777 0504: dt=9.600000, rms=0.529 (0.035%), neg=0, invalid=96777 0505: dt=9.600000, rms=0.529 (0.024%), neg=0, invalid=96777 0506: dt=9.600000, rms=0.529 (0.018%), neg=0, invalid=96777 0507: dt=32.000000, rms=0.528 (0.015%), neg=0, invalid=96777 0508: dt=32.000000, rms=0.528 (0.026%), neg=0, invalid=96777 0509: dt=32.000000, rms=0.528 (-0.195%), neg=0, invalid=96777 0510: dt=2.800000, rms=0.528 (0.013%), neg=0, invalid=96777 0511: dt=2.800000, rms=0.528 (0.013%), neg=0, invalid=96777 0512: dt=4.800000, rms=0.528 (-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=0.552, neg=0, invalid=96777 0513: dt=0.000000, rms=0.552 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.552, neg=0, invalid=96777 0514: dt=0.000000, rms=0.552 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.599, neg=0, invalid=96777 0515: dt=1.402235, rms=0.593 (0.917%), neg=0, invalid=96777 0516: dt=0.384000, rms=0.593 (0.030%), neg=0, invalid=96777 0517: dt=0.384000, rms=0.593 (-0.017%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.593, neg=0, invalid=96777 0518: dt=0.571429, rms=0.592 (0.093%), neg=0, invalid=96777 0519: dt=0.320000, rms=0.592 (0.013%), neg=0, invalid=96777 0520: dt=0.320000, rms=0.592 (-0.009%), 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=0.545, neg=0, invalid=96777 0521: dt=0.174000, rms=0.537 (1.457%), neg=0, invalid=96777 0522: dt=0.142276, rms=0.532 (0.800%), neg=0, invalid=96777 0523: dt=0.448000, rms=0.523 (1.861%), neg=0, invalid=96777 0524: dt=0.028000, rms=0.522 (0.028%), neg=0, invalid=96777 0525: dt=0.028000, rms=0.522 (0.028%), neg=0, invalid=96777 0526: dt=0.028000, rms=0.522 (0.057%), neg=0, invalid=96777 0527: dt=0.028000, rms=0.522 (0.077%), neg=0, invalid=96777 0528: dt=0.028000, rms=0.521 (0.096%), neg=0, invalid=96777 0529: dt=0.028000, rms=0.520 (0.107%), neg=0, invalid=96777 0530: dt=0.028000, rms=0.520 (0.023%), neg=0, invalid=96777 0531: dt=0.028000, rms=0.520 (0.040%), neg=0, invalid=96777 0532: dt=0.028000, rms=0.520 (0.056%), neg=0, invalid=96777 0533: dt=0.028000, rms=0.519 (0.071%), neg=0, invalid=96777 0534: dt=0.028000, rms=0.519 (0.077%), neg=0, invalid=96777 0535: dt=0.028000, rms=0.519 (0.093%), neg=0, invalid=96777 0536: dt=0.028000, rms=0.518 (0.097%), neg=0, invalid=96777 0537: dt=0.028000, rms=0.518 (0.096%), neg=0, invalid=96777 0538: dt=0.028000, rms=0.517 (0.095%), neg=0, invalid=96777 0539: dt=0.028000, rms=0.517 (0.095%), neg=0, invalid=96777 0540: dt=0.028000, rms=0.516 (0.096%), neg=0, invalid=96777 0541: dt=0.028000, rms=0.516 (0.087%), neg=0, invalid=96777 0542: dt=0.028000, rms=0.515 (0.085%), neg=0, invalid=96777 0543: dt=0.028000, rms=0.515 (0.080%), neg=0, invalid=96777 0544: dt=0.028000, rms=0.514 (0.069%), neg=0, invalid=96777 0545: dt=0.028000, rms=0.514 (0.064%), neg=0, invalid=96777 0546: dt=0.028000, rms=0.514 (0.058%), neg=0, invalid=96777 0547: dt=0.028000, rms=0.514 (0.048%), neg=0, invalid=96777 0548: dt=0.028000, rms=0.513 (0.044%), neg=0, invalid=96777 0549: dt=0.028000, rms=0.513 (0.043%), neg=0, invalid=96777 0550: dt=0.028000, rms=0.513 (0.034%), neg=0, invalid=96777 0551: dt=0.028000, rms=0.513 (0.025%), neg=0, invalid=96777 0552: dt=0.028000, rms=0.513 (0.025%), neg=0, invalid=96777 0553: dt=0.028000, rms=0.513 (0.020%), neg=0, invalid=96777 0554: dt=0.000000, rms=0.513 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.513, neg=0, invalid=96777 0555: dt=0.448000, rms=0.507 (1.106%), neg=0, invalid=96777 0556: dt=0.000000, rms=0.507 (-0.000%), neg=0, invalid=96777 0557: dt=0.050000, rms=0.507 (-0.001%), 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=0.504, neg=0, invalid=96777 0558: dt=0.000000, rms=0.504 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.504, neg=0, invalid=96777 0559: dt=129.472000, rms=0.504 (0.049%), neg=0, invalid=96777 0560: dt=129.472000, rms=0.504 (0.020%), neg=0, invalid=96777 0561: dt=129.472000, rms=0.504 (0.022%), neg=0, invalid=96777 0562: dt=129.472000, rms=0.504 (0.021%), neg=0, invalid=96777 0563: dt=129.472000, rms=0.504 (0.019%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.504, neg=0, invalid=96777 0564: dt=36.288000, rms=0.503 (0.149%), neg=0, invalid=96777 0565: dt=36.288000, rms=0.503 (0.071%), neg=0, invalid=96777 0566: dt=36.288000, rms=0.502 (0.060%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0567: dt=36.288000, rms=0.502 (0.049%), neg=0, invalid=96777 0568: dt=36.288000, rms=0.502 (-0.029%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.502, neg=0, invalid=96777 0569: dt=82.944000, rms=0.501 (0.325%), neg=0, invalid=96777 0570: dt=36.288000, rms=0.500 (0.156%), neg=0, invalid=96777 0571: dt=36.288000, rms=0.500 (0.017%), neg=0, invalid=96777 0572: dt=36.288000, rms=0.499 (0.116%), neg=0, invalid=96777 0573: dt=36.288000, rms=0.498 (0.149%), neg=0, invalid=96777 0574: dt=36.288000, rms=0.498 (0.130%), neg=0, invalid=96777 0575: dt=36.288000, rms=0.497 (0.109%), neg=0, invalid=96777 0576: dt=36.288000, rms=0.496 (0.134%), neg=0, invalid=96777 0577: dt=36.288000, rms=0.496 (0.099%), neg=0, invalid=96777 0578: dt=36.288000, rms=0.496 (0.087%), neg=0, invalid=96777 0579: dt=36.288000, rms=0.495 (0.024%), neg=0, invalid=96777 0580: dt=36.288000, rms=0.495 (-0.002%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.496, neg=0, invalid=96777 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0581: dt=38.400000, rms=0.493 (0.574%), neg=0, invalid=96777 0582: dt=11.200000, rms=0.492 (0.246%), neg=0, invalid=96777 0583: dt=11.200000, rms=0.491 (0.085%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0584: dt=11.200000, rms=0.490 (0.262%), neg=0, invalid=96777 0585: dt=11.200000, rms=0.489 (0.294%), neg=0, invalid=96777 0586: dt=11.200000, rms=0.487 (0.244%), neg=0, invalid=96777 0587: dt=11.200000, rms=0.487 (0.169%), neg=0, invalid=96777 0588: dt=11.200000, rms=0.485 (0.217%), neg=0, invalid=96777 0589: dt=11.200000, rms=0.485 (0.174%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0590: dt=11.200000, rms=0.484 (0.176%), neg=0, invalid=96777 0591: dt=11.200000, rms=0.483 (0.150%), neg=0, invalid=96777 0592: dt=11.200000, rms=0.482 (0.237%), neg=0, invalid=96777 0593: dt=11.200000, rms=0.481 (0.165%), neg=0, invalid=96777 0594: dt=11.200000, rms=0.480 (0.173%), neg=0, invalid=96777 0595: dt=11.200000, rms=0.480 (0.123%), neg=0, invalid=96777 0596: dt=11.200000, rms=0.479 (0.126%), neg=0, invalid=96777 0597: dt=11.200000, rms=0.479 (0.119%), neg=0, invalid=96777 0598: dt=11.200000, rms=0.478 (0.092%), neg=0, invalid=96777 0599: dt=11.200000, rms=0.478 (0.056%), neg=0, invalid=96777 0600: dt=11.200000, rms=0.478 (0.014%), neg=0, invalid=96777 0601: dt=11.200000, rms=0.478 (0.047%), neg=0, invalid=96777 0602: dt=11.200000, rms=0.477 (0.050%), neg=0, invalid=96777 0603: dt=11.200000, rms=0.477 (0.049%), neg=0, invalid=96777 0604: dt=11.200000, rms=0.477 (0.027%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.477, neg=0, invalid=96777 0605: dt=38.400000, rms=0.474 (0.529%), neg=0, invalid=96777 0606: dt=6.191571, rms=0.473 (0.204%), neg=0, invalid=96777 0607: dt=6.191571, rms=0.473 (0.083%), neg=0, invalid=96777 0608: dt=6.191571, rms=0.473 (0.090%), neg=0, invalid=96777 0609: dt=6.191571, rms=0.472 (0.099%), neg=0, invalid=96777 0610: dt=6.191571, rms=0.472 (0.112%), neg=0, invalid=96777 0611: dt=6.191571, rms=0.471 (0.101%), neg=0, invalid=96777 0612: dt=6.191571, rms=0.471 (0.075%), neg=0, invalid=96777 0613: dt=44.800000, rms=0.470 (0.098%), neg=0, invalid=96777 0614: dt=2.800000, rms=0.470 (0.006%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.476, neg=0, invalid=96777 0615: dt=4.148148, rms=0.476 (0.109%), neg=0, invalid=96777 0616: dt=2.880000, rms=0.476 (0.026%), neg=0, invalid=96777 0617: dt=2.880000, rms=0.475 (0.003%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 7 iterations, nbhd size=1, neg = 0 0618: dt=2.880000, rms=0.476 (-0.038%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.476, neg=0, invalid=96777 iter 0, gcam->neg = 12 after 11 iterations, nbhd size=1, neg = 0 0619: dt=8.597015, rms=0.475 (0.168%), neg=0, invalid=96777 0620: dt=1.008000, rms=0.475 (0.007%), neg=0, invalid=96777 0621: dt=1.008000, rms=0.475 (0.029%), neg=0, invalid=96777 0622: dt=1.008000, rms=0.474 (0.043%), neg=0, invalid=96777 0623: dt=1.008000, rms=0.474 (0.056%), neg=0, invalid=96777 0624: dt=1.008000, rms=0.474 (0.056%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0625: dt=1.008000, rms=0.474 (0.048%), neg=0, invalid=96777 0626: dt=1.008000, rms=0.473 (0.039%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.478, neg=0, invalid=96777 0627: dt=0.000000, rms=0.478 (0.001%), neg=0, invalid=96777 0628: dt=0.000000, rms=0.478 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.478, neg=0, invalid=96777 0629: dt=0.000000, rms=0.478 (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=0.470, neg=0, invalid=96777 iter 0, gcam->neg = 801 after 20 iterations, nbhd size=2, neg = 0 0630: dt=1.972211, rms=0.424 (9.755%), neg=0, invalid=96777 0631: dt=0.000078, rms=0.424 (-0.004%), neg=0, invalid=96777 0632: dt=0.000078, rms=0.424 (0.000%), neg=0, invalid=96777 0633: dt=0.000078, rms=0.424 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.424, neg=0, invalid=96777 0634: dt=0.000312, rms=0.424 (0.000%), neg=0, invalid=96777 0635: dt=0.000000, rms=0.424 (-0.002%), 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=0.405, neg=0, invalid=96777 0636: dt=0.000000, rms=0.407 (-0.323%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.407, neg=0, invalid=96777 0637: dt=32.368000, rms=0.407 (0.004%), neg=0, invalid=96777 0638: dt=18.496000, rms=0.407 (0.000%), neg=0, invalid=96777 0639: dt=18.496000, rms=0.407 (-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=0.407, neg=0, invalid=96777 0640: dt=0.000000, rms=0.407 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.407, neg=0, invalid=96777 0641: dt=36.288000, rms=0.407 (0.020%), neg=0, invalid=96777 0642: dt=36.288000, rms=0.407 (0.007%), neg=0, invalid=96777 0643: dt=36.288000, rms=0.407 (0.006%), neg=0, invalid=96777 0644: dt=36.288000, rms=0.407 (0.006%), neg=0, invalid=96777 0645: dt=36.288000, rms=0.407 (0.001%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.408, neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0646: dt=11.200000, rms=0.407 (0.071%), neg=0, invalid=96777 0647: dt=8.000000, rms=0.407 (0.015%), neg=0, invalid=96777 0648: dt=8.000000, rms=0.407 (0.019%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0649: dt=8.000000, rms=0.407 (-0.011%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.407, neg=0, invalid=96777 iter 0, gcam->neg = 11 after 8 iterations, nbhd size=1, neg = 0 0650: dt=44.800000, rms=0.405 (0.427%), neg=0, invalid=96777 0651: dt=11.200000, rms=0.405 (0.040%), neg=0, invalid=96777 0652: dt=11.200000, rms=0.405 (0.073%), neg=0, invalid=96777 iter 0, gcam->neg = 6 after 6 iterations, nbhd size=1, neg = 0 0653: dt=11.200000, rms=0.405 (0.108%), neg=0, invalid=96777 0654: dt=11.200000, rms=0.404 (0.010%), neg=0, invalid=96777 iter 0, gcam->neg = 9 after 200 iterations, nbhd size=4, neg = 1 starting rms=0.004, neg=1, removing folds in lattice.... iter 1, dt=0.000875: new neg 0, old_neg 1, delta 1, rms=0.003 (32.188%) 0655: dt=11.200000, rms=0.404 (-0.138%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.408, neg=0, invalid=96777 iter 0, gcam->neg = 10 after 7 iterations, nbhd size=1, neg = 0 0656: dt=2.880000, rms=0.407 (0.040%), neg=0, invalid=96777 0657: dt=0.201923, rms=0.407 (0.003%), neg=0, invalid=96777 0658: dt=0.201923, rms=0.407 (0.012%), neg=0, invalid=96777 0659: dt=0.201923, rms=0.407 (0.021%), neg=0, invalid=96777 0660: dt=0.201923, rms=0.407 (0.030%), neg=0, invalid=96777 0661: dt=0.201923, rms=0.407 (0.035%), neg=0, invalid=96777 0662: dt=0.201923, rms=0.407 (0.039%), neg=0, invalid=96777 0663: dt=0.201923, rms=0.407 (0.041%), neg=0, invalid=96777 0664: dt=0.201923, rms=0.406 (0.041%), neg=0, invalid=96777 0665: dt=0.201923, rms=0.406 (0.040%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.406, neg=0, invalid=96777 iter 0, gcam->neg = 98 after 23 iterations, nbhd size=2, neg = 0 0666: dt=13.824000, rms=0.404 (0.481%), neg=0, invalid=96777 0667: dt=0.003938, rms=0.404 (0.000%), neg=0, invalid=96777 0668: dt=0.003938, rms=0.404 (0.000%), neg=0, invalid=96777 0669: dt=0.003938, rms=0.404 (-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=0.411, neg=0, invalid=96777 0670: dt=0.000000, rms=0.411 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.411, neg=0, invalid=96777 0671: dt=0.000000, rms=0.411 (0.000%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.400, neg=0, invalid=96777 iter 0, gcam->neg = 627 after 30 iterations, nbhd size=3, neg = 0 0672: dt=1.024000, rms=0.383 (4.222%), neg=0, invalid=96777 0673: dt=0.000000, rms=0.383 (0.000%), neg=0, invalid=96777 iter 0, gcam->neg = 666 after 9 iterations, nbhd size=1, neg = 0 0674: dt=0.050000, rms=0.383 (-0.435%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.383, neg=0, invalid=96777 0675: dt=0.000000, rms=0.383 (0.000%), neg=0, invalid=96777 writing output transformation to transforms/talairach.m3z... GCAMwrite registration took 4 hours, 29 minutes and 33 seconds. #-------------------------------------- #@# CA Reg Inv Thu Aug 8 16:34:50 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 16:36:11 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... 10536194 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 1 minutes and 26 seconds. #-------------------------------------- #@# SkullLTA Thu Aug 8 16:37:38 CEST 2013 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta ======= NUMBER OF OPENMP THREADS = 1 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 5 using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach_with_skull_2.log reading '/opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=8.0 skull bounding box = (44, 14, 11) --> (208, 205, 196) using (99, 78, 104) as brain centroid... mean wm in atlas = 126, using box (79,54,81) --> (119, 101,126) to find MRI wm before smoothing, mri peak at 110 after smoothing, mri peak at 110, scaling input intensities by 1.145 scaling channel 0 by 1.14545 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.1 (thresh=-4.1) 1.035 0.007 -0.030 -3.248; 0.002 1.039 0.311 -15.351; 0.034 -0.278 0.903 29.756; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.035 0.007 -0.030 -3.248; 0.002 1.039 0.311 -15.351; 0.034 -0.278 0.903 29.756; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.012 -0.016 -0.073 6.601; 0.037 1.037 0.374 -26.429; 0.067 -0.358 0.912 30.424; 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=-3.9) 1.012 -0.016 -0.073 6.601; 0.037 1.037 0.374 -26.429; 0.067 -0.358 0.912 30.424; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-4.0 (thresh=-3.9) 1.009 -0.016 -0.072 7.020; 0.036 1.034 0.373 -25.911; 0.068 -0.358 0.914 30.247; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.010 -0.016 -0.072 6.881; 0.036 1.033 0.372 -25.739; 0.068 -0.359 0.915 30.158; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3481 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.00975 -0.01640 -0.07248 6.88051; 0.03639 1.03251 0.37245 -25.73854; 0.06766 -0.35886 0.91506 30.15802; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.00975 -0.01640 -0.07248 6.88051; 0.03639 1.03251 0.37245 -25.73854; 0.06766 -0.35886 0.91506 30.15802; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 007: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.010 -0.016 -0.072 6.881; 0.036 1.033 0.372 -25.739; 0.068 -0.359 0.915 30.158; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.9 (old=-4.1) transform before final EM align: 1.010 -0.016 -0.072 6.881; 0.036 1.033 0.372 -25.739; 0.068 -0.359 0.915 30.158; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 382743 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.00975 -0.01640 -0.07248 6.88051; 0.03639 1.03251 0.37245 -25.73854; 0.06766 -0.35886 0.91506 30.15802; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.00975 -0.01640 -0.07248 6.88051; 0.03639 1.03251 0.37245 -25.73854; 0.06766 -0.35886 0.91506 30.15802; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 008: -log(p) = 4.4 after pass:transform: ( 1.01, -0.02, -0.07, 6.88) ( 0.04, 1.03, 0.37, -25.74) ( 0.07, -0.36, 0.92, 30.16) dfp_em_step_func: 009: -log(p) = 4.4 after pass:transform: ( 1.01, -0.02, -0.07, 6.88) ( 0.04, 1.03, 0.37, -25.74) ( 0.07, -0.36, 0.92, 30.16) dfp_em_step_func: 010: -log(p) = 4.4 after pass:transform: ( 1.01, -0.02, -0.07, 6.88) ( 0.04, 1.03, 0.37, -25.74) ( 0.07, -0.36, 0.92, 30.16) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... dfp_em_step_func: 011: -log(p) = 4.4 after pass:transform: ( 1.01, -0.02, -0.07, 6.88) ( 0.04, 1.03, 0.37, -25.74) ( 0.07, -0.36, 0.92, 30.16) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 3 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 013: -log(p) = 4.4 tol 0.000000 final transform: 1.011 -0.016 -0.072 6.881; 0.037 1.033 0.373 -25.739; 0.068 -0.358 0.915 30.158; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull_2.lta... registration took 40 minutes and 13 seconds. #-------------------------------------- #@# SubCort Seg Thu Aug 8 17:17:50 CEST 2013 mri_ca_label -align norm.mgz transforms/talairach.m3z /opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz sysname Linux hostname snake5 machine x86_64 setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 = 0.11505 ( 9) Left_Lateral_Ventricle (4): linear fit = 0.25 x + 0.0 (4274 voxels, overlap=0.007) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (4274 voxels, peak = 7), gca=10.8 gca peak = 0.14982 (20) mri peak = 0.12347 ( 9) Right_Lateral_Ventricle (43): linear fit = 0.35 x + 0.0 (851 voxels, overlap=0.007) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (851 voxels, peak = 7), gca=8.0 gca peak = 0.28003 (97) mri peak = 0.09091 (91) Right_Pallidum (52): linear fit = 0.92 x + 0.0 (335 voxels, overlap=0.241) Right_Pallidum (52): linear fit = 0.92 x + 0.0 (335 voxels, peak = 89), gca=88.8 gca peak = 0.18160 (96) mri peak = 0.11747 (92) Left_Pallidum (13): linear fit = 0.92 x + 0.0 (338 voxels, overlap=0.404) Left_Pallidum (13): linear fit = 0.92 x + 0.0 (338 voxels, peak = 88), gca=87.8 gca peak = 0.27536 (62) mri peak = 0.07051 (58) Right_Hippocampus (53): linear fit = 0.92 x + 0.0 (593 voxels, overlap=0.776) Right_Hippocampus (53): linear fit = 0.92 x + 0.0 (593 voxels, peak = 57), gca=56.7 gca peak = 0.32745 (63) mri peak = 0.07543 (62) Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (637 voxels, overlap=0.996) Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (637 voxels, peak = 58), gca=58.3 gca peak = 0.08597 (105) mri peak = 0.08677 (106) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (45112 voxels, overlap=0.700) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (45112 voxels, peak = 107), gca=106.6 gca peak = 0.09209 (106) mri peak = 0.08778 (109) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (45509 voxels, overlap=0.613) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (45509 voxels, peak = 109), gca=108.6 gca peak = 0.07826 (63) mri peak = 0.04953 (54) Left_Cerebral_Cortex (3): linear fit = 0.88 x + 0.0 (17016 voxels, overlap=0.594) Left_Cerebral_Cortex (3): linear fit = 0.88 x + 0.0 (17016 voxels, peak = 55), gca=55.1 gca peak = 0.08598 (64) mri peak = 0.04978 (51) Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (16497 voxels, overlap=0.424) Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (16497 voxels, peak = 53), gca=52.8 gca peak = 0.24164 (71) mri peak = 0.09000 (70) Right_Caudate (50): linear fit = 0.94 x + 0.0 (700 voxels, overlap=1.013) Right_Caudate (50): linear fit = 0.94 x + 0.0 (700 voxels, peak = 67), gca=67.1 gca peak = 0.18227 (75) mri peak = 0.09213 (68) Left_Caudate (11): linear fit = 0.89 x + 0.0 (966 voxels, overlap=0.499) Left_Caudate (11): linear fit = 0.89 x + 0.0 (966 voxels, peak = 67), gca=67.1 gca peak = 0.10629 (62) mri peak = 0.04739 (51) Left_Cerebellum_Cortex (8): linear fit = 0.92 x + 0.0 (10282 voxels, overlap=0.861) Left_Cerebellum_Cortex (8): linear fit = 0.92 x + 0.0 (10282 voxels, peak = 57), gca=56.7 gca peak = 0.11668 (59) mri peak = 0.05057 (56) Right_Cerebellum_Cortex (47): linear fit = 0.92 x + 0.0 (10639 voxels, overlap=0.913) Right_Cerebellum_Cortex (47): linear fit = 0.92 x + 0.0 (10639 voxels, peak = 54), gca=54.0 gca peak = 0.17849 (88) mri peak = 0.08393 (90) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (5434 voxels, overlap=0.960) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (5434 voxels, peak = 90), gca=90.2 gca peak = 0.16819 (86) mri peak = 0.08571 (90) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (4938 voxels, overlap=0.973) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (4938 voxels, peak = 88), gca=88.2 gca peak = 0.41688 (64) mri peak = 0.10288 (63) Left_Amygdala (18): linear fit = 1.05 x + 0.0 (241 voxels, overlap=1.023) Left_Amygdala (18): linear fit = 1.05 x + 0.0 (241 voxels, peak = 68), gca=67.5 gca peak = 0.42394 (62) mri peak = 0.07365 (58) Right_Amygdala (54): linear fit = 0.94 x + 0.0 (353 voxels, overlap=1.041) Right_Amygdala (54): linear fit = 0.94 x + 0.0 (353 voxels, peak = 58), gca=58.0 gca peak = 0.10041 (96) mri peak = 0.06711 (91) Left_Thalamus_Proper (10): linear fit = 0.96 x + 0.0 (3327 voxels, overlap=0.967) Left_Thalamus_Proper (10): linear fit = 0.96 x + 0.0 (3327 voxels, peak = 93), gca=92.6 gca peak = 0.13978 (88) mri peak = 0.06244 (88) Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (3162 voxels, overlap=0.952) Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (3162 voxels, peak = 86), gca=85.8 gca peak = 0.08514 (81) mri peak = 0.06388 (79) Left_Putamen (12): linear fit = 0.94 x + 0.0 (2191 voxels, overlap=0.679) Left_Putamen (12): linear fit = 0.94 x + 0.0 (2191 voxels, peak = 76), gca=75.7 gca peak = 0.09624 (82) mri peak = 0.06533 (71) Right_Putamen (51): linear fit = 0.88 x + 0.0 (1548 voxels, overlap=0.574) Right_Putamen (51): linear fit = 0.88 x + 0.0 (1548 voxels, peak = 73), gca=72.6 gca peak = 0.07543 (88) mri peak = 0.06900 (90) Brain_Stem (16): linear fit = 1.03 x + 0.0 (10325 voxels, overlap=0.765) Brain_Stem (16): linear fit = 1.03 x + 0.0 (10325 voxels, peak = 91), gca=91.1 gca peak = 0.12757 (95) mri peak = 0.06142 (97) Right_VentralDC (60): linear fit = 1.04 x + 0.0 (973 voxels, overlap=0.820) Right_VentralDC (60): linear fit = 1.04 x + 0.0 (973 voxels, peak = 99), gca=99.3 gca peak = 0.17004 (92) mri peak = 0.06630 (100) Left_VentralDC (28): linear fit = 1.03 x + 0.0 (1154 voxels, overlap=0.859) Left_VentralDC (28): linear fit = 1.03 x + 0.0 (1154 voxels, peak = 95), gca=95.2 gca peak = 0.21361 (36) mri peak = 0.20312 (13) Third_Ventricle (14): linear fit = 0.34 x + 0.0 (64 voxels, overlap=0.060) Third_Ventricle (14): linear fit = 0.34 x + 0.0 (64 voxels, peak = 12), gca=12.1 gca peak = 0.26069 (23) mri peak = 0.12873 (13) Fourth_Ventricle (15): linear fit = 0.38 x + 0.0 (315 voxels, overlap=0.027) Fourth_Ventricle (15): linear fit = 0.38 x + 0.0 (315 voxels, peak = 9), gca=8.9 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak Third_Ventricle = 0.21361 (36) gca peak Fourth_Ventricle = 0.26069 (23) gca peak CSF = 0.14367 (38) gca peak Left_Accumbens_area = 0.57033 (70) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65201 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.31129 (32) gca peak Right_Accumbens_area = 0.30219 (72) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.72939 (42) gca peak WM_hypointensities = 0.14821 (82) gca peak non_WM_hypointensities = 0.10354 (53) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means estimating mean gm scale to be 0.92 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 = 0.11505 ( 9) Left_Lateral_Ventricle (4): linear fit = 0.70 x + 0.0 (4274 voxels, overlap=0.942) Left_Lateral_Ventricle (4): linear fit = 0.70 x + 0.0 (4274 voxels, peak = 8), gca=7.8 gca peak = 0.29325 ( 9) mri peak = 0.12347 ( 9) Right_Lateral_Ventricle (43): linear fit = 0.93 x + 0.0 (851 voxels, overlap=0.997) Right_Lateral_Ventricle (43): linear fit = 0.93 x + 0.0 (851 voxels, peak = 8), gca=8.3 gca peak = 0.32313 (89) mri peak = 0.09091 (91) Right_Pallidum (52): linear fit = 0.98 x + 0.0 (335 voxels, overlap=1.012) Right_Pallidum (52): linear fit = 0.98 x + 0.0 (335 voxels, peak = 87), gca=86.8 gca peak = 0.19545 (88) mri peak = 0.11747 (92) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (338 voxels, overlap=1.003) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (338 voxels, peak = 88), gca=88.0 gca peak = 0.30131 (57) mri peak = 0.07051 (58) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (593 voxels, overlap=1.007) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (593 voxels, peak = 57), gca=57.0 gca peak = 0.28488 (58) mri peak = 0.07543 (62) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (637 voxels, overlap=1.008) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (637 voxels, peak = 58), gca=58.0 gca peak = 0.08542 (107) mri peak = 0.08677 (106) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (45112 voxels, overlap=0.742) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (45112 voxels, peak = 107), gca=107.0 gca peak = 0.08551 (108) mri peak = 0.08778 (109) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (45509 voxels, overlap=0.708) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (45509 voxels, peak = 109), gca=108.5 gca peak = 0.08996 (55) mri peak = 0.04953 (54) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (17016 voxels, overlap=0.975) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (17016 voxels, peak = 54), gca=54.2 gca peak = 0.10529 (53) mri peak = 0.04978 (51) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (16497 voxels, overlap=0.975) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (16497 voxels, peak = 53), gca=53.0 gca peak = 0.22918 (67) mri peak = 0.09000 (70) Right_Caudate (50): linear fit = 1.00 x + 0.0 (700 voxels, overlap=1.007) Right_Caudate (50): linear fit = 1.00 x + 0.0 (700 voxels, peak = 67), gca=67.0 gca peak = 0.18268 (67) mri peak = 0.09213 (68) Left_Caudate (11): linear fit = 1.00 x + 0.0 (966 voxels, overlap=0.999) Left_Caudate (11): linear fit = 1.00 x + 0.0 (966 voxels, peak = 67), gca=67.0 gca peak = 0.11904 (56) mri peak = 0.04739 (51) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (10282 voxels, overlap=1.000) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (10282 voxels, peak = 55), gca=55.2 gca peak = 0.13094 (55) mri peak = 0.05057 (56) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (10639 voxels, overlap=1.000) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (10639 voxels, peak = 56), gca=56.4 gca peak = 0.16673 (89) mri peak = 0.08393 (90) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5434 voxels, overlap=0.990) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5434 voxels, peak = 89), gca=88.6 gca peak = 0.14595 (89) mri peak = 0.08571 (90) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4938 voxels, overlap=0.996) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4938 voxels, peak = 89), gca=88.6 gca peak = 0.33140 (67) mri peak = 0.10288 (63) Left_Amygdala (18): linear fit = 0.95 x + 0.0 (241 voxels, overlap=0.955) Left_Amygdala (18): linear fit = 0.95 x + 0.0 (241 voxels, peak = 64), gca=64.0 gca peak = 0.48017 (58) mri peak = 0.07365 (58) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (353 voxels, overlap=1.027) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (353 voxels, peak = 58), gca=58.0 gca peak = 0.10197 (93) mri peak = 0.06711 (91) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (3327 voxels, overlap=0.983) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (3327 voxels, peak = 94), gca=94.4 gca peak = 0.11274 (83) mri peak = 0.06244 (88) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (3162 voxels, overlap=0.998) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (3162 voxels, peak = 84), gca=84.2 gca peak = 0.09445 (77) mri peak = 0.06388 (79) Left_Putamen (12): linear fit = 0.99 x + 0.0 (2191 voxels, overlap=0.991) Left_Putamen (12): linear fit = 0.99 x + 0.0 (2191 voxels, peak = 76), gca=75.8 gca peak = 0.12421 (67) mri peak = 0.06533 (71) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1548 voxels, overlap=1.001) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1548 voxels, peak = 67), gca=67.0 gca peak = 0.07025 (88) mri peak = 0.06900 (90) Brain_Stem (16): linear fit = 1.00 x + 0.0 (10325 voxels, overlap=0.836) Brain_Stem (16): linear fit = 1.00 x + 0.0 (10325 voxels, peak = 88), gca=87.6 gca peak = 0.13021 (99) mri peak = 0.06142 (97) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (973 voxels, overlap=0.871) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (973 voxels, peak = 99), gca=99.5 gca peak = 0.13821 (95) mri peak = 0.06630 (100) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1154 voxels, overlap=0.917) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1154 voxels, peak = 95), gca=95.0 gca peak = 0.35640 (14) mri peak = 0.20312 (13) Third_Ventricle (14): linear fit = 0.82 x + 0.0 (64 voxels, overlap=0.739) Third_Ventricle (14): linear fit = 0.82 x + 0.0 (64 voxels, peak = 12), gca=11.6 gca peak = 0.33827 ( 9) mri peak = 0.12873 (13) Fourth_Ventricle (15): linear fit = 1.05 x + 0.0 (315 voxels, overlap=0.963) Fourth_Ventricle (15): linear fit = 1.05 x + 0.0 (315 voxels, peak = 9), gca=9.5 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.24950 (33) gca peak CSF = 0.30128 (18) gca peak Left_Accumbens_area = 0.42363 (63) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.59104 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.34941 (29) gca peak Right_Accumbens_area = 0.31038 (68) gca peak Right_vessel = 0.58297 (60) gca peak Right_choroid_plexus = 0.10278 (48) gca peak Fifth_Ventricle = 0.45329 (19) gca peak WM_hypointensities = 0.17311 (83) gca peak non_WM_hypointensities = 0.12130 (54) gca peak Optic_Chiasm = 0.34840 (76) not using caudate to estimate GM means estimating mean gm scale to be 0.99 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 15871 gm and wm labels changed (%11 to gray, %89 to white out of all changed labels) 395 hippocampal voxels changed. 6 amygdala voxels changed. pass 1: 107856 changed. image ll: -2.278, PF=1.000 pass 2: 19554 changed. image ll: -2.276, PF=1.000 pass 3: 7651 changed. pass 4: 3459 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 19 minutes and 50 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/cc_up.lta sub002 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/sub002/mri/transforms/cc_up.lta reading aseg from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/aseg.auto_noCCseg.mgz reading norm from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/norm.mgz 39080 voxels in left wm, 38159 in right wm, xrange [122, 132] searching rotation angles z=[-6 8], y=[-9 5] searching scale 1 Z rot -5.8 searching scale 1 Z rot -5.6 searching scale 1 Z rot -5.3 searching scale 1 Z rot -5.1 searching scale 1 Z rot -4.8 searching scale 1 Z rot -4.6 searching scale 1 Z rot -4.3 searching scale 1 Z rot -4.1 searching scale 1 Z rot -3.8 searching scale 1 Z rot -3.6 searching scale 1 Z rot -3.3 searching scale 1 Z rot -3.1 searching scale 1 Z rot -2.8 searching scale 1 Z rot -2.6 searching scale 1 Z rot -2.3 searching scale 1 Z rot -2.1 searching scale 1 Z rot -1.8 searching scale 1 Z rot -1.6 searching scale 1 Z rot -1.3 searching scale 1 Z rot -1.1 searching scale 1 Z rot -0.8 searching scale 1 Z rot -0.6 searching scale 1 Z rot -0.3 searching scale 1 Z rot -0.1 searching scale 1 Z rot 0.2 searching scale 1 Z rot 0.4 searching scale 1 Z rot 0.7 searching scale 1 Z rot 0.9 searching scale 1 Z rot 1.2 searching scale 1 Z rot 1.4 searching scale 1 Z rot 1.7 searching scale 1 Z rot 1.9 searching scale 1 Z rot 2.2 searching scale 1 Z rot 2.4 searching scale 1 Z rot 2.7 searching scale 1 Z rot 2.9 searching scale 1 Z rot 3.2 searching scale 1 Z rot 3.4 searching scale 1 Z rot 3.7 searching scale 1 Z rot 3.9 searching scale 1 Z rot 4.2 searching scale 1 Z rot 4.4 searching scale 1 Z rot 4.7 searching scale 1 Z rot 4.9 searching scale 1 Z rot 5.2 searching scale 1 Z rot 5.4 searching scale 1 Z rot 5.7 searching scale 1 Z rot 5.9 searching scale 1 Z rot 6.2 searching scale 1 Z rot 6.4 searching scale 1 Z rot 6.7 searching scale 1 Z rot 6.9 searching scale 1 Z rot 7.2 global minimum found at slice 126.0, rotations (-2.05, 0.43) final transformation (x=126.0, yr=-2.053, zr=0.432): 0.999 -0.008 -0.036 6.142; 0.008 1.000 -0.000 45.078; 0.036 -0.000 0.999 27.549; 0.000 0.000 0.000 1.000; updating x range to be [125, 130] in xformed coordinates best xformed slice 128 cc center is found at 128 149 126 eigenvectors: -0.002 0.004 1.000; -0.215 -0.977 0.003; 0.977 -0.215 0.003; error in mid anterior detected - correcting... writing aseg with callosum to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/aseg.auto.mgz... corpus callosum matter segmentation took 0.9 minutes #-------------------------------------- #@# Merge ASeg Thu Aug 8 17:38:36 CEST 2013 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Thu Aug 8 17:38:36 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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... 4572 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 109 gm peak at 56 (56), valley at 31 (31) 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 -nan white matter peak found at 0 gm peak at 0 (0), valley at 6 (-10) csf peak at 0, setting threshold to 0 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 4 minutes and 21 seconds. #-------------------------------------------- #@# Mask BFS Thu Aug 8 17:42:58 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1872837 voxels in mask (pct= 11.16) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Thu Aug 8 17:43:01 CEST 2013 mri_segment brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (107.0): 107.0 +- 4.6 [80.0 --> 125.0] GM (68.0) : 67.1 +- 9.4 [30.0 --> 96.0] setting bottom of white matter range to 76.5 setting top of gray matter range to 85.9 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... 7323 sparsely connected voxels removed... thickening thin strands.... 20 segments, 6642 filled 286 bright non-wm voxels segmented. 3956 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 0.64 minutes reading wm segmentation from wm.seg.mgz... 170 voxels added to wm to prevent paths from MTL structures to cortex 1820 additional wm voxels added 0 additional wm voxels added SEG EDIT: 66007 voxels turned on, 38907 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 0 new 0 115,126,128 old 0 new 0 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 23 found - 23 modified | TOTAL: 23 pass 2 (xy+): 0 found - 23 modified | TOTAL: 23 pass 1 (xy-): 19 found - 19 modified | TOTAL: 42 pass 2 (xy-): 0 found - 19 modified | TOTAL: 42 pass 1 (yz+): 45 found - 45 modified | TOTAL: 87 pass 2 (yz+): 0 found - 45 modified | TOTAL: 87 pass 1 (yz-): 19 found - 19 modified | TOTAL: 106 pass 2 (yz-): 0 found - 19 modified | TOTAL: 106 pass 1 (xz+): 23 found - 23 modified | TOTAL: 129 pass 2 (xz+): 0 found - 23 modified | TOTAL: 129 pass 1 (xz-): 26 found - 26 modified | TOTAL: 155 pass 2 (xz-): 0 found - 26 modified | TOTAL: 155 Iteration Number : 1 pass 1 (+++): 13 found - 13 modified | TOTAL: 13 pass 2 (+++): 0 found - 13 modified | TOTAL: 13 pass 1 (+++): 14 found - 14 modified | TOTAL: 27 pass 2 (+++): 0 found - 14 modified | TOTAL: 27 pass 1 (+++): 9 found - 9 modified | TOTAL: 36 pass 2 (+++): 0 found - 9 modified | TOTAL: 36 pass 1 (+++): 15 found - 15 modified | TOTAL: 51 pass 2 (+++): 0 found - 15 modified | TOTAL: 51 Iteration Number : 1 pass 1 (++): 171 found - 171 modified | TOTAL: 171 pass 2 (++): 0 found - 171 modified | TOTAL: 171 pass 1 (+-): 162 found - 162 modified | TOTAL: 333 pass 2 (+-): 0 found - 162 modified | TOTAL: 333 pass 1 (--): 149 found - 149 modified | TOTAL: 482 pass 2 (--): 0 found - 149 modified | TOTAL: 482 pass 1 (-+): 144 found - 144 modified | TOTAL: 626 pass 2 (-+): 0 found - 144 modified | TOTAL: 626 Iteration Number : 2 pass 1 (xy+): 9 found - 9 modified | TOTAL: 9 pass 2 (xy+): 0 found - 9 modified | TOTAL: 9 pass 1 (xy-): 1 found - 1 modified | TOTAL: 10 pass 2 (xy-): 0 found - 1 modified | TOTAL: 10 pass 1 (yz+): 2 found - 2 modified | TOTAL: 12 pass 2 (yz+): 0 found - 2 modified | TOTAL: 12 pass 1 (yz-): 7 found - 7 modified | TOTAL: 19 pass 2 (yz-): 0 found - 7 modified | TOTAL: 19 pass 1 (xz+): 5 found - 5 modified | TOTAL: 24 pass 2 (xz+): 0 found - 5 modified | TOTAL: 24 pass 1 (xz-): 3 found - 3 modified | TOTAL: 27 pass 2 (xz-): 0 found - 3 modified | TOTAL: 27 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 2 found - 2 modified | TOTAL: 3 pass 2 (--): 0 found - 2 modified | TOTAL: 3 pass 1 (-+): 3 found - 3 modified | TOTAL: 6 pass 2 (-+): 0 found - 3 modified | TOTAL: 6 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 1 found - 1 modified | TOTAL: 1 pass 2 (yz-): 0 found - 1 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 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 = 866 (out of 661130: 0.130988) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Thu Aug 8 17:45:39 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.035 0.007 -0.030 -3.248; 0.002 1.039 0.311 -15.351; 0.034 -0.278 0.903 29.756; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.035 0.007 -0.030 -3.248; 0.002 1.039 0.311 -15.351; 0.034 -0.278 0.903 29.756; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1245 (min = 350, max = 1400), aspect = 0.49 (min = 0.10, max = 0.75) no need to search using seed (126, 117, 152), TAL = (2.0, 24.0, 11.0) talairach voxel to voxel transform 0.965 0.002 0.031 2.228; 0.008 0.881 -0.304 22.582; -0.034 0.271 1.013 -26.103; 0.000 0.000 0.000 1.000; segmentation indicates cc at (126, 117, 152) --> (2.0, 24.0, 11.0) done. writing output to filled.mgz... filling took 1.0 minutes talairach cc position changed to (2.00, 24.00, 11.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, 24.00, 11.00) SRC: (111.51, 80.37, 155.99) search lh wm seed point around talairach space (-16.00, 24.00, 11.00), SRC: (146.26, 80.66, 154.78) 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 17:46:37 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 1 found - 1 modified | TOTAL: 3 pass 2 (xy-): 0 found - 1 modified | TOTAL: 3 pass 1 (yz+): 2 found - 2 modified | TOTAL: 5 pass 2 (yz+): 0 found - 2 modified | TOTAL: 5 pass 1 (yz-): 1 found - 1 modified | TOTAL: 6 pass 2 (yz-): 0 found - 1 modified | TOTAL: 6 pass 1 (xz+): 1 found - 1 modified | TOTAL: 7 pass 2 (xz+): 0 found - 1 modified | TOTAL: 7 pass 1 (xz-): 1 found - 1 modified | TOTAL: 8 pass 2 (xz-): 0 found - 1 modified | TOTAL: 8 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 1 found - 1 modified | TOTAL: 2 pass 2 (--): 0 found - 1 modified | TOTAL: 2 pass 1 (-+): 1 found - 1 modified | TOTAL: 3 pass 2 (-+): 0 found - 1 modified | TOTAL: 3 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 12 (out of 324847: 0.003694) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 30: 485 vertices, 568 faces slice 40: 6210 vertices, 6507 faces slice 50: 17096 vertices, 17505 faces slice 60: 29888 vertices, 30345 faces slice 70: 42910 vertices, 43345 faces slice 80: 55489 vertices, 55876 faces slice 90: 67710 vertices, 68128 faces slice 100: 79985 vertices, 80380 faces slice 110: 92245 vertices, 92655 faces slice 120: 103998 vertices, 104425 faces slice 130: 115128 vertices, 115553 faces slice 140: 125639 vertices, 126012 faces slice 150: 134522 vertices, 134849 faces slice 160: 142620 vertices, 142891 faces slice 170: 149792 vertices, 150016 faces slice 180: 156163 vertices, 156379 faces slice 190: 161191 vertices, 161357 faces slice 200: 163288 vertices, 163328 faces slice 210: 163318 vertices, 163342 faces slice 220: 163318 vertices, 163342 faces slice 230: 163318 vertices, 163342 faces slice 240: 163318 vertices, 163342 faces slice 250: 163318 vertices, 163342 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... 163318 voxel in cpt #1: X=-24 [v=163318,e=490026,f=326684] located at (-27.214685, -24.672211, 39.221371) For the whole surface: X=-24 [v=163318,e=490026,f=326684] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Thu Aug 8 17:46:46 CEST 2013 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 17:46:51 CEST 2013 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts avg radius = 51.3 mm, total surface area = 86638 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.6 minutes Not saving sulc step 000: RMS=0.098 (target=0.015) step 005: RMS=0.073 (target=0.015) step 010: RMS=0.055 (target=0.015) step 015: RMS=0.046 (target=0.015) step 020: RMS=0.039 (target=0.015) step 025: RMS=0.035 (target=0.015) step 030: RMS=0.032 (target=0.015) step 035: RMS=0.030 (target=0.015) step 040: RMS=0.027 (target=0.015) step 045: RMS=0.027 (target=0.015) step 050: RMS=0.026 (target=0.015) step 055: RMS=0.026 (target=0.015) step 060: RMS=0.025 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Thu Aug 8 17:47:30 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.90 +- 0.55 (0.00-->5.85) (max @ vno 121281 --> 121282) face area 0.02 +- 0.03 (-0.17-->0.59) scaling brain by 0.288... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.145, avgs=0 005/300: dt: 0.9000, rms radial error=175.884, avgs=0 010/300: dt: 0.9000, rms radial error=175.323, avgs=0 015/300: dt: 0.9000, rms radial error=174.585, avgs=0 020/300: dt: 0.9000, rms radial error=173.745, avgs=0 025/300: dt: 0.9000, rms radial error=172.847, avgs=0 030/300: dt: 0.9000, rms radial error=171.920, avgs=0 035/300: dt: 0.9000, rms radial error=170.977, avgs=0 040/300: dt: 0.9000, rms radial error=170.026, avgs=0 045/300: dt: 0.9000, rms radial error=169.073, avgs=0 050/300: dt: 0.9000, rms radial error=168.123, avgs=0 055/300: dt: 0.9000, rms radial error=167.180, avgs=0 060/300: dt: 0.9000, rms radial error=166.241, avgs=0 065/300: dt: 0.9000, rms radial error=165.306, avgs=0 070/300: dt: 0.9000, rms radial error=164.376, avgs=0 075/300: dt: 0.9000, rms radial error=163.450, avgs=0 080/300: dt: 0.9000, rms radial error=162.529, avgs=0 085/300: dt: 0.9000, rms radial error=161.613, avgs=0 090/300: dt: 0.9000, rms radial error=160.703, avgs=0 095/300: dt: 0.9000, rms radial error=159.798, avgs=0 100/300: dt: 0.9000, rms radial error=158.898, avgs=0 105/300: dt: 0.9000, rms radial error=158.004, avgs=0 110/300: dt: 0.9000, rms radial error=157.114, avgs=0 115/300: dt: 0.9000, rms radial error=156.229, avgs=0 120/300: dt: 0.9000, rms radial error=155.350, avgs=0 125/300: dt: 0.9000, rms radial error=154.475, avgs=0 130/300: dt: 0.9000, rms radial error=153.605, avgs=0 135/300: dt: 0.9000, rms radial error=152.740, avgs=0 140/300: dt: 0.9000, rms radial error=151.881, avgs=0 145/300: dt: 0.9000, rms radial error=151.026, avgs=0 150/300: dt: 0.9000, rms radial error=150.176, avgs=0 155/300: dt: 0.9000, rms radial error=149.330, avgs=0 160/300: dt: 0.9000, rms radial error=148.490, avgs=0 165/300: dt: 0.9000, rms radial error=147.654, avgs=0 170/300: dt: 0.9000, rms radial error=146.823, avgs=0 175/300: dt: 0.9000, rms radial error=145.997, avgs=0 180/300: dt: 0.9000, rms radial error=145.175, avgs=0 185/300: dt: 0.9000, rms radial error=144.358, avgs=0 190/300: dt: 0.9000, rms radial error=143.546, avgs=0 195/300: dt: 0.9000, rms radial error=142.739, avgs=0 200/300: dt: 0.9000, rms radial error=141.935, avgs=0 205/300: dt: 0.9000, rms radial error=141.137, avgs=0 210/300: dt: 0.9000, rms radial error=140.342, avgs=0 215/300: dt: 0.9000, rms radial error=139.552, avgs=0 220/300: dt: 0.9000, rms radial error=138.767, avgs=0 225/300: dt: 0.9000, rms radial error=137.986, avgs=0 230/300: dt: 0.9000, rms radial error=137.209, avgs=0 235/300: dt: 0.9000, rms radial error=136.436, avgs=0 240/300: dt: 0.9000, rms radial error=135.668, avgs=0 245/300: dt: 0.9000, rms radial error=134.904, avgs=0 250/300: dt: 0.9000, rms radial error=134.145, avgs=0 255/300: dt: 0.9000, rms radial error=133.390, avgs=0 260/300: dt: 0.9000, rms radial error=132.639, avgs=0 265/300: dt: 0.9000, rms radial error=131.892, avgs=0 270/300: dt: 0.9000, rms radial error=131.149, avgs=0 275/300: dt: 0.9000, rms radial error=130.411, avgs=0 280/300: dt: 0.9000, rms radial error=129.677, avgs=0 285/300: dt: 0.9000, rms radial error=128.947, avgs=0 290/300: dt: 0.9000, rms radial error=128.221, avgs=0 295/300: dt: 0.9000, rms radial error=127.498, avgs=0 300/300: dt: 0.9000, rms radial error=126.780, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 19550.91 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00014 epoch 2 (K=40.0), pass 1, starting sse = 3446.64 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00005 epoch 3 (K=160.0), pass 1, starting sse = 388.06 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/11 = 0.00507 epoch 4 (K=640.0), pass 1, starting sse = 24.11 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.09/12 = 0.00732 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 17:53:01 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/sub002/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub002 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=-24 (nv=163318, nf=326684, ne=490026, g=13) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations marking ambiguous vertices... 2474 ambiguous faces found in tessellation segmenting defects... 29 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 29 defects to be corrected 0 vertices coincident reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.7221 (-4.8611) -vertex loglikelihood: -6.5993 (-3.2997) -normal dot loglikelihood: -3.6464 (-3.6464) -quad curv loglikelihood: -6.3981 (-3.1990) Total Loglikelihood : -26.3659 CORRECTING DEFECT 0 (vertices=5, convex hull=21) After retessellation of defect 0, euler #=-25 (161818,484953,323110) : difference with theory (-26) = -1 CORRECTING DEFECT 1 (vertices=83, convex hull=56) After retessellation of defect 1, euler #=-24 (161828,485006,323154) : difference with theory (-25) = -1 CORRECTING DEFECT 2 (vertices=51, convex hull=50) After retessellation of defect 2, euler #=-23 (161840,485058,323195) : difference with theory (-24) = -1 CORRECTING DEFECT 3 (vertices=74, convex hull=72) After retessellation of defect 3, euler #=-22 (161856,485133,323255) : difference with theory (-23) = -1 CORRECTING DEFECT 4 (vertices=9, convex hull=32) After retessellation of defect 4, euler #=-21 (161857,485143,323265) : difference with theory (-22) = -1 CORRECTING DEFECT 5 (vertices=9, convex hull=26) After retessellation of defect 5, euler #=-20 (161859,485156,323277) : difference with theory (-21) = -1 CORRECTING DEFECT 6 (vertices=26, convex hull=31) After retessellation of defect 6, euler #=-19 (161863,485176,323294) : difference with theory (-20) = -1 CORRECTING DEFECT 7 (vertices=25, convex hull=48) After retessellation of defect 7, euler #=-18 (161872,485221,323331) : difference with theory (-19) = -1 CORRECTING DEFECT 8 (vertices=5, convex hull=18) After retessellation of defect 8, euler #=-17 (161872,485225,323336) : difference with theory (-18) = -1 CORRECTING DEFECT 9 (vertices=304, convex hull=132) After retessellation of defect 9, euler #=-17 (161975,485611,323619) : difference with theory (-17) = 0 CORRECTING DEFECT 10 (vertices=129, convex hull=48) After retessellation of defect 10, euler #=-16 (161987,485669,323666) : difference with theory (-16) = 0 CORRECTING DEFECT 11 (vertices=42, convex hull=26) After retessellation of defect 11, euler #=-15 (161991,485688,323682) : difference with theory (-15) = 0 CORRECTING DEFECT 12 (vertices=156, convex hull=66) After retessellation of defect 12, euler #=-14 (162016,485786,323756) : difference with theory (-14) = 0 CORRECTING DEFECT 13 (vertices=15, convex hull=13) After retessellation of defect 13, euler #=-13 (162017,485795,323765) : difference with theory (-13) = 0 CORRECTING DEFECT 14 (vertices=13, convex hull=27) After retessellation of defect 14, euler #=-12 (162022,485819,323785) : difference with theory (-12) = 0 CORRECTING DEFECT 15 (vertices=46, convex hull=24) After retessellation of defect 15, euler #=-11 (162027,485840,323802) : difference with theory (-11) = 0 CORRECTING DEFECT 16 (vertices=33, convex hull=59) After retessellation of defect 16, euler #=-10 (162051,485934,323873) : difference with theory (-10) = 0 CORRECTING DEFECT 17 (vertices=35, convex hull=62) After retessellation of defect 17, euler #=-9 (162069,486013,323935) : difference with theory (-9) = 0 CORRECTING DEFECT 18 (vertices=38, convex hull=29) After retessellation of defect 18, euler #=-8 (162073,486034,323953) : difference with theory (-8) = 0 CORRECTING DEFECT 19 (vertices=24, convex hull=62) After retessellation of defect 19, euler #=-7 (162083,486084,323994) : difference with theory (-7) = 0 CORRECTING DEFECT 20 (vertices=21, convex hull=48) After retessellation of defect 20, euler #=-6 (162093,486131,324032) : difference with theory (-6) = 0 CORRECTING DEFECT 21 (vertices=33, convex hull=32) After retessellation of defect 21, euler #=-5 (162100,486163,324058) : difference with theory (-5) = 0 CORRECTING DEFECT 22 (vertices=104, convex hull=108) After retessellation of defect 22, euler #=-4 (162142,486334,324188) : difference with theory (-4) = 0 CORRECTING DEFECT 23 (vertices=28, convex hull=43) After retessellation of defect 23, euler #=-3 (162151,486374,324220) : difference with theory (-3) = 0 CORRECTING DEFECT 24 (vertices=35, convex hull=21) After retessellation of defect 24, euler #=-2 (162154,486389,324233) : difference with theory (-2) = 0 CORRECTING DEFECT 25 (vertices=34, convex hull=33) After retessellation of defect 25, euler #=-1 (162156,486404,324247) : difference with theory (-1) = 0 CORRECTING DEFECT 26 (vertices=35, convex hull=34) After retessellation of defect 26, euler #=0 (162160,486427,324267) : difference with theory (0) = 0 CORRECTING DEFECT 27 (vertices=51, convex hull=54) After retessellation of defect 27, euler #=1 (162164,486458,324295) : difference with theory (1) = 0 CORRECTING DEFECT 28 (vertices=37, convex hull=69) After retessellation of defect 28, euler #=2 (162178,486528,324352) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.21 (0.08-->7.26) (max @ vno 125026 --> 130478) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.21 (0.08-->7.26) (max @ vno 125026 --> 130478) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 92 mutations (36.5%), 160 crossovers (63.5%), 16 vertices were eliminated building final representation... 1140 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=162178, nf=324352, ne=486528, g=0) writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 15.4 minutes 0 defective edges removing intersecting faces 000: 143 intersecting 001: 17 intersecting 002: 7 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 162178 - 486528 + 324352 = 2 --> 0 holes F =2V-4: 324352 = 324356-4 (0) 2E=3F: 973056 = 973056 (0) total defect index = 0 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 53 intersecting 001: 11 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Thu Aug 8 18:08:36 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub002 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/sub002/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/wm.mgz... 20389 bright wm thresholded. 326 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.orig... computing class statistics... border white: 305608 voxels (1.82%) border gray 333888 voxels (1.99%) WM (92.0): 93.4 +- 9.7 [70.0 --> 110.0] GM (76.0) : 74.6 +- 12.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 48.3 (was 70) setting MAX_BORDER_WHITE to 114.7 (was 105) setting MIN_BORDER_WHITE to 61.0 (was 85) setting MAX_CSF to 35.6 (was 40) setting MAX_GRAY to 95.3 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 54.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 22.8 (was 40) repositioning cortical surface to gray/white boundary reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.21 (0.02-->2.48) (max @ vno 117773 --> 118787) face area 0.28 +- 0.12 (0.00-->2.11) mean absolute distance = 0.77 +- 0.96 3703 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=61 mean inside = 92.7, mean outside = 69.6 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=73.1, 146 (146) missing vertices, mean dist 0.3 [0.7 (%29.1)->0.8 (%70.9))] %61 local maxima, %34 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.26 (0.10-->3.38) (max @ vno 112452 --> 112451) face area 0.28 +- 0.13 (0.00-->1.76) mean absolute distance = 0.38 +- 0.56 3448 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=8275687.5, rms=13.32 001: dt: 0.5000, sse=8102511.5, rms=9.539 (0.000%) 002: dt: 0.5000, sse=8188070.0, rms=7.205 (0.000%) 003: dt: 0.5000, sse=8436538.0, rms=5.718 (0.000%) 004: dt: 0.5000, sse=8620744.0, rms=4.844 (0.000%) 005: dt: 0.5000, sse=8857631.0, rms=4.370 (0.000%) 006: dt: 0.5000, sse=8930440.0, rms=4.154 (0.000%) 007: dt: 0.5000, sse=9014043.0, rms=4.034 (0.000%) 008: dt: 0.5000, sse=9003889.0, rms=3.978 (0.000%) rms = 3.93, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=8987069.0, rms=3.929 (0.000%) 010: dt: 0.2500, sse=5421268.5, rms=2.665 (0.000%) 011: dt: 0.2500, sse=4922603.5, rms=2.224 (0.000%) 012: dt: 0.2500, sse=4626893.0, rms=2.112 (0.000%) 013: dt: 0.2500, sse=4541714.5, rms=2.024 (0.000%) rms = 1.99, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=4449954.5, rms=1.994 (0.000%) 015: dt: 0.1250, sse=4288910.0, rms=1.854 (0.000%) rms = 1.84, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=4247179.5, rms=1.838 (0.000%) positioning took 2.3 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 mean border=78.3, 112 (47) missing vertices, mean dist -0.3 [0.4 (%79.8)->0.2 (%20.2))] %77 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.12-->3.74) (max @ vno 106914 --> 105889) face area 0.35 +- 0.16 (0.00-->2.19) mean absolute distance = 0.23 +- 0.32 3000 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5696138.0, rms=6.74 017: dt: 0.5000, sse=5571937.5, rms=4.228 (0.000%) rms = 4.24, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=5077418.0, rms=3.235 (0.000%) 019: dt: 0.2500, sse=4817492.0, rms=2.390 (0.000%) 020: dt: 0.2500, sse=4722547.0, rms=1.904 (0.000%) 021: dt: 0.2500, sse=4667988.5, rms=1.772 (0.000%) 022: dt: 0.2500, sse=4593165.0, rms=1.665 (0.000%) rms = 1.63, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=4583835.0, rms=1.630 (0.000%) 024: dt: 0.1250, sse=4465102.0, rms=1.507 (0.000%) rms = 1.50, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=4428838.5, rms=1.498 (0.000%) positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group mean border=81.8, 91 (22) missing vertices, mean dist -0.2 [0.2 (%77.5)->0.2 (%22.5))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.07-->4.01) (max @ vno 106914 --> 105889) face area 0.34 +- 0.16 (0.00-->2.55) mean absolute distance = 0.17 +- 0.25 2769 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4949801.0, rms=4.50 026: dt: 0.5000, sse=5238463.5, rms=3.727 (0.000%) rms = 3.99, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=4745555.0, rms=2.357 (0.000%) 028: dt: 0.2500, sse=4624449.0, rms=1.850 (0.000%) 029: dt: 0.2500, sse=4652733.0, rms=1.542 (0.000%) rms = 1.56, time step reduction 2 of 3 to 0.125... 030: dt: 0.1250, sse=4593124.0, rms=1.451 (0.000%) 031: dt: 0.1250, sse=4516467.0, rms=1.325 (0.000%) rms = 1.32, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=4479426.5, rms=1.317 (0.000%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=82.8, 99 (18) missing vertices, mean dist -0.0 [0.2 (%58.1)->0.2 (%41.9))] %91 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=4515783.0, rms=1.79 rms = 2.50, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=4611573.5, rms=1.170 (0.000%) 034: dt: 0.2500, sse=4788554.5, rms=0.994 (0.000%) rms = 1.00, 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=4788534.5, rms=0.986 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 17 non-cortical segments detected only using segment with 1848 vertices erasing segment 1 (vno[0] = 79279) erasing segment 2 (vno[0] = 97128) erasing segment 3 (vno[0] = 101552) erasing segment 4 (vno[0] = 106865) erasing segment 5 (vno[0] = 108150) erasing segment 6 (vno[0] = 115908) erasing segment 7 (vno[0] = 118885) erasing segment 8 (vno[0] = 121878) erasing segment 9 (vno[0] = 122931) erasing segment 10 (vno[0] = 122941) erasing segment 11 (vno[0] = 122951) erasing segment 12 (vno[0] = 123936) erasing segment 13 (vno[0] = 125845) erasing segment 14 (vno[0] = 129542) erasing segment 15 (vno[0] = 129579) erasing segment 16 (vno[0] = 130372) writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/label/lh.cortex.label... writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.curv writing smoothed area to lh.area writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.area vertex spacing 0.89 +- 0.25 (0.06-->4.08) (max @ vno 106914 --> 105889) face area 0.33 +- 0.16 (0.00-->2.68) refinement took 8.1 minutes #-------------------------------------------- #@# Smooth2 lh Thu Aug 8 18:16:43 CEST 2013 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 18:16:48 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 51.5 mm, total surface area = 98637 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=0.079 (target=0.015) step 010: RMS=0.057 (target=0.015) step 015: RMS=0.047 (target=0.015) step 020: RMS=0.040 (target=0.015) step 025: RMS=0.034 (target=0.015) step 030: RMS=0.029 (target=0.015) step 035: RMS=0.025 (target=0.015) step 040: RMS=0.021 (target=0.015) step 045: RMS=0.019 (target=0.015) step 050: RMS=0.018 (target=0.015) step 055: RMS=0.016 (target=0.015) step 060: RMS=0.015 (target=0.015) inflation complete. inflation took 0.7 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 207 vertices thresholded to be in k1 ~ [-0.22 0.45], k2 ~ [-0.25 0.07] total integrated curvature = 0.541*4pi (6.803) --> 0 handles ICI = 1.6, FI = 9.9, variation=170.305 178 vertices thresholded to be in [-0.03 0.02] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 137 vertices thresholded to be in [-0.14 0.14] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.015, std = 0.020 done. #----------------------------------------- #@# Curvature Stats lh Thu Aug 8 18:19:36 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub002 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 [ sub002/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 [ 297 ] Gb_filter = 0 WARN: S lookup min: -0.141974 WARN: S explicit min: 0.000000 vertex = 523 #-------------------------------------------- #@# Sphere lh Thu Aug 8 18:19:41 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 0.270... 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 %20.81 pass 1: epoch 2 of 3 starting distance error %20.79 unfolding complete - removing small folds... starting distance error %20.68 removing remaining folds... final distance error %20.70 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/lh.sphere spherical transformation took 1.15 hours #-------------------------------------------- #@# Surf Reg lh Thu Aug 8 19:28:39 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 = 0.613 curvature mean = 0.042, std = 0.935 curvature mean = 0.024, std = 0.847 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 0.00) sse = 406375.4, tmin=1.3426 d=32.00 min @ (-8.00, -8.00, 0.00) sse = 292306.6, tmin=2.6693 d=16.00 min @ (0.00, 0.00, -4.00) sse = 277955.5, tmin=4.0334 d=8.00 min @ (2.00, 0.00, 0.00) sse = 273601.4, tmin=5.4351 d=4.00 min @ (-1.00, -1.00, 1.00) sse = 270771.8, tmin=6.8509 d=1.00 min @ (0.25, 0.25, 0.00) sse = 270626.5, tmin=9.7036 d=0.50 min @ (0.00, 0.00, 0.12) sse = 270599.8, tmin=11.0924 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 11.09 min curvature mean = 0.008, std = 0.940 curvature mean = 0.012, std = 0.934 curvature mean = 0.004, std = 0.949 curvature mean = 0.006, std = 0.969 curvature mean = 0.001, std = 0.950 curvature mean = 0.002, std = 0.986 2 Reading smoothwm curvature mean = -0.021, std = 0.388 curvature mean = 0.003, std = 0.066 curvature mean = 0.049, std = 0.235 curvature mean = 0.003, std = 0.079 curvature mean = 0.021, std = 0.375 curvature mean = 0.003, std = 0.084 curvature mean = 0.010, std = 0.483 curvature mean = 0.003, std = 0.087 curvature mean = 0.003, std = 0.584 MRISregister() return, current seed 0 writing registered surface to ../surf/lh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white lh Thu Aug 8 20:02:00 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 20:02:03 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 20:02:05 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub002 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... 1305 labels changed using aseg relabeling using gibbs priors... 000: 3454 changed, 162178 examined... 001: 789 changed, 14622 examined... 002: 188 changed, 4322 examined... 003: 63 changed, 1074 examined... 004: 26 changed, 386 examined... 005: 15 changed, 153 examined... 006: 9 changed, 93 examined... 007: 3 changed, 50 examined... 008: 0 changed, 17 examined... 230 labels changed using aseg 000: 143 total segments, 97 labels (308 vertices) changed 001: 46 total segments, 1 labels (3 vertices) changed 002: 45 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 49 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2163 vertices marked for relabeling... 2163 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 1 minutes and 14 seconds. #-------------------------------------------- #@# Make Pial Surf lh Thu Aug 8 20:03:19 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub002 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/sub002/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/wm.mgz... 20389 bright wm thresholded. 326 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.orig... computing class statistics... border white: 305608 voxels (1.82%) border gray 333888 voxels (1.99%) WM (92.0): 93.4 +- 9.7 [70.0 --> 110.0] GM (76.0) : 74.6 +- 12.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 48.3 (was 70) setting MAX_BORDER_WHITE to 114.7 (was 105) setting MIN_BORDER_WHITE to 61.0 (was 85) setting MAX_CSF to 35.6 (was 40) setting MAX_GRAY to 95.3 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 54.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 22.8 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=61 mean inside = 92.7, mean outside = 69.6 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.21 (0.02-->2.48) (max @ vno 117773 --> 118787) face area 0.28 +- 0.12 (0.00-->2.11) mean absolute distance = 0.77 +- 0.96 3703 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown deleting segment 4 with 12 points - only 0.00% unknown deleting segment 5 with 8 points - only 0.00% unknown deleting segment 6 with 25 points - only 0.00% unknown deleting segment 7 with 12 points - only 0.00% unknown mean border=73.1, 146 (146) missing vertices, mean dist 0.3 [0.7 (%29.1)->0.8 (%70.9))] %61 local maxima, %34 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.26 (0.10-->3.38) (max @ vno 112452 --> 112451) face area 0.28 +- 0.13 (0.00-->1.76) mean absolute distance = 0.38 +- 0.56 3451 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=8277498.0, rms=13.32 001: dt: 0.5000, sse=8104297.0, rms=9.538 (0.000%) 002: dt: 0.5000, sse=8189057.0, rms=7.204 (0.000%) 003: dt: 0.5000, sse=8438055.0, rms=5.718 (0.000%) 004: dt: 0.5000, sse=8621839.0, rms=4.844 (0.000%) 005: dt: 0.5000, sse=8859667.0, rms=4.370 (0.000%) 006: dt: 0.5000, sse=8931330.0, rms=4.155 (0.000%) 007: dt: 0.5000, sse=9015885.0, rms=4.034 (0.000%) 008: dt: 0.5000, sse=9004967.0, rms=3.978 (0.000%) rms = 3.93, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=8989411.0, rms=3.929 (0.000%) 010: dt: 0.2500, sse=5421008.5, rms=2.666 (0.000%) 011: dt: 0.2500, sse=4922914.0, rms=2.224 (0.000%) 012: dt: 0.2500, sse=4626976.0, rms=2.112 (0.000%) 013: dt: 0.2500, sse=4542123.0, rms=2.024 (0.000%) rms = 1.99, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=4450310.0, rms=1.994 (0.000%) 015: dt: 0.1250, sse=4289231.5, rms=1.853 (0.000%) rms = 1.84, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=4247387.5, rms=1.838 (0.000%) positioning took 2.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 0 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 2 with 4 points - only 0.00% unknown deleting segment 5 with 62 points - only 29.03% unknown deleting segment 6 with 14 points - only 0.00% unknown deleting segment 7 with 11 points - only 0.00% unknown deleting segment 8 with 29 points - only 0.00% unknown deleting segment 9 with 13 points - only 0.00% unknown mean border=78.3, 112 (47) missing vertices, mean dist -0.3 [0.4 (%79.8)->0.2 (%20.2))] %78 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.12-->3.74) (max @ vno 106914 --> 105889) face area 0.35 +- 0.16 (0.00-->2.19) mean absolute distance = 0.23 +- 0.32 3010 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5700380.0, rms=6.74 017: dt: 0.5000, sse=5576232.5, rms=4.227 (0.000%) rms = 4.24, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=5080995.5, rms=3.234 (0.000%) 019: dt: 0.2500, sse=4820064.5, rms=2.389 (0.000%) 020: dt: 0.2500, sse=4724833.0, rms=1.903 (0.000%) 021: dt: 0.2500, sse=4671011.0, rms=1.772 (0.000%) 022: dt: 0.2500, sse=4595735.0, rms=1.664 (0.000%) rms = 1.63, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=4587611.5, rms=1.630 (0.000%) 024: dt: 0.1250, sse=4469250.5, rms=1.507 (0.000%) rms = 1.50, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=4432582.5, rms=1.497 (0.000%) positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 0 with 2 points - only 0.00% unknown deleting segment 1 with 5 points - only 0.00% unknown deleting segment 3 with 136 points - only 58.82% unknown deleting segment 4 with 12 points - only 0.00% unknown deleting segment 5 with 11 points - only 0.00% unknown deleting segment 6 with 29 points - only 0.00% unknown deleting segment 7 with 12 points - only 0.00% unknown mean border=81.8, 108 (27) missing vertices, mean dist -0.2 [0.2 (%77.5)->0.2 (%22.5))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.07-->4.01) (max @ vno 106914 --> 105889) face area 0.34 +- 0.16 (0.00-->2.26) mean absolute distance = 0.17 +- 0.25 2787 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4956790.0, rms=4.50 026: dt: 0.5000, sse=5243048.5, rms=3.726 (0.000%) rms = 3.99, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=4750395.5, rms=2.356 (0.000%) 028: dt: 0.2500, sse=4629788.5, rms=1.850 (0.000%) 029: dt: 0.2500, sse=4657395.0, rms=1.542 (0.000%) rms = 1.56, time step reduction 2 of 3 to 0.125... 030: dt: 0.1250, sse=4597971.0, rms=1.451 (0.000%) 031: dt: 0.1250, sse=4521950.5, rms=1.325 (0.000%) rms = 1.32, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=4484707.0, rms=1.318 (0.000%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 0 with 2 points - only 0.00% unknown deleting segment 1 with 11 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 136 points - only 58.82% unknown deleting segment 4 with 10 points - only 0.00% unknown deleting segment 5 with 7 points - only 0.00% unknown deleting segment 6 with 11 points - only 0.00% unknown deleting segment 7 with 33 points - only 0.00% unknown deleting segment 8 with 13 points - only 0.00% unknown mean border=82.8, 123 (22) missing vertices, mean dist -0.0 [0.2 (%58.1)->0.2 (%41.9))] %91 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4521456.0, rms=1.80 rms = 2.50, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=4617454.0, rms=1.172 (0.000%) 034: dt: 0.2500, sse=4796951.5, rms=0.995 (0.000%) rms = 1.00, 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=4796746.5, rms=0.987 (0.000%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... smoothing surface for 5 iterations... mean border=51.0, 144 (144) missing vertices, mean dist 1.9 [0.1 (%0.0)->2.2 (%100.0))] %21 local maxima, %61 large gradients and %14 min vals, 1237 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=33542884.0, rms=31.33 001: dt: 0.5000, sse=24071146.0, rms=26.008 (0.000%) 002: dt: 0.5000, sse=17442914.0, rms=21.547 (0.000%) 003: dt: 0.5000, sse=13096878.0, rms=17.941 (0.000%) 004: dt: 0.5000, sse=10597893.0, rms=15.121 (0.000%) 005: dt: 0.5000, sse=9240971.0, rms=12.974 (0.000%) 006: dt: 0.5000, sse=8527073.0, rms=11.354 (0.000%) 007: dt: 0.5000, sse=8051078.5, rms=9.951 (0.000%) 008: dt: 0.5000, sse=7681486.0, rms=8.633 (0.000%) 009: dt: 0.5000, sse=7483358.5, rms=7.368 (0.000%) 010: dt: 0.5000, sse=7441162.5, rms=6.254 (0.000%) 011: dt: 0.5000, sse=7532366.0, rms=5.404 (0.000%) 012: dt: 0.5000, sse=7677448.5, rms=4.865 (0.000%) 013: dt: 0.5000, sse=7882003.5, rms=4.562 (0.000%) 014: dt: 0.5000, sse=7996728.5, rms=4.379 (0.000%) 015: dt: 0.5000, sse=8083462.0, rms=4.260 (0.000%) 016: dt: 0.5000, sse=8105952.5, rms=4.171 (0.000%) 017: dt: 0.5000, sse=8170469.0, rms=4.111 (0.000%) rms = 4.07, time step reduction 1 of 3 to 0.250... 018: dt: 0.5000, sse=8189036.0, rms=4.068 (0.000%) 019: dt: 0.2500, sse=5352816.0, rms=3.085 (0.000%) 020: dt: 0.2500, sse=5082524.5, rms=2.815 (0.000%) 021: dt: 0.2500, sse=4904897.0, rms=2.763 (0.000%) rms = 2.74, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=4858443.0, rms=2.738 (0.000%) 023: dt: 0.1250, sse=4617195.0, rms=2.564 (0.000%) rms = 2.54, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=4586460.0, rms=2.541 (0.000%) positioning took 3.5 minutes mean border=47.4, 504 (17) missing vertices, mean dist 0.2 [0.2 (%40.3)->0.5 (%59.7))] %44 local maxima, %41 large gradients and %10 min vals, 386 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=5666737.0, rms=5.73 025: dt: 0.5000, sse=5772666.5, rms=4.367 (0.000%) rms = 4.35, time step reduction 1 of 3 to 0.250... 026: dt: 0.5000, sse=7566291.5, rms=4.347 (0.000%) 027: dt: 0.2500, sse=5525399.5, rms=3.152 (0.000%) 028: dt: 0.2500, sse=5577510.0, rms=2.825 (0.000%) 029: dt: 0.2500, sse=5397909.5, rms=2.774 (0.000%) 030: dt: 0.2500, sse=5470158.5, rms=2.702 (0.000%) rms = 2.70, time step reduction 2 of 3 to 0.125... 031: dt: 0.1250, sse=5343195.0, rms=2.603 (0.000%) 032: dt: 0.1250, sse=5151511.5, rms=2.459 (0.000%) rms = 2.43, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=5108980.0, rms=2.430 (0.000%) positioning took 1.4 minutes mean border=44.4, 662 (11) missing vertices, mean dist 0.2 [0.2 (%32.8)->0.3 (%67.2))] %64 local maxima, %22 large gradients and %10 min vals, 446 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=5586529.5, rms=4.51 034: dt: 0.5000, sse=5823650.0, rms=4.289 (0.000%) rms = 4.31, time step reduction 1 of 3 to 0.250... 035: dt: 0.2500, sse=5343568.5, rms=3.145 (0.000%) 036: dt: 0.2500, sse=5491674.5, rms=2.678 (0.000%) 037: dt: 0.2500, sse=5479107.5, rms=2.588 (0.000%) rms = 2.56, time step reduction 2 of 3 to 0.125... 038: dt: 0.2500, sse=5516970.5, rms=2.556 (0.000%) 039: dt: 0.1250, sse=5265964.5, rms=2.310 (0.000%) rms = 2.27, time step reduction 3 of 3 to 0.062... 040: dt: 0.1250, sse=5245404.5, rms=2.272 (0.000%) positioning took 1.1 minutes mean border=43.1, 1454 (5) missing vertices, mean dist 0.1 [0.2 (%43.2)->0.2 (%56.8))] %67 local maxima, %18 large gradients and %10 min vals, 294 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/sub002/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=5316321.5, rms=2.76 rms = 3.84, time step reduction 1 of 3 to 0.250... 041: dt: 0.2500, sse=5160718.5, rms=2.365 (0.000%) 042: dt: 0.2500, sse=5316253.5, rms=2.295 (0.000%) rms = 2.30, time step reduction 2 of 3 to 0.125... rms = 2.25, time step reduction 3 of 3 to 0.062... 043: dt: 0.1250, sse=5266903.0, rms=2.252 (0.000%) positioning took 0.7 minutes writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.area.pial vertex spacing 1.00 +- 0.41 (0.07-->7.07) (max @ vno 111435 --> 111419) face area 0.40 +- 0.29 (0.00-->4.99) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 162178 vertices processed 25000 of 162178 vertices processed 50000 of 162178 vertices processed 75000 of 162178 vertices processed 100000 of 162178 vertices processed 125000 of 162178 vertices processed 150000 of 162178 vertices processed 0 of 162178 vertices processed 25000 of 162178 vertices processed 50000 of 162178 vertices processed 75000 of 162178 vertices processed 100000 of 162178 vertices processed 125000 of 162178 vertices processed 150000 of 162178 vertices processed thickness calculation complete, 557:854 truncations. 44192 vertices at 0 distance 120328 vertices at 1 distance 98971 vertices at 2 distance 35103 vertices at 3 distance 9118 vertices at 4 distance 2429 vertices at 5 distance 814 vertices at 6 distance 283 vertices at 7 distance 102 vertices at 8 distance 51 vertices at 9 distance 27 vertices at 10 distance 19 vertices at 11 distance 17 vertices at 12 distance 8 vertices at 13 distance 14 vertices at 14 distance 12 vertices at 15 distance 10 vertices at 16 distance 6 vertices at 17 distance 0 vertices at 18 distance 1 vertices at 19 distance 3 vertices at 20 distance writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.thickness positioning took 17.0 minutes #-------------------------------------------- #@# Surf Volume lh Thu Aug 8 20:20:22 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.volume lh.area.mid mul lh.thickness Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# WM/GM Contrast lh Thu Aug 8 20:20:22 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts pctsurfcon --s sub002 --lh-only Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts/pctsurfcon.log Thu Aug 8 20:20:22 CEST 2013 setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts /opt/freesurfer/5.3.0/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux snake5 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux FREESURFER_HOME /opt/freesurfer/5.3.0 mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/tmp.pctsurfcon.3306/lh.wm.mgh --regheader sub002 --cortex srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/mri/orig.mgz as target reference. Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/label/lh.cortex.label Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 = 125798 Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/label/lh.cortex.label Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/tmp.pctsurfcon.3306/lh.wm.mgh Dim: 162178 1 1 mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/tmp.pctsurfcon.3306/lh.gm.mgh --projfrac 0.3 --regheader sub002 --cortex srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/mri/orig.mgz as target reference. Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/label/lh.cortex.label Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.white Done reading source surface Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 = 144480 Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/label/lh.cortex.label Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/tmp.pctsurfcon.3306/lh.gm.mgh Dim: 162178 1 1 mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/tmp.pctsurfcon.3306/lh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/tmp.pctsurfcon.3306/lh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/surf/lh.w-g.pct.mgh mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.w-g.pct.mgh --annot sub002 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/surf/lh.w-g.pct.mgh --annot sub002 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/stats/lh.w-g.pct.stats --snr sysname Linux hostname snake5 machine x86_64 user fkaule UseRobust 0 Constructing seg from annotation Reading annotation reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Seg base 1000 Loading /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.w-g.pct.mgh Vertex Area is 0.660581 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 1000 unknown 0 0.000 1 1001 bankssts 1908 1358.553 2 1002 caudalanteriorcingulate 1237 841.711 3 1003 caudalmiddlefrontal 3707 2429.536 4 1004 corpuscallosum 0 0.000 5 1005 cuneus 2490 1644.200 6 1006 entorhinal 570 388.561 7 1007 fusiform 5387 3586.849 8 1008 inferiorparietal 8738 5797.738 9 1009 inferiortemporal 6203 4139.783 10 1010 isthmuscingulate 2304 1469.004 11 1011 lateraloccipital 7544 4960.165 12 1012 lateralorbitofrontal 4373 2897.055 13 1013 lingual 4490 2990.144 14 1014 medialorbitofrontal 3123 2057.696 15 1015 middletemporal 6067 4163.659 16 1016 parahippocampal 1546 1015.344 17 1017 paracentral 2075 1301.509 18 1018 parsopercularis 2742 1860.310 19 1019 parsorbitalis 1178 782.502 20 1020 parstriangularis 2322 1553.732 21 1021 pericalcarine 2216 1526.616 22 1022 postcentral 7463 4733.478 23 1023 posteriorcingulate 1929 1285.999 24 1024 precentral 9202 5651.326 25 1025 precuneus 8368 5567.865 26 1026 rostralanteriorcingulate 1594 1070.627 27 1027 rostralmiddlefrontal 10672 7247.876 28 1028 superiorfrontal 13407 9095.433 29 1029 superiorparietal 9674 6236.878 30 1030 superiortemporal 7245 4841.190 31 1031 supramarginal 8068 5468.552 32 1032 frontalpole 419 287.002 33 1033 temporalpole 832 586.120 34 1034 transversetemporal 732 440.409 35 1035 insula 3766 2476.238 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats lh Thu Aug 8 20:20:37 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 sub002 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 1908 1359 3338 2.408 0.420 0.126 0.033 24 2.7 bankssts 1237 842 2268 2.414 0.770 0.141 0.037 21 1.9 caudalanteriorcingulate 3707 2430 6447 2.487 0.490 0.117 0.035 35 5.4 caudalmiddlefrontal 2490 1644 4161 2.151 0.451 0.165 0.059 49 6.1 cuneus 570 389 1979 3.623 0.793 0.159 0.077 11 2.0 entorhinal 5387 3587 11544 2.765 0.711 0.139 0.052 91 11.1 fusiform 8738 5798 14900 2.336 0.394 0.136 0.050 148 17.4 inferiorparietal 6203 4140 12913 2.690 0.725 0.154 0.061 129 15.1 inferiortemporal 2304 1469 4092 2.432 0.877 0.155 0.090 47 7.1 isthmuscingulate 7544 4960 11851 2.100 0.395 0.152 0.056 149 16.9 lateraloccipital 4373 2897 8064 2.481 0.603 0.160 0.073 124 13.9 lateralorbitofrontal 4490 2990 7097 2.150 0.535 0.155 0.061 85 11.2 lingual 3123 2058 5175 2.155 0.810 0.147 0.068 83 9.4 medialorbitofrontal 6067 4164 14504 2.816 0.571 0.145 0.057 140 15.3 middletemporal 1546 1015 2886 2.404 0.613 0.106 0.035 13 2.4 parahippocampal 2075 1302 3416 2.361 0.720 0.126 0.042 29 3.8 paracentral 2742 1860 5691 2.723 0.454 0.127 0.037 31 4.2 parsopercularis 1178 783 2698 2.574 0.580 0.158 0.055 25 2.6 parsorbitalis 2322 1554 4236 2.438 0.418 0.138 0.044 33 4.2 parstriangularis 2216 1527 2696 1.821 0.465 0.141 0.067 37 5.5 pericalcarine 7463 4733 11214 2.078 0.542 0.126 0.041 96 12.4 postcentral 1929 1286 3528 2.624 0.549 0.154 0.059 43 4.5 posteriorcingulate 9202 5651 16225 2.629 0.551 0.118 0.044 105 17.1 precentral 8368 5568 14479 2.422 0.480 0.131 0.044 114 14.0 precuneus 1594 1071 3090 2.436 0.804 0.180 0.091 47 5.4 rostralanteriorcingulate 10672 7248 18731 2.316 0.499 0.152 0.056 196 23.3 rostralmiddlefrontal 13407 9095 26583 2.526 0.607 0.146 0.083 1763 51.0 superiorfrontal 9674 6237 14961 2.180 0.418 0.125 0.035 113 13.7 superiorparietal 7245 4841 15521 2.886 0.584 0.124 0.092 242 13.7 superiortemporal 8068 5469 14809 2.437 0.439 0.139 0.047 134 14.3 supramarginal 419 287 979 2.544 0.519 0.194 0.071 12 1.3 frontalpole 832 586 2930 3.707 0.802 0.156 0.075 14 2.5 temporalpole 732 440 1256 2.497 0.307 0.129 0.041 9 1.3 transversetemporal 3766 2476 7768 3.009 0.826 0.124 0.054 51 7.3 insula #----------------------------------------- #@# Cortical Parc 2 lh Thu Aug 8 20:21:03 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub002 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... 19 labels changed using aseg relabeling using gibbs priors... 000: 10727 changed, 162178 examined... 001: 2554 changed, 41118 examined... 002: 759 changed, 13329 examined... 003: 341 changed, 4318 examined... 004: 152 changed, 1954 examined... 005: 85 changed, 863 examined... 006: 55 changed, 466 examined... 007: 33 changed, 310 examined... 008: 19 changed, 177 examined... 009: 6 changed, 99 examined... 010: 3 changed, 36 examined... 011: 1 changed, 16 examined... 012: 0 changed, 5 examined... 12 labels changed using aseg 000: 337 total segments, 249 labels (2892 vertices) changed 001: 101 total segments, 13 labels (58 vertices) changed 002: 88 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 148 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1262 vertices marked for relabeling... 1262 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 1 minutes and 23 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Thu Aug 8 20:22:26 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 sub002 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 1443 975 2438 2.283 0.512 0.168 0.062 30 3.6 G_and_S_frontomargin 1499 1010 2478 2.151 0.427 0.147 0.049 23 2.8 G_and_S_occipital_inf 1456 842 2306 2.289 0.731 0.131 0.050 29 3.3 G_and_S_paracentral 1954 1275 3341 2.385 0.611 0.142 0.045 33 3.4 G_and_S_subcentral 1006 699 2118 2.369 0.516 0.184 0.077 30 3.0 G_and_S_transv_frontopol 2522 1742 4569 2.426 0.718 0.147 0.055 44 5.5 G_and_S_cingul-Ant 1769 1232 3487 2.599 0.614 0.131 0.036 22 2.6 G_and_S_cingul-Mid-Ant 1530 1051 2810 2.570 0.470 0.135 0.045 23 2.8 G_and_S_cingul-Mid-Post 865 550 2114 3.085 0.533 0.171 0.063 20 2.3 G_cingul-Post-dorsal 505 315 753 1.985 0.832 0.155 0.157 10 1.3 G_cingul-Post-ventral 2221 1463 3913 2.161 0.491 0.175 0.071 55 6.9 G_cuneus 1521 1029 4025 2.937 0.379 0.143 0.052 25 3.0 G_front_inf-Opercular 575 376 1243 2.662 0.473 0.151 0.058 14 1.3 G_front_inf-Orbital 1477 969 3174 2.530 0.408 0.157 0.051 27 3.2 G_front_inf-Triangul 5359 3547 11115 2.491 0.509 0.154 0.060 107 12.9 G_front_middle 9199 6171 20236 2.636 0.644 0.160 0.108 1727 45.9 G_front_sup 578 361 1369 3.301 0.768 0.124 0.045 8 1.0 G_Ins_lg_and_S_cent_ins 859 578 2692 3.636 0.825 0.162 0.112 26 3.0 G_insular_short 2652 1659 5248 2.429 0.366 0.169 0.076 80 8.1 G_occipital_middle 1645 1049 2761 2.154 0.427 0.149 0.052 32 3.5 G_occipital_sup 2043 1322 5176 2.994 0.624 0.157 0.061 49 5.0 G_oc-temp_lat-fusifor 3020 1949 5091 2.108 0.568 0.163 0.072 61 8.8 G_oc-temp_med-Lingual 1392 893 3697 3.150 0.911 0.122 0.044 16 2.5 G_oc-temp_med-Parahip 3282 2178 7192 2.550 0.630 0.170 0.082 110 11.9 G_orbital 3038 2029 5831 2.361 0.403 0.144 0.052 61 6.6 G_pariet_inf-Angular 4341 2946 9366 2.574 0.425 0.151 0.058 101 9.2 G_pariet_inf-Supramar 4170 2663 7674 2.322 0.408 0.135 0.041 63 6.9 G_parietal_sup 2814 1691 4819 2.238 0.477 0.132 0.052 44 5.6 G_postcentral 3727 2133 7748 2.848 0.474 0.121 0.057 59 9.1 G_precentral 3655 2432 7768 2.532 0.529 0.147 0.057 70 7.6 G_precuneus 1075 707 2076 2.149 0.621 0.191 0.092 45 4.3 G_rectus 674 428 1331 2.746 1.005 0.117 0.095 25 2.9 G_subcallosal 500 287 994 2.628 0.258 0.132 0.045 7 0.9 G_temp_sup-G_T_transv 2477 1615 6914 3.139 0.485 0.143 0.199 193 5.8 G_temp_sup-Lateral 853 579 2295 3.572 0.550 0.132 0.083 15 3.1 G_temp_sup-Plan_polar 1514 1062 2916 2.481 0.440 0.131 0.035 19 2.3 G_temp_sup-Plan_tempo 3393 2265 8846 2.912 0.753 0.173 0.080 97 10.3 G_temporal_inf 4130 2822 10653 2.822 0.572 0.159 0.070 125 12.9 G_temporal_middle 358 237 453 2.270 0.495 0.105 0.029 2 0.4 Lat_Fis-ant-Horizont 304 224 503 2.559 0.421 0.112 0.028 3 0.3 Lat_Fis-ant-Vertical 1619 1072 2223 2.377 0.378 0.121 0.037 14 2.5 Lat_Fis-post 2181 1451 3251 1.940 0.374 0.168 0.073 56 6.4 Pole_occipital 2103 1463 6747 3.293 0.887 0.174 0.091 49 7.4 Pole_temporal 2673 1862 3543 2.099 0.653 0.142 0.049 41 5.0 S_calcarine 3348 2175 3826 1.939 0.593 0.113 0.031 21 4.7 S_central 1269 828 2042 2.274 0.493 0.124 0.047 16 2.3 S_cingul-Marginalis 485 333 841 2.894 0.535 0.122 0.031 3 0.6 S_circular_insula_ant 1526 996 2439 2.747 0.573 0.089 0.022 6 1.4 S_circular_insula_inf 2116 1423 3234 2.542 0.407 0.113 0.031 14 2.7 S_circular_insula_sup 796 546 1487 2.753 0.610 0.136 0.042 10 1.4 S_collat_transv_ant 427 285 509 2.007 0.365 0.130 0.032 3 0.6 S_collat_transv_post 2671 1824 3950 2.296 0.425 0.121 0.033 24 3.7 S_front_inf 2306 1560 3336 2.083 0.469 0.132 0.042 28 3.7 S_front_middle 3117 2100 4879 2.319 0.443 0.110 0.032 24 3.8 S_front_sup 805 525 1006 2.254 0.333 0.119 0.029 6 1.0 S_interm_prim-Jensen 3767 2494 4789 2.094 0.325 0.112 0.026 28 4.1 S_intrapariet_and_P_trans 1050 717 1271 1.938 0.358 0.127 0.031 9 1.3 S_oc_middle_and_Lunatus 1788 1180 2352 2.117 0.329 0.109 0.025 12 1.9 S_oc_sup_and_transversal 705 472 849 2.039 0.278 0.115 0.027 5 0.8 S_occipital_ant 1244 828 1671 2.200 0.433 0.108 0.031 10 1.6 S_oc-temp_lat 2815 1946 4287 2.408 0.475 0.115 0.031 21 3.9 S_oc-temp_med_and_Lingual 385 268 553 2.453 0.447 0.127 0.041 3 0.6 S_orbital_lateral 808 548 1246 2.304 0.796 0.128 0.035 7 1.2 S_orbital_med-olfact 1378 924 2144 2.277 0.526 0.158 0.061 30 3.2 S_orbital-H_Shaped 2739 1786 3678 2.187 0.418 0.115 0.040 27 3.6 S_parieto_occipital 1704 1066 1845 2.014 0.709 0.160 0.078 45 5.6 S_pericallosal 3894 2570 4985 2.112 0.446 0.118 0.033 33 5.3 S_postcentral 2030 1364 3033 2.585 0.427 0.109 0.025 13 2.2 S_precentral-inf-part 1679 1136 2391 2.295 0.414 0.109 0.025 11 1.8 S_precentral-sup-part 933 615 1293 1.933 0.732 0.137 0.053 14 2.1 S_suborbital 1918 1305 3083 2.479 0.435 0.125 0.035 19 2.8 S_subparietal 2304 1543 3455 2.482 0.626 0.129 0.039 26 3.8 S_temporal_inf 7184 4898 11561 2.442 0.430 0.120 0.035 76 9.7 S_temporal_sup 429 297 696 2.605 0.379 0.113 0.025 2 0.5 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Thu Aug 8 20:22:56 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub002 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... 1018 labels changed using aseg relabeling using gibbs priors... 000: 3257 changed, 162178 examined... 001: 763 changed, 13667 examined... 002: 198 changed, 4102 examined... 003: 79 changed, 1213 examined... 004: 39 changed, 463 examined... 005: 20 changed, 244 examined... 006: 6 changed, 119 examined... 007: 4 changed, 39 examined... 008: 2 changed, 27 examined... 009: 2 changed, 13 examined... 010: 2 changed, 12 examined... 011: 0 changed, 13 examined... 131 labels changed using aseg 000: 80 total segments, 47 labels (552 vertices) changed 001: 35 total segments, 2 labels (4 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 45 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 842 vertices marked for relabeling... 842 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas40.annot... classification took 1 minutes and 16 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Thu Aug 8 20:24:13 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 sub002 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 2117 1450 4172 2.600 0.692 0.135 0.037 31 3.2 caudalanteriorcingulate 3793 2479 6653 2.500 0.485 0.118 0.035 36 5.7 caudalmiddlefrontal 3548 2344 5746 2.153 0.442 0.149 0.050 60 7.4 cuneus 519 354 1868 3.760 0.767 0.150 0.056 7 1.1 entorhinal 4992 3319 10173 2.721 0.681 0.133 0.044 74 9.3 fusiform 8311 5508 14130 2.322 0.392 0.137 0.050 144 17.0 inferiorparietal 6272 4181 13685 2.734 0.756 0.159 0.068 144 16.8 inferiortemporal 2301 1468 4109 2.431 0.877 0.155 0.091 48 7.1 isthmuscingulate 7732 5087 12054 2.088 0.388 0.152 0.057 153 17.2 lateraloccipital 4894 3210 9081 2.508 0.685 0.164 0.076 142 15.9 lateralorbitofrontal 4489 2986 7083 2.148 0.535 0.156 0.061 85 11.2 lingual 2481 1638 4159 2.080 0.709 0.158 0.075 77 8.5 medialorbitofrontal 8003 5494 17839 2.734 0.557 0.142 0.054 167 18.6 middletemporal 1538 1010 2841 2.391 0.596 0.106 0.035 12 2.4 parahippocampal 2467 1564 4369 2.478 0.733 0.128 0.045 36 4.8 paracentral 2462 1663 5118 2.754 0.454 0.126 0.037 26 3.8 parsopercularis 1342 902 2928 2.689 0.477 0.139 0.048 20 2.5 parsorbitalis 2850 1922 5167 2.418 0.425 0.141 0.043 43 5.2 parstriangularis 2226 1528 2708 1.826 0.470 0.141 0.068 37 5.5 pericalcarine 8325 5296 12367 2.096 0.546 0.127 0.042 105 13.8 postcentral 2152 1435 3867 2.620 0.534 0.151 0.057 45 4.9 posteriorcingulate 9025 5546 15843 2.628 0.552 0.118 0.044 104 17.0 precentral 8041 5338 14146 2.438 0.480 0.134 0.045 114 14.0 precuneus 2102 1411 3766 2.359 0.791 0.168 0.082 52 6.3 rostralanteriorcingulate 7648 5180 13626 2.323 0.507 0.148 0.051 131 15.7 rostralmiddlefrontal 14727 10003 28549 2.447 0.600 0.149 0.084 1804 54.8 superiorfrontal 7867 5076 12219 2.183 0.397 0.122 0.033 87 10.5 superiorparietal 9442 6377 21026 2.907 0.660 0.128 0.084 275 18.4 superiortemporal 7873 5340 14427 2.438 0.440 0.138 0.047 129 13.8 supramarginal 733 445 1262 2.502 0.310 0.129 0.041 8 1.3 transversetemporal 3319 2198 7050 3.008 0.817 0.122 0.053 45 6.1 insula #-------------------------------------------- #@# Tessellate rh Thu Aug 8 20:24:49 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 0 found - 0 modified | TOTAL: 2 pass 1 (yz+): 1 found - 1 modified | TOTAL: 3 pass 2 (yz+): 0 found - 1 modified | TOTAL: 3 pass 1 (yz-): 1 found - 1 modified | TOTAL: 4 pass 2 (yz-): 0 found - 1 modified | TOTAL: 4 pass 1 (xz+): 0 found - 0 modified | TOTAL: 4 pass 1 (xz-): 3 found - 3 modified | TOTAL: 7 pass 2 (xz-): 0 found - 3 modified | TOTAL: 7 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 2 found - 2 modified | TOTAL: 2 pass 2 (--): 0 found - 2 modified | TOTAL: 2 pass 1 (-+): 1 found - 1 modified | TOTAL: 3 pass 2 (-+): 0 found - 1 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 = 10 (out of 314383: 0.003181) 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: 2425 vertices, 2588 faces slice 50: 9338 vertices, 9682 faces slice 60: 19850 vertices, 20243 faces slice 70: 32136 vertices, 32562 faces slice 80: 45543 vertices, 45938 faces slice 90: 58145 vertices, 58605 faces slice 100: 70944 vertices, 71360 faces slice 110: 82751 vertices, 83163 faces slice 120: 94673 vertices, 95112 faces slice 130: 106444 vertices, 106869 faces slice 140: 117806 vertices, 118215 faces slice 150: 128578 vertices, 128945 faces slice 160: 137412 vertices, 137712 faces slice 170: 145518 vertices, 145783 faces slice 180: 152727 vertices, 152983 faces slice 190: 158448 vertices, 158645 faces slice 200: 162265 vertices, 162316 faces slice 210: 162428 vertices, 162448 faces slice 220: 162428 vertices, 162448 faces slice 230: 162428 vertices, 162448 faces slice 240: 162428 vertices, 162448 faces slice 250: 162428 vertices, 162448 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... 162428 voxel in cpt #1: X=-20 [v=162428,e=487344,f=324896] located at (30.741030, -17.895498, 39.739590) For the whole surface: X=-20 [v=162428,e=487344,f=324896] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Thu Aug 8 20:24:59 CEST 2013 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 20:25:04 CEST 2013 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts avg radius = 50.0 mm, total surface area = 86209 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.8 minutes Not saving sulc step 000: RMS=0.098 (target=0.015) step 005: RMS=0.072 (target=0.015) step 010: RMS=0.053 (target=0.015) step 015: RMS=0.045 (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=0.027 (target=0.015) step 040: RMS=0.026 (target=0.015) step 045: RMS=0.024 (target=0.015) step 050: RMS=0.023 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.022 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Thu Aug 8 20:25:50 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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-->5.95) (max @ vno 123027 --> 123028) face area 0.02 +- 0.03 (-0.18-->0.54) scaling brain by 0.292... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.202, avgs=0 005/300: dt: 0.9000, rms radial error=175.942, avgs=0 010/300: dt: 0.9000, rms radial error=175.382, avgs=0 015/300: dt: 0.9000, rms radial error=174.647, avgs=0 020/300: dt: 0.9000, rms radial error=173.811, avgs=0 025/300: dt: 0.9000, rms radial error=172.915, avgs=0 030/300: dt: 0.9000, rms radial error=171.991, avgs=0 035/300: dt: 0.9000, rms radial error=171.051, avgs=0 040/300: dt: 0.9000, rms radial error=170.106, avgs=0 045/300: dt: 0.9000, rms radial error=169.159, avgs=0 050/300: dt: 0.9000, rms radial error=168.213, avgs=0 055/300: dt: 0.9000, rms radial error=167.270, avgs=0 060/300: dt: 0.9000, rms radial error=166.330, avgs=0 065/300: dt: 0.9000, rms radial error=165.395, avgs=0 070/300: dt: 0.9000, rms radial error=164.464, avgs=0 075/300: dt: 0.9000, rms radial error=163.539, avgs=0 080/300: dt: 0.9000, rms radial error=162.618, avgs=0 085/300: dt: 0.9000, rms radial error=161.703, avgs=0 090/300: dt: 0.9000, rms radial error=160.793, avgs=0 095/300: dt: 0.9000, rms radial error=159.889, avgs=0 100/300: dt: 0.9000, rms radial error=158.990, avgs=0 105/300: dt: 0.9000, rms radial error=158.096, avgs=0 110/300: dt: 0.9000, rms radial error=157.207, avgs=0 115/300: dt: 0.9000, rms radial error=156.323, avgs=0 120/300: dt: 0.9000, rms radial error=155.444, avgs=0 125/300: dt: 0.9000, rms radial error=154.570, avgs=0 130/300: dt: 0.9000, rms radial error=153.701, avgs=0 135/300: dt: 0.9000, rms radial error=152.837, avgs=0 140/300: dt: 0.9000, rms radial error=151.978, avgs=0 145/300: dt: 0.9000, rms radial error=151.125, avgs=0 150/300: dt: 0.9000, rms radial error=150.276, avgs=0 155/300: dt: 0.9000, rms radial error=149.431, avgs=0 160/300: dt: 0.9000, rms radial error=148.592, avgs=0 165/300: dt: 0.9000, rms radial error=147.757, avgs=0 170/300: dt: 0.9000, rms radial error=146.927, avgs=0 175/300: dt: 0.9000, rms radial error=146.101, avgs=0 180/300: dt: 0.9000, rms radial error=145.280, avgs=0 185/300: dt: 0.9000, rms radial error=144.464, avgs=0 190/300: dt: 0.9000, rms radial error=143.652, avgs=0 195/300: dt: 0.9000, rms radial error=142.844, avgs=0 200/300: dt: 0.9000, rms radial error=142.041, avgs=0 205/300: dt: 0.9000, rms radial error=141.242, avgs=0 210/300: dt: 0.9000, rms radial error=140.447, avgs=0 215/300: dt: 0.9000, rms radial error=139.657, avgs=0 220/300: dt: 0.9000, rms radial error=138.871, avgs=0 225/300: dt: 0.9000, rms radial error=138.090, avgs=0 230/300: dt: 0.9000, rms radial error=137.313, avgs=0 235/300: dt: 0.9000, rms radial error=136.540, avgs=0 240/300: dt: 0.9000, rms radial error=135.771, avgs=0 245/300: dt: 0.9000, rms radial error=135.007, avgs=0 250/300: dt: 0.9000, rms radial error=134.247, avgs=0 255/300: dt: 0.9000, rms radial error=133.491, avgs=0 260/300: dt: 0.9000, rms radial error=132.739, avgs=0 265/300: dt: 0.9000, rms radial error=131.992, avgs=0 270/300: dt: 0.9000, rms radial error=131.248, avgs=0 275/300: dt: 0.9000, rms radial error=130.509, avgs=0 280/300: dt: 0.9000, rms radial error=129.774, avgs=0 285/300: dt: 0.9000, rms radial error=129.043, avgs=0 290/300: dt: 0.9000, rms radial error=128.316, avgs=0 295/300: dt: 0.9000, rms radial error=127.593, avgs=0 300/300: dt: 0.9000, rms radial error=126.874, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 19353.82 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00016 epoch 2 (K=40.0), pass 1, starting sse = 3355.26 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00003 epoch 3 (K=160.0), pass 1, starting sse = 369.37 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.09/12 = 0.00788 epoch 4 (K=640.0), pass 1, starting sse = 23.43 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.23/20 = 0.01128 final writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.13 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Thu Aug 8 20:33:25 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/sub002/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub002 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=-20 (nv=162428, nf=324896, ne=487344, g=11) 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... 2074 ambiguous faces found in tessellation segmenting defects... 27 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 17 into 16 26 defects to be corrected 0 vertices coincident reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.8100 (-4.9050) -vertex loglikelihood: -6.6243 (-3.3121) -normal dot loglikelihood: -3.6536 (-3.6536) -quad curv loglikelihood: -6.3507 (-3.1753) Total Loglikelihood : -26.4385 CORRECTING DEFECT 0 (vertices=6, convex hull=20) After retessellation of defect 0, euler #=-24 (161140,482924,321760) : difference with theory (-23) = 1 CORRECTING DEFECT 1 (vertices=26, convex hull=37) After retessellation of defect 1, euler #=-23 (161146,482954,321785) : difference with theory (-22) = 1 CORRECTING DEFECT 2 (vertices=28, convex hull=34) After retessellation of defect 2, euler #=-22 (161149,482976,321805) : difference with theory (-21) = 1 CORRECTING DEFECT 3 (vertices=110, convex hull=83) After retessellation of defect 3, euler #=-21 (161166,483064,321877) : difference with theory (-20) = 1 CORRECTING DEFECT 4 (vertices=14, convex hull=28) After retessellation of defect 4, euler #=-20 (161170,483084,321894) : difference with theory (-19) = 1 CORRECTING DEFECT 5 (vertices=33, convex hull=54) After retessellation of defect 5, euler #=-19 (161187,483156,321950) : difference with theory (-18) = 1 CORRECTING DEFECT 6 (vertices=40, convex hull=81) After retessellation of defect 6, euler #=-18 (161195,483211,321998) : difference with theory (-17) = 1 CORRECTING DEFECT 7 (vertices=12, convex hull=18) After retessellation of defect 7, euler #=-17 (161196,483217,322004) : difference with theory (-16) = 1 CORRECTING DEFECT 8 (vertices=13, convex hull=14) After retessellation of defect 8, euler #=-16 (161199,483230,322015) : difference with theory (-15) = 1 CORRECTING DEFECT 9 (vertices=263, convex hull=105) After retessellation of defect 9, euler #=-15 (161210,483311,322086) : difference with theory (-14) = 1 CORRECTING DEFECT 10 (vertices=5, convex hull=24) After retessellation of defect 10, euler #=-14 (161210,483317,322093) : difference with theory (-13) = 1 CORRECTING DEFECT 11 (vertices=8, convex hull=23) After retessellation of defect 11, euler #=-13 (161211,483327,322103) : difference with theory (-12) = 1 CORRECTING DEFECT 12 (vertices=13, convex hull=38) After retessellation of defect 12, euler #=-12 (161216,483355,322127) : difference with theory (-11) = 1 CORRECTING DEFECT 13 (vertices=31, convex hull=27) After retessellation of defect 13, euler #=-11 (161222,483382,322149) : difference with theory (-10) = 1 CORRECTING DEFECT 14 (vertices=92, convex hull=92) After retessellation of defect 14, euler #=-10 (161258,483534,322266) : difference with theory (-9) = 1 CORRECTING DEFECT 15 (vertices=28, convex hull=30) After retessellation of defect 15, euler #=-9 (161261,483553,322283) : difference with theory (-8) = 1 CORRECTING DEFECT 16 (vertices=53, convex hull=41) After retessellation of defect 16, euler #=-7 (161270,483596,322319) : difference with theory (-7) = 0 CORRECTING DEFECT 17 (vertices=59, convex hull=80) After retessellation of defect 17, euler #=-6 (161306,483739,322427) : difference with theory (-6) = 0 CORRECTING DEFECT 18 (vertices=80, convex hull=50) After retessellation of defect 18, euler #=-5 (161324,483811,322482) : difference with theory (-5) = 0 CORRECTING DEFECT 19 (vertices=115, convex hull=63) After retessellation of defect 19, euler #=-4 (161330,483858,322524) : difference with theory (-4) = 0 CORRECTING DEFECT 20 (vertices=27, convex hull=19) After retessellation of defect 20, euler #=-3 (161336,483880,322541) : difference with theory (-3) = 0 CORRECTING DEFECT 21 (vertices=22, convex hull=31) After retessellation of defect 21, euler #=-2 (161337,483893,322554) : difference with theory (-2) = 0 CORRECTING DEFECT 22 (vertices=47, convex hull=43) After retessellation of defect 22, euler #=-1 (161346,483934,322587) : difference with theory (-1) = 0 CORRECTING DEFECT 23 (vertices=24, convex hull=45) After retessellation of defect 23, euler #=0 (161359,483989,322630) : difference with theory (0) = 0 CORRECTING DEFECT 24 (vertices=61, convex hull=90) After retessellation of defect 24, euler #=1 (161382,484095,322714) : difference with theory (1) = 0 CORRECTING DEFECT 25 (vertices=78, convex hull=105) After retessellation of defect 25, euler #=2 (161415,484239,322826) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.21 (0.08-->8.27) (max @ vno 34095 --> 40931) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.21 (0.08-->8.27) (max @ vno 34095 --> 40931) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 142 mutations (41.8%), 198 crossovers (58.2%), 99 vertices were eliminated building final representation... 1013 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=161415, nf=322826, ne=484239, g=0) writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 20.3 minutes 0 defective edges removing intersecting faces 000: 160 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 161415 - 484239 + 322826 = 2 --> 0 holes F =2V-4: 322826 = 322830-4 (0) 2E=3F: 968478 = 968478 (0) total defect index = 0 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 22 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Thu Aug 8 20:53:51 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub002 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/sub002/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/wm.mgz... 19992 bright wm thresholded. 328 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.orig... computing class statistics... border white: 305608 voxels (1.82%) border gray 333888 voxels (1.99%) WM (92.0): 93.4 +- 9.8 [70.0 --> 110.0] GM (76.0) : 74.4 +- 12.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 47.1 (was 70) setting MAX_BORDER_WHITE to 114.8 (was 105) setting MIN_BORDER_WHITE to 60.0 (was 85) setting MAX_CSF to 34.2 (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 21.3 (was 40) repositioning cortical surface to gray/white boundary reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.01-->3.22) (max @ vno 88276 --> 88345) face area 0.28 +- 0.12 (0.00-->1.90) mean absolute distance = 0.72 +- 0.88 3895 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 = 92.8, mean outside = 69.2 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=73.1, 25 (25) missing vertices, mean dist 0.4 [0.6 (%30.0)->0.8 (%70.0))] %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 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.26 (0.11-->4.00) (max @ vno 109067 --> 107853) face area 0.28 +- 0.13 (0.00-->2.60) mean absolute distance = 0.35 +- 0.55 3538 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=8317066.0, rms=13.35 001: dt: 0.5000, sse=8165330.5, rms=9.550 (0.000%) 002: dt: 0.5000, sse=8449409.0, rms=7.326 (0.000%) 003: dt: 0.5000, sse=8621062.0, rms=5.874 (0.000%) 004: dt: 0.5000, sse=8929902.0, rms=5.026 (0.000%) 005: dt: 0.5000, sse=9071069.0, rms=4.546 (0.000%) 006: dt: 0.5000, sse=9274709.0, rms=4.326 (0.000%) 007: dt: 0.5000, sse=9274201.0, rms=4.198 (0.000%) 008: dt: 0.5000, sse=9350852.0, rms=4.140 (0.000%) rms = 4.09, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=9256373.0, rms=4.091 (0.000%) 010: dt: 0.2500, sse=5720867.0, rms=2.771 (0.000%) 011: dt: 0.2500, sse=5169455.5, rms=2.321 (0.000%) 012: dt: 0.2500, sse=4855256.5, rms=2.202 (0.000%) 013: dt: 0.2500, sse=4759121.0, rms=2.112 (0.000%) rms = 2.07, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=4662509.5, rms=2.068 (0.000%) 015: dt: 0.1250, sse=4467816.0, rms=1.889 (0.000%) rms = 1.87, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=4421935.0, rms=1.867 (0.000%) positioning took 2.4 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=77.9, 44 (5) missing vertices, mean dist -0.2 [0.4 (%78.3)->0.2 (%21.7))] %79 local maxima, %16 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.12-->3.57) (max @ vno 95101 --> 88276) face area 0.35 +- 0.16 (0.00-->3.14) mean absolute distance = 0.23 +- 0.33 3311 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5680000.5, rms=6.27 017: dt: 0.5000, sse=5734551.0, rms=3.995 (0.000%) rms = 4.26, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=5213045.5, rms=2.923 (0.000%) 019: dt: 0.2500, sse=4998928.0, rms=2.247 (0.000%) 020: dt: 0.2500, sse=4888233.5, rms=1.849 (0.000%) 021: dt: 0.2500, sse=4858575.0, rms=1.775 (0.000%) 022: dt: 0.2500, sse=4773433.0, rms=1.690 (0.000%) rms = 1.68, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=4783839.5, rms=1.677 (0.000%) 024: dt: 0.1250, sse=4644433.0, rms=1.530 (0.000%) rms = 1.52, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=4604391.5, rms=1.520 (0.000%) positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 4 vertex label from ripped group mean border=81.3, 24 (2) missing vertices, mean dist -0.1 [0.2 (%76.7)->0.2 (%23.3))] %89 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.25 (0.08-->3.73) (max @ vno 95101 --> 88276) face area 0.34 +- 0.16 (0.00-->3.37) mean absolute distance = 0.17 +- 0.26 3000 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5106248.5, rms=4.44 026: dt: 0.5000, sse=5414753.0, rms=3.830 (0.000%) rms = 4.09, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=4915324.0, rms=2.426 (0.000%) 028: dt: 0.2500, sse=4796905.0, rms=1.914 (0.000%) 029: dt: 0.2500, sse=4821499.5, rms=1.594 (0.000%) rms = 1.62, time step reduction 2 of 3 to 0.125... 030: dt: 0.1250, sse=4760085.5, rms=1.489 (0.000%) 031: dt: 0.1250, sse=4681302.0, rms=1.345 (0.000%) rms = 1.33, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=4645796.0, rms=1.335 (0.000%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 4 vertex label from ripped group mean border=82.4, 27 (1) missing vertices, mean dist -0.0 [0.2 (%58.2)->0.2 (%41.8))] %91 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=4677926.5, rms=1.82 rms = 2.60, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=4779034.0, rms=1.175 (0.000%) 034: dt: 0.2500, sse=4958395.5, 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... 035: dt: 0.1250, sse=4959446.5, rms=0.995 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group generating cortex label... 13 non-cortical segments detected only using segment with 2118 vertices erasing segment 0 (vno[0] = 60122) erasing segment 2 (vno[0] = 70346) erasing segment 3 (vno[0] = 98641) erasing segment 4 (vno[0] = 102033) erasing segment 5 (vno[0] = 103304) erasing segment 6 (vno[0] = 105456) erasing segment 7 (vno[0] = 114353) erasing segment 8 (vno[0] = 116649) erasing segment 9 (vno[0] = 118813) erasing segment 10 (vno[0] = 118820) erasing segment 11 (vno[0] = 118832) erasing segment 12 (vno[0] = 122029) writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/label/rh.cortex.label... writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.curv writing smoothed area to rh.area writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.area vertex spacing 0.89 +- 0.25 (0.06-->3.75) (max @ vno 95101 --> 88276) face area 0.33 +- 0.16 (0.00-->3.44) refinement took 8.3 minutes #-------------------------------------------- #@# Smooth2 rh Thu Aug 8 21:02:09 CEST 2013 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 21:02:15 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 50.2 mm, total surface area = 98781 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.113 (target=0.015) step 005: RMS=0.079 (target=0.015) step 010: RMS=0.057 (target=0.015) step 015: RMS=0.047 (target=0.015) step 020: RMS=0.039 (target=0.015) step 025: RMS=0.032 (target=0.015) step 030: RMS=0.027 (target=0.015) step 035: RMS=0.023 (target=0.015) step 040: RMS=0.020 (target=0.015) step 045: RMS=0.018 (target=0.015) step 050: RMS=0.017 (target=0.015) step 055: RMS=0.016 (target=0.015) inflation complete. inflation took 0.7 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 214 vertices thresholded to be in k1 ~ [-0.26 0.52], k2 ~ [-0.25 0.07] total integrated curvature = 0.555*4pi (6.974) --> 0 handles ICI = 1.6, FI = 10.8, variation=181.540 187 vertices thresholded to be in [-0.06 0.01] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 133 vertices thresholded to be in [-0.14 0.14] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.015, std = 0.022 done. #----------------------------------------- #@# Curvature Stats rh Thu Aug 8 21:05:03 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub002 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 [ sub002/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 [ 292 ] Gb_filter = 0 WARN: S lookup min: -0.303609 WARN: S explicit min: 0.000000 vertex = 322 #-------------------------------------------- #@# Sphere rh Thu Aug 8 21:05:09 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 0.272... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=snake, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %21.39 pass 1: epoch 2 of 3 starting distance error %21.26 unfolding complete - removing small folds... starting distance error %21.16 removing remaining folds... final distance error %21.18 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/rh.sphere spherical transformation took 1.28 hours #-------------------------------------------- #@# Surf Reg rh Thu Aug 8 22:21:45 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 = 0.606 curvature mean = 0.027, std = 0.937 curvature mean = 0.022, std = 0.843 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 0.00) sse = 429057.7, tmin=1.5316 d=32.00 min @ (8.00, 8.00, 0.00) sse = 296682.4, tmin=2.8995 d=8.00 min @ (-2.00, 0.00, 0.00) sse = 291731.8, tmin=5.6238 d=4.00 min @ (0.00, 0.00, -1.00) sse = 289867.4, tmin=6.9905 d=2.00 min @ (0.50, 0.00, 0.00) sse = 289076.8, tmin=8.3849 d=0.50 min @ (0.00, -0.12, 0.12) sse = 289007.9, tmin=11.1425 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 11.14 min curvature mean = 0.015, std = 0.939 curvature mean = 0.010, std = 0.928 curvature mean = 0.012, std = 0.946 curvature mean = 0.005, std = 0.965 curvature mean = 0.011, std = 0.946 curvature mean = 0.001, std = 0.983 2 Reading smoothwm curvature mean = -0.022, std = 0.386 curvature mean = 0.006, std = 0.069 curvature mean = 0.050, std = 0.237 curvature mean = 0.007, std = 0.081 curvature mean = 0.026, std = 0.375 curvature mean = 0.007, std = 0.087 curvature mean = 0.014, std = 0.482 curvature mean = 0.007, std = 0.089 curvature mean = 0.005, std = 0.568 MRISregister() return, current seed 0 writing registered surface to ../surf/rh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white rh Thu Aug 8 22:58:34 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 22:58:37 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 22:58:41 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub002 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... 1420 labels changed using aseg relabeling using gibbs priors... 000: 3473 changed, 161415 examined... 001: 803 changed, 14502 examined... 002: 165 changed, 4497 examined... 003: 63 changed, 1016 examined... 004: 30 changed, 362 examined... 005: 12 changed, 194 examined... 006: 10 changed, 81 examined... 007: 6 changed, 49 examined... 008: 3 changed, 38 examined... 009: 1 changed, 20 examined... 010: 0 changed, 7 examined... 224 labels changed using aseg 000: 119 total segments, 79 labels (537 vertices) changed 001: 43 total segments, 3 labels (20 vertices) changed 002: 40 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 43 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2286 vertices marked for relabeling... 2286 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 1 minutes and 32 seconds. #-------------------------------------------- #@# Make Pial Surf rh Thu Aug 8 23:00:14 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub002 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/sub002/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/wm.mgz... 19992 bright wm thresholded. 328 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.orig... computing class statistics... border white: 305608 voxels (1.82%) border gray 333888 voxels (1.99%) WM (92.0): 93.4 +- 9.8 [70.0 --> 110.0] GM (76.0) : 74.4 +- 12.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 47.1 (was 70) setting MAX_BORDER_WHITE to 114.8 (was 105) setting MIN_BORDER_WHITE to 60.0 (was 85) setting MAX_CSF to 34.2 (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 21.3 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=60 mean inside = 92.8, mean outside = 69.2 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/sub002/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.01-->3.22) (max @ vno 88276 --> 88345) face area 0.28 +- 0.12 (0.00-->1.90) mean absolute distance = 0.72 +- 0.88 3975 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 25 points - only 0.00% unknown deleting segment 1 with 7 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown deleting segment 4 with 50 points - only 0.00% unknown deleting segment 5 with 496 points - only 0.00% unknown removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 9 with 3 points - only 0.00% unknown mean border=73.1, 25 (25) missing vertices, mean dist 0.4 [0.6 (%30.0)->0.8 (%70.0))] %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 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.26 (0.11-->4.00) (max @ vno 109067 --> 107853) face area 0.28 +- 0.13 (0.00-->2.60) mean absolute distance = 0.35 +- 0.55 3587 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=8333758.0, rms=13.34 001: dt: 0.5000, sse=8182196.0, rms=9.540 (0.000%) 002: dt: 0.5000, sse=8470299.0, rms=7.319 (0.000%) 003: dt: 0.5000, sse=8647821.0, rms=5.869 (0.000%) 004: dt: 0.5000, sse=8955117.0, rms=5.022 (0.000%) 005: dt: 0.5000, sse=9099352.0, rms=4.543 (0.000%) 006: dt: 0.5000, sse=9303448.0, rms=4.323 (0.000%) 007: dt: 0.5000, sse=9304492.0, rms=4.195 (0.000%) 008: dt: 0.5000, sse=9378339.0, rms=4.137 (0.000%) rms = 4.09, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=9287376.0, rms=4.088 (0.000%) 010: dt: 0.2500, sse=5736678.0, rms=2.770 (0.000%) 011: dt: 0.2500, sse=5185290.0, rms=2.320 (0.000%) 012: dt: 0.2500, sse=4869467.5, rms=2.202 (0.000%) 013: dt: 0.2500, sse=4773433.5, rms=2.112 (0.000%) rms = 2.07, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=4677847.5, rms=2.068 (0.000%) 015: dt: 0.1250, sse=4482472.5, rms=1.889 (0.000%) rms = 1.87, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=4436700.5, rms=1.867 (0.000%) positioning took 2.4 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 24 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 1 with 4 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 5 with 2 points - only 0.00% unknown deleting segment 6 with 72 points - only 0.00% unknown deleting segment 7 with 283 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group deleting segment 15 with 24 points - only 29.17% unknown removing 4 vertex label from ripped group deleting segment 17 with 4 points - only 0.00% unknown deleting segment 18 with 16 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 19 with 4 points - only 0.00% unknown mean border=77.8, 44 (5) missing vertices, mean dist -0.2 [0.4 (%78.3)->0.2 (%21.7))] %80 local maxima, %16 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.09-->3.57) (max @ vno 95101 --> 88276) face area 0.35 +- 0.16 (0.00-->3.14) mean absolute distance = 0.23 +- 0.33 3358 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5699114.5, rms=6.27 017: dt: 0.5000, sse=5750167.5, rms=3.991 (0.000%) rms = 4.25, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=5230811.5, rms=2.920 (0.000%) 019: dt: 0.2500, sse=5019653.5, rms=2.246 (0.000%) 020: dt: 0.2500, sse=4913185.0, rms=1.850 (0.000%) 021: dt: 0.2500, sse=4876328.0, rms=1.775 (0.000%) 022: dt: 0.2500, sse=4794801.5, rms=1.691 (0.000%) rms = 1.68, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=4804935.0, rms=1.678 (0.000%) 024: dt: 0.1250, sse=4666340.5, rms=1.532 (0.000%) rms = 1.52, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=4626848.5, rms=1.521 (0.000%) positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 23 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 2 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 3 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 4 with 2 points - only 0.00% unknown deleting segment 5 with 66 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown deleting segment 7 with 357 points - only 0.00% unknown removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 13 with 24 points - only 29.17% unknown deleting segment 14 with 14 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 15 with 4 points - only 0.00% unknown mean border=81.3, 34 (2) missing vertices, mean dist -0.1 [0.2 (%76.7)->0.2 (%23.3))] %89 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.24 (0.07-->3.73) (max @ vno 95101 --> 88276) face area 0.34 +- 0.16 (0.00-->3.37) mean absolute distance = 0.17 +- 0.26 3098 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5132227.0, rms=4.43 026: dt: 0.5000, sse=5441496.5, rms=3.825 (0.000%) rms = 4.09, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=4940717.5, rms=2.424 (0.000%) 028: dt: 0.2500, sse=4822029.0, rms=1.914 (0.000%) 029: dt: 0.2500, sse=4847129.0, rms=1.595 (0.000%) rms = 1.62, time step reduction 2 of 3 to 0.125... 030: dt: 0.1250, sse=4785154.0, rms=1.491 (0.000%) 031: dt: 0.1250, sse=4705179.0, rms=1.347 (0.000%) rms = 1.34, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=4669167.5, rms=1.337 (0.000%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 23 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown deleting segment 3 with 75 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown deleting segment 5 with 369 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 9 with 30 points - only 43.33% unknown deleting segment 10 with 16 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 11 with 4 points - only 0.00% unknown mean border=82.3, 32 (1) missing vertices, mean dist -0.0 [0.2 (%58.2)->0.2 (%41.8))] %91 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4702632.0, rms=1.82 rms = 2.60, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=4805202.0, rms=1.179 (0.000%) 034: dt: 0.2500, sse=4988136.5, rms=1.006 (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... 035: dt: 0.1250, sse=4988835.0, rms=0.998 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group smoothing surface for 5 iterations... mean border=50.1, 21 (21) missing vertices, mean dist 1.8 [0.1 (%0.0)->2.3 (%100.0))] %17 local maxima, %60 large gradients and %18 min vals, 1494 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=34150712.0, rms=31.67 001: dt: 0.5000, sse=24474122.0, rms=26.267 (0.000%) 002: dt: 0.5000, sse=17722590.0, rms=21.738 (0.000%) 003: dt: 0.5000, sse=13278174.0, rms=18.063 (0.000%) 004: dt: 0.5000, sse=10660978.0, rms=15.162 (0.000%) 005: dt: 0.5000, sse=9172553.0, rms=12.923 (0.000%) 006: dt: 0.5000, sse=8388446.5, rms=11.195 (0.000%) 007: dt: 0.5000, sse=7906671.0, rms=9.716 (0.000%) 008: dt: 0.5000, sse=7596661.0, rms=8.370 (0.000%) 009: dt: 0.5000, sse=7479242.0, rms=7.144 (0.000%) 010: dt: 0.5000, sse=7444399.0, rms=6.139 (0.000%) 011: dt: 0.5000, sse=7613262.0, rms=5.370 (0.000%) 012: dt: 0.5000, sse=7775754.0, rms=4.854 (0.000%) 013: dt: 0.5000, sse=7940431.5, rms=4.521 (0.000%) 014: dt: 0.5000, sse=8061841.0, rms=4.339 (0.000%) 015: dt: 0.5000, sse=8165478.0, rms=4.189 (0.000%) 016: dt: 0.5000, sse=8227836.0, rms=4.111 (0.000%) 017: dt: 0.5000, sse=8254363.0, rms=4.038 (0.000%) rms = 4.01, time step reduction 1 of 3 to 0.250... 018: dt: 0.5000, sse=8280509.0, rms=4.006 (0.000%) 019: dt: 0.2500, sse=5527110.0, rms=3.130 (0.000%) 020: dt: 0.2500, sse=5281470.5, rms=2.884 (0.000%) rms = 2.84, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=5098633.5, rms=2.843 (0.000%) 022: dt: 0.1250, sse=4846981.5, rms=2.690 (0.000%) rms = 2.67, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=4809324.0, rms=2.670 (0.000%) positioning took 3.2 minutes mean border=47.2, 724 (2) missing vertices, mean dist 0.2 [0.2 (%43.5)->0.5 (%56.5))] %40 local maxima, %42 large gradients and %14 min vals, 390 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=5689631.0, rms=5.24 024: dt: 0.5000, sse=5874995.0, rms=4.165 (0.000%) rms = 4.17, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=5432156.0, rms=3.457 (0.000%) 026: dt: 0.2500, sse=5495592.5, rms=3.086 (0.000%) 027: dt: 0.2500, sse=5408624.0, rms=2.927 (0.000%) 028: dt: 0.2500, sse=5454962.0, rms=2.838 (0.000%) 029: dt: 0.2500, sse=5432246.5, rms=2.783 (0.000%) rms = 2.75, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=5497902.0, rms=2.746 (0.000%) 031: dt: 0.1250, sse=5270643.0, rms=2.579 (0.000%) rms = 2.55, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=5244988.5, rms=2.550 (0.000%) positioning took 1.3 minutes mean border=44.4, 909 (1) missing vertices, mean dist 0.2 [0.2 (%33.6)->0.4 (%66.4))] %61 local maxima, %21 large gradients and %13 min vals, 473 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=5684017.0, rms=4.45 033: dt: 0.5000, sse=5879174.0, rms=4.061 (0.000%) rms = 4.14, time step reduction 1 of 3 to 0.250... 034: dt: 0.2500, sse=5464883.0, rms=3.090 (0.000%) 035: dt: 0.2500, sse=5690023.0, rms=2.708 (0.000%) 036: dt: 0.2500, sse=5633554.0, rms=2.621 (0.000%) rms = 2.59, time step reduction 2 of 3 to 0.125... 037: dt: 0.2500, sse=5691973.0, rms=2.592 (0.000%) 038: dt: 0.1250, sse=5451668.5, rms=2.400 (0.000%) rms = 2.37, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=5432180.0, rms=2.373 (0.000%) positioning took 1.1 minutes mean border=43.1, 1810 (1) missing vertices, mean dist 0.1 [0.2 (%43.0)->0.3 (%57.0))] %65 local maxima, %16 large gradients and %13 min vals, 386 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/sub002/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=5503922.5, rms=2.83 rms = 3.78, time step reduction 1 of 3 to 0.250... 040: dt: 0.2500, sse=5343033.5, rms=2.470 (0.000%) 041: dt: 0.2500, sse=5533832.0, rms=2.390 (0.000%) rms = 2.37, time step reduction 2 of 3 to 0.125... 042: dt: 0.2500, sse=5608822.5, rms=2.372 (0.000%) 043: dt: 0.1250, sse=5512340.5, rms=2.247 (0.000%) rms = 2.23, time step reduction 3 of 3 to 0.062... 044: dt: 0.1250, sse=5511996.5, rms=2.234 (0.000%) positioning took 0.8 minutes writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.area.pial vertex spacing 1.00 +- 0.41 (0.08-->6.08) (max @ vno 112370 --> 113418) face area 0.40 +- 0.29 (0.00-->6.39) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 161415 vertices processed 25000 of 161415 vertices processed 50000 of 161415 vertices processed 75000 of 161415 vertices processed 100000 of 161415 vertices processed 125000 of 161415 vertices processed 150000 of 161415 vertices processed 0 of 161415 vertices processed 25000 of 161415 vertices processed 50000 of 161415 vertices processed 75000 of 161415 vertices processed 100000 of 161415 vertices processed 125000 of 161415 vertices processed 150000 of 161415 vertices processed thickness calculation complete, 365:767 truncations. 39775 vertices at 0 distance 116248 vertices at 1 distance 101662 vertices at 2 distance 37656 vertices at 3 distance 10030 vertices at 4 distance 2812 vertices at 5 distance 905 vertices at 6 distance 308 vertices at 7 distance 136 vertices at 8 distance 75 vertices at 9 distance 35 vertices at 10 distance 26 vertices at 11 distance 23 vertices at 12 distance 14 vertices at 13 distance 13 vertices at 14 distance 6 vertices at 15 distance 11 vertices at 16 distance 10 vertices at 17 distance 22 vertices at 18 distance 11 vertices at 19 distance 6 vertices at 20 distance writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.thickness positioning took 16.5 minutes #-------------------------------------------- #@# Surf Volume rh Thu Aug 8 23:16:44 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 23:16:45 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts pctsurfcon --s sub002 --rh-only Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts/pctsurfcon.log Thu Aug 8 23:16:45 CEST 2013 setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts /opt/freesurfer/5.3.0/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux snake5 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux FREESURFER_HOME /opt/freesurfer/5.3.0 mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/tmp.pctsurfcon.18267/rh.wm.mgh --regheader sub002 --cortex srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/mri/orig.mgz as target reference. Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/label/rh.cortex.label Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 = 125441 Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/label/rh.cortex.label Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/tmp.pctsurfcon.18267/rh.wm.mgh Dim: 161415 1 1 mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/tmp.pctsurfcon.18267/rh.gm.mgh --projfrac 0.3 --regheader sub002 --cortex srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/mri/orig.mgz as target reference. Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/label/rh.cortex.label Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.white Done reading source surface Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 = 143811 Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/label/rh.cortex.label Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/tmp.pctsurfcon.18267/rh.gm.mgh Dim: 161415 1 1 mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/tmp.pctsurfcon.18267/rh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/tmp.pctsurfcon.18267/rh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/surf/rh.w-g.pct.mgh mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.w-g.pct.mgh --annot sub002 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/surf/rh.w-g.pct.mgh --annot sub002 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/stats/rh.w-g.pct.stats --snr sysname Linux hostname snake5 machine x86_64 user fkaule UseRobust 0 Constructing seg from annotation Reading annotation reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Seg base 2000 Loading /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.w-g.pct.mgh Vertex Area is 0.665893 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 2000 unknown 0 0.000 1 2001 bankssts 1613 1104.939 2 2002 caudalanteriorcingulate 1478 1023.718 3 2003 caudalmiddlefrontal 3479 2355.313 4 2004 corpuscallosum 0 0.000 5 2005 cuneus 2789 1858.148 6 2006 entorhinal 420 283.363 7 2007 fusiform 5769 3930.761 8 2008 inferiorparietal 11200 7539.997 9 2009 inferiortemporal 5803 3916.349 10 2010 isthmuscingulate 2105 1342.184 11 2011 lateraloccipital 7148 4593.353 12 2012 lateralorbitofrontal 4055 2705.177 13 2013 lingual 5270 3473.353 14 2014 medialorbitofrontal 2784 1895.848 15 2015 middletemporal 5977 4047.395 16 2016 parahippocampal 1128 776.200 17 2017 paracentral 2662 1693.575 18 2018 parsopercularis 3045 2090.832 19 2019 parsorbitalis 1263 882.700 20 2020 parstriangularis 2760 1867.343 21 2021 pericalcarine 2321 1586.182 22 2022 postcentral 7468 4850.527 23 2023 posteriorcingulate 1766 1200.175 24 2024 precentral 7961 5063.128 25 2025 precuneus 8644 5767.969 26 2026 rostralanteriorcingulate 1579 1029.918 27 2027 rostralmiddlefrontal 11351 7817.396 28 2028 superiorfrontal 12638 8630.331 29 2029 superiorparietal 10332 6731.142 30 2030 superiortemporal 5877 3950.300 31 2031 supramarginal 6365 4261.914 32 2032 frontalpole 435 309.395 33 2033 temporalpole 673 460.947 34 2034 transversetemporal 641 381.213 35 2035 insula 3677 2431.106 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats rh Thu Aug 8 23:17:00 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 sub002 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 1613 1105 2837 2.642 0.377 0.113 0.034 16 2.4 bankssts 1478 1024 2713 2.681 0.711 0.142 0.040 23 2.4 caudalanteriorcingulate 3479 2355 6316 2.418 0.444 0.129 0.045 42 6.1 caudalmiddlefrontal 2789 1858 4005 1.969 0.447 0.172 0.070 123 8.4 cuneus 420 283 1663 3.568 0.920 0.168 0.101 8 1.7 entorhinal 5769 3931 11718 2.625 0.605 0.139 0.049 94 11.3 fusiform 11200 7540 20133 2.428 0.459 0.146 0.049 193 22.4 inferiorparietal 5803 3916 12570 2.605 0.639 0.150 0.062 113 15.0 inferiortemporal 2105 1342 3132 2.133 0.889 0.146 0.061 36 4.9 isthmuscingulate 7148 4593 11257 2.210 0.414 0.152 0.057 132 15.7 lateraloccipital 4055 2705 7839 2.595 0.638 0.153 0.066 75 9.9 lateralorbitofrontal 5270 3473 8584 2.284 0.600 0.165 0.070 105 14.7 lingual 2784 1896 4873 2.237 0.714 0.153 0.137 65 7.6 medialorbitofrontal 5977 4047 13994 2.859 0.636 0.146 0.054 106 12.7 middletemporal 1128 776 2141 2.463 0.531 0.124 0.041 11 1.9 parahippocampal 2662 1694 4605 2.469 0.619 0.127 0.045 50 4.6 paracentral 3045 2091 5779 2.492 0.450 0.124 0.035 35 4.6 parsopercularis 1263 883 2644 2.344 0.610 0.139 0.040 17 2.0 parsorbitalis 2760 1867 4788 2.265 0.564 0.137 0.043 38 5.0 parstriangularis 2321 1586 2791 1.850 0.436 0.141 0.096 33 4.9 pericalcarine 7468 4851 11036 2.030 0.599 0.133 0.047 139 16.0 postcentral 1766 1200 3117 2.381 0.834 0.140 0.049 27 3.4 posteriorcingulate 7961 5063 13852 2.520 0.544 0.119 0.042 81 14.4 precentral 8644 5768 14928 2.458 0.501 0.135 0.047 120 17.3 precuneus 1579 1030 3130 2.682 0.603 0.132 0.051 26 3.4 rostralanteriorcingulate 11351 7817 19933 2.266 0.499 0.149 0.057 202 24.2 rostralmiddlefrontal 12638 8630 25666 2.622 0.572 0.151 0.066 265 33.0 superiorfrontal 10332 6731 16404 2.182 0.403 0.140 1.071 195 20.5 superiorparietal 5877 3950 13009 2.944 0.583 0.126 0.043 76 10.9 superiortemporal 6365 4262 11327 2.403 0.485 0.128 0.041 114 11.0 supramarginal 435 309 1051 2.470 0.543 0.207 0.110 16 1.6 frontalpole 673 461 2425 3.689 0.857 0.163 0.068 12 1.9 temporalpole 641 381 1154 2.538 0.344 0.130 0.045 9 1.2 transversetemporal 3677 2431 7937 3.061 0.862 0.135 0.090 110 10.9 insula #----------------------------------------- #@# Cortical Parc 2 rh Thu Aug 8 23:17:33 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub002 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... 12 labels changed using aseg relabeling using gibbs priors... 000: 11329 changed, 161415 examined... 001: 2697 changed, 43014 examined... 002: 834 changed, 13857 examined... 003: 368 changed, 4630 examined... 004: 174 changed, 1978 examined... 005: 100 changed, 1002 examined... 006: 53 changed, 581 examined... 007: 34 changed, 276 examined... 008: 20 changed, 186 examined... 009: 17 changed, 118 examined... 010: 8 changed, 86 examined... 011: 3 changed, 40 examined... 012: 2 changed, 20 examined... 013: 0 changed, 14 examined... 5 labels changed using aseg 000: 338 total segments, 250 labels (3247 vertices) changed 001: 110 total segments, 24 labels (259 vertices) changed 002: 86 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 175 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1494 vertices marked for relabeling... 1494 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 1 minutes and 24 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Thu Aug 8 23:18:57 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 sub002 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 1175 819 2113 2.369 0.600 0.180 0.070 31 3.5 G_and_S_frontomargin 1303 854 2009 2.203 0.431 0.143 0.048 18 2.6 G_and_S_occipital_inf 1671 971 2616 2.244 0.641 0.131 0.052 40 3.2 G_and_S_paracentral 1573 1059 3193 2.634 0.531 0.155 0.049 26 3.2 G_and_S_subcentral 1500 1018 3301 2.518 0.478 0.182 0.076 41 4.4 G_and_S_transv_frontopol 3269 2207 5869 2.518 0.552 0.139 0.047 46 6.6 G_and_S_cingul-Ant 2054 1450 3907 2.609 0.444 0.121 0.030 20 2.6 G_and_S_cingul-Mid-Ant 1832 1290 3447 2.542 0.547 0.128 0.035 20 2.5 G_and_S_cingul-Mid-Post 651 405 1530 2.881 0.799 0.172 0.072 15 1.9 G_cingul-Post-dorsal 340 225 675 2.537 0.810 0.183 0.082 8 1.1 G_cingul-Post-ventral 2499 1715 3611 1.903 0.495 0.185 0.073 57 7.2 G_cuneus 1637 1121 3759 2.757 0.408 0.144 0.054 30 3.6 G_front_inf-Opercular 439 295 1007 2.585 0.426 0.130 0.042 7 0.7 G_front_inf-Orbital 1557 1049 3164 2.389 0.572 0.151 0.051 29 3.4 G_front_inf-Triangul 5032 3428 10616 2.448 0.470 0.161 0.078 113 13.4 G_front_middle 8077 5478 18872 2.751 0.587 0.171 0.085 209 27.7 G_front_sup 570 369 1513 3.518 0.572 0.131 0.061 14 1.2 G_Ins_lg_and_S_cent_ins 735 486 2585 3.926 0.752 0.149 0.090 20 2.3 G_insular_short 2843 1846 5463 2.393 0.423 0.159 0.056 64 6.3 G_occipital_middle 2442 1545 4035 2.173 0.402 0.142 0.043 36 4.1 G_occipital_sup 2586 1695 6493 2.906 0.587 0.155 0.056 61 6.0 G_oc-temp_lat-fusifor 3373 2234 5578 2.218 0.617 0.176 0.080 76 10.6 G_oc-temp_med-Lingual 1422 905 3494 2.882 0.871 0.160 0.148 75 6.9 G_oc-temp_med-Parahip 2933 2003 6824 2.595 0.623 0.167 0.063 63 7.7 G_orbital 4612 3049 9907 2.576 0.512 0.167 0.063 106 11.9 G_pariet_inf-Angular 3278 2193 6827 2.548 0.466 0.139 0.047 55 6.1 G_pariet_inf-Supramar 2870 1884 5371 2.291 0.386 0.145 0.053 52 6.1 G_parietal_sup 2734 1709 4491 2.089 0.496 0.140 0.061 85 8.5 G_postcentral 3208 1892 6767 2.780 0.443 0.122 0.054 43 7.5 G_precentral 3549 2321 7434 2.543 0.442 0.146 3.042 110 9.8 G_precuneus 730 489 1594 2.367 0.607 0.208 0.391 39 3.8 G_rectus 443 300 880 2.599 1.056 0.079 0.028 2 0.4 G_subcallosal 525 305 1054 2.634 0.352 0.130 0.050 8 1.0 G_temp_sup-G_T_transv 1829 1212 5204 3.148 0.526 0.155 0.071 44 5.5 G_temp_sup-Lateral 828 599 2485 3.619 0.610 0.132 0.045 9 1.7 G_temp_sup-Plan_polar 975 652 1915 2.561 0.416 0.123 0.033 11 1.3 G_temp_sup-Plan_tempo 3383 2256 8692 2.807 0.620 0.166 0.079 86 10.9 G_temporal_inf 3388 2310 9423 3.044 0.627 0.160 0.063 77 8.2 G_temporal_middle 463 300 541 1.937 0.409 0.091 0.022 2 0.4 Lat_Fis-ant-Horizont 218 148 352 2.722 0.512 0.119 0.030 2 0.3 Lat_Fis-ant-Vertical 1684 1138 2330 2.400 0.444 0.113 0.033 10 2.3 Lat_Fis-post 3111 1968 4769 2.055 0.422 0.161 0.107 138 9.1 Pole_occipital 2121 1477 5973 2.827 0.928 0.179 0.091 53 7.3 Pole_temporal 2681 1771 3575 2.240 0.625 0.134 0.047 30 5.3 S_calcarine 3309 2224 3681 1.835 0.545 0.113 0.030 21 4.3 S_central 1403 981 2097 2.287 0.526 0.126 0.042 14 2.6 S_cingul-Marginalis 464 309 791 2.883 0.424 0.131 0.050 5 0.8 S_circular_insula_ant 1251 822 2013 2.869 0.591 0.091 0.022 5 1.2 S_circular_insula_inf 1585 1072 2242 2.318 0.468 0.103 0.030 9 1.9 S_circular_insula_sup 1027 686 1754 2.339 0.623 0.133 0.046 15 2.1 S_collat_transv_ant 522 355 716 2.181 0.364 0.148 0.044 6 1.1 S_collat_transv_post 2738 1898 4133 2.165 0.433 0.134 0.038 34 4.3 S_front_inf 2974 2053 4175 2.077 0.380 0.119 0.031 25 3.9 S_front_middle 2856 1964 4211 2.240 0.467 0.125 0.050 53 4.3 S_front_sup 694 474 825 2.078 0.383 0.120 0.055 38 1.9 S_interm_prim-Jensen 4156 2756 5500 2.104 0.388 0.123 0.034 42 5.6 S_intrapariet_and_P_trans 869 581 1405 2.444 0.546 0.163 0.053 16 1.8 S_oc_middle_and_Lunatus 1817 1246 2507 2.158 0.345 0.139 0.040 24 2.8 S_oc_sup_and_transversal 988 652 1642 2.371 0.359 0.122 0.038 11 1.5 S_occipital_ant 1431 974 2019 2.359 0.445 0.110 0.026 9 1.6 S_oc-temp_lat 2639 1855 4289 2.459 0.438 0.121 0.034 23 3.8 S_oc-temp_med_and_Lingual 527 367 655 1.922 0.408 0.134 0.037 4 0.8 S_orbital_lateral 818 565 1231 2.215 0.868 0.118 0.072 11 1.2 S_orbital_med-olfact 1538 1033 2484 2.450 0.603 0.138 0.046 20 3.0 S_orbital-H_Shaped 3307 2166 4512 2.333 0.505 0.119 0.041 30 6.1 S_parieto_occipital 2476 1568 2701 2.031 0.925 0.133 0.049 36 4.7 S_pericallosal 2963 1940 3597 1.981 0.404 0.122 0.035 30 4.1 S_postcentral 2262 1522 3647 2.399 0.412 0.102 0.024 14 2.4 S_precentral-inf-part 1494 1029 1883 2.137 0.482 0.115 0.029 10 1.9 S_precentral-sup-part 387 255 539 2.129 0.800 0.155 0.055 6 0.9 S_suborbital 2326 1578 3948 2.502 0.512 0.143 0.047 34 4.4 S_subparietal 1578 1078 2322 2.305 0.431 0.116 0.028 10 2.0 S_temporal_inf 7597 5171 12127 2.558 0.459 0.117 0.033 70 11.0 S_temporal_sup 337 241 445 2.147 0.324 0.135 0.033 3 0.5 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 rh Thu Aug 8 23:19:22 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub002 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... 959 labels changed using aseg relabeling using gibbs priors... 000: 3377 changed, 161415 examined... 001: 813 changed, 13870 examined... 002: 193 changed, 4425 examined... 003: 79 changed, 1190 examined... 004: 46 changed, 488 examined... 005: 14 changed, 255 examined... 006: 6 changed, 100 examined... 007: 4 changed, 33 examined... 008: 1 changed, 27 examined... 009: 1 changed, 7 examined... 010: 0 changed, 7 examined... 127 labels changed using aseg 000: 67 total segments, 34 labels (207 vertices) changed 001: 33 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... 1322 vertices marked for relabeling... 1322 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas40.annot... classification took 1 minutes and 12 seconds. #----------------------------------------- #@# Parcellation Stats 3 rh Thu Aug 8 23:20:34 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 sub002 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 1653 1136 3208 2.721 0.700 0.144 0.043 27 3.0 caudalanteriorcingulate 3564 2412 6401 2.424 0.451 0.130 0.045 43 6.3 caudalmiddlefrontal 3659 2437 5248 2.010 0.425 0.161 0.061 132 9.7 cuneus 476 327 1682 3.355 1.035 0.162 0.084 8 1.8 entorhinal 5037 3419 10347 2.680 0.599 0.133 0.041 76 8.8 fusiform 10801 7240 18990 2.401 0.462 0.146 0.049 186 21.6 inferiorparietal 6489 4391 13948 2.581 0.636 0.153 0.066 129 17.3 inferiortemporal 2152 1376 3205 2.139 0.885 0.147 0.061 37 5.1 isthmuscingulate 7476 4807 11817 2.211 0.416 0.151 0.057 137 16.2 lateraloccipital 4594 3083 8972 2.556 0.667 0.160 0.078 106 13.1 lateralorbitofrontal 5308 3494 8646 2.284 0.597 0.165 0.070 105 14.7 lingual 2153 1465 4008 2.243 0.759 0.161 0.168 61 6.8 medialorbitofrontal 7282 4941 16404 2.822 0.605 0.141 0.050 120 14.7 middletemporal 1110 762 2098 2.466 0.528 0.123 0.041 11 1.9 parahippocampal 2821 1795 4951 2.486 0.610 0.128 0.045 52 4.8 paracentral 3044 2087 5729 2.496 0.450 0.122 0.035 34 4.5 parsopercularis 1352 925 2795 2.462 0.521 0.133 0.042 19 2.3 parsorbitalis 3108 2100 5525 2.275 0.557 0.146 0.048 51 6.0 parstriangularis 2310 1575 2782 1.855 0.439 0.142 0.097 34 4.9 pericalcarine 7976 5197 11894 2.036 0.587 0.135 0.047 149 17.1 postcentral 1818 1234 3169 2.382 0.822 0.139 0.049 27 3.4 posteriorcingulate 7665 4846 13434 2.521 0.545 0.118 0.042 78 14.0 precentral 8549 5706 14992 2.461 0.503 0.137 0.048 122 17.4 precuneus 1645 1084 3253 2.755 0.514 0.138 0.051 28 3.6 rostralanteriorcingulate 7543 5212 12893 2.217 0.476 0.145 0.057 125 15.7 rostralmiddlefrontal 16428 11254 32323 2.536 0.582 0.150 0.063 328 40.6 superiorfrontal 8695 5673 13901 2.186 0.411 0.139 1.264 172 17.5 superiorparietal 8094 5431 18356 2.975 0.641 0.134 0.054 150 18.0 superiortemporal 5799 3898 10121 2.389 0.473 0.126 0.041 104 10.0 supramarginal 617 368 1106 2.536 0.347 0.130 0.046 8 1.2 transversetemporal 3258 2177 7151 3.065 0.861 0.124 0.059 50 6.1 insula #-------------------------------------------- #@# Refine Pial Surfs w/ T2/FLAIR Thu Aug 8 23:21:01 CEST 2013 bbregister --s sub002 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/T2raw.lta --init-fsl --T2 Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/T2raw.dat.log Thu Aug 8 23:21:02 CEST 2013 setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts /opt/freesurfer/5.3.0/bin/bbregister --s sub002 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/T2raw.lta --init-fsl --T2 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ Linux snake5 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux FREESURFER_HOME /opt/freesurfer/5.3.0 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/template.nii mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/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/sub002/mri/orig/T2raw.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999032, 0.0218052, 0.0381938) j_ras = (0.0265301, 0.991428, 0.127932) k_ras = (0.0350768, -0.128822, 0.991047) writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/template.nii... fslregister --s sub002 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/fslregister --dof 6 --fsvol brainmask.mgz Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/reg.init.dat.fslregister.log Thu Aug 8 23:21:08 CEST 2013 --s sub002 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/fslregister --dof 6 --fsvol brainmask.mgz $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ snake5 Linux snake5 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux nIters 1 -------------------------------------- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/fslregister/refvol.fslregister.nii mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/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/sub002/mri/brainmask.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 4.19095e-09, 0) j_ras = (0, 1.49012e-08, -1) k_ras = (0, 1, 0) writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/fslregister/refvol.fslregister.nii... -------------------------------------- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/fslregister/movvol.fslregister.nii --frame 0 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/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/sub002/mri/transforms/tmp.bbregister.19392/template.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999032, 0.0218052, 0.0381938) j_ras = (0.0265301, 0.991428, 0.127932) k_ras = (0.0350768, -0.128822, 0.991047) keeping frame 0 writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/fslregister/movvol.fslregister.nii... Mov determinant is -0.311049 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/fslregister/movvol.fslregister.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/fslregister/reg0.19435.dat --regheader --fslregout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/reg.init.dat.fsl.mat0 --s sub002 --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/sub002/mri/transforms/tmp.bbregister.19392/fslregister/movvol.fslregister.nii reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/fslregister/reg0.19435.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/sub002/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/sub002/mri/transforms/tmp.bbregister.19392/fslregister/movvol.fslregister.nii Tmov: -------------------- -0.700 0.000 0.000 95.881; 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 -0.022 -0.038 0.000; 0.035 -0.129 0.991 -0.000; -0.027 -0.991 -0.128 0.000; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 0.999 -0.022 -0.038 0.000; 0.035 -0.129 0.991 -0.000; -0.027 -0.991 -0.128 0.000; 0.000 0.000 0.000 1.000; Determinant 0.999999 subject = sub002 RegMat --------------------------- 0.999 -0.022 -0.038 0.000; 0.035 -0.129 0.991 -0.000; -0.027 -0.991 -0.128 0.000; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -0.311049, ref det = -1 Thu Aug 8 23:21:18 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/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/sub002/mri/transforms/tmp.bbregister.19392/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/reg.init.dat.fsl.mat0 Thu Aug 8 23:25:42 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/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/sub002/mri/transforms/tmp.bbregister.19392/reg.init.dat.fsl.mat -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/fslregister/fslmat0.trans.mat -schedule /opt/freesurfer/5.3.0/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s sub002 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/reg.init.dat --fslreg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/reg.init.dat.fsl.mat --noedit tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl ---- FSL registration matrix -------- 0.999 -0.028 -0.022 38.022; -0.025 -0.094 -0.995 271.186; 0.025 0.995 -0.095 8.808; 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/sub002/mri/transforms/tmp.bbregister.19392/template.nii reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/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/sub002/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/sub002/mri/transforms/tmp.bbregister.19392/template.nii Tmov: -------------------- -0.700 0.000 0.000 95.881; 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 = -0.311049, ref det = -1 ---- Input registration matrix (computed) -------- 0.999 -0.025 -0.025 -0.620; 0.022 -0.095 0.995 1.194; -0.028 -0.995 -0.094 -1.620; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 0.999 -0.025 -0.025 -0.620; 0.022 -0.095 0.995 1.194; -0.028 -0.995 -0.094 -1.620; 0.000 0.000 0.000 1.000; Determinant 1 subject = sub002 RegMat --------------------------- 0.999 -0.025 -0.025 -0.620; 0.022 -0.095 0.995 1.194; -0.028 -0.995 -0.094 -1.620; 0.000 0.000 0.000 1.000; Started at Thu Aug 8 23:21:08 CEST 2013 Ended at Thu Aug 8 23:31:41 CEST 2013 fslregister Done To check results, run: tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/reg.init.dat --surf orig mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/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/sub002/scripts mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Linux hostname snake5 machine x86_64 user fkaule movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/template.nii regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/reg.init.dat subject sub002 dof 6 outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/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 1376450912 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.999 -0.025 -0.025 -0.620; 0.022 -0.095 0.995 1.194; -0.028 -0.995 -0.094 -1.620; 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 1.045212 1 -25.0 -25.0 25.0 1.003322 2 -25.0 25.0 -25.0 1.007902 3 -25.0 25.0 25.0 1.026935 4 25.0 -25.0 -25.0 1.013771 5 25.0 -25.0 25.0 1.061154 6 25.0 25.0 -25.0 1.023364 7 25.0 25.0 25.0 1.010720 REL: 8 0.315800 8.192379 1.024047 rel = 0.308384 Initial costs ---------------- Number of surface hits 3047 WM Intensity 57.8110 +/- 8.6409 Ctx Intensity 70.0825 +/- 11.1034 Pct Contrast 18.8163 +/- 18.7598 Cost 0.3158 RelCost 0.3084 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9581 0.9581 0.0 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.8927 0.8927 0.0 21 -4.0000 -4.0000 -4.0000 4.0000 0.0000 -4.0000 0.8505 0.8505 0.0 39 -4.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.8266 0.8266 0.0 120 -4.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.7720 0.7720 0.0 301 0.0000 -4.0000 4.0000 -4.0000 0.0000 0.0000 0.7307 0.7307 0.0 346 0.0000 0.0000 -4.0000 4.0000 0.0000 0.0000 0.7154 0.7154 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.3158 0.3158 0.0 Brute Force -------------------------- Min cost was 0.315800 Number of iterations 729 Search time 2.638000 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 -0.038 0.000 0.000 0.000 0.000 0.000 0.3141953586 9 -0.089 0.000 0.000 0.000 0.000 0.000 0.3140502370 10 -0.067 0.000 0.000 0.000 0.000 0.000 0.3137921398 11 -0.066 0.000 0.000 0.000 0.000 0.000 0.3137911513 17 -0.066 -0.618 0.000 0.000 0.000 0.000 0.2756750169 19 -0.066 -0.587 0.000 0.000 0.000 0.000 0.2751719787 22 -0.066 -0.583 0.000 0.000 0.000 0.000 0.2751619203 26 -0.066 -0.583 1.000 0.000 0.000 0.000 0.1754425269 31 -0.066 -0.583 1.102 0.000 0.000 0.000 0.1711928032 33 -0.066 -0.583 1.196 0.000 0.000 0.000 0.1698448987 34 -0.066 -0.583 1.197 0.000 0.000 0.000 0.1698422257 35 -0.066 -0.583 1.207 0.000 0.000 0.000 0.1698337980 37 -0.066 -0.583 1.204 0.000 0.000 0.000 0.1698317278 38 -0.066 -0.583 1.203 0.000 0.000 0.000 0.1698315153 39 -0.066 -0.583 1.202 0.000 0.000 0.000 0.1698312767 41 -0.066 -0.583 1.201 0.000 0.000 0.000 0.1698309996 48 -0.066 -0.583 1.201 -0.143 0.000 0.000 0.1646940319 50 -0.066 -0.583 1.201 -0.125 0.000 0.000 0.1644750936 53 -0.066 -0.583 1.201 -0.112 0.000 0.000 0.1644734824 54 -0.066 -0.583 1.201 -0.118 0.000 0.000 0.1644524372 55 -0.066 -0.583 1.201 -0.119 0.000 0.000 0.1644516281 63 -0.066 -0.583 1.201 -0.119 -0.087 0.000 0.1642141626 67 -0.066 -0.583 1.201 -0.119 -0.116 0.000 0.1640114329 69 -0.066 -0.583 1.201 -0.119 -0.111 0.000 0.1639960182 77 -0.066 -0.583 1.201 -0.119 -0.111 0.382 0.1597704919 82 -0.066 -0.583 1.201 -0.119 -0.111 0.387 0.1597694456 83 -0.066 -0.583 1.201 -0.119 -0.111 0.385 0.1597666659 92 0.316 -0.583 1.201 -0.119 -0.111 0.385 0.1479585072 93 0.282 -0.583 1.201 -0.119 -0.111 0.385 0.1479536807 97 0.263 -0.583 1.201 -0.119 -0.111 0.385 0.1479532345 98 0.268 -0.583 1.201 -0.119 -0.111 0.385 0.1479499926 99 0.273 -0.583 1.201 -0.119 -0.111 0.385 0.1479497019 100 0.271 -0.583 1.201 -0.119 -0.111 0.385 0.1479482908 108 0.271 -0.651 1.201 -0.119 -0.111 0.385 0.1472668685 109 0.271 -0.655 1.201 -0.119 -0.111 0.385 0.1472428043 111 0.271 -0.692 1.201 -0.119 -0.111 0.385 0.1470721936 114 0.271 -0.690 1.201 -0.119 -0.111 0.385 0.1470695059 116 0.271 -0.689 1.201 -0.119 -0.111 0.385 0.1470688066 124 0.271 -0.689 1.205 -0.119 -0.111 0.385 0.1470313978 125 0.271 -0.689 1.242 -0.119 -0.111 0.385 0.1467459901 128 0.271 -0.689 1.236 -0.119 -0.111 0.385 0.1467363085 137 0.271 -0.689 1.236 -0.135 -0.111 0.385 0.1464510371 138 0.271 -0.689 1.236 -0.181 -0.111 0.385 0.1462013748 140 0.271 -0.689 1.236 -0.171 -0.111 0.385 0.1461816849 141 0.271 -0.689 1.236 -0.172 -0.111 0.385 0.1461805886 153 0.271 -0.689 1.236 -0.172 -0.115 0.385 0.1461751148 154 0.271 -0.689 1.236 -0.172 -0.116 0.385 0.1461750893 162 0.271 -0.689 1.236 -0.172 -0.116 0.481 0.1452244900 163 0.271 -0.689 1.236 -0.172 -0.116 0.475 0.1452053737 165 0.271 -0.689 1.236 -0.172 -0.116 0.474 0.1452050146 174 0.321 -0.689 1.236 -0.172 -0.116 0.474 0.1443831908 175 0.350 -0.689 1.236 -0.172 -0.116 0.474 0.1440496667 179 0.356 -0.689 1.236 -0.172 -0.116 0.474 0.1440469570 180 0.354 -0.689 1.236 -0.172 -0.116 0.474 0.1440446627 181 0.353 -0.689 1.236 -0.172 -0.116 0.474 0.1440445955 189 0.353 -0.657 1.236 -0.172 -0.116 0.474 0.1431075845 191 0.353 -0.637 1.236 -0.172 -0.116 0.474 0.1426990985 193 0.353 -0.635 1.236 -0.172 -0.116 0.474 0.1426940237 203 0.353 -0.635 1.294 -0.172 -0.116 0.474 0.1426287709 205 0.353 -0.635 1.267 -0.172 -0.116 0.474 0.1423279907 207 0.353 -0.635 1.270 -0.172 -0.116 0.474 0.1423240408 209 0.353 -0.635 1.269 -0.172 -0.116 0.474 0.1423230640 219 0.353 -0.635 1.269 -0.184 -0.116 0.474 0.1421965462 220 0.353 -0.635 1.269 -0.195 -0.116 0.474 0.1421919782 221 0.353 -0.635 1.269 -0.190 -0.116 0.474 0.1421769936 223 0.353 -0.635 1.269 -0.191 -0.116 0.474 0.1421761423 235 0.353 -0.635 1.269 -0.191 -0.120 0.474 0.1421721305 236 0.353 -0.635 1.269 -0.191 -0.118 0.474 0.1421696081 244 0.353 -0.635 1.269 -0.191 -0.118 0.532 0.1415484783 245 0.353 -0.635 1.269 -0.191 -0.118 0.542 0.1414569684 249 0.353 -0.635 1.269 -0.191 -0.118 0.548 0.1414469491 251 0.353 -0.635 1.269 -0.191 -0.118 0.550 0.1414460173 253 0.353 -0.635 1.269 -0.191 -0.118 0.549 0.1414459261 263 0.375 -0.635 1.269 -0.191 -0.118 0.549 0.1412665385 264 0.372 -0.635 1.269 -0.191 -0.118 0.549 0.1412527009 265 0.370 -0.635 1.269 -0.191 -0.118 0.549 0.1412521634 275 0.370 -0.646 1.269 -0.191 -0.118 0.549 0.1411436862 276 0.370 -0.648 1.269 -0.191 -0.118 0.549 0.1411432667 296 0.370 -0.648 1.269 -0.185 -0.118 0.549 0.1411159889 297 0.370 -0.648 1.269 -0.184 -0.118 0.549 0.1411140306 298 0.370 -0.648 1.269 -0.181 -0.118 0.549 0.1411132437 301 0.370 -0.648 1.269 -0.182 -0.118 0.549 0.1411126876 310 0.370 -0.648 1.269 -0.182 -0.122 0.549 0.1410933128 312 0.370 -0.648 1.269 -0.182 -0.124 0.549 0.1410913296 322 0.370 -0.648 1.269 -0.182 -0.124 0.566 0.1410126710 323 0.370 -0.648 1.269 -0.182 -0.124 0.564 0.1410103861 334 0.378 -0.648 1.269 -0.182 -0.124 0.564 0.1409838751 336 0.380 -0.648 1.269 -0.182 -0.124 0.564 0.1409838716 339 0.379 -0.648 1.269 -0.182 -0.124 0.564 0.1409830254 349 0.379 -0.646 1.269 -0.182 -0.124 0.564 0.1409792329 359 0.379 -0.646 1.266 -0.182 -0.124 0.564 0.1409789909 361 0.379 -0.646 1.267 -0.182 -0.124 0.564 0.1409778129 373 0.379 -0.646 1.267 -0.185 -0.124 0.564 0.1409715915 387 0.379 -0.646 1.267 -0.185 -0.125 0.564 0.1409707488 398 0.379 -0.646 1.267 -0.185 -0.125 0.570 0.1409646826 410 0.380 -0.646 1.267 -0.185 -0.125 0.570 0.1409638042 421 0.380 -0.645 1.267 -0.185 -0.125 0.570 0.1409606695 443 0.380 -0.645 1.267 -0.186 -0.125 0.570 0.1409603982 453 0.380 -0.645 1.267 -0.186 -0.124 0.570 0.1409583581 454 0.380 -0.645 1.267 -0.186 -0.123 0.570 0.1409575415 465 0.380 -0.645 1.267 -0.186 -0.123 0.571 0.1409573469 Powell done niters = 5 Computing relative cost 0 -25.0 -25.0 -25.0 0.995672 1 -25.0 -25.0 25.0 1.042601 2 -25.0 25.0 -25.0 1.011952 3 -25.0 25.0 25.0 1.001417 4 25.0 -25.0 -25.0 1.005375 5 25.0 -25.0 25.0 1.030164 6 25.0 25.0 -25.0 1.026341 7 25.0 25.0 25.0 1.008419 REL: 8 0.140957 8.121942 1.015243 rel = 0.138841 Number of iterations 5 Min cost was 0.140957 Number of FunctionCalls 467 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 1.789000 sec Parameters at optimum (transmm) 0.38005 -0.64469 1.26704 Parameters at optimum (rotdeg) -0.18598 -0.12277 0.57063 Final costs ---------------- Number of surface hits 3047 WM Intensity 56.9871 +/- 7.9749 Ctx Intensity 69.4327 +/- 8.6816 Pct Contrast 19.7210 +/- 13.7119 Cost 0.1410 RelCost 0.3084 Reg at min cost was 0.999 -0.022 -0.034 -0.249; 0.032 -0.098 0.995 0.538; -0.026 -0.995 -0.098 -0.358; 0.000 0.000 0.000 1.000; Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/bbr.pass1.dat, type = 14 Original Reg 0.999 -0.025 -0.025 -0.620; 0.022 -0.095 0.995 1.194; -0.028 -0.995 -0.094 -1.620; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg 0.000 -0.003 0.010 -0.372; -0.010 0.003 0.001 0.656; -0.002 -0.000 0.003 -1.262; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 1.418080 Computing change in rh position Surface RMS Diff (mm) 1.349605 1.734044 mri_segreg done mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/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/sub002/scripts mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname snake5 machine x86_64 user fkaule movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/template.nii regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/tmp.bbregister.19392/bbr.pass1.dat subject sub002 dof 6 outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 1376706176 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.999 -0.022 -0.034 -0.249; 0.032 -0.098 0.995 0.538; -0.026 -0.995 -0.098 -0.358; 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 1.005681 1 -25.0 -25.0 25.0 1.001206 2 -25.0 25.0 -25.0 1.012760 3 -25.0 25.0 25.0 1.019027 4 25.0 -25.0 -25.0 1.023239 5 25.0 -25.0 25.0 1.021860 6 25.0 25.0 -25.0 1.018151 7 25.0 25.0 25.0 1.018750 REL: 8 0.160538 8.120674 1.015084 rel = 0.158153 Initial costs ---------------- Number of surface hits 306067 WM Intensity 57.2975 +/- 8.3244 Ctx Intensity 69.4291 +/- 8.7579 Pct Contrast 19.2108 +/- 14.0392 Cost 0.1605 RelCost 0.1582 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1584 0.1584 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1579 0.1579 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.1559 0.1559 0.0 6 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 0.1548 0.1548 0.0 9 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 -0.1000 0.1511 0.1511 0.0 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.1491 0.1491 0.0 19 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 0.0000 0.1464 0.1464 0.0 22 -0.1000 -0.1000 -0.1000 0.1000 0.0000 0.0000 0.1457 0.1457 0.0 46 -0.1000 -0.1000 0.0000 0.1000 -0.1000 0.0000 0.1446 0.1446 0.0 49 -0.1000 -0.1000 0.0000 0.1000 0.0000 0.0000 0.1423 0.1423 0.0 293 0.0000 -0.1000 0.0000 0.1000 0.0000 0.1000 0.1422 0.1422 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1410 0.1410 0.0 Brute Force -------------------------- Min cost was 0.140957 Number of iterations 729 Search time 2.641000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 8 -0.025 0.000 0.000 0.000 0.000 0.000 0.1604698779 11 -0.026 0.000 0.000 0.000 0.000 0.000 0.1604692307 12 -0.027 0.000 0.000 0.000 0.000 0.000 0.1604690775 20 -0.027 -0.085 0.000 0.000 0.000 0.000 0.1599344056 21 -0.027 -0.069 0.000 0.000 0.000 0.000 0.1598841461 22 -0.027 -0.066 0.000 0.000 0.000 0.000 0.1598820851 23 -0.027 -0.065 0.000 0.000 0.000 0.000 0.1598819801 31 -0.027 -0.065 -0.050 0.000 0.000 0.000 0.1594113639 32 -0.027 -0.065 -0.083 0.000 0.000 0.000 0.1593761960 33 -0.027 -0.065 -0.072 0.000 0.000 0.000 0.1593607907 34 -0.027 -0.065 -0.071 0.000 0.000 0.000 0.1593605731 35 -0.027 -0.065 -0.070 0.000 0.000 0.000 0.1593605096 44 -0.027 -0.065 -0.070 0.096 0.000 0.000 0.1582018373 45 -0.027 -0.065 -0.070 0.083 0.000 0.000 0.1581597755 46 -0.027 -0.065 -0.070 0.081 0.000 0.000 0.1581593829 48 -0.027 -0.065 -0.070 0.082 0.000 0.000 0.1581592468 56 -0.027 -0.065 -0.070 0.082 0.009 0.000 0.1581555923 57 -0.027 -0.065 -0.070 0.082 0.007 0.000 0.1581551333 68 -0.027 -0.065 -0.070 0.082 0.007 0.031 0.1580046776 70 -0.027 -0.065 -0.070 0.082 0.007 0.039 0.1580007565 71 -0.027 -0.065 -0.070 0.082 0.007 0.037 0.1579999205 72 -0.027 -0.065 -0.070 0.082 0.007 0.036 0.1579999029 82 -0.016 -0.065 -0.070 0.082 0.007 0.036 0.1579976067 83 -0.020 -0.065 -0.070 0.082 0.007 0.036 0.1579957129 84 -0.021 -0.065 -0.070 0.082 0.007 0.036 0.1579953629 86 -0.022 -0.065 -0.070 0.082 0.007 0.036 0.1579952922 93 -0.022 -0.051 -0.070 0.082 0.007 0.036 0.1579751893 94 -0.022 -0.050 -0.070 0.082 0.007 0.036 0.1579748305 95 -0.022 -0.049 -0.070 0.082 0.007 0.036 0.1579745553 104 -0.022 -0.049 -0.112 0.082 0.007 0.036 0.1576380933 105 -0.022 -0.049 -0.139 0.082 0.007 0.036 0.1576224577 106 -0.022 -0.049 -0.129 0.082 0.007 0.036 0.1576082843 115 -0.022 -0.049 -0.129 0.127 0.007 0.036 0.1575930703 116 -0.022 -0.049 -0.129 0.105 0.007 0.036 0.1574967914 117 -0.022 -0.049 -0.129 0.104 0.007 0.036 0.1574965506 127 -0.022 -0.049 -0.129 0.104 0.008 0.036 0.1574965050 138 -0.022 -0.049 -0.129 0.104 0.008 0.038 0.1574956748 147 -0.020 -0.042 -0.151 0.113 0.008 0.039 0.1574506786 148 -0.020 -0.042 -0.152 0.113 0.008 0.039 0.1574505847 150 -0.020 -0.042 -0.152 0.113 0.008 0.039 0.1574505287 161 -0.011 -0.042 -0.152 0.113 0.008 0.039 0.1574457183 162 -0.012 -0.042 -0.152 0.113 0.008 0.039 0.1574455433 163 -0.013 -0.042 -0.152 0.113 0.008 0.039 0.1574454586 173 -0.013 -0.040 -0.152 0.113 0.008 0.039 0.1574453159 174 -0.013 -0.039 -0.152 0.113 0.008 0.039 0.1574453127 184 -0.013 -0.039 -0.152 0.113 0.008 0.047 0.1574429504 185 -0.013 -0.039 -0.152 0.113 0.008 0.045 0.1574422983 203 -0.013 -0.039 -0.152 0.113 0.009 0.045 0.1574421157 215 -0.013 -0.039 -0.152 0.113 0.010 0.045 0.1574420488 226 -0.008 -0.039 -0.152 0.113 0.010 0.045 0.1574415627 227 -0.010 -0.039 -0.152 0.113 0.010 0.045 0.1574413323 236 -0.011 -0.040 -0.152 0.113 0.010 0.045 0.1574411857 237 -0.011 -0.041 -0.152 0.113 0.010 0.045 0.1574410506 251 -0.011 -0.041 -0.152 0.113 0.010 0.046 0.1574410163 268 -0.011 -0.041 -0.152 0.113 0.009 0.046 0.1574409780 282 -0.009 -0.043 -0.152 0.113 0.007 0.047 0.1574406570 288 -0.010 -0.042 -0.152 0.113 0.008 0.047 0.1574406306 294 -0.010 -0.042 -0.152 0.113 0.008 0.047 0.1574406169 312 -0.009 -0.042 -0.152 0.113 0.008 0.047 0.1574406043 341 -0.009 -0.042 -0.152 0.114 0.008 0.047 0.1574405976 351 -0.009 -0.042 -0.152 0.114 0.009 0.047 0.1574404797 352 -0.009 -0.042 -0.152 0.114 0.010 0.047 0.1574404247 356 -0.008 -0.044 -0.152 0.114 0.009 0.048 0.1574402747 360 -0.008 -0.043 -0.152 0.114 0.009 0.047 0.1574401378 361 -0.008 -0.043 -0.152 0.114 0.009 0.047 0.1574401359 367 -0.008 -0.043 -0.152 0.114 0.009 0.047 0.1574401258 394 -0.008 -0.042 -0.152 0.114 0.009 0.047 0.1574399686 415 -0.008 -0.042 -0.152 0.113 0.009 0.047 0.1574399435 430 -0.007 -0.043 -0.152 0.113 0.008 0.048 0.1574399122 435 -0.007 -0.043 -0.152 0.113 0.008 0.048 0.1574398981 437 -0.007 -0.043 -0.152 0.113 0.008 0.048 0.1574398809 475 -0.007 -0.043 -0.152 0.113 0.008 0.049 0.1574398589 492 -0.007 -0.043 -0.152 0.113 0.009 0.049 0.1574398442 513 -0.007 -0.043 -0.152 0.113 0.009 0.049 0.1574398301 514 -0.007 -0.043 -0.153 0.113 0.009 0.049 0.1574397932 569 -0.007 -0.043 -0.153 0.113 0.009 0.049 0.1574397637 635 -0.007 -0.043 -0.153 0.113 0.009 0.049 0.1574397566 Powell done niters = 9 Computing relative cost 0 -25.0 -25.0 -25.0 1.007105 1 -25.0 -25.0 25.0 1.000977 2 -25.0 25.0 -25.0 1.012423 3 -25.0 25.0 25.0 1.019748 4 25.0 -25.0 -25.0 1.024266 5 25.0 -25.0 25.0 1.022357 6 25.0 25.0 -25.0 1.018454 7 25.0 25.0 25.0 1.018845 REL: 8 0.157440 8.124174 1.015522 rel = 0.155033 Number of iterations 9 Min cost was 0.157440 Number of FunctionCalls 706 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 96.378000 sec Parameters at optimum (transmm) -0.00715 -0.04306 -0.15259 Parameters at optimum (rotdeg) 0.11330 0.00929 0.04876 Final costs ---------------- Number of surface hits 306067 WM Intensity 57.2881 +/- 8.2908 Ctx Intensity 69.4207 +/- 8.7837 Pct Contrast 19.2072 +/- 13.9822 Cost 0.1574 RelCost 0.1582 Reg at min cost was 0.999 -0.022 -0.035 -0.256; 0.033 -0.096 0.995 0.495; -0.026 -0.995 -0.096 -0.509; 0.000 0.000 0.000 1.000; Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/T2raw.dat, type = 14 Original Reg 0.999 -0.022 -0.034 -0.249; 0.032 -0.098 0.995 0.538; -0.026 -0.995 -0.098 -0.358; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg 0.000 0.000 0.001 0.008; -0.001 -0.002 -0.000 0.043; 0.000 0.000 -0.002 0.151; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.158104 Computing change in rh position Surface RMS Diff (mm) 0.145179 0.292914 mri_segreg done tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/T2raw.dat --noedit --ltaout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/mri/orig/T2raw.mgz reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 -0.022 -0.035 -0.256; 0.033 -0.096 0.995 0.495; -0.026 -0.995 -0.096 -0.509; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- INFO: loading target /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/mri/orig/T2raw.mgz Tmov: -------------------- -0.700 0.000 0.000 95.881; 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 -0.022 -0.035 -0.256; 0.033 -0.096 0.995 0.495; -0.026 -0.995 -0.096 -0.509; 0.000 0.000 0.000 1.000; Determinant 1 subject = sub002 RegMat --------------------------- 0.999 -0.022 -0.035 -0.256; 0.033 -0.096 0.995 0.495; -0.026 -0.995 -0.096 -0.509; 0.000 0.000 0.000 1.000; transformed matrix: 1.000 -0.001 -0.002 0.174; 0.001 0.999 0.033 0.490; 0.002 -0.033 0.999 0.098; 0.000 0.000 0.000 1.000; transformed matrix: 0.699 -0.017 -0.022 39.493; -0.025 -0.064 -0.663 271.504; 0.016 0.663 -0.064 10.351; 0.000 0.000 0.000 1.000; Cleaning up Started at Thu Aug 8 23:21:02 CEST 2013 Ended at Thu Aug 8 23:34:14 CEST 2013 BBR-Run-Time-Sec 792 bbregister Done To check results, run: tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/T2raw.dat --surf mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/T2.mgz mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/mri/orig/T2raw.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999032, 0.0218052, 0.0381938) j_ras = (0.0265301, 0.991428, 0.127932) k_ras = (0.0350768, -0.128822, 0.991047) INFO: Reading transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/T2raw.lta... Reading transform with LTAreadEx() reading extra input line subject sub002 reading extra input line fscale 0.150000 reading template info from volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig.mgz... INFO: Applying transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/T2raw.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 1.000 -0.001 -0.002 0.174; 0.001 0.999 0.033 0.490; 0.002 -0.033 0.999 0.098; 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/sub002/mri/T2.mgz... mri_normalize -aseg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/aseg.mgz -sigma 4 -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.white identity.nofile -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.white identity.nofile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/T2.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/mri/T2.mgz... computing distance transform computing distance transform computing nonmaximum suppression 18670 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/sub002/mri/T2.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.woT2.pial `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.woT2.pial' mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub002 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/sub002/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/wm.mgz... 20389 bright wm thresholded. 326 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.orig... computing class statistics... border white: 305608 voxels (1.82%) border gray 333888 voxels (1.99%) WM (92.0): 93.4 +- 9.7 [70.0 --> 110.0] GM (76.0) : 74.6 +- 12.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 48.3 (was 70) setting MAX_BORDER_WHITE to 114.7 (was 105) setting MIN_BORDER_WHITE to 61.0 (was 85) setting MAX_CSF to 35.6 (was 40) setting MAX_GRAY to 95.3 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 54.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 22.8 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=61 mean inside = 92.7, mean outside = 69.6 smoothing surface for 5 iterations... reading initial white vertex positions from white... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.89 +- 0.25 (0.02-->4.08) (max @ vno 105889 --> 106914) face area 0.33 +- 0.16 (0.00-->2.68) averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 0 with 2 points - only 0.00% unknown deleting segment 2 with 11 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 3 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 4 with 2 points - only 0.00% unknown deleting segment 6 with 12 points - only 0.00% unknown deleting segment 7 with 8 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 30 points - only 0.00% unknown deleting segment 10 with 12 points - only 0.00% unknown removing 3 vertex label from ripped group 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 (0.06-->4.08) (max @ vno 106914 --> 105889) face area 0.33 +- 0.16 (0.00-->2.68) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4766040.0, rms=0.00 rms = 2.29, time step reduction 1 of 3 to 0.250... rms = 0.59, time step reduction 2 of 3 to 0.125... rms = 0.08, time step reduction 3 of 3 to 0.062... 001: dt: 0.1250, sse=4766040.0, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 0 with 2 points - only 0.00% unknown deleting segment 1 with 11 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 3 with 2 points - only 0.00% unknown deleting segment 4 with 12 points - only 0.00% unknown deleting segment 5 with 8 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown deleting segment 7 with 30 points - only 0.00% unknown deleting segment 8 with 12 points - only 0.00% unknown removing 3 vertex label from ripped group 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 (0.06-->4.08) (max @ vno 106914 --> 105889) face area 0.33 +- 0.16 (0.00-->2.68) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4766040.0, rms=0.00 rms = 2.03, time step reduction 1 of 3 to 0.250... rms = 0.53, time step reduction 2 of 3 to 0.125... rms = 0.07, time step reduction 3 of 3 to 0.062... 002: dt: 0.1250, sse=4766040.0, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 0 with 2 points - only 0.00% unknown deleting segment 1 with 11 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 3 with 2 points - only 0.00% unknown deleting segment 4 with 12 points - only 0.00% unknown deleting segment 5 with 8 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown deleting segment 7 with 30 points - only 0.00% unknown deleting segment 8 with 12 points - only 0.00% unknown removing 3 vertex label from ripped group 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 (0.06-->4.08) (max @ vno 106914 --> 105889) face area 0.33 +- 0.16 (0.00-->2.68) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4766040.0, rms=0.00 rms = 2.29, time step reduction 1 of 3 to 0.250... rms = 0.59, time step reduction 2 of 3 to 0.125... rms = 0.08, time step reduction 3 of 3 to 0.062... 003: dt: 0.1250, sse=4766040.0, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 0 with 2 points - only 0.00% unknown deleting segment 1 with 11 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 3 with 2 points - only 0.00% unknown deleting segment 4 with 12 points - only 0.00% unknown deleting segment 5 with 8 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown deleting segment 7 with 30 points - only 0.00% unknown deleting segment 8 with 12 points - only 0.00% unknown removing 3 vertex label from ripped group 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=4766040.0, rms=0.00 rms = 2.03, time step reduction 1 of 3 to 0.250... rms = 0.53, time step reduction 2 of 3 to 0.125... rms = 0.07, time step reduction 3 of 3 to 0.062... 004: dt: 0.1250, sse=4766040.0, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 3 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 [81.30 212.70], gm=147.00+-21.90, and vertices in regions > 136.0 58159 surface locations found to contain inconsistent values (2108 in, 56051 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=522009.8, rms=0.27 001: dt: 0.5000, sse=493209.2, rms=0.258 (0.000%) 002: dt: 0.5000, sse=475991.9, rms=0.241 (0.000%) 003: dt: 0.5000, sse=467294.1, rms=0.228 (0.000%) 004: dt: 0.5000, sse=460228.8, rms=0.216 (0.000%) 005: dt: 0.5000, sse=455870.2, rms=0.206 (0.000%) 006: dt: 0.5000, sse=452957.9, rms=0.197 (0.000%) 007: dt: 0.5000, sse=451736.1, rms=0.189 (0.000%) 008: dt: 0.5000, sse=451005.8, rms=0.182 (0.000%) 009: dt: 0.5000, sse=451384.6, rms=0.176 (0.000%) 010: dt: 0.5000, sse=450710.3, rms=0.171 (0.000%) 011: dt: 0.5000, sse=450881.6, rms=0.167 (0.000%) 012: dt: 0.5000, sse=450864.9, rms=0.163 (0.000%) 013: dt: 0.5000, sse=450960.5, rms=0.160 (0.000%) 014: dt: 0.5000, sse=450526.3, rms=0.158 (0.000%) 015: dt: 0.5000, sse=450311.5, rms=0.156 (0.000%) 016: dt: 0.5000, sse=449499.1, rms=0.154 (0.000%) 017: dt: 0.5000, sse=449359.0, rms=0.152 (0.000%) 018: dt: 0.5000, sse=448337.1, rms=0.151 (0.000%) 019: dt: 0.5000, sse=448019.9, rms=0.150 (0.000%) 020: dt: 0.5000, sse=446818.6, rms=0.149 (0.000%) 021: dt: 0.5000, sse=446496.1, rms=0.149 (0.000%) 022: dt: 0.5000, sse=445546.1, rms=0.148 (0.000%) 023: dt: 0.5000, sse=444794.8, rms=0.148 (0.000%) 024: dt: 0.5000, sse=443847.1, rms=0.147 (0.000%) 025: dt: 0.5000, sse=443068.0, rms=0.147 (0.000%) 026: dt: 0.5000, sse=441568.9, rms=0.147 (0.000%) 027: dt: 0.5000, sse=441255.9, rms=0.147 (0.000%) 028: dt: 0.5000, sse=440194.6, rms=0.147 (0.000%) 029: dt: 0.5000, sse=439738.7, rms=0.147 (0.000%) 030: dt: 0.5000, sse=438530.6, rms=0.147 (0.000%) positioning took 4.1 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [81.30 218.70], gm=150.00+-22.90, and vertices in regions > 138.5 52018 surface locations found to contain inconsistent values (839 in, 51179 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=46531.7, rms=0.14 031: dt: 0.5000, sse=46095.0, rms=0.136 (0.000%) 032: dt: 0.5000, sse=47367.4, rms=0.122 (0.000%) 033: dt: 0.5000, sse=48962.1, rms=0.113 (0.000%) 034: dt: 0.5000, sse=50287.0, rms=0.107 (0.000%) 035: dt: 0.5000, sse=51504.4, rms=0.101 (0.000%) 036: dt: 0.5000, sse=52693.2, rms=0.096 (0.000%) 037: dt: 0.5000, sse=53796.8, rms=0.091 (0.000%) 038: dt: 0.5000, sse=54834.0, rms=0.087 (0.000%) 039: dt: 0.5000, sse=55909.9, rms=0.082 (0.000%) 040: dt: 0.5000, sse=56892.8, rms=0.079 (0.000%) 041: dt: 0.5000, sse=57865.9, rms=0.075 (0.000%) 042: dt: 0.5000, sse=58734.5, rms=0.072 (0.000%) 043: dt: 0.5000, sse=59589.5, rms=0.069 (0.000%) 044: dt: 0.5000, sse=60364.9, rms=0.066 (0.000%) 045: dt: 0.5000, sse=61180.8, rms=0.063 (0.000%) 046: dt: 0.5000, sse=61857.8, rms=0.061 (0.000%) 047: dt: 0.5000, sse=62521.8, rms=0.059 (0.000%) 048: dt: 0.5000, sse=63131.5, rms=0.057 (0.000%) 049: dt: 0.5000, sse=63755.6, rms=0.055 (0.000%) 050: dt: 0.5000, sse=64314.3, rms=0.053 (0.000%) 051: dt: 0.5000, sse=64831.8, rms=0.052 (0.000%) 052: dt: 0.5000, sse=65303.6, rms=0.050 (0.000%) 053: dt: 0.5000, sse=65795.2, rms=0.049 (0.000%) 054: dt: 0.5000, sse=66184.3, rms=0.048 (0.000%) 055: dt: 0.5000, sse=66592.6, rms=0.047 (0.000%) 056: dt: 0.5000, sse=66902.6, rms=0.045 (0.000%) 057: dt: 0.5000, sse=67230.8, rms=0.044 (0.000%) 058: dt: 0.5000, sse=67489.4, rms=0.043 (0.000%) 059: dt: 0.5000, sse=67699.3, rms=0.042 (0.000%) 060: dt: 0.5000, sse=67941.5, rms=0.041 (0.000%) positioning took 4.3 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [86.50 209.50], gm=148.00+-20.50, and vertices in regions > 137.7 12693 surface locations found to contain inconsistent values (2166 in, 10527 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=8662.8, rms=0.11 061: dt: 0.5000, sse=8608.5, rms=0.108 (0.000%) 062: dt: 0.5000, sse=8404.7, rms=0.101 (0.000%) 063: dt: 0.5000, sse=8253.4, rms=0.095 (0.000%) 064: dt: 0.5000, sse=8144.0, rms=0.090 (0.000%) 065: dt: 0.5000, sse=8071.3, rms=0.085 (0.000%) 066: dt: 0.5000, sse=8025.0, rms=0.081 (0.000%) 067: dt: 0.5000, sse=7979.6, rms=0.078 (0.000%) 068: dt: 0.5000, sse=7932.1, rms=0.075 (0.000%) 069: dt: 0.5000, sse=7886.0, rms=0.072 (0.000%) 070: dt: 0.5000, sse=7852.9, rms=0.069 (0.000%) 071: dt: 0.5000, sse=7827.4, rms=0.066 (0.000%) 072: dt: 0.5000, sse=7811.3, rms=0.064 (0.000%) 073: dt: 0.5000, sse=7807.6, rms=0.061 (0.000%) 074: dt: 0.5000, sse=7799.7, rms=0.058 (0.000%) 075: dt: 0.5000, sse=7793.7, rms=0.056 (0.000%) 076: dt: 0.5000, sse=7792.2, rms=0.054 (0.000%) 077: dt: 0.5000, sse=7789.9, rms=0.052 (0.000%) 078: dt: 0.5000, sse=7796.7, rms=0.050 (0.000%) 079: dt: 0.5000, sse=7797.1, rms=0.048 (0.000%) 080: dt: 0.5000, sse=7805.6, rms=0.046 (0.000%) 081: dt: 0.5000, sse=7812.1, rms=0.044 (0.000%) 082: dt: 0.5000, sse=7825.2, rms=0.042 (0.000%) 083: dt: 0.5000, sse=7830.3, rms=0.041 (0.000%) 084: dt: 0.5000, sse=7840.6, rms=0.039 (0.000%) 085: dt: 0.5000, sse=7851.9, rms=0.038 (0.000%) 086: dt: 0.5000, sse=7864.2, rms=0.037 (0.000%) 087: dt: 0.5000, sse=7874.2, rms=0.036 (0.000%) 088: dt: 0.5000, sse=7883.5, rms=0.035 (0.000%) 089: dt: 0.5000, sse=7891.8, rms=0.034 (0.000%) 090: dt: 0.5000, sse=7896.9, rms=0.033 (0.000%) positioning took 4.2 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [67.40 224.60], gm=146.00+-26.20, and vertices in regions > 132.9 50819 surface locations found to contain inconsistent values (12 in, 50807 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/sub002/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1409.3, rms=0.06 091: dt: 0.5000, sse=1323.0, rms=0.059 (0.000%) 092: dt: 0.5000, sse=1188.5, rms=0.050 (0.000%) 093: dt: 0.5000, sse=1139.4, rms=0.045 (0.000%) 094: dt: 0.5000, sse=1115.3, rms=0.042 (0.000%) 095: dt: 0.5000, sse=1094.7, rms=0.039 (0.000%) 096: dt: 0.5000, sse=1081.3, rms=0.037 (0.000%) 097: dt: 0.5000, sse=1070.9, rms=0.036 (0.000%) 098: dt: 0.5000, sse=1062.7, rms=0.035 (0.000%) 099: dt: 0.5000, sse=1055.0, rms=0.034 (0.000%) 100: dt: 0.5000, sse=1048.7, rms=0.033 (0.000%) 101: dt: 0.5000, sse=1043.7, rms=0.032 (0.000%) 102: dt: 0.5000, sse=1040.3, rms=0.031 (0.000%) 103: dt: 0.5000, sse=1037.3, rms=0.030 (0.000%) 104: dt: 0.5000, sse=1034.1, rms=0.030 (0.000%) 105: dt: 0.5000, sse=1031.7, rms=0.029 (0.000%) 106: dt: 0.5000, sse=1029.2, rms=0.029 (0.000%) 107: dt: 0.5000, sse=1027.3, rms=0.029 (0.000%) 108: dt: 0.5000, sse=1025.3, rms=0.028 (0.000%) 109: dt: 0.5000, sse=1024.1, rms=0.028 (0.000%) 110: dt: 0.5000, sse=1023.2, rms=0.028 (0.000%) 111: dt: 0.5000, sse=1022.6, rms=0.028 (0.000%) 112: dt: 0.5000, sse=1022.3, rms=0.027 (0.000%) 113: dt: 0.5000, sse=1021.3, rms=0.027 (0.000%) 114: dt: 0.5000, sse=1020.7, rms=0.027 (0.000%) 115: dt: 0.5000, sse=1020.2, rms=0.027 (0.000%) 116: dt: 0.5000, sse=1020.0, rms=0.027 (0.000%) 117: dt: 0.5000, sse=1019.9, rms=0.027 (0.000%) 118: dt: 0.5000, sse=1019.7, rms=0.027 (0.000%) 119: dt: 0.5000, sse=1019.5, rms=0.027 (0.000%) 120: dt: 0.5000, sse=1020.1, rms=0.027 (0.000%) positioning took 4.3 minutes writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.area.pial vertex spacing 1.03 +- 0.43 (0.08-->7.06) (max @ vno 111435 --> 111419) face area 0.41 +- 0.31 (0.00-->4.98) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 162178 vertices processed 25000 of 162178 vertices processed 50000 of 162178 vertices processed 75000 of 162178 vertices processed 100000 of 162178 vertices processed 125000 of 162178 vertices processed 150000 of 162178 vertices processed 0 of 162178 vertices processed 25000 of 162178 vertices processed 50000 of 162178 vertices processed 75000 of 162178 vertices processed 100000 of 162178 vertices processed 125000 of 162178 vertices processed 150000 of 162178 vertices processed thickness calculation complete, 605:965 truncations. 41783 vertices at 0 distance 118651 vertices at 1 distance 99728 vertices at 2 distance 36989 vertices at 3 distance 10002 vertices at 4 distance 2858 vertices at 5 distance 963 vertices at 6 distance 326 vertices at 7 distance 126 vertices at 8 distance 55 vertices at 9 distance 35 vertices at 10 distance 24 vertices at 11 distance 18 vertices at 12 distance 10 vertices at 13 distance 12 vertices at 14 distance 16 vertices at 15 distance 9 vertices at 16 distance 9 vertices at 17 distance 2 vertices at 18 distance 3 vertices at 19 distance 3 vertices at 20 distance writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.thickness positioning took 21.1 minutes /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.woT2.pial `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.woT2.pial' mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub002 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/sub002/mri/filled.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/brain.finalsurfs.mgz... reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/wm.mgz... 19992 bright wm thresholded. 328 bright non-wm voxels segmented. reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.orig... computing class statistics... border white: 305608 voxels (1.82%) border gray 333888 voxels (1.99%) WM (92.0): 93.4 +- 9.8 [70.0 --> 110.0] GM (76.0) : 74.4 +- 12.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 47.1 (was 70) setting MAX_BORDER_WHITE to 114.8 (was 105) setting MIN_BORDER_WHITE to 60.0 (was 85) setting MAX_CSF to 34.2 (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 21.3 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=60 mean inside = 92.8, mean outside = 69.2 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/sub002/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.89 +- 0.25 (0.03-->4.00) (max @ vno 107853 --> 109067) face area 0.33 +- 0.16 (0.00-->3.43) averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 24 points - only 0.00% unknown deleting segment 1 with 6 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 1 points - only 0.00% unknown deleting segment 5 with 77 points - only 0.00% unknown deleting segment 6 with 5 points - only 0.00% unknown deleting segment 7 with 472 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 8 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 12 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 13 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 (0.06-->3.75) (max @ vno 95101 --> 88276) face area 0.33 +- 0.16 (0.00-->3.43) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4946121.5, rms=0.00 rms = 1.36, time step reduction 1 of 3 to 0.250... rms = 0.34, time step reduction 2 of 3 to 0.125... rms = 0.04, time step reduction 3 of 3 to 0.062... 001: dt: 0.1250, sse=4946121.5, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 24 points - only 0.00% unknown deleting segment 1 with 6 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 2 with 3 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 77 points - only 0.00% unknown deleting segment 5 with 5 points - only 0.00% unknown deleting segment 6 with 472 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 9 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 10 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 (0.06-->3.75) (max @ vno 95101 --> 88276) face area 0.33 +- 0.16 (0.00-->3.43) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4946121.5, rms=0.00 rms = 1.36, time step reduction 1 of 3 to 0.250... rms = 0.34, time step reduction 2 of 3 to 0.125... rms = 0.04, time step reduction 3 of 3 to 0.062... 002: dt: 0.1250, sse=4946121.5, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 24 points - only 0.00% unknown deleting segment 1 with 6 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 2 with 3 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 77 points - only 0.00% unknown deleting segment 5 with 5 points - only 0.00% unknown deleting segment 6 with 472 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 9 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 10 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 (0.06-->3.75) (max @ vno 95101 --> 88276) face area 0.33 +- 0.16 (0.00-->3.43) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4946121.5, rms=0.00 rms = 1.36, time step reduction 1 of 3 to 0.250... rms = 0.34, time step reduction 2 of 3 to 0.125... rms = 0.04, time step reduction 3 of 3 to 0.062... 003: dt: 0.1250, sse=4946121.5, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 24 points - only 0.00% unknown deleting segment 1 with 6 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 2 with 3 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 77 points - only 0.00% unknown deleting segment 5 with 5 points - only 0.00% unknown deleting segment 6 with 472 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 9 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 10 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=4946121.5, rms=0.00 rms = 1.36, time step reduction 1 of 3 to 0.250... rms = 0.34, time step reduction 2 of 3 to 0.125... rms = 0.04, time step reduction 3 of 3 to 0.062... 004: dt: 0.1250, sse=4946121.5, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group smoothing surface for 5 iterations... reading initial pial vertex positions from woT2.pial... repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [90.20 207.80], gm=149.00+-19.60, and vertices in regions > 139.2 55231 surface locations found to contain inconsistent values (4143 in, 51088 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=546910.6, rms=0.26 001: dt: 0.5000, sse=514420.6, rms=0.253 (0.000%) 002: dt: 0.5000, sse=495108.9, rms=0.238 (0.000%) 003: dt: 0.5000, sse=484468.0, rms=0.226 (0.000%) 004: dt: 0.5000, sse=476251.7, rms=0.215 (0.000%) 005: dt: 0.5000, sse=471347.7, rms=0.205 (0.000%) 006: dt: 0.5000, sse=467727.2, rms=0.197 (0.000%) 007: dt: 0.5000, sse=465879.7, rms=0.190 (0.000%) 008: dt: 0.5000, sse=463983.3, rms=0.184 (0.000%) 009: dt: 0.5000, sse=463124.8, rms=0.178 (0.000%) 010: dt: 0.5000, sse=462071.3, rms=0.174 (0.000%) 011: dt: 0.5000, sse=461640.4, rms=0.170 (0.000%) 012: dt: 0.5000, sse=460878.1, rms=0.167 (0.000%) 013: dt: 0.5000, sse=460294.7, rms=0.164 (0.000%) 014: dt: 0.5000, sse=459589.3, rms=0.161 (0.000%) 015: dt: 0.5000, sse=458760.2, rms=0.159 (0.000%) 016: dt: 0.5000, sse=458094.8, rms=0.157 (0.000%) 017: dt: 0.5000, sse=456837.6, rms=0.156 (0.000%) 018: dt: 0.5000, sse=456292.9, rms=0.155 (0.000%) 019: dt: 0.5000, sse=454951.7, rms=0.154 (0.000%) 020: dt: 0.5000, sse=453750.7, rms=0.153 (0.000%) 021: dt: 0.5000, sse=452578.5, rms=0.152 (0.000%) 022: dt: 0.5000, sse=451501.6, rms=0.152 (0.000%) 023: dt: 0.5000, sse=450358.2, rms=0.151 (0.000%) 024: dt: 0.5000, sse=449395.3, rms=0.151 (0.000%) 025: dt: 0.5000, sse=448435.2, rms=0.151 (0.000%) 026: dt: 0.5000, sse=447607.4, rms=0.151 (0.000%) 027: dt: 0.5000, sse=446392.5, rms=0.151 (0.000%) 028: dt: 0.5000, sse=445177.2, rms=0.151 (0.000%) 029: dt: 0.5000, sse=444232.2, rms=0.151 (0.000%) 030: dt: 0.5000, sse=443181.7, rms=0.151 (0.000%) positioning took 4.2 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [96.90 203.10], gm=150.00+-17.70, and vertices in regions > 141.1 39536 surface locations found to contain inconsistent values (5293 in, 34243 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=48162.5, rms=0.17 031: dt: 0.5000, sse=47843.2, rms=0.164 (0.000%) 032: dt: 0.5000, sse=48514.2, rms=0.154 (0.000%) 033: dt: 0.5000, sse=49544.4, rms=0.145 (0.000%) 034: dt: 0.5000, sse=50520.0, rms=0.139 (0.000%) 035: dt: 0.5000, sse=51356.9, rms=0.133 (0.000%) 036: dt: 0.5000, sse=52187.5, rms=0.127 (0.000%) 037: dt: 0.5000, sse=52974.3, rms=0.122 (0.000%) 038: dt: 0.5000, sse=53779.4, rms=0.117 (0.000%) 039: dt: 0.5000, sse=54595.2, rms=0.112 (0.000%) 040: dt: 0.5000, sse=55391.1, rms=0.108 (0.000%) 041: dt: 0.5000, sse=56232.5, rms=0.103 (0.000%) 042: dt: 0.5000, sse=56987.6, rms=0.099 (0.000%) 043: dt: 0.5000, sse=57735.5, rms=0.096 (0.000%) 044: dt: 0.5000, sse=58471.9, rms=0.092 (0.000%) 045: dt: 0.5000, sse=59184.1, rms=0.089 (0.000%) 046: dt: 0.5000, sse=59841.7, rms=0.086 (0.000%) 047: dt: 0.5000, sse=60478.3, rms=0.083 (0.000%) 048: dt: 0.5000, sse=61077.7, rms=0.080 (0.000%) 049: dt: 0.5000, sse=61640.4, rms=0.077 (0.000%) 050: dt: 0.5000, sse=62170.1, rms=0.075 (0.000%) 051: dt: 0.5000, sse=62651.6, rms=0.072 (0.000%) 052: dt: 0.5000, sse=63104.8, rms=0.070 (0.000%) 053: dt: 0.5000, sse=63556.2, rms=0.068 (0.000%) 054: dt: 0.5000, sse=63980.0, rms=0.066 (0.000%) 055: dt: 0.5000, sse=64350.8, rms=0.064 (0.000%) 056: dt: 0.5000, sse=64702.6, rms=0.062 (0.000%) 057: dt: 0.5000, sse=65028.9, rms=0.060 (0.000%) 058: dt: 0.5000, sse=65340.7, rms=0.058 (0.000%) 059: dt: 0.5000, sse=65644.1, rms=0.057 (0.000%) 060: dt: 0.5000, sse=65887.0, rms=0.055 (0.000%) positioning took 4.2 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [98.70 201.30], gm=150.00+-17.10, and vertices in regions > 141.4 29018 surface locations found to contain inconsistent values (3353 in, 25665 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=8328.2, rms=0.11 061: dt: 0.5000, sse=8281.1, rms=0.105 (0.000%) 062: dt: 0.5000, sse=8165.9, rms=0.100 (0.000%) 063: dt: 0.5000, sse=8081.1, rms=0.095 (0.000%) 064: dt: 0.5000, sse=8015.6, rms=0.091 (0.000%) 065: dt: 0.5000, sse=7958.8, rms=0.087 (0.000%) 066: dt: 0.5000, sse=7917.4, rms=0.084 (0.000%) 067: dt: 0.5000, sse=7877.4, rms=0.081 (0.000%) 068: dt: 0.5000, sse=7832.7, rms=0.078 (0.000%) 069: dt: 0.5000, sse=7793.2, rms=0.076 (0.000%) 070: dt: 0.5000, sse=7760.8, rms=0.073 (0.000%) 071: dt: 0.5000, sse=7732.4, rms=0.070 (0.000%) 072: dt: 0.5000, sse=7712.7, rms=0.068 (0.000%) 073: dt: 0.5000, sse=7694.1, rms=0.066 (0.000%) 074: dt: 0.5000, sse=7677.4, rms=0.064 (0.000%) 075: dt: 0.5000, sse=7670.8, rms=0.061 (0.000%) 076: dt: 0.5000, sse=7659.5, rms=0.059 (0.000%) 077: dt: 0.5000, sse=7652.7, rms=0.057 (0.000%) 078: dt: 0.5000, sse=7652.0, rms=0.056 (0.000%) 079: dt: 0.5000, sse=7650.8, rms=0.054 (0.000%) 080: dt: 0.5000, sse=7653.1, rms=0.052 (0.000%) 081: dt: 0.5000, sse=7652.5, rms=0.051 (0.000%) 082: dt: 0.5000, sse=7656.6, rms=0.049 (0.000%) 083: dt: 0.5000, sse=7659.6, rms=0.048 (0.000%) 084: dt: 0.5000, sse=7663.3, rms=0.047 (0.000%) 085: dt: 0.5000, sse=7671.2, rms=0.046 (0.000%) 086: dt: 0.5000, sse=7672.4, rms=0.044 (0.000%) 087: dt: 0.5000, sse=7676.2, rms=0.043 (0.000%) 088: dt: 0.5000, sse=7679.0, rms=0.042 (0.000%) 089: dt: 0.5000, sse=7682.3, rms=0.041 (0.000%) 090: dt: 0.5000, sse=7686.1, rms=0.040 (0.000%) positioning took 4.1 minutes repositioning pial surface locations using ../mri/T2.mgz locating cortical regions not in the range [99.60 200.40], gm=150.00+-16.80, and vertices in regions > 141.6 23076 surface locations found to contain inconsistent values (1945 in, 21131 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/sub002/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=1771.8, rms=0.08 091: dt: 0.5000, sse=1747.6, rms=0.080 (0.000%) 092: dt: 0.5000, sse=1658.7, rms=0.077 (0.000%) 093: dt: 0.5000, sse=1587.0, rms=0.074 (0.000%) 094: dt: 0.5000, sse=1524.1, rms=0.071 (0.000%) 095: dt: 0.5000, sse=1470.4, rms=0.068 (0.000%) 096: dt: 0.5000, sse=1430.8, rms=0.066 (0.000%) 097: dt: 0.5000, sse=1396.9, rms=0.065 (0.000%) 098: dt: 0.5000, sse=1361.2, rms=0.063 (0.000%) 099: dt: 0.5000, sse=1328.9, rms=0.061 (0.000%) 100: dt: 0.5000, sse=1299.4, rms=0.059 (0.000%) 101: dt: 0.5000, sse=1268.1, rms=0.058 (0.000%) 102: dt: 0.5000, sse=1240.5, rms=0.056 (0.000%) 103: dt: 0.5000, sse=1216.9, rms=0.054 (0.000%) 104: dt: 0.5000, sse=1194.4, rms=0.053 (0.000%) 105: dt: 0.5000, sse=1173.7, rms=0.052 (0.000%) 106: dt: 0.5000, sse=1156.3, rms=0.050 (0.000%) 107: dt: 0.5000, sse=1143.5, rms=0.050 (0.000%) 108: dt: 0.5000, sse=1126.4, rms=0.048 (0.000%) 109: dt: 0.5000, sse=1113.6, rms=0.047 (0.000%) 110: dt: 0.5000, sse=1101.2, rms=0.046 (0.000%) 111: dt: 0.5000, sse=1087.0, rms=0.045 (0.000%) 112: dt: 0.5000, sse=1074.1, rms=0.044 (0.000%) 113: dt: 0.5000, sse=1068.4, rms=0.044 (0.000%) 114: dt: 0.5000, sse=1058.0, rms=0.043 (0.000%) 115: dt: 0.5000, sse=1049.9, rms=0.042 (0.000%) 116: dt: 0.5000, sse=1041.9, rms=0.041 (0.000%) 117: dt: 0.5000, sse=1035.1, rms=0.041 (0.000%) 118: dt: 0.5000, sse=1032.2, rms=0.041 (0.000%) 119: dt: 0.5000, sse=1029.1, rms=0.040 (0.000%) 120: dt: 0.5000, sse=1021.9, rms=0.040 (0.000%) positioning took 5.3 minutes writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.area.pial vertex spacing 1.02 +- 0.43 (0.03-->6.15) (max @ vno 112370 --> 113418) face area 0.40 +- 0.31 (0.00-->6.32) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 161415 vertices processed 25000 of 161415 vertices processed 50000 of 161415 vertices processed 75000 of 161415 vertices processed 100000 of 161415 vertices processed 125000 of 161415 vertices processed 150000 of 161415 vertices processed 0 of 161415 vertices processed 25000 of 161415 vertices processed 50000 of 161415 vertices processed 75000 of 161415 vertices processed 100000 of 161415 vertices processed 125000 of 161415 vertices processed 150000 of 161415 vertices processed thickness calculation complete, 414:852 truncations. 38982 vertices at 0 distance 115625 vertices at 1 distance 101876 vertices at 2 distance 38318 vertices at 3 distance 10423 vertices at 4 distance 3020 vertices at 5 distance 953 vertices at 6 distance 338 vertices at 7 distance 142 vertices at 8 distance 71 vertices at 9 distance 45 vertices at 10 distance 24 vertices at 11 distance 17 vertices at 12 distance 15 vertices at 13 distance 11 vertices at 14 distance 4 vertices at 15 distance 14 vertices at 16 distance 13 vertices at 17 distance 18 vertices at 18 distance 12 vertices at 19 distance 7 vertices at 20 distance writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.thickness positioning took 22.0 minutes #-------------------------------------------- #@# Surf Volume lh Fri Aug 9 00:19:15 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 00:19:17 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 00:19:18 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon sub002 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 = 24 writing volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/ribbon.mgz writing ribbon files #-------------------------------------------- #@# ASeg Stats Fri Aug 9 00:44:43 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002 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 sub002 $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 sub002 sysname Linux hostname snake5 machine x86_64 user fkaule UseRobust 0 atlas_icv (eTIV) = 1487795 mm^3 (det: 1.309391 ) Computing euler number orig.nofix lheno = -24, rheno = -20 orig.nofix lhholes = 13, rhholes = 11 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 301051.478 299221.000 diff= 1830.5 pctdiff= 0.608 rhCtxGM: 289136.374 288108.000 diff= 1028.4 pctdiff= 0.356 lhCtxWM: 272836.406 272641.000 diff= 195.4 pctdiff= 0.072 rhCtxWM: 274536.404 274780.000 diff= -243.6 pctdiff=-0.089 SubCortGMVol 68034.000 SupraTentVol 1234748.663 (1230966.000) diff=3782.663 pctdiff=0.306 SupraTentVolNotVent 1206836.663 (1203054.000) diff=3782.663 pctdiff=0.313 BrainSegVol 1384774.000 (1380497.000) diff=4277.000 pctdiff=0.309 BrainSegVolNotVent 1351349.000 (1353893.663) diff=-2544.663 pctdiff=-0.188 BrainSegVolNotVent 1351349.000 CerebellumVol 148029.000 VentChorVol 27912.000 3rd4th5thCSF 5513.000 CSFVol 1249.000, OptChiasmVol 253.000 MaskVol 1983181.000 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 15712 15712.156 4 5 Left-Inf-Lat-Vent 586 585.676 5 7 Left-Cerebellum-White-Matter 17221 17221.078 6 8 Left-Cerebellum-Cortex 58054 58054.180 7 10 Left-Thalamus-Proper 8295 8294.752 8 11 Left-Caudate 4520 4519.976 9 12 Left-Putamen 7471 7470.748 10 13 Left-Pallidum 2046 2046.089 11 14 3rd-Ventricle 1870 1870.421 12 15 4th-Ventricle 2631 2630.678 13 16 Brain-Stem 23971 23970.787 14 17 Left-Hippocampus 3975 3975.433 15 18 Left-Amygdala 1693 1692.719 16 24 CSF 1208 1207.880 17 26 Left-Accumbens-area 935 935.011 18 28 Left-VentralDC 4588 4588.086 19 30 Left-vessel 116 116.178 20 31 Left-choroid-plexus 1535 1534.951 23 43 Right-Lateral-Ventricle 7505 7504.894 24 44 Right-Inf-Lat-Vent 330 330.009 25 46 Right-Cerebellum-White-Matter 16869 16869.314 26 47 Right-Cerebellum-Cortex 59084 59084.398 27 49 Right-Thalamus-Proper 7459 7458.850 28 50 Right-Caudate 4785 4784.763 29 51 Right-Putamen 6567 6567.062 30 52 Right-Pallidum 1992 1992.300 31 53 Right-Hippocampus 4565 4564.830 32 54 Right-Amygdala 2235 2234.923 33 58 Right-Accumbens-area 818 818.038 34 60 Right-VentralDC 4389 4389.236 35 62 Right-vessel 136 136.460 36 63 Right-choroid-plexus 2202 2201.783 37 72 5th-Ventricle 0 0.000 38 77 WM-hypointensities 1484 1484.361 39 78 Left-WM-hypointensities 0 0.000 40 79 Right-WM-hypointensities 0 0.000 41 80 non-WM-hypointensities 11 10.815 42 81 Left-non-WM-hypointensities 0 0.000 43 82 Right-non-WM-hypointensities 0 0.000 44 85 Optic-Chiasm 263 262.696 45 251 CC_Posterior 816 816.223 46 252 CC_Mid_Posterior 395 394.948 47 253 CC_Central 382 381.718 48 254 CC_Mid_Anterior 435 435.496 49 255 CC_Anterior 875 874.681 Reporting on 45 segmentations mri_segstats done #----------------------------------------- #@# AParc-to-ASeg Fri Aug 9 00:47:43 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002 mri_aparc2aseg --s sub002 --volmask SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer subject sub002 outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.white Reading lh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.pial Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/surf/rh.white Reading rh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.pial Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/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/sub002/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 = 585527 Used brute-force search on 0 voxels Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/aparc+aseg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002 mri_aparc2aseg --s sub002 --volmask --a2009s SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer subject sub002 outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.white Reading lh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.pial Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/surf/rh.white Reading rh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.pial Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/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/sub002/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 = 585527 Used brute-force search on 0 voxels Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# WMParc Fri Aug 9 00:53:00 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002 mri_aparc2aseg --s sub002 --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 sub002 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/sub002/mri/aparc+aseg.mgz Reading lh white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.white Reading lh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.pial Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/surf/rh.white Reading rh pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.pial Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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/sub002/mri/ribbon.mgz Loading filled from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/filled.mgz Ripping vertices labeled as unkown Ripped 8587 vertices from left hemi Ripped 8939 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/sub002/mri/aseg.mgz Loading Ctx Seg File /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 = 1131765 Used brute-force search on 215 voxels Fixing Parahip LH WM Found 13 clusters 0 k 1.000000 1 k 1.000000 2 k 3.000000 3 k 1.000000 4 k 3.000000 5 k 1.000000 6 k 2483.000000 7 k 2.000000 8 k 1.000000 9 k 1.000000 10 k 5.000000 11 k 1.000000 12 k 1.000000 Fixing Parahip RH WM Found 4 clusters 0 k 1.000000 1 k 1.000000 2 k 1.000000 3 k 2104.000000 Writing output aseg to mri/wmparc.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002 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 sub002 --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 sub002 --surf-wm-vol --ctab /opt/freesurfer/5.3.0/WMParcStatsLUT.txt --etiv sysname Linux hostname snake5 machine x86_64 user fkaule UseRobust 0 atlas_icv (eTIV) = 1487795 mm^3 (det: 1.309391 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 301051.478 299221.000 diff= 1830.5 pctdiff= 0.608 rhCtxGM: 289136.374 288108.000 diff= 1028.4 pctdiff= 0.356 lhCtxWM: 272836.406 272641.000 diff= 195.4 pctdiff= 0.072 rhCtxWM: 274536.404 274780.000 diff= -243.6 pctdiff=-0.089 SubCortGMVol 68034.000 SupraTentVol 1234748.663 (1230966.000) diff=3782.663 pctdiff=0.306 SupraTentVolNotVent 1206836.663 (1203054.000) diff=3782.663 pctdiff=0.313 BrainSegVol 1384774.000 (1380497.000) diff=4277.000 pctdiff=0.309 BrainSegVolNotVent 1351349.000 (1353893.663) diff=-2544.663 pctdiff=-0.188 BrainSegVolNotVent 1351349.000 CerebellumVol 148029.000 VentChorVol 27912.000 3rd4th5thCSF 5513.000 CSFVol 1249.000, OptChiasmVol 253.000 MaskVol 1983181.000 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 3831 3831.091 2 3002 wm-lh-caudalanteriorcingulate 3814 3814.421 3 3003 wm-lh-caudalmiddlefrontal 7714 7713.652 4 3004 wm-lh-corpuscallosum 0 0.000 5 3005 wm-lh-cuneus 2420 2419.591 6 3006 wm-lh-entorhinal 768 767.588 7 3007 wm-lh-fusiform 7569 7568.677 8 3008 wm-lh-inferiorparietal 12322 12321.860 9 3009 wm-lh-inferiortemporal 8571 8570.681 10 3010 wm-lh-isthmuscingulate 5372 5372.298 11 3011 wm-lh-lateraloccipital 8528 8528.081 12 3012 wm-lh-lateralorbitofrontal 7503 7503.267 13 3013 wm-lh-lingual 4903 4903.461 14 3014 wm-lh-medialorbitofrontal 4325 4325.258 15 3015 wm-lh-middletemporal 6471 6470.958 16 3016 wm-lh-parahippocampal 2538 2538.227 17 3017 wm-lh-paracentral 4375 4375.143 18 3018 wm-lh-parsopercularis 4565 4565.320 19 3019 wm-lh-parsorbitalis 1055 1054.862 20 3020 wm-lh-parstriangularis 3587 3586.795 21 3021 wm-lh-pericalcarine 2745 2745.437 22 3022 wm-lh-postcentral 8794 8793.513 23 3023 wm-lh-posteriorcingulate 4792 4792.316 24 3024 wm-lh-precentral 16555 16555.076 25 3025 wm-lh-precuneus 14226 14226.451 26 3026 wm-lh-rostralanteriorcingulate 2936 2935.535 27 3027 wm-lh-rostralmiddlefrontal 17354 17353.791 28 3028 wm-lh-superiorfrontal 23529 23528.588 29 3029 wm-lh-superiorparietal 14729 14729.310 30 3030 wm-lh-superiortemporal 10668 10667.562 31 3031 wm-lh-supramarginal 12458 12458.487 32 3032 wm-lh-frontalpole 363 362.975 33 3033 wm-lh-temporalpole 986 985.946 34 3034 wm-lh-transversetemporal 788 788.340 35 3035 wm-lh-insula 9377 9377.229 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 3423 3423.324 120 4002 wm-rh-caudalanteriorcingulate 4456 4456.400 121 4003 wm-rh-caudalmiddlefrontal 6650 6650.487 122 4004 wm-rh-corpuscallosum 0 0.000 123 4005 wm-rh-cuneus 2679 2679.339 124 4006 wm-rh-entorhinal 491 490.770 125 4007 wm-rh-fusiform 8395 8394.559 126 4008 wm-rh-inferiorparietal 15792 15791.956 127 4009 wm-rh-inferiortemporal 7249 7249.257 128 4010 wm-rh-isthmuscingulate 4719 4718.920 129 4011 wm-rh-lateraloccipital 8629 8629.347 130 4012 wm-rh-lateralorbitofrontal 6994 6993.996 131 4013 wm-rh-lingual 5119 5118.712 132 4014 wm-rh-medialorbitofrontal 4042 4041.585 133 4015 wm-rh-middletemporal 7586 7585.990 134 4016 wm-rh-parahippocampal 2100 2099.604 135 4017 wm-rh-paracentral 5214 5213.899 136 4018 wm-rh-parsopercularis 5190 5189.770 137 4019 wm-rh-parsorbitalis 1615 1614.556 138 4020 wm-rh-parstriangularis 4416 4416.242 139 4021 wm-rh-pericalcarine 2832 2831.788 140 4022 wm-rh-postcentral 9337 9336.530 141 4023 wm-rh-posteriorcingulate 4697 4697.445 142 4024 wm-rh-precentral 14892 14892.398 143 4025 wm-rh-precuneus 14794 14793.648 144 4026 wm-rh-rostralanteriorcingulate 2491 2491.264 145 4027 wm-rh-rostralmiddlefrontal 17783 17783.281 146 4028 wm-rh-superiorfrontal 22618 22617.725 147 4029 wm-rh-superiorparietal 14731 14730.840 148 4030 wm-rh-superiortemporal 7759 7759.177 149 4031 wm-rh-supramarginal 9730 9730.302 150 4032 wm-rh-frontalpole 326 325.656 151 4033 wm-rh-temporalpole 679 678.798 152 4034 wm-rh-transversetemporal 550 550.306 153 4035 wm-rh-insula 10108 10108.291 154 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 35120 35119.578 237 5002 Right-UnsegmentedWhiteMatter 38429 38428.828 238 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/sub002/label #-------------------------------------------- #@# BA Labels lh Fri Aug 9 01:05:30 CEST 2013 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.label --trgsubject sub002 --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 = sub002 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/sub002/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178 Number of reverse mapping hits = 554 Checking for and removing duplicates Writing label file ./lh.BA1.label 4683 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.label --trgsubject sub002 --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 = sub002 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/sub002/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178 Number of reverse mapping hits = 1056 Checking for and removing duplicates Writing label file ./lh.BA2.label 8965 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.label --trgsubject sub002 --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 = sub002 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/sub002/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178 Number of reverse mapping hits = 229 Checking for and removing duplicates Writing label file ./lh.BA3a.label 4306 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.label --trgsubject sub002 --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 = sub002 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/sub002/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178 Number of reverse mapping hits = 597 Checking for and removing duplicates Writing label file ./lh.BA3b.label 6580 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.label --trgsubject sub002 --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 = sub002 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/sub002/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178 Number of reverse mapping hits = 970 Checking for and removing duplicates Writing label file ./lh.BA4a.label 6754 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.label --trgsubject sub002 --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 = sub002 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/sub002/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178 Number of reverse mapping hits = 566 Checking for and removing duplicates Writing label file ./lh.BA4p.label 4636 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.label --trgsubject sub002 --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 = sub002 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/sub002/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178 Number of reverse mapping hits = 2907 Checking for and removing duplicates Writing label file ./lh.BA6.label 16496 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.label --trgsubject sub002 --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 = sub002 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/sub002/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178 Number of reverse mapping hits = 525 Checking for and removing duplicates Writing label file ./lh.BA44.label 4706 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.label --trgsubject sub002 --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 = sub002 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/sub002/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178 Number of reverse mapping hits = 1187 Checking for and removing duplicates Writing label file ./lh.BA45.label 4609 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.label --trgsubject sub002 --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 = sub002 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/sub002/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178 Number of reverse mapping hits = 1546 Checking for and removing duplicates Writing label file ./lh.V1.label 6187 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.label --trgsubject sub002 --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 = sub002 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/sub002/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178 Number of reverse mapping hits = 2885 Checking for and removing duplicates Writing label file ./lh.V2.label 10999 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.label --trgsubject sub002 --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 = sub002 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/sub002/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178 Number of reverse mapping hits = 464 Checking for and removing duplicates Writing label file ./lh.MT.label 2482 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.perirhinal.label --trgsubject sub002 --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 = sub002 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/sub002/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178 Number of reverse mapping hits = 153 Checking for and removing duplicates Writing label file ./lh.perirhinal.label 1352 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.thresh.label --trgsubject sub002 --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 = sub002 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/sub002/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178 Number of reverse mapping hits = 127 Checking for and removing duplicates Writing label file ./lh.BA1.thresh.label 1141 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.thresh.label --trgsubject sub002 --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 = sub002 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/sub002/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178 Number of reverse mapping hits = 361 Checking for and removing duplicates Writing label file ./lh.BA2.thresh.label 2453 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.thresh.label --trgsubject sub002 --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 = sub002 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/sub002/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178 Number of reverse mapping hits = 36 Checking for and removing duplicates Writing label file ./lh.BA3a.thresh.label 1540 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.thresh.label --trgsubject sub002 --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 = sub002 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/sub002/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178 Number of reverse mapping hits = 159 Checking for and removing duplicates Writing label file ./lh.BA3b.thresh.label 2155 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.thresh.label --trgsubject sub002 --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 = sub002 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/sub002/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178 Number of reverse mapping hits = 454 Checking for and removing duplicates Writing label file ./lh.BA4a.thresh.label 2773 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.thresh.label --trgsubject sub002 --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 = sub002 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/sub002/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178 Number of reverse mapping hits = 185 Checking for and removing duplicates Writing label file ./lh.BA4p.thresh.label 1734 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.thresh.label --trgsubject sub002 --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 = sub002 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/sub002/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178 Number of reverse mapping hits = 1562 Checking for and removing duplicates Writing label file ./lh.BA6.thresh.label 8597 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.thresh.label --trgsubject sub002 --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 = sub002 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/sub002/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178 Number of reverse mapping hits = 212 Checking for and removing duplicates Writing label file ./lh.BA44.thresh.label 2124 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.thresh.label --trgsubject sub002 --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 = sub002 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/sub002/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178 Number of reverse mapping hits = 529 Checking for and removing duplicates Writing label file ./lh.BA45.thresh.label 1680 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.thresh.label --trgsubject sub002 --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 = sub002 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/sub002/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178 Number of reverse mapping hits = 1126 Checking for and removing duplicates Writing label file ./lh.V1.thresh.label 4531 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.thresh.label --trgsubject sub002 --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 = sub002 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/sub002/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178 Number of reverse mapping hits = 1278 Checking for and removing duplicates Writing label file ./lh.V2.thresh.label 4612 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.thresh.label --trgsubject sub002 --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 = sub002 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/sub002/surf/lh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 162178 Number of reverse mapping hits = 89 Checking for and removing duplicates Writing label file ./lh.MT.thresh.label 602 mri_label2label: Done mris_label2annot --s sub002 --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/sub002/label cmdline mris_label2annot --s sub002 --hemi lh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --l lh.perirhinal.label --a BA --maxstatwinner --noverbose sysname Linux hostname snake5 machine x86_64 user fkaule subject sub002 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/sub002/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 114791 unhit vertices Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/label/lh.BA.annot mris_label2annot --s sub002 --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/sub002/label cmdline mris_label2annot --s sub002 --hemi lh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l lh.BA1.thresh.label --l lh.BA2.thresh.label --l lh.BA3a.thresh.label --l lh.BA3b.thresh.label --l lh.BA4a.thresh.label --l lh.BA4p.thresh.label --l lh.BA6.thresh.label --l lh.BA44.thresh.label --l lh.BA45.thresh.label --l lh.V1.thresh.label --l lh.V2.thresh.label --l lh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose sysname Linux hostname snake5 machine x86_64 user fkaule subject sub002 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/sub002/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 134786 unhit vertices Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/label/lh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab sub002 lh white computing statistics for each annotation in ./lh.BA.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 1253 711 2718 2.609 0.544 0.135 0.053 20 2.7 BA1 4876 3223 8595 2.437 0.522 0.123 0.038 53 7.0 BA2 972 665 1029 1.902 0.349 0.130 0.040 7 1.6 BA3a 2663 1714 4434 2.157 0.591 0.132 0.054 55 5.0 BA3b 1991 1045 4238 3.013 0.731 0.109 0.041 28 3.8 BA4a 1480 874 2695 2.893 0.635 0.108 0.033 10 2.2 BA4p 12325 8106 26696 2.700 0.634 0.140 0.087 1737 49.4 BA6 2711 1823 6359 2.947 0.443 0.124 0.038 32 4.0 BA44 3802 2583 7705 2.553 0.448 0.142 0.045 58 7.3 BA45 3763 2577 5581 1.963 0.473 0.153 0.072 77 11.8 V1 8404 5517 13735 2.208 0.500 0.160 0.062 170 19.6 V2 2089 1397 3463 2.302 0.354 0.132 0.042 27 3.7 MT 1058 711 2857 3.036 0.826 0.133 0.056 15 2.6 perirhinal mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab sub002 lh white computing statistics for each annotation in ./lh.BA.thresh.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 827 441 1808 2.652 0.498 0.137 0.074 16 1.9 BA1 2011 1317 3882 2.479 0.530 0.124 0.037 24 3.2 BA2 788 537 782 1.878 0.338 0.129 0.040 6 1.3 BA3a 1569 1048 2208 1.895 0.416 0.112 0.029 12 2.0 BA3b 2047 1038 4356 3.097 0.664 0.105 0.040 28 4.1 BA4a 1164 708 2018 2.797 0.649 0.110 0.031 7 1.6 BA4p 7098 4655 15293 2.681 0.666 0.145 0.112 1659 38.9 BA6 1711 1145 4114 2.995 0.412 0.129 0.041 21 2.6 BA44 1573 1067 3714 2.647 0.443 0.154 0.051 27 3.3 BA45 3994 2737 5997 1.968 0.464 0.155 0.072 82 12.5 V1 4118 2724 6480 2.108 0.468 0.173 0.073 95 10.8 V2 492 338 962 2.442 0.320 0.137 0.047 7 0.8 MT #-------------------------------------------- #@# BA Labels rh Fri Aug 9 01:10:42 CEST 2013 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.label --trgsubject sub002 --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 = sub002 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/sub002/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415 Number of reverse mapping hits = 524 Checking for and removing duplicates Writing label file ./rh.BA1.label 4486 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.label --trgsubject sub002 --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 = sub002 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/sub002/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415 Number of reverse mapping hits = 741 Checking for and removing duplicates Writing label file ./rh.BA2.label 7428 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.label --trgsubject sub002 --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 = sub002 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/sub002/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415 Number of reverse mapping hits = 238 Checking for and removing duplicates Writing label file ./rh.BA3a.label 4218 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.label --trgsubject sub002 --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 = sub002 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/sub002/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415 Number of reverse mapping hits = 534 Checking for and removing duplicates Writing label file ./rh.BA3b.label 5056 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.label --trgsubject sub002 --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 = sub002 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/sub002/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415 Number of reverse mapping hits = 777 Checking for and removing duplicates Writing label file ./rh.BA4a.label 6524 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.label --trgsubject sub002 --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 = sub002 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/sub002/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415 Number of reverse mapping hits = 455 Checking for and removing duplicates Writing label file ./rh.BA4p.label 4928 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.label --trgsubject sub002 --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 = sub002 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/sub002/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415 Number of reverse mapping hits = 2068 Checking for and removing duplicates Writing label file ./rh.BA6.label 14324 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.label --trgsubject sub002 --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 = sub002 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/sub002/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415 Number of reverse mapping hits = 2037 Checking for and removing duplicates Writing label file ./rh.BA44.label 8949 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.label --trgsubject sub002 --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 = sub002 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/sub002/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415 Number of reverse mapping hits = 2272 Checking for and removing duplicates Writing label file ./rh.BA45.label 7627 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.label --trgsubject sub002 --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 = sub002 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/sub002/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415 Number of reverse mapping hits = 1735 Checking for and removing duplicates Writing label file ./rh.V1.label 6462 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.label --trgsubject sub002 --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 = sub002 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/sub002/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415 Number of reverse mapping hits = 3521 Checking for and removing duplicates Writing label file ./rh.V2.label 11537 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.label --trgsubject sub002 --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 = sub002 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/sub002/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415 Number of reverse mapping hits = 918 Checking for and removing duplicates Writing label file ./rh.MT.label 2850 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.perirhinal.label --trgsubject sub002 --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 = sub002 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/sub002/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415 Number of reverse mapping hits = 96 Checking for and removing duplicates Writing label file ./rh.perirhinal.label 848 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.thresh.label --trgsubject sub002 --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 = sub002 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/sub002/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415 Number of reverse mapping hits = 109 Checking for and removing duplicates Writing label file ./rh.BA1.thresh.label 985 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.thresh.label --trgsubject sub002 --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 = sub002 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/sub002/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415 Number of reverse mapping hits = 236 Checking for and removing duplicates Writing label file ./rh.BA2.thresh.label 2924 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.thresh.label --trgsubject sub002 --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 = sub002 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/sub002/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415 Number of reverse mapping hits = 62 Checking for and removing duplicates Writing label file ./rh.BA3a.thresh.label 1760 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.thresh.label --trgsubject sub002 --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 = sub002 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/sub002/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415 Number of reverse mapping hits = 324 Checking for and removing duplicates Writing label file ./rh.BA3b.thresh.label 2507 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.thresh.label --trgsubject sub002 --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 = sub002 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/sub002/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415 Number of reverse mapping hits = 213 Checking for and removing duplicates Writing label file ./rh.BA4a.thresh.label 1601 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.thresh.label --trgsubject sub002 --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 = sub002 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/sub002/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415 Number of reverse mapping hits = 164 Checking for and removing duplicates Writing label file ./rh.BA4p.thresh.label 1653 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.thresh.label --trgsubject sub002 --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 = sub002 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/sub002/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415 Number of reverse mapping hits = 1082 Checking for and removing duplicates Writing label file ./rh.BA6.thresh.label 8041 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.thresh.label --trgsubject sub002 --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 = sub002 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/sub002/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415 Number of reverse mapping hits = 416 Checking for and removing duplicates Writing label file ./rh.BA44.thresh.label 1428 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.thresh.label --trgsubject sub002 --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 = sub002 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/sub002/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415 Number of reverse mapping hits = 403 Checking for and removing duplicates Writing label file ./rh.BA45.thresh.label 1581 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.thresh.label --trgsubject sub002 --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 = sub002 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/sub002/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415 Number of reverse mapping hits = 1195 Checking for and removing duplicates Writing label file ./rh.V1.thresh.label 4427 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.thresh.label --trgsubject sub002 --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 = sub002 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/sub002/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415 Number of reverse mapping hits = 1542 Checking for and removing duplicates Writing label file ./rh.V2.thresh.label 4979 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.thresh.label --trgsubject sub002 --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 = sub002 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/sub002/surf/rh.white Reading target registration /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 161415 Number of reverse mapping hits = 131 Checking for and removing duplicates Writing label file ./rh.MT.thresh.label 399 mri_label2label: Done mris_label2annot --s sub002 --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/sub002/label cmdline mris_label2annot --s sub002 --hemi rh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --l rh.perirhinal.label --a BA --maxstatwinner --noverbose sysname Linux hostname snake5 machine x86_64 user fkaule subject sub002 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/sub002/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 112972 unhit vertices Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/label/rh.BA.annot mris_label2annot --s sub002 --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/sub002/label cmdline mris_label2annot --s sub002 --hemi rh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l rh.BA1.thresh.label --l rh.BA2.thresh.label --l rh.BA3a.thresh.label --l rh.BA3b.thresh.label --l rh.BA4a.thresh.label --l rh.BA4p.thresh.label --l rh.BA6.thresh.label --l rh.BA44.thresh.label --l rh.BA45.thresh.label --l rh.V1.thresh.label --l rh.V2.thresh.label --l rh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose sysname Linux hostname snake5 machine x86_64 user fkaule subject sub002 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/sub002/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 135499 unhit vertices Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/label/rh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab sub002 rh white computing statistics for each annotation in ./rh.BA.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 1079 641 2252 2.517 0.465 0.148 0.092 62 5.5 BA1 3722 2448 6016 2.276 0.433 0.125 0.034 41 5.4 BA2 1102 729 1080 1.878 0.405 0.133 0.041 10 1.8 BA3a 2526 1644 3649 1.894 0.506 0.129 0.038 29 4.3 BA3b 1922 1062 3806 2.878 0.532 0.111 0.050 36 4.4 BA4a 1368 880 2247 2.599 0.497 0.107 0.032 9 1.8 BA4p 9658 6509 21158 2.713 0.627 0.141 0.065 201 24.7 BA6 4658 3149 9257 2.655 0.429 0.117 0.036 51 6.9 BA44 5741 3937 11576 2.448 0.533 0.148 0.047 95 11.2 BA45 4265 2875 5905 1.927 0.476 0.160 0.099 85 11.9 V1 8997 5858 13897 2.199 0.514 0.163 0.061 235 22.9 V2 2730 1821 4560 2.454 0.429 0.130 0.040 32 4.4 MT 675 440 1860 3.033 0.850 0.152 0.085 10 2.2 perirhinal mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab sub002 rh white computing statistics for each annotation in ./rh.BA.thresh.annot. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 704 411 1539 2.579 0.430 0.151 0.111 53 4.6 BA1 2069 1366 3451 2.262 0.463 0.122 0.034 25 3.0 BA2 950 640 868 1.845 0.362 0.133 0.038 7 1.5 BA3a 2040 1360 2678 1.757 0.435 0.117 0.032 17 2.7 BA3b 1137 631 2465 2.890 0.494 0.118 0.060 15 3.1 BA4a 1124 719 1977 2.736 0.515 0.103 0.033 7 1.7 BA4p 6082 4067 13144 2.669 0.665 0.141 0.066 121 16.5 BA6 1311 919 2984 2.745 0.389 0.125 0.041 17 2.1 BA44 1445 1001 3201 2.524 0.606 0.149 0.048 23 3.0 BA45 4045 2720 5592 1.951 0.474 0.158 0.102 80 11.4 V1 4633 3094 6701 2.071 0.493 0.176 0.071 164 13.8 V2 376 249 736 2.351 0.346 0.126 0.040 4 0.6 MT /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label lh Fri Aug 9 01:15:48 CEST 2013 mris_spherical_average -erode 1 -orig white -t 0.4 -o sub002 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject sub002. processing subject lh.EC_average... reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 1098 points to lh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label sub002 lh white limiting computations to label ./lh.entorhinal_exvivo.label. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 376 235 1293 3.372 0.598 0.150 0.082 9 1.2 ./lh.entorhinal_exvivo.label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label rh Fri Aug 9 01:16:04 CEST 2013 mris_spherical_average -erode 1 -orig white -t 0.4 -o sub002 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label painting output onto subject sub002. processing subject rh.EC_average... reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 809 points to rh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label sub002 rh white limiting computations to label ./rh.entorhinal_exvivo.label. reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/wm.mgz... reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.white... reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.pial... reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/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 322 195 1036 3.334 0.808 0.183 0.099 8 1.7 ./rh.entorhinal_exvivo.label #------------------------------------------ Started at Thu Aug 8 10:53:55 CEST 2013 Ended at Fri Aug 9 01:16:21 CEST 2013 #@#%# recon-all-run-time-hours 14.374 recon-all -s sub002 finished without error at Fri Aug 9 01:16:21 CEST 2013