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- Thu Aug 8 10:54:16 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010
- /opt/freesurfer/5.3.0/bin/recon-all
- -i /home/data/exppsy/forrest_gump/openfmri.org/sub010/anatomy/highres001.nii.gz -cw256 -all -T2 /home/data/exppsy/forrest_gump/openfmri.org/sub010/anatomy/other/t2w001.nii.gz -T2pial -subjid sub010 -sd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- subjid sub010
- 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 snake4 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 96606936 2594756 0 188544 94065044
- -/+ buffers/cache: 2353348 96848344
- Swap: 25165780 532 25165248
- ########################################
- program versions used
- $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
- $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
- mri_convert -all-info
- ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- FLIRT version 5.5
- $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
- mri_convert --version
- stable5
- ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- Program nu_correct, built from:
- Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
- ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ======= NUMBER OF OPENMP THREADS = 1 =======
- ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $
- ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $
- ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:21-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: snake4 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/sub010
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub010/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/orig/001.mgz
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub010/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/anatomy/highres001.nii.gz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.996481, 0.0682576, -0.0486557)
- j_ras = (0.0655887, 0.996358, 0.0544886)
- k_ras = (-0.0521977, -0.0511056, 0.997328)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/orig/001.mgz...
- #--------------------------------------------
- #@# T2/FLAIR Input Thu Aug 8 10:54:34 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub010/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/orig/T2raw.mgz
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub010/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/anatomy/other/t2w001.nii.gz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.996481, 0.0682576, -0.0486557)
- j_ras = (0.0655887, 0.996358, 0.0544886)
- k_ras = (-0.0521977, -0.0511056, 0.997328)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/orig/T2raw.mgz...
- #--------------------------------------------
- #@# MotionCor Thu Aug 8 10:54:48 CEST 2013
- Found 1 runs
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/mri/orig/001.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/rawavg.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/orig.mgz --conform --cw256
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/mri/rawavg.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.996481, 0.0682576, -0.0486557)
- j_ras = (0.0655887, 0.996358, 0.0544886)
- k_ras = (-0.0521977, -0.0511056, 0.997328)
- Original Data has (0.699944, 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/sub010/mri/orig.mgz...
- mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/talairach.xfm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/orig.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Talairach Thu Aug 8 10:55:26 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri
- mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
- talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
- cp transforms/talairach.auto.xfm transforms/talairach.xfm
- #--------------------------------------------
- #@# Talairach Failure Detection Thu Aug 8 10:57:50 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri
- talairach_afd -T 0.005 -xfm transforms/talairach.xfm
- talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6271, pval=0.3663 >= threshold=0.0050)
- awk -f /opt/freesurfer/5.3.0/bin/extract_talairach_avi_QA.awk /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/talairach_avi.log
- tal_QC_AZS /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/talairach_avi.log
- TalAviQA: 0.96447
- z-score: -3
- #--------------------------------------------
- #@# Nu Intensity Correction Thu Aug 8 10:57:50 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/sub010/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 snake4 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
- Thu Aug 8 10:57:50 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.19840
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.19840/nu0.mnc -odt float
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.19840/nu0.mnc -odt float
- $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
- reading from orig.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, -1.07102e-08, 7.45058e-09)
- j_ras = (7.45058e-09, -3.72529e-09, -1)
- k_ras = (-4.42378e-09, 1, 7.45058e-09)
- changing data type from uchar to float (noscale = 0)...
- writing to ./tmp.mri_nu_correct.mni.19840/nu0.mnc...
-
- --------------------------------------------------------
- Iteration 1 Thu Aug 8 10:57:54 CEST 2013
- nu_correct -clobber ./tmp.mri_nu_correct.mni.19840/nu0.mnc ./tmp.mri_nu_correct.mni.19840/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.19840/0/
- [fkaule@snake4:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/] [2013-08-08 10:57:54] 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.19840/0/ ./tmp.mri_nu_correct.mni.19840/nu0.mnc ./tmp.mri_nu_correct.mni.19840/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
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Number of iterations: 27
- CV of field change: 0.000990656
- [fkaule@snake4:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/] [2013-08-08 10:58:24] running:
- /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.19840/nu0.mnc ./tmp.mri_nu_correct.mni.19840/0//template.mnc
- Transforming slices:......................................................................................Done
- Transforming slices:................................................................................................................................................................................................................................................................Done
-
-
- --------------------------------------------------------
- Iteration 2 Thu Aug 8 10:58:31 CEST 2013
- nu_correct -clobber ./tmp.mri_nu_correct.mni.19840/nu1.mnc ./tmp.mri_nu_correct.mni.19840/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.19840/1/
- [fkaule@snake4:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/] [2013-08-08 10:58:32] 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.19840/1/ ./tmp.mri_nu_correct.mni.19840/nu1.mnc ./tmp.mri_nu_correct.mni.19840/nu2.imp
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Number of iterations: 25
- CV of field change: 0.000996627
- [fkaule@snake4:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/] [2013-08-08 10:59:00] running:
- /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.19840/nu1.mnc ./tmp.mri_nu_correct.mni.19840/1//template.mnc
- Transforming slices:......................................................................................Done
- Transforming slices:................................................................................................................................................................................................................................................................Done
-
-
-
- mri_binarize --i ./tmp.mri_nu_correct.mni.19840/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.19840/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/sub010/mri
- cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.19840/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.19840/ones.mgz
- sysname Linux
- hostname snake4
- machine x86_64
- user fkaule
- input ./tmp.mri_nu_correct.mni.19840/nu2.mnc
- frame 0
- nErode3d 0
- nErode2d 0
- output ./tmp.mri_nu_correct.mni.19840/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.19840/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.19840/sum.junk --avgwf ./tmp.mri_nu_correct.mni.19840/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.19840/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.19840/sum.junk --avgwf ./tmp.mri_nu_correct.mni.19840/input.mean.dat
- sysname Linux
- hostname snake4
- machine x86_64
- user fkaule
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.19840/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.19840/input.mean.dat
- mri_segstats done
- mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.19840/ones.mgz --i ./tmp.mri_nu_correct.mni.19840/nu2.mnc --sum ./tmp.mri_nu_correct.mni.19840/sum.junk --avgwf ./tmp.mri_nu_correct.mni.19840/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.19840/ones.mgz --i ./tmp.mri_nu_correct.mni.19840/nu2.mnc --sum ./tmp.mri_nu_correct.mni.19840/sum.junk --avgwf ./tmp.mri_nu_correct.mni.19840/output.mean.dat
- sysname Linux
- hostname snake4
- machine x86_64
- user fkaule
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.19840/ones.mgz
- Loading ./tmp.mri_nu_correct.mni.19840/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.19840/output.mean.dat
- mri_segstats done
- mris_calc -o ./tmp.mri_nu_correct.mni.19840/nu2.mnc ./tmp.mri_nu_correct.mni.19840/nu2.mnc mul .97908922083269502129
- Saving result to './tmp.mri_nu_correct.mni.19840/nu2.mnc' (type = MINC ) [ ok ]
- mri_convert ./tmp.mri_nu_correct.mni.19840/nu2.mnc nu.mgz --like orig.mgz
- mri_convert ./tmp.mri_nu_correct.mni.19840/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.19840/nu2.mnc...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, -1.07102e-08, 7.45058e-09)
- j_ras = (7.45058e-09, -3.72529e-09, -1)
- k_ras = (-4.42378e-09, 1, 7.45058e-09)
- INFO: transform src into the like-volume: orig.mgz
- writing to nu.mgz...
- mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz
- type change took 0 minutes and 7 seconds.
- mapping (10, 205) to ( 3, 110)
-
-
- Thu Aug 8 10:59:46 CEST 2013
- mri_nu_correct.mni done
- mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/talairach.xfm nu.mgz nu.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Intensity Normalization Thu Aug 8 10:59:47 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri
- mri_normalize -g 1 nu.mgz T1.mgz
- using max gradient = 1.000
- reading from nu.mgz...
- normalizing image...
- talairach transform
- 1.292 -0.073 -0.004 4.202;
- 0.035 1.128 0.349 -34.304;
- -0.035 -0.435 1.307 -8.091;
- 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 = 14
- Starting OpenSpline(): npoints = 14
- 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 46 (46), valley at 31 (31)
- csf peak at 23, setting threshold to 38
- 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 48 (48), valley at 37 (37)
- csf peak at 24, setting threshold to 40
- 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 11:02:38 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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=6.0
- skull bounding box = (61, 27, 27) --> (195, 255, 198)
- using (106, 103, 113) as brain centroid...
- mean wm in atlas = 126, using box (90,75,92) --> (122, 131,134) to find MRI wm
- before smoothing, mri peak at 110
- after smoothing, mri peak at 110, scaling input intensities by 1.145
- scaling channel 0 by 1.14545
- initial log_p = -4.9
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -4.763399 @ (-9.091, 9.091, -9.091)
- max log p = -4.729606 @ (13.636, 4.545, 4.545)
- max log p = -4.648008 @ (-6.818, -2.273, -2.273)
- max log p = -4.645391 @ (1.136, -3.409, -3.409)
- max log p = -4.636181 @ (1.705, 6.250, -1.705)
- max log p = -4.636181 @ (0.000, 0.000, 0.000)
- Found translation: (0.6, 14.2, -11.9): log p = -4.636
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.6 (thresh=-4.6)
- 1.236 0.000 0.000 -36.509;
- 0.000 1.194 0.320 -36.794;
- 0.000 -0.320 1.194 -0.626;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1)
- 1.422 0.000 0.000 -60.849;
- 0.000 1.194 0.320 -36.794;
- 0.000 -0.320 1.194 -0.626;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.2500
- ****************************************
- Nine parameter search. iteration 2 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.1 (thresh=-4.1)
- 1.365 0.009 0.086 -62.443;
- -0.050 1.249 0.379 -40.777;
- -0.093 -0.342 1.137 22.251;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 3 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.365 0.009 0.086 -62.443;
- -0.050 1.249 0.379 -40.777;
- -0.096 -0.355 1.180 19.109;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 4 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.365 0.009 0.086 -62.443;
- -0.050 1.249 0.379 -40.777;
- -0.096 -0.355 1.180 19.109;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.0625
- ****************************************
- Nine parameter search. iteration 5 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.363 -0.004 0.093 -61.614;
- -0.038 1.255 0.371 -42.913;
- -0.107 -0.344 1.182 19.272;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 6 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.363 -0.004 0.093 -61.614;
- -0.038 1.258 0.372 -43.297;
- -0.107 -0.344 1.182 19.272;
- 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
- 1.36278 -0.00438 0.09280 -61.61366;
- -0.03776 1.25826 0.37192 -43.29714;
- -0.10746 -0.34419 1.18204 19.27242;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 3481
- Quasinewton: input matrix
- 1.36278 -0.00438 0.09280 -61.61366;
- -0.03776 1.25826 0.37192 -43.29714;
- -0.10746 -0.34419 1.18204 19.27242;
- 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:
- 1.363 -0.004 0.093 -61.614;
- -0.038 1.258 0.372 -43.297;
- -0.107 -0.344 1.182 19.272;
- 0.000 0.000 0.000 1.000;
- pass 1, spacing 8: log(p) = -4.0 (old=-4.9)
- transform before final EM align:
- 1.363 -0.004 0.093 -61.614;
- -0.038 1.258 0.372 -43.297;
- -0.107 -0.344 1.182 19.272;
- 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
- 1.36278 -0.00438 0.09280 -61.61366;
- -0.03776 1.25826 0.37192 -43.29714;
- -0.10746 -0.34419 1.18204 19.27242;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 382743
- Quasinewton: input matrix
- 1.36278 -0.00438 0.09280 -61.61366;
- -0.03776 1.25826 0.37192 -43.29714;
- -0.10746 -0.34419 1.18204 19.27242;
- 0.00000 0.00000 0.00000 1.00000;
- dfp_em_step_func: 010: -log(p) = 4.4
- after pass:transform: ( 1.36, -0.00, 0.09, -61.61)
- ( -0.04, 1.26, 0.37, -43.30)
- ( -0.11, -0.34, 1.18, 19.27)
- dfp_em_step_func: 011: -log(p) = 4.4
- after pass:transform: ( 1.36, -0.00, 0.09, -61.61)
- ( -0.04, 1.26, 0.37, -43.30)
- ( -0.11, -0.34, 1.18, 19.27)
- dfp_em_step_func: 012: -log(p) = 4.4
- after pass:transform: ( 1.36, -0.00, 0.09, -61.61)
- ( -0.04, 1.26, 0.37, -43.30)
- ( -0.11, -0.34, 1.18, 19.27)
- dfp_em_step_func: 013: -log(p) = 4.4
- after pass:transform: ( 1.36, -0.00, 0.09, -61.61)
- ( -0.04, 1.26, 0.37, -43.30)
- ( -0.11, -0.34, 1.18, 19.27)
- dfp_em_step_func: 014: -log(p) = 4.4
- after pass:transform: ( 1.36, -0.00, 0.09, -61.61)
- ( -0.04, 1.26, 0.37, -43.30)
- ( -0.11, -0.34, 1.18, 19.27)
- 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: 016: -log(p) = 4.4 tol 0.000000
- final transform:
- 1.363 -0.004 0.093 -61.614;
- -0.038 1.258 0.372 -43.297;
- -0.107 -0.344 1.182 19.272;
- 0.000 0.000 0.000 1.000;
- writing output transformation to transforms/talairach_with_skull.lta...
- registration took 34 minutes and 43 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=131 y=91 z=115 r=86
- first estimation of the main basin volume: 2755782 voxels
- Looking for seedpoints
- 2 found in the cerebellum
- 11 found in the rest of the brain
- global maximum in x=148, y=88, z=86, 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=14613975146 voxels, voxel volume =1.000
- = 14613975146 mmm3 = 14613975.040 cm3
- done.
- PostAnalyze...Basin Prior
- 56 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=128,y=101, z=112, r=9755 iterations
- ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^
- GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=9 , nb = 46017
- RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=26 , nb = -1034370054
- LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=19 , nb = 1090663681
- RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=9 , nb = -1074963069
- LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=9 , nb = 1077707658
- OTHER CSF_MIN=0, CSF_intensity=6, CSF_MAX=22 , nb = 1071528312
-
- CSF_MAX TRANSITION GM_MIN GM
- GLOBAL
- before analyzing : 9, 12, 22, 41
- after analyzing : 9, 20, 25, 25
- RIGHT_CER
- before analyzing : 26, 22, 15, 60
- after analyzing : 22, 24, 25, 33
- LEFT_CER
- before analyzing : 19, 17, 15, 61
- after analyzing : 17, 22, 25, 31
- RIGHT_BRAIN
- before analyzing : 9, 12, 22, 41
- after analyzing : 9, 20, 25, 25
- LEFT_BRAIN
- before analyzing : 9, 11, 21, 45
- after analyzing : 9, 20, 25, 26
- OTHER
- before analyzing : 22, 51, 79, 94
- after analyzing : 22, 69, 79, 75
- mri_strip_skull: done peeling brain
- highly tesselated surface with 10242 vertices
- matching...70 iterations
- *********************VALIDATION*********************
- curvature mean = -0.014, std = 0.013
- curvature mean = 65.272, std = 8.437
- No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
- before rotation: sse = 1.57, sigma = 2.44
- after rotation: sse = 1.57, sigma = 2.44
- Localization of inacurate regions: Erosion-Dilation steps
- the sse mean is 1.60, its var is 2.07
- before Erosion-Dilatation 0.00% 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...39 iterations
- mri_strip_skull: done peeling brain
- Brain Size = 1394742 voxels, voxel volume = 1.000 mm3
- = 1394742 mmm3 = 1394.742 cm3
- ******************************
- Saving brainmask.auto.mgz
- done
- cp brainmask.auto.mgz brainmask.mgz
- #-------------------------------------
- #@# EM Registration Thu Aug 8 11:37:48 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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=23.1
- skull bounding box = (70, 43, 42) --> (186, 171, 200)
- using (109, 86, 121) as brain centroid...
- mean wm in atlas = 107, using box (95,70,102) --> (123, 101,140) 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 = -4.5
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -4.234900 @ (-9.091, 9.091, -9.091)
- max log p = -4.113619 @ (4.545, 4.545, -4.545)
- max log p = -4.087676 @ (2.273, -2.273, -2.273)
- max log p = -4.074259 @ (-1.136, 1.136, 1.136)
- max log p = -4.065760 @ (1.705, 0.568, -0.568)
- max log p = -4.065760 @ (0.000, 0.000, 0.000)
- Found translation: (-1.7, 13.1, -15.3): log p = -4.066
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.6, old_max_log_p =-4.1 (thresh=-4.1)
- 1.150 0.000 0.000 -20.982;
- 0.000 1.194 0.278 -33.543;
- 0.000 -0.320 1.038 21.380;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.6, old_max_log_p =-3.6 (thresh=-3.6)
- 1.150 0.000 0.000 -20.982;
- 0.000 1.194 0.278 -33.543;
- 0.000 -0.320 1.038 21.380;
- 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=-3.4, old_max_log_p =-3.6 (thresh=-3.6)
- 1.190 -0.019 0.071 -34.107;
- 0.003 1.217 0.284 -37.056;
- -0.072 -0.307 0.997 30.254;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 3 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4)
- 1.168 -0.018 0.070 -31.090;
- 0.003 1.217 0.284 -37.056;
- -0.072 -0.307 0.997 30.254;
- 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=-3.3, old_max_log_p =-3.4 (thresh=-3.4)
- 1.170 0.004 0.066 -33.669;
- -0.015 1.223 0.267 -32.903;
- -0.063 -0.289 1.006 27.154;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 5 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3)
- 1.167 0.004 0.066 -33.293;
- -0.015 1.224 0.267 -33.081;
- -0.063 -0.289 1.006 27.154;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 6 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3)
- 1.167 0.004 0.066 -33.293;
- -0.015 1.226 0.267 -33.259;
- -0.063 -0.289 1.006 27.623;
- 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
- 1.16713 0.00415 0.06623 -33.29273;
- -0.01545 1.22590 0.26728 -33.25930;
- -0.06331 -0.28872 1.00580 27.62313;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 2772
- Quasinewton: input matrix
- 1.16713 0.00415 0.06623 -33.29273;
- -0.01545 1.22590 0.26728 -33.25930;
- -0.06331 -0.28872 1.00580 27.62313;
- 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:
- 1.167 0.004 0.066 -33.293;
- -0.015 1.226 0.267 -33.259;
- -0.063 -0.289 1.006 27.623;
- 0.000 0.000 0.000 1.000;
- pass 1, spacing 8: log(p) = -3.3 (old=-4.5)
- transform before final EM align:
- 1.167 0.004 0.066 -33.293;
- -0.015 1.226 0.267 -33.259;
- -0.063 -0.289 1.006 27.623;
- 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
- 1.16713 0.00415 0.06623 -33.29273;
- -0.01545 1.22590 0.26728 -33.25930;
- -0.06331 -0.28872 1.00580 27.62313;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 312841
- Quasinewton: input matrix
- 1.16713 0.00415 0.06623 -33.29273;
- -0.01545 1.22590 0.26728 -33.25930;
- -0.06331 -0.28872 1.00580 27.62313;
- 0.00000 0.00000 0.00000 1.00000;
- dfp_em_step_func: 010: -log(p) = 3.9
- after pass:transform: ( 1.17, 0.00, 0.07, -33.29)
- ( -0.02, 1.23, 0.27, -33.26)
- ( -0.06, -0.29, 1.01, 27.62)
- dfp_em_step_func: 011: -log(p) = 3.9
- after pass:transform: ( 1.17, 0.00, 0.07, -33.29)
- ( -0.02, 1.23, 0.27, -33.26)
- ( -0.06, -0.29, 1.01, 27.62)
- dfp_em_step_func: 012: -log(p) = 3.8
- after pass:transform: ( 1.17, 0.00, 0.07, -33.29)
- ( -0.02, 1.23, 0.27, -33.26)
- ( -0.06, -0.29, 1.01, 27.62)
- dfp_em_step_func: 013: -log(p) = 3.8
- after pass:transform: ( 1.17, 0.00, 0.07, -33.29)
- ( -0.02, 1.23, 0.27, -33.26)
- ( -0.06, -0.29, 1.01, 27.62)
- dfp_em_step_func: 014: -log(p) = 3.8
- after pass:transform: ( 1.17, 0.00, 0.07, -33.29)
- ( -0.02, 1.23, 0.27, -33.26)
- ( -0.06, -0.29, 1.01, 27.62)
- dfp_em_step_func: 015: -log(p) = 3.8
- after pass:transform: ( 1.17, 0.00, 0.07, -33.29)
- ( -0.02, 1.23, 0.27, -33.26)
- ( -0.06, -0.29, 1.01, 27.62)
- dfp_em_step_func: 016: -log(p) = 3.8
- after pass:transform: ( 1.17, 0.00, 0.07, -33.29)
- ( -0.02, 1.23, 0.27, -33.26)
- ( -0.06, -0.29, 1.01, 27.62)
- dfp_em_step_func: 017: -log(p) = 3.8
- after pass:transform: ( 1.17, 0.00, 0.07, -33.29)
- ( -0.02, 1.23, 0.27, -33.26)
- ( -0.06, -0.29, 1.01, 27.62)
- dfp_em_step_func: 018: -log(p) = 3.8
- after pass:transform: ( 1.17, 0.00, 0.07, -33.29)
- ( -0.02, 1.23, 0.27, -33.26)
- ( -0.06, -0.29, 1.01, 27.62)
- dfp_em_step_func: 019: -log(p) = 3.8
- after pass:transform: ( 1.17, 0.01, 0.07, -33.29)
- ( -0.01, 1.23, 0.27, -33.26)
- ( -0.06, -0.28, 1.01, 27.62)
- dfp_em_step_func: 020: -log(p) = 3.8
- after pass:transform: ( 1.17, 0.01, 0.07, -33.29)
- ( -0.01, 1.23, 0.28, -33.26)
- ( -0.06, -0.28, 1.01, 27.62)
- 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: 021: -log(p) = 3.8
- after pass:transform: ( 1.17, 0.01, 0.07, -33.29)
- ( -0.01, 1.23, 0.28, -33.26)
- ( -0.06, -0.28, 1.01, 27.62)
- dfp_em_step_func: 022: -log(p) = 3.8
- after pass:transform: ( 1.17, 0.01, 0.07, -33.29)
- ( -0.01, 1.23, 0.28, -33.26)
- ( -0.06, -0.28, 1.01, 27.62)
- dfp_em_step_func: 023: -log(p) = 3.8
- after pass:transform: ( 1.17, 0.01, 0.07, -33.29)
- ( -0.01, 1.23, 0.28, -33.26)
- ( -0.06, -0.28, 1.01, 27.62)
- dfp_em_step_func: 024: -log(p) = 3.8
- after pass:transform: ( 1.17, 0.01, 0.07, -33.29)
- ( -0.01, 1.23, 0.28, -33.26)
- ( -0.06, -0.28, 1.01, 27.62)
- 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: 026: -log(p) = 3.8 tol 0.000000
- final transform:
- 1.173 0.007 0.070 -33.293;
- -0.008 1.233 0.277 -33.259;
- -0.059 -0.284 1.012 27.623;
- 0.000 0.000 0.000 1.000;
- writing output transformation to transforms/talairach.lta...
- registration took 26 minutes and 56 seconds.
- #--------------------------------------
- #@# CA Normalize Thu Aug 8 12:04:43 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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=24.1
- skull bounding box = (70, 43, 42) --> (185, 171, 200)
- using (108, 86, 121) as brain centroid...
- mean wm in atlas = 107, using box (94,70,102) --> (122, 101,140) to find MRI wm
- before smoothing, mri peak at 110
- 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
- 1.173 0.007 0.070 -33.293;
- -0.008 1.233 0.277 -33.259;
- -0.059 -0.284 1.012 27.623;
- 0.000 0.000 0.000 1.000;
- INFO: transform used
- finding control points in Left_Cerebral_White_Matter....
- found 41584 control points for structure...
- bounding box (127, 46, 41) --> (185, 139, 197)
- Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 130.0
- 0 of 56 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 40735 control points for structure...
- bounding box (73, 47, 38) --> (129, 135, 197)
- Right_Cerebral_White_Matter: limiting intensities to 99.0 --> 130.0
- 0 of 26 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3012 control points for structure...
- bounding box (131, 117, 69) --> (172, 153, 119)
- Left_Cerebellum_White_Matter: limiting intensities to 103.0 --> 130.0
- 7 of 8 (87.5%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2764 control points for structure...
- bounding box (90, 117, 64) --> (130, 152, 118)
- Right_Cerebellum_White_Matter: limiting intensities to 84.0 --> 130.0
- 0 of 10 (0.0%) samples deleted
- finding control points in Brain_Stem....
- found 3520 control points for structure...
- bounding box (114, 108, 100) --> (142, 163, 128)
- Brain_Stem: limiting intensities to 80.0 --> 130.0
- 1 of 8 (12.5%) samples deleted
- using 108 total control points for intensity normalization...
- bias field = 1.015 +- 0.055
- 0 of 100 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 41584 control points for structure...
- bounding box (127, 46, 41) --> (185, 139, 197)
- Left_Cerebral_White_Matter: limiting intensities to 99.0 --> 131.0
- 0 of 92 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 40735 control points for structure...
- bounding box (73, 47, 38) --> (129, 135, 197)
- Right_Cerebral_White_Matter: limiting intensities to 116.0 --> 131.0
- 69 of 89 (77.5%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3012 control points for structure...
- bounding box (131, 117, 69) --> (172, 153, 119)
- Left_Cerebellum_White_Matter: limiting intensities to 80.0 --> 131.0
- 0 of 39 (0.0%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2764 control points for structure...
- bounding box (90, 117, 64) --> (130, 152, 118)
- Right_Cerebellum_White_Matter: limiting intensities to 91.0 --> 131.0
- 9 of 48 (18.8%) samples deleted
- finding control points in Brain_Stem....
- found 3520 control points for structure...
- bounding box (114, 108, 100) --> (142, 163, 128)
- Brain_Stem: limiting intensities to 71.0 --> 131.0
- 0 of 68 (0.0%) samples deleted
- using 336 total control points for intensity normalization...
- bias field = 0.986 +- 0.066
- 0 of 258 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 41584 control points for structure...
- bounding box (127, 46, 41) --> (185, 139, 197)
- Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 132.0
- 0 of 193 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 40735 control points for structure...
- bounding box (73, 47, 38) --> (129, 135, 197)
- Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0
- 0 of 175 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3012 control points for structure...
- bounding box (131, 117, 69) --> (172, 153, 119)
- Left_Cerebellum_White_Matter: limiting intensities to 75.0 --> 132.0
- 0 of 63 (0.0%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2764 control points for structure...
- bounding box (90, 117, 64) --> (130, 152, 118)
- Right_Cerebellum_White_Matter: limiting intensities to 74.0 --> 132.0
- 0 of 51 (0.0%) samples deleted
- finding control points in Brain_Stem....
- found 3520 control points for structure...
- bounding box (114, 108, 100) --> (142, 163, 128)
- Brain_Stem: limiting intensities to 67.0 --> 132.0
- 0 of 107 (0.0%) samples deleted
- using 589 total control points for intensity normalization...
- bias field = 1.027 +- 0.051
- 1 of 589 control points discarded
- writing normalized volume to norm.mgz...
- writing control points to ctrl_pts.mgz
- freeing GCA...done.
- normalization took 2 minutes and 1 seconds.
- #--------------------------------------
- #@# CA Reg Thu Aug 8 12:06:45 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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) = 1.56 (predicted orig area = 5.1)
- 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=0.879, neg=0, invalid=96777
- 0001: dt=129.472000, rms=0.813 (7.489%), neg=0, invalid=96777
- 0002: dt=221.952000, rms=0.786 (3.298%), neg=0, invalid=96777
- 0003: dt=55.488000, rms=0.782 (0.533%), neg=0, invalid=96777
- 0004: dt=221.952000, rms=0.777 (0.592%), neg=0, invalid=96777
- 0005: dt=129.472000, rms=0.769 (1.125%), neg=0, invalid=96777
- 0006: dt=32.368000, rms=0.768 (0.087%), neg=0, invalid=96777
- 0007: dt=32.368000, rms=0.767 (0.068%), neg=0, invalid=96777
- 0008: dt=32.368000, rms=0.766 (0.119%), neg=0, invalid=96777
- 0009: dt=32.368000, rms=0.765 (0.196%), neg=0, invalid=96777
- 0010: dt=32.368000, rms=0.762 (0.318%), neg=0, invalid=96777
- 0011: dt=32.368000, rms=0.759 (0.410%), neg=0, invalid=96777
- 0012: dt=32.368000, rms=0.756 (0.427%), neg=0, invalid=96777
- 0013: dt=32.368000, rms=0.753 (0.393%), neg=0, invalid=96777
- 0014: dt=32.368000, rms=0.751 (0.341%), neg=0, invalid=96777
- 0015: dt=32.368000, rms=0.748 (0.303%), neg=0, invalid=96777
- 0016: dt=32.368000, rms=0.746 (0.265%), neg=0, invalid=96777
- 0017: dt=32.368000, rms=0.744 (0.246%), neg=0, invalid=96777
- 0018: dt=32.368000, rms=0.743 (0.243%), neg=0, invalid=96777
- 0019: dt=32.368000, rms=0.741 (0.268%), neg=0, invalid=96777
- 0020: dt=32.368000, rms=0.739 (0.286%), neg=0, invalid=96777
- 0021: dt=32.368000, rms=0.737 (0.270%), neg=0, invalid=96777
- 0022: dt=32.368000, rms=0.735 (0.248%), neg=0, invalid=96777
- 0023: dt=32.368000, rms=0.733 (0.216%), neg=0, invalid=96777
- 0024: dt=32.368000, rms=0.732 (0.188%), neg=0, invalid=96777
- 0025: dt=32.368000, rms=0.731 (0.158%), neg=0, invalid=96777
- 0026: dt=32.368000, rms=0.729 (0.157%), neg=0, invalid=96777
- 0027: dt=32.368000, rms=0.728 (0.178%), neg=0, invalid=96777
- 0028: dt=32.368000, rms=0.727 (0.192%), neg=0, invalid=96777
- 0029: dt=32.368000, rms=0.725 (0.193%), neg=0, invalid=96777
- 0030: dt=32.368000, rms=0.724 (0.179%), neg=0, invalid=96777
- 0031: dt=32.368000, rms=0.723 (0.154%), neg=0, invalid=96777
- 0032: dt=32.368000, rms=0.722 (0.133%), neg=0, invalid=96777
- 0033: dt=32.368000, rms=0.721 (0.124%), neg=0, invalid=96777
- 0034: dt=32.368000, rms=0.720 (0.123%), neg=0, invalid=96777
- 0035: dt=517.888000, rms=0.718 (0.302%), neg=0, invalid=96777
- 0036: dt=27.744000, rms=0.718 (0.018%), neg=0, invalid=96777
- 0037: dt=27.744000, rms=0.718 (0.002%), neg=0, invalid=96777
- 0038: dt=27.744000, rms=0.718 (-0.022%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.718, neg=0, invalid=96777
- 0039: dt=32.368000, rms=0.718 (0.025%), neg=0, invalid=96777
- 0040: dt=92.480000, rms=0.717 (0.044%), neg=0, invalid=96777
- 0041: dt=369.920000, rms=0.716 (0.188%), neg=0, invalid=96777
- 0042: dt=32.368000, rms=0.716 (0.017%), neg=0, invalid=96777
- 0043: dt=32.368000, rms=0.716 (0.014%), neg=0, invalid=96777
- 0044: dt=32.368000, rms=0.716 (0.021%), neg=0, invalid=96777
- 0045: dt=32.368000, rms=0.715 (0.028%), neg=0, invalid=96777
- 0046: dt=32.368000, rms=0.715 (0.045%), neg=0, invalid=96777
- 0047: dt=32.368000, rms=0.715 (0.059%), neg=0, invalid=96777
- 0048: dt=32.368000, rms=0.714 (0.075%), neg=0, invalid=96777
- 0049: dt=32.368000, rms=0.714 (0.073%), neg=0, invalid=96777
- 0050: dt=32.368000, rms=0.713 (0.064%), neg=0, invalid=96777
- setting smoothness coefficient to 0.154
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.718, neg=0, invalid=96777
- 0051: dt=145.152000, rms=0.694 (3.277%), neg=0, invalid=96777
- 0052: dt=124.416000, rms=0.680 (1.961%), neg=0, invalid=96777
- 0053: dt=36.288000, rms=0.675 (0.805%), neg=0, invalid=96777
- 0054: dt=103.680000, rms=0.671 (0.539%), neg=0, invalid=96777
- 0055: dt=31.104000, rms=0.667 (0.661%), neg=0, invalid=96777
- 0056: dt=36.288000, rms=0.665 (0.317%), neg=0, invalid=96777
- 0057: dt=124.416000, rms=0.660 (0.691%), neg=0, invalid=96777
- 0058: dt=20.736000, rms=0.658 (0.357%), neg=0, invalid=96777
- 0059: dt=580.608000, rms=0.643 (2.333%), neg=0, invalid=96777
- 0060: dt=25.920000, rms=0.638 (0.636%), neg=0, invalid=96777
- 0061: dt=36.288000, rms=0.637 (0.185%), neg=0, invalid=96777
- 0062: dt=36.288000, rms=0.636 (0.138%), neg=0, invalid=96777
- 0063: dt=36.288000, rms=0.636 (0.132%), neg=0, invalid=96777
- 0064: dt=36.288000, rms=0.635 (0.137%), neg=0, invalid=96777
- 0065: dt=36.288000, rms=0.634 (0.179%), neg=0, invalid=96777
- 0066: dt=36.288000, rms=0.632 (0.307%), neg=0, invalid=96777
- 0067: dt=36.288000, rms=0.630 (0.328%), neg=0, invalid=96777
- 0068: dt=36.288000, rms=0.627 (0.329%), neg=0, invalid=96777
- 0069: dt=36.288000, rms=0.626 (0.302%), neg=0, invalid=96777
- 0070: dt=36.288000, rms=0.623 (0.373%), neg=0, invalid=96777
- 0071: dt=36.288000, rms=0.621 (0.404%), neg=0, invalid=96777
- 0072: dt=36.288000, rms=0.619 (0.333%), neg=0, invalid=96777
- 0073: dt=36.288000, rms=0.617 (0.257%), neg=0, invalid=96777
- 0074: dt=36.288000, rms=0.615 (0.264%), neg=0, invalid=96777
- 0075: dt=36.288000, rms=0.613 (0.326%), neg=0, invalid=96777
- 0076: dt=36.288000, rms=0.612 (0.252%), neg=0, invalid=96777
- 0077: dt=36.288000, rms=0.611 (0.178%), neg=0, invalid=96777
- 0078: dt=36.288000, rms=0.610 (0.153%), neg=0, invalid=96777
- 0079: dt=36.288000, rms=0.609 (0.168%), neg=0, invalid=96777
- 0080: dt=36.288000, rms=0.608 (0.151%), neg=0, invalid=96777
- 0081: dt=36.288000, rms=0.607 (0.131%), neg=0, invalid=96777
- 0082: dt=36.288000, rms=0.606 (0.097%), neg=0, invalid=96777
- 0083: dt=36.288000, rms=0.606 (0.089%), neg=0, invalid=96777
- 0084: dt=36.288000, rms=0.606 (0.042%), neg=0, invalid=96777
- 0085: dt=36.288000, rms=0.606 (-0.019%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.606, neg=0, invalid=96777
- 0086: dt=20.736000, rms=0.606 (0.024%), neg=0, invalid=96777
- 0087: dt=20.736000, rms=0.606 (0.012%), neg=0, invalid=96777
- 0088: dt=20.736000, rms=0.605 (0.011%), neg=0, invalid=96777
- 0089: dt=20.736000, rms=0.605 (-0.029%), neg=0, invalid=96777
- setting smoothness coefficient to 0.588
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.635, neg=0, invalid=96777
- 0090: dt=1.600000, rms=0.635 (0.006%), neg=0, invalid=96777
- 0091: dt=0.175000, rms=0.635 (0.003%), neg=0, invalid=96777
- 0092: dt=0.175000, rms=0.635 (0.000%), neg=0, invalid=96777
- 0093: dt=0.175000, rms=0.635 (-0.001%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.635, neg=0, invalid=96777
- 0094: dt=0.000000, rms=0.635 (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=0.719, neg=0, invalid=96777
- 0095: dt=4.467714, rms=0.698 (3.041%), neg=0, invalid=96777
- 0096: dt=3.180000, rms=0.696 (0.287%), neg=0, invalid=96777
- 0097: dt=0.864000, rms=0.695 (0.013%), neg=0, invalid=96777
- 0098: dt=0.864000, rms=0.695 (-0.006%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.695, neg=0, invalid=96777
- 0099: dt=0.000000, rms=0.695 (0.000%), neg=0, invalid=96777
- setting smoothness coefficient to 5.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.771, neg=0, invalid=96777
- 0100: dt=0.902222, rms=0.769 (0.376%), neg=0, invalid=96777
- 0101: dt=1.792000, rms=0.764 (0.625%), neg=0, invalid=96777
- 0102: dt=1.140187, rms=0.763 (0.147%), neg=0, invalid=96777
- 0103: dt=0.570093, rms=0.762 (0.078%), neg=0, invalid=96777
- 0104: dt=0.570093, rms=0.762 (0.046%), neg=0, invalid=96777
- 0105: dt=0.570093, rms=0.761 (0.028%), neg=0, invalid=96777
- 0106: dt=0.384000, rms=0.761 (0.005%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.761, neg=0, invalid=96777
- 0107: dt=1.584158, rms=0.760 (0.247%), neg=0, invalid=96777
- 0108: dt=0.000000, rms=0.760 (-0.001%), neg=0, invalid=96777
- resetting metric properties...
- setting smoothness coefficient to 10.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.712, neg=0, invalid=96777
- 0109: dt=0.161017, rms=0.703 (1.266%), neg=0, invalid=96777
- 0110: dt=0.000375, rms=0.703 (0.003%), neg=0, invalid=96777
- 0111: dt=0.000375, rms=0.703 (-0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.703, neg=0, invalid=96777
- 0112: dt=0.028000, rms=0.702 (0.083%), neg=0, invalid=96777
- 0113: dt=0.112000, rms=0.701 (0.243%), neg=0, invalid=96777
- 0114: dt=0.028000, rms=0.700 (0.032%), neg=0, invalid=96777
- 0115: dt=0.028000, rms=0.700 (0.029%), neg=0, invalid=96777
- 0116: dt=0.028000, rms=0.700 (0.054%), neg=0, invalid=96777
- 0117: dt=0.028000, rms=0.699 (0.071%), neg=0, invalid=96777
- 0118: dt=0.028000, rms=0.699 (0.085%), neg=0, invalid=96777
- 0119: dt=0.028000, rms=0.698 (0.093%), neg=0, invalid=96777
- 0120: dt=0.028000, rms=0.697 (0.094%), neg=0, invalid=96777
- 0121: dt=0.028000, rms=0.697 (0.093%), neg=0, invalid=96777
- 0122: dt=0.028000, rms=0.696 (0.088%), neg=0, invalid=96777
- renormalizing by structure alignment....
- renormalizing input #0
- gca peak = 0.11725 (24)
- mri peak = 0.15745 ( 7)
- Left_Lateral_Ventricle (4): linear fit = 0.22 x + 0.0 (1009 voxels, overlap=0.005)
- Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (1009 voxels, peak = 5), gca=9.6
- gca peak = 0.14022 (22)
- mri peak = 0.13549 ( 7)
- Right_Lateral_Ventricle (43): linear fit = 0.22 x + 0.0 (681 voxels, overlap=0.006)
- Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (681 voxels, peak = 5), gca=8.8
- gca peak = 0.24234 (100)
- mri peak = 0.08392 (90)
- Right_Pallidum (52): linear fit = 0.90 x + 0.0 (288 voxels, overlap=0.221)
- Right_Pallidum (52): linear fit = 0.90 x + 0.0 (288 voxels, peak = 90), gca=90.5
- gca peak = 0.19192 (97)
- mri peak = 0.09211 (89)
- Left_Pallidum (13): linear fit = 0.92 x + 0.0 (232 voxels, overlap=0.421)
- Left_Pallidum (13): linear fit = 0.92 x + 0.0 (232 voxels, peak = 89), gca=88.8
- gca peak = 0.24007 (63)
- mri peak = 0.11170 (56)
- Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (369 voxels, overlap=0.299)
- Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (369 voxels, peak = 55), gca=55.1
- gca peak = 0.29892 (64)
- mri peak = 0.07546 (56)
- Left_Hippocampus (17): linear fit = 0.85 x + 0.0 (245 voxels, overlap=0.150)
- Left_Hippocampus (17): linear fit = 0.85 x + 0.0 (245 voxels, peak = 54), gca=54.1
- gca peak = 0.12541 (104)
- mri peak = 0.08353 (106)
- Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (44473 voxels, overlap=0.696)
- Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (44473 voxels, peak = 108), gca=107.6
- gca peak = 0.13686 (104)
- mri peak = 0.08740 (108)
- Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (44250 voxels, overlap=0.583)
- Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (44250 voxels, peak = 109), gca=108.7
- gca peak = 0.11691 (63)
- mri peak = 0.06456 (53)
- Left_Cerebral_Cortex (3): linear fit = 0.80 x + 0.0 (12646 voxels, overlap=0.067)
- Left_Cerebral_Cortex (3): linear fit = 0.80 x + 0.0 (12646 voxels, peak = 50), gca=50.1
- gca peak = 0.13270 (63)
- mri peak = 0.06113 (53)
- Right_Cerebral_Cortex (42): linear fit = 0.80 x + 0.0 (13572 voxels, overlap=0.030)
- Right_Cerebral_Cortex (42): linear fit = 0.80 x + 0.0 (13572 voxels, peak = 50), gca=50.1
- gca peak = 0.15182 (70)
- mri peak = 0.08264 (65)
- Right_Caudate (50): linear fit = 0.87 x + 0.0 (408 voxels, overlap=0.217)
- Right_Caudate (50): linear fit = 0.87 x + 0.0 (408 voxels, peak = 61), gca=60.5
- gca peak = 0.14251 (76)
- mri peak = 0.06446 (56)
- Left_Caudate (11): linear fit = 0.82 x + 0.0 (554 voxels, overlap=0.024)
- Left_Caudate (11): linear fit = 0.82 x + 0.0 (554 voxels, peak = 63), gca=62.7
- gca peak = 0.12116 (60)
- mri peak = 0.04686 (53)
- Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (6784 voxels, overlap=0.981)
- Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (6784 voxels, peak = 56), gca=56.1
- gca peak = 0.12723 (61)
- mri peak = 0.04360 (58)
- Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (8805 voxels, overlap=0.974)
- Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (8805 voxels, peak = 57), gca=57.0
- gca peak = 0.22684 (88)
- mri peak = 0.08989 (90)
- Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (5690 voxels, overlap=0.904)
- Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (5690 voxels, peak = 90), gca=90.2
- gca peak = 0.21067 (87)
- mri peak = 0.07613 (89)
- Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (5630 voxels, overlap=0.965)
- Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (5630 voxels, peak = 90), gca=90.0
- gca peak = 0.25455 (62)
- mri peak = 0.15449 (54)
- Left_Amygdala (18): linear fit = 0.86 x + 0.0 (250 voxels, overlap=0.367)
- Left_Amygdala (18): linear fit = 0.86 x + 0.0 (250 voxels, peak = 53), gca=53.0
- gca peak = 0.39668 (62)
- mri peak = 0.09836 (59)
- Right_Amygdala (54): linear fit = 0.94 x + 0.0 (246 voxels, overlap=1.004)
- Right_Amygdala (54): linear fit = 0.94 x + 0.0 (246 voxels, peak = 58), gca=58.0
- gca peak = 0.10129 (93)
- mri peak = 0.05466 (87)
- Left_Thalamus_Proper (10): linear fit = 0.92 x + 0.0 (3847 voxels, overlap=0.681)
- Left_Thalamus_Proper (10): linear fit = 0.92 x + 0.0 (3847 voxels, peak = 85), gca=85.1
- gca peak = 0.12071 (89)
- mri peak = 0.06454 (80)
- Right_Thalamus_Proper (49): linear fit = 0.95 x + 0.0 (3298 voxels, overlap=0.842)
- Right_Thalamus_Proper (49): linear fit = 0.95 x + 0.0 (3298 voxels, peak = 85), gca=85.0
- gca peak = 0.13716 (82)
- mri peak = 0.05280 (75)
- Left_Putamen (12): linear fit = 0.93 x + 0.0 (1846 voxels, overlap=0.877)
- Left_Putamen (12): linear fit = 0.93 x + 0.0 (1846 voxels, peak = 76), gca=75.8
- gca peak = 0.15214 (84)
- mri peak = 0.05720 (74)
- Right_Putamen (51): linear fit = 0.88 x + 0.0 (1623 voxels, overlap=0.454)
- Right_Putamen (51): linear fit = 0.88 x + 0.0 (1623 voxels, peak = 74), gca=74.3
- gca peak = 0.08983 (85)
- mri peak = 0.08109 (83)
- Brain_Stem (16): linear fit = 1.02 x + 0.0 (8543 voxels, overlap=0.777)
- Brain_Stem (16): linear fit = 1.02 x + 0.0 (8543 voxels, peak = 87), gca=87.1
- gca peak = 0.11809 (92)
- mri peak = 0.06588 (97)
- Right_VentralDC (60): linear fit = 1.02 x + 0.0 (666 voxels, overlap=0.876)
- Right_VentralDC (60): linear fit = 1.02 x + 0.0 (666 voxels, peak = 94), gca=94.3
- gca peak = 0.12914 (94)
- mri peak = 0.06316 (95)
- Left_VentralDC (28): linear fit = 1.02 x + 0.0 (845 voxels, overlap=0.889)
- Left_VentralDC (28): linear fit = 1.02 x + 0.0 (845 voxels, peak = 96), gca=96.3
- gca peak = 0.21100 (36)
- mri peak = 0.44444 (10)
- gca peak = 0.13542 (27)
- mri peak = 0.13841 ( 5)
- Fourth_Ventricle (15): linear fit = 0.19 x + 0.0 (173 voxels, overlap=0.018)
- Fourth_Ventricle (15): linear fit = 0.19 x + 0.0 (173 voxels, peak = 5), gca=5.0
- 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 0.85 x + 0.0
- estimating mean wm scale to be 1.04 x + 0.0
- estimating mean csf scale to be 0.40 x + 0.0
- saving intensity scales to talairach.label_intensities.txt
- **************** pass 1 of 1 ************************
- setting smoothness coefficient to 0.008
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.726, neg=0, invalid=96777
- 0123: dt=129.472000, rms=0.721 (0.780%), neg=0, invalid=96777
- 0124: dt=110.976000, rms=0.717 (0.472%), neg=0, invalid=96777
- 0125: dt=55.488000, rms=0.716 (0.151%), neg=0, invalid=96777
- 0126: dt=517.888000, rms=0.712 (0.560%), neg=0, invalid=96777
- 0127: dt=32.368000, rms=0.711 (0.128%), neg=0, invalid=96777
- 0128: dt=110.976000, rms=0.711 (0.095%), neg=0, invalid=96777
- 0129: dt=129.472000, rms=0.710 (0.143%), neg=0, invalid=96777
- 0130: dt=55.488000, rms=0.709 (0.065%), neg=0, invalid=96777
- 0131: dt=1479.680000, rms=0.704 (0.689%), neg=0, invalid=96777
- 0132: dt=32.368000, rms=0.703 (0.200%), neg=0, invalid=96777
- 0133: dt=32.368000, rms=0.703 (0.031%), neg=0, invalid=96777
- 0134: dt=32.368000, rms=0.703 (0.013%), neg=0, invalid=96777
- 0135: dt=32.368000, rms=0.703 (0.011%), neg=0, invalid=96777
- 0136: dt=32.368000, rms=0.702 (0.030%), neg=0, invalid=96777
- 0137: dt=32.368000, rms=0.702 (0.040%), neg=0, invalid=96777
- 0138: dt=32.368000, rms=0.702 (0.054%), neg=0, invalid=96777
- 0139: dt=32.368000, rms=0.701 (0.055%), neg=0, invalid=96777
- 0140: dt=32.368000, rms=0.701 (0.061%), neg=0, invalid=96777
- 0141: dt=32.368000, rms=0.700 (0.066%), neg=0, invalid=96777
- 0142: dt=32.368000, rms=0.700 (0.065%), neg=0, invalid=96777
- 0143: dt=32.368000, rms=0.699 (0.065%), neg=0, invalid=96777
- 0144: dt=32.368000, rms=0.699 (0.078%), neg=0, invalid=96777
- 0145: dt=32.368000, rms=0.698 (0.084%), neg=0, invalid=96777
- 0146: dt=32.368000, rms=0.698 (0.078%), neg=0, invalid=96777
- 0147: dt=32.368000, rms=0.697 (0.082%), neg=0, invalid=96777
- 0148: dt=32.368000, rms=0.697 (0.078%), neg=0, invalid=96777
- 0149: dt=32.368000, rms=0.696 (0.074%), neg=0, invalid=96777
- 0150: dt=32.368000, rms=0.696 (0.072%), neg=0, invalid=96777
- 0151: dt=32.368000, rms=0.695 (0.060%), neg=0, invalid=96777
- 0152: dt=32.368000, rms=0.695 (0.061%), neg=0, invalid=96777
- 0153: dt=32.368000, rms=0.694 (0.059%), neg=0, invalid=96777
- 0154: dt=32.368000, rms=0.694 (0.056%), neg=0, invalid=96777
- 0155: dt=32.368000, rms=0.694 (0.049%), neg=0, invalid=96777
- 0156: dt=32.368000, rms=0.693 (0.049%), neg=0, invalid=96777
- 0157: dt=32.368000, rms=0.693 (0.051%), neg=0, invalid=96777
- 0158: dt=32.368000, rms=0.693 (0.051%), neg=0, invalid=96777
- 0159: dt=32.368000, rms=0.692 (0.052%), neg=0, invalid=96777
- 0160: dt=32.368000, rms=0.692 (0.047%), neg=0, invalid=96777
- 0161: dt=32.368000, rms=0.692 (0.049%), neg=0, invalid=96777
- 0162: dt=32.368000, rms=0.691 (0.048%), neg=0, invalid=96777
- 0163: dt=32.368000, rms=0.691 (0.048%), neg=0, invalid=96777
- 0164: dt=32.368000, rms=0.691 (0.047%), neg=0, invalid=96777
- 0165: dt=32.368000, rms=0.690 (0.044%), neg=0, invalid=96777
- 0166: dt=32.368000, rms=0.690 (0.044%), neg=0, invalid=96777
- 0167: dt=32.368000, rms=0.690 (0.046%), neg=0, invalid=96777
- 0168: dt=32.368000, rms=0.689 (0.044%), neg=0, invalid=96777
- 0169: dt=32.368000, rms=0.689 (0.045%), neg=0, invalid=96777
- 0170: dt=32.368000, rms=0.689 (0.042%), neg=0, invalid=96777
- 0171: dt=32.368000, rms=0.689 (0.039%), neg=0, invalid=96777
- 0172: dt=32.368000, rms=0.688 (0.039%), neg=0, invalid=96777
- 0173: dt=32.368000, rms=0.688 (0.036%), neg=0, invalid=96777
- 0174: dt=32.368000, rms=0.688 (0.038%), neg=0, invalid=96777
- 0175: dt=32.368000, rms=0.687 (0.035%), neg=0, invalid=96777
- 0176: dt=32.368000, rms=0.687 (0.033%), neg=0, invalid=96777
- 0177: dt=32.368000, rms=0.687 (0.034%), neg=0, invalid=96777
- 0178: dt=32.368000, rms=0.687 (0.034%), neg=0, invalid=96777
- 0179: dt=32.368000, rms=0.687 (0.033%), neg=0, invalid=96777
- 0180: dt=32.368000, rms=0.686 (0.032%), neg=0, invalid=96777
- 0181: dt=32.368000, rms=0.686 (0.033%), neg=0, invalid=96777
- 0182: dt=32.368000, rms=0.686 (0.032%), neg=0, invalid=96777
- 0183: dt=32.368000, rms=0.686 (0.030%), neg=0, invalid=96777
- 0184: dt=32.368000, rms=0.685 (0.031%), neg=0, invalid=96777
- 0185: dt=32.368000, rms=0.685 (0.030%), neg=0, invalid=96777
- 0186: dt=32.368000, rms=0.685 (0.029%), neg=0, invalid=96777
- 0187: dt=32.368000, rms=0.685 (0.028%), neg=0, invalid=96777
- 0188: dt=32.368000, rms=0.685 (0.029%), neg=0, invalid=96777
- 0189: dt=32.368000, rms=0.684 (0.028%), neg=0, invalid=96777
- 0190: dt=32.368000, rms=0.684 (0.029%), neg=0, invalid=96777
- 0191: dt=32.368000, rms=0.684 (0.028%), neg=0, invalid=96777
- 0192: dt=32.368000, rms=0.684 (0.028%), neg=0, invalid=96777
- 0193: dt=32.368000, rms=0.684 (0.024%), neg=0, invalid=96777
- 0194: dt=32.368000, rms=0.684 (0.023%), neg=0, invalid=96777
- 0195: dt=517.888000, rms=0.683 (0.043%), neg=0, invalid=96777
- 0196: dt=27.744000, rms=0.683 (0.004%), neg=0, invalid=96777
- 0197: dt=27.744000, rms=0.683 (0.001%), neg=0, invalid=96777
- 0198: dt=27.744000, rms=0.683 (0.002%), neg=0, invalid=96777
- 0199: dt=27.744000, rms=0.683 (-0.001%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.683, neg=0, invalid=96777
- 0200: dt=110.976000, rms=0.683 (0.052%), neg=0, invalid=96777
- 0201: dt=369.920000, rms=0.682 (0.112%), neg=0, invalid=96777
- 0202: dt=129.472000, rms=0.682 (0.071%), neg=0, invalid=96777
- 0203: dt=32.368000, rms=0.682 (0.004%), neg=0, invalid=96777
- 0204: dt=32.368000, rms=0.682 (0.007%), neg=0, invalid=96777
- 0205: dt=32.368000, rms=0.681 (0.012%), neg=0, invalid=96777
- 0206: dt=32.368000, rms=0.681 (0.019%), neg=0, invalid=96777
- 0207: dt=32.368000, rms=0.681 (0.026%), neg=0, invalid=96777
- 0208: dt=32.368000, rms=0.681 (0.028%), neg=0, invalid=96777
- 0209: dt=32.368000, rms=0.681 (0.026%), neg=0, invalid=96777
- 0210: dt=32.368000, rms=0.681 (0.026%), neg=0, invalid=96777
- 0211: dt=32.368000, rms=0.680 (0.021%), neg=0, invalid=96777
- 0212: dt=32.368000, rms=0.680 (0.021%), neg=0, invalid=96777
- 0213: dt=32.368000, rms=0.680 (0.022%), neg=0, invalid=96777
- 0214: dt=32.368000, rms=0.680 (0.021%), neg=0, invalid=96777
- 0215: dt=295.936000, rms=0.680 (0.032%), neg=0, invalid=96777
- 0216: dt=32.368000, rms=0.680 (0.010%), neg=0, invalid=96777
- 0217: dt=32.368000, rms=0.680 (-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=0.680, neg=0, invalid=96777
- 0218: dt=145.152000, rms=0.669 (1.692%), neg=0, invalid=96777
- 0219: dt=36.288000, rms=0.664 (0.677%), neg=0, invalid=96777
- 0220: dt=331.776000, rms=0.653 (1.696%), neg=0, invalid=96777
- 0221: dt=31.104000, rms=0.647 (0.976%), neg=0, invalid=96777
- 0222: dt=36.288000, rms=0.644 (0.347%), neg=0, invalid=96777
- 0223: dt=36.288000, rms=0.643 (0.161%), neg=0, invalid=96777
- 0224: dt=36.288000, rms=0.642 (0.209%), neg=0, invalid=96777
- 0225: dt=36.288000, rms=0.641 (0.143%), neg=0, invalid=96777
- 0226: dt=62.208000, rms=0.640 (0.225%), neg=0, invalid=96777
- 0227: dt=25.920000, rms=0.639 (0.155%), neg=0, invalid=96777
- 0228: dt=36.288000, rms=0.638 (0.167%), neg=0, invalid=96777
- 0229: dt=331.776000, rms=0.633 (0.692%), neg=0, invalid=96777
- 0230: dt=7.776000, rms=0.631 (0.322%), neg=0, invalid=96777
- 0231: dt=1.944000, rms=0.631 (0.055%), neg=0, invalid=96777
- 0232: dt=0.141750, rms=0.631 (0.000%), neg=0, invalid=96777
- 0233: dt=0.035437, rms=0.631 (0.003%), neg=0, invalid=96777
- 0234: dt=0.004430, rms=0.631 (0.000%), neg=0, invalid=96777
- 0235: dt=0.000277, rms=0.631 (0.000%), neg=0, invalid=96777
- 0236: dt=0.000000, rms=0.631 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.631, neg=0, invalid=96777
- 0237: dt=0.000000, rms=0.631 (0.000%), neg=0, invalid=96777
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.635, neg=0, invalid=96777
- 0238: dt=0.000000, rms=0.635 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.635, neg=0, invalid=96777
- 0239: dt=0.000000, rms=0.635 (0.000%), neg=0, invalid=96777
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.647, neg=0, invalid=96777
- 0240: dt=1.008000, rms=0.641 (0.924%), neg=0, invalid=96777
- 0241: dt=1.008000, rms=0.635 (0.862%), neg=0, invalid=96777
- 0242: dt=4.032000, rms=0.615 (3.109%), neg=0, invalid=96777
- 0243: dt=3.456000, rms=0.603 (1.958%), neg=0, invalid=96777
- 0244: dt=11.520000, rms=0.574 (4.800%), neg=0, invalid=96777
- 0245: dt=4.032000, rms=0.571 (0.589%), neg=0, invalid=96777
- 0246: dt=16.128000, rms=0.560 (1.891%), neg=0, invalid=96777
- 0247: dt=5.244444, rms=0.559 (0.237%), neg=0, invalid=96777
- 0248: dt=4.595745, rms=0.558 (0.196%), neg=0, invalid=96777
- 0249: dt=5.000000, rms=0.557 (0.179%), neg=0, invalid=96777
- 0250: dt=4.186047, rms=0.556 (0.149%), neg=0, invalid=96777
- 0251: dt=5.600000, rms=0.555 (0.156%), neg=0, invalid=96777
- 0252: dt=4.689655, rms=0.554 (0.129%), neg=0, invalid=96777
- 0253: dt=4.242424, rms=0.554 (0.106%), neg=0, invalid=96777
- 0254: dt=5.066667, rms=0.553 (0.118%), neg=0, invalid=96777
- 0255: dt=4.521739, rms=0.553 (0.083%), neg=0, invalid=96777
- 0256: dt=11.520000, rms=0.552 (0.101%), neg=0, invalid=96777
- 0257: dt=3.692308, rms=0.551 (0.136%), neg=0, invalid=96777
- 0258: dt=11.520000, rms=0.551 (0.117%), neg=0, invalid=96777
- 0259: dt=2.924731, rms=0.550 (0.096%), neg=0, invalid=96777
- 0260: dt=11.520000, rms=0.550 (0.111%), neg=0, invalid=96777
- 0261: dt=3.456000, rms=0.549 (0.071%), neg=0, invalid=96777
- 0262: dt=9.216000, rms=0.549 (0.076%), neg=0, invalid=96777
- 0263: dt=4.032000, rms=0.548 (0.059%), neg=0, invalid=96777
- 0264: dt=4.032000, rms=0.548 (0.045%), neg=0, invalid=96777
- 0265: dt=4.032000, rms=0.548 (0.030%), neg=0, invalid=96777
- 0266: dt=4.032000, rms=0.548 (0.067%), neg=0, invalid=96777
- 0267: dt=4.032000, rms=0.547 (0.098%), neg=0, invalid=96777
- 0268: dt=4.032000, rms=0.547 (0.101%), neg=0, invalid=96777
- 0269: dt=4.032000, rms=0.546 (0.120%), neg=0, invalid=96777
- 0270: dt=4.032000, rms=0.545 (0.109%), neg=0, invalid=96777
- 0271: dt=4.032000, rms=0.545 (0.140%), neg=0, invalid=96777
- 0272: dt=4.032000, rms=0.544 (0.130%), neg=0, invalid=96777
- 0273: dt=4.032000, rms=0.543 (0.109%), neg=0, invalid=96777
- 0274: dt=4.032000, rms=0.543 (0.096%), neg=0, invalid=96777
- 0275: dt=4.032000, rms=0.542 (0.095%), neg=0, invalid=96777
- 0276: dt=4.032000, rms=0.542 (0.084%), neg=0, invalid=96777
- 0277: dt=4.032000, rms=0.541 (0.082%), neg=0, invalid=96777
- 0278: dt=4.032000, rms=0.541 (0.071%), neg=0, invalid=96777
- 0279: dt=4.032000, rms=0.541 (0.056%), neg=0, invalid=96777
- 0280: dt=4.032000, rms=0.540 (0.060%), neg=0, invalid=96777
- 0281: dt=4.032000, rms=0.540 (0.045%), neg=0, invalid=96777
- 0282: dt=4.032000, rms=0.540 (0.060%), neg=0, invalid=96777
- 0283: dt=4.032000, rms=0.539 (0.058%), neg=0, invalid=96777
- 0284: dt=4.032000, rms=0.539 (0.046%), neg=0, invalid=96777
- 0285: dt=4.032000, rms=0.539 (0.040%), neg=0, invalid=96777
- 0286: dt=4.032000, rms=0.539 (0.030%), neg=0, invalid=96777
- 0287: dt=4.032000, rms=0.539 (0.029%), neg=0, invalid=96777
- 0288: dt=4.032000, rms=0.539 (0.023%), neg=0, invalid=96777
- 0289: dt=4.032000, rms=0.538 (0.027%), neg=0, invalid=96777
- 0290: dt=4.032000, rms=0.538 (0.037%), neg=0, invalid=96777
- 0291: dt=4.032000, rms=0.538 (0.029%), neg=0, invalid=96777
- 0292: dt=4.032000, rms=0.538 (0.027%), neg=0, invalid=96777
- 0293: dt=4.032000, rms=0.538 (0.027%), neg=0, invalid=96777
- 0294: dt=4.032000, rms=0.538 (0.032%), neg=0, invalid=96777
- 0295: dt=4.032000, rms=0.537 (0.020%), neg=0, invalid=96777
- 0296: dt=4.032000, rms=0.537 (0.014%), neg=0, invalid=96777
- 0297: dt=2.880000, rms=0.537 (0.002%), neg=0, invalid=96777
- 0298: dt=2.880000, rms=0.537 (0.004%), neg=0, invalid=96777
- 0299: dt=2.880000, rms=0.537 (-0.003%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.537, neg=0, invalid=96777
- 0300: dt=1.008000, rms=0.537 (0.001%), neg=0, invalid=96777
- 0301: dt=0.063000, rms=0.537 (-0.002%), neg=0, invalid=96777
- setting smoothness coefficient to 1.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.559, neg=0, invalid=96777
- 0302: dt=0.000000, rms=0.559 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.559, neg=0, invalid=96777
- 0303: dt=0.000000, rms=0.559 (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=0.523, neg=0, invalid=96777
- 0304: dt=0.179097, rms=0.514 (1.572%), neg=0, invalid=96777
- 0305: dt=0.028000, rms=0.514 (0.169%), neg=0, invalid=96777
- 0306: dt=0.143858, rms=0.509 (0.800%), neg=0, invalid=96777
- 0307: dt=0.320000, rms=0.503 (1.334%), neg=0, invalid=96777
- 0308: dt=0.007000, rms=0.503 (0.018%), neg=0, invalid=96777
- 0309: dt=0.007000, rms=0.502 (0.015%), neg=0, invalid=96777
- 0310: dt=0.007000, rms=0.502 (0.027%), neg=0, invalid=96777
- 0311: dt=0.007000, rms=0.502 (0.039%), neg=0, invalid=96777
- 0312: dt=0.007000, rms=0.502 (0.047%), neg=0, invalid=96777
- 0313: dt=0.007000, rms=0.502 (0.059%), neg=0, invalid=96777
- 0314: dt=0.007000, rms=0.501 (0.061%), neg=0, invalid=96777
- 0315: dt=0.007000, rms=0.501 (0.069%), neg=0, invalid=96777
- 0316: dt=0.007000, rms=0.501 (0.073%), neg=0, invalid=96777
- 0317: dt=0.007000, rms=0.500 (0.081%), neg=0, invalid=96777
- 0318: dt=0.007000, rms=0.500 (0.081%), neg=0, invalid=96777
- 0319: dt=0.007000, rms=0.499 (0.081%), neg=0, invalid=96777
- 0320: dt=0.007000, rms=0.499 (0.083%), neg=0, invalid=96777
- 0321: dt=0.007000, rms=0.499 (0.083%), neg=0, invalid=96777
- 0322: dt=0.007000, rms=0.498 (0.083%), neg=0, invalid=96777
- 0323: dt=0.007000, rms=0.498 (0.079%), neg=0, invalid=96777
- 0324: dt=0.007000, rms=0.497 (0.077%), neg=0, invalid=96777
- 0325: dt=0.007000, rms=0.497 (0.076%), neg=0, invalid=96777
- 0326: dt=0.007000, rms=0.497 (0.075%), neg=0, invalid=96777
- 0327: dt=0.007000, rms=0.496 (0.075%), neg=0, invalid=96777
- 0328: dt=0.007000, rms=0.496 (0.068%), neg=0, invalid=96777
- 0329: dt=0.007000, rms=0.496 (0.066%), neg=0, invalid=96777
- 0330: dt=0.007000, rms=0.495 (0.063%), neg=0, invalid=96777
- 0331: dt=0.007000, rms=0.495 (0.060%), neg=0, invalid=96777
- 0332: dt=0.007000, rms=0.495 (0.056%), neg=0, invalid=96777
- 0333: dt=0.007000, rms=0.494 (0.051%), neg=0, invalid=96777
- 0334: dt=0.007000, rms=0.494 (0.052%), neg=0, invalid=96777
- 0335: dt=0.007000, rms=0.494 (0.047%), neg=0, invalid=96777
- 0336: dt=0.007000, rms=0.494 (0.044%), neg=0, invalid=96777
- 0337: dt=0.007000, rms=0.494 (0.040%), neg=0, invalid=96777
- 0338: dt=0.007000, rms=0.493 (0.038%), neg=0, invalid=96777
- 0339: dt=0.007000, rms=0.493 (0.036%), neg=0, invalid=96777
- 0340: dt=0.007000, rms=0.493 (0.033%), neg=0, invalid=96777
- 0341: dt=0.007000, rms=0.493 (0.031%), neg=0, invalid=96777
- 0342: dt=0.007000, rms=0.493 (0.027%), neg=0, invalid=96777
- 0343: dt=0.007000, rms=0.493 (0.030%), neg=0, invalid=96777
- 0344: dt=0.007000, rms=0.493 (0.001%), neg=0, invalid=96777
- 0345: dt=0.007000, rms=0.493 (0.002%), neg=0, invalid=96777
- 0346: dt=0.007000, rms=0.493 (0.002%), neg=0, invalid=96777
- 0347: dt=0.320000, rms=0.492 (0.046%), neg=0, invalid=96777
- 0348: dt=0.005001, rms=0.492 (0.003%), neg=0, invalid=96777
- 0349: dt=0.005001, rms=0.492 (0.000%), neg=0, invalid=96777
- 0350: dt=0.005001, rms=0.492 (-0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.492, neg=0, invalid=96777
- 0351: dt=0.112778, rms=0.491 (0.324%), neg=0, invalid=96777
- 0352: dt=0.112000, rms=0.490 (0.244%), neg=0, invalid=96777
- 0353: dt=0.028000, rms=0.489 (0.047%), neg=0, invalid=96777
- 0354: dt=0.028000, rms=0.489 (0.044%), neg=0, invalid=96777
- 0355: dt=0.028000, rms=0.489 (0.086%), neg=0, invalid=96777
- 0356: dt=0.028000, rms=0.488 (0.109%), neg=0, invalid=96777
- 0357: dt=0.028000, rms=0.488 (0.128%), neg=0, invalid=96777
- 0358: dt=0.028000, rms=0.487 (0.142%), neg=0, invalid=96777
- 0359: dt=0.007000, rms=0.487 (0.000%), neg=0, invalid=96777
- 0360: dt=0.007000, rms=0.487 (0.006%), neg=0, invalid=96777
- 0361: dt=0.007000, rms=0.487 (0.007%), neg=0, invalid=96777
- 0362: dt=0.007000, rms=0.487 (0.010%), neg=0, invalid=96777
- 0363: dt=0.007000, rms=0.487 (0.015%), neg=0, invalid=96777
- 0364: dt=0.007000, rms=0.487 (0.017%), neg=0, invalid=96777
- 0365: dt=0.007000, rms=0.486 (0.018%), neg=0, invalid=96777
- 0366: dt=0.007000, rms=0.486 (0.022%), neg=0, invalid=96777
- 0367: dt=0.007000, rms=0.486 (0.018%), neg=0, invalid=96777
- 0368: dt=0.112000, rms=0.486 (0.046%), neg=0, invalid=96777
- 0369: dt=0.096000, rms=0.486 (0.030%), neg=0, invalid=96777
- 0370: dt=0.001500, rms=0.486 (0.004%), neg=0, invalid=96777
- 0371: dt=0.001500, rms=0.486 (0.000%), neg=0, invalid=96777
- 0372: dt=0.001500, rms=0.486 (0.001%), neg=0, invalid=96777
- 0373: dt=0.001500, rms=0.486 (0.001%), neg=0, invalid=96777
- 0374: dt=0.001500, rms=0.486 (-0.000%), 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=0.484, neg=0, invalid=96777
- 0375: dt=32.368000, rms=0.484 (0.004%), neg=0, invalid=96777
- 0376: dt=73.984000, rms=0.484 (0.009%), neg=0, invalid=96777
- 0377: dt=1.734000, rms=0.484 (-0.001%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.484, neg=0, invalid=96777
- 0378: dt=92.480000, rms=0.484 (0.039%), neg=0, invalid=96777
- 0379: dt=129.472000, rms=0.483 (0.062%), neg=0, invalid=96777
- 0380: dt=27.744000, rms=0.483 (0.009%), neg=0, invalid=96777
- 0381: dt=27.744000, rms=0.483 (0.011%), neg=0, invalid=96777
- 0382: dt=27.744000, rms=0.483 (0.014%), neg=0, invalid=96777
- 0383: dt=27.744000, rms=0.483 (0.017%), neg=0, invalid=96777
- 0384: dt=27.744000, rms=0.483 (0.025%), neg=0, invalid=96777
- 0385: dt=27.744000, rms=0.483 (0.026%), neg=0, invalid=96777
- 0386: dt=27.744000, rms=0.483 (0.022%), neg=0, invalid=96777
- 0387: dt=27.744000, rms=0.483 (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=0.483, neg=0, invalid=96777
- 0388: dt=36.288000, rms=0.482 (0.227%), neg=0, invalid=96777
- 0389: dt=36.288000, rms=0.481 (0.112%), neg=0, invalid=96777
- 0390: dt=36.288000, rms=0.481 (0.073%), neg=0, invalid=96777
- 0391: dt=36.288000, rms=0.480 (0.077%), neg=0, invalid=96777
- iter 0, gcam->neg = 2
- after 1 iterations, nbhd size=0, neg = 0
- 0392: dt=36.288000, rms=0.480 (0.014%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0393: dt=36.288000, rms=0.480 (-0.067%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.480, neg=0, invalid=96777
- 0394: dt=82.944000, rms=0.478 (0.529%), neg=0, invalid=96777
- 0395: dt=31.104000, rms=0.477 (0.158%), neg=0, invalid=96777
- 0396: dt=31.104000, rms=0.477 (0.052%), neg=0, invalid=96777
- 0397: dt=31.104000, rms=0.476 (0.138%), neg=0, invalid=96777
- 0398: dt=31.104000, rms=0.475 (0.172%), neg=0, invalid=96777
- 0399: dt=31.104000, rms=0.475 (0.163%), neg=0, invalid=96777
- 0400: dt=31.104000, rms=0.474 (0.109%), neg=0, invalid=96777
- 0401: dt=31.104000, rms=0.473 (0.127%), neg=0, invalid=96777
- 0402: dt=31.104000, rms=0.473 (0.111%), neg=0, invalid=96777
- 0403: dt=31.104000, rms=0.472 (0.136%), neg=0, invalid=96777
- 0404: dt=31.104000, rms=0.472 (0.083%), neg=0, invalid=96777
- 0405: dt=31.104000, rms=0.471 (0.082%), neg=0, invalid=96777
- 0406: dt=25.920000, rms=0.471 (0.018%), neg=0, invalid=96777
- 0407: dt=25.920000, rms=0.471 (0.023%), neg=0, invalid=96777
- 0408: dt=25.920000, rms=0.471 (0.019%), neg=0, invalid=96777
- 0409: dt=25.920000, rms=0.471 (0.019%), neg=0, invalid=96777
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.471, neg=0, invalid=96777
- iter 0, gcam->neg = 9
- after 1 iterations, nbhd size=0, neg = 0
- 0410: dt=32.000000, rms=0.469 (0.610%), neg=0, invalid=96777
- 0411: dt=19.200000, rms=0.467 (0.263%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0412: dt=11.200000, rms=0.466 (0.220%), neg=0, invalid=96777
- 0413: dt=11.200000, rms=0.466 (0.033%), neg=0, invalid=96777
- 0414: dt=11.200000, rms=0.465 (0.282%), neg=0, invalid=96777
- iter 0, gcam->neg = 3
- after 7 iterations, nbhd size=1, neg = 0
- 0415: dt=11.200000, rms=0.464 (0.262%), neg=0, invalid=96777
- iter 0, gcam->neg = 4
- after 1 iterations, nbhd size=0, neg = 0
- 0416: dt=11.200000, rms=0.462 (0.269%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0417: dt=11.200000, rms=0.461 (0.226%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 5 iterations, nbhd size=1, neg = 0
- 0418: dt=11.200000, rms=0.460 (0.218%), neg=0, invalid=96777
- iter 0, gcam->neg = 3
- after 1 iterations, nbhd size=0, neg = 0
- 0419: dt=11.200000, rms=0.459 (0.186%), neg=0, invalid=96777
- 0420: dt=11.200000, rms=0.459 (0.189%), neg=0, invalid=96777
- 0421: dt=11.200000, rms=0.458 (0.198%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0422: dt=11.200000, rms=0.457 (0.180%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 6 iterations, nbhd size=1, neg = 0
- 0423: dt=11.200000, rms=0.456 (0.177%), neg=0, invalid=96777
- 0424: dt=11.200000, rms=0.455 (0.145%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 1 iterations, nbhd size=0, neg = 0
- 0425: dt=11.200000, rms=0.455 (0.125%), neg=0, invalid=96777
- 0426: dt=11.200000, rms=0.454 (0.142%), neg=0, invalid=96777
- 0427: dt=11.200000, rms=0.454 (0.126%), neg=0, invalid=96777
- 0428: dt=11.200000, rms=0.453 (0.157%), neg=0, invalid=96777
- 0429: dt=11.200000, rms=0.452 (0.111%), neg=0, invalid=96777
- 0430: dt=11.200000, rms=0.452 (0.109%), neg=0, invalid=96777
- 0431: dt=11.200000, rms=0.452 (0.036%), neg=0, invalid=96777
- 0432: dt=11.200000, rms=0.452 (0.034%), neg=0, invalid=96777
- 0433: dt=11.200000, rms=0.451 (0.037%), neg=0, invalid=96777
- 0434: dt=11.200000, rms=0.451 (0.046%), neg=0, invalid=96777
- 0435: dt=11.200000, rms=0.451 (0.042%), neg=0, invalid=96777
- 0436: dt=11.200000, rms=0.451 (0.026%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.451, neg=0, invalid=96777
- iter 0, gcam->neg = 12
- after 10 iterations, nbhd size=1, neg = 0
- 0437: dt=44.800000, rms=0.448 (0.712%), neg=0, invalid=96777
- 0438: dt=9.600000, rms=0.447 (0.157%), neg=0, invalid=96777
- 0439: dt=9.600000, rms=0.447 (0.094%), neg=0, invalid=96777
- 0440: dt=9.600000, rms=0.446 (0.120%), neg=0, invalid=96777
- 0441: dt=9.600000, rms=0.445 (0.136%), neg=0, invalid=96777
- 0442: dt=9.600000, rms=0.445 (0.120%), neg=0, invalid=96777
- 0443: dt=9.600000, rms=0.444 (0.110%), neg=0, invalid=96777
- 0444: dt=11.200000, rms=0.444 (0.046%), neg=0, invalid=96777
- 0445: dt=11.200000, rms=0.444 (0.024%), neg=0, invalid=96777
- 0446: dt=11.200000, rms=0.444 (0.041%), neg=0, invalid=96777
- 0447: dt=11.200000, rms=0.444 (0.040%), neg=0, invalid=96777
- 0448: dt=11.200000, rms=0.444 (0.055%), neg=0, invalid=96777
- 0449: dt=11.200000, rms=0.443 (0.067%), neg=0, invalid=96777
- 0450: dt=11.200000, rms=0.443 (0.058%), neg=0, invalid=96777
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.449, neg=0, invalid=96777
- 0451: dt=0.864000, rms=0.449 (-0.001%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.449, neg=0, invalid=96777
- 0452: dt=2.424242, rms=0.448 (0.040%), neg=0, invalid=96777
- 0453: dt=2.880000, rms=0.448 (0.022%), neg=0, invalid=96777
- 0454: dt=2.880000, rms=0.448 (-0.011%), neg=0, invalid=96777
- setting smoothness coefficient to 1.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.458, neg=0, invalid=96777
- 0455: dt=0.448000, rms=0.458 (0.027%), neg=0, invalid=96777
- 0456: dt=0.312500, rms=0.458 (0.007%), neg=0, invalid=96777
- 0457: dt=0.312500, rms=0.458 (-0.009%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.458, neg=0, invalid=96777
- iter 0, gcam->neg = 9
- after 7 iterations, nbhd size=1, neg = 0
- 0458: dt=1.173333, rms=0.457 (0.167%), neg=0, invalid=96777
- 0459: dt=0.004000, rms=0.457 (0.000%), neg=0, invalid=96777
- 0460: dt=0.004000, rms=0.457 (0.000%), neg=0, invalid=96777
- 0461: dt=0.004000, rms=0.457 (0.000%), neg=0, invalid=96777
- 0462: dt=0.004000, rms=0.457 (0.001%), neg=0, invalid=96777
- 0463: dt=0.004000, rms=0.457 (0.001%), neg=0, invalid=96777
- 0464: dt=0.004000, rms=0.457 (-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=0.446, neg=0, invalid=96777
- iter 0, gcam->neg = 919
- after 11 iterations, nbhd size=1, neg = 0
- 0465: dt=1.441713, rms=0.412 (7.562%), neg=0, invalid=96777
- 0466: dt=0.000094, rms=0.412 (-0.014%), neg=0, invalid=96777
- 0467: dt=0.000094, rms=0.412 (0.001%), neg=0, invalid=96777
- 0468: dt=0.000094, rms=0.412 (-0.003%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.412, neg=0, invalid=96777
- 0469: dt=0.000109, rms=0.412 (0.000%), neg=0, invalid=96777
- 0470: dt=0.000000, rms=0.412 (0.000%), neg=0, invalid=96777
- 0471: dt=0.000000, rms=0.412 (0.000%), neg=0, invalid=96777
- label assignment complete, 0 changed (0.00%)
- label assignment complete, 0 changed (0.00%)
- ***************** morphing with label term set to 0 *******************************
- **************** pass 1 of 1 ************************
- setting smoothness coefficient to 0.008
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.404, neg=0, invalid=96777
- 0472: dt=0.003613, rms=0.405 (-0.262%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.405, neg=0, invalid=96777
- 0473: dt=8.092000, rms=0.405 (0.001%), neg=0, invalid=96777
- 0474: dt=8.092000, rms=0.405 (0.000%), neg=0, invalid=96777
- 0475: dt=8.092000, rms=0.405 (-0.000%), neg=0, invalid=96777
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.405, neg=0, invalid=96777
- 0476: dt=0.000000, rms=0.405 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.405, neg=0, invalid=96777
- 0477: dt=31.104000, rms=0.405 (0.026%), neg=0, invalid=96777
- 0478: dt=82.944000, rms=0.405 (0.030%), neg=0, invalid=96777
- 0479: dt=145.152000, rms=0.405 (0.049%), neg=0, invalid=96777
- 0480: dt=36.288000, rms=0.405 (0.007%), neg=0, invalid=96777
- 0481: dt=36.288000, rms=0.405 (0.005%), neg=0, invalid=96777
- 0482: dt=36.288000, rms=0.405 (0.009%), neg=0, invalid=96777
- 0483: dt=36.288000, rms=0.405 (0.014%), neg=0, invalid=96777
- 0484: dt=36.288000, rms=0.404 (0.015%), neg=0, invalid=96777
- 0485: dt=36.288000, rms=0.404 (0.013%), neg=0, invalid=96777
- 0486: dt=36.288000, rms=0.404 (0.009%), neg=0, invalid=96777
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.405, neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 5 iterations, nbhd size=1, neg = 0
- 0487: dt=11.200000, rms=0.405 (0.067%), neg=0, invalid=96777
- 0488: dt=2.800000, rms=0.404 (0.004%), neg=0, invalid=96777
- 0489: dt=2.800000, rms=0.404 (0.011%), neg=0, invalid=96777
- 0490: dt=2.800000, rms=0.404 (0.012%), neg=0, invalid=96777
- 0491: dt=2.800000, rms=0.404 (0.000%), neg=0, invalid=96777
- 0492: dt=2.800000, rms=0.404 (-0.023%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.404, neg=0, invalid=96777
- iter 0, gcam->neg = 16
- after 9 iterations, nbhd size=1, neg = 0
- 0493: dt=19.200000, rms=0.404 (0.183%), neg=0, invalid=96777
- 0494: dt=11.200000, rms=0.403 (0.121%), neg=0, invalid=96777
- 0495: dt=11.200000, rms=0.403 (0.129%), neg=0, invalid=96777
- 0496: dt=11.200000, rms=0.402 (0.192%), neg=0, invalid=96777
- iter 0, gcam->neg = 5
- after 8 iterations, nbhd size=1, neg = 0
- 0497: dt=11.200000, rms=0.401 (0.188%), neg=0, invalid=96777
- iter 0, gcam->neg = 3
- after 1 iterations, nbhd size=0, neg = 0
- 0498: dt=11.200000, rms=0.401 (0.150%), neg=0, invalid=96777
- iter 0, gcam->neg = 6
- after 24 iterations, nbhd size=3, neg = 0
- 0499: dt=11.200000, rms=0.400 (0.043%), neg=0, invalid=96777
- iter 0, gcam->neg = 3
- after 7 iterations, nbhd size=1, neg = 0
- 0500: dt=11.200000, rms=0.400 (0.052%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 5 iterations, nbhd size=1, neg = 0
- 0501: dt=11.200000, rms=0.400 (0.041%), neg=0, invalid=96777
- iter 0, gcam->neg = 3
- after 8 iterations, nbhd size=1, neg = 0
- 0502: dt=25.600000, rms=0.399 (0.162%), neg=0, invalid=96777
- 0503: dt=11.200000, rms=0.399 (0.045%), neg=0, invalid=96777
- 0504: dt=11.200000, rms=0.399 (0.052%), neg=0, invalid=96777
- iter 0, gcam->neg = 2
- after 6 iterations, nbhd size=1, neg = 0
- 0505: dt=11.200000, rms=0.399 (0.076%), neg=0, invalid=96777
- iter 0, gcam->neg = 3
- after 14 iterations, nbhd size=2, neg = 0
- 0506: dt=11.200000, rms=0.398 (0.052%), neg=0, invalid=96777
- iter 0, gcam->neg = 3
- after 11 iterations, nbhd size=1, neg = 0
- 0507: dt=11.200000, rms=0.398 (0.019%), neg=0, invalid=96777
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.400, neg=0, invalid=96777
- 0508: dt=0.044792, rms=0.400 (0.000%), neg=0, invalid=96777
- iter 0, gcam->neg = 29
- after 18 iterations, nbhd size=2, neg = 0
- 0509: dt=4.516129, rms=0.400 (0.142%), neg=0, invalid=96777
- 0510: dt=0.003375, rms=0.400 (0.000%), neg=0, invalid=96777
- 0511: dt=0.003375, rms=0.400 (0.000%), neg=0, invalid=96777
- 0512: dt=0.003375, rms=0.400 (0.000%), neg=0, invalid=96777
- 0513: dt=0.003375, rms=0.400 (0.000%), neg=0, invalid=96777
- 0514: dt=0.003375, rms=0.400 (0.000%), neg=0, invalid=96777
- 0515: dt=0.003375, rms=0.400 (0.000%), neg=0, invalid=96777
- 0516: dt=0.003375, rms=0.400 (0.000%), neg=0, invalid=96777
- 0517: dt=0.003375, rms=0.400 (0.000%), neg=0, invalid=96777
- 0518: dt=0.003375, rms=0.400 (0.000%), neg=0, invalid=96777
- 0519: dt=0.003375, rms=0.400 (0.000%), neg=0, invalid=96777
- 0520: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777
- 0521: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777
- 0522: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777
- 0523: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777
- 0524: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777
- 0525: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777
- 0526: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777
- 0527: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777
- 0528: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777
- 0529: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777
- 0530: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777
- 0531: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777
- 0532: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777
- 0533: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777
- 0534: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777
- 0535: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777
- 0536: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777
- 0537: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777
- 0538: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777
- 0539: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777
- 0540: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777
- 0541: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777
- 0542: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777
- 0543: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777
- 0544: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777
- 0545: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777
- 0546: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777
- 0547: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777
- 0548: dt=0.003375, rms=0.400 (0.001%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.400, neg=0, invalid=96777
- iter 0, gcam->neg = 140
- after 31 iterations, nbhd size=3, neg = 0
- 0549: dt=10.698413, rms=0.398 (0.379%), neg=0, invalid=96777
- 0550: dt=0.002811, rms=0.398 (0.000%), neg=0, invalid=96777
- 0551: dt=0.002811, rms=0.398 (-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=0.402, neg=0, invalid=96777
- 0552: dt=0.000438, rms=0.402 (0.000%), neg=0, invalid=96777
- 0553: dt=0.000000, rms=0.402 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.402, neg=0, invalid=96777
- 0554: dt=0.000375, rms=0.402 (0.000%), neg=0, invalid=96777
- 0555: dt=0.000000, rms=0.402 (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=0.396, neg=0, invalid=96777
- iter 0, gcam->neg = 315
- after 21 iterations, nbhd size=2, neg = 0
- 0556: dt=0.384000, rms=0.388 (1.811%), neg=0, invalid=96777
- 0557: dt=0.000020, rms=0.388 (0.002%), neg=0, invalid=96777
- 0558: dt=0.000020, rms=0.388 (0.000%), neg=0, invalid=96777
- 0559: dt=0.000020, rms=0.388 (0.000%), neg=0, invalid=96777
- 0560: dt=0.000020, rms=0.388 (0.000%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0561: dt=0.001000, rms=0.388 (0.001%), neg=0, invalid=96777
- 0562: dt=0.000109, rms=0.388 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.388, neg=0, invalid=96777
- iter 0, gcam->neg = 72
- after 17 iterations, nbhd size=2, neg = 0
- 0563: dt=0.079545, rms=0.387 (0.267%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0564: dt=0.000012, rms=0.387 (0.001%), neg=0, invalid=96777
- 0565: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777
- 0566: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777
- 0567: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777
- 0568: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777
- 0569: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777
- 0570: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777
- 0571: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777
- 0572: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777
- 0573: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777
- 0574: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777
- 0575: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777
- 0576: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777
- 0577: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777
- 0578: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777
- 0579: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777
- 0580: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777
- 0581: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777
- 0582: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777
- 0583: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777
- 0584: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777
- 0585: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777
- 0586: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777
- 0587: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777
- 0588: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777
- 0589: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777
- 0590: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777
- 0591: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777
- 0592: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777
- 0593: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777
- 0594: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777
- 0595: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777
- 0596: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777
- 0597: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777
- 0598: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777
- 0599: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777
- 0600: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777
- 0601: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777
- 0602: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777
- 0603: dt=0.000012, rms=0.387 (0.000%), neg=0, invalid=96777
- iter 0, gcam->neg = 59
- after 16 iterations, nbhd size=2, neg = 0
- 0604: dt=0.079545, rms=0.386 (0.217%), neg=0, invalid=96777
- 0605: dt=0.000012, rms=0.386 (0.001%), neg=0, invalid=96777
- writing output transformation to transforms/talairach.m3z...
- GCAMwrite
- registration took 3 hours, 45 minutes and 10 seconds.
- #--------------------------------------
- #@# CA Reg Inv Thu Aug 8 15:51:55 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 15:53:50 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...
- 11996396 nonbrain voxels erased
- writing output to nu_noneck.mgz...
- nonbrain removal took 1 minutes and 47 seconds.
- #--------------------------------------
- #@# SkullLTA Thu Aug 8 15:55:38 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=31.3
- skull bounding box = (71, 45, 30) --> (189, 182, 194)
- using (110, 91, 112) as brain centroid...
- mean wm in atlas = 126, using box (96,74,92) --> (124, 107,132) to find MRI wm
- before smoothing, mri peak at 110
- after smoothing, mri peak at 110, scaling input intensities by 1.145
- scaling channel 0 by 1.14545
- ****************************************
- 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)
- 1.248 0.007 0.074 -43.432;
- -0.008 1.233 0.277 -33.259;
- -0.063 -0.306 1.088 21.742;
- 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)
- 1.248 0.007 0.074 -43.432;
- -0.008 1.233 0.277 -33.259;
- -0.063 -0.306 1.088 21.742;
- 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)
- 1.273 0.019 0.041 -43.984;
- -0.010 1.245 0.316 -38.566;
- -0.020 -0.342 1.058 21.291;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 3 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.296 0.019 0.042 -47.167;
- -0.010 1.245 0.316 -38.566;
- -0.020 -0.342 1.058 21.291;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 4 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.296 0.019 0.042 -47.167;
- -0.010 1.245 0.316 -38.566;
- -0.020 -0.342 1.058 21.291;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.0625
- ****************************************
- Nine parameter search. iteration 5 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.291 -0.008 0.053 -46.566;
- 0.011 1.239 0.334 -44.203;
- -0.041 -0.363 1.055 26.091;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 6 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.290 -0.008 0.053 -46.364;
- 0.011 1.239 0.334 -44.203;
- -0.041 -0.363 1.055 26.091;
- 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
- 1.28985 -0.00767 0.05333 -46.36439;
- 0.01112 1.23927 0.33371 -44.20263;
- -0.04089 -0.36328 1.05452 26.09148;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 3481
- Quasinewton: input matrix
- 1.28985 -0.00767 0.05333 -46.36439;
- 0.01112 1.23927 0.33371 -44.20263;
- -0.04089 -0.36328 1.05452 26.09148;
- 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:
- 1.290 -0.008 0.053 -46.364;
- 0.011 1.239 0.334 -44.203;
- -0.041 -0.363 1.055 26.091;
- 0.000 0.000 0.000 1.000;
- pass 1, spacing 8: log(p) = -4.0 (old=-4.2)
- transform before final EM align:
- 1.290 -0.008 0.053 -46.364;
- 0.011 1.239 0.334 -44.203;
- -0.041 -0.363 1.055 26.091;
- 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
- 1.28985 -0.00767 0.05333 -46.36439;
- 0.01112 1.23927 0.33371 -44.20263;
- -0.04089 -0.36328 1.05452 26.09148;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 382743
- Quasinewton: input matrix
- 1.28985 -0.00767 0.05333 -46.36439;
- 0.01112 1.23927 0.33371 -44.20263;
- -0.04089 -0.36328 1.05452 26.09148;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = 4.4 tol 0.000000
- final transform:
- 1.290 -0.008 0.053 -46.364;
- 0.011 1.239 0.334 -44.203;
- -0.041 -0.363 1.055 26.091;
- 0.000 0.000 0.000 1.000;
- writing output transformation to transforms/talairach_with_skull_2.lta...
- registration took 40 minutes and 31 seconds.
- #--------------------------------------
- #@# SubCort Seg Thu Aug 8 16:36:09 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 snake4
- machine x86_64
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 = 0.12811 ( 8)
- Left_Lateral_Ventricle (4): linear fit = 0.25 x + 0.0 (1304 voxels, overlap=0.006)
- Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (1304 voxels, peak = 7), gca=10.8
- gca peak = 0.14982 (20)
- mri peak = 0.10835 ( 6)
- Right_Lateral_Ventricle (43): linear fit = 0.25 x + 0.0 (642 voxels, overlap=0.008)
- Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (642 voxels, peak = 5), gca=8.0
- gca peak = 0.28003 (97)
- mri peak = 0.06855 (87)
- Right_Pallidum (52): linear fit = 0.93 x + 0.0 (253 voxels, overlap=0.332)
- Right_Pallidum (52): linear fit = 0.93 x + 0.0 (253 voxels, peak = 90), gca=89.7
- gca peak = 0.18160 (96)
- mri peak = 0.08019 (92)
- Left_Pallidum (13): linear fit = 0.93 x + 0.0 (251 voxels, overlap=0.258)
- Left_Pallidum (13): linear fit = 0.93 x + 0.0 (251 voxels, peak = 89), gca=88.8
- gca peak = 0.27536 (62)
- mri peak = 0.10516 (56)
- Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (502 voxels, overlap=0.199)
- Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (502 voxels, peak = 54), gca=54.2
- gca peak = 0.32745 (63)
- mri peak = 0.09957 (54)
- Left_Hippocampus (17): linear fit = 0.83 x + 0.0 (576 voxels, overlap=0.386)
- Left_Hippocampus (17): linear fit = 0.83 x + 0.0 (576 voxels, peak = 53), gca=52.6
- gca peak = 0.08597 (105)
- mri peak = 0.08652 (109)
- Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (20917 voxels, overlap=0.608)
- Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (20917 voxels, peak = 109), gca=108.7
- gca peak = 0.09209 (106)
- mri peak = 0.10326 (111)
- Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (19493 voxels, overlap=0.564)
- Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (19493 voxels, peak = 111), gca=110.8
- gca peak = 0.07826 (63)
- mri peak = 0.06236 (53)
- Left_Cerebral_Cortex (3): linear fit = 0.80 x + 0.0 (10571 voxels, overlap=0.170)
- Left_Cerebral_Cortex (3): linear fit = 0.80 x + 0.0 (10571 voxels, peak = 50), gca=50.1
- gca peak = 0.08598 (64)
- mri peak = 0.06339 (52)
- Right_Cerebral_Cortex (42): linear fit = 0.80 x + 0.0 (9805 voxels, overlap=0.110)
- Right_Cerebral_Cortex (42): linear fit = 0.80 x + 0.0 (9805 voxels, peak = 51), gca=50.9
- gca peak = 0.24164 (71)
- mri peak = 0.10212 (65)
- Right_Caudate (50): linear fit = 0.88 x + 0.0 (519 voxels, overlap=0.025)
- Right_Caudate (50): linear fit = 0.88 x + 0.0 (519 voxels, peak = 62), gca=62.1
- gca peak = 0.18227 (75)
- mri peak = 0.10526 (64)
- Left_Caudate (11): linear fit = 0.81 x + 0.0 (665 voxels, overlap=0.024)
- Left_Caudate (11): linear fit = 0.81 x + 0.0 (665 voxels, peak = 61), gca=61.1
- gca peak = 0.10629 (62)
- mri peak = 0.04847 (58)
- Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (5630 voxels, overlap=0.971)
- Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (5630 voxels, peak = 58), gca=58.0
- gca peak = 0.11668 (59)
- mri peak = 0.05438 (58)
- Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (6967 voxels, overlap=0.971)
- Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (6967 voxels, peak = 57), gca=56.9
- gca peak = 0.17849 (88)
- mri peak = 0.10071 (90)
- Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (4265 voxels, overlap=0.960)
- Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (4265 voxels, peak = 90), gca=90.2
- gca peak = 0.16819 (86)
- mri peak = 0.08158 (89)
- Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (3935 voxels, overlap=0.973)
- Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (3935 voxels, peak = 89), gca=89.0
- gca peak = 0.41688 (64)
- mri peak = 0.10000 (54)
- Left_Amygdala (18): linear fit = 0.88 x + 0.0 (217 voxels, overlap=1.036)
- Left_Amygdala (18): linear fit = 0.88 x + 0.0 (217 voxels, peak = 56), gca=56.0
- gca peak = 0.42394 (62)
- mri peak = 0.08115 (64)
- Right_Amygdala (54): linear fit = 1.00 x + 0.0 (196 voxels, overlap=1.036)
- Right_Amygdala (54): linear fit = 1.00 x + 0.0 (196 voxels, peak = 62), gca=62.0
- gca peak = 0.10041 (96)
- mri peak = 0.06387 (84)
- Left_Thalamus_Proper (10): linear fit = 0.92 x + 0.0 (2782 voxels, overlap=0.652)
- Left_Thalamus_Proper (10): linear fit = 0.92 x + 0.0 (2782 voxels, peak = 88), gca=87.8
- gca peak = 0.13978 (88)
- mri peak = 0.07066 (80)
- Right_Thalamus_Proper (49): linear fit = 0.95 x + 0.0 (2740 voxels, overlap=0.821)
- Right_Thalamus_Proper (49): linear fit = 0.95 x + 0.0 (2740 voxels, peak = 84), gca=84.0
- gca peak = 0.08514 (81)
- mri peak = 0.05775 (70)
- Left_Putamen (12): linear fit = 0.88 x + 0.0 (1709 voxels, overlap=0.538)
- Left_Putamen (12): linear fit = 0.88 x + 0.0 (1709 voxels, peak = 71), gca=70.9
- gca peak = 0.09624 (82)
- mri peak = 0.07085 (72)
- Right_Putamen (51): linear fit = 0.88 x + 0.0 (1732 voxels, overlap=0.477)
- Right_Putamen (51): linear fit = 0.88 x + 0.0 (1732 voxels, peak = 73), gca=72.6
- gca peak = 0.07543 (88)
- mri peak = 0.07695 (83)
- Brain_Stem (16): linear fit = 1.00 x + 0.0 (8303 voxels, overlap=0.764)
- Brain_Stem (16): linear fit = 1.00 x + 0.0 (8303 voxels, peak = 88), gca=87.6
- gca peak = 0.12757 (95)
- mri peak = 0.07749 (92)
- Right_VentralDC (60): linear fit = 1.03 x + 0.0 (638 voxels, overlap=0.823)
- Right_VentralDC (60): linear fit = 1.03 x + 0.0 (638 voxels, peak = 98), gca=98.3
- gca peak = 0.17004 (92)
- mri peak = 0.06553 (96)
- Left_VentralDC (28): linear fit = 1.03 x + 0.0 (733 voxels, overlap=0.903)
- Left_VentralDC (28): linear fit = 1.03 x + 0.0 (733 voxels, peak = 95), gca=95.2
- gca peak = 0.21361 (36)
- uniform distribution in MR - rejecting arbitrary fit
- gca peak = 0.26069 (23)
- mri peak = 0.12656 ( 6)
- Fourth_Ventricle (15): linear fit = 0.22 x + 0.0 (107 voxels, overlap=0.029)
- Fourth_Ventricle (15): linear fit = 0.22 x + 0.0 (107 voxels, peak = 5), gca=4.9
- 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 0.86 x + 0.0
- estimating mean wm scale to be 1.04 x + 0.0
- estimating mean csf scale to be 0.40 x + 0.0
- saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
- renormalizing by structure alignment....
- renormalizing input #0
- gca peak = 0.31600 (11)
- mri peak = 0.12811 ( 8)
- Left_Lateral_Ventricle (4): linear fit = 0.52 x + 0.0 (1304 voxels, overlap=0.465)
- Left_Lateral_Ventricle (4): linear fit = 0.52 x + 0.0 (1304 voxels, peak = 6), gca=5.8
- gca peak = 0.29325 ( 9)
- mri peak = 0.10835 ( 6)
- Right_Lateral_Ventricle (43): linear fit = 0.64 x + 0.0 (642 voxels, overlap=0.831)
- Right_Lateral_Ventricle (43): linear fit = 0.64 x + 0.0 (642 voxels, peak = 6), gca=5.8
- gca peak = 0.32313 (90)
- mri peak = 0.06855 (87)
- Right_Pallidum (52): linear fit = 0.95 x + 0.0 (253 voxels, overlap=1.028)
- Right_Pallidum (52): linear fit = 0.95 x + 0.0 (253 voxels, peak = 86), gca=85.9
- gca peak = 0.18461 (89)
- mri peak = 0.08019 (92)
- Left_Pallidum (13): linear fit = 1.00 x + 0.0 (251 voxels, overlap=1.003)
- Left_Pallidum (13): linear fit = 1.00 x + 0.0 (251 voxels, peak = 89), gca=88.6
- gca peak = 0.29894 (54)
- mri peak = 0.10516 (56)
- Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (502 voxels, overlap=1.003)
- Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (502 voxels, peak = 54), gca=54.0
- gca peak = 0.28418 (53)
- mri peak = 0.09957 (54)
- Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (576 voxels, overlap=1.006)
- Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (576 voxels, peak = 53), gca=53.0
- gca peak = 0.08268 (109)
- mri peak = 0.08652 (109)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (20917 voxels, overlap=0.755)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (20917 voxels, peak = 110), gca=109.5
- gca peak = 0.08584 (111)
- mri peak = 0.10326 (111)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (19493 voxels, overlap=0.743)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (19493 voxels, peak = 111), gca=111.0
- gca peak = 0.09713 (50)
- mri peak = 0.06236 (53)
- Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (10571 voxels, overlap=0.989)
- Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (10571 voxels, peak = 50), gca=50.0
- gca peak = 0.11022 (51)
- mri peak = 0.06339 (52)
- Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (9805 voxels, overlap=0.974)
- Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (9805 voxels, peak = 50), gca=50.2
- gca peak = 0.24028 (64)
- mri peak = 0.10212 (65)
- Right_Caudate (50): linear fit = 1.01 x + 0.0 (519 voxels, overlap=1.002)
- Right_Caudate (50): linear fit = 1.01 x + 0.0 (519 voxels, peak = 65), gca=65.0
- gca peak = 0.18407 (61)
- mri peak = 0.10526 (64)
- Left_Caudate (11): linear fit = 1.02 x + 0.0 (665 voxels, overlap=0.984)
- Left_Caudate (11): linear fit = 1.02 x + 0.0 (665 voxels, peak = 63), gca=62.5
- gca peak = 0.11245 (58)
- mri peak = 0.04847 (58)
- Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (5630 voxels, overlap=0.998)
- Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (5630 voxels, peak = 59), gca=59.4
- gca peak = 0.12331 (58)
- mri peak = 0.05438 (58)
- Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (6967 voxels, overlap=1.000)
- Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (6967 voxels, peak = 57), gca=57.1
- gca peak = 0.16635 (89)
- mri peak = 0.10071 (90)
- Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4265 voxels, overlap=0.990)
- Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4265 voxels, peak = 89), gca=88.6
- gca peak = 0.16437 (89)
- mri peak = 0.08158 (89)
- Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (3935 voxels, overlap=0.998)
- Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (3935 voxels, peak = 89), gca=88.6
- gca peak = 0.54117 (56)
- mri peak = 0.10000 (54)
- Left_Amygdala (18): linear fit = 1.04 x + 0.0 (217 voxels, overlap=1.027)
- Left_Amygdala (18): linear fit = 1.04 x + 0.0 (217 voxels, peak = 59), gca=58.5
- gca peak = 0.38630 (63)
- mri peak = 0.08115 (64)
- Right_Amygdala (54): linear fit = 1.00 x + 0.0 (196 voxels, overlap=1.016)
- Right_Amygdala (54): linear fit = 1.00 x + 0.0 (196 voxels, peak = 63), gca=63.0
- gca peak = 0.10601 (88)
- mri peak = 0.06387 (84)
- Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (2782 voxels, overlap=0.997)
- Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (2782 voxels, peak = 89), gca=89.3
- gca peak = 0.14353 (84)
- mri peak = 0.07066 (80)
- Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (2740 voxels, overlap=0.989)
- Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (2740 voxels, peak = 83), gca=82.7
- gca peak = 0.09324 (72)
- mri peak = 0.05775 (70)
- Left_Putamen (12): linear fit = 1.00 x + 0.0 (1709 voxels, overlap=1.000)
- Left_Putamen (12): linear fit = 1.00 x + 0.0 (1709 voxels, peak = 72), gca=72.0
- gca peak = 0.12381 (67)
- mri peak = 0.07085 (72)
- Right_Putamen (51): linear fit = 1.00 x + 0.0 (1732 voxels, overlap=1.000)
- Right_Putamen (51): linear fit = 1.00 x + 0.0 (1732 voxels, peak = 67), gca=67.0
- gca peak = 0.07578 (85)
- mri peak = 0.07695 (83)
- Brain_Stem (16): linear fit = 1.00 x + 0.0 (8303 voxels, overlap=0.755)
- Brain_Stem (16): linear fit = 1.00 x + 0.0 (8303 voxels, peak = 85), gca=84.6
- gca peak = 0.13169 (98)
- mri peak = 0.07749 (92)
- Right_VentralDC (60): linear fit = 1.00 x + 0.0 (638 voxels, overlap=0.872)
- Right_VentralDC (60): linear fit = 1.00 x + 0.0 (638 voxels, peak = 98), gca=98.5
- gca peak = 0.13795 (96)
- mri peak = 0.06553 (96)
- Left_VentralDC (28): linear fit = 1.00 x + 0.0 (733 voxels, overlap=0.928)
- Left_VentralDC (28): linear fit = 1.00 x + 0.0 (733 voxels, peak = 96), gca=96.5
- gca peak = 0.35640 (14)
- uniform distribution in MR - rejecting arbitrary fit
- gca peak = 0.33827 ( 9)
- mri peak = 0.12656 ( 6)
- Fourth_Ventricle (15): linear fit = 0.57 x + 0.0 (107 voxels, overlap=0.470)
- Fourth_Ventricle (15): linear fit = 0.57 x + 0.0 (107 voxels, peak = 5), gca=5.2
- gca peak Unknown = 0.94427 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.24968 (29)
- gca peak Third_Ventricle = 0.35640 (14)
- gca peak Fourth_Ventricle = 0.33827 ( 9)
- gca peak CSF = 0.30128 (18)
- gca peak Left_Accumbens_area = 0.68077 (57)
- gca peak Left_undetermined = 1.00000 (35)
- gca peak Left_vessel = 0.43860 (61)
- gca peak Left_choroid_plexus = 0.09084 (48)
- gca peak Right_Inf_Lat_Vent = 0.33086 (28)
- gca peak Right_Accumbens_area = 0.31095 (63)
- gca peak Right_vessel = 0.53048 (60)
- gca peak Right_choroid_plexus = 0.10423 (48)
- gca peak Fifth_Ventricle = 0.45329 (19)
- gca peak WM_hypointensities = 0.17031 (85)
- gca peak non_WM_hypointensities = 0.11439 (55)
- gca peak Optic_Chiasm = 0.34840 (76)
- not using caudate to estimate GM means
- estimating mean gm scale to be 1.00 x + 0.0
- estimating mean wm scale to be 1.00 x + 0.0
- estimating mean csf scale to be 0.58 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
- 8974 gm and wm labels changed (%11 to gray, %89 to white out of all changed labels)
- 180 hippocampal voxels changed.
- 1 amygdala voxels changed.
- pass 1: 74924 changed. image ll: -2.124, PF=1.000
- pass 2: 14199 changed. image ll: -2.122, PF=1.000
- pass 3: 5409 changed.
- pass 4: 2603 changed.
- writing labeled volume to aseg.auto_noCCseg.mgz...
- auto-labeling took 18 minutes and 52 seconds.
- mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/cc_up.lta sub010
- 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/sub010/mri/transforms/cc_up.lta
- reading aseg from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/aseg.auto_noCCseg.mgz
- reading norm from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/norm.mgz
- 20559 voxels in left wm, 30231 in right wm, xrange [125, 133]
- searching rotation angles z=[-7 7], y=[-4 10]
-
searching scale 1 Z rot -7.5
searching scale 1 Z rot -7.2
searching scale 1 Z rot -7.0
searching scale 1 Z rot -6.7
searching scale 1 Z rot -6.5
searching scale 1 Z rot -6.2
searching scale 1 Z rot -6.0
searching scale 1 Z rot -5.7
searching scale 1 Z rot -5.5
searching scale 1 Z rot -5.2
searching scale 1 Z rot -5.0
searching scale 1 Z rot -4.7
searching scale 1 Z rot -4.5
searching scale 1 Z rot -4.2
searching scale 1 Z rot -4.0
searching scale 1 Z rot -3.7
searching scale 1 Z rot -3.5
searching scale 1 Z rot -3.2
searching scale 1 Z rot -3.0
searching scale 1 Z rot -2.7
searching scale 1 Z rot -2.5
searching scale 1 Z rot -2.2
searching scale 1 Z rot -2.0
searching scale 1 Z rot -1.7
searching scale 1 Z rot -1.5
searching scale 1 Z rot -1.2
searching scale 1 Z rot -1.0
searching scale 1 Z rot -0.7
searching scale 1 Z rot -0.5
searching scale 1 Z rot -0.2
searching scale 1 Z rot 0.0
searching scale 1 Z rot 0.3
searching scale 1 Z rot 0.5
searching scale 1 Z rot 0.8
searching scale 1 Z rot 1.0
searching scale 1 Z rot 1.3
searching scale 1 Z rot 1.5
searching scale 1 Z rot 1.8
searching scale 1 Z rot 2.0
searching scale 1 Z rot 2.3
searching scale 1 Z rot 2.5
searching scale 1 Z rot 2.8
searching scale 1 Z rot 3.0
searching scale 1 Z rot 3.3
searching scale 1 Z rot 3.5
searching scale 1 Z rot 3.8
searching scale 1 Z rot 4.0
searching scale 1 Z rot 4.3
searching scale 1 Z rot 4.5
searching scale 1 Z rot 4.8
searching scale 1 Z rot 5.0
searching scale 1 Z rot 5.3
searching scale 1 Z rot 5.5
searching scale 1 Z rot 5.8
searching scale 1 Z rot 6.0
searching scale 1 Z rot 6.3 global minimum found at slice 129.6, rotations (2.65, -0.46)
- final transformation (x=129.6, yr=2.650, zr=-0.463):
- 0.999 0.008 0.046 -6.994;
- -0.008 1.000 -0.000 45.088;
- -0.046 -0.000 0.999 28.104;
- 0.000 0.000 0.000 1.000;
- updating x range to be [126, 130] in xformed coordinates
- best xformed slice 128
- cc center is found at 128 148 117
- eigenvectors:
- -0.001 0.000 1.000;
- -0.137 -0.991 0.000;
- 0.991 -0.137 0.001;
- writing aseg with callosum to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/aseg.auto.mgz...
- corpus callosum matter segmentation took 0.7 minutes
- #--------------------------------------
- #@# Merge ASeg Thu Aug 8 16:55:43 CEST 2013
- cp aseg.auto.mgz aseg.mgz
- #--------------------------------------------
- #@# Intensity Normalization2 Thu Aug 8 16:55:43 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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...
- 1432 control points removed
- Building bias image
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 0...
- Smoothing with sigma 8
- Applying bias correction
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Iterating 2 times
- ---------------------------------
- 3d normalization pass 1 of 2
- white matter peak found at 111
- white matter peak found at 109
- gm peak at 55 (55), valley at 23 (23)
- csf peak at 27, setting threshold to 45
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- ---------------------------------
- 3d normalization pass 2 of 2
- white matter peak found at 111
- white matter peak found at 110
- gm peak at 56 (56), valley at 24 (24)
- csf peak at 28, setting threshold to 46
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Done iterating ---------------------------------
- writing output to brain.mgz
- 3D bias adjustment took 4 minutes and 24 seconds.
- #--------------------------------------------
- #@# Mask BFS Thu Aug 8 17:00:10 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri
- mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
- threshold mask volume at 5
- DoAbs = 0
- Found 1279546 voxels in mask (pct= 7.63)
- Writing masked volume to brain.finalsurfs.mgz...done.
- #--------------------------------------------
- #@# WM Segmentation Thu Aug 8 17:00:12 CEST 2013
- mri_segment brain.mgz wm.seg.mgz
- doing initial intensity segmentation...
- using local statistics to label ambiguous voxels...
- computing class statistics for intensity windows...
- WM (107.0): 107.2 +- 4.8 [80.0 --> 125.0]
- GM (66.0) : 65.2 +- 10.0 [30.0 --> 96.0]
- setting bottom of white matter range to 75.2
- setting top of gray matter range to 85.2
- doing initial intensity segmentation...
- using local statistics to label ambiguous voxels...
- using local geometry to label remaining ambiguous voxels...
- reclassifying voxels using Gaussian border classifier...
- removing voxels with positive offset direction...
- smoothing T1 volume with sigma = 0.250
- removing 1-dimensional structures...
- 5920 sparsely connected voxels removed...
- thickening thin strands....
- 20 segments, 7387 filled
- 179 bright non-wm voxels segmented.
- 3370 diagonally connected voxels added...
- white matter segmentation took 1.7 minutes
- writing output to wm.seg.mgz...
- mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz
- preserving editing changes in input volume...
- auto filling took 0.62 minutes
- reading wm segmentation from wm.seg.mgz...
- 82 voxels added to wm to prevent paths from MTL structures to cortex
- 1099 additional wm voxels added
- 0 additional wm voxels added
- SEG EDIT: 47958 voxels turned on, 33998 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+): 19 found - 19 modified | TOTAL: 19
- pass 2 (xy+): 0 found - 19 modified | TOTAL: 19
- pass 1 (xy-): 15 found - 15 modified | TOTAL: 34
- pass 2 (xy-): 0 found - 15 modified | TOTAL: 34
- pass 1 (yz+): 27 found - 27 modified | TOTAL: 61
- pass 2 (yz+): 0 found - 27 modified | TOTAL: 61
- pass 1 (yz-): 17 found - 17 modified | TOTAL: 78
- pass 2 (yz-): 0 found - 17 modified | TOTAL: 78
- pass 1 (xz+): 12 found - 12 modified | TOTAL: 90
- pass 2 (xz+): 0 found - 12 modified | TOTAL: 90
- pass 1 (xz-): 11 found - 11 modified | TOTAL: 101
- pass 2 (xz-): 0 found - 11 modified | TOTAL: 101
- Iteration Number : 1
- pass 1 (+++): 11 found - 11 modified | TOTAL: 11
- pass 2 (+++): 0 found - 11 modified | TOTAL: 11
- pass 1 (+++): 13 found - 13 modified | TOTAL: 24
- pass 2 (+++): 0 found - 13 modified | TOTAL: 24
- pass 1 (+++): 12 found - 12 modified | TOTAL: 36
- pass 2 (+++): 0 found - 12 modified | TOTAL: 36
- pass 1 (+++): 15 found - 15 modified | TOTAL: 51
- pass 2 (+++): 0 found - 15 modified | TOTAL: 51
- Iteration Number : 1
- pass 1 (++): 188 found - 188 modified | TOTAL: 188
- pass 2 (++): 0 found - 188 modified | TOTAL: 188
- pass 1 (+-): 146 found - 146 modified | TOTAL: 334
- pass 2 (+-): 0 found - 146 modified | TOTAL: 334
- pass 1 (--): 171 found - 171 modified | TOTAL: 505
- pass 2 (--): 1 found - 172 modified | TOTAL: 506
- pass 3 (--): 0 found - 172 modified | TOTAL: 506
- pass 1 (-+): 166 found - 166 modified | TOTAL: 672
- pass 2 (-+): 0 found - 166 modified | TOTAL: 672
- Iteration Number : 2
- pass 1 (xy+): 5 found - 5 modified | TOTAL: 5
- pass 2 (xy+): 0 found - 5 modified | TOTAL: 5
- pass 1 (xy-): 4 found - 4 modified | TOTAL: 9
- pass 2 (xy-): 0 found - 4 modified | TOTAL: 9
- pass 1 (yz+): 6 found - 6 modified | TOTAL: 15
- pass 2 (yz+): 0 found - 6 modified | TOTAL: 15
- pass 1 (yz-): 5 found - 5 modified | TOTAL: 20
- pass 2 (yz-): 0 found - 5 modified | TOTAL: 20
- pass 1 (xz+): 2 found - 2 modified | TOTAL: 22
- pass 2 (xz+): 0 found - 2 modified | TOTAL: 22
- pass 1 (xz-): 5 found - 5 modified | TOTAL: 27
- pass 2 (xz-): 0 found - 5 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 (++): 2 found - 2 modified | TOTAL: 2
- pass 2 (++): 0 found - 2 modified | TOTAL: 2
- pass 1 (+-): 4 found - 4 modified | TOTAL: 6
- pass 2 (+-): 0 found - 4 modified | TOTAL: 6
- pass 1 (--): 1 found - 1 modified | TOTAL: 7
- pass 2 (--): 0 found - 1 modified | TOTAL: 7
- pass 1 (-+): 2 found - 2 modified | TOTAL: 9
- pass 2 (-+): 0 found - 2 modified | TOTAL: 9
- 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 = 860 (out of 401720: 0.214079)
- binarizing input wm segmentation...
- Ambiguous edge configurations...
- mri_pretess done
- #--------------------------------------------
- #@# Fill Thu Aug 8 17:02:36 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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
- 1.173 0.007 0.070 -33.293;
- -0.008 1.233 0.277 -33.259;
- -0.059 -0.284 1.012 27.623;
- 0.000 0.000 0.000 1.000;
- voxel to talairach voxel transform
- 1.173 0.007 0.070 -33.293;
- -0.008 1.233 0.277 -33.259;
- -0.059 -0.284 1.012 27.623;
- 0.000 0.000 0.000 1.000;
- reading segmented volume aseg.auto_noCCseg.mgz...
- Looking for area (min, max) = (350, 1400)
- area[0] = 1226 (min = 350, max = 1400), aspect = 0.45 (min = 0.10, max = 0.75)
- no need to search
- using seed (127, 107, 95), TAL = (1.0, -33.0, 21.0)
- talairach voxel to voxel transform
- 0.850 -0.017 -0.054 29.210;
- -0.005 0.763 -0.209 30.967;
- 0.048 0.213 0.927 -16.909;
- 0.000 0.000 0.000 1.000;
- segmentation indicates cc at (127, 107, 95) --> (1.0, -33.0, 21.0)
- done.
- writing output to filled.mgz...
- filling took 0.9 minutes
- talairach cc position changed to (1.00, -33.00, 21.00)
- Erasing brainstem...done.
- seed_search_size = 9, min_neighbors = 5
- search rh wm seed point around talairach space:(19.00, -33.00, 21.00) SRC: (114.86, 92.23, 99.16)
- search lh wm seed point around talairach space (-17.00, -33.00, 21.00), SRC: (145.45, 92.04, 100.88)
- 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 17:03:30 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts
- mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz
- Iteration Number : 1
- pass 1 (xy+): 1 found - 1 modified | TOTAL: 1
- pass 2 (xy+): 0 found - 1 modified | TOTAL: 1
- pass 1 (xy-): 3 found - 3 modified | TOTAL: 4
- pass 2 (xy-): 0 found - 3 modified | TOTAL: 4
- pass 1 (yz+): 1 found - 1 modified | TOTAL: 5
- pass 2 (yz+): 0 found - 1 modified | TOTAL: 5
- pass 1 (yz-): 2 found - 2 modified | TOTAL: 7
- pass 2 (yz-): 0 found - 2 modified | TOTAL: 7
- pass 1 (xz+): 0 found - 0 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 (++): 1 found - 1 modified | TOTAL: 1
- pass 2 (++): 0 found - 1 modified | TOTAL: 1
- pass 1 (+-): 0 found - 0 modified | TOTAL: 1
- pass 1 (--): 1 found - 1 modified | TOTAL: 2
- pass 2 (--): 0 found - 1 modified | TOTAL: 2
- pass 1 (-+): 0 found - 0 modified | TOTAL: 2
- Iteration Number : 2
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Total Number of Modified Voxels = 10 (out of 192890: 0.005184)
- 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 50: 3401 vertices, 3592 faces
- slice 60: 10727 vertices, 11043 faces
- slice 70: 20151 vertices, 20468 faces
- slice 80: 29887 vertices, 30243 faces
- slice 90: 38894 vertices, 39231 faces
- slice 100: 48437 vertices, 48774 faces
- slice 110: 57589 vertices, 57925 faces
- slice 120: 66648 vertices, 67010 faces
- slice 130: 75605 vertices, 75952 faces
- slice 140: 85146 vertices, 85508 faces
- slice 150: 93160 vertices, 93476 faces
- slice 160: 99455 vertices, 99705 faces
- slice 170: 105051 vertices, 105292 faces
- slice 180: 109818 vertices, 110015 faces
- slice 190: 112861 vertices, 112993 faces
- slice 200: 113880 vertices, 113928 faces
- slice 210: 113880 vertices, 113928 faces
- slice 220: 113880 vertices, 113928 faces
- slice 230: 113880 vertices, 113928 faces
- slice 240: 113880 vertices, 113928 faces
- slice 250: 113880 vertices, 113928 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...
- 113880 voxel in cpt #1: X=-48 [v=113880,e=341784,f=227856] located at (-26.027784, -18.012205, 33.335861)
- For the whole surface: X=-48 [v=113880,e=341784,f=227856]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Smooth1 lh Thu Aug 8 17:03:38 CEST 2013
- mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 17:03:42 CEST 2013
- mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts
- avg radius = 44.8 mm, total surface area = 59841 mm^2
- writing inflated surface to ../surf/lh.inflated.nofix
- inflation took 0.5 minutes
- Not saving sulc
-
step 000: RMS=0.102 (target=0.015)
step 005: RMS=0.076 (target=0.015)
step 010: RMS=0.055 (target=0.015)
step 015: RMS=0.048 (target=0.015)
step 020: RMS=0.041 (target=0.015)
step 025: RMS=0.036 (target=0.015)
step 030: RMS=0.032 (target=0.015)
step 035: RMS=0.030 (target=0.015)
step 040: RMS=0.028 (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 17:04:09 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts
- mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix
- doing quick spherical unfolding.
- setting seed for random number genererator to 1234
- $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading original vertex positions...
- unfolding cortex into spherical form...
- surface projected - minimizing metric distortion...
- vertex spacing 1.07 +- 0.65 (0.00-->7.38) (max @ vno 51981 --> 52877)
- face area 0.03 +- 0.04 (-0.29-->0.61)
- scaling brain by 0.329...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=176.712, avgs=0
- 005/300: dt: 0.9000, rms radial error=176.454, avgs=0
- 010/300: dt: 0.9000, rms radial error=175.900, avgs=0
- 015/300: dt: 0.9000, rms radial error=175.172, avgs=0
- 020/300: dt: 0.9000, rms radial error=174.341, avgs=0
- 025/300: dt: 0.9000, rms radial error=173.456, avgs=0
- 030/300: dt: 0.9000, rms radial error=172.541, avgs=0
- 035/300: dt: 0.9000, rms radial error=171.607, avgs=0
- 040/300: dt: 0.9000, rms radial error=170.666, avgs=0
- 045/300: dt: 0.9000, rms radial error=169.722, avgs=0
- 050/300: dt: 0.9000, rms radial error=168.777, avgs=0
- 055/300: dt: 0.9000, rms radial error=167.835, avgs=0
- 060/300: dt: 0.9000, rms radial error=166.902, avgs=0
- 065/300: dt: 0.9000, rms radial error=165.973, avgs=0
- 070/300: dt: 0.9000, rms radial error=165.048, avgs=0
- 075/300: dt: 0.9000, rms radial error=164.128, avgs=0
- 080/300: dt: 0.9000, rms radial error=163.212, avgs=0
- 085/300: dt: 0.9000, rms radial error=162.301, avgs=0
- 090/300: dt: 0.9000, rms radial error=161.394, avgs=0
- 095/300: dt: 0.9000, rms radial error=160.492, avgs=0
- 100/300: dt: 0.9000, rms radial error=159.594, avgs=0
- 105/300: dt: 0.9000, rms radial error=158.701, avgs=0
- 110/300: dt: 0.9000, rms radial error=157.813, avgs=0
- 115/300: dt: 0.9000, rms radial error=156.930, avgs=0
- 120/300: dt: 0.9000, rms radial error=156.051, avgs=0
- 125/300: dt: 0.9000, rms radial error=155.176, avgs=0
- 130/300: dt: 0.9000, rms radial error=154.307, avgs=0
- 135/300: dt: 0.9000, rms radial error=153.441, avgs=0
- 140/300: dt: 0.9000, rms radial error=152.581, avgs=0
- 145/300: dt: 0.9000, rms radial error=151.725, avgs=0
- 150/300: dt: 0.9000, rms radial error=150.873, avgs=0
- 155/300: dt: 0.9000, rms radial error=150.026, avgs=0
- 160/300: dt: 0.9000, rms radial error=149.184, avgs=0
- 165/300: dt: 0.9000, rms radial error=148.346, avgs=0
- 170/300: dt: 0.9000, rms radial error=147.512, avgs=0
- 175/300: dt: 0.9000, rms radial error=146.684, avgs=0
- 180/300: dt: 0.9000, rms radial error=145.859, avgs=0
- 185/300: dt: 0.9000, rms radial error=145.039, avgs=0
- 190/300: dt: 0.9000, rms radial error=144.224, avgs=0
- 195/300: dt: 0.9000, rms radial error=143.413, avgs=0
- 200/300: dt: 0.9000, rms radial error=142.606, avgs=0
- 205/300: dt: 0.9000, rms radial error=141.804, avgs=0
- 210/300: dt: 0.9000, rms radial error=141.006, avgs=0
- 215/300: dt: 0.9000, rms radial error=140.213, avgs=0
- 220/300: dt: 0.9000, rms radial error=139.424, avgs=0
- 225/300: dt: 0.9000, rms radial error=138.639, avgs=0
- 230/300: dt: 0.9000, rms radial error=137.859, avgs=0
- 235/300: dt: 0.9000, rms radial error=137.082, avgs=0
- 240/300: dt: 0.9000, rms radial error=136.311, avgs=0
- 245/300: dt: 0.9000, rms radial error=135.544, avgs=0
- 250/300: dt: 0.9000, rms radial error=134.781, avgs=0
- 255/300: dt: 0.9000, rms radial error=134.022, avgs=0
- 260/300: dt: 0.9000, rms radial error=133.268, avgs=0
- 265/300: dt: 0.9000, rms radial error=132.518, avgs=0
- 270/300: dt: 0.9000, rms radial error=131.772, avgs=0
- 275/300: dt: 0.9000, rms radial error=131.030, avgs=0
- 280/300: dt: 0.9000, rms radial error=130.292, avgs=0
- 285/300: dt: 0.9000, rms radial error=129.558, avgs=0
- 290/300: dt: 0.9000, rms radial error=128.829, avgs=0
- 295/300: dt: 0.9000, rms radial error=128.103, avgs=0
- 300/300: dt: 0.9000, rms radial error=127.382, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 13112.08
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00017
- epoch 2 (K=40.0), pass 1, starting sse = 2164.42
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00016
- epoch 3 (K=160.0), pass 1, starting sse = 231.75
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.09/11 = 0.00782
- epoch 4 (K=640.0), pass 1, starting sse = 15.39
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.07/13 = 0.00536
- final writing spherical brain to ../surf/lh.qsphere.nofix
- spherical transformation took 0.07 hours
- distance error %100000.00
- #--------------------------------------------
- #@# Fix Topology lh Thu Aug 8 17:08:04 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/sub010/scripts
- mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub010 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=-48 (nv=113880, nf=227856, ne=341784, g=25)
- 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...
- 2877 ambiguous faces found in tessellation
- segmenting defects...
- 34 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- -merging segment 11 into 8
- 33 defects to be corrected
- 0 vertices coincident
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -9.7635 (-4.8818)
- -vertex loglikelihood: -6.9151 (-3.4575)
- -normal dot loglikelihood: -3.6436 (-3.6436)
- -quad curv loglikelihood: -6.5325 (-3.2663)
- Total Loglikelihood : -26.8548
- CORRECTING DEFECT 0 (vertices=5, convex hull=26)
- After retessellation of defect 0, euler #=-30 (112015,335104,223059) : difference with theory (-30) = 0
- CORRECTING DEFECT 1 (vertices=46, convex hull=86)
- After retessellation of defect 1, euler #=-29 (112037,335207,223141) : difference with theory (-29) = 0
- CORRECTING DEFECT 2 (vertices=338, convex hull=131)
- After retessellation of defect 2, euler #=-29 (112073,335396,223294) : difference with theory (-28) = 1
- CORRECTING DEFECT 3 (vertices=14, convex hull=27)
- After retessellation of defect 3, euler #=-28 (112075,335411,223308) : difference with theory (-27) = 1
- CORRECTING DEFECT 4 (vertices=30, convex hull=64)
- After retessellation of defect 4, euler #=-27 (112090,335483,223366) : difference with theory (-26) = 1
- CORRECTING DEFECT 5 (vertices=38, convex hull=87)
- After retessellation of defect 5, euler #=-26 (112105,335566,223435) : difference with theory (-25) = 1
- CORRECTING DEFECT 6 (vertices=31, convex hull=71)
- After retessellation of defect 6, euler #=-25 (112120,335642,223497) : difference with theory (-24) = 1
- CORRECTING DEFECT 7 (vertices=60, convex hull=90)
- After retessellation of defect 7, euler #=-24 (112152,335773,223597) : difference with theory (-23) = 1
- CORRECTING DEFECT 8 (vertices=41, convex hull=83)
- After retessellation of defect 8, euler #=-22 (112165,335849,223662) : difference with theory (-22) = 0
- CORRECTING DEFECT 9 (vertices=173, convex hull=179)
- After retessellation of defect 9, euler #=-21 (112188,335999,223790) : difference with theory (-21) = 0
- CORRECTING DEFECT 10 (vertices=41, convex hull=80)
- After retessellation of defect 10, euler #=-20 (112217,336117,223880) : difference with theory (-20) = 0
- CORRECTING DEFECT 11 (vertices=50, convex hull=74)
- After retessellation of defect 11, euler #=-19 (112238,336210,223953) : difference with theory (-19) = 0
- CORRECTING DEFECT 12 (vertices=27, convex hull=49)
- After retessellation of defect 12, euler #=-18 (112256,336283,224009) : difference with theory (-18) = 0
- CORRECTING DEFECT 13 (vertices=26, convex hull=81)
- After retessellation of defect 13, euler #=-17 (112269,336353,224067) : difference with theory (-17) = 0
- CORRECTING DEFECT 14 (vertices=88, convex hull=76)
- After retessellation of defect 14, euler #=-16 (112288,336442,224138) : difference with theory (-16) = 0
- CORRECTING DEFECT 15 (vertices=46, convex hull=85)
- After retessellation of defect 15, euler #=-15 (112298,336504,224191) : difference with theory (-15) = 0
- CORRECTING DEFECT 16 (vertices=17, convex hull=20)
- After retessellation of defect 16, euler #=-14 (112302,336521,224205) : difference with theory (-14) = 0
- CORRECTING DEFECT 17 (vertices=16, convex hull=46)
- After retessellation of defect 17, euler #=-13 (112311,336566,224242) : difference with theory (-13) = 0
- CORRECTING DEFECT 18 (vertices=38, convex hull=38)
- After retessellation of defect 18, euler #=-12 (112319,336602,224271) : difference with theory (-12) = 0
- CORRECTING DEFECT 19 (vertices=41, convex hull=30)
- After retessellation of defect 19, euler #=-11 (112326,336634,224297) : difference with theory (-11) = 0
- CORRECTING DEFECT 20 (vertices=25, convex hull=62)
- After retessellation of defect 20, euler #=-10 (112335,336683,224338) : difference with theory (-10) = 0
- CORRECTING DEFECT 21 (vertices=15, convex hull=19)
- After retessellation of defect 21, euler #=-9 (112337,336697,224351) : difference with theory (-9) = 0
- CORRECTING DEFECT 22 (vertices=9, convex hull=25)
- After retessellation of defect 22, euler #=-8 (112343,336722,224371) : difference with theory (-8) = 0
- CORRECTING DEFECT 23 (vertices=61, convex hull=61)
- After retessellation of defect 23, euler #=-7 (112349,336764,224408) : difference with theory (-7) = 0
- CORRECTING DEFECT 24 (vertices=252, convex hull=150)
- After retessellation of defect 24, euler #=-6 (112395,336974,224573) : difference with theory (-6) = 0
- CORRECTING DEFECT 25 (vertices=25, convex hull=53)
- After retessellation of defect 25, euler #=-5 (112407,337035,224623) : difference with theory (-5) = 0
- CORRECTING DEFECT 26 (vertices=21, convex hull=26)
- After retessellation of defect 26, euler #=-4 (112414,337063,224645) : difference with theory (-4) = 0
- CORRECTING DEFECT 27 (vertices=6, convex hull=28)
- After retessellation of defect 27, euler #=-3 (112416,337077,224658) : difference with theory (-3) = 0
- CORRECTING DEFECT 28 (vertices=33, convex hull=69)
- After retessellation of defect 28, euler #=-2 (112432,337151,224717) : difference with theory (-2) = 0
- CORRECTING DEFECT 29 (vertices=37, convex hull=46)
- After retessellation of defect 29, euler #=-1 (112441,337198,224756) : difference with theory (-1) = 0
- CORRECTING DEFECT 30 (vertices=72, convex hull=78)
- After retessellation of defect 30, euler #=0 (112470,337317,224847) : difference with theory (0) = 0
- CORRECTING DEFECT 31 (vertices=98, convex hull=109)
- After retessellation of defect 31, euler #=1 (112497,337448,224952) : difference with theory (1) = 0
- CORRECTING DEFECT 32 (vertices=45, convex hull=89)
- After retessellation of defect 32, euler #=2 (112521,337557,225038) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.88 +- 0.24 (0.04-->11.42) (max @ vno 86901 --> 94849)
- face area 0.00 +- 0.00 (0.00-->0.00)
- performing soap bubble on retessellated vertices for 0 iterations...
- vertex spacing 0.88 +- 0.24 (0.04-->11.42) (max @ vno 86901 --> 94849)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 145 mutations (37.1%), 246 crossovers (62.9%), 222 vertices were eliminated
- building final representation...
- 1359 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=112521, nf=225038, ne=337557, g=0)
- writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 23.2 minutes
- 0 defective edges
- removing intersecting faces
- 000: 247 intersecting
- 001: 14 intersecting
- mris_euler_number ../surf/lh.orig
- euler # = v-e+f = 2g-2: 112521 - 337557 + 225038 = 2 --> 0 holes
- F =2V-4: 225038 = 225042-4 (0)
- 2E=3F: 675114 = 675114 (0)
- total defect index = 0
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts
- mris_remove_intersection ../surf/lh.orig ../surf/lh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 33 intersecting
- 001: 4 intersecting
- writing corrected surface to ../surf/lh.orig
- rm ../surf/lh.inflated
- #--------------------------------------------
- #@# Make White Surf lh Thu Aug 8 17:31:24 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts
- mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub010 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/sub010/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/wm.mgz...
- 13095 bright wm thresholded.
- 240 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.orig...
- computing class statistics...
- border white: 201670 voxels (1.20%)
- border gray 234473 voxels (1.40%)
- WM (91.0): 92.1 +- 10.7 [70.0 --> 110.0]
- GM (73.0) : 71.4 +- 13.2 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 43.8 (was 70)
- setting MAX_BORDER_WHITE to 115.7 (was 105)
- setting MIN_BORDER_WHITE to 57.0 (was 85)
- setting MAX_CSF to 30.6 (was 40)
- setting MAX_GRAY to 94.3 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 50.4 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 17.4 (was 40)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.82 +- 0.22 (0.02-->3.89) (max @ vno 15970 --> 17848)
- face area 0.28 +- 0.12 (0.00-->2.64)
- mean absolute distance = 0.64 +- 0.76
- 2829 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=105, GM=57
- mean inside = 91.7, mean outside = 66.6
- smoothing surface for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- mean border=70.6, 73 (73) missing vertices, mean dist 0.4 [0.4 (%29.9)->0.7 (%70.1))]
- %69 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.92 +- 0.27 (0.08-->5.86) (max @ vno 49307 --> 52883)
- face area 0.28 +- 0.14 (0.00-->5.09)
- mean absolute distance = 0.31 +- 0.47
- 1959 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=6201876.5, rms=13.93
- 001: dt: 0.5000, sse=6300535.0, rms=10.162 (0.000%)
- 002: dt: 0.5000, sse=6480750.5, rms=8.034 (0.000%)
- 003: dt: 0.5000, sse=6603552.0, rms=6.726 (0.000%)
- 004: dt: 0.5000, sse=6743813.5, rms=5.930 (0.000%)
- 005: dt: 0.5000, sse=6841023.0, rms=5.489 (0.000%)
- 006: dt: 0.5000, sse=6893624.5, rms=5.219 (0.000%)
- 007: dt: 0.5000, sse=6924194.5, rms=5.080 (0.000%)
- 008: dt: 0.5000, sse=6928049.0, rms=4.941 (0.000%)
- 009: dt: 0.5000, sse=6892103.0, rms=4.876 (0.000%)
- 010: dt: 0.5000, sse=6868757.5, rms=4.797 (0.000%)
- rms = 4.77, time step reduction 1 of 3 to 0.250...
- 011: dt: 0.5000, sse=6846176.0, rms=4.766 (0.000%)
- 012: dt: 0.2500, sse=4494396.0, rms=3.470 (0.000%)
- 013: dt: 0.2500, sse=4136003.0, rms=3.041 (0.000%)
- 014: dt: 0.2500, sse=3924544.2, rms=2.960 (0.000%)
- 015: dt: 0.2500, sse=3860050.8, rms=2.866 (0.000%)
- rms = 2.84, time step reduction 2 of 3 to 0.125...
- 016: dt: 0.2500, sse=3781857.2, rms=2.843 (0.000%)
- 017: dt: 0.1250, sse=3528814.0, rms=2.519 (0.000%)
- 018: dt: 0.1250, sse=3482855.5, rms=2.466 (0.000%)
- rms = 2.45, time step reduction 3 of 3 to 0.062...
- 019: dt: 0.1250, sse=3453897.2, rms=2.451 (0.000%)
- positioning took 1.9 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 1 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 1 vertex label from ripped group
- mean border=75.3, 92 (10) missing vertices, mean dist -0.2 [0.3 (%77.9)->0.3 (%22.1))]
- %81 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.91 +- 0.26 (0.08-->6.05) (max @ vno 49307 --> 52883)
- face area 0.35 +- 0.17 (0.00-->6.88)
- mean absolute distance = 0.22 +- 0.31
- 2809 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4269646.0, rms=6.34
- 020: dt: 0.5000, sse=4491872.5, rms=4.382 (0.000%)
- rms = 4.77, time step reduction 1 of 3 to 0.250...
- 021: dt: 0.2500, sse=4064394.2, rms=3.159 (0.000%)
- 022: dt: 0.2500, sse=3890573.5, rms=2.627 (0.000%)
- 023: dt: 0.2500, sse=3841361.5, rms=2.188 (0.000%)
- rms = 2.18, time step reduction 2 of 3 to 0.125...
- 024: dt: 0.2500, sse=3835740.2, rms=2.182 (0.000%)
- 025: dt: 0.1250, sse=3668682.2, rms=1.851 (0.000%)
- 026: dt: 0.1250, sse=3629452.0, rms=1.800 (0.000%)
- rms = 1.80, time step reduction 3 of 3 to 0.062...
- 027: dt: 0.1250, sse=3602583.0, rms=1.800 (0.000%)
- positioning took 0.8 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 1 vertex label from ripped group
- mean border=78.9, 104 (7) missing vertices, mean dist -0.1 [0.2 (%76.8)->0.2 (%23.2))]
- %88 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.91 +- 0.26 (0.09-->6.33) (max @ vno 49307 --> 52883)
- face area 0.34 +- 0.17 (0.00-->7.12)
- mean absolute distance = 0.17 +- 0.26
- 2301 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=3951063.5, rms=4.54
- 028: dt: 0.5000, sse=4325509.0, rms=4.440 (0.000%)
- rms = 4.54, time step reduction 1 of 3 to 0.250...
- 029: dt: 0.2500, sse=3903438.8, rms=2.806 (0.000%)
- 030: dt: 0.2500, sse=3766594.8, rms=2.387 (0.000%)
- 031: dt: 0.2500, sse=3835299.5, rms=2.014 (0.000%)
- rms = 2.10, time step reduction 2 of 3 to 0.125...
- 032: dt: 0.1250, sse=3770415.0, rms=1.833 (0.000%)
- 033: dt: 0.1250, sse=3685747.2, rms=1.575 (0.000%)
- rms = 1.54, time step reduction 3 of 3 to 0.062...
- 034: dt: 0.1250, sse=3655808.0, rms=1.540 (0.000%)
- positioning took 0.8 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 1 vertex label from ripped group
- mean border=80.0, 96 (6) missing vertices, mean dist -0.0 [0.2 (%58.8)->0.2 (%41.2))]
- %90 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/sub010/surf/lh.white...
- writing smoothed curvature to lh.curv
- 000: dt: 0.0000, sse=3681861.5, rms=1.97
- rms = 3.05, time step reduction 1 of 3 to 0.250...
- 035: dt: 0.2500, sse=3760503.0, rms=1.311 (0.000%)
- 036: dt: 0.2500, sse=3910438.5, rms=1.152 (0.000%)
- rms = 1.15, time step reduction 2 of 3 to 0.125...
- 037: dt: 0.2500, sse=3993506.0, rms=1.145 (0.000%)
- rms = 1.12, time step reduction 3 of 3 to 0.062...
- 038: dt: 0.1250, sse=4022768.0, rms=1.120 (0.000%)
- positioning took 0.5 minutes
- inhibiting deformation at non-cortical midline structures...
- generating cortex label...
- 10 non-cortical segments detected
- only using segment with 1669 vertices
- erasing segment 1 (vno[0] = 70696)
- erasing segment 2 (vno[0] = 80752)
- erasing segment 3 (vno[0] = 80816)
- erasing segment 4 (vno[0] = 88329)
- erasing segment 5 (vno[0] = 89005)
- erasing segment 6 (vno[0] = 89818)
- erasing segment 7 (vno[0] = 91477)
- erasing segment 8 (vno[0] = 92922)
- erasing segment 9 (vno[0] = 93559)
- writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/label/lh.cortex.label...
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.curv
- writing smoothed area to lh.area
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.area
- vertex spacing 0.90 +- 0.26 (0.08-->6.42) (max @ vno 49307 --> 52883)
- face area 0.34 +- 0.17 (0.00-->7.20)
- refinement took 5.8 minutes
- #--------------------------------------------
- #@# Smooth2 lh Thu Aug 8 17:37:09 CEST 2013
- mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts
- smoothing for 3 iterations
- setting seed for random number generator to 1234
- smoothing surface tessellation for 3 iterations...
- smoothing complete - recomputing first and second fundamental forms...
- #--------------------------------------------
- #@# Inflation2 lh Thu Aug 8 17:37:12 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts
- mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated
- avg radius = 45.0 mm, total surface area = 69548 mm^2
- writing inflated surface to ../surf/lh.inflated
- writing sulcal depths to ../surf/lh.sulc
-
step 000: RMS=0.119 (target=0.015)
step 005: RMS=0.081 (target=0.015)
step 010: RMS=0.059 (target=0.015)
step 015: RMS=0.048 (target=0.015)
step 020: RMS=0.040 (target=0.015)
step 025: RMS=0.033 (target=0.015)
step 030: RMS=0.027 (target=0.015)
step 035: RMS=0.024 (target=0.015)
step 040: RMS=0.021 (target=0.015)
step 045: RMS=0.019 (target=0.015)
step 050: RMS=0.018 (target=0.015)
step 055: RMS=0.016 (target=0.015)
step 060: RMS=0.016 (target=0.015)
- inflation complete.
- inflation took 0.5 minutes
- mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated
- normalizing curvature values.
- averaging curvature patterns 5 times.
- sampling 10 neighbors out to a distance of 10 mm
- 100 vertices thresholded to be in k1 ~ [-0.76 0.46], k2 ~ [-0.30 0.12]
- total integrated curvature = 0.531*4pi (6.670) --> 0 handles
- ICI = 1.4, FI = 8.4, variation=143.686
- 112 vertices thresholded to be in [-0.05 0.05]
- writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level
- curvature mean = 0.000, std = 0.002
- 79 vertices thresholded to be in [-0.26 0.14]
- done.
- writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.019, std = 0.023
- done.
- #-----------------------------------------
- #@# Curvature Stats lh Thu Aug 8 17:39:11 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub010 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 [ sub010/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 [ 235 ]
- Gb_filter = 0
- WARN: S lookup min: -0.685159
- WARN: S explicit min: 0.000000 vertex = 1663
- #--------------------------------------------
- #@# Sphere lh Thu Aug 8 17:39:15 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 0.305...
- 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 %21.17
- pass 1: epoch 2 of 3 starting distance error %21.11
- unfolding complete - removing small folds...
- starting distance error %20.98
- removing remaining folds...
- final distance error %21.01
- MRISunfold() return, current seed 1234
- writing spherical brain to ../surf/lh.sphere
- spherical transformation took 0.84 hours
- #--------------------------------------------
- #@# Surf Reg lh Thu Aug 8 18:29:35 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 = 0.575
- curvature mean = 0.036, std = 0.938
- curvature mean = 0.021, std = 0.867
- Starting MRISrigidBodyAlignGlobal()
- d=32.00 min @ (0.00, -8.00, 0.00) sse = 200972.6, tmin=1.7917
- d=8.00 min @ (2.00, 2.00, -2.00) sse = 194728.5, tmin=3.5916
- d=4.00 min @ (-1.00, 0.00, 0.00) sse = 193221.5, tmin=4.5166
- d=2.00 min @ (0.00, 0.00, 0.50) sse = 193141.8, tmin=5.4543
- d=0.50 min @ (0.00, -0.12, -0.12) sse = 193114.1, tmin=7.3045
- 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 7.30 min
- curvature mean = 0.028, std = 0.968
- curvature mean = 0.009, std = 0.944
- curvature mean = 0.026, std = 0.981
- curvature mean = 0.004, std = 0.975
- curvature mean = 0.026, std = 0.985
- curvature mean = 0.001, std = 0.990
- 2 Reading smoothwm
- curvature mean = -0.028, std = 0.316
- curvature mean = 0.004, std = 0.068
- curvature mean = 0.069, std = 0.341
- curvature mean = 0.004, std = 0.080
- curvature mean = 0.035, std = 0.524
- curvature mean = 0.005, std = 0.087
- curvature mean = 0.019, std = 0.663
- curvature mean = 0.005, std = 0.090
- curvature mean = 0.006, std = 0.776
- MRISregister() return, current seed 0
- writing registered surface to ../surf/lh.sphere.reg...
- expanding nbhd size to 1
- #--------------------------------------------
- #@# Jacobian white lh Thu Aug 8 18:52:14 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 18:52:16 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 18:52:18 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub010 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...
- 894 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2612 changed, 112521 examined...
- 001: 561 changed, 11320 examined...
- 002: 116 changed, 3159 examined...
- 003: 35 changed, 675 examined...
- 004: 11 changed, 211 examined...
- 005: 5 changed, 70 examined...
- 006: 2 changed, 24 examined...
- 007: 3 changed, 13 examined...
- 008: 2 changed, 10 examined...
- 009: 3 changed, 10 examined...
- 010: 0 changed, 13 examined...
- 164 labels changed using aseg
- 000: 108 total segments, 65 labels (199 vertices) changed
- 001: 43 total segments, 1 labels (2 vertices) changed
- 002: 42 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 32 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 1051 vertices marked for relabeling...
- 1051 labels changed in reclassification.
- writing output to ../label/lh.aparc.annot...
- classification took 0 minutes and 50 seconds.
- #--------------------------------------------
- #@# Make Pial Surf lh Thu Aug 8 18:53:08 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts
- mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub010 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/sub010/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/wm.mgz...
- 13095 bright wm thresholded.
- 240 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.orig...
- computing class statistics...
- border white: 201670 voxels (1.20%)
- border gray 234473 voxels (1.40%)
- WM (91.0): 92.1 +- 10.7 [70.0 --> 110.0]
- GM (73.0) : 71.4 +- 13.2 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 43.8 (was 70)
- setting MAX_BORDER_WHITE to 115.7 (was 105)
- setting MIN_BORDER_WHITE to 57.0 (was 85)
- setting MAX_CSF to 30.6 (was 40)
- setting MAX_GRAY to 94.3 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 50.4 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 17.4 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=105, GM=57
- mean inside = 91.7, mean outside = 66.6
- smoothing surface for 5 iterations...
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.82 +- 0.22 (0.02-->3.89) (max @ vno 15970 --> 17848)
- face area 0.28 +- 0.12 (0.00-->2.64)
- mean absolute distance = 0.65 +- 0.77
- 2940 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 23 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 3 with 950 points - only 4.74% unknown
- deleting segment 4 with 19 points - only 0.00% unknown
- deleting segment 6 with 6 points - only 0.00% unknown
- deleting segment 7 with 7 points - only 0.00% unknown
- deleting segment 8 with 13 points - only 0.00% unknown
- deleting segment 9 with 17 points - only 0.00% unknown
- deleting segment 10 with 30 points - only 0.00% unknown
- deleting segment 11 with 5 points - only 0.00% unknown
- mean border=70.6, 75 (73) missing vertices, mean dist 0.4 [0.5 (%29.9)->0.7 (%70.1))]
- %70 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.92 +- 0.27 (0.08-->5.86) (max @ vno 49307 --> 52883)
- face area 0.28 +- 0.14 (0.00-->5.08)
- mean absolute distance = 0.31 +- 0.48
- 1990 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=6236135.5, rms=13.89
- 001: dt: 0.5000, sse=6337606.0, rms=10.134 (0.000%)
- 002: dt: 0.5000, sse=6519611.5, rms=8.011 (0.000%)
- 003: dt: 0.5000, sse=6643135.5, rms=6.709 (0.000%)
- 004: dt: 0.5000, sse=6789308.0, rms=5.916 (0.000%)
- 005: dt: 0.5000, sse=6884693.0, rms=5.478 (0.000%)
- 006: dt: 0.5000, sse=6943840.0, rms=5.208 (0.000%)
- 007: dt: 0.5000, sse=6971964.0, rms=5.070 (0.000%)
- 008: dt: 0.5000, sse=6980964.0, rms=4.933 (0.000%)
- 009: dt: 0.5000, sse=6943480.0, rms=4.871 (0.000%)
- 010: dt: 0.5000, sse=6926897.0, rms=4.792 (0.000%)
- rms = 4.76, time step reduction 1 of 3 to 0.250...
- 011: dt: 0.5000, sse=6898367.0, rms=4.763 (0.000%)
- 012: dt: 0.2500, sse=4528130.5, rms=3.470 (0.000%)
- 013: dt: 0.2500, sse=4167583.8, rms=3.038 (0.000%)
- 014: dt: 0.2500, sse=3953588.5, rms=2.957 (0.000%)
- 015: dt: 0.2500, sse=3887498.2, rms=2.860 (0.000%)
- rms = 2.83, time step reduction 2 of 3 to 0.125...
- 016: dt: 0.2500, sse=3807576.8, rms=2.835 (0.000%)
- 017: dt: 0.1250, sse=3555130.5, rms=2.512 (0.000%)
- 018: dt: 0.1250, sse=3509869.0, rms=2.461 (0.000%)
- rms = 2.45, time step reduction 3 of 3 to 0.062...
- 019: dt: 0.1250, sse=3481148.2, rms=2.449 (0.000%)
- positioning took 1.9 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 19 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 1 with 1 points - only 0.00% unknown
- deleting segment 7 with 857 points - only 5.25% unknown
- removing 4 vertex label from ripped group
- deleting segment 12 with 5 points - only 0.00% unknown
- deleting segment 13 with 15 points - only 0.00% unknown
- deleting segment 14 with 35 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 15 with 4 points - only 0.00% unknown
- mean border=75.3, 93 (9) missing vertices, mean dist -0.2 [0.3 (%77.9)->0.3 (%22.1))]
- %82 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.91 +- 0.26 (0.12-->6.05) (max @ vno 49307 --> 52883)
- face area 0.35 +- 0.17 (0.00-->6.88)
- mean absolute distance = 0.22 +- 0.32
- 2227 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4306171.0, rms=6.34
- 020: dt: 0.5000, sse=4528531.0, rms=4.384 (0.000%)
- rms = 4.76, time step reduction 1 of 3 to 0.250...
- 021: dt: 0.2500, sse=4098567.5, rms=3.164 (0.000%)
- 022: dt: 0.2500, sse=3926800.0, rms=2.635 (0.000%)
- 023: dt: 0.2500, sse=3875310.2, rms=2.198 (0.000%)
- rms = 2.19, time step reduction 2 of 3 to 0.125...
- 024: dt: 0.2500, sse=3872115.0, rms=2.194 (0.000%)
- 025: dt: 0.1250, sse=3703568.0, rms=1.867 (0.000%)
- 026: dt: 0.1250, sse=3667082.5, rms=1.817 (0.000%)
- rms = 1.82, time step reduction 3 of 3 to 0.062...
- 027: dt: 0.1250, sse=3638557.8, rms=1.815 (0.000%)
- positioning took 0.8 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 15 points - only 0.00% unknown
- deleting segment 1 with 36 points - only 11.11% unknown
- removing 2 vertex label from ripped group
- deleting segment 2 with 2 points - only 0.00% unknown
- deleting segment 3 with 933 points - only 4.82% 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 15 points - only 0.00% unknown
- deleting segment 8 with 20 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 9 with 2 points - only 0.00% unknown
- deleting segment 10 with 5 points - only 0.00% unknown
- mean border=78.8, 109 (5) missing vertices, mean dist -0.1 [0.2 (%76.8)->0.2 (%23.2))]
- %89 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.91 +- 0.26 (0.09-->6.33) (max @ vno 49307 --> 52883)
- face area 0.34 +- 0.17 (0.00-->7.12)
- mean absolute distance = 0.17 +- 0.26
- 2322 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=3987435.2, rms=4.52
- 028: dt: 0.5000, sse=4360479.5, rms=4.443 (0.000%)
- rms = 4.54, time step reduction 1 of 3 to 0.250...
- 029: dt: 0.2500, sse=3937313.8, rms=2.815 (0.000%)
- 030: dt: 0.2500, sse=3801524.8, rms=2.401 (0.000%)
- 031: dt: 0.2500, sse=3871084.0, rms=2.033 (0.000%)
- rms = 2.12, time step reduction 2 of 3 to 0.125...
- 032: dt: 0.1250, sse=3806410.5, rms=1.855 (0.000%)
- 033: dt: 0.1250, sse=3722069.0, rms=1.601 (0.000%)
- rms = 1.56, time step reduction 3 of 3 to 0.062...
- 034: dt: 0.1250, sse=3689253.5, rms=1.565 (0.000%)
- positioning took 0.8 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 11 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 3 with 6 points - only 0.00% unknown
- deleting segment 4 with 940 points - only 4.79% unknown
- deleting segment 5 with 6 points - only 0.00% unknown
- deleting segment 6 with 11 points - only 0.00% unknown
- deleting segment 7 with 16 points - only 0.00% unknown
- deleting segment 8 with 19 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 9 with 2 points - only 0.00% unknown
- deleting segment 10 with 5 points - only 0.00% unknown
- mean border=79.9, 118 (4) missing vertices, mean dist -0.0 [0.2 (%58.8)->0.2 (%41.2))]
- %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=3715870.0, rms=1.99
- rms = 3.05, time step reduction 1 of 3 to 0.250...
- 035: dt: 0.2500, sse=3797065.5, rms=1.340 (0.000%)
- 036: dt: 0.2500, sse=3951858.5, rms=1.168 (0.000%)
- rms = 1.16, time step reduction 2 of 3 to 0.125...
- 037: dt: 0.2500, sse=4035628.5, rms=1.157 (0.000%)
- rms = 1.13, time step reduction 3 of 3 to 0.062...
- 038: dt: 0.1250, sse=4063921.5, rms=1.127 (0.000%)
- positioning took 0.5 minutes
- inhibiting deformation at non-cortical midline structures...
- smoothing surface for 5 iterations...
- mean border=46.7, 55 (55) missing vertices, mean dist 1.8 [0.1 (%0.0)->2.3 (%100.0))]
- %17 local maxima, %57 large gradients and %21 min vals, 1181 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=24858422.0, rms=32.46
- 001: dt: 0.5000, sse=17687736.0, rms=26.747 (0.000%)
- 002: dt: 0.5000, sse=12847571.0, rms=22.106 (0.000%)
- 003: dt: 0.5000, sse=9726175.0, rms=18.430 (0.000%)
- 004: dt: 0.5000, sse=7884176.5, rms=15.524 (0.000%)
- 005: dt: 0.5000, sse=6842810.0, rms=13.231 (0.000%)
- 006: dt: 0.5000, sse=6196642.5, rms=11.439 (0.000%)
- 007: dt: 0.5000, sse=5854193.0, rms=9.979 (0.000%)
- 008: dt: 0.5000, sse=5617719.5, rms=8.722 (0.000%)
- 009: dt: 0.5000, sse=5504031.5, rms=7.647 (0.000%)
- 010: dt: 0.5000, sse=5451949.0, rms=6.765 (0.000%)
- 011: dt: 0.5000, sse=5531929.5, rms=6.077 (0.000%)
- 012: dt: 0.5000, sse=5561197.5, rms=5.522 (0.000%)
- 013: dt: 0.5000, sse=5675990.0, rms=5.123 (0.000%)
- 014: dt: 0.5000, sse=5757143.0, rms=4.848 (0.000%)
- 015: dt: 0.5000, sse=5825581.5, rms=4.640 (0.000%)
- 016: dt: 0.5000, sse=5866411.5, rms=4.477 (0.000%)
- 017: dt: 0.5000, sse=5892094.0, rms=4.367 (0.000%)
- 018: dt: 0.5000, sse=5916866.5, rms=4.278 (0.000%)
- rms = 4.23, time step reduction 1 of 3 to 0.250...
- 019: dt: 0.5000, sse=5972314.5, rms=4.232 (0.000%)
- 020: dt: 0.2500, sse=4336481.5, rms=3.580 (0.000%)
- 021: dt: 0.2500, sse=4182995.8, rms=3.401 (0.000%)
- rms = 3.38, time step reduction 2 of 3 to 0.125...
- 022: dt: 0.2500, sse=4078695.0, rms=3.382 (0.000%)
- 023: dt: 0.1250, sse=3912956.0, rms=3.278 (0.000%)
- rms = 3.27, time step reduction 3 of 3 to 0.062...
- 024: dt: 0.1250, sse=3889524.8, rms=3.266 (0.000%)
- positioning took 2.3 minutes
- mean border=44.1, 612 (13) missing vertices, mean dist 0.2 [0.2 (%46.6)->0.6 (%53.4))]
- %35 local maxima, %42 large gradients and %18 min vals, 490 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=4512922.5, rms=5.42
- 025: dt: 0.5000, sse=4742340.5, rms=4.582 (0.000%)
- 026: dt: 0.5000, sse=5974030.5, rms=4.442 (0.000%)
- rms = 4.40, time step reduction 1 of 3 to 0.250...
- 027: dt: 0.5000, sse=5956478.0, rms=4.404 (0.000%)
- 028: dt: 0.2500, sse=4828224.0, rms=3.590 (0.000%)
- 029: dt: 0.2500, sse=4726922.5, rms=3.337 (0.000%)
- rms = 3.31, time step reduction 2 of 3 to 0.125...
- 030: dt: 0.2500, sse=4622455.0, rms=3.309 (0.000%)
- 031: dt: 0.1250, sse=4461873.0, rms=3.163 (0.000%)
- rms = 3.14, time step reduction 3 of 3 to 0.062...
- 032: dt: 0.1250, sse=4438586.0, rms=3.138 (0.000%)
- positioning took 0.8 minutes
- mean border=41.7, 769 (7) missing vertices, mean dist 0.1 [0.2 (%36.9)->0.4 (%63.1))]
- %55 local maxima, %21 large gradients and %18 min vals, 557 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=4684454.0, rms=4.47
- 033: dt: 0.5000, sse=4887963.0, rms=4.203 (0.000%)
- rms = 4.25, time step reduction 1 of 3 to 0.250...
- 034: dt: 0.2500, sse=4608592.5, rms=3.488 (0.000%)
- 035: dt: 0.2500, sse=4814211.5, rms=3.192 (0.000%)
- 036: dt: 0.2500, sse=4767194.0, rms=3.131 (0.000%)
- rms = 3.09, time step reduction 2 of 3 to 0.125...
- 037: dt: 0.2500, sse=4817374.5, rms=3.089 (0.000%)
- 038: dt: 0.1250, sse=4633848.5, rms=2.952 (0.000%)
- rms = 2.93, time step reduction 3 of 3 to 0.062...
- 039: dt: 0.1250, sse=4628728.0, rms=2.930 (0.000%)
- positioning took 0.8 minutes
- mean border=40.4, 1523 (3) missing vertices, mean dist 0.1 [0.2 (%44.4)->0.3 (%55.6))]
- %59 local maxima, %17 large gradients and %18 min vals, 401 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/sub010/surf/lh.pial...
- writing smoothed curvature to lh.curv.pial
- 000: dt: 0.0000, sse=4673022.5, rms=3.26
- rms = 3.94, time step reduction 1 of 3 to 0.250...
- 040: dt: 0.2500, sse=4550543.5, rms=2.969 (0.000%)
- 041: dt: 0.2500, sse=4697228.0, rms=2.882 (0.000%)
- rms = 2.85, time step reduction 2 of 3 to 0.125...
- 042: dt: 0.2500, sse=4765246.5, rms=2.846 (0.000%)
- 043: dt: 0.1250, sse=4665466.0, rms=2.730 (0.000%)
- rms = 2.71, time step reduction 3 of 3 to 0.062...
- 044: dt: 0.1250, sse=4681510.0, rms=2.711 (0.000%)
- positioning took 0.6 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.curv.pial
- writing smoothed area to lh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.area.pial
- vertex spacing 1.05 +- 0.45 (0.08-->8.25) (max @ vno 79788 --> 78779)
- face area 0.44 +- 0.33 (0.00-->9.19)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 112521 vertices processed
- 25000 of 112521 vertices processed
- 50000 of 112521 vertices processed
- 75000 of 112521 vertices processed
- 100000 of 112521 vertices processed
- 0 of 112521 vertices processed
- 25000 of 112521 vertices processed
- 50000 of 112521 vertices processed
- 75000 of 112521 vertices processed
- 100000 of 112521 vertices processed
- thickness calculation complete, 288:998 truncations.
- 24574 vertices at 0 distance
- 73812 vertices at 1 distance
- 71442 vertices at 2 distance
- 31784 vertices at 3 distance
- 8764 vertices at 4 distance
- 2130 vertices at 5 distance
- 632 vertices at 6 distance
- 216 vertices at 7 distance
- 83 vertices at 8 distance
- 57 vertices at 9 distance
- 28 vertices at 10 distance
- 13 vertices at 11 distance
- 18 vertices at 12 distance
- 18 vertices at 13 distance
- 6 vertices at 14 distance
- 15 vertices at 15 distance
- 20 vertices at 16 distance
- 10 vertices at 17 distance
- 8 vertices at 18 distance
- 1 vertices at 19 distance
- 15 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.thickness
- positioning took 11.4 minutes
- #--------------------------------------------
- #@# Surf Volume lh Thu Aug 8 19:04:31 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf
- mris_calc -o lh.area.mid lh.area add lh.area.pial
- Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o lh.area.mid lh.area.mid div 2
- Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o lh.volume lh.area.mid mul lh.thickness
- Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ]
- #-----------------------------------------
- #@# WM/GM Contrast lh Thu Aug 8 19:04:31 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts
- pctsurfcon --s sub010 --lh-only
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts/pctsurfcon.log
- Thu Aug 8 19:04:31 CEST 2013
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts
- /opt/freesurfer/5.3.0/bin/pctsurfcon
- $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $
- Linux snake4 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/sub010/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/tmp.pctsurfcon.31166/lh.wm.mgh --regheader sub010 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/label/lh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 = 87112
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/label/lh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/tmp.pctsurfcon.31166/lh.wm.mgh
- Dim: 112521 1 1
- mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/tmp.pctsurfcon.31166/lh.gm.mgh --projfrac 0.3 --regheader sub010 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/label/lh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.white
- Done reading source surface
- Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 = 100596
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/label/lh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/tmp.pctsurfcon.31166/lh.gm.mgh
- Dim: 112521 1 1
- mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/tmp.pctsurfcon.31166/lh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/tmp.pctsurfcon.31166/lh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/surf/lh.w-g.pct.mgh
- mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.w-g.pct.mgh --annot sub010 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/surf/lh.w-g.pct.mgh --annot sub010 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/stats/lh.w-g.pct.stats --snr
- sysname Linux
- hostname snake4
- 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/sub010/surf/lh.w-g.pct.mgh
- Vertex Area is 0.677656 mm^3
- Generating list of segmentation ids
- Found 36 segmentations
- Computing statistics for each segmentation
- 0 1000 unknown 0 0.000
- 1 1001 bankssts 1374 950.297
- 2 1002 caudalanteriorcingulate 831 560.371
- 3 1003 caudalmiddlefrontal 2328 1552.597
- 4 1004 corpuscallosum 0 0.000
- 5 1005 cuneus 2341 1516.038
- 6 1006 entorhinal 463 358.715
- 7 1007 fusiform 4034 2769.124
- 8 1008 inferiorparietal 6246 4317.512
- 9 1009 inferiortemporal 4634 3226.471
- 10 1010 isthmuscingulate 1325 885.830
- 11 1011 lateraloccipital 6344 4063.706
- 12 1012 lateralorbitofrontal 2862 1972.734
- 13 1013 lingual 4100 2872.105
- 14 1014 medialorbitofrontal 2135 1399.892
- 15 1015 middletemporal 3674 2670.622
- 16 1016 parahippocampal 786 547.957
- 17 1017 paracentral 1577 1051.674
- 18 1018 parsopercularis 1879 1318.475
- 19 1019 parsorbitalis 789 544.669
- 20 1020 parstriangularis 1446 994.055
- 21 1021 pericalcarine 2116 1423.561
- 22 1022 postcentral 5135 3403.305
- 23 1023 posteriorcingulate 1407 926.874
- 24 1024 precentral 6317 4196.049
- 25 1025 precuneus 4869 3313.008
- 26 1026 rostralanteriorcingulate 1071 731.814
- 27 1027 rostralmiddlefrontal 7023 4899.621
- 28 1028 superiorfrontal 8194 5685.728
- 29 1029 superiorparietal 7149 4715.262
- 30 1030 superiortemporal 4004 2770.111
- 31 1031 supramarginal 4432 3006.804
- 32 1032 frontalpole 271 168.141
- 33 1033 temporalpole 682 490.979
- 34 1034 transversetemporal 488 311.560
- 35 1035 insula 2715 1748.682
- Reporting on 34 segmentations
- mri_segstats done
- Cleaning up
- #-----------------------------------------
- #@# Parcellation Stats lh Thu Aug 8 19:04:42 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 sub010 lh white
- computing statistics for each annotation in ../label/lh.aparc.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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
- 1374 950 2563 2.703 0.409 0.124 0.031 13 1.7 bankssts
- 831 560 2102 3.156 0.651 0.190 0.073 27 2.3 caudalanteriorcingulate
- 2328 1553 4236 2.449 0.544 0.135 0.045 32 4.2 caudalmiddlefrontal
- 2341 1516 3529 2.124 0.489 0.170 0.071 52 6.7 cuneus
- 463 359 1737 3.685 1.063 0.148 0.049 7 0.8 entorhinal
- 4034 2769 8812 2.683 0.618 0.161 0.064 97 11.2 fusiform
- 6246 4318 12853 2.547 0.508 0.155 0.062 142 14.8 inferiorparietal
- 4634 3226 10068 2.477 0.687 0.163 0.080 137 12.8 inferiortemporal
- 1325 886 2627 2.721 0.812 0.165 0.091 29 3.3 isthmuscingulate
- 6344 4064 9327 2.052 0.488 0.150 0.053 108 12.9 lateraloccipital
- 2862 1973 6305 2.690 0.709 0.154 0.070 72 7.4 lateralorbitofrontal
- 4100 2872 7176 2.214 0.553 0.180 0.095 140 13.1 lingual
- 2135 1400 4339 2.460 0.829 0.191 0.135 159 11.5 medialorbitofrontal
- 3674 2671 9393 2.749 0.686 0.166 0.070 105 10.8 middletemporal
- 786 548 2286 3.504 0.676 0.147 0.056 20 1.6 parahippocampal
- 1577 1052 2775 2.365 0.523 0.126 0.040 17 2.4 paracentral
- 1879 1318 3832 2.517 0.452 0.141 0.055 39 4.0 parsopercularis
- 789 545 2240 2.916 0.676 0.165 0.068 20 2.1 parsorbitalis
- 1446 994 3095 2.606 0.522 0.156 0.061 31 3.0 parstriangularis
- 2116 1424 2394 1.745 0.447 0.148 0.064 44 5.0 pericalcarine
- 5135 3403 8437 2.127 0.587 0.137 0.049 87 9.8 postcentral
- 1407 927 2665 2.703 0.505 0.149 0.045 28 2.6 posteriorcingulate
- 6317 4196 12756 2.638 0.510 0.125 0.046 83 10.0 precentral
- 4869 3313 8841 2.357 0.568 0.146 0.060 101 12.0 precuneus
- 1071 732 2430 2.798 0.701 0.172 0.075 26 3.2 rostralanteriorcingulate
- 7023 4900 14490 2.405 0.595 0.172 0.072 178 19.4 rostralmiddlefrontal
- 8194 5686 19182 2.757 0.617 0.153 0.068 207 17.3 superiorfrontal
- 7149 4715 11812 2.209 0.464 0.133 0.046 115 13.3 superiorparietal
- 4004 2770 9678 2.808 0.675 0.127 0.044 83 7.4 superiortemporal
- 4432 3007 8834 2.510 0.557 0.157 0.069 112 10.3 supramarginal
- 271 168 770 3.257 0.494 0.205 0.117 10 1.1 frontalpole
- 682 491 2810 3.642 0.928 0.189 0.098 20 2.8 temporalpole
- 488 312 875 2.600 0.319 0.155 0.053 8 1.1 transversetemporal
- 2715 1749 5996 2.927 0.917 0.118 0.136 59 7.4 insula
- #-----------------------------------------
- #@# Cortical Parc 2 lh Thu Aug 8 19:04:55 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub010 lh ../surf/lh.sphere.reg /opt/freesurfer/5.3.0/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot
- setting seed for random number generator to 1234
- using ../mri/aseg.mgz aseg volume to correct midline
- $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading atlas from /opt/freesurfer/5.3.0/average/lh.destrieux.simple.2009-07-29.gcs...
- reading color table from GCSA file....
- average std = 3.9 0.2 using min determinant for regularization = 0.000
- 0 singular and 1066 ill-conditioned covariance matrices regularized
- input 1: CURVATURE FILE, flags 0, avgs 0, name sulc
- input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
- labeling surface...
- 27 labels changed using aseg
- relabeling using gibbs priors...
- 000: 7893 changed, 112521 examined...
- 001: 1975 changed, 30181 examined...
- 002: 569 changed, 10037 examined...
- 003: 242 changed, 3209 examined...
- 004: 87 changed, 1304 examined...
- 005: 61 changed, 506 examined...
- 006: 35 changed, 342 examined...
- 007: 20 changed, 183 examined...
- 008: 12 changed, 121 examined...
- 009: 8 changed, 72 examined...
- 010: 3 changed, 48 examined...
- 011: 0 changed, 18 examined...
- 20 labels changed using aseg
- 000: 229 total segments, 146 labels (1364 vertices) changed
- 001: 91 total segments, 8 labels (63 vertices) changed
- 002: 84 total segments, 1 labels (7 vertices) changed
- 003: 83 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 112 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 556 vertices marked for relabeling...
- 556 labels changed in reclassification.
- writing output to ../label/lh.aparc.a2009s.annot...
- classification took 0 minutes and 57 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 2 lh Thu Aug 8 19:05:53 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 sub010 lh white
- computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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
- 1109 739 2276 2.563 0.677 0.179 0.092 32 3.8 G_and_S_frontomargin
- 1131 789 1972 2.216 0.490 0.144 0.041 17 1.9 G_and_S_occipital_inf
- 1218 789 2462 2.438 0.503 0.139 0.090 23 2.1 G_and_S_paracentral
- 1387 924 3095 2.652 0.518 0.167 0.079 39 3.7 G_and_S_subcentral
- 577 383 1472 2.789 0.591 0.191 0.093 19 1.9 G_and_S_transv_frontopol
- 2197 1513 4613 2.698 0.614 0.155 0.073 45 5.6 G_and_S_cingul-Ant
- 1226 858 2707 2.698 0.817 0.155 0.054 23 2.5 G_and_S_cingul-Mid-Ant
- 1111 756 2055 2.573 0.506 0.123 0.037 13 1.7 G_and_S_cingul-Mid-Post
- 371 250 1046 3.132 0.477 0.205 0.083 13 1.3 G_cingul-Post-dorsal
- 263 169 487 2.624 0.928 0.184 0.238 9 0.9 G_cingul-Post-ventral
- 2136 1360 3236 1.987 0.494 0.176 0.088 58 6.9 G_cuneus
- 1068 746 2703 2.742 0.437 0.172 0.085 36 3.7 G_front_inf-Opercular
- 258 175 717 3.165 0.477 0.164 0.067 6 0.7 G_front_inf-Orbital
- 823 582 2088 2.683 0.486 0.169 0.070 22 1.7 G_front_inf-Triangul
- 3410 2450 8766 2.672 0.573 0.197 0.077 111 11.2 G_front_middle
- 5447 3756 14261 2.896 0.584 0.164 0.083 222 13.5 G_front_sup
- 444 269 1350 3.355 0.906 0.158 0.155 27 2.7 G_Ins_lg_and_S_cent_ins
- 545 334 1878 3.827 0.736 0.123 0.404 13 1.4 G_insular_short
- 1850 1182 3931 2.508 0.426 0.179 0.065 56 4.8 G_occipital_middle
- 1371 869 2231 2.213 0.441 0.152 0.059 31 3.0 G_occipital_sup
- 1637 1071 4041 2.847 0.520 0.182 0.081 53 6.2 G_oc-temp_lat-fusifor
- 2779 1923 4986 2.134 0.538 0.190 0.113 105 10.0 G_oc-temp_med-Lingual
- 1045 749 3417 3.597 0.783 0.143 0.048 21 1.8 G_oc-temp_med-Parahip
- 2031 1393 5750 2.936 0.649 0.182 0.093 72 6.7 G_orbital
- 2199 1536 5634 2.727 0.461 0.188 0.094 77 7.2 G_pariet_inf-Angular
- 2133 1481 5325 2.679 0.569 0.179 0.093 79 6.2 G_pariet_inf-Supramar
- 2642 1714 5334 2.379 0.483 0.149 0.057 55 6.2 G_parietal_sup
- 1889 1232 3588 2.284 0.490 0.145 0.051 37 4.1 G_postcentral
- 2303 1482 5924 2.958 0.376 0.137 0.048 39 4.6 G_precentral
- 2202 1495 5003 2.569 0.573 0.173 0.079 70 7.4 G_precuneus
- 907 568 2217 2.714 0.788 0.236 0.178 70 7.5 G_rectus
- 198 117 349 2.880 1.127 0.133 0.084 4 0.3 G_subcallosal
- 399 251 894 2.759 0.368 0.165 0.087 27 1.0 G_temp_sup-G_T_transv
- 1572 1073 5180 3.209 0.601 0.169 0.068 50 4.9 G_temp_sup-Lateral
- 328 244 1213 3.999 0.888 0.114 0.038 3 0.4 G_temp_sup-Plan_polar
- 763 547 1583 2.500 0.392 0.095 0.021 5 0.7 G_temp_sup-Plan_tempo
- 2843 1986 6968 2.565 0.696 0.181 0.098 110 9.3 G_temporal_inf
- 2091 1540 6671 2.983 0.677 0.191 0.096 80 8.2 G_temporal_middle
- 315 210 639 2.818 0.415 0.143 0.049 6 0.6 Lat_Fis-ant-Horizont
- 106 82 161 2.171 0.272 0.116 0.022 1 0.1 Lat_Fis-ant-Vertical
- 843 557 1141 2.407 0.481 0.130 0.038 7 1.3 Lat_Fis-post
- 2061 1265 2505 1.718 0.458 0.152 0.067 35 4.8 Pole_occipital
- 1529 1118 5501 3.161 0.912 0.207 0.124 63 7.7 Pole_temporal
- 2880 1993 3874 2.034 0.611 0.151 0.062 62 7.3 S_calcarine
- 2585 1764 3191 1.983 0.579 0.111 0.029 16 3.2 S_central
- 936 642 1346 2.216 0.460 0.112 0.026 7 1.1 S_cingul-Marginalis
- 448 310 872 2.735 0.648 0.105 0.026 2 0.5 S_circular_insula_ant
- 1183 798 1860 2.457 0.581 0.103 0.045 13 2.4 S_circular_insula_inf
- 1680 1116 2315 2.343 0.394 0.097 0.027 10 1.7 S_circular_insula_sup
- 1091 776 1909 2.439 0.537 0.108 0.022 8 1.1 S_collat_transv_ant
- 286 186 310 2.002 0.475 0.171 0.052 5 0.5 S_collat_transv_post
- 1682 1140 2476 2.170 0.386 0.126 0.034 16 2.2 S_front_inf
- 1401 964 2130 2.071 0.513 0.143 0.072 22 3.2 S_front_middle
- 2034 1397 3730 2.416 0.528 0.131 0.043 28 3.2 S_front_sup
- 319 207 340 1.937 0.259 0.134 0.035 3 0.5 S_interm_prim-Jensen
- 2941 1970 4126 2.166 0.414 0.113 0.029 25 3.7 S_intrapariet_and_P_trans
- 1077 711 1305 2.026 0.338 0.121 0.034 8 1.4 S_oc_middle_and_Lunatus
- 1085 731 1532 2.204 0.380 0.130 0.038 12 1.7 S_oc_sup_and_transversal
- 582 397 784 2.066 0.327 0.142 0.048 8 1.0 S_occipital_ant
- 809 532 1141 2.448 0.525 0.129 0.036 8 1.3 S_oc-temp_lat
- 1529 1086 3056 2.730 0.724 0.153 0.050 31 3.2 S_oc-temp_med_and_Lingual
- 301 203 432 2.092 0.514 0.129 0.038 3 0.4 S_orbital_lateral
- 545 380 1021 2.363 1.010 0.119 0.045 12 1.0 S_orbital_med-olfact
- 892 628 1505 2.381 0.598 0.144 0.049 12 1.9 S_orbital-H_Shaped
- 1993 1361 2884 2.241 0.467 0.123 0.035 20 2.9 S_parieto_occipital
- 982 607 1308 2.623 0.898 0.166 0.045 24 1.7 S_pericallosal
- 2504 1678 3367 2.074 0.444 0.124 0.040 31 3.8 S_postcentral
- 1490 1013 2427 2.462 0.411 0.118 0.032 16 1.9 S_precentral-inf-part
- 1052 720 1464 2.237 0.366 0.107 0.024 6 1.2 S_precentral-sup-part
- 580 384 999 2.189 0.690 0.178 0.099 28 2.3 S_suborbital
- 846 575 1364 2.304 0.522 0.126 0.039 8 1.3 S_subparietal
- 1372 961 1812 2.054 0.425 0.138 0.040 19 2.1 S_temporal_inf
- 4864 3383 8492 2.556 0.485 0.124 0.036 56 7.2 S_temporal_sup
- 315 225 524 2.518 0.297 0.095 0.018 1 0.3 S_temporal_transverse
- #-----------------------------------------
- #@# Cortical Parc 3 lh Thu Aug 8 19:06:06 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub010 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...
- 779 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2351 changed, 112521 examined...
- 001: 571 changed, 10363 examined...
- 002: 147 changed, 3186 examined...
- 003: 48 changed, 848 examined...
- 004: 23 changed, 286 examined...
- 005: 12 changed, 137 examined...
- 006: 8 changed, 68 examined...
- 007: 8 changed, 47 examined...
- 008: 6 changed, 30 examined...
- 009: 2 changed, 24 examined...
- 010: 2 changed, 12 examined...
- 011: 2 changed, 13 examined...
- 012: 0 changed, 14 examined...
- 163 labels changed using aseg
- 000: 66 total segments, 33 labels (220 vertices) changed
- 001: 33 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 20 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 399 vertices marked for relabeling...
- 399 labels changed in reclassification.
- writing output to ../label/lh.aparc.DKTatlas40.annot...
- classification took 0 minutes and 50 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 3 lh Thu Aug 8 19:06:56 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 sub010 lh white
- computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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
- 1373 935 3202 3.001 0.628 0.166 0.060 32 3.2 caudalanteriorcingulate
- 2337 1569 4298 2.452 0.545 0.134 0.045 32 4.2 caudalmiddlefrontal
- 3150 2057 4686 2.117 0.475 0.153 0.060 61 7.5 cuneus
- 430 330 1473 3.587 1.046 0.149 0.046 6 0.8 entorhinal
- 3635 2476 7715 2.674 0.598 0.155 0.055 77 9.1 fusiform
- 5747 3975 11756 2.525 0.512 0.156 0.062 131 13.7 inferiorparietal
- 4697 3290 10433 2.495 0.699 0.163 0.083 139 12.8 inferiortemporal
- 1341 899 2660 2.723 0.811 0.165 0.091 29 3.3 isthmuscingulate
- 6430 4118 9550 2.058 0.490 0.149 0.053 111 12.9 lateraloccipital
- 3092 2107 7305 2.765 0.749 0.161 0.074 83 8.6 lateralorbitofrontal
- 4079 2865 7164 2.216 0.549 0.179 0.095 135 12.8 lingual
- 1805 1184 3827 2.509 0.851 0.201 0.132 105 10.1 medialorbitofrontal
- 5076 3623 12132 2.702 0.662 0.163 0.067 136 14.7 middletemporal
- 845 590 2468 3.509 0.670 0.149 0.057 21 1.8 parahippocampal
- 1774 1189 3226 2.402 0.539 0.124 0.038 19 2.6 paracentral
- 1743 1217 3563 2.552 0.434 0.145 0.059 39 4.0 parsopercularis
- 926 626 2186 2.805 0.636 0.151 0.052 17 2.1 parsorbitalis
- 1773 1215 3401 2.429 0.522 0.145 0.052 32 3.1 parstriangularis
- 2161 1443 2433 1.740 0.446 0.151 0.069 46 5.7 pericalcarine
- 5674 3757 9270 2.135 0.582 0.138 0.049 97 10.7 postcentral
- 1519 1001 2797 2.665 0.515 0.147 0.044 29 2.8 posteriorcingulate
- 6223 4123 12531 2.644 0.506 0.126 0.046 82 10.1 precentral
- 4635 3157 8648 2.373 0.572 0.153 0.064 107 12.3 precuneus
- 1413 962 3154 2.775 0.698 0.171 0.087 37 4.1 rostralanteriorcingulate
- 4721 3341 10284 2.430 0.600 0.178 0.080 135 14.1 rostralmiddlefrontal
- 9453 6528 21475 2.673 0.637 0.157 0.070 289 21.6 superiorfrontal
- 5816 3854 9805 2.228 0.469 0.132 0.045 91 10.8 superiorparietal
- 5861 4077 14803 2.891 0.750 0.134 0.054 129 12.5 superiortemporal
- 4390 2974 8599 2.495 0.553 0.159 0.070 111 10.3 supramarginal
- 490 313 879 2.594 0.323 0.154 0.052 8 1.1 transversetemporal
- 2432 1568 5544 2.979 0.875 0.111 0.132 38 5.9 insula
- #--------------------------------------------
- #@# Tessellate rh Thu Aug 8 19:07:09 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts
- mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz
- Iteration Number : 1
- pass 1 (xy+): 1 found - 1 modified | TOTAL: 1
- pass 2 (xy+): 0 found - 1 modified | TOTAL: 1
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 1
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 1
- pass 1 (yz-): 2 found - 2 modified | TOTAL: 3
- pass 2 (yz-): 0 found - 2 modified | TOTAL: 3
- pass 1 (xz+): 1 found - 1 modified | TOTAL: 4
- pass 2 (xz+): 0 found - 1 modified | TOTAL: 4
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 4
- Iteration Number : 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 (+++): 2 found - 2 modified | TOTAL: 2
- pass 2 (+++): 0 found - 2 modified | TOTAL: 2
- 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 (--): 0 found - 0 modified | TOTAL: 1
- pass 1 (-+): 1 found - 1 modified | TOTAL: 2
- pass 2 (-+): 0 found - 1 modified | TOTAL: 2
- Iteration Number : 2
- pass 1 (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 : 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 = 9 (out of 191312: 0.004704)
- 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: 43 vertices, 56 faces
- slice 50: 2777 vertices, 2965 faces
- slice 60: 9379 vertices, 9649 faces
- slice 70: 18315 vertices, 18627 faces
- slice 80: 27980 vertices, 28318 faces
- slice 90: 36998 vertices, 37320 faces
- slice 100: 46874 vertices, 47191 faces
- slice 110: 56310 vertices, 56626 faces
- slice 120: 65253 vertices, 65590 faces
- slice 130: 74150 vertices, 74489 faces
- slice 140: 83222 vertices, 83549 faces
- slice 150: 90932 vertices, 91213 faces
- slice 160: 97616 vertices, 97883 faces
- slice 170: 103226 vertices, 103427 faces
- slice 180: 108200 vertices, 108368 faces
- slice 190: 111397 vertices, 111511 faces
- slice 200: 112292 vertices, 112326 faces
- slice 210: 112292 vertices, 112326 faces
- slice 220: 112292 vertices, 112326 faces
- slice 230: 112292 vertices, 112326 faces
- slice 240: 112292 vertices, 112326 faces
- slice 250: 112292 vertices, 112326 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...
- 112292 voxel in cpt #1: X=-34 [v=112292,e=336978,f=224652] located at (23.270029, -17.063156, 35.209133)
- For the whole surface: X=-34 [v=112292,e=336978,f=224652]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Smooth1 rh Thu Aug 8 19:07:16 CEST 2013
- mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts
- setting seed for random number generator to 1234
- smoothing surface tessellation for 10 iterations...
- smoothing complete - recomputing first and second fundamental forms...
- #--------------------------------------------
- #@# Inflation1 rh Thu Aug 8 19:07:20 CEST 2013
- mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts
- avg radius = 44.2 mm, total surface area = 59007 mm^2
- writing inflated surface to ../surf/rh.inflated.nofix
- inflation took 0.5 minutes
- Not saving sulc
-
step 000: RMS=0.102 (target=0.015)
step 005: RMS=0.075 (target=0.015)
step 010: RMS=0.055 (target=0.015)
step 015: RMS=0.046 (target=0.015)
step 020: RMS=0.040 (target=0.015)
step 025: RMS=0.035 (target=0.015)
step 030: RMS=0.032 (target=0.015)
step 035: RMS=0.029 (target=0.015)
step 040: RMS=0.027 (target=0.015)
step 045: RMS=0.026 (target=0.015)
step 050: RMS=0.025 (target=0.015)
step 055: RMS=0.024 (target=0.015)
step 060: RMS=0.024 (target=0.015)
- inflation complete.
- Not saving sulc
- #--------------------------------------------
- #@# QSphere rh Thu Aug 8 19:07:48 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts
- mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix
- doing quick spherical unfolding.
- setting seed for random number genererator to 1234
- $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading original vertex positions...
- unfolding cortex into spherical form...
- surface projected - minimizing metric distortion...
- vertex spacing 1.08 +- 0.64 (0.00-->6.24) (max @ vno 84528 --> 84556)
- face area 0.03 +- 0.04 (-0.05-->0.60)
- scaling brain by 0.333...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=176.635, avgs=0
- 005/300: dt: 0.9000, rms radial error=176.376, avgs=0
- 010/300: dt: 0.9000, rms radial error=175.821, avgs=0
- 015/300: dt: 0.9000, rms radial error=175.093, avgs=0
- 020/300: dt: 0.9000, rms radial error=174.262, avgs=0
- 025/300: dt: 0.9000, rms radial error=173.372, avgs=0
- 030/300: dt: 0.9000, rms radial error=172.450, avgs=0
- 035/300: dt: 0.9000, rms radial error=171.512, avgs=0
- 040/300: dt: 0.9000, rms radial error=170.566, avgs=0
- 045/300: dt: 0.9000, rms radial error=169.619, avgs=0
- 050/300: dt: 0.9000, rms radial error=168.680, avgs=0
- 055/300: dt: 0.9000, rms radial error=167.743, avgs=0
- 060/300: dt: 0.9000, rms radial error=166.810, avgs=0
- 065/300: dt: 0.9000, rms radial error=165.881, avgs=0
- 070/300: dt: 0.9000, rms radial error=164.956, avgs=0
- 075/300: dt: 0.9000, rms radial error=164.036, avgs=0
- 080/300: dt: 0.9000, rms radial error=163.121, avgs=0
- 085/300: dt: 0.9000, rms radial error=162.210, avgs=0
- 090/300: dt: 0.9000, rms radial error=161.304, avgs=0
- 095/300: dt: 0.9000, rms radial error=160.403, avgs=0
- 100/300: dt: 0.9000, rms radial error=159.506, avgs=0
- 105/300: dt: 0.9000, rms radial error=158.614, avgs=0
- 110/300: dt: 0.9000, rms radial error=157.726, avgs=0
- 115/300: dt: 0.9000, rms radial error=156.843, avgs=0
- 120/300: dt: 0.9000, rms radial error=155.965, avgs=0
- 125/300: dt: 0.9000, rms radial error=155.092, avgs=0
- 130/300: dt: 0.9000, rms radial error=154.222, avgs=0
- 135/300: dt: 0.9000, rms radial error=153.358, avgs=0
- 140/300: dt: 0.9000, rms radial error=152.498, avgs=0
- 145/300: dt: 0.9000, rms radial error=151.643, avgs=0
- 150/300: dt: 0.9000, rms radial error=150.792, avgs=0
- 155/300: dt: 0.9000, rms radial error=149.946, avgs=0
- 160/300: dt: 0.9000, rms radial error=149.104, avgs=0
- 165/300: dt: 0.9000, rms radial error=148.267, avgs=0
- 170/300: dt: 0.9000, rms radial error=147.434, avgs=0
- 175/300: dt: 0.9000, rms radial error=146.606, avgs=0
- 180/300: dt: 0.9000, rms radial error=145.782, avgs=0
- 185/300: dt: 0.9000, rms radial error=144.963, avgs=0
- 190/300: dt: 0.9000, rms radial error=144.148, avgs=0
- 195/300: dt: 0.9000, rms radial error=143.337, avgs=0
- 200/300: dt: 0.9000, rms radial error=142.531, avgs=0
- 205/300: dt: 0.9000, rms radial error=141.730, avgs=0
- 210/300: dt: 0.9000, rms radial error=140.932, avgs=0
- 215/300: dt: 0.9000, rms radial error=140.139, avgs=0
- 220/300: dt: 0.9000, rms radial error=139.351, avgs=0
- 225/300: dt: 0.9000, rms radial error=138.567, avgs=0
- 230/300: dt: 0.9000, rms radial error=137.787, avgs=0
- 235/300: dt: 0.9000, rms radial error=137.011, avgs=0
- 240/300: dt: 0.9000, rms radial error=136.240, avgs=0
- 245/300: dt: 0.9000, rms radial error=135.473, avgs=0
- 250/300: dt: 0.9000, rms radial error=134.710, avgs=0
- 255/300: dt: 0.9000, rms radial error=133.951, avgs=0
- 260/300: dt: 0.9000, rms radial error=133.197, avgs=0
- 265/300: dt: 0.9000, rms radial error=132.446, avgs=0
- 270/300: dt: 0.9000, rms radial error=131.700, avgs=0
- 275/300: dt: 0.9000, rms radial error=130.958, avgs=0
- 280/300: dt: 0.9000, rms radial error=130.220, avgs=0
- 285/300: dt: 0.9000, rms radial error=129.487, avgs=0
- 290/300: dt: 0.9000, rms radial error=128.757, avgs=0
- 295/300: dt: 0.9000, rms radial error=128.032, avgs=0
- 300/300: dt: 0.9000, rms radial error=127.310, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 12847.82
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00017
- epoch 2 (K=40.0), pass 1, starting sse = 2075.19
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00021
- epoch 3 (K=160.0), pass 1, starting sse = 210.97
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.12/11 = 0.01123
- epoch 4 (K=640.0), pass 1, starting sse = 11.41
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.26/18 = 0.01451
- final writing spherical brain to ../surf/rh.qsphere.nofix
- spherical transformation took 0.07 hours
- distance error %100000.00
- #--------------------------------------------
- #@# Fix Topology rh Thu Aug 8 19:11:42 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/sub010/scripts
- mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub010 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=-34 (nv=112292, nf=224652, ne=336978, g=18)
- using quasi-homeomorphic spherical map to tessellate cortical surface...
- Correction of the Topology
- Finding true center and radius of Spherical Surface...done
- Surface centered at (0,0,0) with radius 100.0 in 11 iterations
- marking ambiguous vertices...
- 2041 ambiguous faces found in tessellation
- segmenting defects...
- 27 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- 27 defects to be corrected
- 0 vertices coincident
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -9.8867 (-4.9434)
- -vertex loglikelihood: -6.9117 (-3.4559)
- -normal dot loglikelihood: -3.6465 (-3.6465)
- -quad curv loglikelihood: -6.1500 (-3.0750)
- Total Loglikelihood : -26.5949
- CORRECTING DEFECT 0 (vertices=33, convex hull=71)
- After retessellation of defect 0, euler #=-23 (111025,332513,221465) : difference with theory (-24) = -1
- CORRECTING DEFECT 1 (vertices=53, convex hull=101)
- After retessellation of defect 1, euler #=-22 (111056,332649,221571) : difference with theory (-23) = -1
- CORRECTING DEFECT 2 (vertices=16, convex hull=48)
- After retessellation of defect 2, euler #=-21 (111063,332690,221606) : difference with theory (-22) = -1
- CORRECTING DEFECT 3 (vertices=76, convex hull=73)
- After retessellation of defect 3, euler #=-20 (111081,332782,221681) : difference with theory (-21) = -1
- CORRECTING DEFECT 4 (vertices=57, convex hull=83)
- After retessellation of defect 4, euler #=-19 (111100,332874,221755) : difference with theory (-20) = -1
- CORRECTING DEFECT 5 (vertices=27, convex hull=63)
- After retessellation of defect 5, euler #=-18 (111118,332950,221814) : difference with theory (-19) = -1
- CORRECTING DEFECT 6 (vertices=12, convex hull=20)
- After retessellation of defect 6, euler #=-17 (111119,332958,221822) : difference with theory (-18) = -1
- CORRECTING DEFECT 7 (vertices=45, convex hull=77)
- After retessellation of defect 7, euler #=-16 (111136,333039,221887) : difference with theory (-17) = -1
- CORRECTING DEFECT 8 (vertices=55, convex hull=42)
- After retessellation of defect 8, euler #=-15 (111146,333087,221926) : difference with theory (-16) = -1
- CORRECTING DEFECT 9 (vertices=36, convex hull=75)
- After retessellation of defect 9, euler #=-14 (111162,333165,221989) : difference with theory (-15) = -1
- CORRECTING DEFECT 10 (vertices=32, convex hull=57)
- After retessellation of defect 10, euler #=-13 (111175,333225,222037) : difference with theory (-14) = -1
- CORRECTING DEFECT 11 (vertices=83, convex hull=31)
- After retessellation of defect 11, euler #=-12 (111183,333259,222064) : difference with theory (-13) = -1
- CORRECTING DEFECT 12 (vertices=32, convex hull=42)
- After retessellation of defect 12, euler #=-11 (111194,333307,222102) : difference with theory (-12) = -1
- CORRECTING DEFECT 13 (vertices=6, convex hull=29)
- After retessellation of defect 13, euler #=-10 (111196,333321,222115) : difference with theory (-11) = -1
- CORRECTING DEFECT 14 (vertices=25, convex hull=22)
- After retessellation of defect 14, euler #=-9 (111200,333337,222128) : difference with theory (-10) = -1
- CORRECTING DEFECT 15 (vertices=84, convex hull=87)
- After retessellation of defect 15, euler #=-8 (111244,333502,222250) : difference with theory (-9) = -1
- CORRECTING DEFECT 16 (vertices=48, convex hull=61)
- After retessellation of defect 16, euler #=-7 (111258,333567,222302) : difference with theory (-8) = -1
- CORRECTING DEFECT 17 (vertices=19, convex hull=30)
- After retessellation of defect 17, euler #=-6 (111260,333580,222314) : difference with theory (-7) = -1
- CORRECTING DEFECT 18 (vertices=32, convex hull=56)
- After retessellation of defect 18, euler #=-5 (111279,333656,222372) : difference with theory (-6) = -1
- CORRECTING DEFECT 19 (vertices=31, convex hull=29)
- Warning - incorrect dp selected!!!!(-104.593326 >= -104.593328 )
- After retessellation of defect 19, euler #=-4 (111280,333669,222385) : difference with theory (-5) = -1
- CORRECTING DEFECT 20 (vertices=252, convex hull=79)
- After retessellation of defect 20, euler #=-4 (111315,333813,222494) : difference with theory (-4) = 0
- CORRECTING DEFECT 21 (vertices=18, convex hull=46)
- After retessellation of defect 21, euler #=-3 (111326,333861,222532) : difference with theory (-3) = 0
- CORRECTING DEFECT 22 (vertices=90, convex hull=49)
- After retessellation of defect 22, euler #=-2 (111338,333914,222574) : difference with theory (-2) = 0
- CORRECTING DEFECT 23 (vertices=5, convex hull=38)
- After retessellation of defect 23, euler #=-1 (111340,333932,222591) : difference with theory (-1) = 0
- CORRECTING DEFECT 24 (vertices=35, convex hull=61)
- After retessellation of defect 24, euler #=0 (111353,333995,222642) : difference with theory (0) = 0
- CORRECTING DEFECT 25 (vertices=32, convex hull=56)
- After retessellation of defect 25, euler #=1 (111366,334057,222692) : difference with theory (1) = 0
- CORRECTING DEFECT 26 (vertices=44, convex hull=81)
- After retessellation of defect 26, euler #=2 (111391,334167,222778) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.88 +- 0.22 (0.05-->4.93) (max @ vno 5340 --> 7264)
- face area 0.00 +- 0.00 (0.00-->0.00)
- performing soap bubble on retessellated vertices for 0 iterations...
- vertex spacing 0.88 +- 0.22 (0.05-->4.93) (max @ vno 5340 --> 7264)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 97 mutations (35.8%), 174 crossovers (64.2%), 70 vertices were eliminated
- building final representation...
- 901 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=111391, nf=222778, ne=334167, g=0)
- writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 14.7 minutes
- 0 defective edges
- removing intersecting faces
- 000: 118 intersecting
- 001: 12 intersecting
- mris_euler_number ../surf/rh.orig
- euler # = v-e+f = 2g-2: 111391 - 334167 + 222778 = 2 --> 0 holes
- F =2V-4: 222778 = 222782-4 (0)
- 2E=3F: 668334 = 668334 (0)
- total defect index = 0
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts
- mris_remove_intersection ../surf/rh.orig ../surf/rh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 5 intersecting
- writing corrected surface to ../surf/rh.orig
- rm ../surf/rh.inflated
- #--------------------------------------------
- #@# Make White Surf rh Thu Aug 8 19:26:28 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts
- mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub010 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/sub010/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/wm.mgz...
- 12290 bright wm thresholded.
- 241 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.orig...
- computing class statistics...
- border white: 201670 voxels (1.20%)
- border gray 234473 voxels (1.40%)
- WM (91.0): 91.9 +- 10.6 [70.0 --> 110.0]
- GM (73.0) : 71.3 +- 13.5 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 42.5 (was 70)
- setting MAX_BORDER_WHITE to 115.6 (was 105)
- setting MIN_BORDER_WHITE to 56.0 (was 85)
- setting MAX_CSF to 29.1 (was 40)
- setting MAX_GRAY to 94.4 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 49.3 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 15.6 (was 40)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.82 +- 0.22 (0.03-->2.73) (max @ vno 8619 --> 10263)
- face area 0.28 +- 0.12 (0.00-->1.33)
- mean absolute distance = 0.64 +- 0.71
- 3225 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=105, GM=56
- mean inside = 91.3, mean outside = 66.0
- smoothing surface for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- removing 1 vertex label from ripped group
- mean border=70.1, 49 (49) missing vertices, mean dist 0.4 [0.4 (%30.1)->0.7 (%69.9))]
- %71 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.93 +- 0.27 (0.13-->3.59) (max @ vno 88410 --> 89070)
- face area 0.28 +- 0.14 (0.00-->1.54)
- mean absolute distance = 0.31 +- 0.47
- 2338 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=6263519.5, rms=14.16
- 001: dt: 0.5000, sse=6245345.0, rms=10.374 (0.000%)
- 002: dt: 0.5000, sse=6399585.0, rms=8.201 (0.000%)
- 003: dt: 0.5000, sse=6475290.5, rms=6.821 (0.000%)
- 004: dt: 0.5000, sse=6640219.5, rms=5.985 (0.000%)
- 005: dt: 0.5000, sse=6712765.5, rms=5.476 (0.000%)
- 006: dt: 0.5000, sse=6791901.0, rms=5.198 (0.000%)
- 007: dt: 0.5000, sse=6837379.0, rms=5.009 (0.000%)
- 008: dt: 0.5000, sse=6846357.0, rms=4.907 (0.000%)
- 009: dt: 0.5000, sse=6843883.5, rms=4.824 (0.000%)
- 010: dt: 0.5000, sse=6829250.5, rms=4.773 (0.000%)
- 011: dt: 0.5000, sse=6802085.5, rms=4.716 (0.000%)
- rms = 4.68, time step reduction 1 of 3 to 0.250...
- 012: dt: 0.5000, sse=6778209.0, rms=4.683 (0.000%)
- 013: dt: 0.2500, sse=4421098.5, rms=3.302 (0.000%)
- 014: dt: 0.2500, sse=4074072.5, rms=2.871 (0.000%)
- 015: dt: 0.2500, sse=3852660.5, rms=2.789 (0.000%)
- 016: dt: 0.2500, sse=3800534.8, rms=2.710 (0.000%)
- rms = 2.70, time step reduction 2 of 3 to 0.125...
- 017: dt: 0.2500, sse=3720320.8, rms=2.695 (0.000%)
- 018: dt: 0.1250, sse=3456618.2, rms=2.333 (0.000%)
- 019: dt: 0.1250, sse=3420086.8, rms=2.281 (0.000%)
- rms = 2.27, time step reduction 3 of 3 to 0.062...
- 020: dt: 0.1250, sse=3391328.2, rms=2.273 (0.000%)
- positioning took 2.0 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 1 vertex label from ripped group
- removing 1 vertex label from ripped group
- mean border=74.8, 45 (7) missing vertices, mean dist -0.2 [0.3 (%78.4)->0.3 (%21.6))]
- %82 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.91 +- 0.26 (0.09-->3.47) (max @ vno 89159 --> 88482)
- face area 0.35 +- 0.17 (0.00-->2.01)
- mean absolute distance = 0.22 +- 0.33
- 2303 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4232823.5, rms=6.34
- 021: dt: 0.5000, sse=4461567.5, rms=4.430 (0.000%)
- rms = 4.78, time step reduction 1 of 3 to 0.250...
- 022: dt: 0.2500, sse=4019862.2, rms=3.180 (0.000%)
- 023: dt: 0.2500, sse=3836859.8, rms=2.626 (0.000%)
- 024: dt: 0.2500, sse=3785870.2, rms=2.205 (0.000%)
- rms = 2.20, time step reduction 2 of 3 to 0.125...
- 025: dt: 0.2500, sse=3775824.5, rms=2.199 (0.000%)
- 026: dt: 0.1250, sse=3604553.8, rms=1.842 (0.000%)
- 027: dt: 0.1250, sse=3567259.2, rms=1.790 (0.000%)
- rms = 1.79, time step reduction 3 of 3 to 0.062...
- 028: dt: 0.1250, sse=3542844.8, rms=1.789 (0.000%)
- positioning took 0.8 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 1 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 1 vertex label from ripped group
- removing 1 vertex label from ripped group
- mean border=78.2, 42 (7) missing vertices, mean dist -0.1 [0.2 (%75.6)->0.2 (%24.4))]
- %88 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 0.91 +- 0.26 (0.13-->3.47) (max @ vno 89159 --> 88482)
- face area 0.35 +- 0.17 (0.00-->1.98)
- mean absolute distance = 0.17 +- 0.27
- 2375 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=3847400.0, rms=4.31
- rms = 4.44, time step reduction 1 of 3 to 0.250...
- 029: dt: 0.2500, sse=3688419.0, rms=2.969 (0.000%)
- 030: dt: 0.2500, sse=3616075.2, rms=1.973 (0.000%)
- 031: dt: 0.2500, sse=3644289.8, rms=1.850 (0.000%)
- 032: dt: 0.2500, sse=3676542.5, rms=1.774 (0.000%)
- rms = 1.86, time step reduction 2 of 3 to 0.125...
- 033: dt: 0.1250, sse=3626170.8, rms=1.674 (0.000%)
- 034: dt: 0.1250, sse=3554452.8, rms=1.553 (0.000%)
- rms = 1.55, time step reduction 3 of 3 to 0.062...
- 035: dt: 0.1250, sse=3532614.8, rms=1.546 (0.000%)
- positioning took 0.8 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 1 vertex label from ripped group
- removing 1 vertex label from ripped group
- removing 3 vertex label from ripped group
- mean border=79.3, 66 (7) missing vertices, mean dist -0.0 [0.2 (%58.4)->0.2 (%41.6))]
- %89 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/sub010/surf/rh.white...
- writing smoothed curvature to rh.curv
- 000: dt: 0.0000, sse=3554496.5, rms=1.98
- rms = 2.99, time step reduction 1 of 3 to 0.250...
- 036: dt: 0.2500, sse=3647274.8, rms=1.307 (0.000%)
- 037: dt: 0.2500, sse=3806872.8, rms=1.124 (0.000%)
- rms = 1.12, time step reduction 2 of 3 to 0.125...
- 038: dt: 0.2500, sse=3878057.8, rms=1.123 (0.000%)
- rms = 1.09, time step reduction 3 of 3 to 0.062...
- 039: dt: 0.1250, sse=3904920.2, rms=1.091 (0.000%)
- positioning took 0.5 minutes
- inhibiting deformation at non-cortical midline structures...
- generating cortex label...
- 13 non-cortical segments detected
- only using segment with 1747 vertices
- erasing segment 1 (vno[0] = 67108)
- erasing segment 2 (vno[0] = 69658)
- erasing segment 3 (vno[0] = 80395)
- erasing segment 4 (vno[0] = 82178)
- erasing segment 5 (vno[0] = 86152)
- erasing segment 6 (vno[0] = 86160)
- erasing segment 7 (vno[0] = 86197)
- erasing segment 8 (vno[0] = 89141)
- erasing segment 9 (vno[0] = 89757)
- erasing segment 10 (vno[0] = 89802)
- erasing segment 11 (vno[0] = 89809)
- erasing segment 12 (vno[0] = 90446)
- writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/label/rh.cortex.label...
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.curv
- writing smoothed area to rh.area
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.area
- vertex spacing 0.90 +- 0.26 (0.04-->3.59) (max @ vno 89070 --> 88410)
- face area 0.34 +- 0.16 (0.00-->2.15)
- refinement took 5.9 minutes
- #--------------------------------------------
- #@# Smooth2 rh Thu Aug 8 19:32:21 CEST 2013
- mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts
- smoothing for 3 iterations
- setting seed for random number generator to 1234
- smoothing surface tessellation for 3 iterations...
- smoothing complete - recomputing first and second fundamental forms...
- #--------------------------------------------
- #@# Inflation2 rh Thu Aug 8 19:32:25 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts
- mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated
- avg radius = 44.4 mm, total surface area = 69078 mm^2
- writing inflated surface to ../surf/rh.inflated
- writing sulcal depths to ../surf/rh.sulc
-
step 000: RMS=0.118 (target=0.015)
step 005: RMS=0.082 (target=0.015)
step 010: RMS=0.059 (target=0.015)
step 015: RMS=0.047 (target=0.015)
step 020: RMS=0.040 (target=0.015)
step 025: RMS=0.033 (target=0.015)
step 030: RMS=0.028 (target=0.015)
step 035: RMS=0.024 (target=0.015)
step 040: RMS=0.020 (target=0.015)
step 045: RMS=0.018 (target=0.015)
step 050: RMS=0.016 (target=0.015)
step 055: RMS=0.015 (target=0.015)
- inflation complete.
- inflation took 0.4 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
- 107 vertices thresholded to be in k1 ~ [-0.24 0.64], k2 ~ [-0.17 0.10]
- total integrated curvature = 0.614*4pi (7.721) --> 0 handles
- ICI = 1.4, FI = 8.3, variation=142.901
- 114 vertices thresholded to be in [-0.05 0.02]
- writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level
- curvature mean = 0.000, std = 0.002
- 102 vertices thresholded to be in [-0.16 0.23]
- done.
- writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.018, std = 0.023
- done.
- #-----------------------------------------
- #@# Curvature Stats rh Thu Aug 8 19:34:14 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub010 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 [ sub010/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 [ 233 ]
- Gb_filter = 0
- WARN: S lookup min: -0.262075
- WARN: S explicit min: 0.000000 vertex = 790
- #--------------------------------------------
- #@# Sphere rh Thu Aug 8 19:34:18 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 0.307...
- MRISunfold() max_passes = 1 -------
- tol=5.0e-01, sigma=0.0, host=snake, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
- using quadratic fit line minimization
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 1.000000
- desired_rms_height -1.000000
- momentum 0.900000
- nbhd_size 7
- max_nbrs 8
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 1234
- --------------------
- mrisRemoveNegativeArea()
- pass 1: epoch 1 of 3 starting distance error %20.35
- pass 1: epoch 2 of 3 starting distance error %20.28
- unfolding complete - removing small folds...
- starting distance error %20.24
- removing remaining folds...
- final distance error %20.26
- MRISunfold() return, current seed 1234
- writing spherical brain to ../surf/rh.sphere
- spherical transformation took 0.74 hours
- #--------------------------------------------
- #@# Surf Reg rh Thu Aug 8 20:18:43 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 = 0.578
- curvature mean = 0.030, std = 0.941
- curvature mean = 0.021, std = 0.872
- Starting MRISrigidBodyAlignGlobal()
- d=64.00 min @ (0.00, -16.00, 0.00) sse = 311886.0, tmin=0.8804
- d=32.00 min @ (0.00, 8.00, 0.00) sse = 258786.6, tmin=1.7659
- d=16.00 min @ (4.00, 0.00, 4.00) sse = 244398.9, tmin=2.6545
- d=8.00 min @ (-2.00, 0.00, 0.00) sse = 241030.0, tmin=3.6574
- d=4.00 min @ (0.00, -1.00, 0.00) sse = 240748.2, tmin=4.7330
- d=2.00 min @ (0.50, 0.50, 0.00) sse = 240329.7, tmin=5.8162
- d=0.50 min @ (-0.12, -0.12, -0.12) sse = 240299.9, tmin=7.9474
- 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 7.95 min
- curvature mean = 0.006, std = 0.960
- curvature mean = 0.009, std = 0.946
- curvature mean = 0.004, std = 0.973
- curvature mean = 0.004, std = 0.976
- curvature mean = 0.002, std = 0.976
- curvature mean = 0.001, std = 0.990
- 2 Reading smoothwm
- curvature mean = -0.028, std = 0.311
- curvature mean = 0.006, std = 0.071
- curvature mean = 0.068, std = 0.349
- curvature mean = 0.005, std = 0.085
- curvature mean = 0.034, std = 0.528
- curvature mean = 0.005, std = 0.093
- curvature mean = 0.018, std = 0.660
- curvature mean = 0.005, std = 0.096
- curvature mean = 0.006, std = 0.769
- MRISregister() return, current seed 0
- writing registered surface to ../surf/rh.sphere.reg...
- expanding nbhd size to 1
- #--------------------------------------------
- #@# Jacobian white rh Thu Aug 8 20:44:27 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 20:44:29 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 20:44:30 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub010 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...
- 885 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2560 changed, 111391 examined...
- 001: 575 changed, 10957 examined...
- 002: 134 changed, 3173 examined...
- 003: 48 changed, 826 examined...
- 004: 15 changed, 282 examined...
- 005: 11 changed, 92 examined...
- 006: 4 changed, 59 examined...
- 007: 0 changed, 17 examined...
- 144 labels changed using aseg
- 000: 87 total segments, 50 labels (208 vertices) changed
- 001: 37 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 48 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 931 vertices marked for relabeling...
- 931 labels changed in reclassification.
- writing output to ../label/rh.aparc.annot...
- classification took 0 minutes and 51 seconds.
- #--------------------------------------------
- #@# Make Pial Surf rh Thu Aug 8 20:45:21 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts
- mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub010 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/sub010/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/wm.mgz...
- 12290 bright wm thresholded.
- 241 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.orig...
- computing class statistics...
- border white: 201670 voxels (1.20%)
- border gray 234473 voxels (1.40%)
- WM (91.0): 91.9 +- 10.6 [70.0 --> 110.0]
- GM (73.0) : 71.3 +- 13.5 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 42.5 (was 70)
- setting MAX_BORDER_WHITE to 115.6 (was 105)
- setting MIN_BORDER_WHITE to 56.0 (was 85)
- setting MAX_CSF to 29.1 (was 40)
- setting MAX_GRAY to 94.4 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 49.3 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 15.6 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=105, GM=56
- mean inside = 91.3, mean outside = 66.0
- 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/sub010/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.82 +- 0.22 (0.03-->2.73) (max @ vno 8619 --> 10263)
- face area 0.28 +- 0.12 (0.00-->1.33)
- mean absolute distance = 0.64 +- 0.73
- 3313 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 20 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 1 with 3 points - only 0.00% unknown
- deleting segment 2 with 10 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 4 with 1 points - only 0.00% unknown
- deleting segment 5 with 784 points - only 0.00% unknown
- deleting segment 6 with 7 points - only 0.00% unknown
- mean border=70.1, 49 (49) missing vertices, mean dist 0.4 [0.4 (%30.0)->0.7 (%70.0))]
- %72 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.93 +- 0.27 (0.13-->3.59) (max @ vno 88410 --> 89070)
- face area 0.28 +- 0.13 (0.00-->1.56)
- mean absolute distance = 0.31 +- 0.48
- 2063 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=6294467.0, rms=14.14
- 001: dt: 0.5000, sse=6276941.5, rms=10.358 (0.000%)
- 002: dt: 0.5000, sse=6440930.5, rms=8.189 (0.000%)
- 003: dt: 0.5000, sse=6518812.0, rms=6.812 (0.000%)
- 004: dt: 0.5000, sse=6692514.5, rms=5.979 (0.000%)
- 005: dt: 0.5000, sse=6763652.0, rms=5.471 (0.000%)
- 006: dt: 0.5000, sse=6850346.0, rms=5.190 (0.000%)
- 007: dt: 0.5000, sse=6889043.5, rms=5.003 (0.000%)
- 008: dt: 0.5000, sse=6903848.5, rms=4.901 (0.000%)
- 009: dt: 0.5000, sse=6898054.0, rms=4.816 (0.000%)
- 010: dt: 0.5000, sse=6886989.0, rms=4.765 (0.000%)
- 011: dt: 0.5000, sse=6855885.0, rms=4.709 (0.000%)
- rms = 4.68, time step reduction 1 of 3 to 0.250...
- 012: dt: 0.5000, sse=6834797.5, rms=4.676 (0.000%)
- 013: dt: 0.2500, sse=4457324.0, rms=3.299 (0.000%)
- 014: dt: 0.2500, sse=4109140.8, rms=2.870 (0.000%)
- 015: dt: 0.2500, sse=3886174.5, rms=2.786 (0.000%)
- 016: dt: 0.2500, sse=3832405.0, rms=2.706 (0.000%)
- rms = 2.69, time step reduction 2 of 3 to 0.125...
- 017: dt: 0.2500, sse=3750530.8, rms=2.692 (0.000%)
- 018: dt: 0.1250, sse=3486635.0, rms=2.332 (0.000%)
- 019: dt: 0.1250, sse=3450738.5, rms=2.281 (0.000%)
- rms = 2.27, time step reduction 3 of 3 to 0.062...
- 020: dt: 0.1250, sse=3421693.5, rms=2.273 (0.000%)
- positioning took 2.0 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 1 with 46 points - only 23.91% unknown
- removing 4 vertex label from ripped group
- deleting segment 2 with 4 points - only 0.00% unknown
- deleting segment 3 with 14 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 6 with 1 points - only 0.00% unknown
- deleting segment 7 with 563 points - only 0.00% unknown
- deleting segment 9 with 6 points - only 0.00% unknown
- deleting segment 11 with 5 points - only 0.00% unknown
- mean border=74.8, 50 (7) missing vertices, mean dist -0.2 [0.3 (%78.4)->0.3 (%21.6))]
- %82 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.91 +- 0.26 (0.11-->3.46) (max @ vno 89159 --> 88482)
- face area 0.35 +- 0.17 (0.00-->2.01)
- mean absolute distance = 0.22 +- 0.33
- 2403 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4272208.5, rms=6.34
- 021: dt: 0.5000, sse=4503166.5, rms=4.429 (0.000%)
- rms = 4.79, time step reduction 1 of 3 to 0.250...
- 022: dt: 0.2500, sse=4059610.0, rms=3.188 (0.000%)
- 023: dt: 0.2500, sse=3878794.2, rms=2.641 (0.000%)
- 024: dt: 0.2500, sse=3828278.8, rms=2.229 (0.000%)
- rms = 2.22, time step reduction 2 of 3 to 0.125...
- 025: dt: 0.2500, sse=3819842.2, rms=2.225 (0.000%)
- 026: dt: 0.1250, sse=3646417.5, rms=1.879 (0.000%)
- rms = 1.83, time step reduction 3 of 3 to 0.062...
- 027: dt: 0.1250, sse=3609318.8, rms=1.833 (0.000%)
- positioning took 0.8 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- deleting segment 1 with 62 points - only 29.03% unknown
- removing 4 vertex label from ripped group
- deleting segment 2 with 4 points - only 0.00% unknown
- deleting segment 4 with 13 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 5 with 1 points - only 0.00% unknown
- deleting segment 6 with 706 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 8 with 5 points - only 0.00% unknown
- deleting segment 9 with 6 points - only 0.00% unknown
- mean border=78.1, 43 (7) missing vertices, mean dist -0.1 [0.2 (%75.4)->0.2 (%24.6))]
- %88 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 0.91 +- 0.26 (0.12-->3.42) (max @ vno 89159 --> 88482)
- face area 0.35 +- 0.16 (0.00-->1.99)
- mean absolute distance = 0.18 +- 0.27
- 2435 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=3915584.0, rms=4.32
- rms = 4.46, time step reduction 1 of 3 to 0.250...
- 028: dt: 0.2500, sse=3749633.0, rms=2.989 (0.000%)
- 029: dt: 0.2500, sse=3669072.8, rms=2.004 (0.000%)
- 030: dt: 0.2500, sse=3690236.2, rms=1.880 (0.000%)
- 031: dt: 0.2500, sse=3725850.8, rms=1.799 (0.000%)
- rms = 1.89, time step reduction 2 of 3 to 0.125...
- 032: dt: 0.1250, sse=3673796.2, rms=1.698 (0.000%)
- 033: dt: 0.1250, sse=3605017.2, rms=1.579 (0.000%)
- rms = 1.57, time step reduction 3 of 3 to 0.062...
- 034: dt: 0.1250, sse=3577784.2, rms=1.570 (0.000%)
- positioning took 0.8 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 2 vertex label from ripped group
- deleting segment 2 with 62 points - only 29.03% unknown
- deleting segment 3 with 6 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 5 with 14 points - only 0.00% unknown
- deleting segment 6 with 737 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 8 with 5 points - only 0.00% unknown
- deleting segment 9 with 5 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 10 with 3 points - only 0.00% unknown
- mean border=79.3, 67 (7) missing vertices, mean dist -0.0 [0.2 (%58.5)->0.2 (%41.5))]
- %90 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=3604920.8, rms=2.01
- rms = 3.02, time step reduction 1 of 3 to 0.250...
- 035: dt: 0.2500, sse=3700839.2, rms=1.347 (0.000%)
- 036: dt: 0.2500, sse=3864579.0, rms=1.161 (0.000%)
- rms = 1.16, time step reduction 2 of 3 to 0.125...
- rms = 1.14, time step reduction 3 of 3 to 0.062...
- 037: dt: 0.1250, sse=3866826.5, rms=1.144 (0.000%)
- positioning took 0.4 minutes
- inhibiting deformation at non-cortical midline structures...
- smoothing surface for 5 iterations...
- mean border=45.7, 24 (24) missing vertices, mean dist 1.8 [0.1 (%0.0)->2.3 (%100.0))]
- %14 local maxima, %58 large gradients and %23 min vals, 1314 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=25179400.0, rms=32.85
- 001: dt: 0.5000, sse=17927304.0, rms=27.109 (0.000%)
- 002: dt: 0.5000, sse=12997613.0, rms=22.420 (0.000%)
- 003: dt: 0.5000, sse=9794399.0, rms=18.679 (0.000%)
- 004: dt: 0.5000, sse=7898608.5, rms=15.718 (0.000%)
- 005: dt: 0.5000, sse=6833644.0, rms=13.386 (0.000%)
- 006: dt: 0.5000, sse=6199615.0, rms=11.583 (0.000%)
- 007: dt: 0.5000, sse=5835691.5, rms=10.118 (0.000%)
- 008: dt: 0.5000, sse=5583771.0, rms=8.853 (0.000%)
- 009: dt: 0.5000, sse=5490532.0, rms=7.755 (0.000%)
- 010: dt: 0.5000, sse=5434232.0, rms=6.837 (0.000%)
- 011: dt: 0.5000, sse=5495971.5, rms=6.133 (0.000%)
- 012: dt: 0.5000, sse=5562216.5, rms=5.566 (0.000%)
- 013: dt: 0.5000, sse=5669598.0, rms=5.150 (0.000%)
- 014: dt: 0.5000, sse=5748345.0, rms=4.846 (0.000%)
- 015: dt: 0.5000, sse=5847945.5, rms=4.646 (0.000%)
- 016: dt: 0.5000, sse=5871751.5, rms=4.487 (0.000%)
- 017: dt: 0.5000, sse=5920825.5, rms=4.385 (0.000%)
- 018: dt: 0.5000, sse=5928871.0, rms=4.298 (0.000%)
- rms = 4.25, time step reduction 1 of 3 to 0.250...
- 019: dt: 0.5000, sse=5999224.0, rms=4.249 (0.000%)
- 020: dt: 0.2500, sse=4356141.5, rms=3.631 (0.000%)
- 021: dt: 0.2500, sse=4218046.5, rms=3.472 (0.000%)
- rms = 3.46, time step reduction 2 of 3 to 0.125...
- 022: dt: 0.2500, sse=4109447.2, rms=3.457 (0.000%)
- 023: dt: 0.1250, sse=3955508.8, rms=3.368 (0.000%)
- rms = 3.36, time step reduction 3 of 3 to 0.062...
- 024: dt: 0.1250, sse=3928717.8, rms=3.360 (0.000%)
- positioning took 2.4 minutes
- mean border=43.4, 624 (9) missing vertices, mean dist 0.2 [0.2 (%48.8)->0.6 (%51.2))]
- %33 local maxima, %43 large gradients and %19 min vals, 486 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=4482038.5, rms=5.20
- 025: dt: 0.5000, sse=4748793.5, rms=4.491 (0.000%)
- 026: dt: 0.5000, sse=5937889.5, rms=4.380 (0.000%)
- 027: dt: 0.5000, sse=5859295.5, rms=4.323 (0.000%)
- rms = 4.29, time step reduction 1 of 3 to 0.250...
- 028: dt: 0.5000, sse=6508248.0, rms=4.292 (0.000%)
- 029: dt: 0.2500, sse=4775004.5, rms=3.476 (0.000%)
- 030: dt: 0.2500, sse=4748277.0, rms=3.241 (0.000%)
- rms = 3.23, time step reduction 2 of 3 to 0.125...
- 031: dt: 0.2500, sse=4613001.0, rms=3.232 (0.000%)
- 032: dt: 0.1250, sse=4475820.0, rms=3.102 (0.000%)
- rms = 3.08, time step reduction 3 of 3 to 0.062...
- 033: dt: 0.1250, sse=4452397.5, rms=3.084 (0.000%)
- positioning took 0.9 minutes
- mean border=41.1, 678 (7) missing vertices, mean dist 0.1 [0.2 (%38.4)->0.4 (%61.6))]
- %54 local maxima, %22 large gradients and %19 min vals, 577 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=4682343.5, rms=4.34
- 034: dt: 0.5000, sse=4873798.0, rms=4.086 (0.000%)
- rms = 4.14, time step reduction 1 of 3 to 0.250...
- 035: dt: 0.2500, sse=4615343.5, rms=3.440 (0.000%)
- 036: dt: 0.2500, sse=4785714.0, rms=3.160 (0.000%)
- 037: dt: 0.2500, sse=4737580.5, rms=3.103 (0.000%)
- rms = 3.07, time step reduction 2 of 3 to 0.125...
- 038: dt: 0.2500, sse=4786241.0, rms=3.070 (0.000%)
- 039: dt: 0.1250, sse=4629978.0, rms=2.955 (0.000%)
- rms = 2.94, time step reduction 3 of 3 to 0.062...
- 040: dt: 0.1250, sse=4620575.5, rms=2.942 (0.000%)
- positioning took 0.8 minutes
- mean border=39.8, 1486 (6) missing vertices, mean dist 0.1 [0.2 (%45.1)->0.3 (%54.9))]
- %59 local maxima, %17 large gradients and %18 min vals, 414 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/sub010/surf/rh.pial...
- writing smoothed curvature to rh.curv.pial
- 000: dt: 0.0000, sse=4664351.5, rms=3.26
- rms = 3.87, time step reduction 1 of 3 to 0.250...
- 041: dt: 0.2500, sse=4547328.5, rms=2.994 (0.000%)
- 042: dt: 0.2500, sse=4691075.0, rms=2.916 (0.000%)
- rms = 2.88, time step reduction 2 of 3 to 0.125...
- 043: dt: 0.2500, sse=4743708.0, rms=2.884 (0.000%)
- 044: dt: 0.1250, sse=4668799.5, rms=2.780 (0.000%)
- rms = 2.76, time step reduction 3 of 3 to 0.062...
- 045: dt: 0.1250, sse=4683887.0, rms=2.764 (0.000%)
- positioning took 0.6 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.curv.pial
- writing smoothed area to rh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.area.pial
- vertex spacing 1.05 +- 0.45 (0.09-->7.19) (max @ vno 50964 --> 49869)
- face area 0.44 +- 0.33 (0.00-->5.79)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 111391 vertices processed
- 25000 of 111391 vertices processed
- 50000 of 111391 vertices processed
- 75000 of 111391 vertices processed
- 100000 of 111391 vertices processed
- 0 of 111391 vertices processed
- 25000 of 111391 vertices processed
- 50000 of 111391 vertices processed
- 75000 of 111391 vertices processed
- 100000 of 111391 vertices processed
- thickness calculation complete, 340:1064 truncations.
- 23571 vertices at 0 distance
- 71398 vertices at 1 distance
- 71309 vertices at 2 distance
- 32185 vertices at 3 distance
- 9374 vertices at 4 distance
- 2387 vertices at 5 distance
- 766 vertices at 6 distance
- 244 vertices at 7 distance
- 92 vertices at 8 distance
- 45 vertices at 9 distance
- 23 vertices at 10 distance
- 32 vertices at 11 distance
- 15 vertices at 12 distance
- 13 vertices at 13 distance
- 23 vertices at 14 distance
- 24 vertices at 15 distance
- 14 vertices at 16 distance
- 13 vertices at 17 distance
- 8 vertices at 18 distance
- 7 vertices at 19 distance
- 5 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.thickness
- positioning took 11.6 minutes
- #--------------------------------------------
- #@# Surf Volume rh Thu Aug 8 20:56:57 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 20:56:57 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts
- pctsurfcon --s sub010 --rh-only
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts/pctsurfcon.log
- Thu Aug 8 20:56:57 CEST 2013
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts
- /opt/freesurfer/5.3.0/bin/pctsurfcon
- $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $
- Linux snake4 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/sub010/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/tmp.pctsurfcon.978/rh.wm.mgh --regheader sub010 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/label/rh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 = 86344
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/label/rh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/tmp.pctsurfcon.978/rh.wm.mgh
- Dim: 111391 1 1
- mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/tmp.pctsurfcon.978/rh.gm.mgh --projfrac 0.3 --regheader sub010 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/label/rh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.white
- Done reading source surface
- Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 = 99452
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/label/rh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/tmp.pctsurfcon.978/rh.gm.mgh
- Dim: 111391 1 1
- mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/tmp.pctsurfcon.978/rh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/tmp.pctsurfcon.978/rh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/surf/rh.w-g.pct.mgh
- mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.w-g.pct.mgh --annot sub010 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/surf/rh.w-g.pct.mgh --annot sub010 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/stats/rh.w-g.pct.stats --snr
- sysname Linux
- hostname snake4
- 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/sub010/surf/rh.w-g.pct.mgh
- Vertex Area is 0.679864 mm^3
- Generating list of segmentation ids
- Found 36 segmentations
- Computing statistics for each segmentation
- 0 2000 unknown 0 0.000
- 1 2001 bankssts 1491 1053.074
- 2 2002 caudalanteriorcingulate 972 688.321
- 3 2003 caudalmiddlefrontal 2081 1399.162
- 4 2004 corpuscallosum 0 0.000
- 5 2005 cuneus 2409 1575.154
- 6 2006 entorhinal 487 352.277
- 7 2007 fusiform 3287 2291.558
- 8 2008 inferiorparietal 7236 5051.799
- 9 2009 inferiortemporal 3875 2637.674
- 10 2010 isthmuscingulate 1181 779.891
- 11 2011 lateraloccipital 5789 3729.210
- 12 2012 lateralorbitofrontal 3333 2220.578
- 13 2013 lingual 3959 2721.951
- 14 2014 medialorbitofrontal 1903 1315.260
- 15 2015 middletemporal 4185 2969.861
- 16 2016 parahippocampal 649 469.661
- 17 2017 paracentral 1792 1190.402
- 18 2018 parsopercularis 1498 1043.138
- 19 2019 parsorbitalis 896 632.190
- 20 2020 parstriangularis 2141 1451.833
- 21 2021 pericalcarine 2141 1553.410
- 22 2022 postcentral 5066 3373.560
- 23 2023 posteriorcingulate 1409 963.851
- 24 2024 precentral 6364 4293.731
- 25 2025 precuneus 4994 3444.563
- 26 2026 rostralanteriorcingulate 801 578.226
- 27 2027 rostralmiddlefrontal 7005 4895.054
- 28 2028 superiorfrontal 8022 5489.056
- 29 2029 superiorparietal 7019 4653.616
- 30 2030 superiortemporal 4274 2960.927
- 31 2031 supramarginal 3732 2655.914
- 32 2032 frontalpole 323 234.243
- 33 2033 temporalpole 637 427.150
- 34 2034 transversetemporal 377 237.177
- 35 2035 insula 2486 1607.757
- Reporting on 34 segmentations
- mri_segstats done
- Cleaning up
- #-----------------------------------------
- #@# Parcellation Stats rh Thu Aug 8 20:57:09 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 sub010 rh white
- computing statistics for each annotation in ../label/rh.aparc.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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
- 1491 1053 2634 2.391 0.509 0.144 0.040 22 2.5 bankssts
- 972 688 2398 2.885 0.693 0.168 0.052 21 2.1 caudalanteriorcingulate
- 2081 1399 3887 2.507 0.528 0.137 0.058 32 4.3 caudalmiddlefrontal
- 2409 1575 3505 1.925 0.526 0.173 0.081 59 8.0 cuneus
- 487 352 1487 2.883 1.163 0.172 0.092 11 1.9 entorhinal
- 3287 2292 6738 2.574 0.575 0.151 0.055 61 7.0 fusiform
- 7236 5052 14159 2.418 0.589 0.150 0.052 133 15.3 inferiorparietal
- 3875 2638 8060 2.405 0.671 0.155 0.068 119 10.1 inferiortemporal
- 1181 780 2499 2.882 0.681 0.153 0.058 24 2.8 isthmuscingulate
- 5789 3729 9053 2.137 0.527 0.164 0.069 122 14.2 lateraloccipital
- 3333 2221 7179 2.771 0.738 0.165 0.082 118 11.0 lateralorbitofrontal
- 3959 2722 6580 2.202 0.594 0.181 0.089 106 13.4 lingual
- 1903 1315 4226 2.595 0.725 0.177 0.145 107 14.9 medialorbitofrontal
- 4185 2970 11210 2.784 0.787 0.148 0.054 91 8.4 middletemporal
- 649 470 1779 3.143 0.706 0.146 0.053 10 1.3 parahippocampal
- 1792 1190 3318 2.457 0.593 0.131 0.048 26 2.8 paracentral
- 1498 1043 3356 2.688 0.472 0.146 0.057 31 3.7 parsopercularis
- 896 632 2289 2.688 0.544 0.175 0.067 27 2.6 parsorbitalis
- 2141 1452 4330 2.580 0.564 0.136 0.042 31 3.7 parstriangularis
- 2141 1553 2589 1.784 0.423 0.165 0.065 35 5.9 pericalcarine
- 5066 3374 8328 2.105 0.624 0.133 0.040 64 8.9 postcentral
- 1409 964 2957 2.674 0.623 0.166 0.053 30 3.0 posteriorcingulate
- 6364 4294 12788 2.645 0.509 0.130 0.039 72 10.4 precentral
- 4994 3445 9228 2.422 0.544 0.144 0.049 93 10.1 precuneus
- 801 578 2415 3.264 0.715 0.174 0.088 28 2.6 rostralanteriorcingulate
- 7005 4895 15053 2.512 0.640 0.171 0.074 179 19.0 rostralmiddlefrontal
- 8022 5489 18327 2.828 0.578 0.149 0.053 151 16.2 superiorfrontal
- 7019 4654 11696 2.204 0.485 0.145 0.052 132 14.7 superiorparietal
- 4274 2961 10144 2.818 0.636 0.115 0.034 56 6.1 superiortemporal
- 3732 2656 8262 2.554 0.597 0.157 0.066 81 9.4 supramarginal
- 323 234 1061 2.891 0.522 0.273 0.195 21 1.9 frontalpole
- 637 427 2555 3.932 0.725 0.166 0.072 15 1.9 temporalpole
- 377 237 656 2.533 0.352 0.125 0.039 5 0.6 transversetemporal
- 2486 1608 5598 3.081 0.936 0.115 0.059 36 5.4 insula
- #-----------------------------------------
- #@# Cortical Parc 2 rh Thu Aug 8 20:57:21 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub010 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...
- 8 labels changed using aseg
- relabeling using gibbs priors...
- 000: 8222 changed, 111391 examined...
- 001: 1987 changed, 31328 examined...
- 002: 546 changed, 10066 examined...
- 003: 225 changed, 3081 examined...
- 004: 117 changed, 1272 examined...
- 005: 73 changed, 645 examined...
- 006: 24 changed, 414 examined...
- 007: 16 changed, 155 examined...
- 008: 8 changed, 82 examined...
- 009: 1 changed, 40 examined...
- 010: 0 changed, 7 examined...
- 10 labels changed using aseg
- 000: 255 total segments, 174 labels (1677 vertices) changed
- 001: 100 total segments, 19 labels (82 vertices) changed
- 002: 83 total segments, 2 labels (3 vertices) changed
- 003: 81 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 89 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 598 vertices marked for relabeling...
- 598 labels changed in reclassification.
- writing output to ../label/rh.aparc.a2009s.annot...
- classification took 0 minutes and 58 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 2 rh Thu Aug 8 20:58:19 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 sub010 rh white
- computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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
- 904 620 1854 2.377 0.659 0.170 0.095 23 2.5 G_and_S_frontomargin
- 669 489 1404 2.334 0.510 0.185 0.080 18 1.9 G_and_S_occipital_inf
- 1334 846 2625 2.430 0.557 0.145 0.059 25 2.5 G_and_S_paracentral
- 1115 750 2456 2.698 0.449 0.157 0.061 20 3.2 G_and_S_subcentral
- 955 699 2654 2.724 0.671 0.223 0.129 46 4.1 G_and_S_transv_frontopol
- 2280 1594 5294 2.888 0.641 0.157 0.066 54 5.3 G_and_S_cingul-Ant
- 1205 836 2642 2.865 0.527 0.137 0.041 17 1.9 G_and_S_cingul-Mid-Ant
- 1232 841 2458 2.672 0.492 0.134 0.039 16 2.0 G_and_S_cingul-Mid-Post
- 458 305 1236 3.139 0.507 0.191 0.074 13 1.4 G_cingul-Post-dorsal
- 241 157 614 2.960 0.595 0.154 0.075 6 0.7 G_cingul-Post-ventral
- 2221 1497 3237 1.888 0.464 0.177 0.079 52 6.6 G_cuneus
- 986 695 2783 2.865 0.482 0.157 0.068 25 2.9 G_front_inf-Opercular
- 302 204 785 2.682 0.426 0.175 0.067 10 0.9 G_front_inf-Orbital
- 949 633 2397 2.888 0.529 0.175 0.068 26 2.4 G_front_inf-Triangul
- 2754 1898 7082 2.739 0.559 0.192 0.096 92 9.8 G_front_middle
- 5353 3667 14158 2.945 0.591 0.176 0.073 144 15.3 G_front_sup
- 444 266 1314 3.969 0.788 0.118 0.097 8 0.9 G_Ins_lg_and_S_cent_ins
- 551 336 1835 3.543 0.785 0.137 0.089 16 2.4 G_insular_short
- 1897 1292 4684 2.802 0.540 0.203 0.099 69 6.1 G_occipital_middle
- 2088 1325 3248 2.081 0.480 0.161 0.058 41 4.9 G_occipital_sup
- 1184 781 2720 2.771 0.563 0.167 0.072 29 3.2 G_oc-temp_lat-fusifor
- 2574 1753 4722 2.325 0.587 0.201 0.106 84 10.3 G_oc-temp_med-Lingual
- 885 634 2526 3.066 1.065 0.148 0.060 13 2.1 G_oc-temp_med-Parahip
- 2374 1627 6604 2.884 0.727 0.201 0.110 124 10.7 G_orbital
- 2455 1738 6016 2.618 0.584 0.175 0.086 64 7.7 G_pariet_inf-Angular
- 1706 1240 4903 2.810 0.648 0.188 0.084 54 5.8 G_pariet_inf-Supramar
- 1977 1299 4146 2.434 0.500 0.161 0.071 62 6.2 G_parietal_sup
- 1790 1190 3508 2.274 0.551 0.141 0.041 27 3.0 G_postcentral
- 2373 1608 6076 2.877 0.460 0.146 0.047 37 4.7 G_precentral
- 2250 1554 4988 2.476 0.553 0.163 0.061 57 5.5 G_precuneus
- 503 339 1204 2.645 0.662 0.217 0.138 28 3.0 G_rectus
- 317 195 757 3.252 0.777 0.076 0.344 38 8.1 G_subcallosal
- 258 165 536 2.776 0.239 0.120 0.040 3 0.4 G_temp_sup-G_T_transv
- 1455 997 4427 3.053 0.560 0.153 0.058 41 3.3 G_temp_sup-Lateral
- 594 423 1684 3.482 0.777 0.102 0.031 4 0.7 G_temp_sup-Plan_polar
- 476 355 1072 2.495 0.544 0.121 0.034 5 0.7 G_temp_sup-Plan_tempo
- 2333 1597 5898 2.589 0.691 0.179 0.093 105 7.9 G_temporal_inf
- 2491 1792 7858 2.974 0.737 0.166 0.059 72 5.9 G_temporal_middle
- 423 283 704 2.392 0.505 0.101 0.020 2 0.4 Lat_Fis-ant-Horizont
- 165 124 251 2.191 0.354 0.116 0.022 1 0.1 Lat_Fis-ant-Vertical
- 1144 784 1640 2.345 0.393 0.122 0.035 10 1.7 Lat_Fis-post
- 3219 2024 4483 1.950 0.562 0.165 0.071 68 9.5 Pole_occipital
- 1544 1062 5244 3.334 0.843 0.177 0.094 41 5.5 Pole_temporal
- 2345 1689 3225 2.024 0.629 0.164 0.072 48 7.2 S_calcarine
- 2607 1778 3244 1.977 0.609 0.120 0.033 18 3.6 S_central
- 988 695 1560 2.276 0.499 0.122 0.034 12 1.3 S_cingul-Marginalis
- 517 336 978 2.939 0.697 0.118 0.033 4 0.7 S_circular_insula_ant
- 976 648 1505 2.509 0.542 0.081 0.016 3 0.7 S_circular_insula_inf
- 1032 715 1466 2.355 0.362 0.096 0.029 6 1.2 S_circular_insula_sup
- 1038 741 1771 2.309 0.518 0.127 0.035 13 1.5 S_collat_transv_ant
- 484 331 713 2.115 0.462 0.143 0.041 6 0.9 S_collat_transv_post
- 1830 1275 3055 2.248 0.526 0.127 0.036 21 2.8 S_front_inf
- 1701 1200 2754 2.326 0.496 0.143 0.044 21 3.0 S_front_middle
- 1502 1047 2934 2.612 0.569 0.119 0.029 16 1.8 S_front_sup
- 415 276 733 2.390 0.440 0.136 0.040 6 0.7 S_interm_prim-Jensen
- 2613 1743 3543 2.077 0.419 0.116 0.032 21 3.4 S_intrapariet_and_P_trans
- 799 554 960 1.863 0.360 0.128 0.034 6 1.1 S_oc_middle_and_Lunatus
- 1388 955 1919 2.067 0.398 0.135 0.036 17 2.0 S_oc_sup_and_transversal
- 723 468 906 2.134 0.375 0.141 0.045 9 1.5 S_occipital_ant
- 598 394 890 2.206 0.479 0.113 0.034 7 0.7 S_oc-temp_lat
- 1254 905 2344 2.571 0.602 0.121 0.028 11 1.5 S_oc-temp_med_and_Lingual
- 487 318 683 2.274 0.528 0.145 0.053 8 0.9 S_orbital_lateral
- 598 426 942 2.168 0.613 0.116 0.031 7 0.7 S_orbital_med-olfact
- 1254 844 2384 2.747 0.681 0.144 0.051 19 2.4 S_orbital-H_Shaped
- 2020 1388 3023 2.316 0.460 0.125 0.034 20 2.9 S_parieto_occipital
- 1188 766 1753 2.586 0.813 0.146 0.040 23 1.9 S_pericallosal
- 2052 1385 2638 1.989 0.461 0.113 0.029 15 2.5 S_postcentral
- 1204 791 1809 2.589 0.494 0.119 0.033 11 1.6 S_precentral-inf-part
- 1371 938 2214 2.501 0.429 0.121 0.037 13 1.9 S_precentral-sup-part
- 287 197 503 2.257 0.641 0.157 0.076 11 1.1 S_suborbital
- 1051 714 1792 2.397 0.536 0.128 0.034 12 1.5 S_subparietal
- 1029 699 1227 1.873 0.489 0.129 0.038 10 1.3 S_temporal_inf
- 5880 4098 9805 2.370 0.494 0.120 0.031 60 7.7 S_temporal_sup
- 155 113 344 2.638 0.375 0.111 0.023 1 0.2 S_temporal_transverse
- #-----------------------------------------
- #@# Cortical Parc 3 rh Thu Aug 8 20:58:32 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub010 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...
- 880 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2279 changed, 111391 examined...
- 001: 529 changed, 9872 examined...
- 002: 124 changed, 2865 examined...
- 003: 45 changed, 779 examined...
- 004: 26 changed, 246 examined...
- 005: 14 changed, 117 examined...
- 006: 13 changed, 76 examined...
- 007: 12 changed, 58 examined...
- 008: 6 changed, 57 examined...
- 009: 4 changed, 37 examined...
- 010: 3 changed, 18 examined...
- 011: 3 changed, 15 examined...
- 012: 4 changed, 15 examined...
- 013: 2 changed, 16 examined...
- 014: 2 changed, 10 examined...
- 015: 1 changed, 9 examined...
- 016: 1 changed, 9 examined...
- 017: 1 changed, 7 examined...
- 018: 0 changed, 5 examined...
- 212 labels changed using aseg
- 000: 69 total segments, 36 labels (141 vertices) changed
- 001: 33 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 57 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 276 vertices marked for relabeling...
- 276 labels changed in reclassification.
- writing output to ../label/rh.aparc.DKTatlas40.annot...
- classification took 0 minutes and 50 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 3 rh Thu Aug 8 20:59:23 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 sub010 rh white
- computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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
- 1024 720 2470 2.881 0.674 0.166 0.051 21 2.2 caudalanteriorcingulate
- 2148 1442 3962 2.520 0.522 0.136 0.055 32 4.3 caudalmiddlefrontal
- 2860 1896 4163 1.951 0.509 0.168 0.073 64 8.5 cuneus
- 544 395 1498 2.790 1.102 0.167 0.078 11 1.8 entorhinal
- 2834 1957 5736 2.562 0.575 0.147 0.051 51 5.5 fusiform
- 6786 4716 13282 2.418 0.585 0.150 0.053 126 14.3 inferiorparietal
- 4306 2941 9149 2.445 0.676 0.158 0.072 132 11.8 inferiortemporal
- 1181 784 2505 2.876 0.672 0.154 0.058 24 2.7 isthmuscingulate
- 6046 3906 9408 2.133 0.521 0.164 0.067 124 15.0 lateraloccipital
- 3721 2495 8294 2.744 0.755 0.175 0.086 138 13.0 lateralorbitofrontal
- 3962 2731 6658 2.207 0.598 0.181 0.089 107 13.3 lingual
- 1567 1071 3502 2.637 0.770 0.172 0.154 94 13.6 medialorbitofrontal
- 5395 3849 13400 2.701 0.759 0.146 0.051 106 10.2 middletemporal
- 651 468 1752 3.124 0.727 0.143 0.052 10 1.4 parahippocampal
- 1909 1261 3599 2.499 0.604 0.131 0.047 28 3.0 paracentral
- 1533 1069 3391 2.684 0.474 0.145 0.061 32 4.0 parsopercularis
- 978 678 2269 2.596 0.581 0.145 0.045 19 1.9 parsorbitalis
- 2227 1526 4536 2.558 0.574 0.140 0.047 36 4.1 parstriangularis
- 2154 1558 2588 1.779 0.424 0.165 0.065 35 5.9 pericalcarine
- 5434 3625 8899 2.104 0.625 0.133 0.040 67 9.5 postcentral
- 1460 999 3011 2.659 0.626 0.165 0.052 30 3.1 posteriorcingulate
- 6052 4092 12351 2.650 0.514 0.131 0.040 70 10.0 precentral
- 5007 3454 9342 2.418 0.551 0.143 0.049 93 10.1 precuneus
- 825 605 2454 3.181 0.743 0.180 0.088 29 2.7 rostralanteriorcingulate
- 4628 3223 10070 2.529 0.631 0.172 0.075 116 12.7 rostralmiddlefrontal
- 10477 7202 23659 2.765 0.602 0.156 0.062 229 24.1 superiorfrontal
- 6062 4011 10312 2.230 0.489 0.146 0.053 119 13.3 superiorparietal
- 5720 3945 14107 2.899 0.748 0.126 0.041 86 9.9 superiortemporal
- 3545 2520 7877 2.564 0.590 0.160 0.067 80 9.2 supramarginal
- 359 227 632 2.537 0.352 0.126 0.039 5 0.6 transversetemporal
- 2419 1576 5468 3.041 0.913 0.112 0.054 33 4.8 insula
- #--------------------------------------------
- #@# Refine Pial Surfs w/ T2/FLAIR Thu Aug 8 20:59:35 CEST 2013
- bbregister --s sub010 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/T2raw.lta --init-fsl --T2
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/T2raw.dat.log
- Thu Aug 8 20:59:35 CEST 2013
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts
- /opt/freesurfer/5.3.0/bin/bbregister --s sub010 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/T2raw.lta --init-fsl --T2
- $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $
- Linux snake4 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/sub010/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/template.nii
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/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/sub010/mri/orig/T2raw.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.996481, 0.0682576, -0.0486557)
- j_ras = (0.0655887, 0.996358, 0.0544886)
- k_ras = (-0.0521977, -0.0511056, 0.997328)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/template.nii...
- fslregister --s sub010 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/fslregister --dof 6 --fsvol brainmask.mgz
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/reg.init.dat.fslregister.log
- Thu Aug 8 20:59:40 CEST 2013
- --s sub010 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/fslregister --dof 6 --fsvol brainmask.mgz
- $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $
- snake4
- Linux snake4 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/sub010/scripts
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/fslregister/refvol.fslregister.nii
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/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/sub010/mri/brainmask.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, -1.07102e-08, 7.45058e-09)
- j_ras = (7.45058e-09, -3.72529e-09, -1)
- k_ras = (-4.42378e-09, 1, 7.45058e-09)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/fslregister/refvol.fslregister.nii...
- --------------------------------------
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/fslregister/movvol.fslregister.nii --frame 0
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/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/sub010/mri/transforms/tmp.bbregister.1178/template.nii...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.996481, 0.0682576, -0.0486557)
- j_ras = (0.0655887, 0.996358, 0.0544886)
- k_ras = (-0.0521977, -0.0511056, 0.997328)
- keeping frame 0
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/fslregister/movvol.fslregister.nii...
- Mov determinant is -0.311086
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts
- tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/fslregister/movvol.fslregister.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/fslregister/reg0.1218.dat --regheader --fslregout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/reg.init.dat.fsl.mat0 --s sub010 --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/sub010/mri/transforms/tmp.bbregister.1178/fslregister/movvol.fslregister.nii
- reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/fslregister/reg0.1218.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/sub010/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/sub010/mri/transforms/tmp.bbregister.1178/fslregister/movvol.fslregister.nii
- Tmov: --------------------
- -0.700 0.000 0.000 95.892;
- 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) --------
- 0.996 -0.068 0.049 0.000;
- -0.052 -0.051 0.997 0.000;
- -0.066 -0.996 -0.054 -0.000;
- 0.000 0.000 0.000 1.000;
- ---------------------------------------
- ---- Input registration matrix --------
- 0.996 -0.068 0.049 0.000;
- -0.052 -0.051 0.997 0.000;
- -0.066 -0.996 -0.054 -0.000;
- 0.000 0.000 0.000 1.000;
- Determinant 1
- subject = sub010
- RegMat ---------------------------
- 0.996 -0.068 0.049 0.000;
- -0.052 -0.051 0.997 0.000;
- -0.066 -0.996 -0.054 -0.000;
- 0.000 0.000 0.000 1.000;
- FSLOUTPUTTYPE NIFTI
- tkreg2FSL: mov det = -0.311086, ref det = -1
- Thu Aug 8 20:59:49 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts
- flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/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/sub010/mri/transforms/tmp.bbregister.1178/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/reg.init.dat.fsl.mat0
- Thu Aug 8 21:04:13 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts
- flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/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/sub010/mri/transforms/tmp.bbregister.1178/reg.init.dat.fsl.mat -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/fslregister/fslmat0.trans.mat -schedule /opt/freesurfer/5.3.0/bin/flirt.newdefault.20080811.sch
- tkregister2_cmdl --s sub010 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/reg.init.dat --fslreg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/reg.init.dat.fsl.mat --noedit
- tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl
- ---- FSL registration matrix --------
- 0.997 -0.060 0.056 32.987;
- 0.053 -0.050 -0.997 258.619;
- 0.063 0.997 -0.047 -0.014;
- 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/sub010/mri/transforms/tmp.bbregister.1178/template.nii
- reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/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/sub010/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/sub010/mri/transforms/tmp.bbregister.1178/template.nii
- Tmov: --------------------
- -0.700 0.000 0.000 95.892;
- 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 = -0.311086, ref det = -1
- ---- Input registration matrix (computed) --------
- 0.997 -0.063 0.053 0.084;
- -0.056 -0.047 0.997 1.598;
- -0.060 -0.997 -0.050 -0.458;
- 0.000 0.000 0.000 1.000;
- ---------------------------------------
- ---- Input registration matrix --------
- 0.997 -0.063 0.053 0.084;
- -0.056 -0.047 0.997 1.598;
- -0.060 -0.997 -0.050 -0.458;
- 0.000 0.000 0.000 1.000;
- Determinant 1
- subject = sub010
- RegMat ---------------------------
- 0.997 -0.063 0.053 0.084;
- -0.056 -0.047 0.997 1.598;
- -0.060 -0.997 -0.050 -0.458;
- 0.000 0.000 0.000 1.000;
-
- Started at Thu Aug 8 20:59:40 CEST 2013
- Ended at Thu Aug 8 21:10:10 CEST 2013
-
- fslregister Done
-
- To check results, run:
- tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/reg.init.dat --surf orig
-
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/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/sub010/scripts
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/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 snake4
- machine x86_64
- user fkaule
- movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/template.nii
- regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/reg.init.dat
- subject sub010
- dof 6
- outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/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 1376658733
- TransRandMax 0.000000
- RotRandMax 0.000000
- Translations 0.000000 0.000000 0.000000
- Rotations 0.000000 0.000000 0.000000
- Input reg
- 0.997 -0.063 0.053 0.084;
- -0.056 -0.047 0.997 1.598;
- -0.060 -0.997 -0.050 -0.458;
- 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 1.045764
- 1 -25.0 -25.0 25.0 1.015950
- 2 -25.0 25.0 -25.0 1.038444
- 3 -25.0 25.0 25.0 1.048401
- 4 25.0 -25.0 -25.0 1.016484
- 5 25.0 -25.0 25.0 1.008765
- 6 25.0 25.0 -25.0 1.021521
- 7 25.0 25.0 25.0 1.024672
- REL: 8 0.282323 8.220002 1.027500 rel = 0.274766
- Initial costs ----------------
- Number of surface hits 2105
- WM Intensity 55.1658 +/- 10.0304
- Ctx Intensity 67.4505 +/- 11.3538
- Pct Contrast 19.9782 +/- 18.5298
- Cost 0.2823
- RelCost 0.2748
- ------------------------------------
- Brute force preopt -4 4 4, n = 729
- 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9763 0.9763 0.0
- 6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.9580 0.9580 0.0
- 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.9550 0.9550 0.0
- 19 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.0000 0.9120 0.9120 0.0
- 21 -4.0000 -4.0000 -4.0000 4.0000 0.0000 -4.0000 0.8799 0.8799 0.0
- 39 -4.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.8730 0.8730 0.0
- 61 -4.0000 -4.0000 4.0000 -4.0000 4.0000 0.0000 0.8555 0.8555 0.0
- 102 -4.0000 0.0000 -4.0000 4.0000 0.0000 -4.0000 0.7866 0.7866 0.0
- 120 -4.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.7115 0.7115 0.0
- 346 0.0000 0.0000 -4.0000 4.0000 0.0000 0.0000 0.6763 0.6763 0.0
- 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.2823 0.2823 0.0
- Brute Force --------------------------
- Min cost was 0.282323
- Number of iterations 729
- Search time 2.071000 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 0.081 0.000 0.000 0.000 0.000 0.000 0.2798987473
- 8 0.117 0.000 0.000 0.000 0.000 0.000 0.2798302787
- 9 0.103 0.000 0.000 0.000 0.000 0.000 0.2797153885
- 10 0.101 0.000 0.000 0.000 0.000 0.000 0.2797103372
- 11 0.098 0.000 0.000 0.000 0.000 0.000 0.2797057770
- 17 0.098 -1.618 0.000 0.000 0.000 0.000 0.2547975036
- 18 0.098 -0.900 0.000 0.000 0.000 0.000 0.1916273660
- 22 0.098 -0.882 0.000 0.000 0.000 0.000 0.1913300169
- 24 0.098 -0.842 0.000 0.000 0.000 0.000 0.1911925005
- 27 0.098 -0.841 0.000 0.000 0.000 0.000 0.1911923798
- 37 0.098 -0.841 0.382 0.000 0.000 0.000 0.1623420136
- 38 0.098 -0.841 0.534 0.000 0.000 0.000 0.1610038547
- 42 0.098 -0.841 0.554 0.000 0.000 0.000 0.1607820018
- 43 0.098 -0.841 0.559 0.000 0.000 0.000 0.1607775623
- 44 0.098 -0.841 0.557 0.000 0.000 0.000 0.1607767615
- 51 0.098 -0.841 0.557 0.382 0.000 0.000 0.1481033577
- 54 0.098 -0.841 0.557 0.368 0.000 0.000 0.1480194385
- 56 0.098 -0.841 0.557 0.369 0.000 0.000 0.1480192152
- 64 0.098 -0.841 0.557 0.369 -0.046 0.000 0.1478097685
- 65 0.098 -0.841 0.557 0.369 -0.041 0.000 0.1477535978
- 66 0.098 -0.841 0.557 0.369 -0.028 0.000 0.1476978174
- 68 0.098 -0.841 0.557 0.369 -0.027 0.000 0.1476965434
- 69 0.098 -0.841 0.557 0.369 -0.026 0.000 0.1476955927
- 81 0.098 -0.841 0.557 0.369 -0.026 0.001 0.1476955197
- 92 0.072 -0.841 0.557 0.369 -0.026 0.001 0.1475872601
- 94 0.077 -0.841 0.557 0.369 -0.026 0.001 0.1475710673
- 96 0.079 -0.841 0.557 0.369 -0.026 0.001 0.1475692659
- 97 0.080 -0.841 0.557 0.369 -0.026 0.001 0.1475686265
- 98 0.081 -0.841 0.557 0.369 -0.026 0.001 0.1475685489
- 109 0.081 -0.776 0.557 0.369 -0.026 0.001 0.1462220455
- 111 0.081 -0.775 0.557 0.369 -0.026 0.001 0.1462206692
- 117 0.081 -0.775 -0.061 0.369 -0.026 0.001 0.1452707646
- 119 0.081 -0.775 0.243 0.369 -0.026 0.001 0.1393047025
- 122 0.081 -0.775 0.299 0.369 -0.026 0.001 0.1388997789
- 126 0.081 -0.775 0.300 0.369 -0.026 0.001 0.1388984067
- 127 0.081 -0.775 0.301 0.369 -0.026 0.001 0.1388976555
- 133 0.081 -0.775 0.301 0.751 -0.026 0.001 0.1377324858
- 134 0.081 -0.775 0.301 0.573 -0.026 0.001 0.1365577488
- 135 0.081 -0.775 0.301 0.592 -0.026 0.001 0.1361116141
- 136 0.081 -0.775 0.301 0.645 -0.026 0.001 0.1355918373
- 137 0.081 -0.775 0.301 0.646 -0.026 0.001 0.1355870667
- 140 0.081 -0.775 0.301 0.649 -0.026 0.001 0.1355825748
- 141 0.081 -0.775 0.301 0.648 -0.026 0.001 0.1355823258
- 151 0.081 -0.775 0.301 0.648 -0.113 0.001 0.1354293954
- 152 0.081 -0.775 0.301 0.648 -0.074 0.001 0.1352418161
- 153 0.081 -0.775 0.301 0.648 -0.076 0.001 0.1352339243
- 154 0.081 -0.775 0.301 0.648 -0.082 0.001 0.1352173427
- 156 0.081 -0.775 0.301 0.648 -0.087 0.001 0.1352098561
- 157 0.081 -0.775 0.301 0.648 -0.088 0.001 0.1352096761
- 165 0.081 -0.775 0.301 0.648 -0.088 -0.043 0.1329868884
- 167 0.081 -0.775 0.301 0.648 -0.088 -0.108 0.1322049734
- 168 0.081 -0.775 0.301 0.648 -0.088 -0.093 0.1321036264
- 169 0.081 -0.775 0.301 0.648 -0.088 -0.092 0.1321001253
- 170 0.081 -0.775 0.301 0.648 -0.088 -0.087 0.1320964693
- 183 0.091 -0.775 0.301 0.648 -0.088 -0.087 0.1320573402
- 184 0.098 -0.775 0.301 0.648 -0.088 -0.087 0.1320448085
- 194 0.098 -0.639 0.301 0.648 -0.088 -0.087 0.1314103741
- 195 0.098 -0.681 0.301 0.648 -0.088 -0.087 0.1311697645
- 196 0.098 -0.686 0.301 0.648 -0.088 -0.087 0.1311353890
- 199 0.098 -0.691 0.301 0.648 -0.088 -0.087 0.1311227919
- 208 0.098 -0.691 0.129 0.648 -0.088 -0.087 0.1298426937
- 212 0.098 -0.691 0.102 0.648 -0.088 -0.087 0.1295425843
- 221 0.098 -0.691 0.102 0.654 -0.088 -0.087 0.1293195956
- 222 0.098 -0.691 0.102 0.737 -0.088 -0.087 0.1261612594
- 225 0.098 -0.691 0.102 0.750 -0.088 -0.087 0.1259277404
- 227 0.098 -0.691 0.102 0.752 -0.088 -0.087 0.1259261497
- 235 0.098 -0.691 0.102 0.752 -0.106 -0.087 0.1256318091
- 236 0.098 -0.691 0.102 0.752 -0.173 -0.087 0.1256208305
- 239 0.098 -0.691 0.102 0.752 -0.251 -0.087 0.1253173438
- 243 0.098 -0.691 0.102 0.752 -0.242 -0.087 0.1252707117
- 244 0.098 -0.691 0.102 0.752 -0.240 -0.087 0.1252664345
- 245 0.098 -0.691 0.102 0.752 -0.238 -0.087 0.1252650436
- 254 0.098 -0.691 0.102 0.752 -0.238 -0.096 0.1251763466
- 256 0.098 -0.691 0.102 0.752 -0.238 -0.110 0.1251064648
- 257 0.098 -0.691 0.102 0.752 -0.238 -0.113 0.1251023519
- 269 0.077 -0.691 0.102 0.752 -0.238 -0.113 0.1245388016
- 271 0.046 -0.691 0.102 0.752 -0.238 -0.113 0.1241281190
- 282 0.046 -0.677 0.102 0.752 -0.238 -0.113 0.1241026310
- 283 0.046 -0.682 0.102 0.752 -0.238 -0.113 0.1240853142
- 285 0.046 -0.681 0.102 0.752 -0.238 -0.113 0.1240852242
- 293 0.046 -0.681 0.050 0.752 -0.238 -0.113 0.1237052012
- 294 0.046 -0.681 0.052 0.752 -0.238 -0.113 0.1236906944
- 295 0.046 -0.681 0.065 0.752 -0.238 -0.113 0.1236583896
- 297 0.046 -0.681 0.061 0.752 -0.238 -0.113 0.1236475157
- 307 0.046 -0.681 0.061 0.781 -0.238 -0.113 0.1233281206
- 309 0.046 -0.681 0.061 0.773 -0.238 -0.113 0.1232717663
- 319 0.046 -0.681 0.061 0.773 -0.229 -0.113 0.1232119749
- 321 0.046 -0.681 0.061 0.773 -0.223 -0.113 0.1231926702
- 322 0.046 -0.681 0.061 0.773 -0.222 -0.113 0.1231922379
- 330 0.046 -0.681 0.061 0.773 -0.222 -0.128 0.1231715191
- 331 0.046 -0.681 0.061 0.773 -0.222 -0.125 0.1231532928
- 332 0.046 -0.681 0.061 0.773 -0.222 -0.122 0.1231455990
- 333 0.046 -0.681 0.061 0.773 -0.222 -0.121 0.1231455575
- 345 0.044 -0.681 0.061 0.773 -0.222 -0.121 0.1231266858
- 346 0.021 -0.681 0.061 0.773 -0.222 -0.121 0.1230944926
- 348 0.030 -0.681 0.061 0.773 -0.222 -0.121 0.1230583475
- 349 0.031 -0.681 0.061 0.773 -0.222 -0.121 0.1230580732
- 359 0.031 -0.669 0.061 0.773 -0.222 -0.121 0.1229931675
- 360 0.031 -0.671 0.061 0.773 -0.222 -0.121 0.1229877195
- 361 0.031 -0.672 0.061 0.773 -0.222 -0.121 0.1229865998
- 362 0.031 -0.673 0.061 0.773 -0.222 -0.121 0.1229862162
- 373 0.031 -0.673 0.055 0.773 -0.222 -0.121 0.1229802391
- 374 0.031 -0.673 0.057 0.773 -0.222 -0.121 0.1229782452
- 386 0.031 -0.673 0.057 0.774 -0.222 -0.121 0.1229760006
- 387 0.031 -0.673 0.057 0.776 -0.222 -0.121 0.1229747743
- 399 0.031 -0.673 0.057 0.776 -0.218 -0.121 0.1229714520
- 408 0.031 -0.673 0.057 0.776 -0.218 -0.135 0.1229628292
- 409 0.031 -0.673 0.057 0.776 -0.218 -0.130 0.1229276960
- 412 0.017 -0.665 0.053 0.778 -0.215 -0.139 0.1229066164
- 436 0.026 -0.669 0.057 0.776 -0.218 -0.130 0.1229040328
- 437 0.026 -0.670 0.057 0.776 -0.218 -0.130 0.1229031392
- 460 0.026 -0.670 0.057 0.777 -0.218 -0.130 0.1229017014
- 473 0.026 -0.670 0.057 0.777 -0.216 -0.130 0.1229006552
- 484 0.026 -0.670 0.057 0.777 -0.216 -0.131 0.1228965156
- 485 0.026 -0.670 0.057 0.777 -0.216 -0.132 0.1228956624
- 487 0.020 -0.668 0.057 0.778 -0.214 -0.135 0.1228938820
- 493 0.022 -0.669 0.057 0.778 -0.215 -0.134 0.1228919303
- 514 0.022 -0.669 0.057 0.778 -0.215 -0.135 0.1228910971
- 525 0.022 -0.668 0.057 0.778 -0.215 -0.135 0.1228902165
- 537 0.022 -0.668 0.056 0.778 -0.215 -0.135 0.1228893177
- 560 0.022 -0.668 0.056 0.778 -0.216 -0.135 0.1228888567
- 569 0.022 -0.668 0.056 0.778 -0.216 -0.135 0.1228886972
- Powell done niters = 6
- Computing relative cost
- 0 -25.0 -25.0 -25.0 1.014050
- 1 -25.0 -25.0 25.0 1.046470
- 2 -25.0 25.0 -25.0 1.028936
- 3 -25.0 25.0 25.0 1.007599
- 4 25.0 -25.0 -25.0 1.027513
- 5 25.0 -25.0 25.0 1.044016
- 6 25.0 25.0 -25.0 0.991669
- 7 25.0 25.0 25.0 1.022222
- REL: 8 0.122889 8.182476 1.022810 rel = 0.120148
- Number of iterations 6
- Min cost was 0.122889
- Number of FunctionCalls 579
- TolPowell 0.000100
- nMaxItersPowell 36
- OptimizationTime 1.456000 sec
- Parameters at optimum (transmm) 0.02230 -0.66767 0.05609
- Parameters at optimum (rotdeg) 0.77765 -0.21625 -0.13502
- Final costs ----------------
- Number of surface hits 2105
- WM Intensity 54.7066 +/- 8.9338
- Ctx Intensity 67.3044 +/- 9.6627
- Pct Contrast 20.7461 +/- 14.3771
- Cost 0.1229
- RelCost 0.2748
- Reg at min cost was
- 0.997 -0.059 0.055 0.112;
- -0.057 -0.033 0.998 0.936;
- -0.057 -0.998 -0.036 -0.380;
- 0.000 0.000 0.000 1.000;
- Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/bbr.pass1.dat, type = 14
- Original Reg
- 0.997 -0.063 0.053 0.084;
- -0.056 -0.047 0.997 1.598;
- -0.060 -0.997 -0.050 -0.458;
- 0.000 0.000 0.000 1.000;
- Original Reg - Optimal Reg
- -0.000 -0.004 -0.002 -0.028;
- 0.002 -0.014 -0.000 0.662;
- -0.003 0.001 -0.014 -0.078;
- 0.000 0.000 0.000 0.000;
- Computing change in lh position
- LH rmsDiffMean 1.091263
- Computing change in rh position
- Surface RMS Diff (mm) 1.156741 1.927655
- mri_segreg done
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/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/sub010/scripts
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5
- sysname Linux
- hostname snake4
- machine x86_64
- user fkaule
- movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/template.nii
- regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/tmp.bbregister.1178/bbr.pass1.dat
- subject sub010
- dof 6
- outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 1376400309
- TransRandMax 0.000000
- RotRandMax 0.000000
- Translations 0.000000 0.000000 0.000000
- Rotations 0.000000 0.000000 0.000000
- Input reg
- 0.997 -0.059 0.055 0.112;
- -0.057 -0.033 0.998 0.936;
- -0.057 -0.998 -0.036 -0.380;
- 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 1.022829
- 1 -25.0 -25.0 25.0 1.011391
- 2 -25.0 25.0 -25.0 1.008765
- 3 -25.0 25.0 25.0 1.014969
- 4 25.0 -25.0 -25.0 1.019751
- 5 25.0 -25.0 25.0 1.026475
- 6 25.0 25.0 -25.0 1.021876
- 7 25.0 25.0 25.0 1.034910
- REL: 8 0.146833 8.160967 1.020121 rel = 0.143937
- Initial costs ----------------
- Number of surface hits 208855
- WM Intensity 54.9470 +/- 9.6295
- Ctx Intensity 67.1138 +/- 9.7123
- Pct Contrast 20.1534 +/- 14.6898
- Cost 0.1468
- RelCost 0.1439
- ------------------------------------
- Brute force preopt -0.1 0.1 0.1, n = 729
- 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1500 0.1500 0.0
- 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1487 0.1487 0.0
- 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.1437 0.1437 0.0
- 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.1420 0.1420 0.0
- 6 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 0.1405 0.1405 0.0
- 7 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.0000 0.1383 0.1383 0.0
- 8 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.1000 0.1373 0.1373 0.0
- 30 -0.1000 -0.1000 0.0000 -0.1000 0.0000 -0.1000 0.1368 0.1368 0.0
- 31 -0.1000 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.1354 0.1354 0.0
- 34 -0.1000 -0.1000 0.0000 -0.1000 0.1000 0.0000 0.1351 0.1351 0.0
- 35 -0.1000 -0.1000 0.0000 -0.1000 0.1000 0.1000 0.1345 0.1345 0.0
- 88 -0.1000 0.0000 -0.1000 -0.1000 0.1000 0.0000 0.1331 0.1331 0.0
- 93 -0.1000 0.0000 -0.1000 0.0000 0.0000 -0.1000 0.1323 0.1323 0.0
- 94 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.0000 0.1303 0.1303 0.0
- 97 -0.1000 0.0000 -0.1000 0.0000 0.1000 0.0000 0.1302 0.1302 0.0
- 112 -0.1000 0.0000 0.0000 -0.1000 0.0000 0.0000 0.1290 0.1290 0.0
- 120 -0.1000 0.0000 0.0000 0.0000 0.0000 -0.1000 0.1287 0.1287 0.0
- 121 -0.1000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1273 0.1273 0.0
- 337 0.0000 0.0000 -0.1000 0.0000 0.0000 0.0000 0.1253 0.1253 0.0
- 340 0.0000 0.0000 -0.1000 0.0000 0.1000 0.0000 0.1248 0.1248 0.0
- 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1229 0.1229 0.0
- Brute Force --------------------------
- Min cost was 0.122889
- Number of iterations 729
- Search time 1.554000 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 0.082 0.000 0.000 0.000 0.000 0.000 0.1458149024
- 8 0.088 0.000 0.000 0.000 0.000 0.000 0.1458117233
- 9 0.087 0.000 0.000 0.000 0.000 0.000 0.1458113466
- 17 0.087 0.076 0.000 0.000 0.000 0.000 0.1450888197
- 18 0.087 0.074 0.000 0.000 0.000 0.000 0.1450850635
- 19 0.087 0.070 0.000 0.000 0.000 0.000 0.1450798674
- 22 0.087 0.068 0.000 0.000 0.000 0.000 0.1450794793
- 30 0.087 0.068 -0.056 0.000 0.000 0.000 0.1449826744
- 31 0.087 0.068 -0.034 0.000 0.000 0.000 0.1449470763
- 32 0.087 0.068 -0.036 0.000 0.000 0.000 0.1449468939
- 34 0.087 0.068 -0.035 0.000 0.000 0.000 0.1449468147
- 41 0.087 0.068 -0.035 -0.132 0.000 0.000 0.1411851936
- 42 0.087 0.068 -0.035 -0.141 0.000 0.000 0.1411503358
- 43 0.087 0.068 -0.035 -0.147 0.000 0.000 0.1411466191
- 44 0.087 0.068 -0.035 -0.145 0.000 0.000 0.1411462036
- 52 0.087 0.068 -0.035 -0.145 0.069 0.000 0.1403739620
- 54 0.087 0.068 -0.035 -0.145 0.067 0.000 0.1403726556
- 55 0.087 0.068 -0.035 -0.145 0.066 0.000 0.1403725136
- 63 0.087 0.068 -0.035 -0.145 0.066 0.065 0.1394880703
- 65 0.087 0.068 -0.035 -0.145 0.066 0.067 0.1394874522
- 74 0.086 0.068 -0.035 -0.145 0.066 0.067 0.1394860558
- 75 0.082 0.068 -0.035 -0.145 0.066 0.067 0.1394840013
- 85 0.082 0.025 -0.035 -0.145 0.066 0.067 0.1392971198
- 86 0.082 0.031 -0.035 -0.145 0.066 0.067 0.1392769580
- 87 0.082 0.036 -0.035 -0.145 0.066 0.067 0.1392707865
- 96 0.082 0.036 0.048 -0.145 0.066 0.067 0.1381593300
- 97 0.082 0.036 0.055 -0.145 0.066 0.067 0.1381503630
- 98 0.082 0.036 0.056 -0.145 0.066 0.067 0.1381501840
- 106 0.082 0.036 0.056 -0.192 0.066 0.067 0.1377376363
- 108 0.082 0.036 0.056 -0.191 0.066 0.067 0.1377373318
- 117 0.082 0.036 0.056 -0.191 0.087 0.067 0.1376926263
- 118 0.082 0.036 0.056 -0.191 0.084 0.067 0.1376899590
- 119 0.082 0.036 0.056 -0.191 0.083 0.067 0.1376897722
- 127 0.082 0.036 0.056 -0.191 0.083 0.065 0.1376896304
- 129 0.078 0.004 0.148 -0.236 0.100 0.064 0.1375617851
- 135 0.079 0.016 0.113 -0.219 0.093 0.064 0.1374614070
- 136 0.079 0.016 0.113 -0.219 0.093 0.064 0.1374612031
- 139 0.080 0.018 0.109 -0.217 0.093 0.065 0.1374601702
- 142 0.080 0.018 0.108 -0.217 0.092 0.065 0.1374601302
- 153 0.069 0.018 0.108 -0.217 0.092 0.065 0.1374349690
- 154 0.065 0.018 0.108 -0.217 0.092 0.065 0.1374341590
- 155 0.066 0.018 0.108 -0.217 0.092 0.065 0.1374341327
- 163 0.066 0.002 0.108 -0.217 0.092 0.065 0.1373749651
- 164 0.066 -0.004 0.108 -0.217 0.092 0.065 0.1373704933
- 174 0.066 -0.004 0.108 -0.217 0.092 0.063 0.1373698675
- 182 0.066 -0.004 0.108 -0.232 0.092 0.063 0.1373562652
- 183 0.066 -0.004 0.108 -0.227 0.092 0.063 0.1373526036
- 185 0.066 -0.004 0.108 -0.226 0.092 0.063 0.1373525238
- 194 0.066 -0.004 0.108 -0.226 0.096 0.063 0.1373501648
- 195 0.066 -0.004 0.108 -0.226 0.097 0.063 0.1373498926
- 204 0.066 -0.004 0.107 -0.225 0.096 0.063 0.1373497704
- 217 0.065 -0.004 0.107 -0.225 0.096 0.063 0.1373484880
- 218 0.061 -0.004 0.107 -0.225 0.096 0.063 0.1373459604
- 221 0.059 -0.004 0.107 -0.225 0.096 0.063 0.1373455571
- 232 0.059 -0.009 0.107 -0.225 0.096 0.063 0.1373429361
- 234 0.059 -0.008 0.107 -0.225 0.096 0.063 0.1373428382
- 252 0.059 -0.008 0.107 -0.228 0.096 0.063 0.1373409880
- 261 0.059 -0.008 0.107 -0.228 0.099 0.063 0.1373399094
- 262 0.059 -0.008 0.107 -0.228 0.100 0.063 0.1373398462
- 263 0.059 -0.008 0.107 -0.228 0.101 0.063 0.1373398352
- 272 0.059 -0.009 0.109 -0.230 0.101 0.063 0.1373391978
- 273 0.059 -0.009 0.110 -0.230 0.101 0.063 0.1373391866
- 275 0.059 -0.009 0.110 -0.230 0.101 0.063 0.1373391574
- 279 0.059 -0.009 0.111 -0.230 0.101 0.063 0.1373391439
- 280 0.059 -0.009 0.110 -0.230 0.101 0.063 0.1373390156
- 283 0.051 -0.014 0.114 -0.235 0.106 0.062 0.1373388598
- 291 0.055 -0.009 0.110 -0.230 0.101 0.063 0.1373373201
- 301 0.055 -0.013 0.110 -0.230 0.101 0.063 0.1373353841
- 303 0.055 -0.012 0.110 -0.230 0.101 0.063 0.1373352866
- 330 0.055 -0.012 0.110 -0.230 0.104 0.063 0.1373349217
- 343 0.055 -0.012 0.110 -0.230 0.104 0.063 0.1373348630
- 355 0.054 -0.012 0.110 -0.230 0.104 0.063 0.1373346052
- Powell done niters = 6
- Computing relative cost
- 0 -25.0 -25.0 -25.0 1.023859
- 1 -25.0 -25.0 25.0 1.009395
- 2 -25.0 25.0 -25.0 1.009667
- 3 -25.0 25.0 25.0 1.012653
- 4 25.0 -25.0 -25.0 1.018492
- 5 25.0 -25.0 25.0 1.026773
- 6 25.0 25.0 -25.0 1.018917
- 7 25.0 25.0 25.0 1.033462
- REL: 8 0.137335 8.153219 1.019152 rel = 0.134754
- Number of iterations 6
- Min cost was 0.137335
- Number of FunctionCalls 460
- TolPowell 0.000000
- nMaxItersPowell 36
- OptimizationTime 39.149000 sec
- Parameters at optimum (transmm) 0.05420 -0.01155 0.11035
- Parameters at optimum (rotdeg) -0.23004 0.10394 0.06253
- Final costs ----------------
- Number of surface hits 208855
- WM Intensity 54.9646 +/- 9.6236
- Ctx Intensity 67.1014 +/- 9.6266
- Pct Contrast 20.1181 +/- 14.5150
- Cost 0.1373
- RelCost 0.1439
- Reg at min cost was
- 0.997 -0.061 0.054 0.165;
- -0.056 -0.037 0.998 0.923;
- -0.058 -0.997 -0.040 -0.273;
- 0.000 0.000 0.000 1.000;
- Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/T2raw.dat, type = 14
- Original Reg
- 0.997 -0.059 0.055 0.112;
- -0.057 -0.033 0.998 0.936;
- -0.057 -0.998 -0.036 -0.380;
- 0.000 0.000 0.000 1.000;
- Original Reg - Optimal Reg
- 0.000 0.002 0.001 -0.052;
- -0.001 0.004 0.000 0.013;
- 0.002 -0.000 0.004 -0.106;
- 0.000 0.000 0.000 0.000;
- Computing change in lh position
- LH rmsDiffMean 0.192862
- Computing change in rh position
- Surface RMS Diff (mm) 0.200435 0.406761
- mri_segreg done
- tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/T2raw.dat --noedit --ltaout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/mri/orig/T2raw.mgz
- reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 --------
- 0.997 -0.061 0.054 0.165;
- -0.056 -0.037 0.998 0.923;
- -0.058 -0.997 -0.040 -0.273;
- 0.000 0.000 0.000 1.000;
- float2int = 0
- ---------------------------------------
- INFO: loading target /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/mri/orig/T2raw.mgz
- Tmov: --------------------
- -0.700 0.000 0.000 95.892;
- 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 --------
- 0.997 -0.061 0.054 0.165;
- -0.056 -0.037 0.998 0.923;
- -0.058 -0.997 -0.040 -0.273;
- 0.000 0.000 0.000 1.000;
- Determinant 1
- subject = sub010
- RegMat ---------------------------
- 0.997 -0.061 0.054 0.165;
- -0.056 -0.037 0.998 0.923;
- -0.058 -0.997 -0.040 -0.273;
- 0.000 0.000 0.000 1.000;
- transformed matrix:
- 1.000 -0.007 -0.005 -0.052;
- 0.007 1.000 0.014 0.003;
- 0.004 -0.014 1.000 -0.630;
- 0.000 0.000 0.000 1.000;
- transformed matrix:
- 0.698 -0.039 0.038 32.819;
- 0.038 -0.027 -0.665 256.625;
- 0.042 0.665 -0.025 -0.977;
- 0.000 0.000 0.000 1.000;
- Cleaning up
-
- Started at Thu Aug 8 20:59:35 CEST 2013
- Ended at Thu Aug 8 21:11:37 CEST 2013
- BBR-Run-Time-Sec 722
-
- bbregister Done
- To check results, run:
- tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/T2raw.dat --surf
-
- mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/T2.mgz
- mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/mri/orig/T2raw.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.996481, 0.0682576, -0.0486557)
- j_ras = (0.0655887, 0.996358, 0.0544886)
- k_ras = (-0.0521977, -0.0511056, 0.997328)
- INFO: Reading transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/T2raw.lta...
- Reading transform with LTAreadEx()
- reading extra input line subject sub010
- reading extra input line fscale 0.150000
- reading template info from volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/orig.mgz...
- INFO: Applying transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/T2raw.lta...
- ---------------------------------
- INFO: Transform Matrix (linear_ras_to_ras)
- 1.000 -0.007 -0.005 -0.052;
- 0.007 1.000 0.014 0.003;
- 0.004 -0.014 1.000 -0.630;
- 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/sub010/mri/T2.mgz...
- mri_normalize -aseg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/aseg.mgz -sigma 4 -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.white identity.nofile -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.white identity.nofile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/T2.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/mri/T2.mgz...
- computing distance transform
- computing distance transform
- computing nonmaximum suppression
- 8132 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/sub010/mri/T2.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts
- cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.woT2.pial
- `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.woT2.pial'
- mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub010 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/sub010/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/wm.mgz...
- 13095 bright wm thresholded.
- 240 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.orig...
- computing class statistics...
- border white: 201670 voxels (1.20%)
- border gray 234473 voxels (1.40%)
- WM (91.0): 92.1 +- 10.7 [70.0 --> 110.0]
- GM (73.0) : 71.4 +- 13.2 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 43.8 (was 70)
- setting MAX_BORDER_WHITE to 115.7 (was 105)
- setting MIN_BORDER_WHITE to 57.0 (was 85)
- setting MAX_CSF to 30.6 (was 40)
- setting MAX_GRAY to 94.3 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 50.4 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 17.4 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=105, GM=57
- mean inside = 91.7, mean outside = 66.6
- smoothing surface for 5 iterations...
- reading initial white vertex positions from white...
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.90 +- 0.26 (0.02-->6.42) (max @ vno 49307 --> 52883)
- face area 0.34 +- 0.16 (0.00-->7.16)
- 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 2 with 6 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 6 with 924 points - only 4.87% unknown
- deleting segment 7 with 12 points - only 0.00% unknown
- deleting segment 8 with 19 points - only 0.00% unknown
- deleting segment 10 with 6 points - only 0.00% unknown
- deleting segment 11 with 9 points - only 0.00% unknown
- deleting segment 12 with 13 points - only 0.00% unknown
- deleting segment 13 with 17 points - only 0.00% unknown
- deleting segment 14 with 30 points - only 0.00% unknown
- deleting segment 15 with 5 points - only 0.00% unknown
- tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.90 +- 0.26 (0.05-->6.42) (max @ vno 49307 --> 52883)
- face area 0.34 +- 0.16 (0.00-->7.16)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4024837.5, rms=0.00
- rms = 1.07, time step reduction 1 of 3 to 0.250...
- rms = 0.27, time step reduction 2 of 3 to 0.125...
- rms = 0.03, time step reduction 3 of 3 to 0.062...
- 001: dt: 0.1250, sse=4024837.5, rms=0.000 (1.000%)
- positioning took 0.2 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 4 vertex label from ripped group
- deleting segment 3 with 924 points - only 4.87% unknown
- deleting segment 4 with 12 points - only 0.00% unknown
- deleting segment 5 with 19 points - only 0.00% unknown
- deleting segment 6 with 6 points - only 0.00% unknown
- deleting segment 7 with 9 points - only 0.00% unknown
- deleting segment 8 with 13 points - only 0.00% unknown
- deleting segment 9 with 17 points - only 0.00% unknown
- deleting segment 10 with 30 points - only 0.00% unknown
- deleting segment 11 with 5 points - only 0.00% unknown
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.90 +- 0.26 (0.05-->6.42) (max @ vno 49307 --> 52883)
- face area 0.34 +- 0.16 (0.00-->7.16)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4024837.5, rms=0.00
- rms = 1.07, time step reduction 1 of 3 to 0.250...
- rms = 0.27, time step reduction 2 of 3 to 0.125...
- rms = 0.03, time step reduction 3 of 3 to 0.062...
- 002: dt: 0.1250, sse=4024837.5, rms=0.000 (1.000%)
- positioning took 0.2 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 4 vertex label from ripped group
- deleting segment 3 with 924 points - only 4.87% unknown
- deleting segment 4 with 12 points - only 0.00% unknown
- deleting segment 5 with 19 points - only 0.00% unknown
- deleting segment 6 with 6 points - only 0.00% unknown
- deleting segment 7 with 9 points - only 0.00% unknown
- deleting segment 8 with 13 points - only 0.00% unknown
- deleting segment 9 with 17 points - only 0.00% unknown
- deleting segment 10 with 30 points - only 0.00% unknown
- deleting segment 11 with 5 points - only 0.00% unknown
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.26 (0.05-->6.42) (max @ vno 49307 --> 52883)
- face area 0.34 +- 0.16 (0.00-->7.16)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4024837.5, rms=0.00
- rms = 1.07, time step reduction 1 of 3 to 0.250...
- rms = 0.27, time step reduction 2 of 3 to 0.125...
- rms = 0.03, time step reduction 3 of 3 to 0.062...
- 003: dt: 0.1250, sse=4024837.5, rms=0.000 (1.000%)
- positioning took 0.2 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 4 vertex label from ripped group
- deleting segment 3 with 924 points - only 4.87% unknown
- deleting segment 4 with 12 points - only 0.00% unknown
- deleting segment 5 with 19 points - only 0.00% unknown
- deleting segment 6 with 6 points - only 0.00% unknown
- deleting segment 7 with 9 points - only 0.00% unknown
- deleting segment 8 with 13 points - only 0.00% unknown
- deleting segment 9 with 17 points - only 0.00% unknown
- deleting segment 10 with 30 points - only 0.00% unknown
- deleting segment 11 with 5 points - only 0.00% unknown
- tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- repositioning cortical surface to gray/csf boundary.
- smoothing T1 volume with sigma = 2.000
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4024837.5, rms=0.00
- rms = 1.07, time step reduction 1 of 3 to 0.250...
- rms = 0.27, time step reduction 2 of 3 to 0.125...
- rms = 0.03, time step reduction 3 of 3 to 0.062...
- 004: dt: 0.1250, sse=4024837.5, rms=0.000 (1.000%)
- positioning took 0.2 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 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 [89.10 222.90], gm=156.00+-22.30, and vertices in regions > 144.8
- 25335 surface locations found to contain inconsistent values (1995 in, 23340 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=458774.4, rms=0.22
- 001: dt: 0.5000, sse=430848.8, rms=0.215 (0.000%)
- 002: dt: 0.5000, sse=413732.2, rms=0.203 (0.000%)
- 003: dt: 0.5000, sse=402526.7, rms=0.194 (0.000%)
- 004: dt: 0.5000, sse=394554.8, rms=0.186 (0.000%)
- 005: dt: 0.5000, sse=388978.8, rms=0.178 (0.000%)
- 006: dt: 0.5000, sse=384655.2, rms=0.172 (0.000%)
- 007: dt: 0.5000, sse=380914.8, rms=0.167 (0.000%)
- 008: dt: 0.5000, sse=377920.1, rms=0.163 (0.000%)
- 009: dt: 0.5000, sse=375961.9, rms=0.160 (0.000%)
- 010: dt: 0.5000, sse=373370.3, rms=0.157 (0.000%)
- 011: dt: 0.5000, sse=371330.9, rms=0.154 (0.000%)
- 012: dt: 0.5000, sse=369542.8, rms=0.152 (0.000%)
- 013: dt: 0.5000, sse=367807.3, rms=0.151 (0.000%)
- 014: dt: 0.5000, sse=366092.6, rms=0.149 (0.000%)
- 015: dt: 0.5000, sse=364371.3, rms=0.148 (0.000%)
- 016: dt: 0.5000, sse=362689.0, rms=0.148 (0.000%)
- 017: dt: 0.5000, sse=361575.8, rms=0.147 (0.000%)
- 018: dt: 0.5000, sse=359866.9, rms=0.147 (0.000%)
- 019: dt: 0.5000, sse=358425.4, rms=0.147 (0.000%)
- 020: dt: 0.5000, sse=357066.3, rms=0.147 (0.000%)
- 021: dt: 0.5000, sse=356190.8, rms=0.147 (0.000%)
- 022: dt: 0.5000, sse=354647.8, rms=0.148 (0.000%)
- 023: dt: 0.5000, sse=352928.2, rms=0.148 (0.000%)
- 024: dt: 0.5000, sse=351970.6, rms=0.148 (0.000%)
- 025: dt: 0.5000, sse=351171.3, rms=0.149 (0.000%)
- 026: dt: 0.5000, sse=350023.2, rms=0.149 (0.000%)
- 027: dt: 0.5000, sse=348805.7, rms=0.149 (0.000%)
- 028: dt: 0.5000, sse=347812.3, rms=0.150 (0.000%)
- 029: dt: 0.5000, sse=346543.6, rms=0.150 (0.000%)
- 030: dt: 0.5000, sse=345773.7, rms=0.151 (0.000%)
- positioning took 3.0 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [88.00 226.00], gm=157.00+-23.00, and vertices in regions > 145.5
- 20901 surface locations found to contain inconsistent values (661 in, 20240 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=35700.3, rms=0.12
- 031: dt: 0.5000, sse=35536.3, rms=0.117 (0.000%)
- 032: dt: 0.5000, sse=36263.8, rms=0.107 (0.000%)
- 033: dt: 0.5000, sse=37104.3, rms=0.099 (0.000%)
- 034: dt: 0.5000, sse=37836.9, rms=0.094 (0.000%)
- 035: dt: 0.5000, sse=38481.9, rms=0.089 (0.000%)
- 036: dt: 0.5000, sse=39140.8, rms=0.085 (0.000%)
- 037: dt: 0.5000, sse=39729.2, rms=0.081 (0.000%)
- 038: dt: 0.5000, sse=40321.2, rms=0.077 (0.000%)
- 039: dt: 0.5000, sse=40881.0, rms=0.073 (0.000%)
- 040: dt: 0.5000, sse=41432.2, rms=0.070 (0.000%)
- 041: dt: 0.5000, sse=41917.3, rms=0.067 (0.000%)
- 042: dt: 0.5000, sse=42402.4, rms=0.065 (0.000%)
- 043: dt: 0.5000, sse=42878.4, rms=0.062 (0.000%)
- 044: dt: 0.5000, sse=43283.0, rms=0.060 (0.000%)
- 045: dt: 0.5000, sse=43690.0, rms=0.058 (0.000%)
- 046: dt: 0.5000, sse=44037.4, rms=0.056 (0.000%)
- 047: dt: 0.5000, sse=44377.8, rms=0.055 (0.000%)
- 048: dt: 0.5000, sse=44708.8, rms=0.053 (0.000%)
- 049: dt: 0.5000, sse=45008.6, rms=0.052 (0.000%)
- 050: dt: 0.5000, sse=45324.1, rms=0.050 (0.000%)
- 051: dt: 0.5000, sse=45599.2, rms=0.049 (0.000%)
- 052: dt: 0.5000, sse=45824.9, rms=0.048 (0.000%)
- 053: dt: 0.5000, sse=46064.4, rms=0.047 (0.000%)
- 054: dt: 0.5000, sse=46290.4, rms=0.046 (0.000%)
- 055: dt: 0.5000, sse=46508.7, rms=0.046 (0.000%)
- 056: dt: 0.5000, sse=46718.5, rms=0.045 (0.000%)
- 057: dt: 0.5000, sse=46902.8, rms=0.045 (0.000%)
- 058: dt: 0.5000, sse=47088.3, rms=0.044 (0.000%)
- 059: dt: 0.5000, sse=47216.6, rms=0.043 (0.000%)
- 060: dt: 0.5000, sse=47301.2, rms=0.043 (0.000%)
- positioning took 2.9 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [103.10 206.90], gm=155.00+-17.30, and vertices in regions > 146.3
- 13736 surface locations found to contain inconsistent values (5496 in, 8240 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=8089.1, rms=0.18
- 061: dt: 0.5000, sse=7955.0, rms=0.174 (0.000%)
- 062: dt: 0.5000, sse=7539.9, rms=0.163 (0.000%)
- 063: dt: 0.5000, sse=7220.5, rms=0.153 (0.000%)
- 064: dt: 0.5000, sse=6976.5, rms=0.144 (0.000%)
- 065: dt: 0.5000, sse=6799.2, rms=0.137 (0.000%)
- 066: dt: 0.5000, sse=6676.5, rms=0.130 (0.000%)
- 067: dt: 0.5000, sse=6567.2, rms=0.125 (0.000%)
- 068: dt: 0.5000, sse=6474.5, rms=0.120 (0.000%)
- 069: dt: 0.5000, sse=6389.2, rms=0.115 (0.000%)
- 070: dt: 0.5000, sse=6330.9, rms=0.110 (0.000%)
- 071: dt: 0.5000, sse=6282.3, rms=0.105 (0.000%)
- 072: dt: 0.5000, sse=6247.6, rms=0.101 (0.000%)
- 073: dt: 0.5000, sse=6219.6, rms=0.097 (0.000%)
- 074: dt: 0.5000, sse=6204.7, rms=0.093 (0.000%)
- 075: dt: 0.5000, sse=6191.0, rms=0.089 (0.000%)
- 076: dt: 0.5000, sse=6186.2, rms=0.086 (0.000%)
- 077: dt: 0.5000, sse=6182.3, rms=0.083 (0.000%)
- 078: dt: 0.5000, sse=6187.0, rms=0.079 (0.000%)
- 079: dt: 0.5000, sse=6194.9, rms=0.077 (0.000%)
- 080: dt: 0.5000, sse=6204.8, rms=0.074 (0.000%)
- 081: dt: 0.5000, sse=6215.7, rms=0.071 (0.000%)
- 082: dt: 0.5000, sse=6235.3, rms=0.069 (0.000%)
- 083: dt: 0.5000, sse=6246.4, rms=0.067 (0.000%)
- 084: dt: 0.5000, sse=6263.7, rms=0.064 (0.000%)
- 085: dt: 0.5000, sse=6278.4, rms=0.062 (0.000%)
- 086: dt: 0.5000, sse=6290.3, rms=0.060 (0.000%)
- 087: dt: 0.5000, sse=6302.3, rms=0.058 (0.000%)
- 088: dt: 0.5000, sse=6316.3, rms=0.057 (0.000%)
- 089: dt: 0.5000, sse=6324.7, rms=0.055 (0.000%)
- 090: dt: 0.5000, sse=6337.0, rms=0.054 (0.000%)
- positioning took 2.8 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [112.80 199.20], gm=156.00+-14.40, and vertices in regions > 148.8
- 21619 surface locations found to contain inconsistent values (16444 in, 5175 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/sub010/surf/lh.pial...
- writing smoothed curvature to lh.curv.pial
- 000: dt: 0.0000, sse=9710.2, rms=0.29
- 091: dt: 0.5000, sse=9270.5, rms=0.285 (0.000%)
- 092: dt: 0.5000, sse=8617.0, rms=0.274 (0.000%)
- 093: dt: 0.5000, sse=8057.5, rms=0.264 (0.000%)
- 094: dt: 0.5000, sse=7554.5, rms=0.255 (0.000%)
- 095: dt: 0.5000, sse=7106.7, rms=0.247 (0.000%)
- 096: dt: 0.5000, sse=6699.3, rms=0.239 (0.000%)
- 097: dt: 0.5000, sse=6327.3, rms=0.231 (0.000%)
- 098: dt: 0.5000, sse=5978.0, rms=0.224 (0.000%)
- 099: dt: 0.5000, sse=5641.3, rms=0.217 (0.000%)
- 100: dt: 0.5000, sse=5311.4, rms=0.209 (0.000%)
- 101: dt: 0.5000, sse=5000.9, rms=0.202 (0.000%)
- 102: dt: 0.5000, sse=4706.1, rms=0.195 (0.000%)
- 103: dt: 0.5000, sse=4434.0, rms=0.188 (0.000%)
- 104: dt: 0.5000, sse=4177.8, rms=0.182 (0.000%)
- 105: dt: 0.5000, sse=3936.6, rms=0.175 (0.000%)
- 106: dt: 0.5000, sse=3710.8, rms=0.169 (0.000%)
- 107: dt: 0.5000, sse=3498.0, rms=0.163 (0.000%)
- 108: dt: 0.5000, sse=3296.7, rms=0.157 (0.000%)
- 109: dt: 0.5000, sse=3108.9, rms=0.151 (0.000%)
- 110: dt: 0.5000, sse=2931.8, rms=0.145 (0.000%)
- 111: dt: 0.5000, sse=2766.5, rms=0.139 (0.000%)
- 112: dt: 0.5000, sse=2612.9, rms=0.134 (0.000%)
- 113: dt: 0.5000, sse=2471.7, rms=0.128 (0.000%)
- 114: dt: 0.5000, sse=2340.8, rms=0.123 (0.000%)
- 115: dt: 0.5000, sse=2218.6, rms=0.118 (0.000%)
- 116: dt: 0.5000, sse=2109.3, rms=0.113 (0.000%)
- 117: dt: 0.5000, sse=2005.6, rms=0.109 (0.000%)
- 118: dt: 0.5000, sse=1910.7, rms=0.104 (0.000%)
- 119: dt: 0.5000, sse=1824.0, rms=0.100 (0.000%)
- 120: dt: 0.5000, sse=1744.3, rms=0.096 (0.000%)
- positioning took 2.8 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.curv.pial
- writing smoothed area to lh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.area.pial
- vertex spacing 1.07 +- 0.47 (0.08-->8.17) (max @ vno 79788 --> 78779)
- face area 0.44 +- 0.35 (0.00-->7.69)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 112521 vertices processed
- 25000 of 112521 vertices processed
- 50000 of 112521 vertices processed
- 75000 of 112521 vertices processed
- 100000 of 112521 vertices processed
- 0 of 112521 vertices processed
- 25000 of 112521 vertices processed
- 50000 of 112521 vertices processed
- 75000 of 112521 vertices processed
- 100000 of 112521 vertices processed
- thickness calculation complete, 229:1031 truncations.
- 25308 vertices at 0 distance
- 74701 vertices at 1 distance
- 70921 vertices at 2 distance
- 31005 vertices at 3 distance
- 8480 vertices at 4 distance
- 2183 vertices at 5 distance
- 674 vertices at 6 distance
- 207 vertices at 7 distance
- 66 vertices at 8 distance
- 44 vertices at 9 distance
- 26 vertices at 10 distance
- 15 vertices at 11 distance
- 20 vertices at 12 distance
- 18 vertices at 13 distance
- 12 vertices at 14 distance
- 8 vertices at 15 distance
- 15 vertices at 16 distance
- 10 vertices at 17 distance
- 11 vertices at 18 distance
- 4 vertices at 19 distance
- 6 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.thickness
- positioning took 14.5 minutes
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/scripts
- cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.woT2.pial
- `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.woT2.pial'
- mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub010 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/sub010/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/wm.mgz...
- 12290 bright wm thresholded.
- 241 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.orig...
- computing class statistics...
- border white: 201670 voxels (1.20%)
- border gray 234473 voxels (1.40%)
- WM (91.0): 91.9 +- 10.6 [70.0 --> 110.0]
- GM (73.0) : 71.3 +- 13.5 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 42.5 (was 70)
- setting MAX_BORDER_WHITE to 115.6 (was 105)
- setting MIN_BORDER_WHITE to 56.0 (was 85)
- setting MAX_CSF to 29.1 (was 40)
- setting MAX_GRAY to 94.4 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 49.3 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 15.6 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=105, GM=56
- mean inside = 91.3, mean outside = 66.0
- 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/sub010/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.90 +- 0.26 (0.03-->3.59) (max @ vno 88410 --> 89070)
- face area 0.34 +- 0.16 (0.00-->2.13)
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 1 with 59 points - only 30.51% unknown
- deleting segment 2 with 6 points - only 0.00% unknown
- deleting segment 4 with 10 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 7 with 1 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 9 with 810 points - only 0.00% unknown
- deleting segment 10 with 7 points - only 0.00% unknown
- deleting segment 11 with 6 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 12 with 1 points - only 0.00% unknown
- tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.90 +- 0.26 (0.07-->3.46) (max @ vno 60920 --> 61814)
- face area 0.34 +- 0.16 (0.00-->2.13)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=3904294.5, rms=0.00
- rms = 1.47, time step reduction 1 of 3 to 0.250...
- rms = 0.38, time step reduction 2 of 3 to 0.125...
- rms = 0.05, time step reduction 3 of 3 to 0.062...
- 001: dt: 0.1250, sse=3904294.5, rms=0.000 (1.000%)
- positioning took 0.2 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 59 points - only 30.51% unknown
- deleting segment 1 with 6 points - only 0.00% unknown
- deleting segment 2 with 10 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 3 with 1 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 5 with 810 points - only 0.00% unknown
- deleting segment 6 with 7 points - only 0.00% unknown
- deleting segment 7 with 6 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 8 with 1 points - only 0.00% unknown
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.90 +- 0.26 (0.07-->3.46) (max @ vno 60920 --> 61814)
- face area 0.34 +- 0.16 (0.00-->2.13)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=3904294.5, rms=0.00
- rms = 1.47, time step reduction 1 of 3 to 0.250...
- rms = 0.38, time step reduction 2 of 3 to 0.125...
- rms = 0.05, time step reduction 3 of 3 to 0.062...
- 002: dt: 0.1250, sse=3904294.5, rms=0.000 (1.000%)
- positioning took 0.2 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 59 points - only 30.51% unknown
- deleting segment 1 with 6 points - only 0.00% unknown
- deleting segment 2 with 10 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 3 with 1 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 5 with 810 points - only 0.00% unknown
- deleting segment 6 with 7 points - only 0.00% unknown
- deleting segment 7 with 6 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 8 with 1 points - only 0.00% unknown
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.26 (0.07-->3.46) (max @ vno 60920 --> 61814)
- face area 0.34 +- 0.16 (0.00-->2.13)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=3904294.5, rms=0.00
- rms = 1.47, time step reduction 1 of 3 to 0.250...
- rms = 0.38, time step reduction 2 of 3 to 0.125...
- rms = 0.05, time step reduction 3 of 3 to 0.062...
- 003: dt: 0.1250, sse=3904294.5, rms=0.000 (1.000%)
- positioning took 0.2 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 59 points - only 30.51% unknown
- deleting segment 1 with 6 points - only 0.00% unknown
- deleting segment 2 with 10 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 3 with 1 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 5 with 810 points - only 0.00% unknown
- deleting segment 6 with 7 points - only 0.00% unknown
- deleting segment 7 with 6 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 8 with 1 points - only 0.00% unknown
- tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- repositioning cortical surface to gray/csf boundary.
- smoothing T1 volume with sigma = 2.000
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=3904294.5, rms=0.00
- rms = 1.47, time step reduction 1 of 3 to 0.250...
- rms = 0.38, time step reduction 2 of 3 to 0.125...
- rms = 0.05, time step reduction 3 of 3 to 0.062...
- 004: dt: 0.1250, sse=3904294.5, rms=0.000 (1.000%)
- positioning took 0.2 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 [102.60 203.40], gm=153.00+-16.80, and vertices in regions > 144.6
- 32499 surface locations found to contain inconsistent values (6526 in, 25973 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=461334.0, rms=0.25
- 001: dt: 0.5000, sse=433240.8, rms=0.246 (0.000%)
- 002: dt: 0.5000, sse=415716.5, rms=0.232 (0.000%)
- 003: dt: 0.5000, sse=404683.8, rms=0.222 (0.000%)
- 004: dt: 0.5000, sse=396047.9, rms=0.212 (0.000%)
- 005: dt: 0.5000, sse=389515.8, rms=0.204 (0.000%)
- 006: dt: 0.5000, sse=384523.5, rms=0.197 (0.000%)
- 007: dt: 0.5000, sse=380656.6, rms=0.191 (0.000%)
- 008: dt: 0.5000, sse=377785.3, rms=0.185 (0.000%)
- 009: dt: 0.5000, sse=375323.8, rms=0.181 (0.000%)
- 010: dt: 0.5000, sse=373274.1, rms=0.177 (0.000%)
- 011: dt: 0.5000, sse=371203.3, rms=0.174 (0.000%)
- 012: dt: 0.5000, sse=369271.0, rms=0.171 (0.000%)
- 013: dt: 0.5000, sse=367494.1, rms=0.169 (0.000%)
- 014: dt: 0.5000, sse=365989.0, rms=0.167 (0.000%)
- 015: dt: 0.5000, sse=364516.8, rms=0.166 (0.000%)
- 016: dt: 0.5000, sse=363190.2, rms=0.164 (0.000%)
- 017: dt: 0.5000, sse=361709.2, rms=0.163 (0.000%)
- 018: dt: 0.5000, sse=360423.2, rms=0.163 (0.000%)
- 019: dt: 0.5000, sse=358982.1, rms=0.162 (0.000%)
- 020: dt: 0.5000, sse=357685.2, rms=0.162 (0.000%)
- 021: dt: 0.5000, sse=356452.5, rms=0.161 (0.000%)
- 022: dt: 0.5000, sse=355091.5, rms=0.161 (0.000%)
- 023: dt: 0.5000, sse=353877.5, rms=0.161 (0.000%)
- 024: dt: 0.5000, sse=352503.6, rms=0.161 (0.000%)
- 025: dt: 0.5000, sse=351754.4, rms=0.161 (0.000%)
- 026: dt: 0.5000, sse=350467.2, rms=0.161 (0.000%)
- 027: dt: 0.5000, sse=349278.9, rms=0.161 (0.000%)
- 028: dt: 0.5000, sse=348301.2, rms=0.162 (0.000%)
- 029: dt: 0.5000, sse=347300.8, rms=0.162 (0.000%)
- 030: dt: 0.5000, sse=346608.0, rms=0.162 (0.000%)
- positioning took 2.9 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [100.30 207.70], gm=154.00+-17.90, and vertices in regions > 145.0
- 25001 surface locations found to contain inconsistent values (1723 in, 23278 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=36143.1, rms=0.14
- 031: dt: 0.5000, sse=35900.4, rms=0.133 (0.000%)
- 032: dt: 0.5000, sse=36564.6, rms=0.122 (0.000%)
- 033: dt: 0.5000, sse=37401.6, rms=0.115 (0.000%)
- 034: dt: 0.5000, sse=38133.3, rms=0.109 (0.000%)
- 035: dt: 0.5000, sse=38771.1, rms=0.104 (0.000%)
- 036: dt: 0.5000, sse=39402.9, rms=0.099 (0.000%)
- 037: dt: 0.5000, sse=39998.6, rms=0.095 (0.000%)
- 038: dt: 0.5000, sse=40606.3, rms=0.091 (0.000%)
- 039: dt: 0.5000, sse=41163.0, rms=0.087 (0.000%)
- 040: dt: 0.5000, sse=41728.7, rms=0.084 (0.000%)
- 041: dt: 0.5000, sse=42245.6, rms=0.081 (0.000%)
- 042: dt: 0.5000, sse=42753.1, rms=0.078 (0.000%)
- 043: dt: 0.5000, sse=43218.8, rms=0.075 (0.000%)
- 044: dt: 0.5000, sse=43656.8, rms=0.073 (0.000%)
- 045: dt: 0.5000, sse=44066.9, rms=0.070 (0.000%)
- 046: dt: 0.5000, sse=44477.1, rms=0.068 (0.000%)
- 047: dt: 0.5000, sse=44858.4, rms=0.066 (0.000%)
- 048: dt: 0.5000, sse=45200.9, rms=0.064 (0.000%)
- 049: dt: 0.5000, sse=45558.4, rms=0.062 (0.000%)
- 050: dt: 0.5000, sse=45869.6, rms=0.060 (0.000%)
- 051: dt: 0.5000, sse=46134.1, rms=0.059 (0.000%)
- 052: dt: 0.5000, sse=46403.9, rms=0.057 (0.000%)
- 053: dt: 0.5000, sse=46670.9, rms=0.056 (0.000%)
- 054: dt: 0.5000, sse=46913.3, rms=0.055 (0.000%)
- 055: dt: 0.5000, sse=47112.3, rms=0.054 (0.000%)
- 056: dt: 0.5000, sse=47303.3, rms=0.053 (0.000%)
- 057: dt: 0.5000, sse=47512.1, rms=0.051 (0.000%)
- 058: dt: 0.5000, sse=47700.1, rms=0.050 (0.000%)
- 059: dt: 0.5000, sse=47851.7, rms=0.050 (0.000%)
- 060: dt: 0.5000, sse=48009.2, rms=0.049 (0.000%)
- positioning took 2.9 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [97.30 210.70], gm=154.00+-18.90, and vertices in regions > 144.5
- 23565 surface locations found to contain inconsistent values (251 in, 23314 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=5207.5, rms=0.06
- 061: dt: 0.5000, sse=5182.6, rms=0.061 (0.000%)
- 062: dt: 0.5000, sse=5255.6, rms=0.054 (0.000%)
- 063: dt: 0.5000, sse=5333.7, rms=0.050 (0.000%)
- 064: dt: 0.5000, sse=5399.6, rms=0.047 (0.000%)
- 065: dt: 0.5000, sse=5442.4, rms=0.045 (0.000%)
- 066: dt: 0.5000, sse=5466.1, rms=0.044 (0.000%)
- 067: dt: 0.5000, sse=5479.7, rms=0.042 (0.000%)
- 068: dt: 0.5000, sse=5493.1, rms=0.041 (0.000%)
- 069: dt: 0.5000, sse=5506.1, rms=0.040 (0.000%)
- 070: dt: 0.5000, sse=5517.8, rms=0.039 (0.000%)
- 071: dt: 0.5000, sse=5528.1, rms=0.038 (0.000%)
- 072: dt: 0.5000, sse=5539.3, rms=0.037 (0.000%)
- 073: dt: 0.5000, sse=5548.8, rms=0.036 (0.000%)
- 074: dt: 0.5000, sse=5558.5, rms=0.036 (0.000%)
- 075: dt: 0.5000, sse=5567.3, rms=0.035 (0.000%)
- 076: dt: 0.5000, sse=5571.2, rms=0.035 (0.000%)
- 077: dt: 0.5000, sse=5575.4, rms=0.034 (0.000%)
- 078: dt: 0.5000, sse=5580.0, rms=0.034 (0.000%)
- 079: dt: 0.5000, sse=5584.9, rms=0.033 (0.000%)
- 080: dt: 0.5000, sse=5589.2, rms=0.033 (0.000%)
- 081: dt: 0.5000, sse=5594.5, rms=0.033 (0.000%)
- 082: dt: 0.5000, sse=5599.1, rms=0.032 (0.000%)
- 083: dt: 0.5000, sse=5602.4, rms=0.032 (0.000%)
- 084: dt: 0.5000, sse=5605.8, rms=0.032 (0.000%)
- 085: dt: 0.5000, sse=5607.8, rms=0.032 (0.000%)
- 086: dt: 0.5000, sse=5608.6, rms=0.031 (0.000%)
- 087: dt: 0.5000, sse=5611.4, rms=0.031 (0.000%)
- 088: dt: 0.5000, sse=5613.7, rms=0.031 (0.000%)
- 089: dt: 0.5000, sse=5616.2, rms=0.031 (0.000%)
- 090: dt: 0.5000, sse=5616.1, rms=0.031 (0.000%)
- positioning took 2.9 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [102.10 205.90], gm=154.00+-17.30, and vertices in regions > 145.3
- 11360 surface locations found to contain inconsistent values (1534 in, 9826 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/sub010/surf/rh.pial...
- writing smoothed curvature to rh.curv.pial
- 000: dt: 0.0000, sse=945.3, rms=0.06
- 091: dt: 0.5000, sse=937.7, rms=0.060 (0.000%)
- 092: dt: 0.5000, sse=899.3, rms=0.057 (0.000%)
- 093: dt: 0.5000, sse=872.7, rms=0.055 (0.000%)
- 094: dt: 0.5000, sse=848.8, rms=0.052 (0.000%)
- 095: dt: 0.5000, sse=829.0, rms=0.050 (0.000%)
- 096: dt: 0.5000, sse=814.6, rms=0.049 (0.000%)
- 097: dt: 0.5000, sse=803.5, rms=0.048 (0.000%)
- 098: dt: 0.5000, sse=793.9, rms=0.047 (0.000%)
- 099: dt: 0.5000, sse=785.3, rms=0.046 (0.000%)
- 100: dt: 0.5000, sse=776.8, rms=0.045 (0.000%)
- 101: dt: 0.5000, sse=768.7, rms=0.044 (0.000%)
- 102: dt: 0.5000, sse=760.4, rms=0.043 (0.000%)
- 103: dt: 0.5000, sse=753.0, rms=0.042 (0.000%)
- 104: dt: 0.5000, sse=747.5, rms=0.042 (0.000%)
- 105: dt: 0.5000, sse=741.8, rms=0.041 (0.000%)
- 106: dt: 0.5000, sse=735.7, rms=0.040 (0.000%)
- 107: dt: 0.5000, sse=731.4, rms=0.039 (0.000%)
- 108: dt: 0.5000, sse=727.6, rms=0.039 (0.000%)
- 109: dt: 0.5000, sse=723.2, rms=0.038 (0.000%)
- 110: dt: 0.5000, sse=718.4, rms=0.038 (0.000%)
- 111: dt: 0.5000, sse=715.4, rms=0.037 (0.000%)
- 112: dt: 0.5000, sse=711.7, rms=0.037 (0.000%)
- 113: dt: 0.5000, sse=709.7, rms=0.036 (0.000%)
- 114: dt: 0.5000, sse=706.9, rms=0.036 (0.000%)
- 115: dt: 0.5000, sse=703.8, rms=0.036 (0.000%)
- 116: dt: 0.5000, sse=701.3, rms=0.035 (0.000%)
- 117: dt: 0.5000, sse=699.9, rms=0.035 (0.000%)
- 118: dt: 0.5000, sse=699.6, rms=0.035 (0.000%)
- 119: dt: 0.5000, sse=696.8, rms=0.035 (0.000%)
- 120: dt: 0.5000, sse=694.5, rms=0.034 (0.000%)
- positioning took 2.9 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.curv.pial
- writing smoothed area to rh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.area.pial
- vertex spacing 1.06 +- 0.46 (0.03-->7.43) (max @ vno 50964 --> 49869)
- face area 0.44 +- 0.34 (0.00-->5.41)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 111391 vertices processed
- 25000 of 111391 vertices processed
- 50000 of 111391 vertices processed
- 75000 of 111391 vertices processed
- 100000 of 111391 vertices processed
- 0 of 111391 vertices processed
- 25000 of 111391 vertices processed
- 50000 of 111391 vertices processed
- 75000 of 111391 vertices processed
- 100000 of 111391 vertices processed
- thickness calculation complete, 355:1226 truncations.
- 23172 vertices at 0 distance
- 71146 vertices at 1 distance
- 71592 vertices at 2 distance
- 32643 vertices at 3 distance
- 9256 vertices at 4 distance
- 2482 vertices at 5 distance
- 776 vertices at 6 distance
- 263 vertices at 7 distance
- 107 vertices at 8 distance
- 50 vertices at 9 distance
- 29 vertices at 10 distance
- 12 vertices at 11 distance
- 14 vertices at 12 distance
- 5 vertices at 13 distance
- 19 vertices at 14 distance
- 11 vertices at 15 distance
- 14 vertices at 16 distance
- 9 vertices at 17 distance
- 5 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/sub010/surf/rh.thickness
- positioning took 14.4 minutes
- #--------------------------------------------
- #@# Surf Volume lh Thu Aug 8 21:42:01 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf
- mris_calc -o lh.area.mid lh.area add lh.area.pial
- Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o lh.area.mid lh.area.mid div 2
- Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o lh.volume lh.area.mid mul lh.thickness
- Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ]
- #--------------------------------------------
- #@# Surf Volume rh Thu Aug 8 21:42:01 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf
- mris_calc -o rh.area.mid rh.area add rh.area.pial
- Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o rh.area.mid rh.area.mid div 2
- Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o rh.volume rh.area.mid mul rh.thickness
- Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ]
- #--------------------------------------------
- #@# Cortical ribbon mask Thu Aug 8 21:42:01 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri
- mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon sub010
- 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 = 49
- writing volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/ribbon.mgz
- writing ribbon files
- #--------------------------------------------
- #@# ASeg Stats Thu Aug 8 21:55:18 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010
- 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 sub010
- $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 sub010
- sysname Linux
- hostname snake4
- machine x86_64
- user fkaule
- UseRobust 0
- atlas_icv (eTIV) = 925308 mm^3 (det: 2.105359 )
- Computing euler number
- orig.nofix lheno = -48, rheno = -34
- orig.nofix lhholes = 25, rhholes = 18
- Loading mri/aseg.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 215045.047 214126.000 diff= 919.0 pctdiff= 0.427
- rhCtxGM: 216453.318 215813.000 diff= 640.3 pctdiff= 0.296
- lhCtxWM: 159951.796 159955.000 diff= -3.2 pctdiff=-0.002
- rhCtxWM: 161933.369 161722.000 diff= 211.4 pctdiff= 0.131
- SubCortGMVol 57131.000
- SupraTentVol 827705.530 (825177.000) diff=2528.530 pctdiff=0.305
- SupraTentVolNotVent 811627.530 (809099.000) diff=2528.530 pctdiff=0.312
- BrainSegVol 932519.000 (930794.000) diff=1725.000 pctdiff=0.185
- BrainSegVolNotVent 913858.000 (915337.530) diff=-1479.530 pctdiff=-0.162
- BrainSegVolNotVent 913858.000
- CerebellumVol 104471.000
- VentChorVol 16078.000
- 3rd4th5thCSF 2583.000
- CSFVol 897.000, OptChiasmVol 249.000
- MaskVol 1374696.000
- 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 7829 7829.426
- 4 5 Left-Inf-Lat-Vent 339 339.366
- 5 7 Left-Cerebellum-White-Matter 12932 12931.568
- 6 8 Left-Cerebellum-Cortex 39955 39954.531
- 7 10 Left-Thalamus-Proper 6620 6620.007
- 8 11 Left-Caudate 3656 3655.936
- 9 12 Left-Putamen 6330 6329.792
- 10 13 Left-Pallidum 1725 1725.390
- 11 14 3rd-Ventricle 733 733.176
- 12 15 4th-Ventricle 1097 1097.076
- 13 16 Brain-Stem 19373 19373.477
- 14 17 Left-Hippocampus 3640 3640.310
- 15 18 Left-Amygdala 1499 1498.651
- 16 24 CSF 897 897.245
- 17 26 Left-Accumbens-area 736 735.534
- 18 28 Left-VentralDC 3573 3572.699
- 19 30 Left-vessel 188 187.965
- 20 31 Left-choroid-plexus 962 961.815
- 23 43 Right-Lateral-Ventricle 5416 5416.328
- 24 44 Right-Inf-Lat-Vent 307 307.397
- 25 46 Right-Cerebellum-White-Matter 13244 13243.784
- 26 47 Right-Cerebellum-Cortex 40491 40490.508
- 27 49 Right-Thalamus-Proper 6326 6325.789
- 28 50 Right-Caudate 3626 3625.609
- 29 51 Right-Putamen 6094 6093.857
- 30 52 Right-Pallidum 1871 1871.403
- 31 53 Right-Hippocampus 3529 3529.014
- 32 54 Right-Amygdala 1769 1769.435
- 33 58 Right-Accumbens-area 758 757.725
- 34 60 Right-VentralDC 3511 3511.233
- 35 62 Right-vessel 124 124.474
- 36 63 Right-choroid-plexus 1168 1167.699
- 37 72 5th-Ventricle 0 0.000
- 38 77 WM-hypointensities 723 723.212
- 39 78 Left-WM-hypointensities 0 0.000
- 40 79 Right-WM-hypointensities 0 0.000
- 41 80 non-WM-hypointensities 61 60.620
- 42 81 Left-non-WM-hypointensities 0 0.000
- 43 82 Right-non-WM-hypointensities 0 0.000
- 44 85 Optic-Chiasm 242 242.300
- 45 251 CC_Posterior 850 850.278
- 46 252 CC_Mid_Posterior 349 348.652
- 47 253 CC_Central 307 306.991
- 48 254 CC_Mid_Anterior 266 265.577
- 49 255 CC_Anterior 615 614.942
- Reporting on 45 segmentations
- mri_segstats done
- #-----------------------------------------
- #@# AParc-to-ASeg Thu Aug 8 21:58:44 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010
- mri_aparc2aseg --s sub010 --volmask
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- subject sub010
- outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/aparc+aseg.mgz
- useribbon 0
- baseoffset 0
- RipUnknown 0
- Reading lh white surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.white
- Reading lh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.pial
- Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/surf/rh.white
- Reading rh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.pial
- Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/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/sub010/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 = 428041
- Used brute-force search on 0 voxels
- Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/aparc+aseg.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010
- mri_aparc2aseg --s sub010 --volmask --a2009s
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- subject sub010
- outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/aparc.a2009s+aseg.mgz
- useribbon 0
- baseoffset 10100
- RipUnknown 0
- Reading lh white surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.white
- Reading lh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.pial
- Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/surf/rh.white
- Reading rh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.pial
- Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/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/sub010/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 = 428041
- Used brute-force search on 0 voxels
- Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/aparc.a2009s+aseg.mgz
- #-----------------------------------------
- #@# WMParc Thu Aug 8 22:02:45 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010
- mri_aparc2aseg --s sub010 --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 sub010
- 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/sub010/mri/aparc+aseg.mgz
- Reading lh white surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.white
- Reading lh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.pial
- Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/surf/rh.white
- Reading rh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.pial
- Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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/sub010/mri/ribbon.mgz
- Loading filled from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/filled.mgz
- Ripping vertices labeled as unkown
- Ripped 7480 vertices from left hemi
- Ripped 7577 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/sub010/mri/aseg.mgz
- Loading Ctx Seg File /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 = 749163
- Used brute-force search on 32 voxels
- Fixing Parahip LH WM
- Found 5 clusters
- 0 k 9.000000
- 1 k 1194.000000
- 2 k 2.000000
- 3 k 4.000000
- 4 k 49.000000
- Fixing Parahip RH WM
- Found 6 clusters
- 0 k 2.000000
- 1 k 1.000000
- 2 k 2.000000
- 3 k 1.000000
- 4 k 1.000000
- 5 k 1061.000000
- Writing output aseg to mri/wmparc.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010
- 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 sub010 --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 sub010 --surf-wm-vol --ctab /opt/freesurfer/5.3.0/WMParcStatsLUT.txt --etiv
- sysname Linux
- hostname snake4
- machine x86_64
- user fkaule
- UseRobust 0
- atlas_icv (eTIV) = 925308 mm^3 (det: 2.105359 )
- Loading mri/wmparc.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 215045.047 214126.000 diff= 919.0 pctdiff= 0.427
- rhCtxGM: 216453.318 215813.000 diff= 640.3 pctdiff= 0.296
- lhCtxWM: 159951.796 159955.000 diff= -3.2 pctdiff=-0.002
- rhCtxWM: 161933.369 161722.000 diff= 211.4 pctdiff= 0.131
- SubCortGMVol 57131.000
- SupraTentVol 827705.530 (825177.000) diff=2528.530 pctdiff=0.305
- SupraTentVolNotVent 811627.530 (809099.000) diff=2528.530 pctdiff=0.312
- BrainSegVol 932519.000 (930794.000) diff=1725.000 pctdiff=0.185
- BrainSegVolNotVent 913858.000 (915337.530) diff=-1479.530 pctdiff=-0.162
- BrainSegVolNotVent 913858.000
- CerebellumVol 104471.000
- VentChorVol 16078.000
- 3rd4th5thCSF 2583.000
- CSFVol 897.000, OptChiasmVol 249.000
- MaskVol 1374696.000
- 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 3007 3007.497
- 2 3002 wm-lh-caudalanteriorcingulate 1815 1814.583
- 3 3003 wm-lh-caudalmiddlefrontal 4416 4416.122
- 4 3004 wm-lh-corpuscallosum 0 0.000
- 5 3005 wm-lh-cuneus 2213 2212.622
- 6 3006 wm-lh-entorhinal 700 700.151
- 7 3007 wm-lh-fusiform 5229 5229.411
- 8 3008 wm-lh-inferiorparietal 7393 7393.180
- 9 3009 wm-lh-inferiortemporal 4544 4544.138
- 10 3010 wm-lh-isthmuscingulate 3195 3194.569
- 11 3011 wm-lh-lateraloccipital 7121 7120.542
- 12 3012 wm-lh-lateralorbitofrontal 4504 4504.396
- 13 3013 wm-lh-lingual 4379 4378.711
- 14 3014 wm-lh-medialorbitofrontal 2391 2391.337
- 15 3015 wm-lh-middletemporal 3822 3821.702
- 16 3016 wm-lh-parahippocampal 1263 1263.064
- 17 3017 wm-lh-paracentral 2899 2899.385
- 18 3018 wm-lh-parsopercularis 2360 2360.028
- 19 3019 wm-lh-parsorbitalis 632 632.361
- 20 3020 wm-lh-parstriangularis 2051 2050.875
- 21 3021 wm-lh-pericalcarine 2653 2652.559
- 22 3022 wm-lh-postcentral 5421 5421.239
- 23 3023 wm-lh-posteriorcingulate 3201 3201.417
- 24 3024 wm-lh-precentral 10281 10281.124
- 25 3025 wm-lh-precuneus 6670 6670.213
- 26 3026 wm-lh-rostralanteriorcingulate 2855 2854.854
- 27 3027 wm-lh-rostralmiddlefrontal 9121 9120.788
- 28 3028 wm-lh-superiorfrontal 12124 12124.131
- 29 3029 wm-lh-superiorparietal 8530 8529.941
- 30 3030 wm-lh-superiortemporal 4345 4344.885
- 31 3031 wm-lh-supramarginal 5673 5673.487
- 32 3032 wm-lh-frontalpole 125 125.029
- 33 3033 wm-lh-temporalpole 501 500.944
- 34 3034 wm-lh-transversetemporal 598 598.409
- 35 3035 wm-lh-insula 6063 6063.475
- 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 3059 3058.928
- 120 4002 wm-rh-caudalanteriorcingulate 2345 2345.101
- 121 4003 wm-rh-caudalmiddlefrontal 3739 3738.853
- 122 4004 wm-rh-corpuscallosum 0 0.000
- 123 4005 wm-rh-cuneus 2023 2022.947
- 124 4006 wm-rh-entorhinal 568 568.484
- 125 4007 wm-rh-fusiform 4504 4503.506
- 126 4008 wm-rh-inferiorparietal 9271 9271.327
- 127 4009 wm-rh-inferiortemporal 4136 4135.960
- 128 4010 wm-rh-isthmuscingulate 2671 2671.055
- 129 4011 wm-rh-lateraloccipital 6333 6333.224
- 130 4012 wm-rh-lateralorbitofrontal 4706 4706.465
- 131 4013 wm-rh-lingual 4280 4280.259
- 132 4014 wm-rh-medialorbitofrontal 2523 2523.001
- 133 4015 wm-rh-middletemporal 4412 4412.409
- 134 4016 wm-rh-parahippocampal 1130 1129.912
- 135 4017 wm-rh-paracentral 3348 3348.097
- 136 4018 wm-rh-parsopercularis 2198 2198.048
- 137 4019 wm-rh-parsorbitalis 750 749.881
- 138 4020 wm-rh-parstriangularis 2763 2762.996
- 139 4021 wm-rh-pericalcarine 2843 2843.098
- 140 4022 wm-rh-postcentral 5877 5877.005
- 141 4023 wm-rh-posteriorcingulate 3024 3023.799
- 142 4024 wm-rh-precentral 10984 10983.681
- 143 4025 wm-rh-precuneus 7561 7561.242
- 144 4026 wm-rh-rostralanteriorcingulate 1612 1612.110
- 145 4027 wm-rh-rostralmiddlefrontal 9128 9128.189
- 146 4028 wm-rh-superiorfrontal 11986 11985.799
- 147 4029 wm-rh-superiorparietal 8349 8348.782
- 148 4030 wm-rh-superiortemporal 4035 4034.939
- 149 4031 wm-rh-supramarginal 5576 5575.699
- 150 4032 wm-rh-frontalpole 187 186.517
- 151 4033 wm-rh-temporalpole 568 568.127
- 152 4034 wm-rh-transversetemporal 397 397.337
- 153 4035 wm-rh-insula 6007 6006.890
- 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 18696 18696.154
- 237 5002 Right-UnsegmentedWhiteMatter 19159 19158.822
- 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/sub010/label
- #--------------------------------------------
- #@# BA Labels lh Thu Aug 8 22:12:37 CEST 2013
- INFO: fsaverage subject does not exist in SUBJECTS_DIR
- INFO: Creating symlink to fsaverage subject...
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer; ln -s /opt/freesurfer/5.3.0/subjects/fsaverage; cd -
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521
- Number of reverse mapping hits = 96
- Checking for and removing duplicates
- Writing label file ./lh.BA1.label 4225
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521
- Number of reverse mapping hits = 212
- Checking for and removing duplicates
- Writing label file ./lh.BA2.label 8121
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521
- Number of reverse mapping hits = 77
- Checking for and removing duplicates
- Writing label file ./lh.BA3a.label 4154
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521
- Number of reverse mapping hits = 183
- Checking for and removing duplicates
- Writing label file ./lh.BA3b.label 6166
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521
- Number of reverse mapping hits = 84
- Checking for and removing duplicates
- Writing label file ./lh.BA4a.label 5868
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521
- Number of reverse mapping hits = 59
- Checking for and removing duplicates
- Writing label file ./lh.BA4p.label 4129
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521
- Number of reverse mapping hits = 410
- Checking for and removing duplicates
- Writing label file ./lh.BA6.label 13999
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521
- Number of reverse mapping hits = 285
- Checking for and removing duplicates
- Writing label file ./lh.BA44.label 4466
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521
- Number of reverse mapping hits = 319
- Checking for and removing duplicates
- Writing label file ./lh.BA45.label 3741
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521
- Number of reverse mapping hits = 1439
- Checking for and removing duplicates
- Writing label file ./lh.V1.label 6080
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521
- Number of reverse mapping hits = 2375
- Checking for and removing duplicates
- Writing label file ./lh.V2.label 10489
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521
- Number of reverse mapping hits = 238
- Checking for and removing duplicates
- Writing label file ./lh.MT.label 2256
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.perirhinal.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521
- Number of reverse mapping hits = 110
- Checking for and removing duplicates
- Writing label file ./lh.perirhinal.label 1309
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.thresh.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521
- Number of reverse mapping hits = 13
- Checking for and removing duplicates
- Writing label file ./lh.BA1.thresh.label 1027
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.thresh.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521
- Number of reverse mapping hits = 29
- Checking for and removing duplicates
- Writing label file ./lh.BA2.thresh.label 2121
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.thresh.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521
- Number of reverse mapping hits = 26
- Checking for and removing duplicates
- Writing label file ./lh.BA3a.thresh.label 1530
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.thresh.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521
- Number of reverse mapping hits = 104
- Checking for and removing duplicates
- Writing label file ./lh.BA3b.thresh.label 2100
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.thresh.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521
- Number of reverse mapping hits = 33
- Checking for and removing duplicates
- Writing label file ./lh.BA4a.thresh.label 2352
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.thresh.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521
- Number of reverse mapping hits = 22
- Checking for and removing duplicates
- Writing label file ./lh.BA4p.thresh.label 1571
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.thresh.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521
- Number of reverse mapping hits = 148
- Checking for and removing duplicates
- Writing label file ./lh.BA6.thresh.label 7183
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.thresh.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521
- Number of reverse mapping hits = 115
- Checking for and removing duplicates
- Writing label file ./lh.BA44.thresh.label 2027
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.thresh.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521
- Number of reverse mapping hits = 138
- Checking for and removing duplicates
- Writing label file ./lh.BA45.thresh.label 1289
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.thresh.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521
- Number of reverse mapping hits = 1056
- Checking for and removing duplicates
- Writing label file ./lh.V1.thresh.label 4461
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.thresh.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521
- Number of reverse mapping hits = 1262
- Checking for and removing duplicates
- Writing label file ./lh.V2.thresh.label 4596
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.thresh.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 112521
- Number of reverse mapping hits = 39
- Checking for and removing duplicates
- Writing label file ./lh.MT.thresh.label 552
- mri_label2label: Done
- mris_label2annot --s sub010 --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/sub010/label
- cmdline mris_label2annot --s sub010 --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 snake4
- machine x86_64
- user fkaule
- subject sub010
- 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/sub010/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 77718 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/label/lh.BA.annot
- mris_label2annot --s sub010 --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/sub010/label
- cmdline mris_label2annot --s sub010 --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 snake4
- machine x86_64
- user fkaule
- subject sub010
- 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/sub010/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 92228 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/label/lh.BA.thresh.annot
- mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab sub010 lh white
- computing statistics for each annotation in ./lh.BA.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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
- 829 507 1405 1.881 0.756 0.177 0.074 24 2.7 BA1
- 3158 2139 5435 2.277 0.506 0.128 0.038 39 4.9 BA2
- 852 579 838 1.918 0.393 0.134 0.037 7 1.2 BA3a
- 2016 1368 3325 1.977 0.588 0.125 0.045 30 3.3 BA3b
- 1213 776 2944 2.878 0.523 0.109 0.072 15 1.6 BA4a
- 1058 705 1884 2.622 0.506 0.105 0.029 6 1.4 BA4p
- 7180 4860 18198 2.851 0.631 0.141 0.053 127 12.9 BA6
- 2042 1415 4510 2.713 0.461 0.138 0.053 40 4.5 BA44
- 2380 1665 5167 2.549 0.517 0.148 0.052 42 4.1 BA45
- 3648 2441 4555 1.730 0.490 0.156 0.075 76 10.2 V1
- 7807 5115 11855 2.093 0.508 0.169 0.069 168 21.0 V2
- 1723 1182 2922 2.275 0.400 0.153 0.049 30 3.5 MT
- 897 662 3188 3.610 0.865 0.167 0.073 27 2.4 perirhinal
- mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab sub010 lh white
- computing statistics for each annotation in ./lh.BA.thresh.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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
- 507 282 654 1.511 0.555 0.185 0.085 16 2.0 BA1
- 1119 761 1926 2.151 0.501 0.117 0.031 11 1.3 BA2
- 678 454 634 1.948 0.381 0.146 0.043 6 1.2 BA3a
- 1317 907 1778 1.723 0.430 0.105 0.028 9 1.6 BA3b
- 1204 769 2880 2.933 0.471 0.103 0.071 14 1.6 BA4a
- 876 589 1558 2.629 0.467 0.103 0.029 6 1.1 BA4p
- 3855 2591 9579 2.815 0.617 0.139 0.042 53 6.6 BA6
- 1277 879 2896 2.766 0.466 0.147 0.068 33 3.6 BA44
- 983 692 2592 2.764 0.534 0.170 0.048 23 2.0 BA45
- 3888 2602 5015 1.755 0.478 0.156 0.070 68 10.4 V1
- 4162 2704 5731 1.893 0.435 0.176 0.081 110 12.8 V2
- 427 315 797 2.192 0.433 0.154 0.047 7 0.8 MT
- #--------------------------------------------
- #@# BA Labels rh Thu Aug 8 22:16:23 CEST 2013
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391
- Number of reverse mapping hits = 98
- Checking for and removing duplicates
- Writing label file ./rh.BA1.label 4060
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391
- Number of reverse mapping hits = 139
- Checking for and removing duplicates
- Writing label file ./rh.BA2.label 6826
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391
- Number of reverse mapping hits = 87
- Checking for and removing duplicates
- Writing label file ./rh.BA3a.label 4067
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391
- Number of reverse mapping hits = 120
- Checking for and removing duplicates
- Writing label file ./rh.BA3b.label 4642
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391
- Number of reverse mapping hits = 220
- Checking for and removing duplicates
- Writing label file ./rh.BA4a.label 5967
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391
- Number of reverse mapping hits = 160
- Checking for and removing duplicates
- Writing label file ./rh.BA4p.label 4633
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391
- Number of reverse mapping hits = 457
- Checking for and removing duplicates
- Writing label file ./rh.BA6.label 12713
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391
- Number of reverse mapping hits = 406
- Checking for and removing duplicates
- Writing label file ./rh.BA44.label 7318
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391
- Number of reverse mapping hits = 741
- Checking for and removing duplicates
- Writing label file ./rh.BA45.label 6096
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391
- Number of reverse mapping hits = 1665
- Checking for and removing duplicates
- Writing label file ./rh.V1.label 6392
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391
- Number of reverse mapping hits = 2499
- Checking for and removing duplicates
- Writing label file ./rh.V2.label 10515
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391
- Number of reverse mapping hits = 249
- Checking for and removing duplicates
- Writing label file ./rh.MT.label 2181
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.perirhinal.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391
- Number of reverse mapping hits = 65
- Checking for and removing duplicates
- Writing label file ./rh.perirhinal.label 817
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.thresh.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391
- Number of reverse mapping hits = 33
- Checking for and removing duplicates
- Writing label file ./rh.BA1.thresh.label 909
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.thresh.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391
- Number of reverse mapping hits = 61
- Checking for and removing duplicates
- Writing label file ./rh.BA2.thresh.label 2749
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.thresh.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391
- Number of reverse mapping hits = 26
- Checking for and removing duplicates
- Writing label file ./rh.BA3a.thresh.label 1724
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.thresh.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391
- Number of reverse mapping hits = 71
- Checking for and removing duplicates
- Writing label file ./rh.BA3b.thresh.label 2254
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.thresh.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391
- Number of reverse mapping hits = 41
- Checking for and removing duplicates
- Writing label file ./rh.BA4a.thresh.label 1429
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.thresh.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391
- Number of reverse mapping hits = 58
- Checking for and removing duplicates
- Writing label file ./rh.BA4p.thresh.label 1547
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.thresh.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391
- Number of reverse mapping hits = 287
- Checking for and removing duplicates
- Writing label file ./rh.BA6.thresh.label 7246
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.thresh.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391
- Number of reverse mapping hits = 46
- Checking for and removing duplicates
- Writing label file ./rh.BA44.thresh.label 1058
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.thresh.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391
- Number of reverse mapping hits = 165
- Checking for and removing duplicates
- Writing label file ./rh.BA45.thresh.label 1343
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.thresh.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391
- Number of reverse mapping hits = 1139
- Checking for and removing duplicates
- Writing label file ./rh.V1.thresh.label 4371
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.thresh.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391
- Number of reverse mapping hits = 1271
- Checking for and removing duplicates
- Writing label file ./rh.V2.thresh.label 4708
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.thresh.label --trgsubject sub010 --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 = sub010
- 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/sub010/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 111391
- Number of reverse mapping hits = 48
- Checking for and removing duplicates
- Writing label file ./rh.MT.thresh.label 316
- mri_label2label: Done
- mris_label2annot --s sub010 --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/sub010/label
- cmdline mris_label2annot --s sub010 --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 snake4
- machine x86_64
- user fkaule
- subject sub010
- 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/sub010/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 75955 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/label/rh.BA.annot
- mris_label2annot --s sub010 --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/sub010/label
- cmdline mris_label2annot --s sub010 --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 snake4
- machine x86_64
- user fkaule
- subject sub010
- 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/sub010/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 91276 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/label/rh.BA.thresh.annot
- mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab sub010 rh white
- computing statistics for each annotation in ./rh.BA.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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
- 745 436 1729 2.718 0.406 0.163 0.047 15 1.5 BA1
- 2634 1796 4579 2.288 0.530 0.115 0.034 23 4.1 BA2
- 901 588 923 2.072 0.471 0.133 0.041 8 1.4 BA3a
- 1696 1176 2812 2.012 0.594 0.135 0.038 21 2.9 BA3b
- 1334 862 3320 2.935 0.578 0.134 0.058 21 2.3 BA4a
- 1122 780 2129 2.656 0.464 0.119 0.035 9 1.6 BA4p
- 6421 4340 15619 2.902 0.617 0.136 0.040 84 10.7 BA6
- 2715 1866 6069 2.772 0.524 0.135 0.043 41 5.1 BA44
- 3989 2752 9154 2.676 0.596 0.152 0.053 78 8.6 BA45
- 4011 2750 5592 1.926 0.523 0.171 0.074 85 13.4 V1
- 7620 5035 11666 2.131 0.589 0.176 0.078 184 22.4 V2
- 1701 1175 2843 2.316 0.472 0.161 0.070 32 4.1 MT
- 547 400 1651 2.934 1.124 0.176 0.086 13 1.9 perirhinal
- mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab sub010 rh white
- computing statistics for each annotation in ./rh.BA.thresh.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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
- 520 294 1118 2.597 0.377 0.170 0.054 11 1.2 BA1
- 1541 1041 2780 2.272 0.523 0.104 0.027 11 1.7 BA2
- 815 535 801 2.064 0.438 0.136 0.038 7 1.4 BA3a
- 1388 994 2021 1.817 0.488 0.123 0.029 12 1.7 BA3b
- 759 485 2005 3.028 0.568 0.132 0.071 15 1.3 BA4a
- 880 614 1718 2.703 0.470 0.116 0.038 6 1.2 BA4p
- 4205 2836 10451 2.933 0.603 0.140 0.043 60 7.4 BA6
- 717 505 1859 2.751 0.497 0.150 0.067 18 2.0 BA44
- 1040 722 2689 2.888 0.638 0.163 0.056 23 2.4 BA45
- 3823 2617 5263 1.927 0.530 0.170 0.074 82 12.5 V1
- 4172 2802 6222 2.029 0.575 0.187 0.091 108 14.6 V2
- 255 169 523 2.620 0.442 0.157 0.062 4 0.6 MT
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/label
- #--------------------------------------------
- #@# Ex-vivo Entorhinal Cortex Label lh Thu Aug 8 22:20:09 CEST 2013
- INFO: lh.EC_average subject does not exist in SUBJECTS_DIR
- INFO: Creating symlink to lh.EC_average subject...
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer; ln -s /opt/freesurfer/5.3.0/subjects/lh.EC_average; cd -
- mris_spherical_average -erode 1 -orig white -t 0.4 -o sub010 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label
- painting output onto subject sub010.
- processing subject lh.EC_average...
- reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 804 points to lh.entorhinal_exvivo.label...
- mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label sub010 lh white
- limiting computations to label ./lh.entorhinal_exvivo.label.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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
- 275 197 971 2.926 0.840 0.124 0.081 9 0.5 ./lh.entorhinal_exvivo.label
- #--------------------------------------------
- #@# Ex-vivo Entorhinal Cortex Label rh Thu Aug 8 22:20:22 CEST 2013
- INFO: rh.EC_average subject does not exist in SUBJECTS_DIR
- INFO: Creating symlink to rh.EC_average subject...
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer; ln -s /opt/freesurfer/5.3.0/subjects/rh.EC_average; cd -
- mris_spherical_average -erode 1 -orig white -t 0.4 -o sub010 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label
- painting output onto subject sub010.
- processing subject rh.EC_average...
- reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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 734 points to rh.entorhinal_exvivo.label...
- mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label sub010 rh white
- limiting computations to label ./rh.entorhinal_exvivo.label.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/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
- 268 189 829 2.798 1.185 0.125 0.045 3 0.5 ./rh.entorhinal_exvivo.label
- #------------------------------------------
- Started at Thu Aug 8 10:54:16 CEST 2013
- Ended at Thu Aug 8 22:20:36 CEST 2013
- #@#%# recon-all-run-time-hours 11.439
- recon-all -s sub010 finished without error at Thu Aug 8 22:20:36 CEST 2013
|
