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- Thu Aug 8 10:54:16 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009
- /opt/freesurfer/5.3.0/bin/recon-all
- -i /home/data/exppsy/forrest_gump/openfmri.org/sub009/anatomy/highres001.nii.gz -cw256 -all -T2 /home/data/exppsy/forrest_gump/openfmri.org/sub009/anatomy/other/t2w001.nii.gz -T2pial -subjid sub009 -sd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- subjid sub009
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Actual FREESURFER_HOME /opt/freesurfer/5.3.0
- build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
- Linux snake6 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
- cputime unlimited
- filesize unlimited
- datasize unlimited
- stacksize unlimited
- coredumpsize 0 kbytes
- memoryuse unlimited
- vmemoryuse unlimited
- descriptors 1024
- memorylocked 64 kbytes
- maxproc unlimited
- maxlocks unlimited
- maxsignal 16382
- maxmessage 819200
- maxnice 0
- maxrtprio 0
- maxrttime unlimited
- total used free shared buffers cached
- Mem: 99201692 96979476 2222216 0 118440 94733872
- -/+ buffers/cache: 2127164 97074528
- Swap: 25165780 2780 25163000
- ########################################
- program versions used
- $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
- $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
- mri_convert -all-info
- ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- FLIRT version 5.5
- $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
- mri_convert --version
- stable5
- ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- Program nu_correct, built from:
- Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
- ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ======= NUMBER OF OPENMP THREADS = 1 =======
- ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $
- ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $
- ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- #######################################
- GCADIR /opt/freesurfer/5.3.0/average
- GCA RB_all_2008-03-26.gca
- GCASkull RB_all_withskull_2008-03-26.gca
- AvgCurvTif average.curvature.filled.buckner40.tif
- GCSDIR /opt/freesurfer/5.3.0/average
- GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
- #######################################
- -cw256 option is now persistent (remove with -clean-cw256)
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub009/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/orig/001.mgz
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub009/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/anatomy/highres001.nii.gz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.995894, -0.015333, -0.0892185)
- j_ras = (-0.0248655, 0.993977, 0.106735)
- k_ras = (-0.0870445, -0.108515, 0.990277)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/orig/001.mgz...
- #--------------------------------------------
- #@# T2/FLAIR Input Thu Aug 8 10:54:37 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub009/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/orig/T2raw.mgz
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub009/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/anatomy/other/t2w001.nii.gz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.995894, -0.015333, -0.0892185)
- j_ras = (-0.0248655, 0.993977, 0.106735)
- k_ras = (-0.0870445, -0.108515, 0.990277)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/orig/T2raw.mgz...
- #--------------------------------------------
- #@# MotionCor Thu Aug 8 10:54:53 CEST 2013
- Found 1 runs
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/mri/orig/001.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/rawavg.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/orig.mgz --conform --cw256
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/mri/rawavg.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.995894, -0.015333, -0.0892185)
- j_ras = (-0.0248655, 0.993977, 0.106735)
- k_ras = (-0.0870445, -0.108515, 0.990277)
- 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/sub009/mri/orig.mgz...
- mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/talairach.xfm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/orig.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Talairach Thu Aug 8 10:55:33 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri
- mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
- talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
- cp transforms/talairach.auto.xfm transforms/talairach.xfm
- #--------------------------------------------
- #@# Talairach Failure Detection Thu Aug 8 10:58:05 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri
- talairach_afd -T 0.005 -xfm transforms/talairach.xfm
- talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6607, 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/sub009/mri/transforms/talairach_avi.log
- tal_QC_AZS /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/talairach_avi.log
- TalAviQA: 0.96174
- z-score: -3
- #--------------------------------------------
- #@# Nu Intensity Correction Thu Aug 8 10:58:05 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/sub009/mri
- /opt/freesurfer/5.3.0/bin/mri_nu_correct.mni
- --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
- nIters 2
- $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $
- Linux snake6 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
- Thu Aug 8 10:58:05 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.24221
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.24221/nu0.mnc -odt float
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.24221/nu0.mnc -odt float
- $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
- reading from orig.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, -1.86265e-09, 0)
- j_ras = (-7.45058e-09, 0, -1)
- k_ras = (-4.65661e-09, 1, 7.45058e-09)
- changing data type from uchar to float (noscale = 0)...
- writing to ./tmp.mri_nu_correct.mni.24221/nu0.mnc...
-
- --------------------------------------------------------
- Iteration 1 Thu Aug 8 10:58:09 CEST 2013
- nu_correct -clobber ./tmp.mri_nu_correct.mni.24221/nu0.mnc ./tmp.mri_nu_correct.mni.24221/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.24221/0/
- [fkaule@snake6:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/] [2013-08-08 10:58:09] 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.24221/0/ ./tmp.mri_nu_correct.mni.24221/nu0.mnc ./tmp.mri_nu_correct.mni.24221/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
- Number of iterations: 25
- CV of field change: 0.000985702
- [fkaule@snake6:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/] [2013-08-08 10:58:42] running:
- /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.24221/nu0.mnc ./tmp.mri_nu_correct.mni.24221/0//template.mnc
- Transforming slices:......................................................................................Done
- Transforming slices:................................................................................................................................................................................................................................................................Done
-
-
- --------------------------------------------------------
- Iteration 2 Thu Aug 8 10:58:49 CEST 2013
- nu_correct -clobber ./tmp.mri_nu_correct.mni.24221/nu1.mnc ./tmp.mri_nu_correct.mni.24221/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.24221/1/
- [fkaule@snake6:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/] [2013-08-08 10:58:49] 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.24221/1/ ./tmp.mri_nu_correct.mni.24221/nu1.mnc ./tmp.mri_nu_correct.mni.24221/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
- Number of iterations: 17
- CV of field change: 0.000992556
- [fkaule@snake6:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/] [2013-08-08 10:59:12] running:
- /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.24221/nu1.mnc ./tmp.mri_nu_correct.mni.24221/1//template.mnc
- Transforming slices:......................................................................................Done
- Transforming slices:................................................................................................................................................................................................................................................................Done
-
-
-
- mri_binarize --i ./tmp.mri_nu_correct.mni.24221/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.24221/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/sub009/mri
- cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.24221/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.24221/ones.mgz
- sysname Linux
- hostname snake6
- machine x86_64
- user fkaule
- input ./tmp.mri_nu_correct.mni.24221/nu2.mnc
- frame 0
- nErode3d 0
- nErode2d 0
- output ./tmp.mri_nu_correct.mni.24221/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.24221/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.24221/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24221/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.24221/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.24221/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24221/input.mean.dat
- sysname Linux
- hostname snake6
- machine x86_64
- user fkaule
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.24221/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.24221/input.mean.dat
- mri_segstats done
- mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.24221/ones.mgz --i ./tmp.mri_nu_correct.mni.24221/nu2.mnc --sum ./tmp.mri_nu_correct.mni.24221/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24221/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.24221/ones.mgz --i ./tmp.mri_nu_correct.mni.24221/nu2.mnc --sum ./tmp.mri_nu_correct.mni.24221/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24221/output.mean.dat
- sysname Linux
- hostname snake6
- machine x86_64
- user fkaule
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.24221/ones.mgz
- Loading ./tmp.mri_nu_correct.mni.24221/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.24221/output.mean.dat
- mri_segstats done
- mris_calc -o ./tmp.mri_nu_correct.mni.24221/nu2.mnc ./tmp.mri_nu_correct.mni.24221/nu2.mnc mul .98260516135876169345
- Saving result to './tmp.mri_nu_correct.mni.24221/nu2.mnc' (type = MINC ) [ ok ]
- mri_convert ./tmp.mri_nu_correct.mni.24221/nu2.mnc nu.mgz --like orig.mgz
- mri_convert ./tmp.mri_nu_correct.mni.24221/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.24221/nu2.mnc...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, -1.86265e-09, 0)
- j_ras = (-7.45058e-09, 0, -1)
- k_ras = (-4.65661e-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 9 seconds.
- mapping ( 7, 158) to ( 3, 110)
-
-
- Thu Aug 8 11:00:00 CEST 2013
- mri_nu_correct.mni done
- mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/talairach.xfm nu.mgz nu.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Intensity Normalization Thu Aug 8 11:00:01 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri
- mri_normalize -g 1 nu.mgz T1.mgz
- using max gradient = 1.000
- reading from nu.mgz...
- normalizing image...
- talairach transform
- 1.178 0.038 0.046 4.031;
- -0.025 1.063 0.346 -41.083;
- 0.001 -0.446 1.152 -9.389;
- 0.000 0.000 0.000 1.000;
- processing without aseg, no1d=0
- MRInormInit():
- INFO: Modifying talairach volume c_(r,a,s) based on average_305
- MRInormalize():
- MRIsplineNormalize(): npeaks = 17
- Starting OpenSpline(): npoints = 17
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Iterating 2 times
- ---------------------------------
- 3d normalization pass 1 of 2
- white matter peak found at 111
- white matter peak found at 108
- gm peak at 75 (75), valley at 17 (17)
- csf peak at 14, setting threshold to 54
- 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 36 (36)
- csf peak at 10, setting threshold to 35
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Done iterating ---------------------------------
- writing output to T1.mgz
- 3D bias adjustment took 2 minutes and 53 seconds.
- #--------------------------------------------
- #@# Skull Stripping Thu Aug 8 11:02:54 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri
- mri_em_register -skull nu.mgz /opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta
- ======= NUMBER OF OPENMP THREADS = 1 =======
- aligning to atlas containing skull, setting unknown_nbr_spacing = 5
- reading 1 input volumes...
- logging results to talairach_with_skull.log
- reading '/opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca'...
- average std = 23.1 using min determinant for regularization = 53.4
- 0 singular and 5702 ill-conditioned covariance matrices regularized
- reading 'nu.mgz'...
- freeing gibbs priors...done.
- bounding unknown intensity as < 20.2 or > 943.7
- total sample mean = 92.0 (1443 zeros)
- ************************************************
- spacing=8, using 3481 sample points, tol=1.00e-05...
- ************************************************
- register_mri: find_optimal_transform
- find_optimal_transform: nsamples 3481, passno 0, spacing 8
- resetting wm mean[0]: 117 --> 126
- resetting gm mean[0]: 74 --> 74
- input volume #1 is the most T1-like
- using real data threshold=10.0
- skull bounding box = (56, 20, 17) --> (201, 255, 204)
- using (104, 98, 111) as brain centroid...
- mean wm in atlas = 126, using box (86,69,88) --> (121, 127,134) to find MRI wm
- before smoothing, mri peak at 109
- after smoothing, mri peak at 109, scaling input intensities by 1.156
- scaling channel 0 by 1.15596
- initial log_p = -4.8
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -4.547387 @ (-9.091, 9.091, -9.091)
- max log p = -4.444653 @ (4.545, 13.636, -4.545)
- max log p = -4.395447 @ (2.273, -2.273, 2.273)
- max log p = -4.376290 @ (-1.136, -1.136, 1.136)
- max log p = -4.358931 @ (0.568, -0.568, -0.568)
- max log p = -4.358931 @ (0.000, 0.000, 0.000)
- Found translation: (-2.8, 18.7, -10.8): log p = -4.359
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.4 (thresh=-4.4)
- 1.064 0.000 0.000 -11.039;
- 0.000 1.148 0.453 -41.755;
- 0.000 -0.432 0.988 42.330;
- 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)
- 1.144 0.000 0.000 -21.299;
- 0.000 1.105 0.296 -20.559;
- 0.000 -0.278 1.038 21.616;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 2 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1)
- 1.144 0.000 0.000 -21.299;
- 0.000 1.105 0.296 -20.559;
- 0.000 -0.278 1.038 21.616;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.2500
- ****************************************
- Nine parameter search. iteration 3 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.1 (thresh=-4.1)
- 1.121 0.036 0.008 -24.844;
- -0.038 1.133 0.268 -17.144;
- 0.000 -0.232 1.009 18.195;
- 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)
- 1.121 0.036 0.008 -24.844;
- -0.038 1.133 0.268 -17.144;
- 0.000 -0.232 1.009 18.195;
- 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)
- 1.123 0.036 0.008 -25.021;
- -0.038 1.133 0.268 -17.144;
- 0.000 -0.232 1.010 18.092;
- 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
- 1.12280 0.03577 0.00846 -25.02088;
- -0.03812 1.13299 0.26790 -17.14352;
- 0.00000 -0.23178 1.00976 18.09197;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 3481
- Quasinewton: input matrix
- 1.12280 0.03577 0.00846 -25.02088;
- -0.03812 1.13299 0.26790 -17.14352;
- 0.00000 -0.23178 1.00976 18.09197;
- 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:
- 1.123 0.036 0.008 -25.021;
- -0.038 1.133 0.268 -17.144;
- 0.000 -0.232 1.010 18.092;
- 0.000 0.000 0.000 1.000;
- pass 1, spacing 8: log(p) = -4.0 (old=-4.8)
- transform before final EM align:
- 1.123 0.036 0.008 -25.021;
- -0.038 1.133 0.268 -17.144;
- 0.000 -0.232 1.010 18.092;
- 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
- 1.12280 0.03577 0.00846 -25.02088;
- -0.03812 1.13299 0.26790 -17.14352;
- 0.00000 -0.23178 1.00976 18.09197;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 382743
- Quasinewton: input matrix
- 1.12280 0.03577 0.00846 -25.02088;
- -0.03812 1.13299 0.26790 -17.14352;
- 0.00000 -0.23178 1.00976 18.09197;
- 0.00000 0.00000 0.00000 1.00000;
- dfp_em_step_func: 009: -log(p) = 4.4
- after pass:transform: ( 1.12, 0.04, 0.01, -25.02)
- ( -0.04, 1.13, 0.27, -17.14)
- ( -0.00, -0.23, 1.01, 18.09)
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization...
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = 4.4 tol 0.000000
- final transform:
- 1.123 0.036 0.008 -25.021;
- -0.038 1.133 0.268 -17.144;
- -0.000 -0.232 1.010 18.092;
- 0.000 0.000 0.000 1.000;
- writing output transformation to transforms/talairach_with_skull.lta...
- registration took 29 minutes and 25 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=88 z=112 r=93
- first estimation of the main basin volume: 3459359 voxels
- Looking for seedpoints
- 2 found in the cerebellum
- 16 found in the rest of the brain
- global maximum in x=150, y=87, z=72, Imax=255
- CSF=12, WM_intensity=110, WM_VARIANCE=5
- WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110
- preflooding height equal to 10 percent
- done.
- Analyze...
- main basin size=20174662590 voxels, voxel volume =1.000
- = 20174662590 mmm3 = 20174661.632 cm3
- done.
- PostAnalyze...Basin Prior
- 98 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=130,y=100, z=110, r=10562 iterations
- ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^
- GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=9 , nb = 45587
- RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=15 , nb = -1032719808
- LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=12 , nb = 1099334728
- RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=9 , nb = -1061402847
- LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=8 , nb = 1082764002
- OTHER CSF_MIN=2, CSF_intensity=10, CSF_MAX=24 , nb = 1070255838
-
- CSF_MAX TRANSITION GM_MIN GM
- GLOBAL
- before analyzing : 9, 11, 24, 56
- after analyzing : 9, 20, 25, 29
- RIGHT_CER
- before analyzing : 15, 16, 20, 61
- after analyzing : 15, 22, 25, 31
- LEFT_CER
- before analyzing : 12, 16, 30, 59
- after analyzing : 12, 25, 30, 33
- RIGHT_BRAIN
- before analyzing : 9, 12, 26, 54
- after analyzing : 9, 21, 26, 29
- LEFT_BRAIN
- before analyzing : 8, 10, 22, 54
- after analyzing : 8, 20, 25, 28
- OTHER
- before analyzing : 24, 58, 83, 93
- after analyzing : 24, 74, 83, 78
- mri_strip_skull: done peeling brain
- highly tesselated surface with 10242 vertices
- matching...71 iterations
- *********************VALIDATION*********************
- curvature mean = -0.013, std = 0.013
- curvature mean = 70.185, std = 8.838
- No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
- before rotation: sse = 2.78, sigma = 4.84
- after rotation: sse = 2.78, sigma = 4.84
- Localization of inacurate regions: Erosion-Dilation steps
- the sse mean is 3.23, its var is 5.52
- before Erosion-Dilatation 1.18% 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...41 iterations
- mri_strip_skull: done peeling brain
- Brain Size = 1742949 voxels, voxel volume = 1.000 mm3
- = 1742949 mmm3 = 1742.949 cm3
- ******************************
- Saving brainmask.auto.mgz
- done
- cp brainmask.auto.mgz brainmask.mgz
- #-------------------------------------
- #@# EM Registration Thu Aug 8 11:32:47 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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=23.0
- skull bounding box = (66, 40, 34) --> (191, 179, 197)
- using (108, 86, 116) as brain centroid...
- mean wm in atlas = 107, using box (93,69,96) --> (123, 103,136) to find MRI wm
- before smoothing, mri peak at 109
- after smoothing, mri peak at 109, scaling input intensities by 0.982
- scaling channel 0 by 0.981651
- initial log_p = -4.4
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -4.030836 @ (-9.091, 27.273, -9.091)
- max log p = -3.875740 @ (4.545, -13.636, -4.545)
- max log p = -3.829614 @ (-2.273, 2.273, 2.273)
- max log p = -3.783844 @ (3.409, 1.136, -1.136)
- max log p = -3.783844 @ (0.000, 0.000, 0.000)
- max log p = -3.783844 @ (0.000, 0.000, 0.000)
- Found translation: (-3.4, 17.0, -12.5): log p = -3.784
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.6, old_max_log_p =-3.8 (thresh=-3.8)
- 1.140 0.140 0.053 -42.102;
- -0.150 1.063 0.399 -9.357;
- 0.000 -0.390 0.833 54.385;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p =-3.6 (thresh=-3.6)
- 1.143 0.025 -0.099 -14.797;
- 0.000 1.118 0.276 -21.293;
- 0.139 -0.245 0.943 2.459;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 2 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p =-3.5 (thresh=-3.5)
- 1.057 0.024 -0.092 -4.177;
- 0.018 1.077 0.397 -33.521;
- 0.138 -0.389 0.899 29.133;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 3 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p =-3.5 (thresh=-3.5)
- 1.057 0.024 -0.092 -4.177;
- 0.018 1.077 0.397 -33.521;
- 0.138 -0.389 0.899 29.133;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.2500
- ****************************************
- Nine parameter search. iteration 4 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.4, old_max_log_p =-3.5 (thresh=-3.5)
- 1.083 0.038 -0.021 -18.504;
- -0.027 1.099 0.338 -23.505;
- 0.069 -0.318 0.927 26.206;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 5 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.4 (thresh=-3.4)
- 1.083 0.038 -0.021 -18.504;
- -0.025 1.108 0.375 -28.734;
- 0.070 -0.354 0.916 32.782;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 6 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3)
- 1.083 0.038 -0.021 -18.504;
- -0.025 1.108 0.375 -28.734;
- 0.070 -0.354 0.916 32.782;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.0625
- ****************************************
- Nine parameter search. iteration 7 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3)
- 1.084 0.047 -0.018 -19.865;
- -0.035 1.110 0.359 -25.815;
- 0.070 -0.337 0.925 29.655;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 8 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3)
- 1.086 0.047 -0.018 -20.209;
- -0.035 1.106 0.358 -25.307;
- 0.070 -0.337 0.925 29.655;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 9 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3)
- 1.086 0.047 -0.018 -20.209;
- -0.035 1.106 0.358 -25.307;
- 0.070 -0.337 0.925 29.655;
- 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
- 1.08629 0.04736 -0.01826 -20.20926;
- -0.03464 1.10598 0.35761 -25.30689;
- 0.07002 -0.33722 0.92503 29.65523;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 2772
- Quasinewton: input matrix
- 1.08629 0.04736 -0.01826 -20.20926;
- -0.03464 1.10598 0.35761 -25.30689;
- 0.07002 -0.33722 0.92503 29.65523;
- 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: 012: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 1.086 0.047 -0.018 -20.209;
- -0.035 1.106 0.358 -25.307;
- 0.070 -0.337 0.925 29.655;
- 0.000 0.000 0.000 1.000;
- pass 1, spacing 8: log(p) = -3.3 (old=-4.4)
- transform before final EM align:
- 1.086 0.047 -0.018 -20.209;
- -0.035 1.106 0.358 -25.307;
- 0.070 -0.337 0.925 29.655;
- 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
- 1.08629 0.04736 -0.01826 -20.20926;
- -0.03464 1.10598 0.35761 -25.30689;
- 0.07002 -0.33722 0.92503 29.65523;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 312841
- Quasinewton: input matrix
- 1.08629 0.04736 -0.01826 -20.20926;
- -0.03464 1.10598 0.35761 -25.30689;
- 0.07002 -0.33722 0.92503 29.65523;
- 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: 014: -log(p) = 3.9 tol 0.000000
- final transform:
- 1.086 0.047 -0.018 -20.209;
- -0.035 1.106 0.358 -25.307;
- 0.070 -0.337 0.925 29.655;
- 0.000 0.000 0.000 1.000;
- writing output transformation to transforms/talairach.lta...
- registration took 37 minutes and 38 seconds.
- #--------------------------------------
- #@# CA Normalize Thu Aug 8 12:10:25 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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=23.0
- skull bounding box = (66, 40, 34) --> (191, 179, 197)
- using (108, 86, 116) as brain centroid...
- mean wm in atlas = 107, using box (93,69,96) --> (123, 103,136) to find MRI wm
- before smoothing, mri peak at 109
- after smoothing, mri peak at 109, scaling input intensities by 0.982
- scaling channel 0 by 0.981651
- using 244171 sample points...
- INFO: compute sample coordinates transform
- 1.086 0.047 -0.018 -20.209;
- -0.035 1.106 0.358 -25.307;
- 0.070 -0.337 0.925 29.655;
- 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, 43, 32) --> (192, 149, 197)
- Left_Cerebral_White_Matter: limiting intensities to 100.0 --> 166.0
- 0 of 19 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 40735 control points for structure...
- bounding box (72, 41, 33) --> (134, 139, 199)
- Right_Cerebral_White_Matter: limiting intensities to 100.0 --> 166.0
- 0 of 10 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3012 control points for structure...
- bounding box (131, 122, 63) --> (176, 162, 117)
- Left_Cerebellum_White_Matter: limiting intensities to 91.0 --> 166.0
- 0 of 10 (0.0%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2764 control points for structure...
- bounding box (87, 122, 63) --> (131, 159, 120)
- Right_Cerebellum_White_Matter: limiting intensities to 95.0 --> 166.0
- 0 of 7 (0.0%) samples deleted
- finding control points in Brain_Stem....
- found 3520 control points for structure...
- bounding box (116, 109, 97) --> (146, 170, 128)
- Brain_Stem: limiting intensities to 83.0 --> 166.0
- 0 of 14 (0.0%) samples deleted
- using 60 total control points for intensity normalization...
- bias field = 0.937 +- 0.079
- 0 of 60 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 41584 control points for structure...
- bounding box (127, 43, 32) --> (192, 149, 197)
- Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 154.0
- 0 of 92 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 40735 control points for structure...
- bounding box (72, 41, 33) --> (134, 139, 199)
- Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 154.0
- 0 of 97 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3012 control points for structure...
- bounding box (131, 122, 63) --> (176, 162, 117)
- Left_Cerebellum_White_Matter: limiting intensities to 81.0 --> 154.0
- 0 of 33 (0.0%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2764 control points for structure...
- bounding box (87, 122, 63) --> (131, 159, 120)
- Right_Cerebellum_White_Matter: limiting intensities to 79.0 --> 154.0
- 0 of 53 (0.0%) samples deleted
- finding control points in Brain_Stem....
- found 3520 control points for structure...
- bounding box (116, 109, 97) --> (146, 170, 128)
- Brain_Stem: limiting intensities to 72.0 --> 154.0
- 0 of 56 (0.0%) samples deleted
- using 331 total control points for intensity normalization...
- bias field = 1.002 +- 0.051
- 0 of 331 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 41584 control points for structure...
- bounding box (127, 43, 32) --> (192, 149, 197)
- Left_Cerebral_White_Matter: limiting intensities to 93.0 --> 152.0
- 0 of 189 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 40735 control points for structure...
- bounding box (72, 41, 33) --> (134, 139, 199)
- Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 152.0
- 0 of 203 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3012 control points for structure...
- bounding box (131, 122, 63) --> (176, 162, 117)
- Left_Cerebellum_White_Matter: limiting intensities to 80.0 --> 152.0
- 0 of 63 (0.0%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2764 control points for structure...
- bounding box (87, 122, 63) --> (131, 159, 120)
- Right_Cerebellum_White_Matter: limiting intensities to 79.0 --> 152.0
- 0 of 36 (0.0%) samples deleted
- finding control points in Brain_Stem....
- found 3520 control points for structure...
- bounding box (116, 109, 97) --> (146, 170, 128)
- Brain_Stem: limiting intensities to 72.0 --> 152.0
- 0 of 64 (0.0%) samples deleted
- using 555 total control points for intensity normalization...
- bias field = 1.010 +- 0.042
- 0 of 555 control points discarded
- writing normalized volume to norm.mgz...
- writing control points to ctrl_pts.mgz
- freeing GCA...done.
- normalization took 2 minutes and 4 seconds.
- #--------------------------------------
- #@# CA Reg Thu Aug 8 12:12:30 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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) = 1.25 (predicted orig area = 6.4)
- 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=0.943, neg=0, invalid=96777
- 0001: dt=129.472000, rms=0.856 (9.248%), neg=0, invalid=96777
- 0002: dt=129.472000, rms=0.841 (1.783%), neg=0, invalid=96777
- 0003: dt=295.936000, rms=0.823 (2.113%), neg=0, invalid=96777
- 0004: dt=73.984000, rms=0.818 (0.612%), neg=0, invalid=96777
- 0005: dt=443.904000, rms=0.809 (1.128%), neg=0, invalid=96777
- 0006: dt=55.488000, rms=0.804 (0.535%), neg=0, invalid=96777
- 0007: dt=443.904000, rms=0.800 (0.614%), neg=0, invalid=96777
- 0008: dt=92.480000, rms=0.795 (0.586%), neg=0, invalid=96777
- 0009: dt=110.976000, rms=0.794 (0.132%), neg=0, invalid=96777
- 0010: dt=110.976000, rms=0.792 (0.229%), neg=0, invalid=96777
- 0011: dt=110.976000, rms=0.789 (0.325%), neg=0, invalid=96777
- 0012: dt=110.976000, rms=0.786 (0.403%), neg=0, invalid=96777
- 0013: dt=110.976000, rms=0.783 (0.462%), neg=0, invalid=96777
- 0014: dt=110.976000, rms=0.778 (0.563%), neg=0, invalid=96777
- 0015: dt=110.976000, rms=0.774 (0.526%), neg=0, invalid=96777
- 0016: dt=110.976000, rms=0.770 (0.464%), neg=0, invalid=96777
- 0017: dt=110.976000, rms=0.767 (0.399%), neg=0, invalid=96777
- 0018: dt=110.976000, rms=0.764 (0.455%), neg=0, invalid=96777
- 0019: dt=110.976000, rms=0.760 (0.446%), neg=0, invalid=96777
- 0020: dt=110.976000, rms=0.758 (0.379%), neg=0, invalid=96777
- 0021: dt=110.976000, rms=0.755 (0.304%), neg=0, invalid=96777
- 0022: dt=110.976000, rms=0.753 (0.310%), neg=0, invalid=96777
- 0023: dt=110.976000, rms=0.750 (0.393%), neg=0, invalid=96777
- 0024: dt=110.976000, rms=0.747 (0.358%), neg=0, invalid=96777
- 0025: dt=110.976000, rms=0.745 (0.303%), neg=0, invalid=96777
- 0026: dt=110.976000, rms=0.743 (0.283%), neg=0, invalid=96777
- 0027: dt=110.976000, rms=0.740 (0.329%), neg=0, invalid=96777
- 0028: dt=110.976000, rms=0.738 (0.332%), neg=0, invalid=96777
- 0029: dt=110.976000, rms=0.736 (0.272%), neg=0, invalid=96777
- 0030: dt=110.976000, rms=0.734 (0.233%), neg=0, invalid=96777
- 0031: dt=110.976000, rms=0.733 (0.221%), neg=0, invalid=96777
- 0032: dt=110.976000, rms=0.731 (0.209%), neg=0, invalid=96777
- 0033: dt=110.976000, rms=0.730 (0.183%), neg=0, invalid=96777
- 0034: dt=110.976000, rms=0.729 (0.147%), neg=0, invalid=96777
- 0035: dt=110.976000, rms=0.728 (0.140%), neg=0, invalid=96777
- 0036: dt=110.976000, rms=0.726 (0.174%), neg=0, invalid=96777
- 0037: dt=110.976000, rms=0.725 (0.152%), neg=0, invalid=96777
- 0038: dt=110.976000, rms=0.725 (0.111%), neg=0, invalid=96777
- 0039: dt=110.976000, rms=0.724 (0.094%), neg=0, invalid=96777
- 0040: dt=443.904000, rms=0.723 (0.122%), neg=0, invalid=96777
- 0041: dt=8.092000, rms=0.723 (-0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.723, neg=0, invalid=96777
- 0042: dt=27.744000, rms=0.723 (0.015%), neg=0, invalid=96777
- 0043: dt=32.368000, rms=0.723 (0.008%), neg=0, invalid=96777
- 0044: dt=32.368000, rms=0.723 (0.009%), neg=0, invalid=96777
- 0045: dt=32.368000, rms=0.723 (0.014%), neg=0, invalid=96777
- 0046: dt=32.368000, rms=0.723 (0.009%), neg=0, invalid=96777
- 0047: dt=32.368000, rms=0.723 (0.010%), neg=0, invalid=96777
- 0048: dt=32.368000, rms=0.722 (0.031%), neg=0, invalid=96777
- 0049: dt=32.368000, rms=0.722 (0.037%), neg=0, invalid=96777
- 0050: dt=32.368000, rms=0.722 (0.038%), neg=0, invalid=96777
- 0051: dt=32.368000, rms=0.722 (0.015%), neg=0, invalid=96777
- setting smoothness coefficient to 0.154
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.731, neg=0, invalid=96777
- 0052: dt=145.152000, rms=0.719 (1.570%), neg=0, invalid=96777
- 0053: dt=62.208000, rms=0.713 (0.887%), neg=0, invalid=96777
- 0054: dt=20.736000, rms=0.711 (0.304%), neg=0, invalid=96777
- 0055: dt=145.152000, rms=0.704 (1.012%), neg=0, invalid=96777
- 0056: dt=25.920000, rms=0.700 (0.482%), neg=0, invalid=96777
- 0057: dt=103.680000, rms=0.697 (0.437%), neg=0, invalid=96777
- 0058: dt=20.736000, rms=0.695 (0.304%), neg=0, invalid=96777
- 0059: dt=103.680000, rms=0.691 (0.523%), neg=0, invalid=96777
- 0060: dt=9.072000, rms=0.691 (0.113%), neg=0, invalid=96777
- 0061: dt=9.072000, rms=0.690 (0.077%), neg=0, invalid=96777
- 0062: dt=9.072000, rms=0.690 (0.077%), neg=0, invalid=96777
- 0063: dt=9.072000, rms=0.689 (0.088%), neg=0, invalid=96777
- 0064: dt=9.072000, rms=0.688 (0.109%), neg=0, invalid=96777
- 0065: dt=9.072000, rms=0.687 (0.153%), neg=0, invalid=96777
- 0066: dt=9.072000, rms=0.686 (0.212%), neg=0, invalid=96777
- 0067: dt=9.072000, rms=0.684 (0.237%), neg=0, invalid=96777
- 0068: dt=9.072000, rms=0.682 (0.233%), neg=0, invalid=96777
- 0069: dt=9.072000, rms=0.681 (0.224%), neg=0, invalid=96777
- 0070: dt=9.072000, rms=0.680 (0.209%), neg=0, invalid=96777
- 0071: dt=9.072000, rms=0.678 (0.200%), neg=0, invalid=96777
- 0072: dt=9.072000, rms=0.677 (0.199%), neg=0, invalid=96777
- 0073: dt=9.072000, rms=0.675 (0.208%), neg=0, invalid=96777
- 0074: dt=9.072000, rms=0.674 (0.220%), neg=0, invalid=96777
- 0075: dt=9.072000, rms=0.672 (0.213%), neg=0, invalid=96777
- 0076: dt=9.072000, rms=0.671 (0.196%), neg=0, invalid=96777
- 0077: dt=9.072000, rms=0.670 (0.181%), neg=0, invalid=96777
- 0078: dt=9.072000, rms=0.669 (0.170%), neg=0, invalid=96777
- 0079: dt=9.072000, rms=0.668 (0.168%), neg=0, invalid=96777
- 0080: dt=9.072000, rms=0.667 (0.165%), neg=0, invalid=96777
- 0081: dt=9.072000, rms=0.666 (0.152%), neg=0, invalid=96777
- 0082: dt=9.072000, rms=0.665 (0.138%), neg=0, invalid=96777
- 0083: dt=9.072000, rms=0.664 (0.136%), neg=0, invalid=96777
- 0084: dt=9.072000, rms=0.663 (0.140%), neg=0, invalid=96777
- 0085: dt=9.072000, rms=0.662 (0.139%), neg=0, invalid=96777
- 0086: dt=9.072000, rms=0.661 (0.133%), neg=0, invalid=96777
- 0087: dt=9.072000, rms=0.660 (0.123%), neg=0, invalid=96777
- 0088: dt=9.072000, rms=0.659 (0.112%), neg=0, invalid=96777
- 0089: dt=82.944000, rms=0.659 (0.029%), neg=0, invalid=96777
- 0090: dt=82.944000, rms=0.659 (0.070%), neg=0, invalid=96777
- 0091: dt=82.944000, rms=0.659 (-0.684%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.659, neg=0, invalid=96777
- 0092: dt=9.072000, rms=0.659 (0.042%), neg=0, invalid=96777
- 0093: dt=15.552000, rms=0.658 (0.033%), neg=0, invalid=96777
- 0094: dt=15.552000, rms=0.658 (-0.001%), neg=0, invalid=96777
- setting smoothness coefficient to 0.588
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.687, neg=0, invalid=96777
- 0095: dt=7.245283, rms=0.686 (0.088%), neg=0, invalid=96777
- 0096: dt=4.800000, rms=0.686 (0.035%), neg=0, invalid=96777
- 0097: dt=4.800000, rms=0.686 (0.008%), neg=0, invalid=96777
- 0098: dt=4.800000, rms=0.686 (-0.040%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.686, neg=0, invalid=96777
- 0099: dt=0.000000, rms=0.686 (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=0.758, neg=0, invalid=96777
- 0100: dt=4.958678, rms=0.746 (1.494%), neg=0, invalid=96777
- 0101: dt=3.090909, rms=0.746 (0.108%), neg=0, invalid=96777
- 0102: dt=3.090909, rms=0.746 (-0.008%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.746, neg=0, invalid=96777
- 0103: dt=0.000000, rms=0.746 (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=0.831, neg=0, invalid=96777
- 0104: dt=0.640625, rms=0.830 (0.200%), neg=0, invalid=96777
- 0105: dt=1.792000, rms=0.826 (0.441%), neg=0, invalid=96777
- 0106: dt=3.634146, rms=0.818 (1.034%), neg=0, invalid=96777
- 0107: dt=0.250000, rms=0.817 (0.021%), neg=0, invalid=96777
- 0108: dt=0.250000, rms=0.817 (-0.005%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.817, neg=0, invalid=96777
- 0109: dt=0.500000, rms=0.817 (0.081%), neg=0, invalid=96777
- 0110: dt=0.448000, rms=0.817 (0.019%), neg=0, invalid=96777
- 0111: dt=0.448000, rms=0.816 (0.019%), neg=0, invalid=96777
- 0112: dt=0.448000, rms=0.816 (0.023%), neg=0, invalid=96777
- 0113: dt=0.448000, rms=0.816 (0.020%), neg=0, invalid=96777
- 0114: dt=0.448000, rms=0.816 (-0.011%), 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=0.759, neg=0, invalid=96777
- 0115: dt=0.448000, rms=0.735 (3.238%), neg=0, invalid=96777
- 0116: dt=0.000000, rms=0.735 (0.005%), neg=0, invalid=96777
- 0117: dt=0.050000, rms=0.735 (-0.555%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.735, neg=0, invalid=96777
- 0118: dt=0.000000, rms=0.735 (0.000%), neg=0, invalid=96777
- renormalizing by structure alignment....
- renormalizing input #0
- gca peak = 0.11725 (24)
- mri peak = 0.12602 ( 7)
- Left_Lateral_Ventricle (4): linear fit = 0.25 x + 0.0 (1403 voxels, overlap=0.006)
- Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (1403 voxels, peak = 6), gca=9.6
- gca peak = 0.14022 (22)
- mri peak = 0.14839 ( 9)
- Right_Lateral_Ventricle (43): linear fit = 0.28 x + 0.0 (1135 voxels, overlap=0.007)
- Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (1135 voxels, peak = 6), gca=8.8
- gca peak = 0.24234 (100)
- mri peak = 0.06586 (90)
- Right_Pallidum (52): linear fit = 0.89 x + 0.0 (411 voxels, overlap=0.889)
- Right_Pallidum (52): linear fit = 0.89 x + 0.0 (411 voxels, peak = 90), gca=89.5
- gca peak = 0.19192 (97)
- mri peak = 0.06932 (98)
- Left_Pallidum (13): linear fit = 0.96 x + 0.0 (316 voxels, overlap=0.899)
- Left_Pallidum (13): linear fit = 0.96 x + 0.0 (316 voxels, peak = 94), gca=93.6
- gca peak = 0.24007 (63)
- mri peak = 0.06304 (54)
- Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (480 voxels, overlap=0.729)
- Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (480 voxels, peak = 55), gca=55.1
- gca peak = 0.29892 (64)
- mri peak = 0.09093 (58)
- Left_Hippocampus (17): linear fit = 0.89 x + 0.0 (448 voxels, overlap=0.692)
- Left_Hippocampus (17): linear fit = 0.89 x + 0.0 (448 voxels, peak = 57), gca=57.3
- gca peak = 0.12541 (104)
- mri peak = 0.07831 (106)
- Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (54261 voxels, overlap=0.812)
- Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (54261 voxels, peak = 106), gca=105.6
- gca peak = 0.13686 (104)
- mri peak = 0.08418 (107)
- Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (55024 voxels, overlap=0.713)
- Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (55024 voxels, peak = 108), gca=107.6
- gca peak = 0.11691 (63)
- mri peak = 0.05989 (51)
- Left_Cerebral_Cortex (3): linear fit = 0.82 x + 0.0 (14984 voxels, overlap=0.186)
- Left_Cerebral_Cortex (3): linear fit = 0.82 x + 0.0 (14984 voxels, peak = 52), gca=52.0
- gca peak = 0.13270 (63)
- mri peak = 0.06439 (51)
- Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (14237 voxels, overlap=0.058)
- Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (14237 voxels, peak = 52), gca=52.0
- gca peak = 0.15182 (70)
- mri peak = 0.08129 (99)
- Right_Caudate (50): linear fit = 0.75 x + 0.0 (348 voxels, overlap=0.015)
- Right_Caudate (50): linear fit = 0.75 x + 0.0 (348 voxels, peak = 52), gca=52.2
- gca peak = 0.14251 (76)
- mri peak = 0.06402 (68)
- Left_Caudate (11): linear fit = 0.89 x + 0.0 (413 voxels, overlap=0.515)
- Left_Caudate (11): linear fit = 0.89 x + 0.0 (413 voxels, peak = 68), gca=68.0
- gca peak = 0.12116 (60)
- mri peak = 0.03405 (56)
- Left_Cerebellum_Cortex (8): linear fit = 0.92 x + 0.0 (7629 voxels, overlap=0.839)
- Left_Cerebellum_Cortex (8): linear fit = 0.92 x + 0.0 (7629 voxels, peak = 55), gca=54.9
- gca peak = 0.12723 (61)
- mri peak = 0.03984 (56)
- Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (9635 voxels, overlap=0.972)
- Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (9635 voxels, peak = 59), gca=58.9
- gca peak = 0.22684 (88)
- mri peak = 0.08304 (94)
- Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (6490 voxels, overlap=0.843)
- Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (6490 voxels, peak = 93), gca=92.8
- gca peak = 0.21067 (87)
- mri peak = 0.06685 (93)
- Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (5978 voxels, overlap=0.923)
- Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (5978 voxels, peak = 92), gca=91.8
- gca peak = 0.25455 (62)
- mri peak = 0.08174 (61)
- Left_Amygdala (18): linear fit = 0.93 x + 0.0 (326 voxels, overlap=0.595)
- Left_Amygdala (18): linear fit = 0.93 x + 0.0 (326 voxels, peak = 57), gca=57.4
- gca peak = 0.39668 (62)
- mri peak = 0.10628 (55)
- Right_Amygdala (54): linear fit = 0.88 x + 0.0 (239 voxels, overlap=0.239)
- Right_Amygdala (54): linear fit = 0.88 x + 0.0 (239 voxels, peak = 54), gca=54.2
- gca peak = 0.10129 (93)
- mri peak = 0.04774 (90)
- Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (4655 voxels, overlap=0.988)
- Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (4655 voxels, peak = 91), gca=90.7
- gca peak = 0.12071 (89)
- mri peak = 0.06468 (76)
- Right_Thalamus_Proper (49): linear fit = 0.94 x + 0.0 (2818 voxels, overlap=0.796)
- Right_Thalamus_Proper (49): linear fit = 0.94 x + 0.0 (2818 voxels, peak = 84), gca=84.1
- gca peak = 0.13716 (82)
- mri peak = 0.05848 (80)
- Left_Putamen (12): linear fit = 0.96 x + 0.0 (1773 voxels, overlap=0.949)
- Left_Putamen (12): linear fit = 0.96 x + 0.0 (1773 voxels, peak = 79), gca=79.1
- gca peak = 0.15214 (84)
- mri peak = 0.03921 (92)
- Right_Putamen (51): linear fit = 1.12 x + 0.0 (2027 voxels, overlap=0.239)
- Right_Putamen (51): linear fit = 1.12 x + 0.0 (2027 voxels, peak = 94), gca=94.5
- gca peak = 0.08983 (85)
- mri peak = 0.06970 (88)
- Brain_Stem (16): linear fit = 1.07 x + 0.0 (9927 voxels, overlap=0.778)
- Brain_Stem (16): linear fit = 1.07 x + 0.0 (9927 voxels, peak = 91), gca=90.5
- gca peak = 0.11809 (92)
- mri peak = 0.05692 (95)
- Right_VentralDC (60): linear fit = 1.03 x + 0.0 (773 voxels, overlap=0.751)
- Right_VentralDC (60): linear fit = 1.03 x + 0.0 (773 voxels, peak = 95), gca=95.2
- gca peak = 0.12914 (94)
- mri peak = 0.06803 (96)
- Left_VentralDC (28): linear fit = 1.03 x + 0.0 (978 voxels, overlap=0.836)
- Left_VentralDC (28): linear fit = 1.03 x + 0.0 (978 voxels, peak = 97), gca=97.3
- gca peak = 0.21100 (36)
- uniform distribution in MR - rejecting arbitrary fit
- gca peak = 0.13542 (27)
- mri peak = 0.19355 ( 8)
- Fourth_Ventricle (15): linear fit = 0.28 x + 0.0 (313 voxels, overlap=0.024)
- Fourth_Ventricle (15): linear fit = 0.28 x + 0.0 (313 voxels, peak = 7), gca=7.4
- 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 0.87 x + 0.0
- estimating mean wm scale to be 1.02 x + 0.0
- estimating mean csf scale to be 0.40 x + 0.0
- saving intensity scales to 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=0.752, neg=0, invalid=96777
- 0119: dt=129.472000, rms=0.746 (0.816%), neg=0, invalid=96777
- 0120: dt=129.472000, rms=0.744 (0.259%), neg=0, invalid=96777
- 0121: dt=129.472000, rms=0.743 (0.197%), neg=0, invalid=96777
- 0122: dt=92.480000, rms=0.742 (0.084%), neg=0, invalid=96777
- 0123: dt=129.472000, rms=0.741 (0.128%), neg=0, invalid=96777
- 0124: dt=92.480000, rms=0.741 (0.058%), neg=0, invalid=96777
- 0125: dt=129.472000, rms=0.740 (0.100%), neg=0, invalid=96777
- 0126: dt=92.480000, rms=0.740 (0.040%), neg=0, invalid=96777
- 0127: dt=92.480000, rms=0.739 (0.065%), neg=0, invalid=96777
- 0128: dt=92.480000, rms=0.738 (0.096%), neg=0, invalid=96777
- 0129: dt=92.480000, rms=0.737 (0.113%), neg=0, invalid=96777
- 0130: dt=92.480000, rms=0.737 (0.110%), neg=0, invalid=96777
- 0131: dt=92.480000, rms=0.736 (0.142%), neg=0, invalid=96777
- 0132: dt=92.480000, rms=0.735 (0.151%), neg=0, invalid=96777
- 0133: dt=92.480000, rms=0.733 (0.144%), neg=0, invalid=96777
- 0134: dt=92.480000, rms=0.732 (0.138%), neg=0, invalid=96777
- 0135: dt=92.480000, rms=0.731 (0.146%), neg=0, invalid=96777
- 0136: dt=92.480000, rms=0.730 (0.157%), neg=0, invalid=96777
- 0137: dt=92.480000, rms=0.729 (0.144%), neg=0, invalid=96777
- 0138: dt=92.480000, rms=0.728 (0.134%), neg=0, invalid=96777
- 0139: dt=92.480000, rms=0.727 (0.135%), neg=0, invalid=96777
- 0140: dt=92.480000, rms=0.726 (0.128%), neg=0, invalid=96777
- 0141: dt=92.480000, rms=0.725 (0.124%), neg=0, invalid=96777
- 0142: dt=92.480000, rms=0.725 (0.121%), neg=0, invalid=96777
- 0143: dt=92.480000, rms=0.724 (0.112%), neg=0, invalid=96777
- 0144: dt=92.480000, rms=0.723 (0.108%), neg=0, invalid=96777
- 0145: dt=92.480000, rms=0.722 (0.124%), neg=0, invalid=96777
- 0146: dt=92.480000, rms=0.721 (0.113%), neg=0, invalid=96777
- 0147: dt=92.480000, rms=0.720 (0.104%), neg=0, invalid=96777
- 0148: dt=92.480000, rms=0.720 (0.131%), neg=0, invalid=96777
- 0149: dt=92.480000, rms=0.719 (0.112%), neg=0, invalid=96777
- 0150: dt=92.480000, rms=0.718 (0.093%), neg=0, invalid=96777
- 0151: dt=92.480000, rms=0.717 (0.132%), neg=0, invalid=96777
- 0152: dt=92.480000, rms=0.716 (0.122%), neg=0, invalid=96777
- 0153: dt=92.480000, rms=0.716 (0.067%), neg=0, invalid=96777
- 0154: dt=92.480000, rms=0.715 (0.067%), neg=0, invalid=96777
- 0155: dt=92.480000, rms=0.715 (0.094%), neg=0, invalid=96777
- 0156: dt=92.480000, rms=0.714 (0.091%), neg=0, invalid=96777
- 0157: dt=92.480000, rms=0.713 (0.077%), neg=0, invalid=96777
- 0158: dt=92.480000, rms=0.713 (0.065%), neg=0, invalid=96777
- 0159: dt=92.480000, rms=0.712 (0.071%), neg=0, invalid=96777
- 0160: dt=92.480000, rms=0.712 (0.090%), neg=0, invalid=96777
- 0161: dt=92.480000, rms=0.711 (0.077%), neg=0, invalid=96777
- 0162: dt=92.480000, rms=0.711 (0.060%), neg=0, invalid=96777
- 0163: dt=92.480000, rms=0.710 (0.049%), neg=0, invalid=96777
- 0164: dt=92.480000, rms=0.710 (0.060%), neg=0, invalid=96777
- 0165: dt=92.480000, rms=0.710 (0.069%), neg=0, invalid=96777
- 0166: dt=92.480000, rms=0.709 (0.060%), neg=0, invalid=96777
- 0167: dt=92.480000, rms=0.709 (0.046%), neg=0, invalid=96777
- 0168: dt=92.480000, rms=0.708 (0.039%), neg=0, invalid=96777
- 0169: dt=92.480000, rms=0.708 (0.053%), neg=0, invalid=96777
- 0170: dt=92.480000, rms=0.708 (0.055%), neg=0, invalid=96777
- 0171: dt=92.480000, rms=0.707 (0.050%), neg=0, invalid=96777
- 0172: dt=92.480000, rms=0.707 (0.038%), neg=0, invalid=96777
- 0173: dt=92.480000, rms=0.707 (0.057%), neg=0, invalid=96777
- 0174: dt=92.480000, rms=0.706 (0.048%), neg=0, invalid=96777
- 0175: dt=92.480000, rms=0.706 (0.024%), neg=0, invalid=96777
- 0176: dt=92.480000, rms=0.706 (0.039%), neg=0, invalid=96777
- 0177: dt=92.480000, rms=0.705 (0.060%), neg=0, invalid=96777
- 0178: dt=92.480000, rms=0.705 (0.015%), neg=0, invalid=96777
- 0179: dt=92.480000, rms=0.705 (0.011%), neg=0, invalid=96777
- 0180: dt=129.472000, rms=0.705 (0.053%), neg=0, invalid=96777
- 0181: dt=0.000000, rms=0.705 (0.001%), neg=0, invalid=96777
- 0182: dt=0.850000, rms=0.705 (-0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.705, neg=0, invalid=96777
- 0183: dt=92.480000, rms=0.705 (0.045%), neg=0, invalid=96777
- 0184: dt=129.472000, rms=0.704 (0.135%), neg=0, invalid=96777
- 0185: dt=27.744000, rms=0.704 (0.007%), neg=0, invalid=96777
- 0186: dt=27.744000, rms=0.704 (0.002%), neg=0, invalid=96777
- 0187: dt=27.744000, rms=0.704 (0.002%), neg=0, invalid=96777
- 0188: dt=27.744000, rms=0.704 (0.005%), neg=0, invalid=96777
- 0189: dt=27.744000, rms=0.703 (0.033%), neg=0, invalid=96777
- 0190: dt=27.744000, rms=0.703 (0.042%), neg=0, invalid=96777
- 0191: dt=27.744000, rms=0.703 (0.037%), neg=0, invalid=96777
- 0192: dt=27.744000, rms=0.703 (0.027%), neg=0, invalid=96777
- 0193: dt=27.744000, rms=0.702 (0.012%), neg=0, invalid=96777
- 0194: dt=27.744000, rms=0.702 (0.003%), neg=0, invalid=96777
- 0195: dt=369.920000, rms=0.702 (0.063%), neg=0, invalid=96777
- 0196: dt=18.496000, rms=0.702 (0.005%), neg=0, invalid=96777
- 0197: dt=18.496000, rms=0.702 (0.000%), neg=0, invalid=96777
- 0198: dt=18.496000, rms=0.702 (-0.009%), neg=0, invalid=96777
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.703, neg=0, invalid=96777
- 0199: dt=124.416000, rms=0.699 (0.601%), neg=0, invalid=96777
- 0200: dt=31.104000, rms=0.694 (0.701%), neg=0, invalid=96777
- 0201: dt=25.920000, rms=0.692 (0.215%), neg=0, invalid=96777
- 0202: dt=124.416000, rms=0.688 (0.587%), neg=0, invalid=96777
- 0203: dt=25.920000, rms=0.685 (0.423%), neg=0, invalid=96777
- 0204: dt=103.680000, rms=0.683 (0.379%), neg=0, invalid=96777
- 0205: dt=20.736000, rms=0.680 (0.417%), neg=0, invalid=96777
- 0206: dt=82.944000, rms=0.678 (0.248%), neg=0, invalid=96777
- 0207: dt=25.920000, rms=0.676 (0.294%), neg=0, invalid=96777
- 0208: dt=25.920000, rms=0.676 (0.104%), neg=0, invalid=96777
- 0209: dt=103.680000, rms=0.674 (0.287%), neg=0, invalid=96777
- 0210: dt=20.736000, rms=0.672 (0.237%), neg=0, invalid=96777
- 0211: dt=497.664000, rms=0.662 (1.531%), neg=0, invalid=96777
- 0212: dt=36.288000, rms=0.659 (0.377%), neg=0, invalid=96777
- 0213: dt=9.072000, rms=0.659 (0.047%), neg=0, invalid=96777
- 0214: dt=9.072000, rms=0.659 (0.025%), neg=0, invalid=96777
- 0215: dt=9.072000, rms=0.659 (0.025%), neg=0, invalid=96777
- 0216: dt=9.072000, rms=0.658 (0.035%), neg=0, invalid=96777
- 0217: dt=9.072000, rms=0.658 (0.060%), neg=0, invalid=96777
- 0218: dt=9.072000, rms=0.658 (0.081%), neg=0, invalid=96777
- 0219: dt=9.072000, rms=0.657 (0.097%), neg=0, invalid=96777
- 0220: dt=9.072000, rms=0.656 (0.100%), neg=0, invalid=96777
- 0221: dt=9.072000, rms=0.656 (0.027%), neg=0, invalid=96777
- 0222: dt=9.072000, rms=0.656 (0.026%), neg=0, invalid=96777
- 0223: dt=0.567000, rms=0.656 (0.002%), neg=0, invalid=96777
- 0224: dt=0.017719, rms=0.656 (0.000%), neg=0, invalid=96777
- 0225: dt=0.002215, rms=0.656 (0.000%), neg=0, invalid=96777
- 0226: dt=0.002215, rms=0.656 (0.000%), neg=0, invalid=96777
- 0227: dt=0.001107, rms=0.656 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.656, neg=0, invalid=96777
- 0228: dt=145.152000, rms=0.651 (0.710%), neg=0, invalid=96777
- 0229: dt=36.288000, rms=0.650 (0.150%), neg=0, invalid=96777
- 0230: dt=145.152000, rms=0.648 (0.362%), neg=0, invalid=96777
- 0231: dt=9.072000, rms=0.648 (0.019%), neg=0, invalid=96777
- 0232: dt=9.072000, rms=0.648 (0.018%), neg=0, invalid=96777
- 0233: dt=9.072000, rms=0.648 (0.023%), neg=0, invalid=96777
- 0234: dt=9.072000, rms=0.647 (0.036%), neg=0, invalid=96777
- 0235: dt=9.072000, rms=0.647 (0.058%), neg=0, invalid=96777
- 0236: dt=9.072000, rms=0.646 (0.083%), neg=0, invalid=96777
- 0237: dt=9.072000, rms=0.646 (0.101%), neg=0, invalid=96777
- 0238: dt=9.072000, rms=0.645 (0.105%), neg=0, invalid=96777
- 0239: dt=9.072000, rms=0.644 (0.105%), neg=0, invalid=96777
- 0240: dt=9.072000, rms=0.644 (0.102%), neg=0, invalid=96777
- 0241: dt=9.072000, rms=0.643 (0.100%), neg=0, invalid=96777
- 0242: dt=9.072000, rms=0.642 (0.094%), neg=0, invalid=96777
- 0243: dt=9.072000, rms=0.642 (0.096%), neg=0, invalid=96777
- 0244: dt=9.072000, rms=0.641 (0.097%), neg=0, invalid=96777
- 0245: dt=9.072000, rms=0.640 (0.119%), neg=0, invalid=96777
- 0246: dt=9.072000, rms=0.640 (0.123%), neg=0, invalid=96777
- 0247: dt=9.072000, rms=0.639 (0.124%), neg=0, invalid=96777
- 0248: dt=9.072000, rms=0.638 (0.121%), neg=0, invalid=96777
- 0249: dt=9.072000, rms=0.637 (0.118%), neg=0, invalid=96777
- 0250: dt=9.072000, rms=0.637 (0.112%), neg=0, invalid=96777
- 0251: dt=9.072000, rms=0.636 (0.098%), neg=0, invalid=96777
- 0252: dt=9.072000, rms=0.635 (0.103%), neg=0, invalid=96777
- 0253: dt=9.072000, rms=0.635 (0.098%), neg=0, invalid=96777
- 0254: dt=9.072000, rms=0.634 (0.099%), neg=0, invalid=96777
- 0255: dt=9.072000, rms=0.633 (0.104%), neg=0, invalid=96777
- 0256: dt=9.072000, rms=0.633 (0.101%), neg=0, invalid=96777
- 0257: dt=9.072000, rms=0.632 (0.096%), neg=0, invalid=96777
- 0258: dt=9.072000, rms=0.632 (0.096%), neg=0, invalid=96777
- 0259: dt=9.072000, rms=0.631 (0.093%), neg=0, invalid=96777
- 0260: dt=9.072000, rms=0.630 (0.089%), neg=0, invalid=96777
- 0261: dt=9.072000, rms=0.630 (0.086%), neg=0, invalid=96777
- 0262: dt=9.072000, rms=0.629 (0.087%), neg=0, invalid=96777
- 0263: dt=9.072000, rms=0.629 (0.083%), neg=0, invalid=96777
- 0264: dt=9.072000, rms=0.628 (0.078%), neg=0, invalid=96777
- 0265: dt=9.072000, rms=0.628 (0.079%), neg=0, invalid=96777
- 0266: dt=9.072000, rms=0.627 (0.074%), neg=0, invalid=96777
- 0267: dt=9.072000, rms=0.627 (0.071%), neg=0, invalid=96777
- 0268: dt=9.072000, rms=0.627 (0.006%), neg=0, invalid=96777
- 0269: dt=9.072000, rms=0.627 (0.015%), neg=0, invalid=96777
- 0270: dt=9.072000, rms=0.627 (0.017%), neg=0, invalid=96777
- 0271: dt=9.072000, rms=0.627 (0.021%), neg=0, invalid=96777
- 0272: dt=9.072000, rms=0.626 (0.027%), neg=0, invalid=96777
- 0273: dt=9.072000, rms=0.626 (0.031%), neg=0, invalid=96777
- 0274: dt=9.072000, rms=0.626 (0.033%), neg=0, invalid=96777
- 0275: dt=9.072000, rms=0.626 (0.034%), neg=0, invalid=96777
- 0276: dt=9.072000, rms=0.626 (0.035%), neg=0, invalid=96777
- 0277: dt=9.072000, rms=0.625 (0.037%), neg=0, invalid=96777
- 0278: dt=9.072000, rms=0.625 (0.040%), neg=0, invalid=96777
- 0279: dt=9.072000, rms=0.625 (0.041%), neg=0, invalid=96777
- 0280: dt=9.072000, rms=0.625 (0.043%), neg=0, invalid=96777
- 0281: dt=9.072000, rms=0.624 (0.046%), neg=0, invalid=96777
- 0282: dt=9.072000, rms=0.624 (0.044%), neg=0, invalid=96777
- 0283: dt=9.072000, rms=0.624 (0.046%), neg=0, invalid=96777
- 0284: dt=9.072000, rms=0.623 (0.043%), neg=0, invalid=96777
- 0285: dt=9.072000, rms=0.623 (0.042%), neg=0, invalid=96777
- 0286: dt=9.072000, rms=0.623 (0.045%), neg=0, invalid=96777
- 0287: dt=9.072000, rms=0.623 (0.044%), neg=0, invalid=96777
- 0288: dt=9.072000, rms=0.622 (0.049%), neg=0, invalid=96777
- 0289: dt=9.072000, rms=0.622 (0.047%), neg=0, invalid=96777
- 0290: dt=9.072000, rms=0.622 (0.049%), neg=0, invalid=96777
- 0291: dt=9.072000, rms=0.621 (0.046%), neg=0, invalid=96777
- 0292: dt=9.072000, rms=0.621 (0.049%), neg=0, invalid=96777
- 0293: dt=9.072000, rms=0.621 (0.043%), neg=0, invalid=96777
- 0294: dt=9.072000, rms=0.621 (0.044%), neg=0, invalid=96777
- 0295: dt=9.072000, rms=0.620 (0.043%), neg=0, invalid=96777
- 0296: dt=9.072000, rms=0.620 (0.041%), neg=0, invalid=96777
- 0297: dt=9.072000, rms=0.620 (0.043%), neg=0, invalid=96777
- 0298: dt=9.072000, rms=0.620 (0.042%), neg=0, invalid=96777
- 0299: dt=9.072000, rms=0.619 (0.042%), neg=0, invalid=96777
- 0300: dt=9.072000, rms=0.619 (0.043%), neg=0, invalid=96777
- 0301: dt=9.072000, rms=0.619 (0.041%), neg=0, invalid=96777
- 0302: dt=9.072000, rms=0.619 (0.041%), neg=0, invalid=96777
- 0303: dt=9.072000, rms=0.618 (0.041%), neg=0, invalid=96777
- 0304: dt=9.072000, rms=0.618 (0.041%), neg=0, invalid=96777
- 0305: dt=9.072000, rms=0.618 (0.042%), neg=0, invalid=96777
- 0306: dt=9.072000, rms=0.617 (0.040%), neg=0, invalid=96777
- 0307: dt=9.072000, rms=0.617 (0.041%), neg=0, invalid=96777
- 0308: dt=9.072000, rms=0.617 (0.038%), neg=0, invalid=96777
- 0309: dt=9.072000, rms=0.617 (0.039%), neg=0, invalid=96777
- 0310: dt=9.072000, rms=0.617 (0.040%), neg=0, invalid=96777
- 0311: dt=9.072000, rms=0.616 (0.038%), neg=0, invalid=96777
- 0312: dt=9.072000, rms=0.616 (0.038%), neg=0, invalid=96777
- 0313: dt=9.072000, rms=0.616 (0.036%), neg=0, invalid=96777
- 0314: dt=9.072000, rms=0.616 (0.035%), neg=0, invalid=96777
- 0315: dt=9.072000, rms=0.615 (0.037%), neg=0, invalid=96777
- 0316: dt=9.072000, rms=0.615 (0.035%), neg=0, invalid=96777
- 0317: dt=9.072000, rms=0.615 (0.037%), neg=0, invalid=96777
- 0318: dt=9.072000, rms=0.615 (0.037%), neg=0, invalid=96777
- 0319: dt=9.072000, rms=0.614 (0.036%), neg=0, invalid=96777
- 0320: dt=9.072000, rms=0.614 (0.035%), neg=0, invalid=96777
- 0321: dt=9.072000, rms=0.614 (0.036%), neg=0, invalid=96777
- 0322: dt=9.072000, rms=0.614 (0.033%), neg=0, invalid=96777
- 0323: dt=9.072000, rms=0.614 (0.031%), neg=0, invalid=96777
- 0324: dt=9.072000, rms=0.613 (0.033%), neg=0, invalid=96777
- 0325: dt=9.072000, rms=0.613 (0.032%), neg=0, invalid=96777
- 0326: dt=9.072000, rms=0.613 (0.029%), neg=0, invalid=96777
- 0327: dt=9.072000, rms=0.613 (0.030%), neg=0, invalid=96777
- 0328: dt=9.072000, rms=0.613 (0.031%), neg=0, invalid=96777
- 0329: dt=9.072000, rms=0.613 (0.029%), neg=0, invalid=96777
- 0330: dt=9.072000, rms=0.612 (0.030%), neg=0, invalid=96777
- 0331: dt=9.072000, rms=0.612 (0.029%), neg=0, invalid=96777
- 0332: dt=9.072000, rms=0.612 (0.030%), neg=0, invalid=96777
- 0333: dt=9.072000, rms=0.612 (0.030%), neg=0, invalid=96777
- 0334: dt=9.072000, rms=0.612 (0.028%), neg=0, invalid=96777
- 0335: dt=9.072000, rms=0.611 (0.027%), neg=0, invalid=96777
- 0336: dt=9.072000, rms=0.611 (0.026%), neg=0, invalid=96777
- 0337: dt=9.072000, rms=0.611 (0.024%), neg=0, invalid=96777
- 0338: dt=9.072000, rms=0.611 (0.026%), neg=0, invalid=96777
- 0339: dt=9.072000, rms=0.611 (0.028%), neg=0, invalid=96777
- 0340: dt=9.072000, rms=0.611 (0.028%), neg=0, invalid=96777
- 0341: dt=9.072000, rms=0.610 (0.029%), neg=0, invalid=96777
- 0342: dt=9.072000, rms=0.610 (0.028%), neg=0, invalid=96777
- 0343: dt=9.072000, rms=0.610 (0.026%), neg=0, invalid=96777
- 0344: dt=9.072000, rms=0.610 (0.024%), neg=0, invalid=96777
- 0345: dt=9.072000, rms=0.610 (0.022%), neg=0, invalid=96777
- 0346: dt=580.608000, rms=0.609 (0.106%), neg=0, invalid=96777
- 0347: dt=20.736000, rms=0.609 (0.045%), neg=0, invalid=96777
- 0348: dt=20.736000, rms=0.609 (0.011%), neg=0, invalid=96777
- 0349: dt=20.736000, rms=0.609 (0.014%), neg=0, invalid=96777
- 0350: dt=20.736000, rms=0.609 (0.015%), neg=0, invalid=96777
- 0351: dt=20.736000, rms=0.609 (0.018%), neg=0, invalid=96777
- 0352: dt=20.736000, rms=0.608 (0.027%), neg=0, invalid=96777
- 0353: dt=20.736000, rms=0.608 (0.020%), neg=0, invalid=96777
- 0354: dt=20.736000, rms=0.608 (0.022%), neg=0, invalid=96777
- 0355: dt=20.736000, rms=0.608 (0.023%), neg=0, invalid=96777
- 0356: dt=20.736000, rms=0.608 (0.026%), neg=0, invalid=96777
- 0357: dt=20.736000, rms=0.608 (0.036%), neg=0, invalid=96777
- 0358: dt=20.736000, rms=0.607 (0.038%), neg=0, invalid=96777
- 0359: dt=20.736000, rms=0.607 (0.035%), neg=0, invalid=96777
- 0360: dt=20.736000, rms=0.607 (0.028%), neg=0, invalid=96777
- 0361: dt=20.736000, rms=0.607 (0.038%), neg=0, invalid=96777
- 0362: dt=20.736000, rms=0.607 (0.041%), neg=0, invalid=96777
- 0363: dt=20.736000, rms=0.606 (0.042%), neg=0, invalid=96777
- 0364: dt=20.736000, rms=0.606 (0.042%), neg=0, invalid=96777
- 0365: dt=20.736000, rms=0.606 (0.041%), neg=0, invalid=96777
- 0366: dt=20.736000, rms=0.606 (0.036%), neg=0, invalid=96777
- 0367: dt=20.736000, rms=0.605 (0.035%), neg=0, invalid=96777
- 0368: dt=20.736000, rms=0.605 (0.033%), neg=0, invalid=96777
- 0369: dt=20.736000, rms=0.605 (0.034%), neg=0, invalid=96777
- 0370: dt=20.736000, rms=0.605 (0.041%), neg=0, invalid=96777
- 0371: dt=20.736000, rms=0.605 (0.037%), neg=0, invalid=96777
- 0372: dt=20.736000, rms=0.604 (0.037%), neg=0, invalid=96777
- 0373: dt=20.736000, rms=0.604 (0.034%), neg=0, invalid=96777
- 0374: dt=20.736000, rms=0.604 (0.040%), neg=0, invalid=96777
- 0375: dt=20.736000, rms=0.604 (0.040%), neg=0, invalid=96777
- 0376: dt=20.736000, rms=0.603 (0.034%), neg=0, invalid=96777
- 0377: dt=20.736000, rms=0.603 (0.034%), neg=0, invalid=96777
- 0378: dt=20.736000, rms=0.603 (0.032%), neg=0, invalid=96777
- 0379: dt=20.736000, rms=0.603 (0.036%), neg=0, invalid=96777
- 0380: dt=20.736000, rms=0.603 (0.036%), neg=0, invalid=96777
- 0381: dt=20.736000, rms=0.602 (0.037%), neg=0, invalid=96777
- 0382: dt=20.736000, rms=0.602 (0.031%), neg=0, invalid=96777
- 0383: dt=20.736000, rms=0.602 (0.035%), neg=0, invalid=96777
- 0384: dt=20.736000, rms=0.602 (0.036%), neg=0, invalid=96777
- 0385: dt=20.736000, rms=0.602 (0.033%), neg=0, invalid=96777
- 0386: dt=20.736000, rms=0.601 (0.031%), neg=0, invalid=96777
- 0387: dt=20.736000, rms=0.601 (0.032%), neg=0, invalid=96777
- 0388: dt=20.736000, rms=0.601 (0.035%), neg=0, invalid=96777
- 0389: dt=20.736000, rms=0.601 (0.034%), neg=0, invalid=96777
- 0390: dt=20.736000, rms=0.601 (0.030%), neg=0, invalid=96777
- 0391: dt=20.736000, rms=0.600 (0.029%), neg=0, invalid=96777
- 0392: dt=20.736000, rms=0.600 (0.034%), neg=0, invalid=96777
- 0393: dt=20.736000, rms=0.600 (0.032%), neg=0, invalid=96777
- 0394: dt=20.736000, rms=0.600 (0.027%), neg=0, invalid=96777
- 0395: dt=20.736000, rms=0.600 (0.028%), neg=0, invalid=96777
- 0396: dt=20.736000, rms=0.599 (0.028%), neg=0, invalid=96777
- 0397: dt=20.736000, rms=0.599 (0.032%), neg=0, invalid=96777
- 0398: dt=20.736000, rms=0.599 (0.033%), neg=0, invalid=96777
- 0399: dt=20.736000, rms=0.599 (0.029%), neg=0, invalid=96777
- 0400: dt=20.736000, rms=0.599 (0.024%), neg=0, invalid=96777
- 0401: dt=20.736000, rms=0.599 (0.028%), neg=0, invalid=96777
- 0402: dt=20.736000, rms=0.598 (0.028%), neg=0, invalid=96777
- 0403: dt=20.736000, rms=0.598 (0.026%), neg=0, invalid=96777
- 0404: dt=20.736000, rms=0.598 (0.030%), neg=0, invalid=96777
- 0405: dt=20.736000, rms=0.598 (0.028%), neg=0, invalid=96777
- 0406: dt=20.736000, rms=0.598 (0.025%), neg=0, invalid=96777
- 0407: dt=20.736000, rms=0.598 (0.025%), neg=0, invalid=96777
- 0408: dt=20.736000, rms=0.597 (0.024%), neg=0, invalid=96777
- 0409: dt=20.736000, rms=0.597 (0.024%), neg=0, invalid=96777
- 0410: dt=6.480000, rms=0.597 (0.004%), neg=0, invalid=96777
- 0411: dt=6.480000, rms=0.597 (-0.001%), neg=0, invalid=96777
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.605, neg=0, invalid=96777
- 0412: dt=38.400000, rms=0.602 (0.539%), neg=0, invalid=96777
- 0413: dt=38.400000, rms=0.597 (0.816%), neg=0, invalid=96777
- 0414: dt=9.600000, rms=0.596 (0.163%), neg=0, invalid=96777
- 0415: dt=11.200000, rms=0.594 (0.197%), neg=0, invalid=96777
- 0416: dt=19.200000, rms=0.593 (0.191%), neg=0, invalid=96777
- 0417: dt=7.734807, rms=0.592 (0.225%), neg=0, invalid=96777
- 0418: dt=11.200000, rms=0.591 (0.155%), neg=0, invalid=96777
- 0419: dt=19.200000, rms=0.590 (0.260%), neg=0, invalid=96777
- 0420: dt=7.218045, rms=0.589 (0.156%), neg=0, invalid=96777
- 0421: dt=44.800000, rms=0.585 (0.531%), neg=0, invalid=96777
- 0422: dt=7.366906, rms=0.585 (0.134%), neg=0, invalid=96777
- 0423: dt=44.800000, rms=0.582 (0.502%), neg=0, invalid=96777
- 0424: dt=11.200000, rms=0.581 (0.096%), neg=0, invalid=96777
- 0425: dt=44.800000, rms=0.580 (0.236%), neg=0, invalid=96777
- 0426: dt=6.400000, rms=0.579 (0.127%), neg=0, invalid=96777
- 0427: dt=11.200000, rms=0.578 (0.180%), neg=0, invalid=96777
- 0428: dt=11.200000, rms=0.577 (0.107%), neg=0, invalid=96777
- 0429: dt=19.200000, rms=0.577 (0.106%), neg=0, invalid=96777
- 0430: dt=6.400000, rms=0.576 (0.072%), neg=0, invalid=96777
- 0431: dt=19.200000, rms=0.576 (0.104%), neg=0, invalid=96777
- 0432: dt=9.600000, rms=0.575 (0.108%), neg=0, invalid=96777
- 0433: dt=9.600000, rms=0.575 (0.069%), neg=0, invalid=96777
- 0434: dt=25.600000, rms=0.574 (0.154%), neg=0, invalid=96777
- 0435: dt=6.521739, rms=0.573 (0.077%), neg=0, invalid=96777
- 0436: dt=44.800000, rms=0.572 (0.285%), neg=0, invalid=96777
- 0437: dt=11.200000, rms=0.572 (0.051%), neg=0, invalid=96777
- 0438: dt=32.000000, rms=0.571 (0.125%), neg=0, invalid=96777
- 0439: dt=6.776471, rms=0.570 (0.089%), neg=0, invalid=96777
- 0440: dt=44.800000, rms=0.569 (0.202%), neg=0, invalid=96777
- 0441: dt=6.400000, rms=0.569 (0.063%), neg=0, invalid=96777
- 0442: dt=19.200000, rms=0.568 (0.074%), neg=0, invalid=96777
- 0443: dt=6.400000, rms=0.568 (0.045%), neg=0, invalid=96777
- 0444: dt=6.400000, rms=0.568 (0.040%), neg=0, invalid=96777
- 0445: dt=6.400000, rms=0.568 (0.063%), neg=0, invalid=96777
- 0446: dt=6.400000, rms=0.567 (0.083%), neg=0, invalid=96777
- 0447: dt=6.400000, rms=0.566 (0.105%), neg=0, invalid=96777
- 0448: dt=6.400000, rms=0.566 (0.115%), neg=0, invalid=96777
- 0449: dt=6.400000, rms=0.565 (0.125%), neg=0, invalid=96777
- 0450: dt=6.400000, rms=0.564 (0.139%), neg=0, invalid=96777
- 0451: dt=6.400000, rms=0.564 (0.148%), neg=0, invalid=96777
- 0452: dt=6.400000, rms=0.563 (0.147%), neg=0, invalid=96777
- 0453: dt=6.400000, rms=0.562 (0.150%), neg=0, invalid=96777
- 0454: dt=6.400000, rms=0.561 (0.157%), neg=0, invalid=96777
- 0455: dt=6.400000, rms=0.560 (0.165%), neg=0, invalid=96777
- 0456: dt=6.400000, rms=0.559 (0.166%), neg=0, invalid=96777
- 0457: dt=6.400000, rms=0.558 (0.154%), neg=0, invalid=96777
- 0458: dt=6.400000, rms=0.557 (0.145%), neg=0, invalid=96777
- 0459: dt=6.400000, rms=0.557 (0.132%), neg=0, invalid=96777
- 0460: dt=6.400000, rms=0.556 (0.129%), neg=0, invalid=96777
- 0461: dt=6.400000, rms=0.555 (0.125%), neg=0, invalid=96777
- 0462: dt=6.400000, rms=0.555 (0.130%), neg=0, invalid=96777
- 0463: dt=6.400000, rms=0.554 (0.020%), neg=0, invalid=96777
- 0464: dt=6.400000, rms=0.554 (0.029%), neg=0, invalid=96777
- 0465: dt=6.400000, rms=0.554 (0.030%), neg=0, invalid=96777
- 0466: dt=6.400000, rms=0.554 (0.035%), neg=0, invalid=96777
- 0467: dt=6.400000, rms=0.554 (0.029%), neg=0, invalid=96777
- 0468: dt=6.400000, rms=0.554 (0.030%), neg=0, invalid=96777
- 0469: dt=6.400000, rms=0.553 (0.041%), neg=0, invalid=96777
- 0470: dt=6.400000, rms=0.553 (0.041%), neg=0, invalid=96777
- 0471: dt=6.400000, rms=0.553 (0.043%), neg=0, invalid=96777
- 0472: dt=6.400000, rms=0.553 (0.055%), neg=0, invalid=96777
- 0473: dt=6.400000, rms=0.552 (0.059%), neg=0, invalid=96777
- 0474: dt=6.400000, rms=0.552 (0.064%), neg=0, invalid=96777
- 0475: dt=6.400000, rms=0.552 (0.065%), neg=0, invalid=96777
- 0476: dt=6.400000, rms=0.551 (0.065%), neg=0, invalid=96777
- 0477: dt=6.400000, rms=0.551 (0.070%), neg=0, invalid=96777
- 0478: dt=6.400000, rms=0.550 (0.067%), neg=0, invalid=96777
- 0479: dt=6.400000, rms=0.550 (0.064%), neg=0, invalid=96777
- 0480: dt=6.400000, rms=0.550 (0.058%), neg=0, invalid=96777
- 0481: dt=6.400000, rms=0.549 (0.064%), neg=0, invalid=96777
- 0482: dt=6.400000, rms=0.549 (0.061%), neg=0, invalid=96777
- 0483: dt=6.400000, rms=0.549 (0.062%), neg=0, invalid=96777
- 0484: dt=6.400000, rms=0.548 (0.057%), neg=0, invalid=96777
- 0485: dt=6.400000, rms=0.548 (0.058%), neg=0, invalid=96777
- 0486: dt=6.400000, rms=0.548 (0.056%), neg=0, invalid=96777
- 0487: dt=6.400000, rms=0.547 (0.059%), neg=0, invalid=96777
- 0488: dt=6.400000, rms=0.547 (0.060%), neg=0, invalid=96777
- 0489: dt=6.400000, rms=0.547 (0.060%), neg=0, invalid=96777
- 0490: dt=6.400000, rms=0.547 (0.058%), neg=0, invalid=96777
- 0491: dt=6.400000, rms=0.546 (0.052%), neg=0, invalid=96777
- 0492: dt=6.400000, rms=0.546 (0.049%), neg=0, invalid=96777
- 0493: dt=6.400000, rms=0.546 (0.046%), neg=0, invalid=96777
- 0494: dt=6.400000, rms=0.545 (0.048%), neg=0, invalid=96777
- 0495: dt=6.400000, rms=0.545 (0.045%), neg=0, invalid=96777
- 0496: dt=6.400000, rms=0.545 (0.044%), neg=0, invalid=96777
- 0497: dt=6.400000, rms=0.545 (0.045%), neg=0, invalid=96777
- 0498: dt=6.400000, rms=0.544 (0.043%), neg=0, invalid=96777
- 0499: dt=6.400000, rms=0.544 (0.040%), neg=0, invalid=96777
- 0500: dt=6.400000, rms=0.544 (0.039%), neg=0, invalid=96777
- 0501: dt=6.400000, rms=0.544 (0.036%), neg=0, invalid=96777
- 0502: dt=6.400000, rms=0.544 (0.034%), neg=0, invalid=96777
- 0503: dt=6.400000, rms=0.544 (0.033%), neg=0, invalid=96777
- 0504: dt=6.400000, rms=0.543 (0.035%), neg=0, invalid=96777
- 0505: dt=6.400000, rms=0.543 (0.038%), neg=0, invalid=96777
- 0506: dt=6.400000, rms=0.543 (0.045%), neg=0, invalid=96777
- 0507: dt=6.400000, rms=0.543 (0.039%), neg=0, invalid=96777
- 0508: dt=6.400000, rms=0.542 (0.033%), neg=0, invalid=96777
- 0509: dt=6.400000, rms=0.542 (0.029%), neg=0, invalid=96777
- 0510: dt=6.400000, rms=0.542 (0.032%), neg=0, invalid=96777
- 0511: dt=6.400000, rms=0.542 (0.024%), neg=0, invalid=96777
- 0512: dt=6.400000, rms=0.542 (0.027%), neg=0, invalid=96777
- 0513: dt=6.400000, rms=0.542 (0.023%), neg=0, invalid=96777
- 0514: dt=6.400000, rms=0.542 (0.029%), neg=0, invalid=96777
- 0515: dt=6.400000, rms=0.541 (0.028%), neg=0, invalid=96777
- 0516: dt=6.400000, rms=0.541 (0.022%), neg=0, invalid=96777
- 0517: dt=6.400000, rms=0.541 (0.024%), neg=0, invalid=96777
- 0518: dt=6.400000, rms=0.541 (0.022%), neg=0, invalid=96777
- 0519: dt=1.600000, rms=0.541 (0.001%), neg=0, invalid=96777
- 0520: dt=1.600000, rms=0.541 (-0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.541, neg=0, invalid=96777
- 0521: dt=38.400000, rms=0.539 (0.327%), neg=0, invalid=96777
- 0522: dt=19.200000, rms=0.539 (0.102%), neg=0, invalid=96777
- 0523: dt=2.800000, rms=0.539 (0.004%), neg=0, invalid=96777
- 0524: dt=2.800000, rms=0.539 (0.012%), neg=0, invalid=96777
- 0525: dt=2.800000, rms=0.539 (0.017%), neg=0, invalid=96777
- 0526: dt=2.800000, rms=0.539 (0.011%), neg=0, invalid=96777
- 0527: dt=2.800000, rms=0.538 (0.016%), neg=0, invalid=96777
- 0528: dt=2.800000, rms=0.538 (0.016%), neg=0, invalid=96777
- 0529: dt=2.800000, rms=0.538 (0.016%), neg=0, invalid=96777
- 0530: dt=32.000000, rms=0.538 (0.035%), neg=0, invalid=96777
- 0531: dt=8.000000, rms=0.538 (0.009%), neg=0, invalid=96777
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.564, neg=0, invalid=96777
- 0532: dt=0.000000, rms=0.564 (0.003%), neg=0, invalid=96777
- 0533: dt=0.000000, rms=0.564 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.564, neg=0, invalid=96777
- 0534: dt=0.000000, rms=0.564 (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=0.615, neg=0, invalid=96777
- 0535: dt=1.122762, rms=0.611 (0.633%), neg=0, invalid=96777
- 0536: dt=0.275000, rms=0.611 (0.021%), neg=0, invalid=96777
- 0537: dt=0.275000, rms=0.611 (-0.009%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.611, neg=0, invalid=96777
- 0538: dt=0.541667, rms=0.610 (0.109%), neg=0, invalid=96777
- 0539: dt=0.384000, rms=0.610 (0.023%), neg=0, invalid=96777
- 0540: dt=0.384000, rms=0.610 (-0.012%), 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=0.554, neg=0, invalid=96777
- 0541: dt=0.384000, rms=0.536 (3.354%), neg=0, invalid=96777
- 0542: dt=0.005000, rms=0.536 (0.012%), neg=0, invalid=96777
- 0543: dt=0.005000, rms=0.536 (0.012%), neg=0, invalid=96777
- 0544: dt=0.005000, rms=0.535 (0.025%), neg=0, invalid=96777
- 0545: dt=0.005000, rms=0.535 (0.013%), neg=0, invalid=96777
- 0546: dt=0.005000, rms=0.535 (0.024%), neg=0, invalid=96777
- 0547: dt=0.005000, rms=0.535 (0.034%), neg=0, invalid=96777
- 0548: dt=0.005000, rms=0.535 (0.044%), neg=0, invalid=96777
- 0549: dt=0.005000, rms=0.535 (0.052%), neg=0, invalid=96777
- 0550: dt=0.005000, rms=0.534 (0.057%), neg=0, invalid=96777
- 0551: dt=0.005000, rms=0.534 (0.063%), neg=0, invalid=96777
- 0552: dt=0.005000, rms=0.534 (0.068%), neg=0, invalid=96777
- 0553: dt=0.005000, rms=0.533 (0.071%), neg=0, invalid=96777
- 0554: dt=0.005000, rms=0.533 (0.074%), neg=0, invalid=96777
- 0555: dt=0.005000, rms=0.532 (0.076%), neg=0, invalid=96777
- 0556: dt=0.005000, rms=0.532 (0.077%), neg=0, invalid=96777
- 0557: dt=0.005000, rms=0.532 (0.078%), neg=0, invalid=96777
- 0558: dt=0.005000, rms=0.531 (0.079%), neg=0, invalid=96777
- 0559: dt=0.005000, rms=0.531 (0.078%), neg=0, invalid=96777
- 0560: dt=0.005000, rms=0.530 (0.078%), neg=0, invalid=96777
- 0561: dt=0.005000, rms=0.530 (0.075%), neg=0, invalid=96777
- 0562: dt=0.005000, rms=0.529 (0.074%), neg=0, invalid=96777
- 0563: dt=0.005000, rms=0.529 (0.073%), neg=0, invalid=96777
- 0564: dt=0.005000, rms=0.529 (0.070%), neg=0, invalid=96777
- 0565: dt=0.005000, rms=0.528 (0.071%), neg=0, invalid=96777
- 0566: dt=0.005000, rms=0.528 (0.068%), neg=0, invalid=96777
- 0567: dt=0.005000, rms=0.528 (0.065%), neg=0, invalid=96777
- 0568: dt=0.005000, rms=0.527 (0.060%), neg=0, invalid=96777
- 0569: dt=0.005000, rms=0.527 (0.060%), neg=0, invalid=96777
- 0570: dt=0.005000, rms=0.527 (0.060%), neg=0, invalid=96777
- 0571: dt=0.005000, rms=0.526 (0.054%), neg=0, invalid=96777
- 0572: dt=0.005000, rms=0.526 (0.053%), neg=0, invalid=96777
- 0573: dt=0.005000, rms=0.526 (0.050%), neg=0, invalid=96777
- 0574: dt=0.005000, rms=0.526 (0.047%), neg=0, invalid=96777
- 0575: dt=0.005000, rms=0.525 (0.045%), neg=0, invalid=96777
- 0576: dt=0.005000, rms=0.525 (0.043%), neg=0, invalid=96777
- 0577: dt=0.005000, rms=0.525 (0.040%), neg=0, invalid=96777
- 0578: dt=0.005000, rms=0.525 (0.041%), neg=0, invalid=96777
- 0579: dt=0.005000, rms=0.525 (0.033%), neg=0, invalid=96777
- 0580: dt=0.005000, rms=0.524 (0.034%), neg=0, invalid=96777
- 0581: dt=0.005000, rms=0.524 (0.029%), neg=0, invalid=96777
- 0582: dt=0.005000, rms=0.524 (0.031%), neg=0, invalid=96777
- 0583: dt=0.005000, rms=0.524 (0.028%), neg=0, invalid=96777
- 0584: dt=0.005000, rms=0.524 (0.028%), neg=0, invalid=96777
- 0585: dt=0.005000, rms=0.524 (0.023%), neg=0, invalid=96777
- 0586: dt=0.005000, rms=0.524 (0.023%), neg=0, invalid=96777
- 0587: dt=0.112000, rms=0.523 (0.022%), neg=0, invalid=96777
- 0588: dt=0.003500, rms=0.523 (0.003%), neg=0, invalid=96777
- 0589: dt=0.003500, rms=0.523 (0.001%), neg=0, invalid=96777
- 0590: dt=0.001750, rms=0.523 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.523, neg=0, invalid=96777
- 0591: dt=0.007000, rms=0.523 (0.021%), neg=0, invalid=96777
- 0592: dt=0.007000, rms=0.523 (0.022%), neg=0, invalid=96777
- 0593: dt=0.114062, rms=0.521 (0.359%), neg=0, invalid=96777
- 0594: dt=0.112000, rms=0.520 (0.265%), neg=0, invalid=96777
- 0595: dt=0.007000, rms=0.520 (0.015%), neg=0, invalid=96777
- 0596: dt=0.007000, rms=0.520 (0.013%), neg=0, invalid=96777
- 0597: dt=0.007000, rms=0.520 (0.023%), neg=0, invalid=96777
- 0598: dt=0.007000, rms=0.519 (0.033%), neg=0, invalid=96777
- 0599: dt=0.007000, rms=0.519 (0.043%), neg=0, invalid=96777
- 0600: dt=0.007000, rms=0.519 (0.049%), neg=0, invalid=96777
- 0601: dt=0.007000, rms=0.519 (0.054%), neg=0, invalid=96777
- 0602: dt=0.007000, rms=0.518 (0.060%), neg=0, invalid=96777
- 0603: dt=0.007000, rms=0.518 (0.059%), neg=0, invalid=96777
- 0604: dt=0.007000, rms=0.518 (0.062%), neg=0, invalid=96777
- 0605: dt=0.007000, rms=0.517 (0.061%), neg=0, invalid=96777
- 0606: dt=0.007000, rms=0.517 (0.064%), neg=0, invalid=96777
- 0607: dt=0.007000, rms=0.517 (0.063%), neg=0, invalid=96777
- 0608: dt=0.007000, rms=0.516 (0.063%), neg=0, invalid=96777
- 0609: dt=0.007000, rms=0.516 (0.059%), neg=0, invalid=96777
- 0610: dt=0.007000, rms=0.516 (0.055%), neg=0, invalid=96777
- 0611: dt=0.007000, rms=0.516 (0.053%), neg=0, invalid=96777
- 0612: dt=0.007000, rms=0.515 (0.048%), neg=0, invalid=96777
- 0613: dt=0.007000, rms=0.515 (0.045%), neg=0, invalid=96777
- 0614: dt=0.007000, rms=0.515 (0.039%), neg=0, invalid=96777
- 0615: dt=0.007000, rms=0.515 (0.036%), neg=0, invalid=96777
- 0616: dt=0.007000, rms=0.515 (0.033%), neg=0, invalid=96777
- 0617: dt=0.007000, rms=0.514 (0.030%), neg=0, invalid=96777
- 0618: dt=0.007000, rms=0.514 (0.021%), neg=0, invalid=96777
- 0619: dt=0.007000, rms=0.514 (0.023%), neg=0, invalid=96777
- 0620: dt=0.007000, rms=0.514 (0.018%), neg=0, invalid=96777
- 0621: dt=0.000000, rms=0.514 (-0.003%), neg=0, invalid=96777
- label assignment complete, 0 changed (0.00%)
- *********************************************************************************************
- *********************************************************************************************
- *********************************************************************************************
- ********************* ALLOWING NEGATIVE NODES IN DEFORMATION ********************************
- *********************************************************************************************
- *********************************************************************************************
- *********************************************************************************************
- **************** pass 1 of 1 ************************
- setting smoothness coefficient to 0.008
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.512, neg=0, invalid=96777
- 0622: dt=32.368000, rms=0.512 (0.006%), neg=0, invalid=96777
- 0623: dt=18.496000, rms=0.512 (0.001%), neg=0, invalid=96777
- 0624: dt=18.496000, rms=0.512 (-0.003%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.512, neg=0, invalid=96777
- 0625: dt=129.472000, rms=0.512 (0.047%), neg=0, invalid=96777
- 0626: dt=92.480000, rms=0.512 (0.022%), neg=0, invalid=96777
- 0627: dt=92.480000, rms=0.512 (0.017%), neg=0, invalid=96777
- 0628: dt=92.480000, rms=0.511 (0.040%), neg=0, invalid=96777
- 0629: dt=92.480000, rms=0.511 (0.011%), neg=0, invalid=96777
- 0630: dt=92.480000, rms=0.511 (0.053%), neg=0, invalid=96777
- 0631: dt=92.480000, rms=0.511 (0.017%), neg=0, invalid=96777
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.511, neg=0, invalid=96777
- 0632: dt=36.288000, rms=0.510 (0.186%), neg=0, invalid=96777
- 0633: dt=36.288000, rms=0.509 (0.109%), neg=0, invalid=96777
- 0634: dt=36.288000, rms=0.509 (0.034%), neg=0, invalid=96777
- 0635: dt=36.288000, rms=0.509 (0.016%), neg=0, invalid=96777
- 0636: dt=36.288000, rms=0.509 (-0.038%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.509, neg=0, invalid=96777
- 0637: dt=82.944000, rms=0.507 (0.431%), neg=0, invalid=96777
- 0638: dt=9.072000, rms=0.507 (0.072%), neg=0, invalid=96777
- 0639: dt=9.072000, rms=0.506 (0.041%), neg=0, invalid=96777
- 0640: dt=9.072000, rms=0.506 (0.047%), neg=0, invalid=96777
- 0641: dt=9.072000, rms=0.506 (0.054%), neg=0, invalid=96777
- 0642: dt=9.072000, rms=0.506 (0.052%), neg=0, invalid=96777
- 0643: dt=9.072000, rms=0.505 (0.068%), neg=0, invalid=96777
- 0644: dt=9.072000, rms=0.505 (0.074%), neg=0, invalid=96777
- 0645: dt=9.072000, rms=0.504 (0.079%), neg=0, invalid=96777
- 0646: dt=9.072000, rms=0.504 (0.072%), neg=0, invalid=96777
- 0647: dt=103.680000, rms=0.504 (0.072%), neg=0, invalid=96777
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.504, neg=0, invalid=96777
- iter 0, gcam->neg = 80
- after 10 iterations, nbhd size=1, neg = 0
- 0648: dt=38.400000, rms=0.499 (0.902%), neg=0, invalid=96777
- 0649: dt=5.468927, rms=0.498 (0.206%), neg=0, invalid=96777
- 0650: dt=5.468927, rms=0.498 (0.160%), neg=0, invalid=96777
- 0651: dt=5.468927, rms=0.497 (0.213%), neg=0, invalid=96777
- 0652: dt=5.468927, rms=0.495 (0.243%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 5 iterations, nbhd size=1, neg = 0
- 0653: dt=5.468927, rms=0.494 (0.220%), neg=0, invalid=96777
- 0654: dt=5.468927, rms=0.493 (0.202%), neg=0, invalid=96777
- 0655: dt=5.468927, rms=0.492 (0.198%), neg=0, invalid=96777
- 0656: dt=5.468927, rms=0.491 (0.175%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 1 iterations, nbhd size=0, neg = 0
- 0657: dt=5.468927, rms=0.491 (0.136%), neg=0, invalid=96777
- 0658: dt=5.468927, rms=0.490 (0.120%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 5 iterations, nbhd size=1, neg = 0
- 0659: dt=5.468927, rms=0.490 (0.105%), neg=0, invalid=96777
- iter 0, gcam->neg = 4
- after 7 iterations, nbhd size=1, neg = 0
- 0660: dt=44.800000, rms=0.488 (0.259%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 7 iterations, nbhd size=1, neg = 0
- 0661: dt=6.400000, rms=0.488 (0.044%), neg=0, invalid=96777
- 0662: dt=6.400000, rms=0.488 (0.046%), neg=0, invalid=96777
- 0663: dt=6.400000, rms=0.488 (0.059%), neg=0, invalid=96777
- 0664: dt=6.400000, rms=0.487 (0.068%), neg=0, invalid=96777
- 0665: dt=6.400000, rms=0.487 (0.066%), neg=0, invalid=96777
- 0666: dt=6.400000, rms=0.487 (0.085%), neg=0, invalid=96777
- 0667: dt=6.400000, rms=0.486 (0.098%), neg=0, invalid=96777
- 0668: dt=6.400000, rms=0.486 (0.099%), neg=0, invalid=96777
- 0669: dt=6.400000, rms=0.485 (0.097%), neg=0, invalid=96777
- iter 0, gcam->neg = 2
- after 7 iterations, nbhd size=1, neg = 0
- 0670: dt=32.000000, rms=0.485 (0.035%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.485, neg=0, invalid=96777
- iter 0, gcam->neg = 3
- after 0 iterations, nbhd size=0, neg = 0
- 0671: dt=25.600000, rms=0.483 (0.437%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 5 iterations, nbhd size=1, neg = 0
- 0672: dt=4.761905, rms=0.482 (0.167%), neg=0, invalid=96777
- 0673: dt=4.761905, rms=0.481 (0.131%), neg=0, invalid=96777
- 0674: dt=4.761905, rms=0.481 (0.127%), neg=0, invalid=96777
- 0675: dt=4.761905, rms=0.480 (0.141%), neg=0, invalid=96777
- 0676: dt=4.761905, rms=0.479 (0.162%), neg=0, invalid=96777
- 0677: dt=4.761905, rms=0.479 (0.152%), neg=0, invalid=96777
- 0678: dt=4.761905, rms=0.478 (0.141%), neg=0, invalid=96777
- iter 0, gcam->neg = 2
- after 5 iterations, nbhd size=1, neg = 0
- 0679: dt=4.761905, rms=0.477 (0.122%), neg=0, invalid=96777
- 0680: dt=4.761905, rms=0.477 (0.096%), neg=0, invalid=96777
- 0681: dt=19.200000, rms=0.477 (0.041%), neg=0, invalid=96777
- 0682: dt=19.200000, rms=0.477 (0.038%), neg=0, invalid=96777
- 0683: dt=19.200000, rms=0.476 (0.091%), neg=0, invalid=96777
- 0684: dt=19.200000, rms=0.475 (0.124%), neg=0, invalid=96777
- iter 0, gcam->neg = 2
- after 6 iterations, nbhd size=1, neg = 0
- 0685: dt=19.200000, rms=0.476 (-0.168%), neg=0, invalid=96777
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.479, neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 5 iterations, nbhd size=1, neg = 0
- 0686: dt=2.304000, rms=0.479 (0.046%), neg=0, invalid=96777
- iter 0, gcam->neg = 6
- after 6 iterations, nbhd size=1, neg = 0
- 0687: dt=1.008000, rms=0.479 (0.040%), neg=0, invalid=96777
- 0688: dt=1.008000, rms=0.479 (0.033%), neg=0, invalid=96777
- 0689: dt=1.008000, rms=0.478 (0.054%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 1 iterations, nbhd size=0, neg = 0
- 0690: dt=1.008000, rms=0.478 (0.031%), neg=0, invalid=96777
- 0691: dt=1.008000, rms=0.478 (-0.012%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.478, neg=0, invalid=96777
- iter 0, gcam->neg = 16
- after 8 iterations, nbhd size=1, neg = 0
- 0692: dt=2.880000, rms=0.478 (0.049%), neg=0, invalid=96777
- iter 0, gcam->neg = 24
- after 10 iterations, nbhd size=1, neg = 0
- 0693: dt=3.081967, rms=0.478 (0.090%), neg=0, invalid=96777
- iter 0, gcam->neg = 19
- after 8 iterations, nbhd size=1, neg = 0
- 0694: dt=2.880000, rms=0.477 (0.073%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 5 iterations, nbhd size=1, neg = 0
- 0695: dt=2.880000, rms=0.477 (0.097%), neg=0, invalid=96777
- iter 0, gcam->neg = 7
- after 6 iterations, nbhd size=1, neg = 0
- 0696: dt=2.880000, rms=0.476 (0.154%), neg=0, invalid=96777
- iter 0, gcam->neg = 32
- after 13 iterations, nbhd size=1, neg = 0
- 0697: dt=2.880000, rms=0.475 (0.133%), neg=0, invalid=96777
- iter 0, gcam->neg = 36
- after 14 iterations, nbhd size=1, neg = 0
- 0698: dt=2.880000, rms=0.475 (0.148%), neg=0, invalid=96777
- iter 0, gcam->neg = 92
- after 23 iterations, nbhd size=1, neg = 0
- 0699: dt=2.880000, rms=0.474 (0.078%), neg=0, invalid=96777
- iter 0, gcam->neg = 40
- after 14 iterations, nbhd size=1, neg = 0
- 0700: dt=2.880000, rms=0.474 (0.133%), neg=0, invalid=96777
- iter 0, gcam->neg = 35
- after 10 iterations, nbhd size=1, neg = 0
- 0701: dt=2.880000, rms=0.473 (0.196%), neg=0, invalid=96777
- iter 0, gcam->neg = 24
- after 11 iterations, nbhd size=1, neg = 0
- 0702: dt=2.880000, rms=0.471 (0.286%), neg=0, invalid=96777
- iter 0, gcam->neg = 22
- after 9 iterations, nbhd size=1, neg = 0
- 0703: dt=2.880000, rms=0.470 (0.369%), neg=0, invalid=96777
- iter 0, gcam->neg = 16
- after 8 iterations, nbhd size=1, neg = 0
- 0704: dt=2.880000, rms=0.468 (0.366%), neg=0, invalid=96777
- iter 0, gcam->neg = 40
- after 8 iterations, nbhd size=1, neg = 0
- 0705: dt=2.880000, rms=0.467 (0.320%), neg=0, invalid=96777
- iter 0, gcam->neg = 43
- after 9 iterations, nbhd size=1, neg = 0
- 0706: dt=2.880000, rms=0.465 (0.251%), neg=0, invalid=96777
- iter 0, gcam->neg = 52
- after 11 iterations, nbhd size=1, neg = 0
- 0707: dt=2.880000, rms=0.464 (0.216%), neg=0, invalid=96777
- iter 0, gcam->neg = 71
- after 12 iterations, nbhd size=1, neg = 0
- 0708: dt=2.880000, rms=0.464 (0.135%), neg=0, invalid=96777
- iter 0, gcam->neg = 79
- after 13 iterations, nbhd size=1, neg = 0
- 0709: dt=2.880000, rms=0.463 (0.077%), neg=0, invalid=96777
- iter 0, gcam->neg = 31
- after 8 iterations, nbhd size=1, neg = 0
- 0710: dt=2.880000, rms=0.463 (-0.012%), neg=0, invalid=96777
- 0711: dt=0.000000, rms=0.463 (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=0.469, neg=0, invalid=96777
- 0712: dt=0.000000, rms=0.469 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.469, neg=0, invalid=96777
- 0713: dt=0.000000, rms=0.469 (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=0.460, neg=0, invalid=96777
- iter 0, gcam->neg = 995
- after 41 iterations, nbhd size=3, neg = 0
- 0714: dt=1.536000, rms=0.422 (8.230%), neg=0, invalid=96777
- 0715: dt=0.000016, rms=0.422 (-0.004%), neg=0, invalid=96777
- 0716: dt=0.000016, rms=0.422 (0.000%), neg=0, invalid=96777
- 0717: dt=0.000016, rms=0.422 (0.000%), neg=0, invalid=96777
- 0718: dt=0.000016, rms=0.422 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.422, neg=0, invalid=96777
- 0719: dt=0.000188, rms=0.422 (0.000%), neg=0, invalid=96777
- 0720: dt=0.000000, rms=0.422 (0.000%), neg=0, invalid=96777
- label assignment complete, 0 changed (0.00%)
- label assignment complete, 0 changed (0.00%)
- ***************** morphing with label term set to 0 *******************************
- **************** pass 1 of 1 ************************
- setting smoothness coefficient to 0.008
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.412, neg=0, invalid=96777
- 0721: dt=18.496000, rms=0.413 (-0.304%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.413, neg=0, invalid=96777
- 0722: dt=32.368000, rms=0.413 (0.003%), neg=0, invalid=96777
- 0723: dt=5.780000, rms=0.413 (0.000%), neg=0, invalid=96777
- 0724: dt=5.780000, rms=0.413 (-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=0.413, neg=0, invalid=96777
- 0725: dt=7.776000, rms=0.413 (0.006%), neg=0, invalid=96777
- 0726: dt=0.567000, rms=0.413 (0.000%), neg=0, invalid=96777
- 0727: dt=0.567000, rms=0.413 (0.000%), neg=0, invalid=96777
- 0728: dt=0.567000, rms=0.413 (0.000%), neg=0, invalid=96777
- 0729: dt=0.567000, rms=0.413 (-0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.413, neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 200 iterations, nbhd size=1, neg = 2
- starting rms=0.006, neg=2, removing folds in lattice....
- iter 1, dt=0.000000: new neg 2, old_neg 2, delta 0, rms=0.006 (0.000%)
- ---------- unfolding failed - restoring original position --------------------
- 0730: dt=36.288000, rms=0.413 (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=0.413, neg=0, invalid=96777
- iter 0, gcam->neg = 13
- after 200 iterations, nbhd size=2, neg = 2
- starting rms=0.008, neg=2, removing folds in lattice....
- iter 1, dt=0.000023: new neg 1, old_neg 2, delta 1, rms=0.006 (28.961%)
- iter 2, dt=0.000061: new neg 0, old_neg 1, delta 1, rms=0.003 (41.141%)
- 0731: dt=6.400000, rms=0.413 (0.002%), neg=0, invalid=96777
- iter 0, gcam->neg = 20
- after 200 iterations, nbhd size=4, neg = 2
- starting rms=0.008, neg=2, removing folds in lattice....
- iter 1, dt=0.000023: new neg 1, old_neg 2, delta 1, rms=0.005 (27.551%)
- iter 2, dt=0.000061: new neg 0, old_neg 1, delta 1, rms=0.003 (41.000%)
- 0732: dt=9.600000, rms=0.413 (-0.066%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.413, neg=0, invalid=96777
- iter 0, gcam->neg = 46
- after 200 iterations, nbhd size=2, neg = 5
- starting rms=0.005, neg=5, removing folds in lattice....
- iter 1, dt=0.000031: new neg 0, old_neg 5, delta 5, rms=0.003 (35.752%)
- 0733: dt=38.400000, rms=0.413 (0.208%), neg=0, invalid=96777
- iter 0, gcam->neg = 2
- after 26 iterations, nbhd size=4, neg = 0
- 0734: dt=4.800000, rms=0.413 (0.020%), neg=0, invalid=96777
- 0735: dt=4.800000, rms=0.412 (0.041%), neg=0, invalid=96777
- 0736: dt=4.800000, rms=0.412 (0.061%), neg=0, invalid=96777
- iter 0, gcam->neg = 2
- after 5 iterations, nbhd size=1, neg = 0
- 0737: dt=4.800000, rms=0.412 (0.077%), neg=0, invalid=96777
- 0738: dt=4.800000, rms=0.411 (0.087%), neg=0, invalid=96777
- iter 0, gcam->neg = 3
- after 14 iterations, nbhd size=2, neg = 0
- 0739: dt=4.800000, rms=0.411 (-0.002%), neg=0, invalid=96777
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.413, neg=0, invalid=96777
- 0740: dt=0.001688, rms=0.413 (0.000%), neg=0, invalid=96777
- iter 0, gcam->neg = 44
- after 37 iterations, nbhd size=4, neg = 0
- 0741: dt=3.105882, rms=0.412 (0.207%), neg=0, invalid=96777
- 0742: dt=0.011248, rms=0.412 (0.000%), neg=0, invalid=96777
- 0743: dt=0.011248, rms=0.412 (0.001%), neg=0, invalid=96777
- 0744: dt=0.011248, rms=0.412 (0.002%), neg=0, invalid=96777
- 0745: dt=0.011248, rms=0.412 (0.002%), neg=0, invalid=96777
- 0746: dt=0.011248, rms=0.412 (0.003%), neg=0, invalid=96777
- 0747: dt=0.011248, rms=0.412 (0.004%), neg=0, invalid=96777
- 0748: dt=0.011248, rms=0.412 (0.004%), neg=0, invalid=96777
- 0749: dt=0.011248, rms=0.412 (0.005%), neg=0, invalid=96777
- 0750: dt=0.011248, rms=0.412 (0.005%), neg=0, invalid=96777
- 0751: dt=0.011248, rms=0.412 (0.006%), neg=0, invalid=96777
- 0752: dt=0.011248, rms=0.412 (0.006%), neg=0, invalid=96777
- 0753: dt=0.011248, rms=0.412 (0.007%), neg=0, invalid=96777
- 0754: dt=0.011248, rms=0.412 (0.007%), neg=0, invalid=96777
- 0755: dt=0.011248, rms=0.412 (0.007%), neg=0, invalid=96777
- 0756: dt=0.011248, rms=0.412 (0.007%), neg=0, invalid=96777
- 0757: dt=0.011248, rms=0.412 (0.008%), neg=0, invalid=96777
- 0758: dt=0.011248, rms=0.412 (0.008%), neg=0, invalid=96777
- 0759: dt=0.011248, rms=0.412 (0.008%), neg=0, invalid=96777
- 0760: dt=0.011248, rms=0.412 (0.008%), neg=0, invalid=96777
- 0761: dt=0.011248, rms=0.412 (0.008%), neg=0, invalid=96777
- 0762: dt=0.011248, rms=0.412 (0.008%), neg=0, invalid=96777
- 0763: dt=0.011248, rms=0.412 (0.008%), neg=0, invalid=96777
- 0764: dt=0.011248, rms=0.412 (0.008%), neg=0, invalid=96777
- 0765: dt=0.011248, rms=0.412 (0.008%), neg=0, invalid=96777
- 0766: dt=0.011248, rms=0.412 (0.008%), neg=0, invalid=96777
- 0767: dt=0.011248, rms=0.412 (0.008%), neg=0, invalid=96777
- 0768: dt=0.011248, rms=0.411 (0.008%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.411, neg=0, invalid=96777
- iter 0, gcam->neg = 103
- after 200 iterations, nbhd size=4, neg = 4
- starting rms=0.005, neg=4, removing folds in lattice....
- iter 1, dt=0.000047: new neg 0, old_neg 4, delta 4, rms=0.003 (45.413%)
- 0769: dt=9.216000, rms=0.409 (0.517%), neg=0, invalid=96777
- 0770: dt=0.045000, rms=0.409 (0.001%), neg=0, invalid=96777
- 0771: dt=0.045000, rms=0.409 (0.002%), neg=0, invalid=96777
- 0772: dt=0.045000, rms=0.409 (0.004%), neg=0, invalid=96777
- 0773: dt=0.045000, rms=0.409 (0.006%), neg=0, invalid=96777
- 0774: dt=0.045000, rms=0.409 (0.008%), neg=0, invalid=96777
- 0775: dt=0.045000, rms=0.409 (0.010%), neg=0, invalid=96777
- 0776: dt=0.045000, rms=0.409 (0.012%), neg=0, invalid=96777
- 0777: dt=0.045000, rms=0.409 (0.013%), neg=0, invalid=96777
- 0778: dt=0.045000, rms=0.409 (0.015%), neg=0, invalid=96777
- 0779: dt=0.045000, rms=0.409 (0.016%), neg=0, invalid=96777
- 0780: dt=0.045000, rms=0.409 (0.017%), neg=0, invalid=96777
- 0781: dt=0.045000, rms=0.409 (0.018%), neg=0, invalid=96777
- 0782: dt=0.045000, rms=0.409 (0.018%), neg=0, invalid=96777
- 0783: dt=0.045000, rms=0.409 (0.018%), neg=0, invalid=96777
- 0784: dt=0.045000, rms=0.409 (0.018%), neg=0, invalid=96777
- 0785: dt=0.045000, rms=0.409 (0.019%), neg=0, invalid=96777
- 0786: dt=0.045000, rms=0.408 (0.019%), neg=0, invalid=96777
- 0787: dt=0.045000, rms=0.408 (0.019%), neg=0, invalid=96777
- 0788: dt=0.045000, rms=0.408 (0.019%), neg=0, invalid=96777
- 0789: dt=0.045000, rms=0.408 (0.019%), neg=0, invalid=96777
- 0790: dt=0.045000, rms=0.408 (0.019%), neg=0, invalid=96777
- iter 0, gcam->neg = 78
- after 200 iterations, nbhd size=4, neg = 2
- starting rms=0.003, neg=2, removing folds in lattice....
- iter 1, dt=0.000039: new neg 0, old_neg 2, delta 2, rms=0.003 (25.772%)
- 0791: dt=9.072626, rms=0.408 (0.160%), neg=0, invalid=96777
- 0792: dt=0.003938, rms=0.408 (0.000%), neg=0, invalid=96777
- setting smoothness coefficient to 1.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.411, neg=0, invalid=96777
- 0793: dt=0.000000, rms=0.411 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.411, neg=0, invalid=96777
- 0794: dt=0.000000, rms=0.411 (0.000%), neg=0, invalid=96777
- iter 0, gcam->neg = 11
- after 200 iterations, nbhd size=1, neg = 2
- starting rms=0.004, neg=2, removing folds in lattice....
- iter 1, dt=0.000611: new neg 0, old_neg 2, delta 2, rms=0.002 (58.131%)
- 0795: dt=0.100000, rms=0.411 (-0.086%), 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=0.405, neg=0, invalid=96777
- iter 0, gcam->neg = 421
- after 31 iterations, nbhd size=3, neg = 0
- 0796: dt=0.506734, rms=0.395 (2.419%), neg=0, invalid=96777
- 0797: dt=0.000027, rms=0.395 (0.002%), neg=0, invalid=96777
- 0798: dt=0.000027, rms=0.395 (0.000%), neg=0, invalid=96777
- 0799: dt=0.000027, rms=0.395 (0.000%), neg=0, invalid=96777
- 0800: dt=0.000027, rms=0.395 (0.000%), neg=0, invalid=96777
- 0801: dt=0.000250, rms=0.395 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.395, neg=0, invalid=96777
- iter 0, gcam->neg = 17
- after 7 iterations, nbhd size=1, neg = 0
- 0802: dt=0.024000, rms=0.395 (0.053%), neg=0, invalid=96777
- 0803: dt=0.000060, rms=0.395 (0.000%), neg=0, invalid=96777
- 0804: dt=0.000060, rms=0.395 (0.000%), neg=0, invalid=96777
- 0805: dt=0.000060, rms=0.395 (0.000%), neg=0, invalid=96777
- 0806: dt=0.000060, rms=0.395 (0.001%), neg=0, invalid=96777
- 0807: dt=0.000060, rms=0.395 (0.001%), neg=0, invalid=96777
- 0808: dt=0.000060, rms=0.395 (0.001%), neg=0, invalid=96777
- 0809: dt=0.000060, rms=0.395 (0.001%), neg=0, invalid=96777
- 0810: dt=0.000060, rms=0.395 (0.001%), neg=0, invalid=96777
- 0811: dt=0.000060, rms=0.395 (0.001%), neg=0, invalid=96777
- 0812: dt=0.000060, rms=0.395 (0.001%), neg=0, invalid=96777
- 0813: dt=0.000060, rms=0.395 (0.001%), neg=0, invalid=96777
- 0814: dt=0.000060, rms=0.395 (0.001%), neg=0, invalid=96777
- 0815: dt=0.000060, rms=0.395 (0.001%), neg=0, invalid=96777
- 0816: dt=0.000060, rms=0.395 (0.001%), neg=0, invalid=96777
- 0817: dt=0.000060, rms=0.395 (0.001%), neg=0, invalid=96777
- 0818: dt=0.000060, rms=0.395 (0.001%), neg=0, invalid=96777
- 0819: dt=0.000060, rms=0.395 (0.001%), neg=0, invalid=96777
- 0820: dt=0.000060, rms=0.395 (0.001%), neg=0, invalid=96777
- 0821: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777
- 0822: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777
- 0823: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777
- 0824: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777
- 0825: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777
- 0826: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777
- 0827: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777
- 0828: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777
- 0829: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777
- 0830: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777
- 0831: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777
- 0832: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777
- 0833: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777
- 0834: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777
- 0835: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777
- 0836: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777
- 0837: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777
- 0838: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777
- 0839: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777
- 0840: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777
- 0841: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777
- 0842: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777
- 0843: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777
- 0844: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777
- 0845: dt=0.000060, rms=0.395 (0.002%), neg=0, invalid=96777
- writing output transformation to transforms/talairach.m3z...
- GCAMwrite
- registration took 4 hours, 38 minutes and 37 seconds.
- #--------------------------------------
- #@# CA Reg Inv Thu Aug 8 16:51:07 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri
- mri_ca_register -invert-and-save transforms/talairach.m3z
- Loading, Inverting, Saving, Exiting ...
- Reading transforms/talairach.m3z
- Inverting GCAM
- Saving inverse
- #--------------------------------------
- #@# Remove Neck Thu Aug 8 16:52:34 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...
- 11240145 nonbrain voxels erased
- writing output to nu_noneck.mgz...
- nonbrain removal took 1 minutes and 25 seconds.
- #--------------------------------------
- #@# SkullLTA Thu Aug 8 16:54:00 CEST 2013
- mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta
- ======= NUMBER OF OPENMP THREADS = 1 =======
- aligning to atlas containing skull, setting unknown_nbr_spacing = 5
- using previously computed transform transforms/talairach.lta
- reading 1 input volumes...
- logging results to talairach_with_skull_2.log
- reading '/opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca'...
- average std = 23.1 using min determinant for regularization = 53.4
- 0 singular and 5702 ill-conditioned covariance matrices regularized
- reading 'nu_noneck.mgz'...
- freeing gibbs priors...done.
- bounding unknown intensity as < 20.2 or > 943.7
- total sample mean = 92.0 (1443 zeros)
- ************************************************
- spacing=8, using 3481 sample points, tol=1.00e-05...
- ************************************************
- register_mri: find_optimal_transform
- find_optimal_transform: nsamples 3481, passno 0, spacing 8
- resetting wm mean[0]: 117 --> 126
- resetting gm mean[0]: 74 --> 74
- input volume #1 is the most T1-like
- using real data threshold=11.0
- skull bounding box = (55, 20, 16) --> (207, 204, 195)
- using (106, 81, 106) as brain centroid...
- mean wm in atlas = 126, using box (87,58,84) --> (124, 103,128) to find MRI wm
- before smoothing, mri peak at 109
- after smoothing, mri peak at 110, scaling input intensities by 1.145
- scaling channel 0 by 1.14545
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.2 (thresh=-4.2)
- 1.168 0.051 -0.020 -31.157;
- -0.035 1.106 0.358 -25.307;
- 0.070 -0.337 0.925 29.655;
- 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)
- 1.168 0.051 -0.020 -31.157;
- -0.035 1.106 0.358 -25.307;
- 0.070 -0.337 0.925 29.655;
- 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)
- 1.125 0.014 -0.028 -18.873;
- -0.001 1.105 0.290 -22.213;
- 0.071 -0.279 1.000 13.411;
- 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)
- 1.104 0.013 -0.028 -16.161;
- -0.003 1.134 0.262 -21.735;
- 0.070 -0.238 0.990 10.595;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.0625
- ****************************************
- Nine parameter search. iteration 4 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.107 0.006 -0.038 -14.701;
- 0.005 1.132 0.252 -21.601;
- 0.079 -0.228 0.989 8.610;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 5 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.107 0.006 -0.038 -14.701;
- 0.005 1.132 0.252 -21.601;
- 0.079 -0.228 0.989 8.610;
- 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
- 1.10678 0.00590 -0.03797 -14.70059;
- 0.00517 1.13224 0.25242 -21.60137;
- 0.07881 -0.22815 0.98872 8.60961;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 3481
- Quasinewton: input matrix
- 1.10678 0.00590 -0.03797 -14.70059;
- 0.00517 1.13224 0.25242 -21.60137;
- 0.07881 -0.22815 0.98872 8.60961;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 007: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 1.107 0.006 -0.038 -14.701;
- 0.005 1.132 0.252 -21.601;
- 0.079 -0.228 0.989 8.610;
- 0.000 0.000 0.000 1.000;
- pass 1, spacing 8: log(p) = -4.0 (old=-4.2)
- transform before final EM align:
- 1.107 0.006 -0.038 -14.701;
- 0.005 1.132 0.252 -21.601;
- 0.079 -0.228 0.989 8.610;
- 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
- 1.10678 0.00590 -0.03797 -14.70059;
- 0.00517 1.13224 0.25242 -21.60137;
- 0.07881 -0.22815 0.98872 8.60961;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 382743
- Quasinewton: input matrix
- 1.10678 0.00590 -0.03797 -14.70059;
- 0.00517 1.13224 0.25242 -21.60137;
- 0.07881 -0.22815 0.98872 8.60961;
- 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: 009: -log(p) = 4.4 tol 0.000000
- final transform:
- 1.107 0.006 -0.038 -14.701;
- 0.005 1.132 0.252 -21.601;
- 0.079 -0.228 0.989 8.610;
- 0.000 0.000 0.000 1.000;
- writing output transformation to transforms/talairach_with_skull_2.lta...
- registration took 29 minutes and 29 seconds.
- #--------------------------------------
- #@# SubCort Seg Thu Aug 8 17:23:29 CEST 2013
- mri_ca_label -align norm.mgz transforms/talairach.m3z /opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz
- sysname Linux
- hostname snake6
- machine x86_64
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 = 0.12812 ( 7)
- Left_Lateral_Ventricle (4): linear fit = 0.25 x + 0.0 (3501 voxels, overlap=0.007)
- Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (3501 voxels, peak = 7), gca=10.8
- gca peak = 0.14982 (20)
- mri peak = 0.12164 ( 7)
- Right_Lateral_Ventricle (43): linear fit = 0.31 x + 0.0 (3208 voxels, overlap=0.008)
- Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (3208 voxels, peak = 6), gca=8.0
- gca peak = 0.28003 (97)
- mri peak = 0.09887 (92)
- Right_Pallidum (52): linear fit = 0.94 x + 0.0 (123 voxels, overlap=0.826)
- Right_Pallidum (52): linear fit = 0.94 x + 0.0 (123 voxels, peak = 91), gca=90.7
- gca peak = 0.18160 (96)
- mri peak = 0.08158 (92)
- Left_Pallidum (13): linear fit = 0.94 x + 0.0 (379 voxels, overlap=0.566)
- Left_Pallidum (13): linear fit = 0.94 x + 0.0 (379 voxels, peak = 91), gca=90.7
- gca peak = 0.27536 (62)
- mri peak = 0.09023 (51)
- Right_Hippocampus (53): linear fit = 0.82 x + 0.0 (528 voxels, overlap=0.182)
- Right_Hippocampus (53): linear fit = 0.82 x + 0.0 (528 voxels, peak = 51), gca=51.1
- gca peak = 0.32745 (63)
- mri peak = 0.10369 (58)
- Left_Hippocampus (17): linear fit = 0.90 x + 0.0 (498 voxels, overlap=0.606)
- Left_Hippocampus (17): linear fit = 0.90 x + 0.0 (498 voxels, peak = 57), gca=57.0
- gca peak = 0.08597 (105)
- mri peak = 0.08517 (106)
- Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (27442 voxels, overlap=0.743)
- Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (27442 voxels, peak = 107), gca=106.6
- gca peak = 0.09209 (106)
- mri peak = 0.08847 (108)
- Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (28941 voxels, overlap=0.613)
- Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (28941 voxels, peak = 109), gca=108.6
- gca peak = 0.07826 (63)
- mri peak = 0.06440 (51)
- Left_Cerebral_Cortex (3): linear fit = 0.82 x + 0.0 (11820 voxels, overlap=0.307)
- Left_Cerebral_Cortex (3): linear fit = 0.82 x + 0.0 (11820 voxels, peak = 52), gca=52.0
- gca peak = 0.08598 (64)
- mri peak = 0.06742 (51)
- Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (9630 voxels, overlap=0.266)
- Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (9630 voxels, peak = 53), gca=52.8
- gca peak = 0.24164 (71)
- mri peak = 0.10762 (66)
- Right_Caudate (50): linear fit = 0.90 x + 0.0 (332 voxels, overlap=0.181)
- Right_Caudate (50): linear fit = 0.90 x + 0.0 (332 voxels, peak = 64), gca=64.3
- gca peak = 0.18227 (75)
- mri peak = 0.08796 (68)
- Left_Caudate (11): linear fit = 0.87 x + 0.0 (689 voxels, overlap=0.452)
- Left_Caudate (11): linear fit = 0.87 x + 0.0 (689 voxels, peak = 65), gca=64.9
- gca peak = 0.10629 (62)
- mri peak = 0.04888 (56)
- Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (6222 voxels, overlap=0.995)
- Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (6222 voxels, peak = 58), gca=58.0
- gca peak = 0.11668 (59)
- mri peak = 0.05288 (56)
- Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (7596 voxels, overlap=0.987)
- Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (7596 voxels, peak = 57), gca=56.9
- gca peak = 0.17849 (88)
- mri peak = 0.08781 (94)
- Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (5856 voxels, overlap=0.921)
- Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (5856 voxels, peak = 92), gca=92.0
- gca peak = 0.16819 (86)
- mri peak = 0.09458 (93)
- Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (5069 voxels, overlap=0.973)
- Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (5069 voxels, peak = 90), gca=89.9
- gca peak = 0.41688 (64)
- mri peak = 0.11359 (61)
- Left_Amygdala (18): linear fit = 0.94 x + 0.0 (244 voxels, overlap=1.037)
- Left_Amygdala (18): linear fit = 0.94 x + 0.0 (244 voxels, peak = 60), gca=59.8
- gca peak = 0.42394 (62)
- mri peak = 0.10630 (58)
- Right_Amygdala (54): linear fit = 0.92 x + 0.0 (258 voxels, overlap=0.617)
- Right_Amygdala (54): linear fit = 0.92 x + 0.0 (258 voxels, peak = 57), gca=56.7
- gca peak = 0.10041 (96)
- mri peak = 0.07153 (90)
- Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (3048 voxels, overlap=0.814)
- Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (3048 voxels, peak = 92), gca=91.7
- gca peak = 0.13978 (88)
- mri peak = 0.06806 (89)
- Right_Thalamus_Proper (49): linear fit = 0.95 x + 0.0 (2683 voxels, overlap=0.920)
- Right_Thalamus_Proper (49): linear fit = 0.95 x + 0.0 (2683 voxels, peak = 84), gca=84.0
- gca peak = 0.08514 (81)
- mri peak = 0.05583 (80)
- Left_Putamen (12): linear fit = 0.90 x + 0.0 (2027 voxels, overlap=0.673)
- Left_Putamen (12): linear fit = 0.90 x + 0.0 (2027 voxels, peak = 73), gca=73.3
- gca peak = 0.09624 (82)
- mri peak = 0.05650 (72)
- Right_Putamen (51): linear fit = 0.93 x + 0.0 (2538 voxels, overlap=0.687)
- Right_Putamen (51): linear fit = 0.93 x + 0.0 (2538 voxels, peak = 76), gca=75.8
- gca peak = 0.07543 (88)
- mri peak = 0.06768 (88)
- Brain_Stem (16): linear fit = 1.03 x + 0.0 (10689 voxels, overlap=0.765)
- Brain_Stem (16): linear fit = 1.03 x + 0.0 (10689 voxels, peak = 91), gca=91.1
- gca peak = 0.12757 (95)
- mri peak = 0.06738 (93)
- Right_VentralDC (60): linear fit = 1.01 x + 0.0 (878 voxels, overlap=0.822)
- Right_VentralDC (60): linear fit = 1.01 x + 0.0 (878 voxels, peak = 96), gca=96.4
- gca peak = 0.17004 (92)
- mri peak = 0.06801 (96)
- Left_VentralDC (28): linear fit = 1.03 x + 0.0 (987 voxels, overlap=0.843)
- Left_VentralDC (28): linear fit = 1.03 x + 0.0 (987 voxels, peak = 95), gca=95.2
- gca peak = 0.21361 (36)
- mri peak = 0.17391 (11)
- gca peak = 0.26069 (23)
- mri peak = 0.17595 ( 8)
- Fourth_Ventricle (15): linear fit = 0.26 x + 0.0 (127 voxels, overlap=0.024)
- Fourth_Ventricle (15): linear fit = 0.26 x + 0.0 (127 voxels, peak = 6), gca=6.1
- gca peak Unknown = 0.94427 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.31795 (35)
- gca peak Third_Ventricle = 0.21361 (36)
- gca peak Fourth_Ventricle = 0.26069 (23)
- gca peak CSF = 0.14367 (38)
- gca peak Left_Accumbens_area = 0.57033 (70)
- gca peak Left_undetermined = 1.00000 (35)
- gca peak Left_vessel = 0.65201 (62)
- gca peak Left_choroid_plexus = 0.09084 (48)
- gca peak Right_Inf_Lat_Vent = 0.31129 (32)
- gca peak Right_Accumbens_area = 0.30219 (72)
- gca peak Right_vessel = 0.83418 (60)
- gca peak Right_choroid_plexus = 0.10189 (48)
- gca peak Fifth_Ventricle = 0.72939 (42)
- gca peak WM_hypointensities = 0.14821 (82)
- gca peak non_WM_hypointensities = 0.10354 (53)
- gca peak Optic_Chiasm = 0.34849 (76)
- not using caudate to estimate GM means
- estimating mean gm scale to be 0.87 x + 0.0
- estimating mean wm scale to be 1.02 x + 0.0
- estimating mean csf scale to be 0.40 x + 0.0
- saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
- renormalizing by structure alignment....
- renormalizing input #0
- gca peak = 0.31600 (11)
- mri peak = 0.12812 ( 7)
- Left_Lateral_Ventricle (4): linear fit = 0.70 x + 0.0 (3501 voxels, overlap=0.942)
- Left_Lateral_Ventricle (4): linear fit = 0.70 x + 0.0 (3501 voxels, peak = 8), gca=7.8
- gca peak = 0.29325 ( 9)
- mri peak = 0.12164 ( 7)
- Right_Lateral_Ventricle (43): linear fit = 0.76 x + 0.0 (3208 voxels, overlap=0.969)
- Right_Lateral_Ventricle (43): linear fit = 0.76 x + 0.0 (3208 voxels, peak = 7), gca=6.9
- gca peak = 0.30470 (91)
- mri peak = 0.09887 (92)
- Right_Pallidum (52): linear fit = 1.00 x + 0.0 (123 voxels, overlap=1.010)
- Right_Pallidum (52): linear fit = 1.00 x + 0.0 (123 voxels, peak = 91), gca=90.5
- gca peak = 0.18129 (91)
- mri peak = 0.08158 (92)
- Left_Pallidum (13): linear fit = 0.99 x + 0.0 (379 voxels, overlap=1.007)
- Left_Pallidum (13): linear fit = 0.99 x + 0.0 (379 voxels, peak = 90), gca=89.6
- gca peak = 0.32446 (51)
- mri peak = 0.09023 (51)
- Right_Hippocampus (53): linear fit = 0.98 x + 0.0 (528 voxels, overlap=1.002)
- Right_Hippocampus (53): linear fit = 0.98 x + 0.0 (528 voxels, peak = 50), gca=49.7
- gca peak = 0.33359 (57)
- mri peak = 0.10369 (58)
- Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (498 voxels, overlap=1.007)
- Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (498 voxels, peak = 57), gca=57.0
- gca peak = 0.08541 (107)
- mri peak = 0.08517 (106)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (27442 voxels, overlap=0.780)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (27442 voxels, peak = 106), gca=106.5
- gca peak = 0.08551 (108)
- mri peak = 0.08847 (108)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (28941 voxels, overlap=0.708)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (28941 voxels, peak = 108), gca=108.0
- gca peak = 0.09514 (52)
- mri peak = 0.06440 (51)
- Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (11820 voxels, overlap=0.985)
- Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (11820 voxels, peak = 53), gca=53.3
- gca peak = 0.10560 (53)
- mri peak = 0.06742 (51)
- Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (9630 voxels, overlap=0.987)
- Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (9630 voxels, peak = 52), gca=52.2
- gca peak = 0.26783 (64)
- mri peak = 0.10762 (66)
- Right_Caudate (50): linear fit = 0.99 x + 0.0 (332 voxels, overlap=0.993)
- Right_Caudate (50): linear fit = 0.99 x + 0.0 (332 voxels, peak = 63), gca=63.0
- gca peak = 0.17966 (65)
- mri peak = 0.08796 (68)
- Left_Caudate (11): linear fit = 1.01 x + 0.0 (689 voxels, overlap=0.999)
- Left_Caudate (11): linear fit = 1.01 x + 0.0 (689 voxels, peak = 66), gca=66.0
- gca peak = 0.11193 (57)
- mri peak = 0.04888 (56)
- Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (6222 voxels, overlap=0.994)
- Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (6222 voxels, peak = 58), gca=58.4
- gca peak = 0.12335 (58)
- mri peak = 0.05288 (56)
- Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (7596 voxels, overlap=1.000)
- Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (7596 voxels, peak = 56), gca=56.0
- gca peak = 0.17369 (92)
- mri peak = 0.08781 (94)
- Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5856 voxels, overlap=0.994)
- Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5856 voxels, peak = 92), gca=91.5
- gca peak = 0.15955 (90)
- mri peak = 0.09458 (93)
- Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5069 voxels, overlap=1.000)
- Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5069 voxels, peak = 90), gca=89.6
- gca peak = 0.34609 (59)
- mri peak = 0.11359 (61)
- Left_Amygdala (18): linear fit = 1.02 x + 0.0 (244 voxels, overlap=1.012)
- Left_Amygdala (18): linear fit = 1.02 x + 0.0 (244 voxels, peak = 60), gca=60.5
- gca peak = 0.50707 (57)
- mri peak = 0.10630 (58)
- Right_Amygdala (54): linear fit = 1.00 x + 0.0 (258 voxels, overlap=1.023)
- Right_Amygdala (54): linear fit = 1.00 x + 0.0 (258 voxels, peak = 57), gca=57.0
- gca peak = 0.10969 (90)
- mri peak = 0.07153 (90)
- Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3048 voxels, overlap=0.997)
- Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3048 voxels, peak = 90), gca=89.6
- gca peak = 0.14487 (84)
- mri peak = 0.06806 (89)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (2683 voxels, overlap=1.000)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (2683 voxels, peak = 84), gca=83.6
- gca peak = 0.09690 (79)
- mri peak = 0.05583 (80)
- Left_Putamen (12): linear fit = 1.00 x + 0.0 (2027 voxels, overlap=0.997)
- Left_Putamen (12): linear fit = 1.00 x + 0.0 (2027 voxels, peak = 79), gca=79.0
- gca peak = 0.12049 (70)
- mri peak = 0.05650 (72)
- Right_Putamen (51): linear fit = 1.00 x + 0.0 (2538 voxels, overlap=1.002)
- Right_Putamen (51): linear fit = 1.00 x + 0.0 (2538 voxels, peak = 70), gca=69.7
- gca peak = 0.07047 (88)
- mri peak = 0.06768 (88)
- Brain_Stem (16): linear fit = 1.00 x + 0.0 (10689 voxels, overlap=0.836)
- Brain_Stem (16): linear fit = 1.00 x + 0.0 (10689 voxels, peak = 88), gca=87.6
- gca peak = 0.14090 (96)
- mri peak = 0.06738 (93)
- Right_VentralDC (60): linear fit = 1.00 x + 0.0 (878 voxels, overlap=0.866)
- Right_VentralDC (60): linear fit = 1.00 x + 0.0 (878 voxels, peak = 96), gca=95.5
- gca peak = 0.13753 (96)
- mri peak = 0.06801 (96)
- Left_VentralDC (28): linear fit = 1.00 x + 0.0 (987 voxels, overlap=0.914)
- Left_VentralDC (28): linear fit = 1.00 x + 0.0 (987 voxels, peak = 96), gca=96.5
- gca peak = 0.35640 (14)
- mri peak = 0.17391 (11)
- gca peak = 0.33827 ( 9)
- mri peak = 0.17595 ( 8)
- Fourth_Ventricle (15): linear fit = 0.68 x + 0.0 (127 voxels, overlap=0.932)
- Fourth_Ventricle (15): linear fit = 0.68 x + 0.0 (127 voxels, peak = 6), gca=6.1
- gca peak Unknown = 0.94427 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.27695 (32)
- gca peak Third_Ventricle = 0.35640 (14)
- gca peak CSF = 0.30128 (18)
- gca peak Left_Accumbens_area = 0.44858 (60)
- gca peak Left_undetermined = 1.00000 (35)
- gca peak Left_vessel = 0.42679 (62)
- gca peak Left_choroid_plexus = 0.09164 (48)
- gca peak Right_Inf_Lat_Vent = 0.31192 (26)
- gca peak Right_Accumbens_area = 0.38912 (65)
- gca peak Right_vessel = 0.58264 (60)
- gca peak Right_choroid_plexus = 0.10280 (48)
- gca peak Fifth_Ventricle = 0.45329 (19)
- gca peak WM_hypointensities = 0.17302 (83)
- gca peak non_WM_hypointensities = 0.11232 (54)
- gca peak Optic_Chiasm = 0.34849 (76)
- not using caudate to estimate GM means
- estimating mean gm scale to be 1.00 x + 0.0
- estimating mean wm scale to be 1.00 x + 0.0
- estimating mean csf scale to be 0.71 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
- 11984 gm and wm labels changed (%13 to gray, %87 to white out of all changed labels)
- 311 hippocampal voxels changed.
- 7 amygdala voxels changed.
- pass 1: 91688 changed. image ll: -2.211, PF=1.000
- pass 2: 16871 changed. image ll: -2.209, PF=1.000
- pass 3: 6520 changed.
- pass 4: 3025 changed.
- writing labeled volume to aseg.auto_noCCseg.mgz...
- auto-labeling took 19 minutes and 14 seconds.
- mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/cc_up.lta sub009
- 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/sub009/mri/transforms/cc_up.lta
- reading aseg from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/aseg.auto_noCCseg.mgz
- reading norm from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/norm.mgz
- 22980 voxels in left wm, 35154 in right wm, xrange [127, 135]
- searching rotation angles z=[-9 5], y=[-9 5]
-
searching scale 1 Z rot -9.0
searching scale 1 Z rot -8.7
searching scale 1 Z rot -8.5
searching scale 1 Z rot -8.2
searching scale 1 Z rot -8.0
searching scale 1 Z rot -7.7
searching scale 1 Z rot -7.5
searching scale 1 Z rot -7.2
searching scale 1 Z rot -7.0
searching scale 1 Z rot -6.7
searching scale 1 Z rot -6.5
searching scale 1 Z rot -6.2
searching scale 1 Z rot -6.0
searching scale 1 Z rot -5.7
searching scale 1 Z rot -5.5
searching scale 1 Z rot -5.2
searching scale 1 Z rot -5.0
searching scale 1 Z rot -4.7
searching scale 1 Z rot -4.5
searching scale 1 Z rot -4.2
searching scale 1 Z rot -4.0
searching scale 1 Z rot -3.7
searching scale 1 Z rot -3.5
searching scale 1 Z rot -3.2
searching scale 1 Z rot -3.0
searching scale 1 Z rot -2.7
searching scale 1 Z rot -2.5
searching scale 1 Z rot -2.2
searching scale 1 Z rot -2.0
searching scale 1 Z rot -1.7
searching scale 1 Z rot -1.5
searching scale 1 Z rot -1.2
searching scale 1 Z rot -1.0
searching scale 1 Z rot -0.7
searching scale 1 Z rot -0.5
searching scale 1 Z rot -0.2
searching scale 1 Z rot 0.0
searching scale 1 Z rot 0.3
searching scale 1 Z rot 0.5
searching scale 1 Z rot 0.8
searching scale 1 Z rot 1.0
searching scale 1 Z rot 1.3
searching scale 1 Z rot 1.5
searching scale 1 Z rot 1.8
searching scale 1 Z rot 2.0
searching scale 1 Z rot 2.3
searching scale 1 Z rot 2.5
searching scale 1 Z rot 2.8
searching scale 1 Z rot 3.0
searching scale 1 Z rot 3.3
searching scale 1 Z rot 3.5
searching scale 1 Z rot 3.8
searching scale 1 Z rot 4.0
searching scale 1 Z rot 4.3
searching scale 1 Z rot 4.5
searching scale 1 Z rot 4.8 global minimum found at slice 131.0, rotations (-1.91, -2.00)
- final transformation (x=131.0, yr=-1.915, zr=-1.998):
- 0.999 0.035 -0.033 -1.928;
- -0.035 0.999 0.001 53.484;
- 0.033 0.000 0.999 13.685;
- 0.000 0.000 0.000 1.000;
- updating x range to be [125, 131] in xformed coordinates
- best xformed slice 128
- cc center is found at 128 154 110
- eigenvectors:
- -0.000 -0.002 1.000;
- -0.223 -0.975 -0.002;
- 0.975 -0.223 -0.000;
- error in mid anterior detected - correcting...
- error in mid anterior detected - correcting...
- error in mid anterior detected - correcting...
- writing aseg with callosum to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/aseg.auto.mgz...
- corpus callosum matter segmentation took 0.8 minutes
- #--------------------------------------
- #@# Merge ASeg Thu Aug 8 17:43:29 CEST 2013
- cp aseg.auto.mgz aseg.mgz
- #--------------------------------------------
- #@# Intensity Normalization2 Thu Aug 8 17:43:29 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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...
- 2439 control points removed
- Building bias image
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 0...
- Smoothing with sigma 8
- Applying bias correction
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Iterating 2 times
- ---------------------------------
- 3d normalization pass 1 of 2
- white matter peak found at 111
- white matter peak found at 109
- gm peak at 56 (56), valley at 30 (30)
- csf peak at 28, setting threshold to 46
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- ---------------------------------
- 3d normalization pass 2 of 2
- white matter peak found at 111
- white matter peak found at 110
- gm peak at 56 (56), valley at 30 (30)
- 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 19 seconds.
- #--------------------------------------------
- #@# Mask BFS Thu Aug 8 17:47:50 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri
- mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
- threshold mask volume at 5
- DoAbs = 0
- Found 1589890 voxels in mask (pct= 9.48)
- Writing masked volume to brain.finalsurfs.mgz...done.
- #--------------------------------------------
- #@# WM Segmentation Thu Aug 8 17:47:52 CEST 2013
- mri_segment brain.mgz wm.seg.mgz
- doing initial intensity segmentation...
- using local statistics to label ambiguous voxels...
- computing class statistics for intensity windows...
- WM (108.0): 107.5 +- 4.6 [80.0 --> 125.0]
- GM (66.0) : 65.5 +- 9.6 [30.0 --> 96.0]
- setting bottom of white matter range to 75.0
- setting top of gray matter range to 84.6
- 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...
- 7605 sparsely connected voxels removed...
- thickening thin strands....
- 20 segments, 8722 filled
- 751 bright non-wm voxels segmented.
- 4251 diagonally connected voxels added...
- white matter segmentation took 1.8 minutes
- writing output to wm.seg.mgz...
- mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz
- preserving editing changes in input volume...
- auto filling took 0.72 minutes
- reading wm segmentation from wm.seg.mgz...
- 195 voxels added to wm to prevent paths from MTL structures to cortex
- 1290 additional wm voxels added
- 0 additional wm voxels added
- SEG EDIT: 65476 voxels turned on, 47719 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+): 18 found - 18 modified | TOTAL: 18
- pass 2 (xy+): 0 found - 18 modified | TOTAL: 18
- pass 1 (xy-): 21 found - 21 modified | TOTAL: 39
- pass 2 (xy-): 0 found - 21 modified | TOTAL: 39
- pass 1 (yz+): 25 found - 25 modified | TOTAL: 64
- pass 2 (yz+): 0 found - 25 modified | TOTAL: 64
- pass 1 (yz-): 20 found - 20 modified | TOTAL: 84
- pass 2 (yz-): 0 found - 20 modified | TOTAL: 84
- pass 1 (xz+): 19 found - 19 modified | TOTAL: 103
- pass 2 (xz+): 0 found - 19 modified | TOTAL: 103
- pass 1 (xz-): 18 found - 18 modified | TOTAL: 121
- pass 2 (xz-): 0 found - 18 modified | TOTAL: 121
- Iteration Number : 1
- pass 1 (+++): 4 found - 4 modified | TOTAL: 4
- pass 2 (+++): 0 found - 4 modified | TOTAL: 4
- pass 1 (+++): 6 found - 6 modified | TOTAL: 10
- pass 2 (+++): 0 found - 6 modified | TOTAL: 10
- pass 1 (+++): 2 found - 2 modified | TOTAL: 12
- pass 2 (+++): 0 found - 2 modified | TOTAL: 12
- pass 1 (+++): 16 found - 16 modified | TOTAL: 28
- pass 2 (+++): 0 found - 16 modified | TOTAL: 28
- Iteration Number : 1
- pass 1 (++): 241 found - 241 modified | TOTAL: 241
- pass 2 (++): 0 found - 241 modified | TOTAL: 241
- pass 1 (+-): 226 found - 226 modified | TOTAL: 467
- pass 2 (+-): 0 found - 226 modified | TOTAL: 467
- pass 1 (--): 240 found - 240 modified | TOTAL: 707
- pass 2 (--): 0 found - 240 modified | TOTAL: 707
- pass 1 (-+): 210 found - 210 modified | TOTAL: 917
- pass 2 (-+): 0 found - 210 modified | TOTAL: 917
- Iteration Number : 2
- pass 1 (xy+): 6 found - 6 modified | TOTAL: 6
- pass 2 (xy+): 0 found - 6 modified | TOTAL: 6
- pass 1 (xy-): 2 found - 2 modified | TOTAL: 8
- pass 2 (xy-): 0 found - 2 modified | TOTAL: 8
- pass 1 (yz+): 2 found - 2 modified | TOTAL: 10
- pass 2 (yz+): 0 found - 2 modified | TOTAL: 10
- pass 1 (yz-): 2 found - 2 modified | TOTAL: 12
- pass 2 (yz-): 0 found - 2 modified | TOTAL: 12
- pass 1 (xz+): 4 found - 4 modified | TOTAL: 16
- pass 2 (xz+): 0 found - 4 modified | TOTAL: 16
- pass 1 (xz-): 4 found - 4 modified | TOTAL: 20
- pass 2 (xz-): 0 found - 4 modified | TOTAL: 20
- Iteration Number : 2
- pass 1 (+++): 2 found - 2 modified | TOTAL: 2
- pass 2 (+++): 0 found - 2 modified | TOTAL: 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 2
- Iteration Number : 2
- pass 1 (++): 1 found - 1 modified | TOTAL: 1
- pass 2 (++): 0 found - 1 modified | TOTAL: 1
- pass 1 (+-): 0 found - 0 modified | TOTAL: 1
- pass 1 (--): 0 found - 0 modified | TOTAL: 1
- pass 1 (-+): 1 found - 1 modified | TOTAL: 2
- pass 2 (-+): 0 found - 1 modified | TOTAL: 2
- Iteration Number : 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 = 1090 (out of 531379: 0.205127)
- binarizing input wm segmentation...
- Ambiguous edge configurations...
- mri_pretess done
- #--------------------------------------------
- #@# Fill Thu Aug 8 17:50:27 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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
- 1.086 0.047 -0.018 -20.209;
- -0.035 1.106 0.358 -25.307;
- 0.070 -0.337 0.925 29.655;
- 0.000 0.000 0.000 1.000;
- voxel to talairach voxel transform
- 1.086 0.047 -0.018 -20.209;
- -0.035 1.106 0.358 -25.307;
- 0.070 -0.337 0.925 29.655;
- 0.000 0.000 0.000 1.000;
- reading segmented volume aseg.auto_noCCseg.mgz...
- Looking for area (min, max) = (350, 1400)
- area[0] = 1112 (min = 350, max = 1400), aspect = 0.51 (min = 0.10, max = 0.75)
- no need to search
- using seed (125, 121, 151), TAL = (3.0, 23.0, 7.0)
- talairach voxel to voxel transform
- 0.918 -0.030 0.030 16.898;
- 0.046 0.807 -0.311 30.586;
- -0.053 0.297 0.965 -22.188;
- 0.000 0.000 0.000 1.000;
- segmentation indicates cc at (125, 121, 151) --> (3.0, 23.0, 7.0)
- done.
- writing output to filled.mgz...
- filling took 0.9 minutes
- talairach cc position changed to (3.00, 23.00, 7.00)
- Erasing brainstem...done.
- seed_search_size = 9, min_neighbors = 5
- search rh wm seed point around talairach space:(21.00, 23.00, 7.00) SRC: (115.93, 86.18, 153.82)
- search lh wm seed point around talairach space (-15.00, 23.00, 7.00), SRC: (148.97, 87.83, 151.92)
- 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 17:51:25 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts
- mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz
- Iteration Number : 1
- pass 1 (xy+): 4 found - 4 modified | TOTAL: 4
- pass 2 (xy+): 0 found - 4 modified | TOTAL: 4
- pass 1 (xy-): 1 found - 1 modified | TOTAL: 5
- pass 2 (xy-): 0 found - 1 modified | TOTAL: 5
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 5
- pass 1 (yz-): 1 found - 1 modified | TOTAL: 6
- pass 2 (yz-): 0 found - 1 modified | TOTAL: 6
- pass 1 (xz+): 2 found - 2 modified | TOTAL: 8
- pass 2 (xz+): 0 found - 2 modified | TOTAL: 8
- pass 1 (xz-): 1 found - 1 modified | TOTAL: 9
- pass 2 (xz-): 0 found - 1 modified | TOTAL: 9
- Iteration Number : 1
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 1
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 1 found - 1 modified | TOTAL: 1
- pass 2 (+-): 0 found - 1 modified | TOTAL: 1
- pass 1 (--): 2 found - 2 modified | TOTAL: 3
- pass 2 (--): 0 found - 2 modified | TOTAL: 3
- pass 1 (-+): 1 found - 1 modified | TOTAL: 4
- pass 2 (-+): 0 found - 1 modified | TOTAL: 4
- Iteration Number : 2
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Total Number of Modified Voxels = 13 (out of 255110: 0.005096)
- Ambiguous edge configurations...
- mri_pretess done
- mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix
- $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- slice 40: 1168 vertices, 1282 faces
- slice 50: 7596 vertices, 7910 faces
- slice 60: 17706 vertices, 18109 faces
- slice 70: 29558 vertices, 29921 faces
- slice 80: 41414 vertices, 41840 faces
- slice 90: 53057 vertices, 53438 faces
- slice 100: 65191 vertices, 65598 faces
- slice 110: 77122 vertices, 77499 faces
- slice 120: 88225 vertices, 88598 faces
- slice 130: 98943 vertices, 99314 faces
- slice 140: 109309 vertices, 109688 faces
- slice 150: 118462 vertices, 118769 faces
- slice 160: 126731 vertices, 127041 faces
- slice 170: 134510 vertices, 134788 faces
- slice 180: 140690 vertices, 140900 faces
- slice 190: 145394 vertices, 145564 faces
- slice 200: 147202 vertices, 147234 faces
- slice 210: 147202 vertices, 147234 faces
- slice 220: 147202 vertices, 147234 faces
- slice 230: 147202 vertices, 147234 faces
- slice 240: 147202 vertices, 147234 faces
- slice 250: 147202 vertices, 147234 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...
- 147202 voxel in cpt #1: X=-32 [v=147202,e=441702,f=294468] located at (-29.049103, -19.310961, 36.435368)
- For the whole surface: X=-32 [v=147202,e=441702,f=294468]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Smooth1 lh Thu Aug 8 17:51:32 CEST 2013
- mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 17:51:37 CEST 2013
- mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts
- avg radius = 47.5 mm, total surface area = 75597 mm^2
- writing inflated surface to ../surf/lh.inflated.nofix
- inflation took 0.6 minutes
- Not saving sulc
-
step 000: RMS=0.105 (target=0.015)
step 005: RMS=0.077 (target=0.015)
step 010: RMS=0.056 (target=0.015)
step 015: RMS=0.046 (target=0.015)
step 020: RMS=0.039 (target=0.015)
step 025: RMS=0.034 (target=0.015)
step 030: RMS=0.030 (target=0.015)
step 035: RMS=0.028 (target=0.015)
step 040: RMS=0.025 (target=0.015)
step 045: RMS=0.024 (target=0.015)
step 050: RMS=0.023 (target=0.015)
step 055: RMS=0.023 (target=0.015)
step 060: RMS=0.022 (target=0.015)
- inflation complete.
- Not saving sulc
- #--------------------------------------------
- #@# QSphere lh Thu Aug 8 17:52:11 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts
- mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix
- doing quick spherical unfolding.
- setting seed for random number genererator to 1234
- $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading original vertex positions...
- unfolding cortex into spherical form...
- surface projected - minimizing metric distortion...
- vertex spacing 0.94 +- 0.57 (0.00-->6.24) (max @ vno 60200 --> 61427)
- face area 0.02 +- 0.03 (-0.09-->0.68)
- scaling brain by 0.304...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=176.422, avgs=0
- 005/300: dt: 0.9000, rms radial error=176.162, avgs=0
- 010/300: dt: 0.9000, rms radial error=175.603, avgs=0
- 015/300: dt: 0.9000, rms radial error=174.875, avgs=0
- 020/300: dt: 0.9000, rms radial error=174.047, avgs=0
- 025/300: dt: 0.9000, rms radial error=173.161, avgs=0
- 030/300: dt: 0.9000, rms radial error=172.244, avgs=0
- 035/300: dt: 0.9000, rms radial error=171.311, avgs=0
- 040/300: dt: 0.9000, rms radial error=170.369, avgs=0
- 045/300: dt: 0.9000, rms radial error=169.426, avgs=0
- 050/300: dt: 0.9000, rms radial error=168.483, avgs=0
- 055/300: dt: 0.9000, rms radial error=167.542, avgs=0
- 060/300: dt: 0.9000, rms radial error=166.605, avgs=0
- 065/300: dt: 0.9000, rms radial error=165.673, avgs=0
- 070/300: dt: 0.9000, rms radial error=164.746, avgs=0
- 075/300: dt: 0.9000, rms radial error=163.823, avgs=0
- 080/300: dt: 0.9000, rms radial error=162.905, avgs=0
- 085/300: dt: 0.9000, rms radial error=161.992, avgs=0
- 090/300: dt: 0.9000, rms radial error=161.084, avgs=0
- 095/300: dt: 0.9000, rms radial error=160.181, avgs=0
- 100/300: dt: 0.9000, rms radial error=159.283, avgs=0
- 105/300: dt: 0.9000, rms radial error=158.389, avgs=0
- 110/300: dt: 0.9000, rms radial error=157.501, avgs=0
- 115/300: dt: 0.9000, rms radial error=156.617, avgs=0
- 120/300: dt: 0.9000, rms radial error=155.738, avgs=0
- 125/300: dt: 0.9000, rms radial error=154.864, avgs=0
- 130/300: dt: 0.9000, rms radial error=153.994, avgs=0
- 135/300: dt: 0.9000, rms radial error=153.129, avgs=0
- 140/300: dt: 0.9000, rms radial error=152.269, avgs=0
- 145/300: dt: 0.9000, rms radial error=151.413, avgs=0
- 150/300: dt: 0.9000, rms radial error=150.562, avgs=0
- 155/300: dt: 0.9000, rms radial error=149.716, avgs=0
- 160/300: dt: 0.9000, rms radial error=148.874, avgs=0
- 165/300: dt: 0.9000, rms radial error=148.036, avgs=0
- 170/300: dt: 0.9000, rms radial error=147.203, avgs=0
- 175/300: dt: 0.9000, rms radial error=146.375, avgs=0
- 180/300: dt: 0.9000, rms radial error=145.551, avgs=0
- 185/300: dt: 0.9000, rms radial error=144.732, avgs=0
- 190/300: dt: 0.9000, rms radial error=143.917, avgs=0
- 195/300: dt: 0.9000, rms radial error=143.107, avgs=0
- 200/300: dt: 0.9000, rms radial error=142.301, avgs=0
- 205/300: dt: 0.9000, rms radial error=141.500, avgs=0
- 210/300: dt: 0.9000, rms radial error=140.703, avgs=0
- 215/300: dt: 0.9000, rms radial error=139.910, avgs=0
- 220/300: dt: 0.9000, rms radial error=139.122, avgs=0
- 225/300: dt: 0.9000, rms radial error=138.338, avgs=0
- 230/300: dt: 0.9000, rms radial error=137.558, avgs=0
- 235/300: dt: 0.9000, rms radial error=136.783, avgs=0
- 240/300: dt: 0.9000, rms radial error=136.012, avgs=0
- 245/300: dt: 0.9000, rms radial error=135.246, avgs=0
- 250/300: dt: 0.9000, rms radial error=134.483, avgs=0
- 255/300: dt: 0.9000, rms radial error=133.725, avgs=0
- 260/300: dt: 0.9000, rms radial error=132.971, avgs=0
- 265/300: dt: 0.9000, rms radial error=132.222, avgs=0
- 270/300: dt: 0.9000, rms radial error=131.476, avgs=0
- 275/300: dt: 0.9000, rms radial error=130.735, avgs=0
- 280/300: dt: 0.9000, rms radial error=129.998, avgs=0
- 285/300: dt: 0.9000, rms radial error=129.265, avgs=0
- 290/300: dt: 0.9000, rms radial error=128.537, avgs=0
- 295/300: dt: 0.9000, rms radial error=127.812, avgs=0
- 300/300: dt: 0.9000, rms radial error=127.092, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 17467.02
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00011
- epoch 2 (K=40.0), pass 1, starting sse = 3038.68
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00005
- epoch 3 (K=160.0), pass 1, starting sse = 330.76
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.08/11 = 0.00711
- epoch 4 (K=640.0), pass 1, starting sse = 18.04
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.08/12 = 0.00686
- final writing spherical brain to ../surf/lh.qsphere.nofix
- spherical transformation took 0.08 hours
- distance error %100000.00
- #--------------------------------------------
- #@# Fix Topology lh Thu Aug 8 17:56:58 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/sub009/scripts
- mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub009 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=-32 (nv=147202, nf=294468, ne=441702, g=17)
- using quasi-homeomorphic spherical map to tessellate cortical surface...
- Correction of the Topology
- Finding true center and radius of Spherical Surface...done
- Surface centered at (0,0,0) with radius 100.0 in 9 iterations
- marking ambiguous vertices...
- 2257 ambiguous faces found in tessellation
- segmenting defects...
- 24 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- -merging segment 16 into 15
- 23 defects to be corrected
- 0 vertices coincident
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -9.8358 (-4.9179)
- -vertex loglikelihood: -6.7138 (-3.3569)
- -normal dot loglikelihood: -3.6666 (-3.6666)
- -quad curv loglikelihood: -6.0725 (-3.0363)
- Total Loglikelihood : -26.2887
- CORRECTING DEFECT 0 (vertices=33, convex hull=63)
- After retessellation of defect 0, euler #=-21 (145827,436937,291089) : difference with theory (-20) = 1
- CORRECTING DEFECT 1 (vertices=22, convex hull=75)
- After retessellation of defect 1, euler #=-20 (145835,436990,291135) : difference with theory (-19) = 1
- CORRECTING DEFECT 2 (vertices=28, convex hull=62)
- After retessellation of defect 2, euler #=-19 (145846,437047,291182) : difference with theory (-18) = 1
- CORRECTING DEFECT 3 (vertices=25, convex hull=57)
- After retessellation of defect 3, euler #=-18 (145861,437110,291231) : difference with theory (-17) = 1
- CORRECTING DEFECT 4 (vertices=427, convex hull=194)
- After retessellation of defect 4, euler #=-17 (145884,437269,291368) : difference with theory (-16) = 1
- CORRECTING DEFECT 5 (vertices=80, convex hull=79)
- After retessellation of defect 5, euler #=-16 (145918,437411,291477) : difference with theory (-15) = 1
- CORRECTING DEFECT 6 (vertices=10, convex hull=22)
- After retessellation of defect 6, euler #=-15 (145919,437420,291486) : difference with theory (-14) = 1
- CORRECTING DEFECT 7 (vertices=34, convex hull=46)
- After retessellation of defect 7, euler #=-14 (145929,437466,291523) : difference with theory (-13) = 1
- CORRECTING DEFECT 8 (vertices=19, convex hull=48)
- After retessellation of defect 8, euler #=-13 (145935,437500,291552) : difference with theory (-12) = 1
- CORRECTING DEFECT 9 (vertices=23, convex hull=22)
- Warning - incorrect dp selected!!!!(-80.689924 >= -80.689926 )
- After retessellation of defect 9, euler #=-12 (145936,437510,291562) : difference with theory (-11) = 1
- CORRECTING DEFECT 10 (vertices=32, convex hull=52)
- After retessellation of defect 10, euler #=-11 (145946,437562,291605) : difference with theory (-10) = 1
- CORRECTING DEFECT 11 (vertices=63, convex hull=38)
- After retessellation of defect 11, euler #=-10 (145955,437601,291636) : difference with theory (-9) = 1
- CORRECTING DEFECT 12 (vertices=32, convex hull=65)
- After retessellation of defect 12, euler #=-9 (145977,437695,291709) : difference with theory (-8) = 1
- CORRECTING DEFECT 13 (vertices=42, convex hull=45)
- After retessellation of defect 13, euler #=-8 (145986,437738,291744) : difference with theory (-7) = 1
- CORRECTING DEFECT 14 (vertices=103, convex hull=68)
- After retessellation of defect 14, euler #=-7 (146014,437850,291829) : difference with theory (-6) = 1
- CORRECTING DEFECT 15 (vertices=27, convex hull=43)
- After retessellation of defect 15, euler #=-5 (146021,437892,291866) : difference with theory (-5) = 0
- CORRECTING DEFECT 16 (vertices=7, convex hull=27)
- After retessellation of defect 16, euler #=-4 (146022,437902,291876) : difference with theory (-4) = 0
- CORRECTING DEFECT 17 (vertices=121, convex hull=43)
- After retessellation of defect 17, euler #=-3 (146032,437950,291915) : difference with theory (-3) = 0
- CORRECTING DEFECT 18 (vertices=16, convex hull=54)
- After retessellation of defect 18, euler #=-2 (146040,437993,291951) : difference with theory (-2) = 0
- CORRECTING DEFECT 19 (vertices=20, convex hull=62)
- After retessellation of defect 19, euler #=-1 (146050,438045,291994) : difference with theory (-1) = 0
- CORRECTING DEFECT 20 (vertices=51, convex hull=65)
- After retessellation of defect 20, euler #=0 (146069,438134,292065) : difference with theory (0) = 0
- CORRECTING DEFECT 21 (vertices=145, convex hull=101)
- After retessellation of defect 21, euler #=1 (146103,438280,292178) : difference with theory (1) = 0
- CORRECTING DEFECT 22 (vertices=32, convex hull=59)
- After retessellation of defect 22, euler #=2 (146118,438348,292232) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.88 +- 0.21 (0.11-->7.41) (max @ vno 68747 --> 72328)
- face area 0.00 +- 0.00 (0.00-->0.00)
- performing soap bubble on retessellated vertices for 0 iterations...
- vertex spacing 0.88 +- 0.21 (0.11-->7.41) (max @ vno 68747 --> 72328)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 90 mutations (33.2%), 181 crossovers (66.8%), 108 vertices were eliminated
- building final representation...
- 1084 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=146118, nf=292232, ne=438348, g=0)
- writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 18.9 minutes
- 0 defective edges
- removing intersecting faces
- 000: 125 intersecting
- mris_euler_number ../surf/lh.orig
- euler # = v-e+f = 2g-2: 146118 - 438348 + 292232 = 2 --> 0 holes
- F =2V-4: 292232 = 292236-4 (0)
- 2E=3F: 876696 = 876696 (0)
- total defect index = 0
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts
- mris_remove_intersection ../surf/lh.orig ../surf/lh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 21 intersecting
- writing corrected surface to ../surf/lh.orig
- rm ../surf/lh.inflated
- #--------------------------------------------
- #@# Make White Surf lh Thu Aug 8 18:15:59 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts
- mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub009 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/sub009/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/wm.mgz...
- 18938 bright wm thresholded.
- 815 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.orig...
- computing class statistics...
- border white: 259466 voxels (1.55%)
- border gray 303507 voxels (1.81%)
- WM (91.0): 92.8 +- 10.6 [70.0 --> 110.0]
- GM (74.0) : 72.4 +- 12.9 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 46.1 (was 70)
- setting MAX_BORDER_WHITE to 115.6 (was 105)
- setting MIN_BORDER_WHITE to 59.0 (was 85)
- setting MAX_CSF to 33.3 (was 40)
- setting MAX_GRAY to 94.4 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 52.6 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 20.4 (was 40)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.81 +- 0.22 (0.02-->3.23) (max @ vno 72318 --> 72328)
- face area 0.27 +- 0.12 (0.00-->2.15)
- mean absolute distance = 0.65 +- 0.76
- 3334 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=105, GM=59
- mean inside = 92.6, mean outside = 67.5
- smoothing surface for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- mean border=72.0, 185 (185) missing vertices, mean dist 0.3 [0.5 (%32.9)->0.7 (%67.1))]
- %67 local maxima, %28 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.92 +- 0.26 (0.11-->5.09) (max @ vno 72328 --> 69994)
- face area 0.27 +- 0.13 (0.00-->2.63)
- mean absolute distance = 0.29 +- 0.46
- 2565 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=8181313.0, rms=13.80
- 001: dt: 0.5000, sse=8284825.0, rms=9.980 (0.000%)
- 002: dt: 0.5000, sse=8638677.0, rms=7.805 (0.000%)
- 003: dt: 0.5000, sse=8709959.0, rms=6.394 (0.000%)
- 004: dt: 0.5000, sse=9058297.0, rms=5.564 (0.000%)
- 005: dt: 0.5000, sse=9033870.0, rms=5.081 (0.000%)
- 006: dt: 0.5000, sse=9298963.0, rms=4.838 (0.000%)
- 007: dt: 0.5000, sse=9143655.0, rms=4.682 (0.000%)
- 008: dt: 0.5000, sse=9303874.0, rms=4.605 (0.000%)
- 009: dt: 0.5000, sse=9127403.0, rms=4.541 (0.000%)
- rms = 4.50, time step reduction 1 of 3 to 0.250...
- 010: dt: 0.5000, sse=9231868.0, rms=4.501 (0.000%)
- 011: dt: 0.2500, sse=5948398.5, rms=3.175 (0.000%)
- 012: dt: 0.2500, sse=5499109.5, rms=2.691 (0.000%)
- 013: dt: 0.2500, sse=5181864.0, rms=2.601 (0.000%)
- 014: dt: 0.2500, sse=5098457.0, rms=2.507 (0.000%)
- rms = 2.48, time step reduction 2 of 3 to 0.125...
- 015: dt: 0.2500, sse=4977274.5, rms=2.478 (0.000%)
- 016: dt: 0.1250, sse=4707268.5, rms=2.202 (0.000%)
- rms = 2.17, time step reduction 3 of 3 to 0.062...
- 017: dt: 0.1250, sse=4652214.0, rms=2.167 (0.000%)
- positioning took 2.3 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- removing 1 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 3 vertex label from ripped group
- mean border=76.4, 133 (52) missing vertices, mean dist -0.2 [0.3 (%77.4)->0.2 (%22.6))]
- %80 local maxima, %16 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.90 +- 0.26 (0.09-->5.30) (max @ vno 72328 --> 69994)
- face area 0.35 +- 0.17 (0.00-->3.81)
- mean absolute distance = 0.21 +- 0.28
- 2468 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5664017.0, rms=5.99
- 018: dt: 0.5000, sse=5908087.0, rms=4.141 (0.000%)
- rms = 4.67, time step reduction 1 of 3 to 0.250...
- 019: dt: 0.2500, sse=5362265.0, rms=2.966 (0.000%)
- 020: dt: 0.2500, sse=5184648.0, rms=2.442 (0.000%)
- 021: dt: 0.2500, sse=5103986.5, rms=2.045 (0.000%)
- rms = 2.02, time step reduction 2 of 3 to 0.125...
- 022: dt: 0.2500, sse=5091900.0, rms=2.018 (0.000%)
- 023: dt: 0.1250, sse=4899920.0, rms=1.759 (0.000%)
- rms = 1.72, time step reduction 3 of 3 to 0.062...
- 024: dt: 0.1250, sse=4848903.5, rms=1.719 (0.000%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 1 vertex label from ripped group
- removing 3 vertex label from ripped group
- mean border=80.1, 85 (28) missing vertices, mean dist -0.1 [0.2 (%79.1)->0.2 (%20.9))]
- %89 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.25 (0.08-->5.42) (max @ vno 72328 --> 69994)
- face area 0.34 +- 0.16 (0.00-->3.96)
- mean absolute distance = 0.15 +- 0.23
- 2774 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5305572.5, rms=4.53
- 025: dt: 0.5000, sse=5513302.0, rms=4.234 (0.000%)
- rms = 4.45, time step reduction 1 of 3 to 0.250...
- 026: dt: 0.2500, sse=5033679.0, rms=2.658 (0.000%)
- 027: dt: 0.2500, sse=4937652.0, rms=2.240 (0.000%)
- 028: dt: 0.2500, sse=5013818.0, rms=1.848 (0.000%)
- rms = 1.92, time step reduction 2 of 3 to 0.125...
- 029: dt: 0.1250, sse=4939601.5, rms=1.701 (0.000%)
- 030: dt: 0.1250, sse=4841204.5, rms=1.497 (0.000%)
- rms = 1.48, time step reduction 3 of 3 to 0.062...
- 031: dt: 0.1250, sse=4807466.0, rms=1.476 (0.000%)
- positioning took 1.1 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- removing 1 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 3 vertex label from ripped group
- mean border=81.3, 75 (24) missing vertices, mean dist -0.0 [0.2 (%59.8)->0.2 (%40.2))]
- %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
- writing white matter surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.white...
- writing smoothed curvature to lh.curv
- 000: dt: 0.0000, sse=4838137.5, rms=1.92
- rms = 3.10, time step reduction 1 of 3 to 0.250...
- 032: dt: 0.2500, sse=4908938.0, rms=1.213 (0.000%)
- 033: dt: 0.2500, sse=5051706.5, rms=1.117 (0.000%)
- rms = 1.12, time step reduction 2 of 3 to 0.125...
- rms = 1.10, time step reduction 3 of 3 to 0.062...
- 034: dt: 0.1250, sse=5054505.0, rms=1.102 (0.000%)
- positioning took 0.6 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 1 vertex label from ripped group
- removing 4 vertex label from ripped group
- generating cortex label...
- 13 non-cortical segments detected
- only using segment with 1519 vertices
- erasing segment 1 (vno[0] = 73398)
- erasing segment 2 (vno[0] = 76481)
- erasing segment 3 (vno[0] = 77591)
- erasing segment 4 (vno[0] = 85337)
- erasing segment 5 (vno[0] = 87185)
- erasing segment 6 (vno[0] = 94733)
- erasing segment 7 (vno[0] = 100948)
- erasing segment 8 (vno[0] = 102918)
- erasing segment 9 (vno[0] = 114820)
- erasing segment 10 (vno[0] = 115581)
- erasing segment 11 (vno[0] = 115607)
- erasing segment 12 (vno[0] = 117125)
- writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/label/lh.cortex.label...
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.curv
- writing smoothed area to lh.area
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.area
- vertex spacing 0.89 +- 0.25 (0.02-->5.47) (max @ vno 72328 --> 69994)
- face area 0.33 +- 0.16 (0.00-->4.05)
- refinement took 7.1 minutes
- #--------------------------------------------
- #@# Smooth2 lh Thu Aug 8 18:23:07 CEST 2013
- mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts
- smoothing for 3 iterations
- setting seed for random number generator to 1234
- smoothing surface tessellation for 3 iterations...
- smoothing complete - recomputing first and second fundamental forms...
- #--------------------------------------------
- #@# Inflation2 lh Thu Aug 8 18:23:12 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts
- mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated
- avg radius = 47.7 mm, total surface area = 88198 mm^2
- writing inflated surface to ../surf/lh.inflated
- writing sulcal depths to ../surf/lh.sulc
-
step 000: RMS=0.121 (target=0.015)
step 005: RMS=0.084 (target=0.015)
step 010: RMS=0.061 (target=0.015)
step 015: RMS=0.049 (target=0.015)
step 020: RMS=0.041 (target=0.015)
step 025: RMS=0.034 (target=0.015)
step 030: RMS=0.028 (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=0.017 (target=0.015)
step 055: RMS=0.017 (target=0.015)
step 060: RMS=0.015 (target=0.015)
- inflation complete.
- inflation took 0.6 minutes
- mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated
- normalizing curvature values.
- averaging curvature patterns 5 times.
- sampling 10 neighbors out to a distance of 10 mm
- 178 vertices thresholded to be in k1 ~ [-1.06 0.29], k2 ~ [-0.24 0.14]
- total integrated curvature = 0.513*4pi (6.452) --> 0 handles
- ICI = 1.5, FI = 9.2, variation=157.807
- 146 vertices thresholded to be in [-0.04 0.02]
- writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level
- curvature mean = 0.000, std = 0.001
- 111 vertices thresholded to be in [-0.26 0.15]
- done.
- writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.016, std = 0.022
- done.
- #-----------------------------------------
- #@# Curvature Stats lh Thu Aug 8 18:25:39 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub009 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 [ sub009/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 [ 292 ]
- Gb_filter = 0
- WARN: S lookup min: -0.281872
- WARN: S explicit min: 0.000000 vertex = 349
- #--------------------------------------------
- #@# Sphere lh Thu Aug 8 18:25:44 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 0.280...
- MRISunfold() max_passes = 1 -------
- tol=5.0e-01, sigma=0.0, host=snake, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
- using quadratic fit line minimization
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 1.000000
- desired_rms_height -1.000000
- momentum 0.900000
- nbhd_size 7
- max_nbrs 8
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 1234
- --------------------
- mrisRemoveNegativeArea()
- pass 1: epoch 1 of 3 starting distance error %20.42
- pass 1: epoch 2 of 3 starting distance error %20.30
- unfolding complete - removing small folds...
- starting distance error %20.19
- removing remaining folds...
- final distance error %20.21
- MRISunfold() return, current seed 1234
- writing spherical brain to ../surf/lh.sphere
- spherical transformation took 0.99 hours
- #--------------------------------------------
- #@# Surf Reg lh Thu Aug 8 19:25:24 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 = 0.576
- curvature mean = 0.038, std = 0.934
- curvature mean = 0.026, std = 0.845
- Starting MRISrigidBodyAlignGlobal()
- d=64.00 min @ (0.00, -16.00, 0.00) sse = 357180.1, tmin=1.1687
- d=32.00 min @ (8.00, 8.00, 0.00) sse = 295199.3, tmin=2.3467
- d=16.00 min @ (0.00, -4.00, -4.00) sse = 287773.8, tmin=3.5194
- d=8.00 min @ (0.00, 2.00, 2.00) sse = 285320.1, tmin=4.7325
- d=4.00 min @ (-1.00, -1.00, 0.00) sse = 283934.3, tmin=5.9771
- d=2.00 min @ (0.00, 0.00, -0.50) sse = 283738.5, tmin=7.2418
- d=1.00 min @ (0.25, 0.00, 0.00) sse = 283649.9, tmin=8.5086
- d=0.50 min @ (-0.12, -0.12, -0.12) sse = 283648.4, tmin=9.7731
- 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 9.77 min
- curvature mean = 0.014, std = 0.956
- curvature mean = 0.014, std = 0.930
- curvature mean = 0.014, std = 0.968
- curvature mean = 0.007, std = 0.967
- curvature mean = 0.013, std = 0.970
- curvature mean = 0.002, std = 0.985
- 2 Reading smoothwm
- curvature mean = -0.025, std = 0.323
- curvature mean = 0.004, std = 0.066
- curvature mean = 0.078, std = 0.301
- curvature mean = 0.003, std = 0.078
- curvature mean = 0.036, std = 0.488
- curvature mean = 0.003, std = 0.084
- curvature mean = 0.022, std = 0.629
- curvature mean = 0.003, std = 0.088
- curvature mean = 0.008, std = 0.747
- MRISregister() return, current seed 0
- writing registered surface to ../surf/lh.sphere.reg...
- expanding nbhd size to 1
- #--------------------------------------------
- #@# Jacobian white lh Thu Aug 8 19:53:51 CEST 2013
- mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white
- reading surface from ../surf/lh.white...
- writing curvature file ../surf/lh.jacobian_white
- #--------------------------------------------
- #@# AvgCurv lh Thu Aug 8 19:53:54 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts
- mrisp_paint -a 5 /opt/freesurfer/5.3.0/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv
- averaging curvature patterns 5 times...
- reading surface from ../surf/lh.sphere.reg...
- reading template parameterization from /opt/freesurfer/5.3.0/average/lh.average.curvature.filled.buckner40.tif...
- writing curvature file to ../surf/lh.avg_curv...
- #-----------------------------------------
- #@# Cortical Parc lh Thu Aug 8 19:53:56 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub009 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...
- 1620 labels changed using aseg
- relabeling using gibbs priors...
- 000: 3282 changed, 146118 examined...
- 001: 751 changed, 14004 examined...
- 002: 205 changed, 4211 examined...
- 003: 55 changed, 1157 examined...
- 004: 23 changed, 377 examined...
- 005: 8 changed, 132 examined...
- 006: 3 changed, 43 examined...
- 007: 1 changed, 20 examined...
- 008: 2 changed, 6 examined...
- 009: 1 changed, 10 examined...
- 010: 1 changed, 9 examined...
- 011: 0 changed, 5 examined...
- 225 labels changed using aseg
- 000: 151 total segments, 109 labels (675 vertices) changed
- 001: 44 total segments, 7 labels (46 vertices) changed
- 002: 37 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...
- 1710 vertices marked for relabeling...
- 1710 labels changed in reclassification.
- writing output to ../label/lh.aparc.annot...
- classification took 1 minutes and 7 seconds.
- #--------------------------------------------
- #@# Make Pial Surf lh Thu Aug 8 19:55:03 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts
- mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub009 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/sub009/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/wm.mgz...
- 18938 bright wm thresholded.
- 815 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.orig...
- computing class statistics...
- border white: 259466 voxels (1.55%)
- border gray 303507 voxels (1.81%)
- WM (91.0): 92.8 +- 10.6 [70.0 --> 110.0]
- GM (74.0) : 72.4 +- 12.9 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 46.1 (was 70)
- setting MAX_BORDER_WHITE to 115.6 (was 105)
- setting MIN_BORDER_WHITE to 59.0 (was 85)
- setting MAX_CSF to 33.3 (was 40)
- setting MAX_GRAY to 94.4 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 52.6 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 20.4 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=105, GM=59
- mean inside = 92.6, mean outside = 67.5
- smoothing surface for 5 iterations...
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.81 +- 0.22 (0.02-->3.23) (max @ vno 72318 --> 72328)
- face area 0.27 +- 0.12 (0.00-->2.15)
- mean absolute distance = 0.65 +- 0.76
- 3346 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 1 with 11 points - only 0.00% unknown
- deleting segment 2 with 6 points - only 0.00% unknown
- deleting segment 3 with 654 points - only 0.00% unknown
- deleting segment 4 with 19 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 18 points - only 0.00% unknown
- deleting segment 8 with 14 points - only 0.00% unknown
- mean border=72.0, 185 (185) missing vertices, mean dist 0.3 [0.5 (%32.9)->0.7 (%67.1))]
- %68 local maxima, %28 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.92 +- 0.26 (0.11-->5.09) (max @ vno 72328 --> 69994)
- face area 0.27 +- 0.13 (0.00-->2.63)
- mean absolute distance = 0.29 +- 0.45
- 2572 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=8202595.5, rms=13.78
- 001: dt: 0.5000, sse=8317187.0, rms=9.964 (0.000%)
- 002: dt: 0.5000, sse=8675203.0, rms=7.792 (0.000%)
- 003: dt: 0.5000, sse=8750276.0, rms=6.385 (0.000%)
- 004: dt: 0.5000, sse=9099968.0, rms=5.558 (0.000%)
- 005: dt: 0.5000, sse=9076132.0, rms=5.076 (0.000%)
- 006: dt: 0.5000, sse=9343738.0, rms=4.833 (0.000%)
- 007: dt: 0.5000, sse=9184572.0, rms=4.677 (0.000%)
- 008: dt: 0.5000, sse=9348068.0, rms=4.601 (0.000%)
- 009: dt: 0.5000, sse=9168776.0, rms=4.536 (0.000%)
- rms = 4.50, time step reduction 1 of 3 to 0.250...
- 010: dt: 0.5000, sse=9275467.0, rms=4.497 (0.000%)
- 011: dt: 0.2500, sse=5971632.0, rms=3.170 (0.000%)
- 012: dt: 0.2500, sse=5520908.0, rms=2.688 (0.000%)
- 013: dt: 0.2500, sse=5201493.5, rms=2.597 (0.000%)
- 014: dt: 0.2500, sse=5117343.5, rms=2.503 (0.000%)
- rms = 2.47, time step reduction 2 of 3 to 0.125...
- 015: dt: 0.2500, sse=4996641.5, rms=2.474 (0.000%)
- 016: dt: 0.1250, sse=4726252.5, rms=2.200 (0.000%)
- rms = 2.16, time step reduction 3 of 3 to 0.062...
- 017: dt: 0.1250, sse=4671087.5, rms=2.165 (0.000%)
- positioning took 2.3 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- deleting segment 0 with 3 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 3 with 1 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 4 with 4 points - only 0.00% unknown
- deleting segment 5 with 569 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 6 with 3 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 8 with 2 points - only 0.00% unknown
- deleting segment 10 with 6 points - only 0.00% unknown
- deleting segment 11 with 7 points - only 0.00% unknown
- deleting segment 12 with 19 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 15 with 11 points - only 0.00% unknown
- deleting segment 16 with 15 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 17 with 3 points - only 0.00% unknown
- mean border=76.4, 135 (52) missing vertices, mean dist -0.2 [0.3 (%77.3)->0.2 (%22.7))]
- %80 local maxima, %16 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.90 +- 0.25 (0.09-->5.30) (max @ vno 72328 --> 69994)
- face area 0.35 +- 0.16 (0.00-->3.81)
- mean absolute distance = 0.21 +- 0.28
- 2480 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5686639.0, rms=5.98
- 018: dt: 0.5000, sse=5928499.5, rms=4.134 (0.000%)
- rms = 4.66, time step reduction 1 of 3 to 0.250...
- 019: dt: 0.2500, sse=5382237.5, rms=2.961 (0.000%)
- 020: dt: 0.2500, sse=5206576.5, rms=2.437 (0.000%)
- 021: dt: 0.2500, sse=5124761.5, rms=2.042 (0.000%)
- rms = 2.01, time step reduction 2 of 3 to 0.125...
- 022: dt: 0.2500, sse=5111591.0, rms=2.014 (0.000%)
- 023: dt: 0.1250, sse=4920777.0, rms=1.757 (0.000%)
- rms = 1.72, time step reduction 3 of 3 to 0.062...
- 024: dt: 0.1250, sse=4869989.0, rms=1.717 (0.000%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 5 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 2 with 5 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 3 with 1 points - only 0.00% unknown
- deleting segment 4 with 7 points - only 0.00% unknown
- deleting segment 5 with 629 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 7 with 2 points - only 0.00% unknown
- deleting segment 8 with 17 points - only 0.00% unknown
- deleting segment 9 with 20 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 10 with 4 points - only 0.00% unknown
- deleting segment 13 with 8 points - only 0.00% unknown
- deleting segment 14 with 14 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 15 with 3 points - only 0.00% unknown
- mean border=80.1, 90 (29) missing vertices, mean dist -0.1 [0.2 (%79.1)->0.2 (%20.9))]
- %89 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.25 (0.04-->5.42) (max @ vno 72328 --> 69994)
- face area 0.34 +- 0.16 (0.00-->3.96)
- mean absolute distance = 0.15 +- 0.23
- 2797 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5327450.0, rms=4.52
- 025: dt: 0.5000, sse=5535659.0, rms=4.227 (0.000%)
- rms = 4.45, time step reduction 1 of 3 to 0.250...
- 026: dt: 0.2500, sse=5055721.5, rms=2.653 (0.000%)
- 027: dt: 0.2500, sse=4959688.0, rms=2.236 (0.000%)
- 028: dt: 0.2500, sse=5037968.5, rms=1.846 (0.000%)
- rms = 1.92, time step reduction 2 of 3 to 0.125...
- 029: dt: 0.1250, sse=4963726.0, rms=1.699 (0.000%)
- 030: dt: 0.1250, sse=4864778.0, rms=1.497 (0.000%)
- rms = 1.48, time step reduction 3 of 3 to 0.062...
- 031: dt: 0.1250, sse=4831304.5, rms=1.477 (0.000%)
- positioning took 1.1 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 5 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 2 with 5 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 3 with 1 points - only 0.00% unknown
- deleting segment 4 with 7 points - only 0.00% unknown
- deleting segment 5 with 648 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 6 with 2 points - only 0.00% unknown
- deleting segment 7 with 17 points - only 0.00% unknown
- deleting segment 8 with 19 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 9 with 4 points - only 0.00% unknown
- deleting segment 10 with 15 points - only 0.00% unknown
- deleting segment 11 with 14 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 12 with 3 points - only 0.00% unknown
- mean border=81.2, 86 (24) missing vertices, mean dist -0.0 [0.2 (%59.8)->0.2 (%40.2))]
- %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=4863136.0, rms=1.92
- rms = 3.09, time step reduction 1 of 3 to 0.250...
- 032: dt: 0.2500, sse=4935760.5, rms=1.215 (0.000%)
- 033: dt: 0.2500, sse=5081568.5, rms=1.118 (0.000%)
- rms = 1.12, time step reduction 2 of 3 to 0.125...
- rms = 1.10, time step reduction 3 of 3 to 0.062...
- 034: dt: 0.1250, sse=5082797.5, rms=1.103 (0.000%)
- positioning took 0.6 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 1 vertex label from ripped group
- deleting segment 1 with 1 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 2 with 4 points - only 0.00% unknown
- smoothing surface for 5 iterations...
- mean border=49.1, 175 (175) missing vertices, mean dist 1.6 [0.1 (%0.0)->2.1 (%100.0))]
- %16 local maxima, %56 large gradients and %24 min vals, 1580 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=30720990.0, rms=31.38
- 001: dt: 0.5000, sse=21866200.0, rms=25.815 (0.000%)
- 002: dt: 0.5000, sse=15775913.0, rms=21.187 (0.000%)
- 003: dt: 0.5000, sse=11803336.0, rms=17.441 (0.000%)
- 004: dt: 0.5000, sse=9533108.0, rms=14.470 (0.000%)
- 005: dt: 0.5000, sse=8256870.0, rms=12.194 (0.000%)
- 006: dt: 0.5000, sse=7530437.5, rms=10.492 (0.000%)
- 007: dt: 0.5000, sse=7055526.5, rms=9.062 (0.000%)
- 008: dt: 0.5000, sse=6810970.0, rms=7.796 (0.000%)
- 009: dt: 0.5000, sse=6691887.0, rms=6.671 (0.000%)
- 010: dt: 0.5000, sse=6741076.0, rms=5.786 (0.000%)
- 011: dt: 0.5000, sse=6920722.0, rms=5.132 (0.000%)
- 012: dt: 0.5000, sse=7093514.5, rms=4.706 (0.000%)
- 013: dt: 0.5000, sse=7282325.0, rms=4.422 (0.000%)
- 014: dt: 0.5000, sse=7366286.5, rms=4.258 (0.000%)
- 015: dt: 0.5000, sse=7475775.0, rms=4.132 (0.000%)
- 016: dt: 0.5000, sse=7495378.0, rms=4.064 (0.000%)
- 017: dt: 0.5000, sse=7551958.0, rms=3.999 (0.000%)
- rms = 3.96, time step reduction 1 of 3 to 0.250...
- 018: dt: 0.5000, sse=7551811.5, rms=3.958 (0.000%)
- 019: dt: 0.2500, sse=5331480.0, rms=3.253 (0.000%)
- 020: dt: 0.2500, sse=5099851.0, rms=3.057 (0.000%)
- rms = 3.03, time step reduction 2 of 3 to 0.125...
- 021: dt: 0.2500, sse=4986196.5, rms=3.034 (0.000%)
- 022: dt: 0.1250, sse=4792820.5, rms=2.940 (0.000%)
- rms = 2.93, time step reduction 3 of 3 to 0.062...
- 023: dt: 0.1250, sse=4762591.0, rms=2.929 (0.000%)
- positioning took 3.0 minutes
- mean border=46.8, 793 (12) missing vertices, mean dist 0.2 [0.2 (%48.5)->0.6 (%51.5))]
- %33 local maxima, %43 large gradients and %19 min vals, 541 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=5474551.0, rms=5.04
- 024: dt: 0.5000, sse=5761867.5, rms=4.133 (0.000%)
- rms = 4.12, time step reduction 1 of 3 to 0.250...
- 025: dt: 0.5000, sse=7465571.5, rms=4.116 (0.000%)
- 026: dt: 0.2500, sse=5631418.0, rms=3.287 (0.000%)
- 027: dt: 0.2500, sse=5642405.0, rms=3.051 (0.000%)
- rms = 3.00, time step reduction 2 of 3 to 0.125...
- 028: dt: 0.2500, sse=5502221.5, rms=3.004 (0.000%)
- 029: dt: 0.1250, sse=5307892.0, rms=2.853 (0.000%)
- rms = 2.82, time step reduction 3 of 3 to 0.062...
- 030: dt: 0.1250, sse=5292795.5, rms=2.821 (0.000%)
- positioning took 0.9 minutes
- mean border=44.2, 992 (7) missing vertices, mean dist 0.1 [0.2 (%36.7)->0.4 (%63.3))]
- %54 local maxima, %22 large gradients and %19 min vals, 629 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=5655667.5, rms=4.45
- 031: dt: 0.5000, sse=5853190.5, rms=3.992 (0.000%)
- rms = 4.08, time step reduction 1 of 3 to 0.250...
- 032: dt: 0.2500, sse=5500425.0, rms=3.226 (0.000%)
- 033: dt: 0.2500, sse=5725797.5, rms=2.917 (0.000%)
- 034: dt: 0.2500, sse=5645297.5, rms=2.840 (0.000%)
- rms = 2.80, time step reduction 2 of 3 to 0.125...
- 035: dt: 0.2500, sse=5700974.0, rms=2.802 (0.000%)
- 036: dt: 0.1250, sse=5498973.5, rms=2.674 (0.000%)
- rms = 2.65, time step reduction 3 of 3 to 0.062...
- 037: dt: 0.1250, sse=5487813.0, rms=2.647 (0.000%)
- positioning took 1.0 minutes
- mean border=42.9, 2039 (5) missing vertices, mean dist 0.1 [0.2 (%43.0)->0.3 (%57.0))]
- %59 local maxima, %17 large gradients and %18 min vals, 514 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/sub009/surf/lh.pial...
- writing smoothed curvature to lh.curv.pial
- 000: dt: 0.0000, sse=5567807.0, rms=3.14
- rms = 3.78, time step reduction 1 of 3 to 0.250...
- 038: dt: 0.2500, sse=5401296.0, rms=2.806 (0.000%)
- 039: dt: 0.2500, sse=5550118.0, rms=2.697 (0.000%)
- rms = 2.67, time step reduction 2 of 3 to 0.125...
- 040: dt: 0.2500, sse=5639928.5, rms=2.672 (0.000%)
- 041: dt: 0.1250, sse=5526929.5, rms=2.556 (0.000%)
- rms = 2.53, time step reduction 3 of 3 to 0.062...
- 042: dt: 0.1250, sse=5536103.0, rms=2.530 (0.000%)
- positioning took 0.7 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.curv.pial
- writing smoothed area to lh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.area.pial
- vertex spacing 1.00 +- 0.42 (0.07-->7.19) (max @ vno 98031 --> 96995)
- face area 0.40 +- 0.30 (0.00-->5.20)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 146118 vertices processed
- 25000 of 146118 vertices processed
- 50000 of 146118 vertices processed
- 75000 of 146118 vertices processed
- 100000 of 146118 vertices processed
- 125000 of 146118 vertices processed
- 0 of 146118 vertices processed
- 25000 of 146118 vertices processed
- 50000 of 146118 vertices processed
- 75000 of 146118 vertices processed
- 100000 of 146118 vertices processed
- 125000 of 146118 vertices processed
- thickness calculation complete, 263:496 truncations.
- 32479 vertices at 0 distance
- 100939 vertices at 1 distance
- 96911 vertices at 2 distance
- 36297 vertices at 3 distance
- 9817 vertices at 4 distance
- 2623 vertices at 5 distance
- 740 vertices at 6 distance
- 272 vertices at 7 distance
- 131 vertices at 8 distance
- 82 vertices at 9 distance
- 56 vertices at 10 distance
- 38 vertices at 11 distance
- 30 vertices at 12 distance
- 20 vertices at 13 distance
- 21 vertices at 14 distance
- 10 vertices at 15 distance
- 4 vertices at 16 distance
- 6 vertices at 17 distance
- 5 vertices at 18 distance
- 9 vertices at 19 distance
- 10 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.thickness
- positioning took 14.3 minutes
- #--------------------------------------------
- #@# Surf Volume lh Thu Aug 8 20:09:20 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf
- mris_calc -o lh.area.mid lh.area add lh.area.pial
- Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o lh.area.mid lh.area.mid div 2
- Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o lh.volume lh.area.mid mul lh.thickness
- Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ]
- #-----------------------------------------
- #@# WM/GM Contrast lh Thu Aug 8 20:09:20 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts
- pctsurfcon --s sub009 --lh-only
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts/pctsurfcon.log
- Thu Aug 8 20:09:20 CEST 2013
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts
- /opt/freesurfer/5.3.0/bin/pctsurfcon
- $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $
- Linux snake6 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
- FREESURFER_HOME /opt/freesurfer/5.3.0
- mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/tmp.pctsurfcon.8644/lh.wm.mgh --regheader sub009 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/label/lh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 = 111541
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/label/lh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/tmp.pctsurfcon.8644/lh.wm.mgh
- Dim: 146118 1 1
- mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/tmp.pctsurfcon.8644/lh.gm.mgh --projfrac 0.3 --regheader sub009 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/label/lh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.white
- Done reading source surface
- Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 = 129823
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/label/lh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/tmp.pctsurfcon.8644/lh.gm.mgh
- Dim: 146118 1 1
- mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/tmp.pctsurfcon.8644/lh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/tmp.pctsurfcon.8644/lh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/surf/lh.w-g.pct.mgh
- mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.w-g.pct.mgh --annot sub009 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/surf/lh.w-g.pct.mgh --annot sub009 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/stats/lh.w-g.pct.stats --snr
- sysname Linux
- hostname snake6
- machine x86_64
- user fkaule
- UseRobust 0
- Constructing seg from annotation
- Reading annotation
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
- Seg base 1000
- Loading /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.w-g.pct.mgh
- Vertex Area is 0.663559 mm^3
- Generating list of segmentation ids
- Found 36 segmentations
- Computing statistics for each segmentation
- 0 1000 unknown 0 0.000
- 1 1001 bankssts 1387 995.230
- 2 1002 caudalanteriorcingulate 1626 1103.811
- 3 1003 caudalmiddlefrontal 3071 2022.123
- 4 1004 corpuscallosum 0 0.000
- 5 1005 cuneus 2101 1369.660
- 6 1006 entorhinal 758 516.569
- 7 1007 fusiform 5734 3788.897
- 8 1008 inferiorparietal 8907 5993.643
- 9 1009 inferiortemporal 5247 3557.660
- 10 1010 isthmuscingulate 1716 1104.740
- 11 1011 lateraloccipital 8358 5448.021
- 12 1012 lateralorbitofrontal 4001 2628.918
- 13 1013 lingual 3929 2727.612
- 14 1014 medialorbitofrontal 3404 2217.685
- 15 1015 middletemporal 4927 3422.167
- 16 1016 parahippocampal 1095 731.138
- 17 1017 paracentral 2194 1430.574
- 18 1018 parsopercularis 3344 2239.959
- 19 1019 parsorbitalis 1215 797.758
- 20 1020 parstriangularis 1773 1217.633
- 21 1021 pericalcarine 2164 1473.465
- 22 1022 postcentral 6120 4006.338
- 23 1023 posteriorcingulate 2209 1499.423
- 24 1024 precentral 7841 4942.984
- 25 1025 precuneus 6922 4586.249
- 26 1026 rostralanteriorcingulate 1820 1169.508
- 27 1027 rostralmiddlefrontal 8948 6107.701
- 28 1028 superiorfrontal 10472 7041.768
- 29 1029 superiorparietal 8961 5873.902
- 30 1030 superiortemporal 5536 3678.935
- 31 1031 supramarginal 6946 4625.763
- 32 1032 frontalpole 384 262.584
- 33 1033 temporalpole 959 630.734
- 34 1034 transversetemporal 787 487.875
- 35 1035 insula 3661 2414.259
- Reporting on 34 segmentations
- mri_segstats done
- Cleaning up
- #-----------------------------------------
- #@# Parcellation Stats lh Thu Aug 8 20:09:34 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 sub009 lh white
- computing statistics for each annotation in ../label/lh.aparc.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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
- 1387 995 2235 2.235 0.477 0.113 0.028 12 1.7 bankssts
- 1626 1104 3261 2.570 0.535 0.122 0.033 18 2.3 caudalanteriorcingulate
- 3071 2022 5110 2.379 0.416 0.138 0.113 47 22.3 caudalmiddlefrontal
- 2101 1370 3273 2.083 0.421 0.166 0.064 42 5.3 cuneus
- 758 517 2025 3.059 0.661 0.121 0.035 6 1.2 entorhinal
- 5734 3789 12012 2.692 0.598 0.165 0.088 240 22.3 fusiform
- 8907 5994 14437 2.195 0.446 0.148 0.056 168 20.2 inferiorparietal
- 5247 3558 10575 2.585 0.578 0.162 0.083 145 14.9 inferiortemporal
- 1716 1105 2951 2.471 0.678 0.167 0.087 47 6.6 isthmuscingulate
- 8358 5448 13029 2.116 0.486 0.163 0.068 171 20.4 lateraloccipital
- 4001 2629 6708 2.369 0.683 0.168 0.074 102 12.3 lateralorbitofrontal
- 3929 2728 6162 2.077 0.520 0.166 0.072 77 11.7 lingual
- 3404 2218 5612 2.183 0.699 0.147 0.116 167 10.7 medialorbitofrontal
- 4927 3422 10198 2.520 0.576 0.168 0.075 178 14.8 middletemporal
- 1095 731 1764 2.171 0.494 0.124 0.109 91 5.2 parahippocampal
- 2194 1431 3646 2.295 0.552 0.119 0.035 22 3.0 paracentral
- 3344 2240 6250 2.447 0.413 0.144 0.049 56 6.2 parsopercularis
- 1215 798 2373 2.400 0.525 0.185 0.082 34 4.1 parsorbitalis
- 1773 1218 2985 2.195 0.441 0.162 0.078 554 3.6 parstriangularis
- 2164 1473 2485 1.742 0.476 0.180 0.084 42 8.1 pericalcarine
- 6120 4006 8641 1.907 0.551 0.137 0.053 112 13.1 postcentral
- 2209 1499 4126 2.565 0.496 0.160 0.060 49 5.4 posteriorcingulate
- 7841 4943 13190 2.407 0.477 0.125 0.039 89 12.6 precentral
- 6922 4586 11437 2.321 0.467 0.150 0.058 140 14.6 precuneus
- 1820 1170 3307 2.524 0.595 0.153 0.078 38 6.9 rostralanteriorcingulate
- 8948 6108 15238 2.185 0.499 0.172 0.073 219 24.6 rostralmiddlefrontal
- 10472 7042 19699 2.440 0.512 0.147 0.050 171 20.8 superiorfrontal
- 8961 5874 13047 2.033 0.371 0.148 0.048 159 17.2 superiorparietal
- 5536 3679 11333 2.708 0.577 0.132 0.042 98 9.6 superiortemporal
- 6946 4626 11929 2.367 0.477 0.145 0.047 115 13.2 supramarginal
- 384 263 872 2.413 0.503 0.237 0.342 39 8.2 frontalpole
- 959 631 3408 3.699 0.690 0.164 0.075 21 2.8 temporalpole
- 787 488 1385 2.464 0.344 0.132 0.052 13 1.4 transversetemporal
- 3661 2414 7627 3.035 0.757 0.128 0.057 75 9.0 insula
- #-----------------------------------------
- #@# Cortical Parc 2 lh Thu Aug 8 20:09:53 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub009 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...
- 10 labels changed using aseg
- relabeling using gibbs priors...
- 000: 10264 changed, 146118 examined...
- 001: 2502 changed, 39264 examined...
- 002: 784 changed, 12919 examined...
- 003: 346 changed, 4393 examined...
- 004: 185 changed, 1924 examined...
- 005: 87 changed, 1026 examined...
- 006: 57 changed, 486 examined...
- 007: 25 changed, 325 examined...
- 008: 13 changed, 134 examined...
- 009: 9 changed, 66 examined...
- 010: 1 changed, 57 examined...
- 011: 1 changed, 8 examined...
- 012: 0 changed, 6 examined...
- 5 labels changed using aseg
- 000: 334 total segments, 247 labels (2782 vertices) changed
- 001: 105 total segments, 18 labels (37 vertices) changed
- 002: 87 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 109 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 1071 vertices marked for relabeling...
- 1071 labels changed in reclassification.
- writing output to ../label/lh.aparc.a2009s.annot...
- classification took 1 minutes and 13 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 2 lh Thu Aug 8 20:11:07 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 sub009 lh white
- computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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
- 1365 918 2157 2.068 0.585 0.186 0.111 48 4.6 G_and_S_frontomargin
- 2229 1475 3859 2.166 0.555 0.159 0.059 45 5.5 G_and_S_occipital_inf
- 1592 1003 2955 2.348 0.592 0.136 0.041 22 2.7 G_and_S_paracentral
- 1605 1086 3020 2.425 0.464 0.156 0.073 50 5.2 G_and_S_subcentral
- 872 627 1786 2.264 0.476 0.213 0.184 50 9.3 G_and_S_transv_frontopol
- 3429 2238 5679 2.374 0.481 0.140 0.057 55 9.0 G_and_S_cingul-Ant
- 1709 1135 3257 2.564 0.499 0.132 0.042 21 2.8 G_and_S_cingul-Mid-Ant
- 1672 1146 2867 2.428 0.361 0.139 0.046 25 3.2 G_and_S_cingul-Mid-Post
- 779 484 1792 2.990 0.525 0.189 0.084 22 2.7 G_cingul-Post-dorsal
- 264 160 402 2.151 0.684 0.166 0.093 8 0.8 G_cingul-Post-ventral
- 1928 1269 3030 2.018 0.441 0.178 0.074 43 5.6 G_cuneus
- 1889 1268 4274 2.556 0.412 0.157 0.060 44 4.3 G_front_inf-Opercular
- 503 327 1028 2.487 0.439 0.185 0.078 16 1.8 G_front_inf-Orbital
- 1466 983 2654 2.282 0.441 0.177 0.096 555 3.6 G_front_inf-Triangul
- 4437 2985 9047 2.382 0.468 0.175 0.068 112 12.2 G_front_middle
- 7530 5011 16116 2.548 0.527 0.153 0.056 142 16.8 G_front_sup
- 572 361 1294 3.109 0.631 0.142 0.100 18 2.7 G_Ins_lg_and_S_cent_ins
- 864 544 2622 3.787 0.620 0.152 0.079 41 3.1 G_insular_short
- 2050 1344 4383 2.509 0.401 0.192 0.086 69 6.4 G_occipital_middle
- 1382 883 2118 2.077 0.438 0.161 0.060 28 3.2 G_occipital_sup
- 2272 1435 5009 2.839 0.522 0.175 0.082 68 7.4 G_oc-temp_lat-fusifor
- 2631 1820 4534 2.054 0.539 0.184 0.104 66 9.7 G_oc-temp_med-Lingual
- 1355 887 3220 2.771 0.772 0.114 0.037 11 2.1 G_oc-temp_med-Parahip
- 2986 1938 5823 2.391 0.676 0.187 0.093 101 11.2 G_orbital
- 2960 1995 5474 2.232 0.400 0.165 0.072 75 9.3 G_pariet_inf-Angular
- 3825 2523 7701 2.527 0.446 0.158 0.058 84 8.6 G_pariet_inf-Supramar
- 3884 2557 6625 2.127 0.397 0.164 0.062 91 9.5 G_parietal_sup
- 2242 1435 3306 1.882 0.467 0.145 0.059 42 4.9 G_postcentral
- 3058 1833 6313 2.640 0.375 0.130 0.046 43 5.5 G_precentral
- 3345 2205 6455 2.384 0.480 0.164 0.078 95 8.7 G_precuneus
- 1264 836 2581 2.323 0.631 0.216 0.140 67 8.1 G_rectus
- 436 269 826 2.897 0.793 0.122 0.401 91 1.1 G_subcallosal
- 554 332 1113 2.542 0.259 0.136 0.059 11 1.1 G_temp_sup-G_T_transv
- 2173 1408 5507 2.867 0.563 0.161 0.058 66 5.0 G_temp_sup-Lateral
- 683 465 1907 3.653 0.595 0.120 0.035 6 1.0 G_temp_sup-Plan_polar
- 847 575 1546 2.442 0.461 0.105 0.027 6 1.0 G_temp_sup-Plan_tempo
- 2936 1981 7047 2.716 0.598 0.175 0.104 112 10.4 G_temporal_inf
- 2719 1902 6489 2.601 0.575 0.192 0.100 142 10.8 G_temporal_middle
- 313 213 429 2.158 0.409 0.118 0.027 3 0.3 Lat_Fis-ant-Horizont
- 287 192 405 2.545 0.440 0.144 0.051 3 0.5 Lat_Fis-ant-Vertical
- 1470 989 1955 2.258 0.392 0.129 0.037 13 2.4 Lat_Fis-post
- 2758 1736 4060 2.050 0.448 0.175 0.076 65 7.4 Pole_occipital
- 2495 1677 7344 3.124 0.711 0.167 0.092 132 9.4 Pole_temporal
- 2672 1813 3352 1.953 0.608 0.162 0.079 73 10.7 S_calcarine
- 2801 1858 3030 1.790 0.574 0.116 0.031 22 3.6 S_central
- 1182 783 1555 2.152 0.502 0.131 0.038 16 1.8 S_cingul-Marginalis
- 501 335 847 3.134 0.483 0.145 0.049 5 1.1 S_circular_insula_ant
- 1434 962 2262 2.733 0.502 0.092 0.025 7 1.5 S_circular_insula_inf
- 2045 1374 3034 2.452 0.496 0.119 0.033 15 2.9 S_circular_insula_sup
- 1126 767 2203 2.672 0.618 0.158 0.099 42 5.2 S_collat_transv_ant
- 393 256 413 2.020 0.355 0.159 0.059 5 0.9 S_collat_transv_post
- 2419 1659 3284 2.069 0.381 0.141 0.042 30 4.2 S_front_inf
- 1612 1084 2341 2.185 0.479 0.158 0.062 29 3.6 S_front_middle
- 2379 1624 3364 2.161 0.418 0.119 0.125 29 20.4 S_front_sup
- 434 298 576 2.038 0.280 0.118 0.030 3 0.6 S_interm_prim-Jensen
- 3646 2407 4459 1.953 0.301 0.126 0.032 40 5.0 S_intrapariet_and_P_trans
- 1320 903 1708 1.948 0.405 0.134 0.042 14 2.2 S_oc_middle_and_Lunatus
- 1524 1015 1907 2.017 0.428 0.128 0.036 15 2.2 S_oc_sup_and_transversal
- 1103 765 1470 2.151 0.425 0.143 0.047 16 2.0 S_occipital_ant
- 1297 860 1887 2.329 0.379 0.152 0.056 21 2.9 S_oc-temp_lat
- 2045 1457 3087 2.354 0.501 0.134 0.075 81 5.9 S_oc-temp_med_and_Lingual
- 428 300 589 2.000 0.375 0.166 0.052 7 1.0 S_orbital_lateral
- 917 615 1224 2.081 0.785 0.103 0.033 6 1.0 S_orbital_med-olfact
- 1416 955 2161 2.186 0.567 0.161 0.057 26 3.3 S_orbital-H_Shaped
- 2193 1422 2851 2.203 0.442 0.124 0.035 22 3.3 S_parieto_occipital
- 1399 933 1780 2.268 0.624 0.138 0.073 32 4.8 S_pericallosal
- 3225 2119 3933 1.994 0.384 0.125 0.037 34 4.9 S_postcentral
- 1419 935 2001 2.337 0.358 0.105 0.026 9 1.5 S_precentral-inf-part
- 1404 929 1856 2.253 0.431 0.138 0.041 16 2.2 S_precentral-sup-part
- 567 388 602 1.645 0.292 0.114 0.021 4 0.5 S_suborbital
- 1525 1058 2304 2.228 0.376 0.154 0.048 24 3.0 S_subparietal
- 1338 897 1869 2.314 0.532 0.137 0.049 18 2.6 S_temporal_inf
- 6793 4661 9959 2.213 0.469 0.131 0.038 89 10.4 S_temporal_sup
- 330 231 411 2.073 0.241 0.122 0.026 2 0.4 S_temporal_transverse
- #-----------------------------------------
- #@# Cortical Parc 3 lh Thu Aug 8 20:11:27 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub009 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...
- 830 labels changed using aseg
- relabeling using gibbs priors...
- 000: 3063 changed, 146118 examined...
- 001: 754 changed, 12773 examined...
- 002: 184 changed, 4121 examined...
- 003: 72 changed, 1135 examined...
- 004: 27 changed, 395 examined...
- 005: 9 changed, 125 examined...
- 006: 4 changed, 53 examined...
- 007: 3 changed, 25 examined...
- 008: 1 changed, 13 examined...
- 009: 0 changed, 5 examined...
- 47 labels changed using aseg
- 000: 70 total segments, 37 labels (417 vertices) changed
- 001: 35 total segments, 2 labels (3 vertices) changed
- 002: 33 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 33 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 974 vertices marked for relabeling...
- 974 labels changed in reclassification.
- writing output to ../label/lh.aparc.DKTatlas40.annot...
- classification took 1 minutes and 5 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 3 lh Thu Aug 8 20:12:31 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 sub009 lh white
- computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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
- 2086 1428 3891 2.514 0.513 0.129 0.037 24 3.2 caudalanteriorcingulate
- 3203 2110 5335 2.393 0.427 0.138 0.110 48 22.5 caudalmiddlefrontal
- 2874 1879 4160 2.045 0.407 0.156 0.057 49 6.7 cuneus
- 690 464 1878 3.077 0.686 0.123 0.037 6 1.2 entorhinal
- 5215 3450 10385 2.665 0.584 0.165 0.089 225 20.7 fusiform
- 8189 5512 13053 2.162 0.426 0.146 0.056 152 18.5 inferiorparietal
- 5400 3668 11544 2.629 0.591 0.161 0.084 151 15.5 inferiortemporal
- 1709 1096 2930 2.469 0.687 0.167 0.088 47 6.7 isthmuscingulate
- 8516 5545 13322 2.118 0.490 0.164 0.069 178 21.1 lateraloccipital
- 4464 2936 7497 2.309 0.730 0.168 0.087 128 14.2 lateralorbitofrontal
- 3941 2734 6174 2.075 0.520 0.167 0.072 78 11.8 lingual
- 2558 1699 4373 2.140 0.668 0.165 0.156 167 12.1 medialorbitofrontal
- 6621 4606 13255 2.497 0.571 0.163 0.068 206 17.9 middletemporal
- 1048 698 1719 2.165 0.501 0.124 0.114 91 5.1 parahippocampal
- 2458 1604 4232 2.337 0.553 0.120 0.034 26 3.4 paracentral
- 3065 2046 5779 2.469 0.402 0.145 0.050 53 5.8 parsopercularis
- 1227 806 2306 2.445 0.521 0.157 0.054 22 2.9 parsorbitalis
- 2569 1738 4204 2.192 0.448 0.162 0.072 570 5.6 parstriangularis
- 2162 1475 2506 1.742 0.474 0.180 0.083 42 7.9 pericalcarine
- 6837 4495 9568 1.925 0.549 0.138 0.052 122 14.2 postcentral
- 2317 1577 4214 2.543 0.491 0.158 0.057 48 5.5 posteriorcingulate
- 7733 4870 13058 2.411 0.475 0.126 0.040 90 12.6 precentral
- 6699 4451 11347 2.335 0.466 0.154 0.062 144 14.8 precuneus
- 2347 1501 4001 2.481 0.594 0.141 0.055 39 5.3 rostralanteriorcingulate
- 6003 4097 10198 2.187 0.489 0.169 0.065 132 15.6 rostralmiddlefrontal
- 12354 8331 23469 2.398 0.520 0.156 0.064 260 34.5 superiorfrontal
- 7491 4891 11055 2.046 0.358 0.145 0.045 130 13.9 superiorparietal
- 7838 5198 16683 2.756 0.704 0.135 0.048 140 15.8 superiortemporal
- 6923 4612 11872 2.362 0.476 0.146 0.048 116 13.4 supramarginal
- 761 473 1347 2.454 0.344 0.133 0.053 13 1.4 transversetemporal
- 3219 2127 6977 3.125 0.716 0.124 0.050 62 6.7 insula
- #--------------------------------------------
- #@# Tessellate rh Thu Aug 8 20:12:51 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts
- mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz
- Iteration Number : 1
- pass 1 (xy+): 4 found - 4 modified | TOTAL: 4
- pass 2 (xy+): 0 found - 4 modified | TOTAL: 4
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 4
- pass 1 (yz+): 3 found - 3 modified | TOTAL: 7
- pass 2 (yz+): 0 found - 3 modified | TOTAL: 7
- pass 1 (yz-): 1 found - 1 modified | TOTAL: 8
- pass 2 (yz-): 0 found - 1 modified | TOTAL: 8
- pass 1 (xz+): 4 found - 4 modified | TOTAL: 12
- pass 2 (xz+): 0 found - 4 modified | TOTAL: 12
- pass 1 (xz-): 1 found - 1 modified | TOTAL: 13
- pass 2 (xz-): 0 found - 1 modified | TOTAL: 13
- Iteration Number : 1
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 1
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 4 found - 4 modified | TOTAL: 4
- pass 2 (--): 0 found - 4 modified | TOTAL: 4
- pass 1 (-+): 1 found - 1 modified | TOTAL: 5
- pass 2 (-+): 0 found - 1 modified | TOTAL: 5
- 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 = 18 (out of 253619: 0.007097)
- 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: 297 vertices, 355 faces
- slice 50: 6084 vertices, 6352 faces
- slice 60: 15679 vertices, 16077 faces
- slice 70: 27718 vertices, 28118 faces
- slice 80: 39087 vertices, 39471 faces
- slice 90: 50806 vertices, 51217 faces
- slice 100: 62947 vertices, 63363 faces
- slice 110: 74553 vertices, 74945 faces
- slice 120: 85960 vertices, 86378 faces
- slice 130: 96968 vertices, 97362 faces
- slice 140: 107791 vertices, 108174 faces
- slice 150: 117190 vertices, 117512 faces
- slice 160: 125522 vertices, 125796 faces
- slice 170: 132989 vertices, 133271 faces
- slice 180: 139840 vertices, 140065 faces
- slice 190: 144792 vertices, 144961 faces
- slice 200: 147148 vertices, 147173 faces
- slice 210: 147156 vertices, 147176 faces
- slice 220: 147156 vertices, 147176 faces
- slice 230: 147156 vertices, 147176 faces
- slice 240: 147156 vertices, 147176 faces
- slice 250: 147156 vertices, 147176 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...
- 147156 voxel in cpt #1: X=-20 [v=147156,e=441528,f=294352] located at (24.144629, -17.471710, 38.149364)
- For the whole surface: X=-20 [v=147156,e=441528,f=294352]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Smooth1 rh Thu Aug 8 20:12:58 CEST 2013
- mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts
- setting seed for random number generator to 1234
- smoothing surface tessellation for 10 iterations...
- smoothing complete - recomputing first and second fundamental forms...
- #--------------------------------------------
- #@# Inflation1 rh Thu Aug 8 20:13:03 CEST 2013
- mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts
- avg radius = 47.7 mm, total surface area = 75769 mm^2
- writing inflated surface to ../surf/rh.inflated.nofix
- inflation took 0.7 minutes
- Not saving sulc
-
step 000: RMS=0.103 (target=0.015)
step 005: RMS=0.075 (target=0.015)
step 010: RMS=0.054 (target=0.015)
step 015: RMS=0.044 (target=0.015)
step 020: RMS=0.037 (target=0.015)
step 025: RMS=0.032 (target=0.015)
step 030: RMS=0.029 (target=0.015)
step 035: RMS=0.026 (target=0.015)
step 040: RMS=0.023 (target=0.015)
step 045: RMS=0.023 (target=0.015)
step 050: RMS=0.021 (target=0.015)
step 055: RMS=0.020 (target=0.015)
step 060: RMS=0.020 (target=0.015)
- inflation complete.
- Not saving sulc
- #--------------------------------------------
- #@# QSphere rh Thu Aug 8 20:13:44 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts
- mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix
- doing quick spherical unfolding.
- setting seed for random number genererator to 1234
- $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading original vertex positions...
- unfolding cortex into spherical form...
- surface projected - minimizing metric distortion...
- vertex spacing 0.95 +- 0.56 (0.00-->6.55) (max @ vno 109603 --> 109604)
- face area 0.02 +- 0.03 (-0.11-->0.64)
- scaling brain by 0.306...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=176.258, avgs=0
- 005/300: dt: 0.9000, rms radial error=175.998, avgs=0
- 010/300: dt: 0.9000, rms radial error=175.441, avgs=0
- 015/300: dt: 0.9000, rms radial error=174.711, avgs=0
- 020/300: dt: 0.9000, rms radial error=173.880, avgs=0
- 025/300: dt: 0.9000, rms radial error=172.991, avgs=0
- 030/300: dt: 0.9000, rms radial error=172.068, avgs=0
- 035/300: dt: 0.9000, rms radial error=171.129, avgs=0
- 040/300: dt: 0.9000, rms radial error=170.183, avgs=0
- 045/300: dt: 0.9000, rms radial error=169.235, avgs=0
- 050/300: dt: 0.9000, rms radial error=168.289, avgs=0
- 055/300: dt: 0.9000, rms radial error=167.346, avgs=0
- 060/300: dt: 0.9000, rms radial error=166.406, avgs=0
- 065/300: dt: 0.9000, rms radial error=165.471, avgs=0
- 070/300: dt: 0.9000, rms radial error=164.540, avgs=0
- 075/300: dt: 0.9000, rms radial error=163.614, avgs=0
- 080/300: dt: 0.9000, rms radial error=162.692, avgs=0
- 085/300: dt: 0.9000, rms radial error=161.778, avgs=0
- 090/300: dt: 0.9000, rms radial error=160.872, avgs=0
- 095/300: dt: 0.9000, rms radial error=159.970, avgs=0
- 100/300: dt: 0.9000, rms radial error=159.074, avgs=0
- 105/300: dt: 0.9000, rms radial error=158.182, avgs=0
- 110/300: dt: 0.9000, rms radial error=157.295, avgs=0
- 115/300: dt: 0.9000, rms radial error=156.414, avgs=0
- 120/300: dt: 0.9000, rms radial error=155.537, avgs=0
- 125/300: dt: 0.9000, rms radial error=154.666, avgs=0
- 130/300: dt: 0.9000, rms radial error=153.799, avgs=0
- 135/300: dt: 0.9000, rms radial error=152.937, avgs=0
- 140/300: dt: 0.9000, rms radial error=152.079, avgs=0
- 145/300: dt: 0.9000, rms radial error=151.226, avgs=0
- 150/300: dt: 0.9000, rms radial error=150.378, avgs=0
- 155/300: dt: 0.9000, rms radial error=149.534, avgs=0
- 160/300: dt: 0.9000, rms radial error=148.695, avgs=0
- 165/300: dt: 0.9000, rms radial error=147.861, avgs=0
- 170/300: dt: 0.9000, rms radial error=147.031, avgs=0
- 175/300: dt: 0.9000, rms radial error=146.206, avgs=0
- 180/300: dt: 0.9000, rms radial error=145.386, avgs=0
- 185/300: dt: 0.9000, rms radial error=144.570, avgs=0
- 190/300: dt: 0.9000, rms radial error=143.758, avgs=0
- 195/300: dt: 0.9000, rms radial error=142.951, avgs=0
- 200/300: dt: 0.9000, rms radial error=142.148, avgs=0
- 205/300: dt: 0.9000, rms radial error=141.350, avgs=0
- 210/300: dt: 0.9000, rms radial error=140.556, avgs=0
- 215/300: dt: 0.9000, rms radial error=139.767, avgs=0
- 220/300: dt: 0.9000, rms radial error=138.982, avgs=0
- 225/300: dt: 0.9000, rms radial error=138.201, avgs=0
- 230/300: dt: 0.9000, rms radial error=137.424, avgs=0
- 235/300: dt: 0.9000, rms radial error=136.652, avgs=0
- 240/300: dt: 0.9000, rms radial error=135.885, avgs=0
- 245/300: dt: 0.9000, rms radial error=135.121, avgs=0
- 250/300: dt: 0.9000, rms radial error=134.362, avgs=0
- 255/300: dt: 0.9000, rms radial error=133.607, avgs=0
- 260/300: dt: 0.9000, rms radial error=132.856, avgs=0
- 265/300: dt: 0.9000, rms radial error=132.109, avgs=0
- 270/300: dt: 0.9000, rms radial error=131.366, avgs=0
- 275/300: dt: 0.9000, rms radial error=130.628, avgs=0
- 280/300: dt: 0.9000, rms radial error=129.893, avgs=0
- 285/300: dt: 0.9000, rms radial error=129.163, avgs=0
- 290/300: dt: 0.9000, rms radial error=128.437, avgs=0
- 295/300: dt: 0.9000, rms radial error=127.715, avgs=0
- 300/300: dt: 0.9000, rms radial error=126.996, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 17388.32
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00016
- epoch 2 (K=40.0), pass 1, starting sse = 2987.17
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00014
- epoch 3 (K=160.0), pass 1, starting sse = 323.75
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.12/12 = 0.00964
- epoch 4 (K=640.0), pass 1, starting sse = 18.55
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.25/22 = 0.01155
- final writing spherical brain to ../surf/rh.qsphere.nofix
- spherical transformation took 0.10 hours
- distance error %100000.00
- #--------------------------------------------
- #@# Fix Topology rh Thu Aug 8 20:19:37 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/sub009/scripts
- mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub009 rh
- reading spherical homeomorphism from 'qsphere.nofix'
- using genetic algorithm with optimized parameters
- setting seed for random number genererator to 1234
- *************************************************************
- Topology Correction Parameters
- retessellation mode: genetic search
- number of patches/generation : 10
- number of generations : 10
- surface mri loglikelihood coefficient : 1.0
- volume mri loglikelihood coefficient : 10.0
- normal dot loglikelihood coefficient : 1.0
- quadratic curvature loglikelihood coefficient : 1.0
- volume resolution : 2
- eliminate vertices during search : 1
- initial patch selection : 1
- select all defect vertices : 0
- ordering dependant retessellation: 0
- use precomputed edge table : 0
- smooth retessellated patch : 2
- match retessellated patch : 1
- verbose mode : 0
- *************************************************************
- INFO: assuming .mgz format
- $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- before topology correction, eno=-20 (nv=147156, nf=294352, ne=441528, g=11)
- using quasi-homeomorphic spherical map to tessellate cortical surface...
- Correction of the Topology
- Finding true center and radius of Spherical Surface...done
- Surface centered at (0,0,0) with radius 100.0 in 10 iterations
- marking ambiguous vertices...
- 1820 ambiguous faces found in tessellation
- segmenting defects...
- 20 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- 20 defects to be corrected
- 0 vertices coincident
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -9.9143 (-4.9571)
- -vertex loglikelihood: -6.7225 (-3.3612)
- -normal dot loglikelihood: -3.6256 (-3.6256)
- -quad curv loglikelihood: -6.5992 (-3.2996)
- Total Loglikelihood : -26.8615
- CORRECTING DEFECT 0 (vertices=16, convex hull=56)
- After retessellation of defect 0, euler #=-17 (145994,437409,291398) : difference with theory (-17) = 0
- CORRECTING DEFECT 1 (vertices=42, convex hull=77)
- After retessellation of defect 1, euler #=-16 (146017,437511,291478) : difference with theory (-16) = 0
- CORRECTING DEFECT 2 (vertices=57, convex hull=101)
- After retessellation of defect 2, euler #=-15 (146049,437646,291582) : difference with theory (-15) = 0
- CORRECTING DEFECT 3 (vertices=15, convex hull=30)
- After retessellation of defect 3, euler #=-14 (146053,437668,291601) : difference with theory (-14) = 0
- CORRECTING DEFECT 4 (vertices=22, convex hull=73)
- After retessellation of defect 4, euler #=-13 (146068,437744,291663) : difference with theory (-13) = 0
- CORRECTING DEFECT 5 (vertices=15, convex hull=31)
- After retessellation of defect 5, euler #=-12 (146072,437767,291683) : difference with theory (-12) = 0
- CORRECTING DEFECT 6 (vertices=56, convex hull=131)
- After retessellation of defect 6, euler #=-11 (146100,437904,291793) : difference with theory (-11) = 0
- CORRECTING DEFECT 7 (vertices=18, convex hull=24)
- After retessellation of defect 7, euler #=-10 (146103,437919,291806) : difference with theory (-10) = 0
- CORRECTING DEFECT 8 (vertices=457, convex hull=274)
- After retessellation of defect 8, euler #=-9 (146119,438110,291982) : difference with theory (-9) = 0
- CORRECTING DEFECT 9 (vertices=40, convex hull=20)
- After retessellation of defect 9, euler #=-8 (146123,438130,291999) : difference with theory (-8) = 0
- CORRECTING DEFECT 10 (vertices=10, convex hull=13)
- After retessellation of defect 10, euler #=-7 (146124,438135,292004) : difference with theory (-7) = 0
- CORRECTING DEFECT 11 (vertices=118, convex hull=165)
- After retessellation of defect 11, euler #=-6 (146166,438341,292169) : difference with theory (-6) = 0
- CORRECTING DEFECT 12 (vertices=76, convex hull=70)
- After retessellation of defect 12, euler #=-5 (146200,438476,292271) : difference with theory (-5) = 0
- CORRECTING DEFECT 13 (vertices=7, convex hull=24)
- After retessellation of defect 13, euler #=-4 (146202,438490,292284) : difference with theory (-4) = 0
- CORRECTING DEFECT 14 (vertices=15, convex hull=14)
- After retessellation of defect 14, euler #=-3 (146203,438497,292291) : difference with theory (-3) = 0
- CORRECTING DEFECT 15 (vertices=64, convex hull=46)
- After retessellation of defect 15, euler #=-2 (146208,438532,292322) : difference with theory (-2) = 0
- CORRECTING DEFECT 16 (vertices=22, convex hull=26)
- After retessellation of defect 16, euler #=-1 (146209,438544,292334) : difference with theory (-1) = 0
- CORRECTING DEFECT 17 (vertices=29, convex hull=77)
- After retessellation of defect 17, euler #=0 (146224,438619,292395) : difference with theory (0) = 0
- CORRECTING DEFECT 18 (vertices=55, convex hull=80)
- After retessellation of defect 18, euler #=1 (146244,438714,292471) : difference with theory (1) = 0
- CORRECTING DEFECT 19 (vertices=35, convex hull=33)
- After retessellation of defect 19, euler #=2 (146248,438738,292492) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.88 +- 0.22 (0.11-->7.99) (max @ vno 80780 --> 80800)
- 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 (0.11-->7.99) (max @ vno 80780 --> 80800)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 79 mutations (36.7%), 136 crossovers (63.3%), 164 vertices were eliminated
- building final representation...
- 908 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=146248, nf=292492, ne=438738, g=0)
- writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 27.0 minutes
- 0 defective edges
- removing intersecting faces
- 000: 153 intersecting
- 001: 2 intersecting
- mris_euler_number ../surf/rh.orig
- euler # = v-e+f = 2g-2: 146248 - 438738 + 292492 = 2 --> 0 holes
- F =2V-4: 292492 = 292496-4 (0)
- 2E=3F: 877476 = 877476 (0)
- total defect index = 0
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts
- mris_remove_intersection ../surf/rh.orig ../surf/rh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 16 intersecting
- 001: 4 intersecting
- writing corrected surface to ../surf/rh.orig
- rm ../surf/rh.inflated
- #--------------------------------------------
- #@# Make White Surf rh Thu Aug 8 20:46:44 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts
- mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub009 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/sub009/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/wm.mgz...
- 19164 bright wm thresholded.
- 814 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.orig...
- computing class statistics...
- border white: 259466 voxels (1.55%)
- border gray 303507 voxels (1.81%)
- WM (92.0): 93.0 +- 10.6 [70.0 --> 110.0]
- GM (74.0) : 72.2 +- 13.0 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 44.0 (was 70)
- setting MAX_BORDER_WHITE to 115.6 (was 105)
- setting MIN_BORDER_WHITE to 57.0 (was 85)
- setting MAX_CSF to 30.9 (was 40)
- setting MAX_GRAY to 94.4 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 50.5 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 17.9 (was 40)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.81 +- 0.22 (0.02-->2.66) (max @ vno 79769 --> 80799)
- face area 0.27 +- 0.12 (0.00-->1.76)
- mean absolute distance = 0.67 +- 0.76
- 3877 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 = 92.8, mean outside = 66.9
- smoothing surface for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- removing 3 vertex label from ripped group
- mean border=70.8, 60 (60) missing vertices, mean dist 0.4 [0.5 (%30.5)->0.8 (%69.5))]
- %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 1
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.92 +- 0.27 (0.06-->4.62) (max @ vno 80799 --> 79769)
- face area 0.27 +- 0.13 (0.00-->2.93)
- mean absolute distance = 0.31 +- 0.45
- 2699 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=8750270.0, rms=14.49
- 001: dt: 0.5000, sse=8701720.0, rms=10.592 (0.000%)
- 002: dt: 0.5000, sse=8905935.0, rms=8.311 (0.000%)
- 003: dt: 0.5000, sse=8952658.0, rms=6.782 (0.000%)
- 004: dt: 0.5000, sse=9183209.0, rms=5.832 (0.000%)
- 005: dt: 0.5000, sse=9228581.0, rms=5.261 (0.000%)
- 006: dt: 0.5000, sse=9405899.0, rms=4.963 (0.000%)
- 007: dt: 0.5000, sse=9364875.0, rms=4.779 (0.000%)
- 008: dt: 0.5000, sse=9414885.0, rms=4.684 (0.000%)
- 009: dt: 0.5000, sse=9330527.0, rms=4.603 (0.000%)
- rms = 4.56, time step reduction 1 of 3 to 0.250...
- 010: dt: 0.5000, sse=9347492.0, rms=4.560 (0.000%)
- 011: dt: 0.2500, sse=6068557.5, rms=3.252 (0.000%)
- 012: dt: 0.2500, sse=5611800.0, rms=2.777 (0.000%)
- 013: dt: 0.2500, sse=5301363.5, rms=2.682 (0.000%)
- 014: dt: 0.2500, sse=5209381.5, rms=2.584 (0.000%)
- rms = 2.55, time step reduction 2 of 3 to 0.125...
- 015: dt: 0.2500, sse=5096611.5, rms=2.548 (0.000%)
- 016: dt: 0.1250, sse=4827331.5, rms=2.288 (0.000%)
- rms = 2.25, time step reduction 3 of 3 to 0.062...
- 017: dt: 0.1250, sse=4771513.5, rms=2.251 (0.000%)
- positioning took 2.2 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 1 vertex label from ripped group
- removing 3 vertex label from ripped group
- mean border=75.7, 61 (6) missing vertices, mean dist -0.2 [0.3 (%78.9)->0.2 (%21.1))]
- %81 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.90 +- 0.26 (0.06-->4.92) (max @ vno 80799 --> 79769)
- face area 0.35 +- 0.17 (0.00-->4.22)
- mean absolute distance = 0.21 +- 0.27
- 2522 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5950757.0, rms=6.43
- 018: dt: 0.5000, sse=6106958.5, rms=4.340 (0.000%)
- rms = 4.77, time step reduction 1 of 3 to 0.250...
- 019: dt: 0.2500, sse=5552593.0, rms=3.126 (0.000%)
- 020: dt: 0.2500, sse=5360413.0, rms=2.562 (0.000%)
- 021: dt: 0.2500, sse=5281753.0, rms=2.157 (0.000%)
- rms = 2.13, time step reduction 2 of 3 to 0.125...
- 022: dt: 0.2500, sse=5269842.0, rms=2.132 (0.000%)
- 023: dt: 0.1250, sse=5055385.5, rms=1.847 (0.000%)
- rms = 1.80, time step reduction 3 of 3 to 0.062...
- 024: dt: 0.1250, sse=4995741.0, rms=1.797 (0.000%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 3 vertex label from ripped group
- mean border=79.7, 66 (3) missing vertices, mean dist -0.1 [0.2 (%80.5)->0.2 (%19.5))]
- %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.25 (0.10-->5.10) (max @ vno 80799 --> 79769)
- face area 0.34 +- 0.16 (0.00-->4.34)
- mean absolute distance = 0.15 +- 0.22
- 2643 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5549135.0, rms=4.88
- 025: dt: 0.5000, sse=5665896.5, rms=4.369 (0.000%)
- rms = 4.56, time step reduction 1 of 3 to 0.250...
- 026: dt: 0.2500, sse=5164925.0, rms=2.733 (0.000%)
- 027: dt: 0.2500, sse=5055262.5, rms=2.336 (0.000%)
- 028: dt: 0.2500, sse=5154182.0, rms=1.924 (0.000%)
- rms = 2.01, time step reduction 2 of 3 to 0.125...
- 029: dt: 0.1250, sse=5073879.0, rms=1.763 (0.000%)
- 030: dt: 0.1250, sse=4973509.0, rms=1.543 (0.000%)
- rms = 1.52, time step reduction 3 of 3 to 0.062...
- 031: dt: 0.1250, sse=4934952.0, rms=1.518 (0.000%)
- positioning took 1.1 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 3 vertex label from ripped group
- mean border=81.0, 52 (1) missing vertices, mean dist -0.0 [0.2 (%60.3)->0.1 (%39.7))]
- %92 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- writing white matter surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.white...
- writing smoothed curvature to rh.curv
- 000: dt: 0.0000, sse=4962267.5, rms=1.94
- rms = 3.25, time step reduction 1 of 3 to 0.250...
- 032: dt: 0.2500, sse=5031940.5, rms=1.215 (0.000%)
- 033: dt: 0.2500, sse=5172706.5, rms=1.143 (0.000%)
- rms = 1.14, time step reduction 2 of 3 to 0.125...
- 034: dt: 0.2500, sse=5274603.0, rms=1.143 (0.000%)
- rms = 1.12, time step reduction 3 of 3 to 0.062...
- 035: dt: 0.1250, sse=5311404.5, rms=1.116 (0.000%)
- positioning took 0.6 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- generating cortex label...
- 13 non-cortical segments detected
- only using segment with 1610 vertices
- erasing segment 1 (vno[0] = 87431)
- erasing segment 2 (vno[0] = 90706)
- erasing segment 3 (vno[0] = 102106)
- erasing segment 4 (vno[0] = 103142)
- erasing segment 5 (vno[0] = 103149)
- erasing segment 6 (vno[0] = 103219)
- erasing segment 7 (vno[0] = 106604)
- erasing segment 8 (vno[0] = 107511)
- erasing segment 9 (vno[0] = 109450)
- erasing segment 10 (vno[0] = 113247)
- erasing segment 11 (vno[0] = 113282)
- erasing segment 12 (vno[0] = 116705)
- writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/label/rh.cortex.label...
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.curv
- writing smoothed area to rh.area
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.area
- vertex spacing 0.89 +- 0.25 (0.04-->5.20) (max @ vno 80799 --> 79769)
- face area 0.34 +- 0.16 (0.00-->4.40)
- refinement took 7.1 minutes
- #--------------------------------------------
- #@# Smooth2 rh Thu Aug 8 20:53:51 CEST 2013
- mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts
- smoothing for 3 iterations
- setting seed for random number generator to 1234
- smoothing surface tessellation for 3 iterations...
- smoothing complete - recomputing first and second fundamental forms...
- #--------------------------------------------
- #@# Inflation2 rh Thu Aug 8 20:53:55 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts
- mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated
- avg radius = 47.9 mm, total surface area = 88544 mm^2
- writing inflated surface to ../surf/rh.inflated
- writing sulcal depths to ../surf/rh.sulc
-
step 000: RMS=0.121 (target=0.015)
step 005: RMS=0.082 (target=0.015)
step 010: RMS=0.060 (target=0.015)
step 015: RMS=0.048 (target=0.015)
step 020: RMS=0.039 (target=0.015)
step 025: RMS=0.033 (target=0.015)
step 030: RMS=0.027 (target=0.015)
step 035: RMS=0.023 (target=0.015)
step 040: RMS=0.019 (target=0.015)
step 045: RMS=0.017 (target=0.015)
step 050: RMS=0.016 (target=0.015)
- inflation complete.
- inflation took 0.5 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
- 188 vertices thresholded to be in k1 ~ [-0.26 0.37], k2 ~ [-0.13 0.11]
- total integrated curvature = 0.465*4pi (5.845) --> 1 handles
- ICI = 1.6, FI = 11.9, variation=198.417
- 140 vertices thresholded to be in [-0.02 0.02]
- writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level
- curvature mean = 0.000, std = 0.001
- 139 vertices thresholded to be in [-0.16 0.15]
- done.
- writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.016, std = 0.024
- done.
- #-----------------------------------------
- #@# Curvature Stats rh Thu Aug 8 20:56:18 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub009 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 [ sub009/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 [ 273 ]
- Gb_filter = 0
- WARN: S lookup min: -0.238989
- WARN: S explicit min: 0.000000 vertex = 170
- #--------------------------------------------
- #@# Sphere rh Thu Aug 8 20:56:24 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 0.283...
- MRISunfold() max_passes = 1 -------
- tol=5.0e-01, sigma=0.0, host=snake, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
- using quadratic fit line minimization
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 1.000000
- desired_rms_height -1.000000
- momentum 0.900000
- nbhd_size 7
- max_nbrs 8
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 1234
- --------------------
- mrisRemoveNegativeArea()
- pass 1: epoch 1 of 3 starting distance error %19.30
- pass 1: epoch 2 of 3 starting distance error %19.24
- unfolding complete - removing small folds...
- starting distance error %19.19
- removing remaining folds...
- final distance error %19.21
- MRISunfold() return, current seed 1234
- writing spherical brain to ../surf/rh.sphere
- spherical transformation took 0.98 hours
- #--------------------------------------------
- #@# Surf Reg rh Thu Aug 8 21:55:17 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 = 0.564
- curvature mean = 0.014, std = 0.929
- curvature mean = 0.025, std = 0.844
- Starting MRISrigidBodyAlignGlobal()
- d=64.00 min @ (16.00, 0.00, 0.00) sse = 412168.3, tmin=1.3556
- d=32.00 min @ (-8.00, -8.00, 0.00) sse = 327821.5, tmin=2.6979
- d=16.00 min @ (-4.00, 0.00, 4.00) sse = 302534.3, tmin=4.0419
- d=8.00 min @ (2.00, 2.00, 0.00) sse = 294141.2, tmin=5.4223
- d=4.00 min @ (1.00, 0.00, -1.00) sse = 292668.7, tmin=6.8288
- d=2.00 min @ (-0.50, -0.50, 0.50) sse = 292154.8, tmin=8.2403
- d=1.00 min @ (-0.25, 0.00, -0.25) sse = 292002.5, tmin=9.6176
- d=0.50 min @ (0.12, 0.12, 0.00) sse = 291966.3, tmin=11.0210
- tol=1.0e+00, sigma=0.5, host=snake, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
- using quadratic fit line minimization
- MRISrigidBodyAlignGlobal() done 11.02 min
- curvature mean = -0.007, std = 0.932
- curvature mean = 0.012, std = 0.930
- curvature mean = -0.010, std = 0.941
- curvature mean = 0.006, std = 0.966
- curvature mean = -0.011, std = 0.940
- curvature mean = 0.002, std = 0.984
- 2 Reading smoothwm
- curvature mean = -0.024, std = 0.309
- curvature mean = 0.005, std = 0.069
- curvature mean = 0.077, std = 0.314
- curvature mean = 0.005, std = 0.083
- curvature mean = 0.039, std = 0.507
- curvature mean = 0.005, std = 0.088
- curvature mean = 0.021, std = 0.656
- curvature mean = 0.006, std = 0.091
- curvature mean = 0.007, std = 0.776
- MRISregister() return, current seed 0
- writing registered surface to ../surf/rh.sphere.reg...
- expanding nbhd size to 1
- #--------------------------------------------
- #@# Jacobian white rh Thu Aug 8 22:28:55 CEST 2013
- mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white
- reading surface from ../surf/rh.white...
- writing curvature file ../surf/rh.jacobian_white
- #--------------------------------------------
- #@# AvgCurv rh Thu Aug 8 22:28:57 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts
- mrisp_paint -a 5 /opt/freesurfer/5.3.0/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv
- averaging curvature patterns 5 times...
- reading surface from ../surf/rh.sphere.reg...
- reading template parameterization from /opt/freesurfer/5.3.0/average/rh.average.curvature.filled.buckner40.tif...
- writing curvature file to ../surf/rh.avg_curv...
- #-----------------------------------------
- #@# Cortical Parc rh Thu Aug 8 22:29:00 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub009 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...
- 1209 labels changed using aseg
- relabeling using gibbs priors...
- 000: 3289 changed, 146248 examined...
- 001: 798 changed, 13951 examined...
- 002: 197 changed, 4307 examined...
- 003: 88 changed, 1223 examined...
- 004: 46 changed, 528 examined...
- 005: 17 changed, 256 examined...
- 006: 9 changed, 98 examined...
- 007: 3 changed, 40 examined...
- 008: 2 changed, 16 examined...
- 009: 4 changed, 13 examined...
- 010: 3 changed, 23 examined...
- 011: 1 changed, 17 examined...
- 012: 0 changed, 9 examined...
- 170 labels changed using aseg
- 000: 129 total segments, 91 labels (443 vertices) changed
- 001: 42 total segments, 4 labels (21 vertices) changed
- 002: 38 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 42 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 1931 vertices marked for relabeling...
- 1931 labels changed in reclassification.
- writing output to ../label/rh.aparc.annot...
- classification took 1 minutes and 11 seconds.
- #--------------------------------------------
- #@# Make Pial Surf rh Thu Aug 8 22:30:11 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts
- mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub009 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/sub009/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/wm.mgz...
- 19164 bright wm thresholded.
- 814 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.orig...
- computing class statistics...
- border white: 259466 voxels (1.55%)
- border gray 303507 voxels (1.81%)
- WM (92.0): 93.0 +- 10.6 [70.0 --> 110.0]
- GM (74.0) : 72.2 +- 13.0 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 44.0 (was 70)
- setting MAX_BORDER_WHITE to 115.6 (was 105)
- setting MIN_BORDER_WHITE to 57.0 (was 85)
- setting MAX_CSF to 30.9 (was 40)
- setting MAX_GRAY to 94.4 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 50.5 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 17.9 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=105, GM=57
- mean inside = 92.8, mean outside = 66.9
- 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/sub009/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.81 +- 0.22 (0.02-->2.66) (max @ vno 79769 --> 80799)
- face area 0.27 +- 0.12 (0.00-->1.76)
- mean absolute distance = 0.67 +- 0.76
- 3914 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 15 points - only 0.00% unknown
- deleting segment 3 with 333 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 4 with 3 points - only 0.00% unknown
- deleting segment 7 with 8 points - only 0.00% unknown
- deleting segment 8 with 7 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 9 with 3 points - only 0.00% unknown
- deleting segment 10 with 29 points - only 0.00% unknown
- mean border=70.8, 61 (61) missing vertices, mean dist 0.4 [0.5 (%30.5)->0.8 (%69.5))]
- %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 1
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.92 +- 0.26 (0.06-->4.62) (max @ vno 80799 --> 79769)
- face area 0.27 +- 0.13 (0.00-->2.93)
- mean absolute distance = 0.31 +- 0.45
- 2701 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=8763778.0, rms=14.48
- 001: dt: 0.5000, sse=8717599.0, rms=10.586 (0.000%)
- 002: dt: 0.5000, sse=8921043.0, rms=8.306 (0.000%)
- 003: dt: 0.5000, sse=8975575.0, rms=6.778 (0.000%)
- 004: dt: 0.5000, sse=9204313.0, rms=5.828 (0.000%)
- 005: dt: 0.5000, sse=9255857.0, rms=5.259 (0.000%)
- 006: dt: 0.5000, sse=9432396.0, rms=4.961 (0.000%)
- 007: dt: 0.5000, sse=9394983.0, rms=4.777 (0.000%)
- 008: dt: 0.5000, sse=9439806.0, rms=4.682 (0.000%)
- 009: dt: 0.5000, sse=9361114.0, rms=4.602 (0.000%)
- rms = 4.56, time step reduction 1 of 3 to 0.250...
- 010: dt: 0.5000, sse=9373735.0, rms=4.559 (0.000%)
- 011: dt: 0.2500, sse=6083314.5, rms=3.252 (0.000%)
- 012: dt: 0.2500, sse=5624215.0, rms=2.777 (0.000%)
- 013: dt: 0.2500, sse=5313463.5, rms=2.682 (0.000%)
- 014: dt: 0.2500, sse=5220910.0, rms=2.585 (0.000%)
- rms = 2.55, time step reduction 2 of 3 to 0.125...
- 015: dt: 0.2500, sse=5107566.0, rms=2.548 (0.000%)
- 016: dt: 0.1250, sse=4839035.5, rms=2.289 (0.000%)
- rms = 2.25, time step reduction 3 of 3 to 0.062...
- 017: dt: 0.1250, sse=4783469.5, rms=2.252 (0.000%)
- positioning took 2.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 36 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 1 with 4 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 5 with 16 points - only 0.00% unknown
- deleting segment 6 with 297 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 7 with 3 points - only 0.00% unknown
- deleting segment 8 with 11 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 10 with 18 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 11 with 3 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 12 with 3 points - only 0.00% unknown
- deleting segment 13 with 34 points - only 0.00% unknown
- mean border=75.7, 65 (8) missing vertices, mean dist -0.2 [0.3 (%78.9)->0.2 (%21.1))]
- %82 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.90 +- 0.25 (0.06-->4.92) (max @ vno 80799 --> 79769)
- face area 0.35 +- 0.17 (0.00-->4.22)
- mean absolute distance = 0.21 +- 0.27
- 2540 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5964654.0, rms=6.43
- 018: dt: 0.5000, sse=6123459.0, rms=4.336 (0.000%)
- rms = 4.76, time step reduction 1 of 3 to 0.250...
- 019: dt: 0.2500, sse=5567103.0, rms=3.123 (0.000%)
- 020: dt: 0.2500, sse=5374869.5, rms=2.560 (0.000%)
- 021: dt: 0.2500, sse=5296525.0, rms=2.156 (0.000%)
- rms = 2.13, time step reduction 2 of 3 to 0.125...
- 022: dt: 0.2500, sse=5284441.0, rms=2.132 (0.000%)
- 023: dt: 0.1250, sse=5069048.5, rms=1.847 (0.000%)
- rms = 1.80, time step reduction 3 of 3 to 0.062...
- 024: dt: 0.1250, sse=5009618.5, rms=1.797 (0.000%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 19 points - only 0.00% unknown
- deleting segment 1 with 13 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 2 with 2 points - only 0.00% unknown
- deleting segment 3 with 294 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 4 with 4 points - only 0.00% unknown
- deleting segment 5 with 14 points - only 0.00% unknown
- deleting segment 7 with 33 points - only 0.00% unknown
- deleting segment 8 with 10 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 9 with 3 points - only 0.00% unknown
- deleting segment 10 with 40 points - only 0.00% unknown
- mean border=79.7, 69 (3) missing vertices, mean dist -0.1 [0.2 (%80.4)->0.2 (%19.6))]
- %91 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.25 (0.10-->5.10) (max @ vno 80799 --> 79769)
- face area 0.34 +- 0.16 (0.00-->4.34)
- mean absolute distance = 0.15 +- 0.22
- 2666 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5564047.0, rms=4.88
- 025: dt: 0.5000, sse=5684758.5, rms=4.366 (0.000%)
- rms = 4.56, time step reduction 1 of 3 to 0.250...
- 026: dt: 0.2500, sse=5182205.5, rms=2.732 (0.000%)
- 027: dt: 0.2500, sse=5070397.5, rms=2.336 (0.000%)
- 028: dt: 0.2500, sse=5170511.5, rms=1.924 (0.000%)
- rms = 2.01, time step reduction 2 of 3 to 0.125...
- 029: dt: 0.1250, sse=5089885.0, rms=1.763 (0.000%)
- 030: dt: 0.1250, sse=4988666.5, rms=1.544 (0.000%)
- rms = 1.52, time step reduction 3 of 3 to 0.062...
- 031: dt: 0.1250, sse=4950042.0, rms=1.519 (0.000%)
- positioning took 1.1 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 22 points - only 0.00% unknown
- deleting segment 4 with 13 points - only 0.00% unknown
- deleting segment 5 with 307 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 6 with 4 points - only 0.00% unknown
- deleting segment 7 with 16 points - only 0.00% unknown
- deleting segment 8 with 21 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 10 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 11 with 3 points - only 0.00% unknown
- deleting segment 12 with 34 points - only 0.00% unknown
- mean border=80.9, 56 (1) missing vertices, mean dist -0.0 [0.2 (%60.2)->0.1 (%39.8))]
- %93 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- repositioning cortical surface to gray/csf boundary.
- smoothing T1 volume with sigma = 2.000
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4977131.0, rms=1.94
- rms = 3.24, time step reduction 1 of 3 to 0.250...
- 032: dt: 0.2500, sse=5048153.0, rms=1.214 (0.000%)
- 033: dt: 0.2500, sse=5190069.5, rms=1.144 (0.000%)
- rms = 1.14, time step reduction 2 of 3 to 0.125...
- 034: dt: 0.2500, sse=5292632.5, rms=1.144 (0.000%)
- rms = 1.12, time step reduction 3 of 3 to 0.062...
- 035: dt: 0.1250, sse=5328846.0, rms=1.117 (0.000%)
- positioning took 0.6 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- deleting segment 5 with 3 points - only 0.00% unknown
- smoothing surface for 5 iterations...
- mean border=47.1, 88 (88) missing vertices, mean dist 1.7 [0.1 (%0.0)->2.2 (%100.0))]
- %15 local maxima, %58 large gradients and %23 min vals, 1039 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=33695572.0, rms=32.95
- 001: dt: 0.5000, sse=24109036.0, rms=27.266 (0.000%)
- 002: dt: 0.5000, sse=17436482.0, rms=22.508 (0.000%)
- 003: dt: 0.5000, sse=12950371.0, rms=18.625 (0.000%)
- 004: dt: 0.5000, sse=10276401.0, rms=15.538 (0.000%)
- 005: dt: 0.5000, sse=8813430.0, rms=13.154 (0.000%)
- 006: dt: 0.5000, sse=7984159.0, rms=11.361 (0.000%)
- 007: dt: 0.5000, sse=7484004.5, rms=9.851 (0.000%)
- 008: dt: 0.5000, sse=7189707.5, rms=8.521 (0.000%)
- 009: dt: 0.5000, sse=7017868.5, rms=7.286 (0.000%)
- 010: dt: 0.5000, sse=7024291.5, rms=6.271 (0.000%)
- 011: dt: 0.5000, sse=7163269.0, rms=5.507 (0.000%)
- 012: dt: 0.5000, sse=7435373.0, rms=5.011 (0.000%)
- 013: dt: 0.5000, sse=7562700.5, rms=4.698 (0.000%)
- 014: dt: 0.5000, sse=7753237.5, rms=4.520 (0.000%)
- 015: dt: 0.5000, sse=7852165.5, rms=4.389 (0.000%)
- 016: dt: 0.5000, sse=7904825.0, rms=4.320 (0.000%)
- 017: dt: 0.5000, sse=7932647.0, rms=4.251 (0.000%)
- rms = 4.22, time step reduction 1 of 3 to 0.250...
- 018: dt: 0.5000, sse=7944391.5, rms=4.219 (0.000%)
- 019: dt: 0.2500, sse=5529934.0, rms=3.422 (0.000%)
- 020: dt: 0.2500, sse=5269636.5, rms=3.206 (0.000%)
- rms = 3.18, time step reduction 2 of 3 to 0.125...
- 021: dt: 0.2500, sse=5108067.5, rms=3.180 (0.000%)
- 022: dt: 0.1250, sse=4893078.0, rms=3.057 (0.000%)
- rms = 3.04, time step reduction 3 of 3 to 0.062...
- 023: dt: 0.1250, sse=4848967.5, rms=3.044 (0.000%)
- positioning took 3.0 minutes
- mean border=45.0, 745 (8) missing vertices, mean dist 0.1 [0.2 (%50.3)->0.5 (%49.7))]
- %32 local maxima, %45 large gradients and %19 min vals, 314 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=5475894.0, rms=4.77
- 024: dt: 0.5000, sse=5843607.0, rms=4.123 (0.000%)
- rms = 4.21, time step reduction 1 of 3 to 0.250...
- 025: dt: 0.2500, sse=5424345.0, rms=3.471 (0.000%)
- 026: dt: 0.2500, sse=5570535.5, rms=3.199 (0.000%)
- 027: dt: 0.2500, sse=5477197.5, rms=3.092 (0.000%)
- 028: dt: 0.2500, sse=5540206.5, rms=3.038 (0.000%)
- rms = 3.01, time step reduction 2 of 3 to 0.125...
- 029: dt: 0.2500, sse=5515802.0, rms=3.011 (0.000%)
- 030: dt: 0.1250, sse=5327823.0, rms=2.869 (0.000%)
- rms = 2.84, time step reduction 3 of 3 to 0.062...
- 031: dt: 0.1250, sse=5312098.5, rms=2.843 (0.000%)
- positioning took 1.1 minutes
- mean border=42.5, 857 (5) missing vertices, mean dist 0.1 [0.2 (%37.7)->0.4 (%62.3))]
- %54 local maxima, %23 large gradients and %19 min vals, 471 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=5656001.0, rms=4.41
- 032: dt: 0.5000, sse=5915675.0, rms=4.144 (0.000%)
- rms = 4.25, time step reduction 1 of 3 to 0.250...
- 033: dt: 0.2500, sse=5534863.0, rms=3.273 (0.000%)
- 034: dt: 0.2500, sse=5785543.5, rms=2.939 (0.000%)
- 035: dt: 0.2500, sse=5721019.0, rms=2.871 (0.000%)
- rms = 2.84, time step reduction 2 of 3 to 0.125...
- 036: dt: 0.2500, sse=5785428.0, rms=2.836 (0.000%)
- 037: dt: 0.1250, sse=5551452.5, rms=2.664 (0.000%)
- rms = 2.64, time step reduction 3 of 3 to 0.062...
- 038: dt: 0.1250, sse=5536021.0, rms=2.642 (0.000%)
- positioning took 1.0 minutes
- mean border=41.1, 1949 (2) missing vertices, mean dist 0.1 [0.2 (%44.6)->0.3 (%55.4))]
- %59 local maxima, %18 large gradients and %18 min vals, 406 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/sub009/surf/rh.pial...
- writing smoothed curvature to rh.curv.pial
- 000: dt: 0.0000, sse=5609083.0, rms=3.08
- rms = 3.99, time step reduction 1 of 3 to 0.250...
- 039: dt: 0.2500, sse=5448987.0, rms=2.732 (0.000%)
- 040: dt: 0.2500, sse=5656892.0, rms=2.662 (0.000%)
- rms = 2.64, time step reduction 2 of 3 to 0.125...
- 041: dt: 0.2500, sse=5735981.5, rms=2.645 (0.000%)
- 042: dt: 0.1250, sse=5619942.5, rms=2.509 (0.000%)
- rms = 2.49, time step reduction 3 of 3 to 0.062...
- 043: dt: 0.1250, sse=5632522.0, rms=2.494 (0.000%)
- positioning took 0.7 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.curv.pial
- writing smoothed area to rh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.area.pial
- vertex spacing 1.01 +- 0.41 (0.07-->8.67) (max @ vno 102156 --> 102155)
- face area 0.40 +- 0.30 (0.00-->6.82)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 146248 vertices processed
- 25000 of 146248 vertices processed
- 50000 of 146248 vertices processed
- 75000 of 146248 vertices processed
- 100000 of 146248 vertices processed
- 125000 of 146248 vertices processed
- 0 of 146248 vertices processed
- 25000 of 146248 vertices processed
- 50000 of 146248 vertices processed
- 75000 of 146248 vertices processed
- 100000 of 146248 vertices processed
- 125000 of 146248 vertices processed
- thickness calculation complete, 251:385 truncations.
- 33011 vertices at 0 distance
- 99243 vertices at 1 distance
- 97132 vertices at 2 distance
- 38100 vertices at 3 distance
- 9947 vertices at 4 distance
- 2514 vertices at 5 distance
- 792 vertices at 6 distance
- 278 vertices at 7 distance
- 118 vertices at 8 distance
- 71 vertices at 9 distance
- 50 vertices at 10 distance
- 34 vertices at 11 distance
- 32 vertices at 12 distance
- 24 vertices at 13 distance
- 18 vertices at 14 distance
- 23 vertices at 15 distance
- 17 vertices at 16 distance
- 14 vertices at 17 distance
- 10 vertices at 18 distance
- 7 vertices at 19 distance
- 15 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.thickness
- positioning took 14.6 minutes
- #--------------------------------------------
- #@# Surf Volume rh Thu Aug 8 22:44:48 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf
- mris_calc -o rh.area.mid rh.area add rh.area.pial
- Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o rh.area.mid rh.area.mid div 2
- Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o rh.volume rh.area.mid mul rh.thickness
- Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ]
- #-----------------------------------------
- #@# WM/GM Contrast rh Thu Aug 8 22:44:49 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts
- pctsurfcon --s sub009 --rh-only
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts/pctsurfcon.log
- Thu Aug 8 22:44:49 CEST 2013
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts
- /opt/freesurfer/5.3.0/bin/pctsurfcon
- $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $
- Linux snake6 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
- FREESURFER_HOME /opt/freesurfer/5.3.0
- mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/tmp.pctsurfcon.21186/rh.wm.mgh --regheader sub009 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/label/rh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 = 111831
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/label/rh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/tmp.pctsurfcon.21186/rh.wm.mgh
- Dim: 146248 1 1
- mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/tmp.pctsurfcon.21186/rh.gm.mgh --projfrac 0.3 --regheader sub009 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/label/rh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.white
- Done reading source surface
- Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 = 130305
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/label/rh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/tmp.pctsurfcon.21186/rh.gm.mgh
- Dim: 146248 1 1
- mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/tmp.pctsurfcon.21186/rh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/tmp.pctsurfcon.21186/rh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/surf/rh.w-g.pct.mgh
- mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.w-g.pct.mgh --annot sub009 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/surf/rh.w-g.pct.mgh --annot sub009 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/stats/rh.w-g.pct.stats --snr
- sysname Linux
- hostname snake6
- machine x86_64
- user fkaule
- UseRobust 0
- Constructing seg from annotation
- Reading annotation
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
- Seg base 2000
- Loading /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.w-g.pct.mgh
- Vertex Area is 0.666197 mm^3
- Generating list of segmentation ids
- Found 36 segmentations
- Computing statistics for each segmentation
- 0 2000 unknown 0 0.000
- 1 2001 bankssts 1112 775.413
- 2 2002 caudalanteriorcingulate 981 688.921
- 3 2003 caudalmiddlefrontal 3731 2507.108
- 4 2004 corpuscallosum 0 0.000
- 5 2005 cuneus 2007 1316.870
- 6 2006 entorhinal 444 318.865
- 7 2007 fusiform 5076 3432.738
- 8 2008 inferiorparietal 8077 5455.833
- 9 2009 inferiortemporal 4898 3307.569
- 10 2010 isthmuscingulate 2076 1313.176
- 11 2011 lateraloccipital 8015 5289.354
- 12 2012 lateralorbitofrontal 4462 2926.592
- 13 2013 lingual 4273 2907.199
- 14 2014 medialorbitofrontal 2909 1908.565
- 15 2015 middletemporal 5190 3501.465
- 16 2016 parahippocampal 949 651.578
- 17 2017 paracentral 3230 2076.418
- 18 2018 parsopercularis 2120 1440.617
- 19 2019 parsorbitalis 1326 885.209
- 20 2020 parstriangularis 2291 1521.716
- 21 2021 pericalcarine 2025 1375.701
- 22 2022 postcentral 7665 5076.688
- 23 2023 posteriorcingulate 2332 1529.350
- 24 2024 precentral 7001 4552.345
- 25 2025 precuneus 6642 4384.634
- 26 2026 rostralanteriorcingulate 1180 755.048
- 27 2027 rostralmiddlefrontal 9506 6418.618
- 28 2028 superiorfrontal 11897 7992.842
- 29 2029 superiorparietal 9643 6390.857
- 30 2030 superiortemporal 5716 3874.690
- 31 2031 supramarginal 6513 4446.536
- 32 2032 frontalpole 426 289.887
- 33 2033 temporalpole 606 405.228
- 34 2034 transversetemporal 647 376.329
- 35 2035 insula 3907 2588.489
- Reporting on 34 segmentations
- mri_segstats done
- Cleaning up
- #-----------------------------------------
- #@# Parcellation Stats rh Thu Aug 8 22:45:14 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 sub009 rh white
- computing statistics for each annotation in ../label/rh.aparc.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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
- 1112 775 2055 2.592 0.403 0.127 0.040 13 1.8 bankssts
- 981 689 1862 2.283 0.665 0.153 0.035 19 1.5 caudalanteriorcingulate
- 3731 2507 6377 2.329 0.426 0.145 0.047 61 7.0 caudalmiddlefrontal
- 2007 1317 3048 2.033 0.438 0.171 0.066 42 5.2 cuneus
- 444 319 1695 3.408 0.704 0.147 0.063 6 1.3 entorhinal
- 5076 3433 9838 2.587 0.505 0.148 0.059 141 11.0 fusiform
- 8077 5456 13955 2.260 0.451 0.155 0.061 172 19.0 inferiorparietal
- 4898 3308 9558 2.422 0.703 0.164 0.073 141 14.1 inferiortemporal
- 2076 1313 3414 2.300 0.772 0.170 0.079 63 7.1 isthmuscingulate
- 8015 5289 13510 2.234 0.474 0.164 0.078 196 19.2 lateraloccipital
- 4462 2927 8009 2.526 0.661 0.169 0.086 113 15.3 lateralorbitofrontal
- 4273 2907 6715 2.100 0.549 0.168 0.070 89 11.6 lingual
- 2909 1909 5117 2.308 0.649 0.163 0.097 106 9.8 medialorbitofrontal
- 5190 3501 11531 2.688 0.618 0.156 0.064 120 13.3 middletemporal
- 949 652 1671 2.240 0.510 0.116 0.032 7 1.3 parahippocampal
- 3230 2076 5406 2.377 0.515 0.140 0.046 44 5.9 paracentral
- 2120 1441 3928 2.411 0.400 0.134 0.045 30 3.7 parsopercularis
- 1326 885 2655 2.349 0.528 0.167 0.096 41 3.2 parsorbitalis
- 2291 1522 3847 2.270 0.434 0.159 0.075 52 5.1 parstriangularis
- 2025 1376 2406 1.745 0.361 0.160 0.070 34 5.6 pericalcarine
- 7665 5077 11290 1.965 0.534 0.140 0.046 136 14.2 postcentral
- 2332 1529 4030 2.345 0.679 0.170 0.068 56 5.6 posteriorcingulate
- 7001 4552 12396 2.431 0.492 0.133 0.089 266 27.7 precentral
- 6642 4385 10711 2.275 0.457 0.156 0.070 144 14.7 precuneus
- 1180 755 2315 2.868 0.647 0.154 0.061 25 2.9 rostralanteriorcingulate
- 9506 6419 16447 2.269 0.459 0.171 0.071 233 25.7 rostralmiddlefrontal
- 11897 7993 23437 2.601 0.493 0.154 0.056 225 26.8 superiorfrontal
- 9643 6391 13990 1.981 0.418 0.152 0.048 179 18.8 superiorparietal
- 5716 3875 12325 2.793 0.542 0.145 0.058 110 11.8 superiortemporal
- 6513 4447 11256 2.311 0.450 0.141 0.056 140 13.3 supramarginal
- 426 290 1001 2.561 0.412 0.203 0.081 13 1.3 frontalpole
- 606 405 1891 3.464 0.740 0.182 0.126 33 3.9 temporalpole
- 647 376 1139 2.596 0.366 0.139 0.066 14 1.6 transversetemporal
- 3907 2588 7513 2.823 0.825 0.134 0.076 74 10.0 insula
- #-----------------------------------------
- #@# Cortical Parc 2 rh Thu Aug 8 22:45:45 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub009 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...
- 0 labels changed using aseg
- relabeling using gibbs priors...
- 000: 10805 changed, 146248 examined...
- 001: 2667 changed, 40876 examined...
- 002: 853 changed, 13541 examined...
- 003: 364 changed, 4664 examined...
- 004: 192 changed, 2025 examined...
- 005: 103 changed, 1083 examined...
- 006: 48 changed, 578 examined...
- 007: 17 changed, 258 examined...
- 008: 12 changed, 110 examined...
- 009: 5 changed, 51 examined...
- 010: 4 changed, 26 examined...
- 011: 4 changed, 20 examined...
- 012: 2 changed, 16 examined...
- 013: 0 changed, 9 examined...
- 0 labels changed using aseg
- 000: 341 total segments, 257 labels (2958 vertices) changed
- 001: 97 total segments, 15 labels (24 vertices) changed
- 002: 82 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 160 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 1163 vertices marked for relabeling...
- 1163 labels changed in reclassification.
- writing output to ../label/rh.aparc.a2009s.annot...
- classification took 1 minutes and 36 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 2 rh Thu Aug 8 22:47:22 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 sub009 rh white
- computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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
- 1101 743 1776 2.124 0.496 0.180 0.075 30 3.7 G_and_S_frontomargin
- 1548 1063 3003 2.446 0.421 0.153 0.050 27 3.2 G_and_S_occipital_inf
- 1810 1154 3351 2.421 0.557 0.148 0.047 27 3.5 G_and_S_paracentral
- 1607 1081 3279 2.617 0.442 0.160 0.053 31 3.3 G_and_S_subcentral
- 1030 710 2244 2.433 0.402 0.205 0.117 45 5.1 G_and_S_transv_frontopol
- 3657 2442 6734 2.562 0.582 0.145 0.051 60 7.7 G_and_S_cingul-Ant
- 1650 1149 3431 2.700 0.508 0.143 0.044 25 3.0 G_and_S_cingul-Mid-Ant
- 2012 1317 3462 2.434 0.472 0.154 0.064 38 4.4 G_and_S_cingul-Mid-Post
- 902 554 2064 2.847 0.624 0.199 0.089 33 3.1 G_cingul-Post-dorsal
- 352 225 837 2.811 0.691 0.165 0.092 10 1.2 G_cingul-Post-ventral
- 1757 1117 2624 2.002 0.453 0.186 0.080 44 5.9 G_cuneus
- 1657 1109 3745 2.617 0.466 0.154 0.059 33 3.7 G_front_inf-Opercular
- 306 197 594 2.295 0.365 0.146 0.177 10 0.5 G_front_inf-Orbital
- 1142 761 2329 2.450 0.420 0.179 0.067 31 3.1 G_front_inf-Triangul
- 4706 3200 9598 2.377 0.451 0.186 0.081 139 14.3 G_front_middle
- 7827 5157 16715 2.655 0.494 0.164 0.062 168 18.8 G_front_sup
- 577 376 1335 3.303 0.593 0.130 0.066 13 1.3 G_Ins_lg_and_S_cent_ins
- 707 475 2014 3.391 0.793 0.162 0.106 18 2.5 G_insular_short
- 2948 1955 6403 2.486 0.447 0.192 0.141 131 9.6 G_occipital_middle
- 2101 1342 3312 2.081 0.443 0.154 0.052 39 4.1 G_occipital_sup
- 2146 1360 4946 2.729 0.497 0.166 0.068 96 5.6 G_oc-temp_lat-fusifor
- 2860 1902 4840 2.154 0.574 0.185 0.086 76 9.5 G_oc-temp_med-Lingual
- 1340 858 3096 2.705 0.870 0.134 0.074 22 3.4 G_oc-temp_med-Parahip
- 3349 2170 7080 2.553 0.708 0.188 0.122 131 13.3 G_orbital
- 2605 1759 5175 2.315 0.424 0.171 0.076 75 8.1 G_pariet_inf-Angular
- 3300 2264 6909 2.444 0.433 0.161 0.075 108 8.7 G_pariet_inf-Supramar
- 3607 2409 5369 1.935 0.419 0.151 0.048 73 7.1 G_parietal_sup
- 2890 1856 4555 1.986 0.448 0.150 0.052 60 6.2 G_postcentral
- 2469 1537 5330 2.649 0.368 0.141 0.181 221 20.4 G_precentral
- 3072 1982 6044 2.428 0.427 0.181 0.102 105 8.5 G_precuneus
- 809 517 1632 2.380 0.630 0.211 0.194 60 4.9 G_rectus
- 435 293 890 2.695 0.715 0.139 0.120 13 1.5 G_subcallosal
- 505 287 1056 2.832 0.431 0.156 0.080 15 1.5 G_temp_sup-G_T_transv
- 2151 1420 5877 3.051 0.496 0.173 0.091 69 5.8 G_temp_sup-Lateral
- 597 441 1688 3.347 0.589 0.146 0.059 9 1.1 G_temp_sup-Plan_polar
- 681 467 1203 2.408 0.488 0.101 0.025 5 0.6 G_temp_sup-Plan_tempo
- 2266 1541 4791 2.444 0.770 0.182 0.089 89 7.7 G_temporal_inf
- 3027 2034 7962 2.849 0.574 0.173 0.079 91 9.8 G_temporal_middle
- 479 309 634 2.126 0.416 0.119 0.029 4 0.6 Lat_Fis-ant-Horizont
- 122 80 164 2.259 0.298 0.119 0.041 1 0.2 Lat_Fis-ant-Vertical
- 1665 1113 2151 2.231 0.432 0.117 0.037 14 2.6 Lat_Fis-post
- 3400 2238 5239 2.031 0.537 0.181 0.067 79 9.0 Pole_occipital
- 1972 1350 5553 3.001 0.736 0.181 0.111 81 9.3 Pole_temporal
- 2288 1602 2915 2.011 0.564 0.141 0.051 29 4.6 S_calcarine
- 2921 1983 3212 1.776 0.537 0.114 0.030 21 3.7 S_central
- 1657 1132 2382 2.173 0.371 0.133 0.041 21 2.6 S_cingul-Marginalis
- 534 354 1020 2.924 0.571 0.153 0.075 12 1.7 S_circular_insula_ant
- 1312 867 2026 2.581 0.532 0.096 0.023 7 1.4 S_circular_insula_inf
- 1336 894 1874 2.331 0.359 0.121 0.037 11 2.0 S_circular_insula_sup
- 919 630 1693 2.460 0.637 0.122 0.039 14 1.5 S_collat_transv_ant
- 383 254 427 2.034 0.383 0.165 0.053 6 0.8 S_collat_transv_post
- 2913 1951 4417 2.183 0.409 0.146 0.052 50 6.1 S_front_inf
- 2234 1522 3382 2.212 0.418 0.149 0.054 38 4.5 S_front_middle
- 2846 1926 4073 2.315 0.363 0.127 0.034 31 4.1 S_front_sup
- 788 540 1043 2.005 0.347 0.148 0.050 13 1.4 S_interm_prim-Jensen
- 3093 2080 3917 1.937 0.374 0.138 0.043 43 5.4 S_intrapariet_and_P_trans
- 1523 1013 1883 2.059 0.335 0.125 0.039 12 2.3 S_oc_middle_and_Lunatus
- 1193 841 1684 2.056 0.319 0.135 0.038 14 1.7 S_oc_sup_and_transversal
- 685 471 1073 2.292 0.347 0.138 0.052 11 1.4 S_occipital_ant
- 1546 1043 2368 2.419 0.513 0.151 0.057 28 3.2 S_oc-temp_lat
- 1873 1364 2731 2.221 0.358 0.118 0.029 12 2.3 S_oc-temp_med_and_Lingual
- 401 274 508 2.046 0.345 0.150 0.050 4 0.8 S_orbital_lateral
- 919 638 1258 2.184 0.752 0.120 0.042 11 1.9 S_orbital_med-olfact
- 1815 1211 2967 2.491 0.612 0.155 0.055 31 4.3 S_orbital-H_Shaped
- 2346 1566 3005 2.034 0.432 0.140 0.041 30 4.0 S_parieto_occipital
- 1901 1209 1910 1.817 0.745 0.151 0.055 42 4.7 S_pericallosal
- 3876 2607 4872 1.958 0.367 0.121 0.037 52 5.6 S_postcentral
- 1783 1188 2413 2.228 0.438 0.123 0.033 16 2.4 S_precentral-inf-part
- 946 645 1377 2.247 0.392 0.117 0.031 7 1.2 S_precentral-sup-part
- 81 58 123 2.189 0.839 0.122 0.025 1 0.1 S_suborbital
- 1558 1044 2228 2.165 0.355 0.146 0.049 23 2.9 S_subparietal
- 1534 1041 2261 2.267 0.530 0.135 0.041 19 2.5 S_temporal_inf
- 6194 4189 9727 2.388 0.436 0.136 0.042 83 10.9 S_temporal_sup
- 331 232 537 2.860 0.399 0.133 0.030 2 0.5 S_temporal_transverse
- #-----------------------------------------
- #@# Cortical Parc 3 rh Thu Aug 8 22:49:10 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub009 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...
- 825 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2826 changed, 146248 examined...
- 001: 650 changed, 12116 examined...
- 002: 159 changed, 3587 examined...
- 003: 62 changed, 936 examined...
- 004: 33 changed, 363 examined...
- 005: 21 changed, 186 examined...
- 006: 6 changed, 121 examined...
- 007: 3 changed, 37 examined...
- 008: 1 changed, 15 examined...
- 009: 0 changed, 7 examined...
- 76 labels changed using aseg
- 000: 63 total segments, 30 labels (172 vertices) changed
- 001: 33 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 41 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 1150 vertices marked for relabeling...
- 1150 labels changed in reclassification.
- writing output to ../label/rh.aparc.DKTatlas40.annot...
- classification took 1 minutes and 8 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 3 rh Thu Aug 8 22:50:20 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 sub009 rh white
- computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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
- 950 671 1813 2.288 0.670 0.157 0.036 19 1.5 caudalanteriorcingulate
- 3735 2508 6447 2.342 0.421 0.145 0.047 61 7.1 caudalmiddlefrontal
- 2626 1704 3888 1.993 0.455 0.164 0.061 52 6.4 cuneus
- 415 298 1644 3.421 0.721 0.148 0.066 6 1.2 entorhinal
- 4508 3026 8443 2.571 0.499 0.146 0.052 119 9.4 fusiform
- 7565 5137 13257 2.268 0.452 0.157 0.062 166 18.0 inferiorparietal
- 5406 3666 10731 2.450 0.693 0.166 0.078 163 15.8 inferiortemporal
- 2098 1332 3464 2.315 0.766 0.170 0.078 63 7.1 isthmuscingulate
- 8368 5525 14115 2.229 0.477 0.163 0.077 199 19.5 lateraloccipital
- 5155 3374 9106 2.440 0.700 0.167 0.087 137 17.8 lateralorbitofrontal
- 4245 2885 6666 2.100 0.548 0.169 0.070 89 11.5 lingual
- 2414 1577 4299 2.323 0.680 0.164 0.107 98 8.6 medialorbitofrontal
- 6045 4082 12948 2.646 0.594 0.151 0.059 130 14.4 middletemporal
- 954 652 1671 2.236 0.511 0.116 0.032 7 1.3 parahippocampal
- 3339 2146 5629 2.385 0.513 0.140 0.046 46 6.1 paracentral
- 2224 1505 4129 2.423 0.408 0.137 0.046 33 4.3 parsopercularis
- 1364 891 2533 2.347 0.523 0.156 0.094 39 3.3 parsorbitalis
- 2582 1713 4433 2.297 0.430 0.162 0.074 59 5.9 parstriangularis
- 2052 1400 2449 1.747 0.360 0.159 0.069 34 5.6 pericalcarine
- 8420 5563 12323 1.979 0.534 0.139 0.045 131 15.2 postcentral
- 2421 1586 4152 2.351 0.674 0.168 0.067 57 5.8 posteriorcingulate
- 6758 4389 11965 2.429 0.491 0.133 0.091 265 27.3 precentral
- 6616 4367 10782 2.284 0.453 0.157 0.071 147 14.7 precuneus
- 1290 844 2494 2.795 0.665 0.144 0.052 24 2.6 rostralanteriorcingulate
- 6249 4222 10699 2.234 0.428 0.172 0.072 156 16.8 rostralmiddlefrontal
- 15254 10279 29586 2.549 0.505 0.157 0.059 304 35.9 superiorfrontal
- 8189 5484 12051 1.986 0.409 0.151 0.048 155 15.8 superiorparietal
- 7418 5006 16243 2.835 0.598 0.149 0.068 168 18.7 superiortemporal
- 6295 4283 10588 2.275 0.456 0.143 0.058 150 13.4 supramarginal
- 640 372 1132 2.599 0.365 0.139 0.066 14 1.6 transversetemporal
- 3278 2194 6657 2.929 0.747 0.135 0.061 54 7.2 insula
- #--------------------------------------------
- #@# Refine Pial Surfs w/ T2/FLAIR Thu Aug 8 22:50:42 CEST 2013
- bbregister --s sub009 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/T2raw.lta --init-fsl --T2
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/T2raw.dat.log
- Thu Aug 8 22:50:42 CEST 2013
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts
- /opt/freesurfer/5.3.0/bin/bbregister --s sub009 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/T2raw.lta --init-fsl --T2
- $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $
- Linux snake6 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
- FREESURFER_HOME /opt/freesurfer/5.3.0
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/template.nii
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/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/sub009/mri/orig/T2raw.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.995894, -0.015333, -0.0892185)
- j_ras = (-0.0248655, 0.993977, 0.106735)
- k_ras = (-0.0870445, -0.108515, 0.990277)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/template.nii...
- fslregister --s sub009 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/fslregister --dof 6 --fsvol brainmask.mgz
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/reg.init.dat.fslregister.log
- Thu Aug 8 22:50:50 CEST 2013
- --s sub009 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/fslregister --dof 6 --fsvol brainmask.mgz
- $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $
- snake6
- Linux snake6 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
- nIters 1
- --------------------------------------
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/fslregister/refvol.fslregister.nii
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/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/sub009/mri/brainmask.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, -1.86265e-09, 0)
- j_ras = (-7.45058e-09, 0, -1)
- k_ras = (-4.65661e-09, 1, 7.45058e-09)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/fslregister/refvol.fslregister.nii...
- --------------------------------------
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/fslregister/movvol.fslregister.nii --frame 0
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/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/sub009/mri/transforms/tmp.bbregister.21801/template.nii...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.995894, -0.015333, -0.0892184)
- j_ras = (-0.0248655, 0.993977, 0.106735)
- k_ras = (-0.0870445, -0.108515, 0.990277)
- keeping frame 0
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/fslregister/movvol.fslregister.nii...
- Mov determinant is -0.311086
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts
- tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/fslregister/movvol.fslregister.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/fslregister/reg0.21844.dat --regheader --fslregout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/reg.init.dat.fsl.mat0 --s sub009 --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/sub009/mri/transforms/tmp.bbregister.21801/fslregister/movvol.fslregister.nii
- reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/fslregister/reg0.21844.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/sub009/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/sub009/mri/transforms/tmp.bbregister.21801/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 0.015 0.089 -0.000;
- -0.087 -0.109 0.990 -0.000;
- 0.025 -0.994 -0.107 -0.000;
- 0.000 0.000 0.000 1.000;
- ---------------------------------------
- ---- Input registration matrix --------
- 0.996 0.015 0.089 -0.000;
- -0.087 -0.109 0.990 -0.000;
- 0.025 -0.994 -0.107 -0.000;
- 0.000 0.000 0.000 1.000;
- Determinant 1
- subject = sub009
- RegMat ---------------------------
- 0.996 0.015 0.089 -0.000;
- -0.087 -0.109 0.990 -0.000;
- 0.025 -0.994 -0.107 -0.000;
- 0.000 0.000 0.000 1.000;
- FSLOUTPUTTYPE NIFTI
- tkreg2FSL: mov det = -0.311086, ref det = -1
- Thu Aug 8 22:50:59 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts
- flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/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/sub009/mri/transforms/tmp.bbregister.21801/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/reg.init.dat.fsl.mat0
- Thu Aug 8 22:55:23 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts
- flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/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/sub009/mri/transforms/tmp.bbregister.21801/reg.init.dat.fsl.mat -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/fslregister/fslmat0.trans.mat -schedule /opt/freesurfer/5.3.0/bin/flirt.newdefault.20080811.sch
- tkregister2_cmdl --s sub009 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/reg.init.dat --fslreg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/reg.init.dat.fsl.mat --noedit
- tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl
- ---- FSL registration matrix --------
- 0.995 0.024 0.101 16.537;
- 0.103 -0.096 -0.990 257.759;
- -0.015 0.995 -0.098 13.660;
- 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/sub009/mri/transforms/tmp.bbregister.21801/template.nii
- reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/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/sub009/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/sub009/mri/transforms/tmp.bbregister.21801/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) --------
- 0.995 0.015 0.103 0.059;
- -0.101 -0.098 0.990 0.554;
- 0.024 -0.995 -0.096 -0.937;
- 0.000 0.000 0.000 1.000;
- ---------------------------------------
- ---- Input registration matrix --------
- 0.995 0.015 0.103 0.059;
- -0.101 -0.098 0.990 0.554;
- 0.024 -0.995 -0.096 -0.937;
- 0.000 0.000 0.000 1.000;
- Determinant 0.999999
- subject = sub009
- RegMat ---------------------------
- 0.995 0.015 0.103 0.059;
- -0.101 -0.098 0.990 0.554;
- 0.024 -0.995 -0.096 -0.937;
- 0.000 0.000 0.000 1.000;
-
- Started at Thu Aug 8 22:50:50 CEST 2013
- Ended at Thu Aug 8 23:01:48 CEST 2013
-
- fslregister Done
-
- To check results, run:
- tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/reg.init.dat --surf orig
-
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/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/sub009/scripts
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5
- sysname Linux
- hostname snake6
- machine x86_64
- user fkaule
- movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/template.nii
- regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/reg.init.dat
- subject sub009
- dof 6
- outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/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 1376322642
- TransRandMax 0.000000
- RotRandMax 0.000000
- Translations 0.000000 0.000000 0.000000
- Rotations 0.000000 0.000000 0.000000
- Input reg
- 0.995 0.015 0.103 0.059;
- -0.101 -0.098 0.990 0.554;
- 0.024 -0.995 -0.096 -0.937;
- 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 1.033315
- 1 -25.0 -25.0 25.0 1.003318
- 2 -25.0 25.0 -25.0 1.012121
- 3 -25.0 25.0 25.0 1.004161
- 4 25.0 -25.0 -25.0 0.997893
- 5 25.0 -25.0 25.0 1.036592
- 6 25.0 25.0 -25.0 0.998662
- 7 25.0 25.0 25.0 1.021020
- REL: 8 0.438956 8.107082 1.013385 rel = 0.433158
- Initial costs ----------------
- Number of surface hits 2772
- WM Intensity 58.3193 +/- 11.9758
- Ctx Intensity 69.8534 +/- 15.2890
- Pct Contrast 17.2580 +/- 24.0963
- Cost 0.4390
- RelCost 0.4332
- ------------------------------------
- Brute force preopt -4 4 4, n = 729
- 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 1.0064 1.0064 0.0
- 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.9726 0.9726 0.0
- 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.9475 0.9475 0.0
- 19 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.0000 0.9111 0.9111 0.0
- 21 -4.0000 -4.0000 -4.0000 4.0000 0.0000 -4.0000 0.8812 0.8812 0.0
- 39 -4.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.8571 0.8571 0.0
- 118 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.0000 0.8418 0.8418 0.0
- 120 -4.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.7935 0.7935 0.0
- 301 0.0000 -4.0000 4.0000 -4.0000 0.0000 0.0000 0.7808 0.7808 0.0
- 346 0.0000 0.0000 -4.0000 4.0000 0.0000 0.0000 0.6768 0.6768 0.0
- 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.4390 0.4390 0.0
- Brute Force --------------------------
- Min cost was 0.438956
- Number of iterations 729
- Search time 2.153000 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
- 5 -0.618 0.000 0.000 0.000 0.000 0.000 0.4240294907
- 7 -0.440 0.000 0.000 0.000 0.000 0.000 0.4209544114
- 8 -0.437 0.000 0.000 0.000 0.000 0.000 0.4209177264
- 10 -0.401 0.000 0.000 0.000 0.000 0.000 0.4207867888
- 12 -0.388 0.000 0.000 0.000 0.000 0.000 0.4207430928
- 14 -0.371 0.000 0.000 0.000 0.000 0.000 0.4207299772
- 15 -0.375 0.000 0.000 0.000 0.000 0.000 0.4207209116
- 17 -0.374 0.000 0.000 0.000 0.000 0.000 0.4207208115
- 21 -0.374 -1.618 0.000 0.000 0.000 0.000 0.2981514008
- 22 -0.374 -1.514 0.000 0.000 0.000 0.000 0.2917458273
- 25 -0.374 -1.293 0.000 0.000 0.000 0.000 0.2877179964
- 26 -0.374 -1.291 0.000 0.000 0.000 0.000 0.2875827155
- 27 -0.374 -1.155 0.000 0.000 0.000 0.000 0.2853981573
- 28 -0.374 -1.194 0.000 0.000 0.000 0.000 0.2852815210
- 29 -0.374 -1.182 0.000 0.000 0.000 0.000 0.2852194566
- 31 -0.374 -1.183 0.000 0.000 0.000 0.000 0.2852184333
- 32 -0.374 -1.184 0.000 0.000 0.000 0.000 0.2852181365
- 35 -0.374 -1.184 1.000 0.000 0.000 0.000 0.1932573450
- 43 -0.374 -1.184 1.090 0.000 0.000 0.000 0.1913017908
- 46 -0.374 -1.184 1.084 0.000 0.000 0.000 0.1912798821
- 55 -0.374 -1.184 1.084 0.133 0.000 0.000 0.1841702737
- 56 -0.374 -1.184 1.084 0.151 0.000 0.000 0.1839889615
- 58 -0.374 -1.184 1.084 0.148 0.000 0.000 0.1839844981
- 59 -0.374 -1.184 1.084 0.149 0.000 0.000 0.1839841188
- 66 -0.374 -1.184 1.084 0.149 -0.051 0.000 0.1830259769
- 68 -0.374 -1.184 1.084 0.149 -0.054 0.000 0.1830052049
- 70 -0.374 -1.184 1.084 0.149 -0.058 0.000 0.1829965795
- 78 -0.374 -1.184 1.084 0.149 -0.058 0.382 0.1630476874
- 79 -0.374 -1.184 1.084 0.149 -0.058 0.369 0.1628444379
- 81 -0.374 -1.184 1.084 0.149 -0.058 0.355 0.1628186469
- 82 -0.374 -1.184 1.084 0.149 -0.058 0.359 0.1627995908
- 83 -0.374 -1.184 1.084 0.149 -0.058 0.361 0.1627976520
- 92 -0.210 -1.184 1.084 0.149 -0.058 0.361 0.1584671673
- 94 -0.219 -1.184 1.084 0.149 -0.058 0.361 0.1584428926
- 96 -0.231 -1.184 1.084 0.149 -0.058 0.361 0.1584313808
- 97 -0.230 -1.184 1.084 0.149 -0.058 0.361 0.1584308908
- 106 -0.230 -1.141 1.084 0.149 -0.058 0.361 0.1579965593
- 119 -0.230 -1.141 0.875 0.149 -0.058 0.361 0.1536496762
- 122 -0.230 -1.141 0.834 0.149 -0.058 0.361 0.1531940783
- 123 -0.230 -1.141 0.836 0.149 -0.058 0.361 0.1531877192
- 124 -0.230 -1.141 0.840 0.149 -0.058 0.361 0.1531710905
- 127 -0.230 -1.141 0.842 0.149 -0.058 0.361 0.1531677108
- 128 -0.230 -1.141 0.843 0.149 -0.058 0.361 0.1531676964
- 135 -0.230 -1.141 0.843 0.531 -0.058 0.361 0.1473128666
- 136 -0.230 -1.141 0.843 0.380 -0.058 0.361 0.1403563629
- 139 -0.230 -1.141 0.843 0.378 -0.058 0.361 0.1403523950
- 141 -0.230 -1.141 0.843 0.377 -0.058 0.361 0.1403518831
- 149 -0.230 -1.141 0.843 0.377 -0.051 0.361 0.1403306435
- 153 -0.230 -1.141 0.843 0.377 -0.052 0.361 0.1403305798
- 160 -0.230 -1.141 0.843 0.377 -0.052 0.431 0.1400911137
- 161 -0.230 -1.141 0.843 0.377 -0.052 0.407 0.1399985170
- 162 -0.230 -1.141 0.843 0.377 -0.052 0.406 0.1399968466
- 164 -0.230 -1.141 0.843 0.377 -0.052 0.403 0.1399957568
- 165 -0.230 -1.141 0.843 0.377 -0.052 0.404 0.1399953869
- 167 -0.085 -1.098 0.602 0.606 -0.045 0.448 0.1343285674
- 173 -0.140 -1.115 0.694 0.519 -0.048 0.431 0.1339098551
- 174 -0.124 -1.110 0.666 0.545 -0.047 0.436 0.1333603664
- 175 -0.116 -1.108 0.654 0.557 -0.047 0.438 0.1333080120
- 176 -0.117 -1.108 0.654 0.556 -0.047 0.438 0.1333075260
- 177 -0.117 -1.108 0.655 0.555 -0.047 0.438 0.1333070076
- 178 -0.117 -1.108 0.655 0.555 -0.047 0.438 0.1333068951
- 186 -0.147 -1.108 0.655 0.555 -0.047 0.438 0.1322486410
- 188 -0.201 -1.108 0.655 0.555 -0.047 0.438 0.1313617889
- 190 -0.205 -1.108 0.655 0.555 -0.047 0.438 0.1313573967
- 199 -0.205 -1.041 0.655 0.555 -0.047 0.438 0.1304728631
- 201 -0.205 -1.056 0.655 0.555 -0.047 0.438 0.1303537402
- 203 -0.205 -1.062 0.655 0.555 -0.047 0.438 0.1303375048
- 204 -0.205 -1.063 0.655 0.555 -0.047 0.438 0.1303345283
- 205 -0.205 -1.068 0.655 0.555 -0.047 0.438 0.1303331739
- 206 -0.205 -1.066 0.655 0.555 -0.047 0.438 0.1303305412
- 215 -0.205 -1.066 0.497 0.555 -0.047 0.438 0.1273900231
- 216 -0.205 -1.066 0.504 0.555 -0.047 0.438 0.1273858699
- 221 -0.205 -1.066 0.508 0.555 -0.047 0.438 0.1273838560
- 222 -0.205 -1.066 0.507 0.555 -0.047 0.438 0.1273838362
- 230 -0.205 -1.066 0.507 0.555 -0.047 0.473 0.1265646605
- 232 -0.205 -1.066 0.507 0.555 -0.047 0.486 0.1264997243
- 233 -0.205 -1.066 0.507 0.555 -0.047 0.485 0.1264982170
- 241 -0.205 -1.066 0.507 0.555 -0.086 0.485 0.1258425191
- 245 -0.205 -1.066 0.507 0.555 -0.082 0.485 0.1258343048
- 253 -0.150 -1.050 0.414 0.643 -0.079 0.502 0.1257550182
- 254 -0.176 -1.057 0.459 0.601 -0.080 0.494 0.1251218396
- 256 -0.173 -1.057 0.454 0.605 -0.080 0.495 0.1251110666
- 258 -0.173 -1.056 0.453 0.606 -0.080 0.495 0.1251104986
- 260 -0.173 -1.056 0.453 0.606 -0.080 0.495 0.1251104486
- 272 -0.180 -1.056 0.453 0.606 -0.080 0.495 0.1250839290
- 274 -0.179 -1.056 0.453 0.606 -0.080 0.495 0.1250831880
- 285 -0.179 -1.035 0.453 0.606 -0.080 0.495 0.1249916686
- 286 -0.179 -1.038 0.453 0.606 -0.080 0.495 0.1249898323
- 287 -0.179 -1.037 0.453 0.606 -0.080 0.495 0.1249891314
- 296 -0.179 -1.037 0.451 0.606 -0.080 0.495 0.1249798103
- 297 -0.179 -1.037 0.445 0.606 -0.080 0.495 0.1249734194
- 299 -0.179 -1.037 0.443 0.606 -0.080 0.495 0.1249723968
- 300 -0.179 -1.037 0.442 0.606 -0.080 0.495 0.1249707811
- 301 -0.179 -1.037 0.440 0.606 -0.080 0.495 0.1249696578
- 303 -0.179 -1.037 0.441 0.606 -0.080 0.495 0.1249696544
- 310 -0.179 -1.037 0.441 0.606 -0.080 0.502 0.1249610311
- 312 -0.179 -1.037 0.441 0.606 -0.080 0.499 0.1249563349
- 321 -0.179 -1.037 0.441 0.606 -0.102 0.499 0.1247580194
- 323 -0.179 -1.037 0.441 0.606 -0.101 0.499 0.1247561821
- 324 -0.179 -1.037 0.441 0.606 -0.100 0.499 0.1247561150
- 332 -0.176 -1.036 0.436 0.610 -0.100 0.500 0.1247265205
- 334 -0.174 -1.036 0.433 0.613 -0.100 0.500 0.1247207955
- 335 -0.174 -1.036 0.433 0.613 -0.100 0.501 0.1247206597
- 350 -0.171 -1.036 0.433 0.613 -0.100 0.501 0.1247089616
- 363 -0.171 -1.037 0.433 0.613 -0.100 0.501 0.1247087942
- 373 -0.171 -1.037 0.438 0.613 -0.100 0.501 0.1247017144
- 374 -0.171 -1.037 0.437 0.613 -0.100 0.501 0.1247012166
- 394 -0.171 -1.037 0.437 0.613 -0.103 0.501 0.1246933981
- 408 -0.171 -1.037 0.437 0.613 -0.103 0.500 0.1246930870
- 421 -0.169 -1.037 0.437 0.613 -0.103 0.500 0.1246919227
- 423 -0.170 -1.037 0.437 0.613 -0.103 0.500 0.1246918112
- 434 -0.170 -1.035 0.437 0.613 -0.103 0.500 0.1246912973
- 444 -0.170 -1.035 0.438 0.613 -0.103 0.500 0.1246909621
- 464 -0.170 -1.035 0.438 0.613 -0.104 0.500 0.1246907325
- Powell done niters = 5
- Computing relative cost
- 0 -25.0 -25.0 -25.0 1.033704
- 1 -25.0 -25.0 25.0 0.994621
- 2 -25.0 25.0 -25.0 1.003955
- 3 -25.0 25.0 25.0 0.989554
- 4 25.0 -25.0 -25.0 1.024186
- 5 25.0 -25.0 25.0 1.047537
- 6 25.0 25.0 -25.0 1.035593
- 7 25.0 25.0 25.0 1.032315
- REL: 8 0.124691 8.161465 1.020183 rel = 0.122224
- Number of iterations 5
- Min cost was 0.124691
- Number of FunctionCalls 476
- TolPowell 0.000100
- nMaxItersPowell 36
- OptimizationTime 1.377000 sec
- Parameters at optimum (transmm) -0.16965 -1.03536 0.43834
- Parameters at optimum (rotdeg) 0.61290 -0.10434 0.50048
- Final costs ----------------
- Number of surface hits 2772
- WM Intensity 56.7404 +/- 11.0330
- Ctx Intensity 69.2588 +/- 10.1336
- Pct Contrast 20.2576 +/- 13.5904
- Cost 0.1247
- RelCost 0.4332
- Reg at min cost was
- 0.995 0.017 0.094 -0.114;
- -0.093 -0.087 0.992 -0.471;
- 0.025 -0.996 -0.085 -0.493;
- 0.000 0.000 0.000 1.000;
- Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/bbr.pass1.dat, type = 14
- Original Reg
- 0.995 0.015 0.103 0.059;
- -0.101 -0.098 0.990 0.554;
- 0.024 -0.995 -0.096 -0.937;
- 0.000 0.000 0.000 1.000;
- Original Reg - Optimal Reg
- -0.001 -0.003 0.009 0.173;
- -0.008 -0.011 -0.002 1.025;
- -0.001 0.001 -0.011 -0.444;
- 0.000 0.000 0.000 0.000;
- Computing change in lh position
- LH rmsDiffMean 1.782706
- Computing change in rh position
- Surface RMS Diff (mm) 1.619904 2.444892
- mri_segreg done
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/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/sub009/scripts
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5
- sysname Linux
- hostname snake6
- machine x86_64
- user fkaule
- movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/template.nii
- regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/tmp.bbregister.21801/bbr.pass1.dat
- subject sub009
- dof 6
- outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 1376026366
- TransRandMax 0.000000
- RotRandMax 0.000000
- Translations 0.000000 0.000000 0.000000
- Rotations 0.000000 0.000000 0.000000
- Input reg
- 0.995 0.017 0.094 -0.114;
- -0.093 -0.087 0.992 -0.471;
- 0.025 -0.996 -0.085 -0.493;
- 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 1.016423
- 1 -25.0 -25.0 25.0 0.997811
- 2 -25.0 25.0 -25.0 0.994115
- 3 -25.0 25.0 25.0 0.997896
- 4 25.0 -25.0 -25.0 1.006045
- 5 25.0 -25.0 25.0 1.023716
- 6 25.0 25.0 -25.0 1.014273
- 7 25.0 25.0 25.0 1.015183
- REL: 8 0.134087 8.065463 1.008183 rel = 0.132999
- Initial costs ----------------
- Number of surface hits 277390
- WM Intensity 56.8589 +/- 10.5831
- Ctx Intensity 69.3526 +/- 10.1667
- Pct Contrast 20.1370 +/- 13.7599
- Cost 0.1341
- RelCost 0.1330
- ------------------------------------
- Brute force preopt -0.1 0.1 0.1, n = 729
- 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1445 0.1445 0.0
- 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1394 0.1394 0.0
- 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.1363 0.1363 0.0
- 13 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.1325 0.1325 0.0
- 31 -0.1000 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.1323 0.1323 0.0
- 40 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.0000 0.1308 0.1308 0.0
- 58 -0.1000 -0.1000 0.1000 -0.1000 0.0000 0.0000 0.1300 0.1300 0.0
- 94 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.0000 0.1291 0.1291 0.0
- 120 -0.1000 0.0000 0.0000 0.0000 0.0000 -0.1000 0.1272 0.1272 0.0
- 121 -0.1000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1264 0.1264 0.0
- 184 -0.1000 0.1000 -0.1000 0.1000 0.0000 0.0000 0.1259 0.1259 0.0
- 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1247 0.1247 0.0
- Brute Force --------------------------
- Min cost was 0.124691
- Number of iterations 729
- Search time 2.098000 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 0.145 0.000 0.000 0.000 0.000 0.000 0.1316677242
- 9 0.152 0.000 0.000 0.000 0.000 0.000 0.1316635766
- 11 0.150 0.000 0.000 0.000 0.000 0.000 0.1316633193
- 19 0.150 0.055 0.000 0.000 0.000 0.000 0.1313455337
- 21 0.150 0.053 0.000 0.000 0.000 0.000 0.1313449322
- 29 0.150 0.053 -0.028 0.000 0.000 0.000 0.1312292684
- 32 0.150 0.053 -0.029 0.000 0.000 0.000 0.1312291729
- 39 0.150 0.053 -0.029 0.010 0.000 0.000 0.1311202670
- 40 0.150 0.053 -0.029 0.028 0.000 0.000 0.1310242261
- 41 0.150 0.053 -0.029 0.031 0.000 0.000 0.1310228484
- 42 0.150 0.053 -0.029 0.030 0.000 0.000 0.1310225481
- 50 0.150 0.053 -0.029 0.030 -0.014 0.000 0.1309972377
- 59 0.150 0.053 -0.029 0.030 -0.014 0.041 0.1308405624
- 60 0.150 0.053 -0.029 0.030 -0.014 0.035 0.1308394115
- 61 0.150 0.053 -0.029 0.030 -0.014 0.037 0.1308388734
- 70 0.208 0.074 -0.041 0.042 -0.019 0.051 0.1305962841
- 71 0.202 0.072 -0.039 0.041 -0.018 0.050 0.1305877315
- 73 0.201 0.071 -0.039 0.040 -0.018 0.049 0.1305873916
- 74 0.201 0.071 -0.039 0.040 -0.018 0.049 0.1305873201
- 76 0.201 0.071 -0.039 0.040 -0.018 0.049 0.1305873163
- 84 0.201 0.071 -0.039 0.040 -0.018 0.060 0.1305733172
- 85 0.201 0.071 -0.039 0.040 -0.018 0.059 0.1305730463
- 86 0.201 0.071 -0.039 0.040 -0.018 0.058 0.1305729202
- 96 0.201 0.070 -0.039 0.040 -0.018 0.058 0.1305728490
- 104 0.201 0.070 -0.064 0.040 -0.018 0.058 0.1304761187
- 106 0.201 0.070 -0.065 0.040 -0.018 0.058 0.1304759000
- 115 0.201 0.070 -0.065 0.049 -0.018 0.058 0.1304516466
- 116 0.201 0.070 -0.065 0.052 -0.018 0.058 0.1304494602
- 126 0.201 0.070 -0.065 0.052 -0.016 0.058 0.1304490328
- 136 0.205 0.072 -0.066 0.053 -0.016 0.059 0.1304467687
- 139 0.205 0.072 -0.066 0.053 -0.016 0.059 0.1304467412
- 149 0.205 0.072 -0.066 0.053 -0.016 0.064 0.1304450677
- 150 0.205 0.072 -0.066 0.053 -0.016 0.063 0.1304449994
- 151 0.205 0.072 -0.066 0.053 -0.016 0.062 0.1304449540
- 160 0.205 0.077 -0.066 0.053 -0.016 0.062 0.1304409792
- 162 0.205 0.078 -0.066 0.053 -0.016 0.062 0.1304405442
- 163 0.205 0.082 -0.066 0.053 -0.016 0.062 0.1304401267
- 165 0.205 0.081 -0.066 0.053 -0.016 0.062 0.1304398427
- 173 0.205 0.081 -0.075 0.053 -0.016 0.062 0.1304264829
- 174 0.205 0.081 -0.077 0.053 -0.016 0.062 0.1304255022
- 175 0.205 0.081 -0.078 0.053 -0.016 0.062 0.1304250495
- 186 0.205 0.081 -0.078 0.060 -0.016 0.062 0.1304060388
- 187 0.205 0.081 -0.078 0.063 -0.016 0.062 0.1304034358
- 206 0.205 0.081 -0.078 0.063 -0.016 0.063 0.1304033850
- 207 0.206 0.081 -0.078 0.063 -0.016 0.063 0.1304032411
- 211 0.207 0.081 -0.078 0.064 -0.016 0.063 0.1304032101
- 213 0.208 0.082 -0.079 0.064 -0.017 0.063 0.1304031668
- 217 0.211 0.091 -0.091 0.075 -0.017 0.067 0.1303761680
- 222 0.212 0.098 -0.099 0.082 -0.017 0.070 0.1303711430
- 224 0.212 0.097 -0.098 0.080 -0.017 0.069 0.1303711384
- 225 0.212 0.097 -0.098 0.081 -0.017 0.069 0.1303711251
- 227 0.212 0.097 -0.098 0.081 -0.017 0.069 0.1303710919
- 241 0.212 0.097 -0.098 0.081 -0.017 0.074 0.1303698309
- 251 0.212 0.095 -0.098 0.081 -0.017 0.073 0.1303694306
- 253 0.212 0.096 -0.098 0.081 -0.017 0.073 0.1303692453
- 260 0.212 0.096 -0.101 0.081 -0.017 0.073 0.1303668534
- 261 0.212 0.096 -0.104 0.081 -0.017 0.073 0.1303647895
- 264 0.212 0.096 -0.105 0.081 -0.017 0.073 0.1303644396
- 273 0.206 0.094 -0.104 0.080 -0.016 0.071 0.1303617292
- 275 0.206 0.093 -0.104 0.080 -0.016 0.071 0.1303617012
- 280 0.205 0.093 -0.103 0.080 -0.016 0.071 0.1303616720
- 288 0.205 0.093 -0.103 0.080 -0.023 0.071 0.1303598366
- 289 0.205 0.093 -0.103 0.080 -0.021 0.071 0.1303594426
- 290 0.205 0.093 -0.103 0.080 -0.022 0.071 0.1303594143
- 297 0.206 0.095 -0.106 0.082 -0.022 0.072 0.1303587789
- 298 0.206 0.095 -0.106 0.082 -0.022 0.072 0.1303587783
- 299 0.206 0.095 -0.106 0.082 -0.022 0.072 0.1303587650
- 319 0.206 0.097 -0.106 0.082 -0.022 0.072 0.1303587302
- 338 0.205 0.096 -0.106 0.082 -0.022 0.072 0.1303586955
- 405 0.205 0.096 -0.105 0.082 -0.022 0.071 0.1303586909
- Powell done niters = 5
- Computing relative cost
- 0 -25.0 -25.0 -25.0 1.016213
- 1 -25.0 -25.0 25.0 0.998353
- 2 -25.0 25.0 -25.0 0.994860
- 3 -25.0 25.0 25.0 0.997565
- 4 25.0 -25.0 -25.0 1.004759
- 5 25.0 -25.0 25.0 1.023781
- 6 25.0 25.0 -25.0 1.011973
- 7 25.0 25.0 25.0 1.014206
- REL: 8 0.130359 8.061709 1.007714 rel = 0.129361
- Number of iterations 5
- Min cost was 0.130359
- Number of FunctionCalls 429
- TolPowell 0.000000
- nMaxItersPowell 36
- OptimizationTime 62.251000 sec
- Parameters at optimum (transmm) 0.20508 0.09636 -0.10549
- Parameters at optimum (rotdeg) 0.08156 -0.02152 0.07146
- Final costs ----------------
- Number of surface hits 277390
- WM Intensity 56.8648 +/- 10.6213
- Ctx Intensity 69.3155 +/- 10.1226
- Pct Contrast 20.0837 +/- 13.7341
- Cost 0.1304
- RelCost 0.1330
- Reg at min cost was
- 0.995 0.018 0.093 0.092;
- -0.091 -0.086 0.992 -0.374;
- 0.025 -0.996 -0.084 -0.599;
- 0.000 0.000 0.000 1.000;
- Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/T2raw.dat, type = 14
- Original Reg
- 0.995 0.017 0.094 -0.114;
- -0.093 -0.087 0.992 -0.471;
- 0.025 -0.996 -0.085 -0.493;
- 0.000 0.000 0.000 1.000;
- Original Reg - Optimal Reg
- -0.000 -0.000 0.001 -0.206;
- -0.001 -0.001 -0.000 -0.097;
- -0.000 0.000 -0.001 0.106;
- 0.000 0.000 0.000 0.000;
- Computing change in lh position
- LH rmsDiffMean 0.177186
- Computing change in rh position
- Surface RMS Diff (mm) 0.189640 0.307027
- mri_segreg done
- tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/T2raw.dat --noedit --ltaout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/mri/orig/T2raw.mgz
- reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 --------
- 0.995 0.018 0.093 0.092;
- -0.091 -0.086 0.992 -0.374;
- 0.025 -0.996 -0.084 -0.599;
- 0.000 0.000 0.000 1.000;
- float2int = 0
- ---------------------------------------
- INFO: loading target /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/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 --------
- 0.995 0.018 0.093 0.092;
- -0.091 -0.086 0.992 -0.374;
- 0.025 -0.996 -0.084 -0.599;
- 0.000 0.000 0.000 1.000;
- Determinant 0.999999
- subject = sub009
- RegMat ---------------------------
- 0.995 0.018 0.093 0.092;
- -0.091 -0.086 0.992 -0.374;
- 0.025 -0.996 -0.084 -0.599;
- 0.000 0.000 0.000 1.000;
- transformed matrix:
- 1.000 -0.000 -0.004 -0.159;
- 0.000 1.000 0.023 -0.357;
- 0.004 -0.023 1.000 1.003;
- 0.000 0.000 0.000 1.000;
- transformed matrix:
- 0.697 0.017 0.061 17.690;
- 0.065 -0.056 -0.661 256.433;
- -0.012 0.664 -0.057 12.498;
- 0.000 0.000 0.000 1.000;
- Cleaning up
-
- Started at Thu Aug 8 22:50:42 CEST 2013
- Ended at Thu Aug 8 23:03:44 CEST 2013
- BBR-Run-Time-Sec 782
-
- bbregister Done
- To check results, run:
- tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/T2raw.dat --surf
-
- mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/T2.mgz
- mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/mri/orig/T2raw.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.995894, -0.015333, -0.0892185)
- j_ras = (-0.0248655, 0.993977, 0.106735)
- k_ras = (-0.0870445, -0.108515, 0.990277)
- INFO: Reading transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/T2raw.lta...
- Reading transform with LTAreadEx()
- reading extra input line subject sub009
- reading extra input line fscale 0.150000
- reading template info from volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/orig.mgz...
- INFO: Applying transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/transforms/T2raw.lta...
- ---------------------------------
- INFO: Transform Matrix (linear_ras_to_ras)
- 1.000 -0.000 -0.004 -0.159;
- 0.000 1.000 0.023 -0.357;
- 0.004 -0.023 1.000 1.003;
- 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/sub009/mri/T2.mgz...
- mri_normalize -aseg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/aseg.mgz -sigma 4 -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.white identity.nofile -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.white identity.nofile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/T2.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/mri/T2.mgz...
- computing distance transform
- computing distance transform
- computing nonmaximum suppression
- 13976 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/sub009/mri/T2.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts
- cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.woT2.pial
- `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.woT2.pial'
- mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub009 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/sub009/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/wm.mgz...
- 18938 bright wm thresholded.
- 815 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.orig...
- computing class statistics...
- border white: 259466 voxels (1.55%)
- border gray 303507 voxels (1.81%)
- WM (91.0): 92.8 +- 10.6 [70.0 --> 110.0]
- GM (74.0) : 72.4 +- 12.9 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 46.1 (was 70)
- setting MAX_BORDER_WHITE to 115.6 (was 105)
- setting MIN_BORDER_WHITE to 59.0 (was 85)
- setting MAX_CSF to 33.3 (was 40)
- setting MAX_GRAY to 94.4 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 52.6 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 20.4 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=105, GM=59
- mean inside = 92.6, mean outside = 67.5
- smoothing surface for 5 iterations...
- reading initial white vertex positions from white...
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.89 +- 0.26 (0.02-->5.47) (max @ vno 69994 --> 72328)
- face area 0.33 +- 0.16 (0.00-->4.03)
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 5 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 2 with 2 points - only 0.00% unknown
- deleting segment 3 with 11 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 6 points - only 0.00% unknown
- deleting segment 6 with 654 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 7 with 3 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 8 with 2 points - only 0.00% unknown
- deleting segment 9 with 19 points - only 0.00% unknown
- deleting segment 10 with 19 points - only 0.00% unknown
- deleting segment 11 with 6 points - only 0.00% unknown
- deleting segment 12 with 18 points - only 0.00% unknown
- deleting segment 13 with 14 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 14 with 1 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 15 with 3 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 16 with 3 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 17 with 3 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 18 with 1 points - only 0.00% unknown
- tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.89 +- 0.25 (0.02-->5.47) (max @ vno 72328 --> 69994)
- face area 0.33 +- 0.16 (0.00-->4.03)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5036635.5, rms=0.00
- rms = 1.17, time step reduction 1 of 3 to 0.250...
- rms = 0.30, time step reduction 2 of 3 to 0.125...
- rms = 0.04, time step reduction 3 of 3 to 0.062...
- 001: dt: 0.1250, sse=5036635.5, rms=0.000 (1.000%)
- positioning took 0.4 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 5 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 1 with 2 points - only 0.00% unknown
- deleting segment 2 with 11 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 3 with 1 points - only 0.00% unknown
- deleting segment 4 with 6 points - only 0.00% unknown
- deleting segment 5 with 654 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 6 with 3 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 7 with 2 points - only 0.00% unknown
- deleting segment 8 with 19 points - only 0.00% unknown
- deleting segment 9 with 19 points - only 0.00% unknown
- deleting segment 10 with 6 points - only 0.00% unknown
- deleting segment 11 with 18 points - only 0.00% unknown
- deleting segment 12 with 14 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 13 with 1 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 14 with 3 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 15 with 3 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 16 with 3 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 17 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 0.89 +- 0.25 (0.02-->5.47) (max @ vno 72328 --> 69994)
- face area 0.33 +- 0.16 (0.00-->4.03)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5036635.5, rms=0.00
- rms = 1.17, time step reduction 1 of 3 to 0.250...
- rms = 0.30, time step reduction 2 of 3 to 0.125...
- rms = 0.04, time step reduction 3 of 3 to 0.062...
- 002: dt: 0.1250, sse=5036635.5, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 5 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 1 with 2 points - only 0.00% unknown
- deleting segment 2 with 11 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 3 with 1 points - only 0.00% unknown
- deleting segment 4 with 6 points - only 0.00% unknown
- deleting segment 5 with 654 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 6 with 3 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 7 with 2 points - only 0.00% unknown
- deleting segment 8 with 19 points - only 0.00% unknown
- deleting segment 9 with 19 points - only 0.00% unknown
- deleting segment 10 with 6 points - only 0.00% unknown
- deleting segment 11 with 18 points - only 0.00% unknown
- deleting segment 12 with 14 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 13 with 1 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 14 with 3 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 15 with 3 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 16 with 3 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 17 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 0.89 +- 0.25 (0.02-->5.47) (max @ vno 72328 --> 69994)
- face area 0.33 +- 0.16 (0.00-->4.03)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5036635.5, rms=0.00
- rms = 1.17, time step reduction 1 of 3 to 0.250...
- rms = 0.30, time step reduction 2 of 3 to 0.125...
- rms = 0.04, time step reduction 3 of 3 to 0.062...
- 003: dt: 0.1250, sse=5036635.5, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 5 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 1 with 2 points - only 0.00% unknown
- deleting segment 2 with 11 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 3 with 1 points - only 0.00% unknown
- deleting segment 4 with 6 points - only 0.00% unknown
- deleting segment 5 with 654 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 6 with 3 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 7 with 2 points - only 0.00% unknown
- deleting segment 8 with 19 points - only 0.00% unknown
- deleting segment 9 with 19 points - only 0.00% unknown
- deleting segment 10 with 6 points - only 0.00% unknown
- deleting segment 11 with 18 points - only 0.00% unknown
- deleting segment 12 with 14 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 13 with 1 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 14 with 3 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 15 with 3 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 16 with 3 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 17 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=5036635.5, rms=0.00
- rms = 1.17, time step reduction 1 of 3 to 0.250...
- rms = 0.30, time step reduction 2 of 3 to 0.125...
- rms = 0.04, time step reduction 3 of 3 to 0.062...
- 004: dt: 0.1250, sse=5036635.5, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 1 vertex label from ripped group
- deleting segment 1 with 1 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 2 with 3 points - only 0.00% unknown
- 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 [93.50 210.50], gm=152.00+-19.50, and vertices in regions > 142.2
- 49201 surface locations found to contain inconsistent values (3727 in, 45474 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=545821.2, rms=0.24
- 001: dt: 0.5000, sse=512763.5, rms=0.235 (0.000%)
- 002: dt: 0.5000, sse=492109.2, rms=0.221 (0.000%)
- 003: dt: 0.5000, sse=478890.5, rms=0.210 (0.000%)
- 004: dt: 0.5000, sse=468479.1, rms=0.201 (0.000%)
- 005: dt: 0.5000, sse=460928.7, rms=0.192 (0.000%)
- 006: dt: 0.5000, sse=454852.8, rms=0.185 (0.000%)
- 007: dt: 0.5000, sse=450161.5, rms=0.179 (0.000%)
- 008: dt: 0.5000, sse=446411.6, rms=0.174 (0.000%)
- 009: dt: 0.5000, sse=443463.4, rms=0.170 (0.000%)
- 010: dt: 0.5000, sse=440539.3, rms=0.166 (0.000%)
- 011: dt: 0.5000, sse=438160.5, rms=0.162 (0.000%)
- 012: dt: 0.5000, sse=435969.0, rms=0.160 (0.000%)
- 013: dt: 0.5000, sse=433968.7, rms=0.157 (0.000%)
- 014: dt: 0.5000, sse=431918.1, rms=0.156 (0.000%)
- 015: dt: 0.5000, sse=430199.5, rms=0.154 (0.000%)
- 016: dt: 0.5000, sse=428447.1, rms=0.153 (0.000%)
- 017: dt: 0.5000, sse=426984.7, rms=0.152 (0.000%)
- 018: dt: 0.5000, sse=425236.5, rms=0.151 (0.000%)
- 019: dt: 0.5000, sse=423691.1, rms=0.150 (0.000%)
- 020: dt: 0.5000, sse=422392.0, rms=0.150 (0.000%)
- 021: dt: 0.5000, sse=421291.2, rms=0.149 (0.000%)
- 022: dt: 0.5000, sse=419910.5, rms=0.149 (0.000%)
- 023: dt: 0.5000, sse=418554.5, rms=0.149 (0.000%)
- 024: dt: 0.5000, sse=417560.7, rms=0.149 (0.000%)
- 025: dt: 0.5000, sse=416196.1, rms=0.149 (0.000%)
- 026: dt: 0.5000, sse=415011.2, rms=0.149 (0.000%)
- 027: dt: 0.5000, sse=413737.7, rms=0.149 (0.000%)
- 028: dt: 0.5000, sse=412626.5, rms=0.149 (0.000%)
- 029: dt: 0.5000, sse=411409.8, rms=0.150 (0.000%)
- 030: dt: 0.5000, sse=410304.5, rms=0.150 (0.000%)
- positioning took 3.9 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [93.00 213.00], gm=153.00+-20.00, and vertices in regions > 143.0
- 41790 surface locations found to contain inconsistent values (1450 in, 40340 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=42761.6, rms=0.13
- 031: dt: 0.5000, sse=42489.0, rms=0.124 (0.000%)
- 032: dt: 0.5000, sse=43547.5, rms=0.112 (0.000%)
- 033: dt: 0.5000, sse=44796.3, rms=0.104 (0.000%)
- 034: dt: 0.5000, sse=45835.6, rms=0.099 (0.000%)
- 035: dt: 0.5000, sse=46688.0, rms=0.094 (0.000%)
- 036: dt: 0.5000, sse=47513.7, rms=0.089 (0.000%)
- 037: dt: 0.5000, sse=48284.1, rms=0.085 (0.000%)
- 038: dt: 0.5000, sse=49045.8, rms=0.081 (0.000%)
- 039: dt: 0.5000, sse=49766.2, rms=0.077 (0.000%)
- 040: dt: 0.5000, sse=50454.8, rms=0.074 (0.000%)
- 041: dt: 0.5000, sse=51093.2, rms=0.071 (0.000%)
- 042: dt: 0.5000, sse=51700.8, rms=0.068 (0.000%)
- 043: dt: 0.5000, sse=52256.1, rms=0.066 (0.000%)
- 044: dt: 0.5000, sse=52807.4, rms=0.063 (0.000%)
- 045: dt: 0.5000, sse=53337.2, rms=0.061 (0.000%)
- 046: dt: 0.5000, sse=53795.3, rms=0.059 (0.000%)
- 047: dt: 0.5000, sse=54250.1, rms=0.057 (0.000%)
- 048: dt: 0.5000, sse=54667.7, rms=0.056 (0.000%)
- 049: dt: 0.5000, sse=55090.1, rms=0.054 (0.000%)
- 050: dt: 0.5000, sse=55411.9, rms=0.053 (0.000%)
- 051: dt: 0.5000, sse=55740.8, rms=0.051 (0.000%)
- 052: dt: 0.5000, sse=56052.9, rms=0.050 (0.000%)
- 053: dt: 0.5000, sse=56331.7, rms=0.049 (0.000%)
- 054: dt: 0.5000, sse=56591.1, rms=0.048 (0.000%)
- 055: dt: 0.5000, sse=56808.3, rms=0.047 (0.000%)
- 056: dt: 0.5000, sse=57023.4, rms=0.046 (0.000%)
- 057: dt: 0.5000, sse=57233.9, rms=0.045 (0.000%)
- 058: dt: 0.5000, sse=57386.6, rms=0.045 (0.000%)
- 059: dt: 0.5000, sse=57561.9, rms=0.044 (0.000%)
- 060: dt: 0.5000, sse=57688.0, rms=0.043 (0.000%)
- positioning took 3.9 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [91.50 214.50], gm=153.00+-20.50, and vertices in regions > 142.7
- 40779 surface locations found to contain inconsistent values (255 in, 40524 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=6171.3, rms=0.05
- 061: dt: 0.5000, sse=6159.9, rms=0.053 (0.000%)
- 062: dt: 0.5000, sse=6243.5, rms=0.047 (0.000%)
- 063: dt: 0.5000, sse=6319.6, rms=0.043 (0.000%)
- 064: dt: 0.5000, sse=6379.4, rms=0.041 (0.000%)
- 065: dt: 0.5000, sse=6416.9, rms=0.039 (0.000%)
- 066: dt: 0.5000, sse=6437.3, rms=0.038 (0.000%)
- 067: dt: 0.5000, sse=6448.1, rms=0.037 (0.000%)
- 068: dt: 0.5000, sse=6457.0, rms=0.036 (0.000%)
- 069: dt: 0.5000, sse=6463.1, rms=0.035 (0.000%)
- 070: dt: 0.5000, sse=6472.0, rms=0.033 (0.000%)
- 071: dt: 0.5000, sse=6479.8, rms=0.033 (0.000%)
- 072: dt: 0.5000, sse=6487.4, rms=0.032 (0.000%)
- 073: dt: 0.5000, sse=6494.8, rms=0.031 (0.000%)
- 074: dt: 0.5000, sse=6500.6, rms=0.030 (0.000%)
- 075: dt: 0.5000, sse=6508.4, rms=0.030 (0.000%)
- 076: dt: 0.5000, sse=6513.4, rms=0.029 (0.000%)
- 077: dt: 0.5000, sse=6519.9, rms=0.029 (0.000%)
- 078: dt: 0.5000, sse=6527.2, rms=0.028 (0.000%)
- 079: dt: 0.5000, sse=6530.8, rms=0.028 (0.000%)
- 080: dt: 0.5000, sse=6534.9, rms=0.028 (0.000%)
- 081: dt: 0.5000, sse=6538.8, rms=0.027 (0.000%)
- 082: dt: 0.5000, sse=6543.6, rms=0.027 (0.000%)
- 083: dt: 0.5000, sse=6547.2, rms=0.027 (0.000%)
- 084: dt: 0.5000, sse=6550.2, rms=0.027 (0.000%)
- 085: dt: 0.5000, sse=6552.5, rms=0.026 (0.000%)
- 086: dt: 0.5000, sse=6555.2, rms=0.026 (0.000%)
- 087: dt: 0.5000, sse=6558.0, rms=0.026 (0.000%)
- 088: dt: 0.5000, sse=6560.3, rms=0.026 (0.000%)
- 089: dt: 0.5000, sse=6564.6, rms=0.026 (0.000%)
- 090: dt: 0.5000, sse=6565.5, rms=0.026 (0.000%)
- positioning took 3.8 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [91.50 214.50], gm=153.00+-20.50, and vertices in regions > 142.7
- 40410 surface locations found to contain inconsistent values (65 in, 40345 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/sub009/surf/lh.pial...
- writing smoothed curvature to lh.curv.pial
- 000: dt: 0.0000, sse=780.8, rms=0.03
- 091: dt: 0.5000, sse=781.5, rms=0.031 (0.000%)
- 092: dt: 0.5000, sse=771.2, rms=0.029 (0.000%)
- 093: dt: 0.5000, sse=764.6, rms=0.029 (0.000%)
- 094: dt: 0.5000, sse=758.2, rms=0.028 (0.000%)
- 095: dt: 0.5000, sse=752.9, rms=0.027 (0.000%)
- 096: dt: 0.5000, sse=748.3, rms=0.026 (0.000%)
- 097: dt: 0.5000, sse=745.5, rms=0.026 (0.000%)
- 098: dt: 0.5000, sse=743.0, rms=0.026 (0.000%)
- 099: dt: 0.5000, sse=740.3, rms=0.025 (0.000%)
- 100: dt: 0.5000, sse=737.5, rms=0.025 (0.000%)
- 101: dt: 0.5000, sse=736.0, rms=0.025 (0.000%)
- 102: dt: 0.5000, sse=733.7, rms=0.024 (0.000%)
- 103: dt: 0.5000, sse=732.3, rms=0.024 (0.000%)
- 104: dt: 0.5000, sse=729.8, rms=0.024 (0.000%)
- 105: dt: 0.5000, sse=728.5, rms=0.024 (0.000%)
- 106: dt: 0.5000, sse=726.5, rms=0.023 (0.000%)
- 107: dt: 0.5000, sse=724.8, rms=0.023 (0.000%)
- 108: dt: 0.5000, sse=723.3, rms=0.023 (0.000%)
- 109: dt: 0.5000, sse=723.5, rms=0.023 (0.000%)
- 110: dt: 0.5000, sse=721.8, rms=0.022 (0.000%)
- 111: dt: 0.5000, sse=720.9, rms=0.022 (0.000%)
- 112: dt: 0.5000, sse=721.7, rms=0.022 (0.000%)
- 113: dt: 0.5000, sse=720.4, rms=0.022 (0.000%)
- 114: dt: 0.5000, sse=719.6, rms=0.022 (0.000%)
- 115: dt: 0.5000, sse=719.1, rms=0.022 (0.000%)
- 116: dt: 0.5000, sse=718.0, rms=0.022 (0.000%)
- 117: dt: 0.5000, sse=717.3, rms=0.022 (0.000%)
- 118: dt: 0.5000, sse=717.8, rms=0.022 (0.000%)
- 119: dt: 0.5000, sse=717.7, rms=0.022 (0.000%)
- 120: dt: 0.5000, sse=717.9, rms=0.022 (0.000%)
- positioning took 3.7 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.curv.pial
- writing smoothed area to lh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.area.pial
- vertex spacing 1.01 +- 0.43 (0.05-->7.19) (max @ vno 98031 --> 96995)
- face area 0.40 +- 0.31 (0.00-->5.22)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 146118 vertices processed
- 25000 of 146118 vertices processed
- 50000 of 146118 vertices processed
- 75000 of 146118 vertices processed
- 100000 of 146118 vertices processed
- 125000 of 146118 vertices processed
- 0 of 146118 vertices processed
- 25000 of 146118 vertices processed
- 50000 of 146118 vertices processed
- 75000 of 146118 vertices processed
- 100000 of 146118 vertices processed
- 125000 of 146118 vertices processed
- thickness calculation complete, 234:454 truncations.
- 31267 vertices at 0 distance
- 100158 vertices at 1 distance
- 97139 vertices at 2 distance
- 37480 vertices at 3 distance
- 10338 vertices at 4 distance
- 2816 vertices at 5 distance
- 812 vertices at 6 distance
- 264 vertices at 7 distance
- 122 vertices at 8 distance
- 85 vertices at 9 distance
- 50 vertices at 10 distance
- 40 vertices at 11 distance
- 23 vertices at 12 distance
- 19 vertices at 13 distance
- 12 vertices at 14 distance
- 13 vertices at 15 distance
- 8 vertices at 16 distance
- 5 vertices at 17 distance
- 6 vertices at 18 distance
- 10 vertices at 19 distance
- 9 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.thickness
- positioning took 19.4 minutes
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/scripts
- cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.woT2.pial
- `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.woT2.pial'
- mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub009 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/sub009/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/wm.mgz...
- 19164 bright wm thresholded.
- 814 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.orig...
- computing class statistics...
- border white: 259466 voxels (1.55%)
- border gray 303507 voxels (1.81%)
- WM (92.0): 93.0 +- 10.6 [70.0 --> 110.0]
- GM (74.0) : 72.2 +- 13.0 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 44.0 (was 70)
- setting MAX_BORDER_WHITE to 115.6 (was 105)
- setting MIN_BORDER_WHITE to 57.0 (was 85)
- setting MAX_CSF to 30.9 (was 40)
- setting MAX_GRAY to 94.4 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 50.5 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 17.9 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=105, GM=57
- mean inside = 92.8, mean outside = 66.9
- 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/sub009/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.89 +- 0.25 (0.02-->5.20) (max @ vno 79769 --> 80799)
- face area 0.33 +- 0.16 (0.00-->4.37)
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 15 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- removing 3 vertex label from ripped group
- deleting segment 4 with 3 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 6 with 17 points - only 0.00% unknown
- deleting segment 7 with 314 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 8 with 4 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 10 with 1 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 11 with 4 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 12 with 1 points - only 0.00% unknown
- deleting segment 13 with 5 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 14 with 1 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 15 with 3 points - only 0.00% unknown
- deleting segment 16 with 29 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 17 with 2 points - only 0.00% unknown
- tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.89 +- 0.25 (0.04-->5.20) (max @ vno 80799 --> 79769)
- face area 0.33 +- 0.16 (0.00-->4.37)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5283345.5, rms=0.00
- rms = 1.44, 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=5283345.5, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 15 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- removing 3 vertex label from ripped group
- deleting segment 2 with 3 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 4 with 17 points - only 0.00% unknown
- deleting segment 5 with 314 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 6 with 4 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 7 with 1 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 8 with 4 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 9 with 1 points - only 0.00% unknown
- deleting segment 10 with 5 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 11 with 1 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 12 with 3 points - only 0.00% unknown
- deleting segment 13 with 29 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 14 with 2 points - only 0.00% unknown
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.89 +- 0.25 (0.04-->5.20) (max @ vno 80799 --> 79769)
- face area 0.33 +- 0.16 (0.00-->4.37)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5283345.5, rms=0.00
- rms = 1.44, 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=5283345.5, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 15 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- removing 3 vertex label from ripped group
- deleting segment 2 with 3 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 4 with 17 points - only 0.00% unknown
- deleting segment 5 with 314 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 6 with 4 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 7 with 1 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 8 with 4 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 9 with 1 points - only 0.00% unknown
- deleting segment 10 with 5 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 11 with 1 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 12 with 3 points - only 0.00% unknown
- deleting segment 13 with 29 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 14 with 2 points - only 0.00% unknown
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.89 +- 0.25 (0.04-->5.20) (max @ vno 80799 --> 79769)
- face area 0.33 +- 0.16 (0.00-->4.37)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5283345.5, rms=0.00
- rms = 1.44, 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=5283345.5, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 15 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- removing 3 vertex label from ripped group
- deleting segment 2 with 3 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 4 with 17 points - only 0.00% unknown
- deleting segment 5 with 314 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 6 with 4 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 7 with 1 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 8 with 4 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 9 with 1 points - only 0.00% unknown
- deleting segment 10 with 5 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 11 with 1 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 12 with 3 points - only 0.00% unknown
- deleting segment 13 with 29 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 14 with 2 points - only 0.00% unknown
- tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- repositioning cortical surface to gray/csf boundary.
- smoothing T1 volume with sigma = 2.000
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5283345.5, rms=0.00
- rms = 1.44, 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=5283345.5, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 3 vertex label from ripped group
- deleting segment 6 with 3 points - only 0.00% unknown
- smoothing surface for 5 iterations...
- reading initial pial vertex positions from woT2.pial...
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [92.00 212.00], gm=152.00+-20.00, and vertices in regions > 142.0
- 54992 surface locations found to contain inconsistent values (4218 in, 50774 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=553568.6, rms=0.23
- 001: dt: 0.5000, sse=517982.0, rms=0.224 (0.000%)
- 002: dt: 0.5000, sse=496008.7, rms=0.209 (0.000%)
- 003: dt: 0.5000, sse=482069.6, rms=0.197 (0.000%)
- 004: dt: 0.5000, sse=470726.9, rms=0.188 (0.000%)
- 005: dt: 0.5000, sse=462433.6, rms=0.180 (0.000%)
- 006: dt: 0.5000, sse=456190.8, rms=0.173 (0.000%)
- 007: dt: 0.5000, sse=451191.1, rms=0.167 (0.000%)
- 008: dt: 0.5000, sse=447166.4, rms=0.162 (0.000%)
- 009: dt: 0.5000, sse=443656.5, rms=0.157 (0.000%)
- 010: dt: 0.5000, sse=440653.6, rms=0.154 (0.000%)
- 011: dt: 0.5000, sse=438000.7, rms=0.151 (0.000%)
- 012: dt: 0.5000, sse=435878.2, rms=0.149 (0.000%)
- 013: dt: 0.5000, sse=433847.7, rms=0.147 (0.000%)
- 014: dt: 0.5000, sse=431588.1, rms=0.145 (0.000%)
- 015: dt: 0.5000, sse=429934.3, rms=0.144 (0.000%)
- 016: dt: 0.5000, sse=428059.9, rms=0.143 (0.000%)
- 017: dt: 0.5000, sse=426326.9, rms=0.142 (0.000%)
- 018: dt: 0.5000, sse=424761.1, rms=0.141 (0.000%)
- 019: dt: 0.5000, sse=422935.0, rms=0.141 (0.000%)
- 020: dt: 0.5000, sse=421328.0, rms=0.141 (0.000%)
- 021: dt: 0.5000, sse=419715.2, rms=0.140 (0.000%)
- 022: dt: 0.5000, sse=418351.8, rms=0.140 (0.000%)
- 023: dt: 0.5000, sse=417144.2, rms=0.140 (0.000%)
- 024: dt: 0.5000, sse=415696.4, rms=0.140 (0.000%)
- 025: dt: 0.5000, sse=414073.3, rms=0.141 (0.000%)
- 026: dt: 0.5000, sse=412813.5, rms=0.141 (0.000%)
- 027: dt: 0.5000, sse=411663.8, rms=0.141 (0.000%)
- 028: dt: 0.5000, sse=410353.9, rms=0.141 (0.000%)
- 029: dt: 0.5000, sse=409229.2, rms=0.142 (0.000%)
- 030: dt: 0.5000, sse=407916.7, rms=0.142 (0.000%)
- positioning took 4.0 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [95.00 209.00], gm=152.00+-19.00, and vertices in regions > 142.5
- 39232 surface locations found to contain inconsistent values (3272 in, 35960 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=42389.2, rms=0.12
- 031: dt: 0.5000, sse=42143.1, rms=0.120 (0.000%)
- 032: dt: 0.5000, sse=42833.0, rms=0.110 (0.000%)
- 033: dt: 0.5000, sse=43754.8, rms=0.102 (0.000%)
- 034: dt: 0.5000, sse=44552.0, rms=0.097 (0.000%)
- 035: dt: 0.5000, sse=45223.8, rms=0.092 (0.000%)
- 036: dt: 0.5000, sse=45882.4, rms=0.087 (0.000%)
- 037: dt: 0.5000, sse=46532.7, rms=0.083 (0.000%)
- 038: dt: 0.5000, sse=47153.7, rms=0.079 (0.000%)
- 039: dt: 0.5000, sse=47770.9, rms=0.075 (0.000%)
- 040: dt: 0.5000, sse=48403.9, rms=0.072 (0.000%)
- 041: dt: 0.5000, sse=48977.2, rms=0.069 (0.000%)
- 042: dt: 0.5000, sse=49550.5, rms=0.066 (0.000%)
- 043: dt: 0.5000, sse=50075.6, rms=0.063 (0.000%)
- 044: dt: 0.5000, sse=50585.0, rms=0.061 (0.000%)
- 045: dt: 0.5000, sse=51057.1, rms=0.059 (0.000%)
- 046: dt: 0.5000, sse=51506.5, rms=0.057 (0.000%)
- 047: dt: 0.5000, sse=51927.9, rms=0.055 (0.000%)
- 048: dt: 0.5000, sse=52297.9, rms=0.053 (0.000%)
- 049: dt: 0.5000, sse=52670.6, rms=0.052 (0.000%)
- 050: dt: 0.5000, sse=52984.2, rms=0.050 (0.000%)
- 051: dt: 0.5000, sse=53287.6, rms=0.049 (0.000%)
- 052: dt: 0.5000, sse=53577.7, rms=0.048 (0.000%)
- 053: dt: 0.5000, sse=53851.3, rms=0.047 (0.000%)
- 054: dt: 0.5000, sse=54110.2, rms=0.046 (0.000%)
- 055: dt: 0.5000, sse=54312.0, rms=0.045 (0.000%)
- 056: dt: 0.5000, sse=54524.5, rms=0.044 (0.000%)
- 057: dt: 0.5000, sse=54719.0, rms=0.043 (0.000%)
- 058: dt: 0.5000, sse=54878.2, rms=0.043 (0.000%)
- 059: dt: 0.5000, sse=55031.9, rms=0.042 (0.000%)
- 060: dt: 0.5000, sse=55190.9, rms=0.041 (0.000%)
- positioning took 3.9 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [87.50 216.50], gm=152.00+-21.50, and vertices in regions > 141.2
- 46443 surface locations found to contain inconsistent values (76 in, 46367 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=6303.0, rms=0.07
- 061: dt: 0.5000, sse=6212.9, rms=0.071 (0.000%)
- 062: dt: 0.5000, sse=6267.5, rms=0.060 (0.000%)
- 063: dt: 0.5000, sse=6378.5, rms=0.054 (0.000%)
- 064: dt: 0.5000, sse=6483.5, rms=0.051 (0.000%)
- 065: dt: 0.5000, sse=6559.6, rms=0.048 (0.000%)
- 066: dt: 0.5000, sse=6609.5, rms=0.045 (0.000%)
- 067: dt: 0.5000, sse=6643.6, rms=0.044 (0.000%)
- 068: dt: 0.5000, sse=6674.2, rms=0.042 (0.000%)
- 069: dt: 0.5000, sse=6704.0, rms=0.040 (0.000%)
- 070: dt: 0.5000, sse=6731.9, rms=0.039 (0.000%)
- 071: dt: 0.5000, sse=6756.5, rms=0.038 (0.000%)
- 072: dt: 0.5000, sse=6778.3, rms=0.037 (0.000%)
- 073: dt: 0.5000, sse=6796.7, rms=0.036 (0.000%)
- 074: dt: 0.5000, sse=6813.0, rms=0.035 (0.000%)
- 075: dt: 0.5000, sse=6827.6, rms=0.034 (0.000%)
- 076: dt: 0.5000, sse=6840.5, rms=0.033 (0.000%)
- 077: dt: 0.5000, sse=6850.6, rms=0.033 (0.000%)
- 078: dt: 0.5000, sse=6860.6, rms=0.032 (0.000%)
- 079: dt: 0.5000, sse=6868.9, rms=0.031 (0.000%)
- 080: dt: 0.5000, sse=6877.5, rms=0.031 (0.000%)
- 081: dt: 0.5000, sse=6884.9, rms=0.031 (0.000%)
- 082: dt: 0.5000, sse=6892.0, rms=0.030 (0.000%)
- 083: dt: 0.5000, sse=6897.8, rms=0.030 (0.000%)
- 084: dt: 0.5000, sse=6903.8, rms=0.030 (0.000%)
- 085: dt: 0.5000, sse=6909.2, rms=0.029 (0.000%)
- 086: dt: 0.5000, sse=6913.9, rms=0.029 (0.000%)
- 087: dt: 0.5000, sse=6918.3, rms=0.029 (0.000%)
- 088: dt: 0.5000, sse=6921.5, rms=0.029 (0.000%)
- 089: dt: 0.5000, sse=6924.7, rms=0.029 (0.000%)
- 090: dt: 0.5000, sse=6928.1, rms=0.029 (0.000%)
- positioning took 3.8 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [86.00 218.00], gm=152.00+-22.00, and vertices in regions > 141.0
- 46811 surface locations found to contain inconsistent values (17 in, 46794 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/sub009/surf/rh.pial...
- writing smoothed curvature to rh.curv.pial
- 000: dt: 0.0000, sse=920.2, rms=0.04
- 091: dt: 0.5000, sse=902.4, rms=0.039 (0.000%)
- 092: dt: 0.5000, sse=858.5, rms=0.034 (0.000%)
- 093: dt: 0.5000, sse=846.2, rms=0.032 (0.000%)
- 094: dt: 0.5000, sse=840.8, rms=0.031 (0.000%)
- 095: dt: 0.5000, sse=836.5, rms=0.030 (0.000%)
- 096: dt: 0.5000, sse=833.2, rms=0.030 (0.000%)
- 097: dt: 0.5000, sse=830.5, rms=0.030 (0.000%)
- 098: dt: 0.5000, sse=828.1, rms=0.029 (0.000%)
- 099: dt: 0.5000, sse=826.3, rms=0.029 (0.000%)
- 100: dt: 0.5000, sse=824.3, rms=0.029 (0.000%)
- 101: dt: 0.5000, sse=822.5, rms=0.028 (0.000%)
- 102: dt: 0.5000, sse=820.9, rms=0.028 (0.000%)
- 103: dt: 0.5000, sse=819.9, rms=0.028 (0.000%)
- 104: dt: 0.5000, sse=818.6, rms=0.028 (0.000%)
- 105: dt: 0.5000, sse=817.3, rms=0.028 (0.000%)
- 106: dt: 0.5000, sse=816.2, rms=0.027 (0.000%)
- 107: dt: 0.5000, sse=815.2, rms=0.027 (0.000%)
- 108: dt: 0.5000, sse=814.3, rms=0.027 (0.000%)
- 109: dt: 0.5000, sse=813.5, rms=0.027 (0.000%)
- 110: dt: 0.5000, sse=812.8, rms=0.027 (0.000%)
- 111: dt: 0.5000, sse=812.3, rms=0.027 (0.000%)
- 112: dt: 0.5000, sse=811.6, rms=0.027 (0.000%)
- 113: dt: 0.5000, sse=811.2, rms=0.027 (0.000%)
- 114: dt: 0.5000, sse=811.0, rms=0.027 (0.000%)
- 115: dt: 0.5000, sse=811.4, rms=0.027 (0.000%)
- 116: dt: 0.5000, sse=811.0, rms=0.027 (0.000%)
- 117: dt: 0.5000, sse=810.6, rms=0.027 (0.000%)
- 118: dt: 0.5000, sse=810.2, rms=0.026 (0.000%)
- 119: dt: 0.5000, sse=810.0, rms=0.026 (0.000%)
- 120: dt: 0.5000, sse=809.9, rms=0.026 (0.000%)
- positioning took 3.7 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.curv.pial
- writing smoothed area to rh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.area.pial
- vertex spacing 1.02 +- 0.43 (0.08-->8.58) (max @ vno 102156 --> 102155)
- face area 0.41 +- 0.31 (0.00-->6.68)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 146248 vertices processed
- 25000 of 146248 vertices processed
- 50000 of 146248 vertices processed
- 75000 of 146248 vertices processed
- 100000 of 146248 vertices processed
- 125000 of 146248 vertices processed
- 0 of 146248 vertices processed
- 25000 of 146248 vertices processed
- 50000 of 146248 vertices processed
- 75000 of 146248 vertices processed
- 100000 of 146248 vertices processed
- 125000 of 146248 vertices processed
- thickness calculation complete, 284:405 truncations.
- 31600 vertices at 0 distance
- 98547 vertices at 1 distance
- 97474 vertices at 2 distance
- 38998 vertices at 3 distance
- 10460 vertices at 4 distance
- 2837 vertices at 5 distance
- 830 vertices at 6 distance
- 308 vertices at 7 distance
- 110 vertices at 8 distance
- 71 vertices at 9 distance
- 43 vertices at 10 distance
- 41 vertices at 11 distance
- 41 vertices at 12 distance
- 16 vertices at 13 distance
- 25 vertices at 14 distance
- 26 vertices at 15 distance
- 17 vertices at 16 distance
- 11 vertices at 17 distance
- 12 vertices at 18 distance
- 5 vertices at 19 distance
- 18 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.thickness
- positioning took 19.0 minutes
- #--------------------------------------------
- #@# Surf Volume lh Thu Aug 8 23:43:47 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf
- mris_calc -o lh.area.mid lh.area add lh.area.pial
- Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o lh.area.mid lh.area.mid div 2
- Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o lh.volume lh.area.mid mul lh.thickness
- Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ]
- #--------------------------------------------
- #@# Surf Volume rh Thu Aug 8 23:43:48 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf
- mris_calc -o rh.area.mid rh.area add rh.area.pial
- Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o rh.area.mid rh.area.mid div 2
- Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o rh.volume rh.area.mid mul rh.thickness
- Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ]
- #--------------------------------------------
- #@# Cortical ribbon mask Thu Aug 8 23:43:48 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri
- mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon sub009
- 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 = 5
- writing volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/ribbon.mgz
- writing ribbon files
- #--------------------------------------------
- #@# ASeg Stats Fri Aug 9 00:03:59 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009
- 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 sub009
- $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 sub009
- sysname Linux
- hostname snake6
- machine x86_64
- user fkaule
- UseRobust 0
- atlas_icv (eTIV) = 1198514 mm^3 (det: 1.625434 )
- Computing euler number
- orig.nofix lheno = -32, rheno = -20
- orig.nofix lhholes = 17, rhholes = 11
- Loading mri/aseg.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 250723.462 249908.000 diff= 815.5 pctdiff= 0.325
- rhCtxGM: 256030.872 254885.000 diff= 1145.9 pctdiff= 0.448
- lhCtxWM: 212144.737 211877.500 diff= 267.2 pctdiff= 0.126
- rhCtxWM: 212485.812 212659.500 diff= -173.7 pctdiff=-0.082
- SubCortGMVol 59766.000
- SupraTentVol 1021635.883 (1018698.000) diff=2937.883 pctdiff=0.288
- SupraTentVolNotVent 992174.883 (989237.000) diff=2937.883 pctdiff=0.296
- BrainSegVol 1164260.000 (1161362.000) diff=2898.000 pctdiff=0.249
- BrainSegVolNotVent 1130776.000 (1132546.883) diff=-1770.883 pctdiff=-0.157
- BrainSegVolNotVent 1130776.000
- CerebellumVol 141255.000
- VentChorVol 29461.000
- 3rd4th5thCSF 4023.000
- CSFVol 1142.000, OptChiasmVol 267.000
- MaskVol 1709725.000
- 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 13306 13305.957
- 4 5 Left-Inf-Lat-Vent 238 237.695
- 5 7 Left-Cerebellum-White-Matter 18453 18452.689
- 6 8 Left-Cerebellum-Cortex 52582 52581.742
- 7 10 Left-Thalamus-Proper 6965 6965.113
- 8 11 Left-Caudate 3863 3863.370
- 9 12 Left-Putamen 6716 6716.408
- 10 13 Left-Pallidum 1892 1891.845
- 11 14 3rd-Ventricle 1460 1459.907
- 12 15 4th-Ventricle 1635 1634.819
- 13 16 Brain-Stem 23763 23762.811
- 14 17 Left-Hippocampus 3429 3428.875
- 15 18 Left-Amygdala 1480 1479.961
- 16 24 CSF 1144 1143.941
- 17 26 Left-Accumbens-area 856 855.577
- 18 28 Left-VentralDC 3880 3879.935
- 19 30 Left-vessel 29 29.245
- 20 31 Left-choroid-plexus 1099 1099.359
- 23 43 Right-Lateral-Ventricle 12914 12913.826
- 24 44 Right-Inf-Lat-Vent 217 216.662
- 25 46 Right-Cerebellum-White-Matter 18133 18133.016
- 26 47 Right-Cerebellum-Cortex 54267 54266.852
- 27 49 Right-Thalamus-Proper 6384 6383.620
- 28 50 Right-Caudate 3911 3911.343
- 29 51 Right-Putamen 7260 7260.207
- 30 52 Right-Pallidum 1645 1644.907
- 31 53 Right-Hippocampus 3514 3513.790
- 32 54 Right-Amygdala 1593 1593.034
- 33 58 Right-Accumbens-area 782 782.409
- 34 60 Right-VentralDC 3878 3877.557
- 35 62 Right-vessel 101 101.259
- 36 63 Right-choroid-plexus 1502 1501.959
- 37 72 5th-Ventricle 0 0.000
- 38 77 WM-hypointensities 1684 1684.251
- 39 78 Left-WM-hypointensities 0 0.000
- 40 79 Right-WM-hypointensities 0 0.000
- 41 80 non-WM-hypointensities 14 13.978
- 42 81 Left-non-WM-hypointensities 0 0.000
- 43 82 Right-non-WM-hypointensities 0 0.000
- 44 85 Optic-Chiasm 277 276.815
- 45 251 CC_Posterior 633 633.104
- 46 252 CC_Mid_Posterior 328 327.517
- 47 253 CC_Central 315 315.145
- 48 254 CC_Mid_Anterior 399 399.062
- 49 255 CC_Anterior 700 700.434
- Reporting on 45 segmentations
- mri_segstats done
- #-----------------------------------------
- #@# AParc-to-ASeg Fri Aug 9 00:07:17 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009
- mri_aparc2aseg --s sub009 --volmask
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- subject sub009
- outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/aparc+aseg.mgz
- useribbon 0
- baseoffset 0
- RipUnknown 0
- Reading lh white surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.white
- Reading lh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.pial
- Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/surf/rh.white
- Reading rh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.pial
- Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/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/sub009/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 = 503309
- Used brute-force search on 0 voxels
- Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/aparc+aseg.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009
- mri_aparc2aseg --s sub009 --volmask --a2009s
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- subject sub009
- outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/aparc.a2009s+aseg.mgz
- useribbon 0
- baseoffset 10100
- RipUnknown 0
- Reading lh white surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.white
- Reading lh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.pial
- Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/surf/rh.white
- Reading rh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.pial
- Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/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/sub009/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 = 503309
- Used brute-force search on 0 voxels
- Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/aparc.a2009s+aseg.mgz
- #-----------------------------------------
- #@# WMParc Fri Aug 9 00:12:12 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009
- mri_aparc2aseg --s sub009 --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 sub009
- 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/sub009/mri/aparc+aseg.mgz
- Reading lh white surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.white
- Reading lh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.pial
- Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/surf/rh.white
- Reading rh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.pial
- Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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/sub009/mri/ribbon.mgz
- Loading filled from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/filled.mgz
- Ripping vertices labeled as unkown
- Ripped 7601 vertices from left hemi
- Ripped 7375 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/sub009/mri/aseg.mgz
- Loading Ctx Seg File /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 = 926878
- Used brute-force search on 220 voxels
- Fixing Parahip LH WM
- Found 10 clusters
- 0 k 1672.000000
- 1 k 1.000000
- 2 k 1.000000
- 3 k 1.000000
- 4 k 1.000000
- 5 k 6.000000
- 6 k 2.000000
- 7 k 1.000000
- 8 k 32.000000
- 9 k 1.000000
- Fixing Parahip RH WM
- Found 5 clusters
- 0 k 3.000000
- 1 k 2.000000
- 2 k 1.000000
- 3 k 1373.000000
- 4 k 2.000000
- Writing output aseg to mri/wmparc.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009
- 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 sub009 --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 sub009 --surf-wm-vol --ctab /opt/freesurfer/5.3.0/WMParcStatsLUT.txt --etiv
- sysname Linux
- hostname snake6
- machine x86_64
- user fkaule
- UseRobust 0
- atlas_icv (eTIV) = 1198514 mm^3 (det: 1.625434 )
- Loading mri/wmparc.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 250723.462 249908.000 diff= 815.5 pctdiff= 0.325
- rhCtxGM: 256030.872 254885.000 diff= 1145.9 pctdiff= 0.448
- lhCtxWM: 212144.737 211877.500 diff= 267.2 pctdiff= 0.126
- rhCtxWM: 212485.812 212659.500 diff= -173.7 pctdiff=-0.082
- SubCortGMVol 59766.000
- SupraTentVol 1021635.883 (1018698.000) diff=2937.883 pctdiff=0.288
- SupraTentVolNotVent 992174.883 (989237.000) diff=2937.883 pctdiff=0.296
- BrainSegVol 1164260.000 (1161362.000) diff=2898.000 pctdiff=0.249
- BrainSegVolNotVent 1130776.000 (1132546.883) diff=-1770.883 pctdiff=-0.157
- BrainSegVolNotVent 1130776.000
- CerebellumVol 141255.000
- VentChorVol 29461.000
- 3rd4th5thCSF 4023.000
- CSFVol 1142.000, OptChiasmVol 267.000
- MaskVol 1709725.000
- 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 1805 1804.976
- 2 3002 wm-lh-caudalanteriorcingulate 3722 3722.377
- 3 3003 wm-lh-caudalmiddlefrontal 5819 5818.831
- 4 3004 wm-lh-corpuscallosum 0 0.000
- 5 3005 wm-lh-cuneus 1739 1739.438
- 6 3006 wm-lh-entorhinal 1174 1173.700
- 7 3007 wm-lh-fusiform 6099 6099.014
- 8 3008 wm-lh-inferiorparietal 10880 10880.184
- 9 3009 wm-lh-inferiortemporal 6232 6231.960
- 10 3010 wm-lh-isthmuscingulate 3386 3385.789
- 11 3011 wm-lh-lateraloccipital 9315 9315.484
- 12 3012 wm-lh-lateralorbitofrontal 6493 6493.025
- 13 3013 wm-lh-lingual 3892 3891.911
- 14 3014 wm-lh-medialorbitofrontal 3614 3613.732
- 15 3015 wm-lh-middletemporal 5669 5669.354
- 16 3016 wm-lh-parahippocampal 1681 1681.262
- 17 3017 wm-lh-paracentral 3500 3500.263
- 18 3018 wm-lh-parsopercularis 4456 4455.846
- 19 3019 wm-lh-parsorbitalis 1002 1001.512
- 20 3020 wm-lh-parstriangularis 2758 2758.121
- 21 3021 wm-lh-pericalcarine 2592 2592.143
- 22 3022 wm-lh-postcentral 6460 6459.997
- 23 3023 wm-lh-posteriorcingulate 4768 4768.479
- 24 3024 wm-lh-precentral 12316 12316.146
- 25 3025 wm-lh-precuneus 10587 10587.366
- 26 3026 wm-lh-rostralanteriorcingulate 2807 2807.190
- 27 3027 wm-lh-rostralmiddlefrontal 11997 11996.839
- 28 3028 wm-lh-superiorfrontal 15458 15458.268
- 29 3029 wm-lh-superiorparietal 10976 10976.164
- 30 3030 wm-lh-superiortemporal 6779 6779.273
- 31 3031 wm-lh-supramarginal 9299 9299.476
- 32 3032 wm-lh-frontalpole 242 241.536
- 33 3033 wm-lh-temporalpole 725 725.089
- 34 3034 wm-lh-transversetemporal 792 792.341
- 35 3035 wm-lh-insula 9900 9900.117
- 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 1754 1754.114
- 120 4002 wm-rh-caudalanteriorcingulate 2418 2417.562
- 121 4003 wm-rh-caudalmiddlefrontal 6421 6421.150
- 122 4004 wm-rh-corpuscallosum 0 0.000
- 123 4005 wm-rh-cuneus 1710 1709.773
- 124 4006 wm-rh-entorhinal 512 511.662
- 125 4007 wm-rh-fusiform 6470 6469.794
- 126 4008 wm-rh-inferiorparietal 10519 10519.486
- 127 4009 wm-rh-inferiortemporal 5595 5595.008
- 128 4010 wm-rh-isthmuscingulate 4005 4004.809
- 129 4011 wm-rh-lateraloccipital 8468 8467.862
- 130 4012 wm-rh-lateralorbitofrontal 6680 6680.200
- 131 4013 wm-rh-lingual 4140 4139.808
- 132 4014 wm-rh-medialorbitofrontal 3026 3025.862
- 133 4015 wm-rh-middletemporal 5180 5180.194
- 134 4016 wm-rh-parahippocampal 1393 1393.051
- 135 4017 wm-rh-paracentral 5542 5542.227
- 136 4018 wm-rh-parsopercularis 3170 3169.978
- 137 4019 wm-rh-parsorbitalis 1120 1120.104
- 138 4020 wm-rh-parstriangularis 3305 3305.098
- 139 4021 wm-rh-pericalcarine 2445 2445.323
- 140 4022 wm-rh-postcentral 8501 8500.583
- 141 4023 wm-rh-posteriorcingulate 4458 4458.224
- 142 4024 wm-rh-precentral 11362 11362.404
- 143 4025 wm-rh-precuneus 9609 9609.014
- 144 4026 wm-rh-rostralanteriorcingulate 2202 2202.296
- 145 4027 wm-rh-rostralmiddlefrontal 12301 12300.676
- 146 4028 wm-rh-superiorfrontal 17984 17984.150
- 147 4029 wm-rh-superiorparietal 12043 12043.066
- 148 4030 wm-rh-superiortemporal 6955 6954.842
- 149 4031 wm-rh-supramarginal 9802 9802.221
- 150 4032 wm-rh-frontalpole 272 271.942
- 151 4033 wm-rh-temporalpole 591 591.352
- 152 4034 wm-rh-transversetemporal 616 616.153
- 153 4035 wm-rh-insula 9805 9805.454
- 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 24313 24312.592
- 237 5002 Right-UnsegmentedWhiteMatter 23325 23325.129
- 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/sub009/label
- #--------------------------------------------
- #@# BA Labels lh Fri Aug 9 00:22:49 CEST 2013
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118
- Number of reverse mapping hits = 243
- Checking for and removing duplicates
- Writing label file ./lh.BA1.label 4372
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118
- Number of reverse mapping hits = 475
- Checking for and removing duplicates
- Writing label file ./lh.BA2.label 8384
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118
- Number of reverse mapping hits = 134
- Checking for and removing duplicates
- Writing label file ./lh.BA3a.label 4211
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118
- Number of reverse mapping hits = 303
- Checking for and removing duplicates
- Writing label file ./lh.BA3b.label 6286
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118
- Number of reverse mapping hits = 626
- Checking for and removing duplicates
- Writing label file ./lh.BA4a.label 6410
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118
- Number of reverse mapping hits = 350
- Checking for and removing duplicates
- Writing label file ./lh.BA4p.label 4420
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118
- Number of reverse mapping hits = 1248
- Checking for and removing duplicates
- Writing label file ./lh.BA6.label 14837
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118
- Number of reverse mapping hits = 863
- Checking for and removing duplicates
- Writing label file ./lh.BA44.label 5044
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118
- Number of reverse mapping hits = 1296
- Checking for and removing duplicates
- Writing label file ./lh.BA45.label 4718
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118
- Number of reverse mapping hits = 1647
- Checking for and removing duplicates
- Writing label file ./lh.V1.label 6288
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118
- Number of reverse mapping hits = 2674
- Checking for and removing duplicates
- Writing label file ./lh.V2.label 10788
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118
- Number of reverse mapping hits = 739
- Checking for and removing duplicates
- Writing label file ./lh.MT.label 2757
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.perirhinal.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118
- Number of reverse mapping hits = 168
- Checking for and removing duplicates
- Writing label file ./lh.perirhinal.label 1367
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.thresh.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118
- Number of reverse mapping hits = 82
- Checking for and removing duplicates
- Writing label file ./lh.BA1.thresh.label 1096
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.thresh.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118
- Number of reverse mapping hits = 74
- Checking for and removing duplicates
- Writing label file ./lh.BA2.thresh.label 2166
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.thresh.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118
- Number of reverse mapping hits = 15
- Checking for and removing duplicates
- Writing label file ./lh.BA3a.thresh.label 1519
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.thresh.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118
- Number of reverse mapping hits = 82
- Checking for and removing duplicates
- Writing label file ./lh.BA3b.thresh.label 2078
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.thresh.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118
- Number of reverse mapping hits = 247
- Checking for and removing duplicates
- Writing label file ./lh.BA4a.thresh.label 2566
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.thresh.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118
- Number of reverse mapping hits = 126
- Checking for and removing duplicates
- Writing label file ./lh.BA4p.thresh.label 1675
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.thresh.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118
- Number of reverse mapping hits = 604
- Checking for and removing duplicates
- Writing label file ./lh.BA6.thresh.label 7639
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.thresh.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118
- Number of reverse mapping hits = 443
- Checking for and removing duplicates
- Writing label file ./lh.BA44.thresh.label 2355
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.thresh.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118
- Number of reverse mapping hits = 633
- Checking for and removing duplicates
- Writing label file ./lh.BA45.thresh.label 1784
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.thresh.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118
- Number of reverse mapping hits = 1212
- Checking for and removing duplicates
- Writing label file ./lh.V1.thresh.label 4617
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.thresh.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118
- Number of reverse mapping hits = 1181
- Checking for and removing duplicates
- Writing label file ./lh.V2.thresh.label 4515
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.thresh.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146118
- Number of reverse mapping hits = 160
- Checking for and removing duplicates
- Writing label file ./lh.MT.thresh.label 673
- mri_label2label: Done
- mris_label2annot --s sub009 --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/sub009/label
- cmdline mris_label2annot --s sub009 --hemi lh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --l lh.perirhinal.label --a BA --maxstatwinner --noverbose
- sysname Linux
- hostname snake6
- machine x86_64
- user fkaule
- subject sub009
- 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/sub009/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 103427 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/label/lh.BA.annot
- mris_label2annot --s sub009 --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/sub009/label
- cmdline mris_label2annot --s sub009 --hemi lh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l lh.BA1.thresh.label --l lh.BA2.thresh.label --l lh.BA3a.thresh.label --l lh.BA3b.thresh.label --l lh.BA4a.thresh.label --l lh.BA4p.thresh.label --l lh.BA6.thresh.label --l lh.BA44.thresh.label --l lh.BA45.thresh.label --l lh.V1.thresh.label --l lh.V2.thresh.label --l lh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose
- sysname Linux
- hostname snake6
- machine x86_64
- user fkaule
- subject sub009
- 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/sub009/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 121505 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/label/lh.BA.thresh.annot
- mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab sub009 lh white
- computing statistics for each annotation in ./lh.BA.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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
- 1133 667 2086 2.282 0.490 0.173 0.074 31 3.4 BA1
- 3885 2607 6069 2.228 0.408 0.129 0.043 61 7.4 BA2
- 860 583 863 1.914 0.441 0.154 0.046 9 1.7 BA3a
- 2207 1513 3238 1.883 0.551 0.124 0.041 27 3.1 BA3b
- 1850 1146 4022 2.843 0.482 0.118 0.033 17 2.6 BA4a
- 1344 822 2168 2.596 0.459 0.099 0.030 9 1.6 BA4p
- 9292 6036 20367 2.710 0.528 0.135 0.042 120 15.7 BA6
- 2910 1966 5800 2.559 0.400 0.136 0.044 44 5.0 BA44
- 3682 2499 6445 2.296 0.437 0.161 0.068 592 8.0 BA45
- 3821 2607 5020 1.855 0.498 0.171 0.083 73 12.8 V1
- 8091 5275 12048 2.103 0.448 0.170 0.072 169 21.8 V2
- 2511 1712 4489 2.412 0.461 0.162 0.059 50 6.1 MT
- 1105 749 2333 2.690 0.648 0.126 0.080 65 2.5 perirhinal
- mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab sub009 lh white
- computing statistics for each annotation in ./lh.BA.thresh.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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
- 714 414 1322 2.262 0.515 0.179 0.083 22 2.2 BA1
- 1382 922 2244 2.152 0.336 0.109 0.026 11 1.5 BA2
- 710 469 651 1.903 0.382 0.150 0.044 8 1.3 BA3a
- 1324 921 1579 1.564 0.337 0.114 0.030 12 1.6 BA3b
- 1786 1098 3916 2.880 0.482 0.115 0.030 15 2.5 BA4a
- 1095 689 1705 2.500 0.455 0.103 0.029 7 1.3 BA4p
- 5234 3357 11657 2.715 0.539 0.132 0.044 69 8.9 BA6
- 1990 1355 4155 2.608 0.374 0.138 0.043 29 3.4 BA44
- 1695 1114 3150 2.399 0.406 0.172 0.064 56 4.1 BA45
- 4041 2764 5343 1.849 0.486 0.170 0.082 76 13.5 V1
- 4023 2633 6097 2.114 0.441 0.185 0.088 95 12.5 V2
- 619 439 1091 2.273 0.490 0.167 0.061 12 1.5 MT
- #--------------------------------------------
- #@# BA Labels rh Fri Aug 9 00:27:33 CEST 2013
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248
- Number of reverse mapping hits = 656
- Checking for and removing duplicates
- Writing label file ./rh.BA1.label 4618
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248
- Number of reverse mapping hits = 1333
- Checking for and removing duplicates
- Writing label file ./rh.BA2.label 8020
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248
- Number of reverse mapping hits = 188
- Checking for and removing duplicates
- Writing label file ./rh.BA3a.label 4168
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248
- Number of reverse mapping hits = 341
- Checking for and removing duplicates
- Writing label file ./rh.BA3b.label 4863
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248
- Number of reverse mapping hits = 393
- Checking for and removing duplicates
- Writing label file ./rh.BA4a.label 6140
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248
- Number of reverse mapping hits = 218
- Checking for and removing duplicates
- Writing label file ./rh.BA4p.label 4691
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248
- Number of reverse mapping hits = 1114
- Checking for and removing duplicates
- Writing label file ./rh.BA6.label 13370
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248
- Number of reverse mapping hits = 1345
- Checking for and removing duplicates
- Writing label file ./rh.BA44.label 8257
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248
- Number of reverse mapping hits = 1586
- Checking for and removing duplicates
- Writing label file ./rh.BA45.label 6941
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248
- Number of reverse mapping hits = 1243
- Checking for and removing duplicates
- Writing label file ./rh.V1.label 5970
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248
- Number of reverse mapping hits = 2681
- Checking for and removing duplicates
- Writing label file ./rh.V2.label 10697
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248
- Number of reverse mapping hits = 636
- Checking for and removing duplicates
- Writing label file ./rh.MT.label 2568
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.perirhinal.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248
- Number of reverse mapping hits = 43
- Checking for and removing duplicates
- Writing label file ./rh.perirhinal.label 795
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.thresh.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248
- Number of reverse mapping hits = 200
- Checking for and removing duplicates
- Writing label file ./rh.BA1.thresh.label 1076
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.thresh.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248
- Number of reverse mapping hits = 495
- Checking for and removing duplicates
- Writing label file ./rh.BA2.thresh.label 3183
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.thresh.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248
- Number of reverse mapping hits = 62
- Checking for and removing duplicates
- Writing label file ./rh.BA3a.thresh.label 1760
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.thresh.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248
- Number of reverse mapping hits = 182
- Checking for and removing duplicates
- Writing label file ./rh.BA3b.thresh.label 2365
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.thresh.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248
- Number of reverse mapping hits = 163
- Checking for and removing duplicates
- Writing label file ./rh.BA4a.thresh.label 1551
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.thresh.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248
- Number of reverse mapping hits = 75
- Checking for and removing duplicates
- Writing label file ./rh.BA4p.thresh.label 1564
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.thresh.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248
- Number of reverse mapping hits = 452
- Checking for and removing duplicates
- Writing label file ./rh.BA6.thresh.label 7411
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.thresh.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248
- Number of reverse mapping hits = 245
- Checking for and removing duplicates
- Writing label file ./rh.BA44.thresh.label 1257
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.thresh.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248
- Number of reverse mapping hits = 238
- Checking for and removing duplicates
- Writing label file ./rh.BA45.thresh.label 1416
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.thresh.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248
- Number of reverse mapping hits = 811
- Checking for and removing duplicates
- Writing label file ./rh.V1.thresh.label 4043
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.thresh.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248
- Number of reverse mapping hits = 1126
- Checking for and removing duplicates
- Writing label file ./rh.V2.thresh.label 4563
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.thresh.label --trgsubject sub009 --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 = sub009
- 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/sub009/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 146248
- Number of reverse mapping hits = 82
- Checking for and removing duplicates
- Writing label file ./rh.MT.thresh.label 350
- mri_label2label: Done
- mris_label2annot --s sub009 --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/sub009/label
- cmdline mris_label2annot --s sub009 --hemi rh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --l rh.perirhinal.label --a BA --maxstatwinner --noverbose
- sysname Linux
- hostname snake6
- machine x86_64
- user fkaule
- subject sub009
- 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/sub009/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 102322 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/label/rh.BA.annot
- mris_label2annot --s sub009 --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/sub009/label
- cmdline mris_label2annot --s sub009 --hemi rh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l rh.BA1.thresh.label --l rh.BA2.thresh.label --l rh.BA3a.thresh.label --l rh.BA3b.thresh.label --l rh.BA4a.thresh.label --l rh.BA4p.thresh.label --l rh.BA6.thresh.label --l rh.BA44.thresh.label --l rh.BA45.thresh.label --l rh.V1.thresh.label --l rh.V2.thresh.label --l rh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose
- sysname Linux
- hostname snake6
- machine x86_64
- user fkaule
- subject sub009
- 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/sub009/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 123231 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/label/rh.BA.thresh.annot
- mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab sub009 rh white
- computing statistics for each annotation in ./rh.BA.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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
- 1201 752 2408 2.357 0.430 0.168 0.063 29 2.9 BA1
- 4871 3243 7867 2.233 0.367 0.129 0.042 83 8.0 BA2
- 1068 695 1123 1.974 0.421 0.135 0.042 10 1.8 BA3a
- 2069 1396 3072 1.864 0.539 0.126 0.036 27 3.1 BA3b
- 1682 1072 3660 2.838 0.485 0.123 0.034 17 2.4 BA4a
- 1195 786 1996 2.524 0.396 0.123 0.155 83 2.7 BA4p
- 8163 5331 18011 2.771 0.496 0.140 0.066 225 29.6 BA6
- 3864 2594 7764 2.573 0.452 0.139 0.046 56 6.9 BA44
- 5023 3345 9641 2.429 0.439 0.162 0.078 124 12.3 BA45
- 3665 2525 5299 1.957 0.425 0.168 0.069 70 10.1 V1
- 8214 5385 12922 2.169 0.489 0.172 0.069 176 21.8 V2
- 2352 1578 3926 2.397 0.405 0.134 0.105 60 4.2 MT
- 559 389 1634 2.852 0.748 0.143 0.054 7 1.4 perirhinal
- mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab sub009 rh white
- computing statistics for each annotation in ./rh.BA.thresh.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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
- 845 525 1619 2.228 0.401 0.180 0.065 24 2.3 BA1
- 2627 1759 4183 2.179 0.331 0.124 0.040 33 4.3 BA2
- 907 605 862 1.915 0.391 0.143 0.045 8 1.8 BA3a
- 1707 1144 2170 1.706 0.426 0.115 0.031 19 2.1 BA3b
- 1121 689 2556 2.912 0.530 0.126 0.037 12 1.8 BA4a
- 942 621 1522 2.546 0.364 0.116 0.182 80 2.1 BA4p
- 4752 3056 10420 2.749 0.478 0.142 0.083 177 23.0 BA6
- 1051 712 2456 2.662 0.486 0.145 0.056 19 2.2 BA44
- 1181 799 2516 2.555 0.389 0.167 0.061 28 2.9 BA45
- 3502 2407 4947 1.944 0.423 0.163 0.065 62 9.2 V1
- 4069 2720 6184 2.063 0.522 0.184 0.078 99 12.3 V2
- 313 205 621 2.406 0.453 0.146 0.518 35 0.8 MT
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/label
- #--------------------------------------------
- #@# Ex-vivo Entorhinal Cortex Label lh Fri Aug 9 00:32:22 CEST 2013
- mris_spherical_average -erode 1 -orig white -t 0.4 -o sub009 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label
- painting output onto subject sub009.
- processing subject lh.EC_average...
- reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 1011 points to lh.entorhinal_exvivo.label...
- mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label sub009 lh white
- limiting computations to label ./lh.entorhinal_exvivo.label.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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
- 374 242 1174 3.103 0.694 0.111 0.030 3 0.6 ./lh.entorhinal_exvivo.label
- #--------------------------------------------
- #@# Ex-vivo Entorhinal Cortex Label rh Fri Aug 9 00:32:37 CEST 2013
- mris_spherical_average -erode 1 -orig white -t 0.4 -o sub009 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label
- painting output onto subject sub009.
- processing subject rh.EC_average...
- reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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 753 points to rh.entorhinal_exvivo.label...
- mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label sub009 rh white
- limiting computations to label ./rh.entorhinal_exvivo.label.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub009/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
- 288 182 1047 3.223 0.784 0.144 0.066 4 0.9 ./rh.entorhinal_exvivo.label
- #------------------------------------------
- Started at Thu Aug 8 10:54:16 CEST 2013
- Ended at Fri Aug 9 00:32:53 CEST 2013
- #@#%# recon-all-run-time-hours 13.644
- recon-all -s sub009 finished without error at Fri Aug 9 00:32:53 CEST 2013
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