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- Thu Aug 8 10:54:17 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014
- /opt/freesurfer/5.3.0/bin/recon-all
- -i /home/data/exppsy/forrest_gump/openfmri.org/sub014/anatomy/highres001.nii.gz -cw256 -all -T2 /home/data/exppsy/forrest_gump/openfmri.org/sub014/anatomy/other/t2w001.nii.gz -T2pial -subjid sub014 -sd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- subjid sub014
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Actual FREESURFER_HOME /opt/freesurfer/5.3.0
- build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
- Linux snake5 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
- cputime unlimited
- filesize unlimited
- datasize unlimited
- stacksize unlimited
- coredumpsize 0 kbytes
- memoryuse unlimited
- vmemoryuse unlimited
- descriptors 1024
- memorylocked 64 kbytes
- maxproc unlimited
- maxlocks unlimited
- maxsignal 16382
- maxmessage 819200
- maxnice 0
- maxrtprio 0
- maxrttime unlimited
- total used free shared buffers cached
- Mem: 99201692 96748076 2453616 0 177160 93969012
- -/+ buffers/cache: 2601904 96599788
- Swap: 25165780 3620 25162160
- ########################################
- program versions used
- $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
- $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
- mri_convert -all-info
- ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- FLIRT version 5.5
- $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
- mri_convert --version
- stable5
- ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- Program nu_correct, built from:
- Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
- ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ======= NUMBER OF OPENMP THREADS = 1 =======
- ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:21-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:21-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:21-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:21-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:21-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $
- ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:21-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $
- ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:21-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:21-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:22-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:22-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:22-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- #######################################
- GCADIR /opt/freesurfer/5.3.0/average
- GCA RB_all_2008-03-26.gca
- GCASkull RB_all_withskull_2008-03-26.gca
- AvgCurvTif average.curvature.filled.buckner40.tif
- GCSDIR /opt/freesurfer/5.3.0/average
- GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
- #######################################
- -cw256 option is now persistent (remove with -clean-cw256)
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub014/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/orig/001.mgz
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub014/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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/sub014/anatomy/highres001.nii.gz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.999671, 0.0251903, -0.0048728)
- j_ras = (0.0252193, 0.999664, -0.00597949)
- k_ras = (-0.00472054, 0.00610041, 0.99997)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/orig/001.mgz...
- #--------------------------------------------
- #@# T2/FLAIR Input Thu Aug 8 10:54:35 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub014/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/orig/T2raw.mgz
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub014/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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/sub014/anatomy/other/t2w001.nii.gz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.999671, 0.0251903, -0.0048728)
- j_ras = (0.0252193, 0.999664, -0.00597949)
- k_ras = (-0.00472054, 0.00610041, 0.99997)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/orig/T2raw.mgz...
- #--------------------------------------------
- #@# MotionCor Thu Aug 8 10:54:50 CEST 2013
- Found 1 runs
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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/sub014/mri/orig/001.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/rawavg.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/orig.mgz --conform --cw256
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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/sub014/mri/rawavg.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.999671, 0.0251903, -0.0048728)
- j_ras = (0.0252193, 0.999664, -0.00597949)
- k_ras = (-0.00472054, 0.00610041, 0.99997)
- Original Data has (0.699974, 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/sub014/mri/orig.mgz...
- mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/talairach.xfm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/orig.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Talairach Thu Aug 8 10:55:30 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 10:58:14 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri
- talairach_afd -T 0.005 -xfm transforms/talairach.xfm
- talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7657, pval=0.6675 >= threshold=0.0050)
- awk -f /opt/freesurfer/5.3.0/bin/extract_talairach_avi_QA.awk /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/talairach_avi.log
- tal_QC_AZS /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/talairach_avi.log
- TalAviQA: 0.96701
- z-score: -2
- #--------------------------------------------
- #@# Nu Intensity Correction Thu Aug 8 10:58:14 CEST 2013
- mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri
- /opt/freesurfer/5.3.0/bin/mri_nu_correct.mni
- --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
- nIters 2
- $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $
- Linux snake5 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
- Thu Aug 8 10:58:14 CEST 2013
- Program nu_correct, built from:
- Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
- tmpdir is ./tmp.mri_nu_correct.mni.13078
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.13078/nu0.mnc -odt float
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.13078/nu0.mnc -odt float
- $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
- reading from orig.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, -4.89672e-09, 4.65661e-10)
- j_ras = (0, 0, -1)
- k_ras = (1.16779e-09, 1, -9.31323e-10)
- changing data type from uchar to float (noscale = 0)...
- writing to ./tmp.mri_nu_correct.mni.13078/nu0.mnc...
-
- --------------------------------------------------------
- Iteration 1 Thu Aug 8 10:58:18 CEST 2013
- nu_correct -clobber ./tmp.mri_nu_correct.mni.13078/nu0.mnc ./tmp.mri_nu_correct.mni.13078/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.13078/0/
- [fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/] [2013-08-08 10:58:18] running:
- /opt/freesurfer/5.3.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.13078/0/ ./tmp.mri_nu_correct.mni.13078/nu0.mnc ./tmp.mri_nu_correct.mni.13078/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
- Number of iterations: 23
- CV of field change: 0.000995735
- [fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/] [2013-08-08 10:58:52] running:
- /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.13078/nu0.mnc ./tmp.mri_nu_correct.mni.13078/0//template.mnc
- Transforming slices:......................................................................................Done
- Transforming slices:................................................................................................................................................................................................................................................................Done
-
-
- --------------------------------------------------------
- Iteration 2 Thu Aug 8 10:59:00 CEST 2013
- nu_correct -clobber ./tmp.mri_nu_correct.mni.13078/nu1.mnc ./tmp.mri_nu_correct.mni.13078/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.13078/1/
- [fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/] [2013-08-08 10:59:00] 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.13078/1/ ./tmp.mri_nu_correct.mni.13078/nu1.mnc ./tmp.mri_nu_correct.mni.13078/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: 0.000985405
- [fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/] [2013-08-08 10:59:29] running:
- /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.13078/nu1.mnc ./tmp.mri_nu_correct.mni.13078/1//template.mnc
- Transforming slices:......................................................................................Done
- Transforming slices:................................................................................................................................................................................................................................................................Done
-
-
-
- mri_binarize --i ./tmp.mri_nu_correct.mni.13078/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.13078/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/sub014/mri
- cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.13078/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.13078/ones.mgz
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- input ./tmp.mri_nu_correct.mni.13078/nu2.mnc
- frame 0
- nErode3d 0
- nErode2d 0
- output ./tmp.mri_nu_correct.mni.13078/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.13078/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.13078/sum.junk --avgwf ./tmp.mri_nu_correct.mni.13078/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.13078/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.13078/sum.junk --avgwf ./tmp.mri_nu_correct.mni.13078/input.mean.dat
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.13078/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.13078/input.mean.dat
- mri_segstats done
- mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.13078/ones.mgz --i ./tmp.mri_nu_correct.mni.13078/nu2.mnc --sum ./tmp.mri_nu_correct.mni.13078/sum.junk --avgwf ./tmp.mri_nu_correct.mni.13078/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.13078/ones.mgz --i ./tmp.mri_nu_correct.mni.13078/nu2.mnc --sum ./tmp.mri_nu_correct.mni.13078/sum.junk --avgwf ./tmp.mri_nu_correct.mni.13078/output.mean.dat
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.13078/ones.mgz
- Loading ./tmp.mri_nu_correct.mni.13078/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.13078/output.mean.dat
- mri_segstats done
- mris_calc -o ./tmp.mri_nu_correct.mni.13078/nu2.mnc ./tmp.mri_nu_correct.mni.13078/nu2.mnc mul .96599755336283500046
- Saving result to './tmp.mri_nu_correct.mni.13078/nu2.mnc' (type = MINC ) [ ok ]
- mri_convert ./tmp.mri_nu_correct.mni.13078/nu2.mnc nu.mgz --like orig.mgz
- mri_convert ./tmp.mri_nu_correct.mni.13078/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.13078/nu2.mnc...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, -4.89672e-09, 4.65661e-10)
- j_ras = (0, 0, -1)
- k_ras = (1.16779e-09, 1, -9.31322e-10)
- INFO: transform src into the like-volume: orig.mgz
- writing to nu.mgz...
- mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz
- type change took 0 minutes and 8 seconds.
- mapping (10, 200) to ( 3, 110)
-
-
- Thu Aug 8 11:00:21 CEST 2013
- mri_nu_correct.mni done
- mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/talairach.xfm nu.mgz nu.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Intensity Normalization Thu Aug 8 11:00:22 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri
- mri_normalize -g 1 nu.mgz T1.mgz
- using max gradient = 1.000
- reading from nu.mgz...
- normalizing image...
- talairach transform
- 1.198 -0.010 0.045 7.245;
- -0.008 1.171 0.207 -28.613;
- -0.046 -0.317 1.275 9.062;
- 0.000 0.000 0.000 1.000;
- processing without aseg, no1d=0
- MRInormInit():
- INFO: Modifying talairach volume c_(r,a,s) based on average_305
- MRInormalize():
- MRIsplineNormalize(): npeaks = 14
- Starting OpenSpline(): npoints = 14
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Iterating 2 times
- ---------------------------------
- 3d normalization pass 1 of 2
- white matter peak found at 111
- white matter peak found at 109
- gm peak at 54 (54), valley at 43 (43)
- csf peak at 12, setting threshold to 40
- 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 52 (52), valley at 39 (39)
- csf peak at 12, setting threshold to 38
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Done iterating ---------------------------------
- writing output to T1.mgz
- 3D bias adjustment took 2 minutes and 49 seconds.
- #--------------------------------------------
- #@# Skull Stripping Thu Aug 8 11:03:11 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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=7.0
- skull bounding box = (59, 25, 29) --> (195, 255, 201)
- using (104, 102, 115) as brain centroid...
- mean wm in atlas = 126, using box (87,74,94) --> (120, 130,136) to find MRI wm
- before smoothing, mri peak at 111
- after smoothing, mri peak at 110, scaling input intensities by 1.145
- scaling channel 0 by 1.14545
- initial log_p = -5.0
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -4.762351 @ (-9.091, 9.091, -9.091)
- max log p = -4.596579 @ (4.545, 4.545, -4.545)
- max log p = -4.549440 @ (2.273, 2.273, 2.273)
- max log p = -4.549440 @ (0.000, 0.000, 0.000)
- max log p = -4.547785 @ (0.568, 0.568, -1.705)
- max log p = -4.547785 @ (0.000, 0.000, 0.000)
- Found translation: (-1.7, 16.5, -13.1): log p = -4.548
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.5 (thresh=-4.5)
- 1.150 0.000 0.000 -20.824;
- 0.000 1.226 0.161 -18.855;
- 0.000 -0.139 1.055 -5.049;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.150 0.000 0.000 -20.824;
- 0.000 1.226 0.161 -18.855;
- 0.000 -0.139 1.055 -5.049;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.2500
- ****************************************
- Nine parameter search. iteration 2 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-4.0 (thresh=-4.0)
- 1.170 0.042 0.008 -30.324;
- -0.036 1.191 0.226 -18.470;
- 0.000 -0.223 1.061 2.436;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 3 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 1.170 0.042 0.008 -30.324;
- -0.036 1.191 0.226 -18.470;
- 0.000 -0.223 1.061 2.436;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.0625
- ****************************************
- Nine parameter search. iteration 4 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 1.174 0.044 -0.001 -30.469;
- -0.035 1.191 0.208 -16.894;
- 0.009 -0.203 1.066 -0.761;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 5 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 1.178 0.044 -0.001 -31.018;
- -0.035 1.191 0.208 -16.894;
- 0.009 -0.203 1.066 -0.761;
- 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
- 1.17825 0.04386 -0.00078 -31.01841;
- -0.03545 1.19137 0.20761 -16.89371;
- 0.00900 -0.20328 1.06618 -0.76057;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 3481
- Quasinewton: input matrix
- 1.17825 0.04386 -0.00078 -31.01841;
- -0.03545 1.19137 0.20761 -16.89371;
- 0.00900 -0.20328 1.06618 -0.76057;
- 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:
- 1.178 0.044 -0.001 -31.018;
- -0.035 1.191 0.208 -16.894;
- 0.009 -0.203 1.066 -0.761;
- 0.000 0.000 0.000 1.000;
- pass 1, spacing 8: log(p) = -3.9 (old=-5.0)
- transform before final EM align:
- 1.178 0.044 -0.001 -31.018;
- -0.035 1.191 0.208 -16.894;
- 0.009 -0.203 1.066 -0.761;
- 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
- 1.17825 0.04386 -0.00078 -31.01841;
- -0.03545 1.19137 0.20761 -16.89371;
- 0.00900 -0.20328 1.06618 -0.76057;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 382743
- Quasinewton: input matrix
- 1.17825 0.04386 -0.00078 -31.01841;
- -0.03545 1.19137 0.20761 -16.89371;
- 0.00900 -0.20328 1.06618 -0.76057;
- 0.00000 0.00000 0.00000 1.00000;
- dfp_em_step_func: 009: -log(p) = 4.3
- after pass:transform: ( 1.18, 0.04, -0.00, -31.02)
- ( -0.04, 1.19, 0.21, -16.89)
- ( 0.01, -0.20, 1.07, -0.76)
- dfp_em_step_func: 010: -log(p) = 4.3
- after pass:transform: ( 1.18, 0.04, -0.00, -31.02)
- ( -0.04, 1.19, 0.21, -16.89)
- ( 0.01, -0.20, 1.07, -0.76)
- dfp_em_step_func: 011: -log(p) = 4.3
- after pass:transform: ( 1.18, 0.04, -0.00, -31.02)
- ( -0.04, 1.19, 0.21, -16.89)
- ( 0.01, -0.20, 1.07, -0.76)
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization...
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 013: -log(p) = 4.3 tol 0.000000
- final transform:
- 1.178 0.044 -0.001 -31.018;
- -0.035 1.191 0.208 -16.894;
- 0.009 -0.203 1.066 -0.761;
- 0.000 0.000 0.000 1.000;
- writing output transformation to transforms/talairach_with_skull.lta...
- registration took 30 minutes and 3 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=130 y=90 z=121 r=82
- first estimation of the main basin volume: 2373406 voxels
- Looking for seedpoints
- 2 found in the cerebellum
- 15 found in the rest of the brain
- global maximum in x=151, y=86, z=82, 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=19239101242 voxels, voxel volume =1.000
- = 19239101242 mmm3 = 19239100.416 cm3
- done.
- PostAnalyze...Basin Prior
- 110 basins merged thanks to atlas
- ***** 0 basin(s) merged in 1 iteration(s)
- ***** 0 voxel(s) added to the main basin
- done.
- Weighting the input with prior template
- ****************TEMPLATE DEFORMATION****************
- second estimation of the COG coord: x=128,y=99, z=116, r=9051 iterations
- ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^
- GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=9 , nb = 45260
- RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=19 , nb = -1031314490
- LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=25 , nb = 1090759654
- RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=8 , nb = -1062781127
- LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=9 , nb = 1078783504
- OTHER CSF_MIN=0, CSF_intensity=4, CSF_MAX=17 , nb = 1057087772
- Problem with the least square interpolation in GM_MIN calculation.
-
- CSF_MAX TRANSITION GM_MIN GM
- GLOBAL
- before analyzing : 9, 13, 28, 50
- after analyzing : 9, 23, 28, 29
- RIGHT_CER
- before analyzing : 19, 18, 17, 58
- after analyzing : 18, 22, 25, 31
- LEFT_CER
- before analyzing : 25, 27, 30, 60
- after analyzing : 25, 29, 30, 36
- RIGHT_BRAIN
- before analyzing : 8, 12, 28, 50
- after analyzing : 8, 22, 28, 29
- LEFT_BRAIN
- before analyzing : 9, 13, 28, 50
- after analyzing : 9, 23, 28, 29
- OTHER
- before analyzing : 17, 55, 85, 95
- after analyzing : 17, 75, 85, 80
- mri_strip_skull: done peeling brain
- highly tesselated surface with 10242 vertices
- matching...68 iterations
- *********************VALIDATION*********************
- curvature mean = -0.014, std = 0.012
- curvature mean = 66.573, std = 7.816
- No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
- before rotation: sse = 1.63, sigma = 2.54
- after rotation: sse = 1.63, sigma = 2.54
- Localization of inacurate regions: Erosion-Dilation steps
- the sse mean is 1.64, its var is 1.97
- before Erosion-Dilatation 0.00% of inacurate vertices
- after Erosion-Dilatation 0.00% of inacurate vertices
- Validation of the shape of the surface done.
- Scaling of atlas fields onto current surface fields
- ********FINAL ITERATIVE TEMPLATE DEFORMATION********
- Compute Local values csf/gray
- Fine Segmentation...36 iterations
- mri_strip_skull: done peeling brain
- Brain Size = 1424599 voxels, voxel volume = 1.000 mm3
- = 1424599 mmm3 = 1424.599 cm3
- ******************************
- Saving brainmask.auto.mgz
- done
- cp brainmask.auto.mgz brainmask.mgz
- #-------------------------------------
- #@# EM Registration Thu Aug 8 11:33:41 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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=20.9
- skull bounding box = (66, 44, 44) --> (187, 160, 199)
- using (106, 83, 122) as brain centroid...
- mean wm in atlas = 107, using box (91,69,103) --> (120, 97,141) to find MRI wm
- before smoothing, mri peak at 110
- after smoothing, mri peak at 110, scaling input intensities by 0.973
- scaling channel 0 by 0.972727
- initial log_p = -4.5
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -4.157252 @ (-9.091, 27.273, -9.091)
- max log p = -3.964982 @ (4.545, -13.636, -4.545)
- max log p = -3.964982 @ (0.000, 0.000, 0.000)
- max log p = -3.936896 @ (1.136, 1.136, -3.409)
- max log p = -3.932051 @ (-1.705, 2.841, 2.841)
- max log p = -3.932051 @ (0.000, 0.000, 0.000)
- Found translation: (-5.1, 17.6, -14.2): log p = -3.932
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p =-3.9 (thresh=-3.9)
- 1.140 0.148 0.022 -41.242;
- -0.161 1.210 0.180 -3.872;
- 0.000 -0.112 0.997 -2.487;
- 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 =-3.5 (thresh=-3.5)
- 1.151 -0.008 -0.018 -22.085;
- -0.010 1.194 0.309 -30.168;
- 0.023 -0.289 1.037 15.141;
- 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)
- 1.151 -0.008 -0.018 -22.085;
- -0.012 1.130 0.158 -6.923;
- 0.021 -0.130 1.068 -11.040;
- 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)
- 1.151 -0.008 -0.018 -22.085;
- -0.012 1.130 0.158 -6.923;
- 0.021 -0.130 1.068 -11.040;
- 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=-3.3, old_max_log_p =-3.5 (thresh=-3.5)
- 1.150 0.025 0.021 -27.725;
- -0.054 1.167 0.196 -11.240;
- -0.014 -0.169 1.083 -2.416;
- 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 =-3.3 (thresh=-3.3)
- 1.150 0.025 0.021 -27.725;
- -0.054 1.167 0.196 -11.240;
- -0.014 -0.169 1.083 -2.416;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.0625
- ****************************************
- Nine parameter search. iteration 6 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.3 (thresh=-3.3)
- 1.148 0.043 0.033 -30.045;
- -0.073 1.168 0.186 -8.269;
- -0.024 -0.159 1.084 -2.202;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 7 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2)
- 1.149 0.026 0.012 -26.163;
- -0.054 1.169 0.187 -10.321;
- -0.005 -0.159 1.083 -4.156;
- 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
- 1.14917 0.02601 0.01176 -26.16338;
- -0.05403 1.16887 0.18651 -10.32084;
- -0.00514 -0.15856 1.08324 -4.15601;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 2772
- Quasinewton: input matrix
- 1.14917 0.02601 0.01176 -26.16338;
- -0.05403 1.16887 0.18651 -10.32084;
- -0.00514 -0.15856 1.08324 -4.15601;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 4 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 1.149 0.026 0.012 -26.163;
- -0.054 1.169 0.187 -10.321;
- -0.005 -0.159 1.083 -4.156;
- 0.000 0.000 0.000 1.000;
- pass 1, spacing 8: log(p) = -3.2 (old=-4.5)
- transform before final EM align:
- 1.149 0.026 0.012 -26.163;
- -0.054 1.169 0.187 -10.321;
- -0.005 -0.159 1.083 -4.156;
- 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
- 1.14917 0.02601 0.01176 -26.16338;
- -0.05403 1.16887 0.18651 -10.32084;
- -0.00514 -0.15856 1.08324 -4.15601;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 312841
- Quasinewton: input matrix
- 1.14917 0.02601 0.01176 -26.16338;
- -0.05403 1.16887 0.18651 -10.32084;
- -0.00514 -0.15856 1.08324 -4.15601;
- 0.00000 0.00000 0.00000 1.00000;
- dfp_em_step_func: 011: -log(p) = 3.8
- after pass:transform: ( 1.15, 0.03, 0.01, -26.16)
- ( -0.05, 1.17, 0.19, -10.32)
- ( -0.01, -0.16, 1.08, -4.16)
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization...
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 013: -log(p) = 3.8 tol 0.000000
- final transform:
- 1.149 0.026 0.012 -26.163;
- -0.054 1.169 0.187 -10.321;
- -0.005 -0.159 1.083 -4.156;
- 0.000 0.000 0.000 1.000;
- writing output transformation to transforms/talairach.lta...
- registration took 31 minutes and 23 seconds.
- #--------------------------------------
- #@# CA Normalize Thu Aug 8 12:05:04 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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=20.9
- skull bounding box = (66, 44, 44) --> (187, 160, 199)
- using (106, 83, 122) as brain centroid...
- mean wm in atlas = 107, using box (91,69,103) --> (120, 97,141) to find MRI wm
- before smoothing, mri peak at 110
- after smoothing, mri peak at 110, scaling input intensities by 0.973
- scaling channel 0 by 0.972727
- using 244171 sample points...
- INFO: compute sample coordinates transform
- 1.149 0.026 0.012 -26.163;
- -0.054 1.169 0.187 -10.321;
- -0.005 -0.159 1.083 -4.156;
- 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, 42, 45) --> (186, 139, 197)
- Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0
- 0 of 53 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 40735 control points for structure...
- bounding box (73, 42, 45) --> (129, 137, 197)
- Right_Cerebral_White_Matter: limiting intensities to 98.0 --> 132.0
- 0 of 29 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3012 control points for structure...
- bounding box (130, 115, 70) --> (172, 155, 118)
- Left_Cerebellum_White_Matter: limiting intensities to 82.0 --> 132.0
- 0 of 16 (0.0%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2764 control points for structure...
- bounding box (88, 115, 67) --> (129, 151, 119)
- Right_Cerebellum_White_Matter: limiting intensities to 83.0 --> 132.0
- 0 of 14 (0.0%) samples deleted
- finding control points in Brain_Stem....
- found 3520 control points for structure...
- bounding box (114, 108, 101) --> (143, 167, 129)
- Brain_Stem: limiting intensities to 79.0 --> 132.0
- 0 of 16 (0.0%) samples deleted
- using 128 total control points for intensity normalization...
- bias field = 1.006 +- 0.057
- 0 of 128 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 41584 control points for structure...
- bounding box (127, 42, 45) --> (186, 139, 197)
- Left_Cerebral_White_Matter: limiting intensities to 99.0 --> 131.0
- 0 of 83 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 40735 control points for structure...
- bounding box (73, 42, 45) --> (129, 137, 197)
- Right_Cerebral_White_Matter: limiting intensities to 99.0 --> 131.0
- 0 of 91 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3012 control points for structure...
- bounding box (130, 115, 70) --> (172, 155, 118)
- Left_Cerebellum_White_Matter: limiting intensities to 86.0 --> 131.0
- 1 of 23 (4.3%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2764 control points for structure...
- bounding box (88, 115, 67) --> (129, 151, 119)
- Right_Cerebellum_White_Matter: limiting intensities to 80.0 --> 131.0
- 0 of 43 (0.0%) samples deleted
- finding control points in Brain_Stem....
- found 3520 control points for structure...
- bounding box (114, 108, 101) --> (143, 167, 129)
- Brain_Stem: limiting intensities to 70.0 --> 131.0
- 0 of 55 (0.0%) samples deleted
- using 295 total control points for intensity normalization...
- bias field = 0.991 +- 0.050
- 0 of 294 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 41584 control points for structure...
- bounding box (127, 42, 45) --> (186, 139, 197)
- Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 130.0
- 0 of 187 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 40735 control points for structure...
- bounding box (73, 42, 45) --> (129, 137, 197)
- Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 130.0
- 0 of 196 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3012 control points for structure...
- bounding box (130, 115, 70) --> (172, 155, 118)
- Left_Cerebellum_White_Matter: limiting intensities to 80.0 --> 130.0
- 0 of 89 (0.0%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2764 control points for structure...
- bounding box (88, 115, 67) --> (129, 151, 119)
- Right_Cerebellum_White_Matter: limiting intensities to 76.0 --> 130.0
- 0 of 68 (0.0%) samples deleted
- finding control points in Brain_Stem....
- found 3520 control points for structure...
- bounding box (114, 108, 101) --> (143, 167, 129)
- Brain_Stem: limiting intensities to 68.0 --> 130.0
- 0 of 108 (0.0%) samples deleted
- using 648 total control points for intensity normalization...
- bias field = 1.008 +- 0.041
- 0 of 648 control points discarded
- writing normalized volume to norm.mgz...
- writing control points to ctrl_pts.mgz
- freeing GCA...done.
- normalization took 2 minutes and 3 seconds.
- #--------------------------------------
- #@# CA Reg Thu Aug 8 12:07:07 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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) = 1.49 (predicted orig area = 5.4)
- 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=0.878, neg=0, invalid=96777
- 0001: dt=129.472000, rms=0.799 (9.026%), neg=0, invalid=96777
- 0002: dt=129.472000, rms=0.787 (1.489%), neg=0, invalid=96777
- 0003: dt=129.472000, rms=0.773 (1.853%), neg=0, invalid=96777
- 0004: dt=110.976000, rms=0.769 (0.487%), neg=0, invalid=96777
- 0005: dt=221.952000, rms=0.759 (1.271%), neg=0, invalid=96777
- 0006: dt=73.984000, rms=0.757 (0.331%), neg=0, invalid=96777
- 0007: dt=1183.744000, rms=0.739 (2.355%), neg=0, invalid=96777
- 0008: dt=129.472000, rms=0.737 (0.284%), neg=0, invalid=96777
- 0009: dt=129.472000, rms=0.734 (0.309%), neg=0, invalid=96777
- 0010: dt=110.976000, rms=0.734 (0.108%), neg=0, invalid=96777
- 0011: dt=110.976000, rms=0.732 (0.224%), neg=0, invalid=96777
- 0012: dt=110.976000, rms=0.730 (0.273%), neg=0, invalid=96777
- 0013: dt=110.976000, rms=0.728 (0.293%), neg=0, invalid=96777
- 0014: dt=110.976000, rms=0.726 (0.309%), neg=0, invalid=96777
- 0015: dt=110.976000, rms=0.722 (0.438%), neg=0, invalid=96777
- 0016: dt=110.976000, rms=0.720 (0.396%), neg=0, invalid=96777
- 0017: dt=110.976000, rms=0.717 (0.304%), neg=0, invalid=96777
- 0018: dt=110.976000, rms=0.715 (0.256%), neg=0, invalid=96777
- 0019: dt=110.976000, rms=0.713 (0.337%), neg=0, invalid=96777
- 0020: dt=110.976000, rms=0.710 (0.363%), neg=0, invalid=96777
- 0021: dt=110.976000, rms=0.709 (0.275%), neg=0, invalid=96777
- 0022: dt=110.976000, rms=0.707 (0.176%), neg=0, invalid=96777
- 0023: dt=110.976000, rms=0.706 (0.251%), neg=0, invalid=96777
- 0024: dt=110.976000, rms=0.703 (0.333%), neg=0, invalid=96777
- 0025: dt=110.976000, rms=0.701 (0.257%), neg=0, invalid=96777
- 0026: dt=110.976000, rms=0.700 (0.193%), neg=0, invalid=96777
- 0027: dt=110.976000, rms=0.699 (0.174%), neg=0, invalid=96777
- 0028: dt=110.976000, rms=0.697 (0.275%), neg=0, invalid=96777
- 0029: dt=110.976000, rms=0.695 (0.222%), neg=0, invalid=96777
- 0030: dt=110.976000, rms=0.694 (0.151%), neg=0, invalid=96777
- 0031: dt=110.976000, rms=0.694 (0.084%), neg=0, invalid=96777
- 0032: dt=110.976000, rms=0.693 (0.128%), neg=0, invalid=96777
- 0033: dt=110.976000, rms=0.691 (0.193%), neg=0, invalid=96777
- 0034: dt=110.976000, rms=0.690 (0.140%), neg=0, invalid=96777
- 0035: dt=110.976000, rms=0.690 (0.065%), neg=0, invalid=96777
- 0036: dt=110.976000, rms=0.690 (0.048%), neg=0, invalid=96777
- 0037: dt=129.472000, rms=0.689 (0.155%), neg=0, invalid=96777
- 0038: dt=0.000000, rms=0.689 (-0.006%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.689, neg=0, invalid=96777
- 0039: dt=32.368000, rms=0.689 (0.018%), neg=0, invalid=96777
- 0040: dt=73.984000, rms=0.688 (0.028%), neg=0, invalid=96777
- 0041: dt=129.472000, rms=0.688 (0.072%), neg=0, invalid=96777
- 0042: dt=369.920000, rms=0.687 (0.073%), neg=0, invalid=96777
- 0043: dt=443.904000, rms=0.686 (0.217%), neg=0, invalid=96777
- 0044: dt=18.496000, rms=0.686 (0.005%), neg=0, invalid=96777
- 0045: dt=18.496000, rms=0.686 (-0.005%), neg=0, invalid=96777
- setting smoothness coefficient to 0.154
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.693, neg=0, invalid=96777
- 0046: dt=82.944000, rms=0.688 (0.688%), neg=0, invalid=96777
- 0047: dt=62.208000, rms=0.679 (1.220%), neg=0, invalid=96777
- 0048: dt=15.552000, rms=0.678 (0.221%), neg=0, invalid=96777
- 0049: dt=15.552000, rms=0.677 (0.177%), neg=0, invalid=96777
- 0050: dt=15.552000, rms=0.675 (0.256%), neg=0, invalid=96777
- 0051: dt=15.552000, rms=0.672 (0.373%), neg=0, invalid=96777
- 0052: dt=15.552000, rms=0.669 (0.507%), neg=0, invalid=96777
- 0053: dt=15.552000, rms=0.665 (0.597%), neg=0, invalid=96777
- 0054: dt=15.552000, rms=0.661 (0.619%), neg=0, invalid=96777
- 0055: dt=15.552000, rms=0.657 (0.583%), neg=0, invalid=96777
- 0056: dt=15.552000, rms=0.654 (0.545%), neg=0, invalid=96777
- 0057: dt=15.552000, rms=0.650 (0.501%), neg=0, invalid=96777
- 0058: dt=15.552000, rms=0.647 (0.450%), neg=0, invalid=96777
- 0059: dt=15.552000, rms=0.645 (0.422%), neg=0, invalid=96777
- 0060: dt=15.552000, rms=0.642 (0.403%), neg=0, invalid=96777
- 0061: dt=15.552000, rms=0.640 (0.384%), neg=0, invalid=96777
- 0062: dt=15.552000, rms=0.637 (0.354%), neg=0, invalid=96777
- 0063: dt=15.552000, rms=0.635 (0.325%), neg=0, invalid=96777
- 0064: dt=15.552000, rms=0.633 (0.295%), neg=0, invalid=96777
- 0065: dt=15.552000, rms=0.632 (0.256%), neg=0, invalid=96777
- 0066: dt=15.552000, rms=0.630 (0.225%), neg=0, invalid=96777
- 0067: dt=15.552000, rms=0.629 (0.214%), neg=0, invalid=96777
- 0068: dt=15.552000, rms=0.628 (0.200%), neg=0, invalid=96777
- 0069: dt=15.552000, rms=0.627 (0.166%), neg=0, invalid=96777
- 0070: dt=15.552000, rms=0.626 (0.130%), neg=0, invalid=96777
- 0071: dt=15.552000, rms=0.625 (0.107%), neg=0, invalid=96777
- 0072: dt=15.552000, rms=0.625 (0.094%), neg=0, invalid=96777
- 0073: dt=145.152000, rms=0.624 (0.131%), neg=0, invalid=96777
- 0074: dt=3.888000, rms=0.624 (0.000%), neg=0, invalid=96777
- 0075: dt=3.888000, rms=0.624 (0.002%), neg=0, invalid=96777
- 0076: dt=3.888000, rms=0.624 (-0.005%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.624, neg=0, invalid=96777
- 0077: dt=25.920000, rms=0.623 (0.047%), neg=0, invalid=96777
- 0078: dt=82.944000, rms=0.623 (0.115%), neg=0, invalid=96777
- 0079: dt=0.000810, rms=0.623 (-0.003%), neg=0, invalid=96777
- setting smoothness coefficient to 0.588
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.647, neg=0, invalid=96777
- 0080: dt=7.483871, rms=0.646 (0.118%), neg=0, invalid=96777
- 0081: dt=6.400000, rms=0.646 (0.035%), neg=0, invalid=96777
- 0082: dt=6.400000, rms=0.646 (0.000%), neg=0, invalid=96777
- 0083: dt=6.400000, rms=0.646 (-0.100%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.646, neg=0, invalid=96777
- 0084: dt=0.000000, rms=0.646 (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=0.705, neg=0, invalid=96777
- 0085: dt=4.871111, rms=0.694 (1.472%), neg=0, invalid=96777
- 0086: dt=1.008000, rms=0.694 (0.025%), neg=0, invalid=96777
- 0087: dt=1.008000, rms=0.694 (0.011%), neg=0, invalid=96777
- 0088: dt=1.008000, rms=0.694 (-0.041%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.694, neg=0, invalid=96777
- 0089: dt=0.000000, rms=0.694 (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=0.765, neg=0, invalid=96777
- 0090: dt=0.892523, rms=0.762 (0.328%), neg=0, invalid=96777
- 0091: dt=1.792000, rms=0.758 (0.522%), neg=0, invalid=96777
- 0092: dt=1.280000, rms=0.757 (0.137%), neg=0, invalid=96777
- 0093: dt=1.280000, rms=0.756 (0.115%), neg=0, invalid=96777
- 0094: dt=1.280000, rms=0.756 (-0.097%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.756, neg=0, invalid=96777
- 0095: dt=1.109756, rms=0.755 (0.202%), neg=0, invalid=96777
- 0096: dt=0.000000, rms=0.755 (-0.002%), 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=0.702, neg=0, invalid=96777
- 0097: dt=0.161279, rms=0.693 (1.272%), neg=0, invalid=96777
- 0098: dt=0.000000, rms=0.693 (0.002%), neg=0, invalid=96777
- 0099: dt=0.050000, rms=0.693 (-0.029%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.693, neg=0, invalid=96777
- 0100: dt=0.304717, rms=0.690 (0.417%), neg=0, invalid=96777
- 0101: dt=0.080960, rms=0.689 (0.155%), neg=0, invalid=96777
- 0102: dt=0.080960, rms=0.689 (0.022%), neg=0, invalid=96777
- 0103: dt=0.080960, rms=0.688 (0.039%), neg=0, invalid=96777
- 0104: dt=0.080960, rms=0.688 (0.083%), neg=0, invalid=96777
- 0105: dt=0.080960, rms=0.687 (0.122%), neg=0, invalid=96777
- 0106: dt=0.080960, rms=0.686 (0.139%), neg=0, invalid=96777
- 0107: dt=0.080960, rms=0.685 (0.128%), neg=0, invalid=96777
- 0108: dt=0.080960, rms=0.684 (0.109%), neg=0, invalid=96777
- 0109: dt=0.080960, rms=0.684 (0.084%), neg=0, invalid=96777
- 0110: dt=0.000000, rms=0.684 (0.001%), neg=0, invalid=96777
- 0111: dt=0.050000, rms=0.684 (-0.003%), neg=0, invalid=96777
- renormalizing by structure alignment....
- renormalizing input #0
- gca peak = 0.11725 (24)
- mri peak = 0.12121 ( 9)
- Left_Lateral_Ventricle (4): linear fit = 0.31 x + 0.0 (723 voxels, overlap=0.006)
- Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (723 voxels, peak = 8), gca=9.6
- gca peak = 0.14022 (22)
- mri peak = 0.13797 ( 8)
- Right_Lateral_Ventricle (43): linear fit = 0.32 x + 0.0 (611 voxels, overlap=0.007)
- Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (611 voxels, peak = 7), gca=8.8
- gca peak = 0.24234 (100)
- mri peak = 0.06731 (84)
- Right_Pallidum (52): linear fit = 0.83 x + 0.0 (239 voxels, overlap=0.042)
- Right_Pallidum (52): linear fit = 0.83 x + 0.0 (239 voxels, peak = 84), gca=83.5
- gca peak = 0.19192 (97)
- mri peak = 0.06821 (75)
- Left_Pallidum (13): linear fit = 0.77 x + 0.0 (166 voxels, overlap=0.159)
- Left_Pallidum (13): linear fit = 0.77 x + 0.0 (166 voxels, peak = 75), gca=75.2
- gca peak = 0.24007 (63)
- mri peak = 0.07331 (55)
- Right_Hippocampus (53): linear fit = 0.86 x + 0.0 (500 voxels, overlap=0.378)
- Right_Hippocampus (53): linear fit = 0.86 x + 0.0 (500 voxels, peak = 54), gca=53.9
- gca peak = 0.29892 (64)
- mri peak = 0.10426 (56)
- Left_Hippocampus (17): linear fit = 0.85 x + 0.0 (512 voxels, overlap=0.449)
- Left_Hippocampus (17): linear fit = 0.85 x + 0.0 (512 voxels, peak = 54), gca=54.1
- gca peak = 0.12541 (104)
- mri peak = 0.08393 (108)
- Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (48558 voxels, overlap=0.696)
- Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (48558 voxels, peak = 109), gca=108.7
- gca peak = 0.13686 (104)
- mri peak = 0.08475 (110)
- Left_Cerebral_White_Matter (2): linear fit = 1.07 x + 0.0 (51712 voxels, overlap=0.583)
- Left_Cerebral_White_Matter (2): linear fit = 1.07 x + 0.0 (51712 voxels, peak = 111), gca=110.8
- gca peak = 0.11691 (63)
- mri peak = 0.05598 (50)
- Left_Cerebral_Cortex (3): linear fit = 0.77 x + 0.0 (13597 voxels, overlap=0.067)
- Left_Cerebral_Cortex (3): linear fit = 0.77 x + 0.0 (13597 voxels, peak = 49), gca=48.8
- gca peak = 0.13270 (63)
- mri peak = 0.05132 (55)
- Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (13408 voxels, overlap=0.203)
- Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (13408 voxels, peak = 52), gca=52.0
- gca peak = 0.15182 (70)
- mri peak = 0.08571 (65)
- Right_Caudate (50): linear fit = 0.88 x + 0.0 (467 voxels, overlap=0.473)
- Right_Caudate (50): linear fit = 0.88 x + 0.0 (467 voxels, peak = 61), gca=61.2
- gca peak = 0.14251 (76)
- mri peak = 0.07851 (72)
- Left_Caudate (11): linear fit = 0.81 x + 0.0 (528 voxels, overlap=0.094)
- Left_Caudate (11): linear fit = 0.81 x + 0.0 (528 voxels, peak = 62), gca=61.9
- gca peak = 0.12116 (60)
- mri peak = 0.04144 (56)
- Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (8245 voxels, overlap=0.992)
- Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (8245 voxels, peak = 58), gca=57.9
- gca peak = 0.12723 (61)
- mri peak = 0.05070 (57)
- Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (8772 voxels, overlap=0.973)
- Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (8772 voxels, peak = 59), gca=58.9
- gca peak = 0.22684 (88)
- mri peak = 0.07339 (90)
- Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (5371 voxels, overlap=0.770)
- Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (5371 voxels, peak = 93), gca=92.8
- gca peak = 0.21067 (87)
- mri peak = 0.08788 (91)
- Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (5116 voxels, overlap=0.868)
- Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (5116 voxels, peak = 90), gca=90.0
- gca peak = 0.25455 (62)
- mri peak = 0.12016 (56)
- Left_Amygdala (18): linear fit = 0.85 x + 0.0 (262 voxels, overlap=0.513)
- Left_Amygdala (18): linear fit = 0.85 x + 0.0 (262 voxels, peak = 52), gca=52.4
- gca peak = 0.39668 (62)
- mri peak = 0.11583 (60)
- Right_Amygdala (54): linear fit = 0.95 x + 0.0 (268 voxels, overlap=0.997)
- Right_Amygdala (54): linear fit = 0.95 x + 0.0 (268 voxels, peak = 59), gca=59.2
- gca peak = 0.10129 (93)
- mri peak = 0.04503 (89)
- Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4058 voxels, overlap=0.990)
- Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4058 voxels, peak = 93), gca=93.5
- gca peak = 0.12071 (89)
- mri peak = 0.05834 (90)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3348 voxels, overlap=0.972)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3348 voxels, peak = 89), gca=88.6
- gca peak = 0.13716 (82)
- mri peak = 0.09114 (72)
- Left_Putamen (12): linear fit = 0.89 x + 0.0 (1603 voxels, overlap=0.673)
- Left_Putamen (12): linear fit = 0.89 x + 0.0 (1603 voxels, peak = 73), gca=73.4
- gca peak = 0.15214 (84)
- mri peak = 0.07559 (72)
- Right_Putamen (51): linear fit = 0.87 x + 0.0 (1572 voxels, overlap=0.638)
- Right_Putamen (51): linear fit = 0.87 x + 0.0 (1572 voxels, peak = 73), gca=72.7
- gca peak = 0.08983 (85)
- mri peak = 0.07776 (88)
- Brain_Stem (16): linear fit = 1.03 x + 0.0 (8721 voxels, overlap=0.777)
- Brain_Stem (16): linear fit = 1.03 x + 0.0 (8721 voxels, peak = 88), gca=88.0
- gca peak = 0.11809 (92)
- mri peak = 0.05556 (96)
- Right_VentralDC (60): linear fit = 1.03 x + 0.0 (590 voxels, overlap=0.878)
- Right_VentralDC (60): linear fit = 1.03 x + 0.0 (590 voxels, peak = 95), gca=95.2
- gca peak = 0.12914 (94)
- mri peak = 0.05868 (82)
- Left_VentralDC (28): linear fit = 1.03 x + 0.0 (638 voxels, overlap=0.830)
- Left_VentralDC (28): linear fit = 1.03 x + 0.0 (638 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 = 0.18920 ( 8)
- Fourth_Ventricle (15): linear fit = 0.22 x + 0.0 (252 voxels, overlap=0.022)
- Fourth_Ventricle (15): linear fit = 0.22 x + 0.0 (252 voxels, peak = 6), gca=6.1
- gca peak Unknown = 0.94427 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.21802 (40)
- gca peak Third_Ventricle = 0.21100 (36)
- gca peak Fourth_Ventricle = 0.13542 (27)
- gca peak CSF = 0.17123 (45)
- gca peak Left_Accumbens_area = 0.25875 (69)
- gca peak Left_undetermined = 0.96240 (36)
- gca peak Left_vessel = 0.33262 (65)
- gca peak Left_choroid_plexus = 0.09846 (46)
- gca peak Right_Inf_Lat_Vent = 0.28113 (34)
- gca peak Right_Accumbens_area = 0.27120 (72)
- gca peak Right_vessel = 0.61915 (60)
- gca peak Right_choroid_plexus = 0.12775 (51)
- gca peak Fifth_Ventricle = 0.45329 (44)
- gca peak WM_hypointensities = 0.11729 (81)
- gca peak non_WM_hypointensities = 0.10912 (56)
- gca peak Optic_Chiasm = 0.33287 (75)
- label assignment complete, 0 changed (0.00%)
- not using caudate to estimate GM means
- estimating mean gm scale to be 0.85 x + 0.0
- estimating mean wm scale to be 1.06 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=0.730, neg=0, invalid=96777
- 0112: dt=129.472000, rms=0.723 (1.057%), neg=0, invalid=96777
- 0113: dt=92.480000, rms=0.721 (0.179%), neg=0, invalid=96777
- 0114: dt=110.976000, rms=0.719 (0.272%), neg=0, invalid=96777
- 0115: dt=73.984000, rms=0.718 (0.110%), neg=0, invalid=96777
- 0116: dt=295.936000, rms=0.717 (0.255%), neg=0, invalid=96777
- 0117: dt=32.368000, rms=0.716 (0.106%), neg=0, invalid=96777
- 0118: dt=92.480000, rms=0.715 (0.063%), neg=0, invalid=96777
- 0119: dt=129.472000, rms=0.715 (0.127%), neg=0, invalid=96777
- 0120: dt=55.488000, rms=0.714 (0.038%), neg=0, invalid=96777
- 0121: dt=55.488000, rms=0.714 (0.046%), neg=0, invalid=96777
- 0122: dt=55.488000, rms=0.713 (0.068%), neg=0, invalid=96777
- 0123: dt=55.488000, rms=0.713 (0.086%), neg=0, invalid=96777
- 0124: dt=55.488000, rms=0.712 (0.107%), neg=0, invalid=96777
- 0125: dt=55.488000, rms=0.711 (0.113%), neg=0, invalid=96777
- 0126: dt=55.488000, rms=0.710 (0.112%), neg=0, invalid=96777
- 0127: dt=55.488000, rms=0.710 (0.110%), neg=0, invalid=96777
- 0128: dt=55.488000, rms=0.709 (0.108%), neg=0, invalid=96777
- 0129: dt=55.488000, rms=0.708 (0.118%), neg=0, invalid=96777
- 0130: dt=55.488000, rms=0.707 (0.118%), neg=0, invalid=96777
- 0131: dt=55.488000, rms=0.706 (0.116%), neg=0, invalid=96777
- 0132: dt=55.488000, rms=0.706 (0.107%), neg=0, invalid=96777
- 0133: dt=55.488000, rms=0.705 (0.103%), neg=0, invalid=96777
- 0134: dt=55.488000, rms=0.704 (0.099%), neg=0, invalid=96777
- 0135: dt=55.488000, rms=0.704 (0.101%), neg=0, invalid=96777
- 0136: dt=55.488000, rms=0.703 (0.092%), neg=0, invalid=96777
- 0137: dt=55.488000, rms=0.702 (0.089%), neg=0, invalid=96777
- 0138: dt=55.488000, rms=0.702 (0.084%), neg=0, invalid=96777
- 0139: dt=55.488000, rms=0.701 (0.075%), neg=0, invalid=96777
- 0140: dt=55.488000, rms=0.701 (0.076%), neg=0, invalid=96777
- 0141: dt=55.488000, rms=0.700 (0.069%), neg=0, invalid=96777
- 0142: dt=55.488000, rms=0.700 (0.069%), neg=0, invalid=96777
- 0143: dt=55.488000, rms=0.699 (0.067%), neg=0, invalid=96777
- 0144: dt=55.488000, rms=0.699 (0.065%), neg=0, invalid=96777
- 0145: dt=55.488000, rms=0.698 (0.062%), neg=0, invalid=96777
- 0146: dt=55.488000, rms=0.698 (0.060%), neg=0, invalid=96777
- 0147: dt=55.488000, rms=0.697 (0.058%), neg=0, invalid=96777
- 0148: dt=55.488000, rms=0.697 (0.055%), neg=0, invalid=96777
- 0149: dt=55.488000, rms=0.697 (0.060%), neg=0, invalid=96777
- 0150: dt=55.488000, rms=0.696 (0.052%), neg=0, invalid=96777
- 0151: dt=55.488000, rms=0.696 (0.044%), neg=0, invalid=96777
- 0152: dt=55.488000, rms=0.696 (0.043%), neg=0, invalid=96777
- 0153: dt=55.488000, rms=0.695 (0.046%), neg=0, invalid=96777
- 0154: dt=55.488000, rms=0.695 (0.044%), neg=0, invalid=96777
- 0155: dt=55.488000, rms=0.695 (0.042%), neg=0, invalid=96777
- 0156: dt=55.488000, rms=0.694 (0.039%), neg=0, invalid=96777
- 0157: dt=55.488000, rms=0.694 (0.030%), neg=0, invalid=96777
- 0158: dt=55.488000, rms=0.694 (0.032%), neg=0, invalid=96777
- 0159: dt=55.488000, rms=0.694 (0.037%), neg=0, invalid=96777
- 0160: dt=55.488000, rms=0.694 (0.042%), neg=0, invalid=96777
- 0161: dt=55.488000, rms=0.693 (0.040%), neg=0, invalid=96777
- 0162: dt=55.488000, rms=0.693 (0.033%), neg=0, invalid=96777
- 0163: dt=55.488000, rms=0.693 (0.025%), neg=0, invalid=96777
- 0164: dt=55.488000, rms=0.693 (0.033%), neg=0, invalid=96777
- 0165: dt=55.488000, rms=0.692 (0.035%), neg=0, invalid=96777
- 0166: dt=55.488000, rms=0.692 (0.036%), neg=0, invalid=96777
- 0167: dt=55.488000, rms=0.692 (0.034%), neg=0, invalid=96777
- 0168: dt=55.488000, rms=0.692 (0.031%), neg=0, invalid=96777
- 0169: dt=55.488000, rms=0.691 (0.033%), neg=0, invalid=96777
- 0170: dt=55.488000, rms=0.691 (0.037%), neg=0, invalid=96777
- 0171: dt=55.488000, rms=0.691 (0.034%), neg=0, invalid=96777
- 0172: dt=55.488000, rms=0.691 (0.029%), neg=0, invalid=96777
- 0173: dt=55.488000, rms=0.691 (0.029%), neg=0, invalid=96777
- 0174: dt=55.488000, rms=0.690 (0.029%), neg=0, invalid=96777
- 0175: dt=55.488000, rms=0.690 (0.032%), neg=0, invalid=96777
- 0176: dt=55.488000, rms=0.690 (0.031%), neg=0, invalid=96777
- 0177: dt=55.488000, rms=0.690 (0.033%), neg=0, invalid=96777
- 0178: dt=55.488000, rms=0.689 (0.030%), neg=0, invalid=96777
- 0179: dt=55.488000, rms=0.689 (0.029%), neg=0, invalid=96777
- 0180: dt=55.488000, rms=0.689 (0.034%), neg=0, invalid=96777
- 0181: dt=55.488000, rms=0.689 (0.034%), neg=0, invalid=96777
- 0182: dt=55.488000, rms=0.689 (0.032%), neg=0, invalid=96777
- 0183: dt=55.488000, rms=0.688 (0.029%), neg=0, invalid=96777
- 0184: dt=55.488000, rms=0.688 (0.031%), neg=0, invalid=96777
- 0185: dt=55.488000, rms=0.688 (0.030%), neg=0, invalid=96777
- 0186: dt=55.488000, rms=0.688 (0.030%), neg=0, invalid=96777
- 0187: dt=55.488000, rms=0.688 (0.031%), neg=0, invalid=96777
- 0188: dt=55.488000, rms=0.687 (0.027%), neg=0, invalid=96777
- 0189: dt=55.488000, rms=0.687 (0.028%), neg=0, invalid=96777
- 0190: dt=55.488000, rms=0.687 (0.030%), neg=0, invalid=96777
- 0191: dt=55.488000, rms=0.687 (0.032%), neg=0, invalid=96777
- 0192: dt=55.488000, rms=0.687 (0.029%), neg=0, invalid=96777
- 0193: dt=55.488000, rms=0.686 (0.026%), neg=0, invalid=96777
- 0194: dt=55.488000, rms=0.686 (0.025%), neg=0, invalid=96777
- 0195: dt=55.488000, rms=0.686 (0.024%), neg=0, invalid=96777
- 0196: dt=3551.232000, rms=0.685 (0.114%), neg=0, invalid=96777
- 0197: dt=27.744000, rms=0.685 (0.012%), neg=0, invalid=96777
- 0198: dt=27.744000, rms=0.685 (0.003%), neg=0, invalid=96777
- 0199: dt=27.744000, rms=0.685 (0.000%), neg=0, invalid=96777
- 0200: dt=27.744000, rms=0.685 (-0.003%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.685, neg=0, invalid=96777
- 0201: dt=129.472000, rms=0.684 (0.103%), neg=0, invalid=96777
- 0202: dt=129.472000, rms=0.684 (0.065%), neg=0, invalid=96777
- 0203: dt=221.952000, rms=0.683 (0.093%), neg=0, invalid=96777
- 0204: dt=32.368000, rms=0.683 (0.020%), neg=0, invalid=96777
- 0205: dt=32.368000, rms=0.683 (0.007%), neg=0, invalid=96777
- 0206: dt=32.368000, rms=0.683 (0.006%), neg=0, invalid=96777
- 0207: dt=32.368000, rms=0.683 (0.008%), neg=0, invalid=96777
- 0208: dt=32.368000, rms=0.683 (0.024%), neg=0, invalid=96777
- 0209: dt=32.368000, rms=0.683 (0.039%), neg=0, invalid=96777
- 0210: dt=32.368000, rms=0.682 (0.039%), neg=0, invalid=96777
- 0211: dt=32.368000, rms=0.682 (0.028%), neg=0, invalid=96777
- 0212: dt=32.368000, rms=0.682 (0.028%), neg=0, invalid=96777
- 0213: dt=32.368000, rms=0.682 (0.022%), neg=0, invalid=96777
- 0214: dt=32.368000, rms=0.682 (0.017%), neg=0, invalid=96777
- 0215: dt=129.472000, rms=0.682 (0.028%), neg=0, invalid=96777
- 0216: dt=13.872000, rms=0.682 (-0.003%), neg=0, invalid=96777
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.682, neg=0, invalid=96777
- 0217: dt=103.680000, rms=0.678 (0.657%), neg=0, invalid=96777
- 0218: dt=36.288000, rms=0.673 (0.688%), neg=0, invalid=96777
- 0219: dt=124.416000, rms=0.669 (0.558%), neg=0, invalid=96777
- 0220: dt=31.104000, rms=0.665 (0.642%), neg=0, invalid=96777
- 0221: dt=36.288000, rms=0.664 (0.192%), neg=0, invalid=96777
- 0222: dt=82.944000, rms=0.661 (0.430%), neg=0, invalid=96777
- 0223: dt=15.552000, rms=0.660 (0.200%), neg=0, invalid=96777
- 0224: dt=145.152000, rms=0.657 (0.487%), neg=0, invalid=96777
- 0225: dt=36.288000, rms=0.654 (0.363%), neg=0, invalid=96777
- 0226: dt=20.736000, rms=0.654 (0.088%), neg=0, invalid=96777
- 0227: dt=497.664000, rms=0.644 (1.449%), neg=0, invalid=96777
- 0228: dt=9.072000, rms=0.643 (0.136%), neg=0, invalid=96777
- 0229: dt=9.072000, rms=0.643 (0.077%), neg=0, invalid=96777
- 0230: dt=9.072000, rms=0.642 (0.039%), neg=0, invalid=96777
- 0231: dt=1.134000, rms=0.642 (0.011%), neg=0, invalid=96777
- 0232: dt=0.567000, rms=0.642 (0.002%), neg=0, invalid=96777
- 0233: dt=0.141750, rms=0.642 (0.000%), neg=0, invalid=96777
- 0234: dt=103.680000, rms=0.641 (0.201%), neg=0, invalid=96777
- 0235: dt=31.104000, rms=0.640 (0.150%), neg=0, invalid=96777
- 0236: dt=36.288000, rms=0.640 (0.082%), neg=0, invalid=96777
- 0237: dt=82.944000, rms=0.639 (0.130%), neg=0, invalid=96777
- 0238: dt=20.736000, rms=0.638 (0.095%), neg=0, invalid=96777
- 0239: dt=580.608000, rms=0.634 (0.730%), neg=0, invalid=96777
- 0240: dt=15.552000, rms=0.632 (0.317%), neg=0, invalid=96777
- 0241: dt=20.736000, rms=0.631 (0.067%), neg=0, invalid=96777
- 0242: dt=497.664000, rms=0.629 (0.389%), neg=0, invalid=96777
- 0243: dt=25.920000, rms=0.627 (0.239%), neg=0, invalid=96777
- 0244: dt=36.288000, rms=0.627 (0.075%), neg=0, invalid=96777
- 0245: dt=62.208000, rms=0.626 (0.062%), neg=0, invalid=96777
- 0246: dt=36.288000, rms=0.626 (0.053%), neg=0, invalid=96777
- 0247: dt=36.288000, rms=0.626 (0.036%), neg=0, invalid=96777
- 0248: dt=36.288000, rms=0.625 (0.051%), neg=0, invalid=96777
- 0249: dt=36.288000, rms=0.625 (0.069%), neg=0, invalid=96777
- 0250: dt=36.288000, rms=0.624 (0.086%), neg=0, invalid=96777
- 0251: dt=36.288000, rms=0.624 (0.117%), neg=0, invalid=96777
- 0252: dt=36.288000, rms=0.623 (0.148%), neg=0, invalid=96777
- 0253: dt=36.288000, rms=0.622 (0.150%), neg=0, invalid=96777
- 0254: dt=36.288000, rms=0.621 (0.166%), neg=0, invalid=96777
- 0255: dt=36.288000, rms=0.620 (0.174%), neg=0, invalid=96777
- 0256: dt=36.288000, rms=0.618 (0.200%), neg=0, invalid=96777
- 0257: dt=36.288000, rms=0.617 (0.176%), neg=0, invalid=96777
- 0258: dt=36.288000, rms=0.616 (0.168%), neg=0, invalid=96777
- 0259: dt=36.288000, rms=0.615 (0.177%), neg=0, invalid=96777
- 0260: dt=36.288000, rms=0.614 (0.186%), neg=0, invalid=96777
- 0261: dt=36.288000, rms=0.613 (0.172%), neg=0, invalid=96777
- 0262: dt=36.288000, rms=0.612 (0.159%), neg=0, invalid=96777
- 0263: dt=36.288000, rms=0.611 (0.156%), neg=0, invalid=96777
- 0264: dt=36.288000, rms=0.610 (0.158%), neg=0, invalid=96777
- 0265: dt=36.288000, rms=0.609 (0.152%), neg=0, invalid=96777
- 0266: dt=36.288000, rms=0.608 (0.130%), neg=0, invalid=96777
- 0267: dt=36.288000, rms=0.608 (0.133%), neg=0, invalid=96777
- 0268: dt=36.288000, rms=0.607 (0.125%), neg=0, invalid=96777
- 0269: dt=36.288000, rms=0.606 (0.134%), neg=0, invalid=96777
- 0270: dt=36.288000, rms=0.605 (0.109%), neg=0, invalid=96777
- 0271: dt=36.288000, rms=0.605 (0.100%), neg=0, invalid=96777
- 0272: dt=36.288000, rms=0.604 (0.093%), neg=0, invalid=96777
- 0273: dt=36.288000, rms=0.604 (0.101%), neg=0, invalid=96777
- 0274: dt=36.288000, rms=0.603 (0.102%), neg=0, invalid=96777
- 0275: dt=36.288000, rms=0.603 (0.078%), neg=0, invalid=96777
- 0276: dt=36.288000, rms=0.602 (0.073%), neg=0, invalid=96777
- 0277: dt=36.288000, rms=0.602 (0.073%), neg=0, invalid=96777
- 0278: dt=36.288000, rms=0.601 (0.079%), neg=0, invalid=96777
- 0279: dt=36.288000, rms=0.601 (0.079%), neg=0, invalid=96777
- 0280: dt=36.288000, rms=0.600 (0.067%), neg=0, invalid=96777
- 0281: dt=36.288000, rms=0.600 (0.057%), neg=0, invalid=96777
- 0282: dt=36.288000, rms=0.600 (0.075%), neg=0, invalid=96777
- 0283: dt=36.288000, rms=0.599 (0.078%), neg=0, invalid=96777
- 0284: dt=36.288000, rms=0.599 (0.068%), neg=0, invalid=96777
- 0285: dt=36.288000, rms=0.598 (0.051%), neg=0, invalid=96777
- 0286: dt=36.288000, rms=0.598 (0.048%), neg=0, invalid=96777
- 0287: dt=36.288000, rms=0.598 (0.072%), neg=0, invalid=96777
- 0288: dt=36.288000, rms=0.597 (0.064%), neg=0, invalid=96777
- 0289: dt=36.288000, rms=0.597 (0.058%), neg=0, invalid=96777
- 0290: dt=36.288000, rms=0.597 (0.051%), neg=0, invalid=96777
- 0291: dt=36.288000, rms=0.596 (0.045%), neg=0, invalid=96777
- 0292: dt=36.288000, rms=0.596 (0.035%), neg=0, invalid=96777
- 0293: dt=36.288000, rms=0.596 (0.049%), neg=0, invalid=96777
- 0294: dt=36.288000, rms=0.595 (0.062%), neg=0, invalid=96777
- 0295: dt=36.288000, rms=0.595 (0.058%), neg=0, invalid=96777
- 0296: dt=36.288000, rms=0.595 (0.054%), neg=0, invalid=96777
- 0297: dt=36.288000, rms=0.595 (0.047%), neg=0, invalid=96777
- 0298: dt=36.288000, rms=0.594 (0.045%), neg=0, invalid=96777
- 0299: dt=36.288000, rms=0.594 (0.039%), neg=0, invalid=96777
- 0300: dt=36.288000, rms=0.594 (0.047%), neg=0, invalid=96777
- 0301: dt=36.288000, rms=0.593 (0.045%), neg=0, invalid=96777
- 0302: dt=36.288000, rms=0.593 (0.049%), neg=0, invalid=96777
- 0303: dt=36.288000, rms=0.593 (0.034%), neg=0, invalid=96777
- 0304: dt=36.288000, rms=0.593 (0.039%), neg=0, invalid=96777
- 0305: dt=36.288000, rms=0.592 (0.044%), neg=0, invalid=96777
- 0306: dt=36.288000, rms=0.592 (0.053%), neg=0, invalid=96777
- 0307: dt=36.288000, rms=0.592 (0.041%), neg=0, invalid=96777
- 0308: dt=36.288000, rms=0.592 (0.038%), neg=0, invalid=96777
- 0309: dt=36.288000, rms=0.591 (0.045%), neg=0, invalid=96777
- 0310: dt=36.288000, rms=0.591 (0.035%), neg=0, invalid=96777
- 0311: dt=36.288000, rms=0.591 (0.034%), neg=0, invalid=96777
- 0312: dt=36.288000, rms=0.591 (0.031%), neg=0, invalid=96777
- 0313: dt=36.288000, rms=0.591 (0.030%), neg=0, invalid=96777
- 0314: dt=36.288000, rms=0.590 (0.036%), neg=0, invalid=96777
- 0315: dt=36.288000, rms=0.590 (0.029%), neg=0, invalid=96777
- 0316: dt=36.288000, rms=0.590 (0.029%), neg=0, invalid=96777
- 0317: dt=36.288000, rms=0.590 (0.025%), neg=0, invalid=96777
- 0318: dt=36.288000, rms=0.590 (0.030%), neg=0, invalid=96777
- 0319: dt=36.288000, rms=0.590 (0.028%), neg=0, invalid=96777
- 0320: dt=36.288000, rms=0.589 (0.022%), neg=0, invalid=96777
- 0321: dt=36.288000, rms=0.589 (0.034%), neg=0, invalid=96777
- 0322: dt=36.288000, rms=0.589 (0.025%), neg=0, invalid=96777
- 0323: dt=36.288000, rms=0.589 (0.020%), neg=0, invalid=96777
- 0324: dt=331.776000, rms=0.589 (0.036%), neg=0, invalid=96777
- 0325: dt=2.268000, rms=0.589 (0.000%), neg=0, invalid=96777
- 0326: dt=2.268000, rms=0.589 (-0.001%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.589, neg=0, invalid=96777
- 0327: dt=36.288000, rms=0.588 (0.150%), neg=0, invalid=96777
- 0328: dt=124.416000, rms=0.586 (0.301%), neg=0, invalid=96777
- 0329: dt=15.552000, rms=0.586 (0.054%), neg=0, invalid=96777
- 0330: dt=25.920000, rms=0.586 (0.020%), neg=0, invalid=96777
- 0331: dt=25.920000, rms=0.585 (0.043%), neg=0, invalid=96777
- 0332: dt=25.920000, rms=0.585 (0.046%), neg=0, invalid=96777
- 0333: dt=25.920000, rms=0.585 (0.058%), neg=0, invalid=96777
- 0334: dt=25.920000, rms=0.584 (0.062%), neg=0, invalid=96777
- 0335: dt=25.920000, rms=0.584 (0.066%), neg=0, invalid=96777
- 0336: dt=25.920000, rms=0.584 (0.062%), neg=0, invalid=96777
- 0337: dt=25.920000, rms=0.583 (0.058%), neg=0, invalid=96777
- 0338: dt=25.920000, rms=0.583 (0.053%), neg=0, invalid=96777
- 0339: dt=25.920000, rms=0.583 (0.049%), neg=0, invalid=96777
- 0340: dt=25.920000, rms=0.582 (0.055%), neg=0, invalid=96777
- 0341: dt=25.920000, rms=0.582 (0.050%), neg=0, invalid=96777
- 0342: dt=25.920000, rms=0.582 (0.043%), neg=0, invalid=96777
- 0343: dt=25.920000, rms=0.582 (0.040%), neg=0, invalid=96777
- 0344: dt=25.920000, rms=0.582 (0.036%), neg=0, invalid=96777
- 0345: dt=25.920000, rms=0.581 (0.037%), neg=0, invalid=96777
- 0346: dt=25.920000, rms=0.581 (0.041%), neg=0, invalid=96777
- 0347: dt=25.920000, rms=0.581 (0.038%), neg=0, invalid=96777
- 0348: dt=25.920000, rms=0.581 (0.040%), neg=0, invalid=96777
- 0349: dt=25.920000, rms=0.580 (0.040%), neg=0, invalid=96777
- 0350: dt=25.920000, rms=0.580 (0.043%), neg=0, invalid=96777
- 0351: dt=25.920000, rms=0.580 (0.035%), neg=0, invalid=96777
- 0352: dt=25.920000, rms=0.580 (0.026%), neg=0, invalid=96777
- 0353: dt=25.920000, rms=0.580 (0.030%), neg=0, invalid=96777
- 0354: dt=25.920000, rms=0.579 (0.036%), neg=0, invalid=96777
- 0355: dt=25.920000, rms=0.579 (0.034%), neg=0, invalid=96777
- 0356: dt=25.920000, rms=0.579 (0.029%), neg=0, invalid=96777
- 0357: dt=25.920000, rms=0.579 (0.023%), neg=0, invalid=96777
- 0358: dt=25.920000, rms=0.579 (0.030%), neg=0, invalid=96777
- 0359: dt=25.920000, rms=0.579 (0.026%), neg=0, invalid=96777
- 0360: dt=25.920000, rms=0.578 (0.028%), neg=0, invalid=96777
- 0361: dt=25.920000, rms=0.578 (0.017%), neg=0, invalid=96777
- 0362: dt=25.920000, rms=0.578 (0.025%), neg=0, invalid=96777
- 0363: dt=25.920000, rms=0.578 (0.024%), neg=0, invalid=96777
- 0364: dt=25.920000, rms=0.578 (0.019%), neg=0, invalid=96777
- 0365: dt=145.152000, rms=0.578 (0.032%), neg=0, invalid=96777
- 0366: dt=0.000000, rms=0.578 (-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=0.586, neg=0, invalid=96777
- 0367: dt=19.200000, rms=0.585 (0.236%), neg=0, invalid=96777
- 0368: dt=32.000000, rms=0.583 (0.389%), neg=0, invalid=96777
- 0369: dt=4.800000, rms=0.582 (0.126%), neg=0, invalid=96777
- 0370: dt=44.800000, rms=0.580 (0.287%), neg=0, invalid=96777
- 0371: dt=10.678571, rms=0.578 (0.468%), neg=0, invalid=96777
- 0372: dt=3.428571, rms=0.577 (0.062%), neg=0, invalid=96777
- 0373: dt=32.000000, rms=0.576 (0.157%), neg=0, invalid=96777
- 0374: dt=10.797546, rms=0.574 (0.371%), neg=0, invalid=96777
- 0375: dt=4.800000, rms=0.574 (0.058%), neg=0, invalid=96777
- 0376: dt=44.800000, rms=0.572 (0.328%), neg=0, invalid=96777
- 0377: dt=11.548387, rms=0.570 (0.321%), neg=0, invalid=96777
- 0378: dt=4.800000, rms=0.570 (0.048%), neg=0, invalid=96777
- 0379: dt=4.800000, rms=0.570 (0.046%), neg=0, invalid=96777
- 0380: dt=4.800000, rms=0.569 (0.079%), neg=0, invalid=96777
- 0381: dt=4.800000, rms=0.568 (0.126%), neg=0, invalid=96777
- 0382: dt=4.800000, rms=0.567 (0.170%), neg=0, invalid=96777
- 0383: dt=4.800000, rms=0.566 (0.189%), neg=0, invalid=96777
- 0384: dt=4.800000, rms=0.565 (0.204%), neg=0, invalid=96777
- 0385: dt=4.800000, rms=0.564 (0.214%), neg=0, invalid=96777
- 0386: dt=4.800000, rms=0.563 (0.217%), neg=0, invalid=96777
- 0387: dt=4.800000, rms=0.562 (0.210%), neg=0, invalid=96777
- 0388: dt=4.800000, rms=0.560 (0.230%), neg=0, invalid=96777
- 0389: dt=4.800000, rms=0.559 (0.225%), neg=0, invalid=96777
- 0390: dt=4.800000, rms=0.558 (0.225%), neg=0, invalid=96777
- 0391: dt=4.800000, rms=0.557 (0.217%), neg=0, invalid=96777
- 0392: dt=4.800000, rms=0.555 (0.217%), neg=0, invalid=96777
- 0393: dt=4.800000, rms=0.554 (0.204%), neg=0, invalid=96777
- 0394: dt=4.800000, rms=0.553 (0.198%), neg=0, invalid=96777
- 0395: dt=4.800000, rms=0.552 (0.182%), neg=0, invalid=96777
- 0396: dt=4.800000, rms=0.551 (0.173%), neg=0, invalid=96777
- 0397: dt=4.800000, rms=0.550 (0.159%), neg=0, invalid=96777
- 0398: dt=4.800000, rms=0.549 (0.160%), neg=0, invalid=96777
- 0399: dt=4.800000, rms=0.549 (0.151%), neg=0, invalid=96777
- 0400: dt=4.800000, rms=0.548 (0.148%), neg=0, invalid=96777
- 0401: dt=4.800000, rms=0.547 (0.139%), neg=0, invalid=96777
- 0402: dt=4.800000, rms=0.546 (0.135%), neg=0, invalid=96777
- 0403: dt=4.800000, rms=0.546 (0.129%), neg=0, invalid=96777
- 0404: dt=4.800000, rms=0.545 (0.121%), neg=0, invalid=96777
- 0405: dt=4.800000, rms=0.544 (0.116%), neg=0, invalid=96777
- 0406: dt=4.800000, rms=0.544 (0.109%), neg=0, invalid=96777
- 0407: dt=4.800000, rms=0.543 (0.101%), neg=0, invalid=96777
- 0408: dt=4.800000, rms=0.543 (0.093%), neg=0, invalid=96777
- 0409: dt=4.800000, rms=0.542 (0.087%), neg=0, invalid=96777
- 0410: dt=4.800000, rms=0.542 (0.079%), neg=0, invalid=96777
- 0411: dt=4.800000, rms=0.541 (0.074%), neg=0, invalid=96777
- 0412: dt=4.800000, rms=0.541 (0.071%), neg=0, invalid=96777
- 0413: dt=4.800000, rms=0.541 (0.073%), neg=0, invalid=96777
- 0414: dt=4.800000, rms=0.540 (0.068%), neg=0, invalid=96777
- 0415: dt=4.800000, rms=0.540 (0.069%), neg=0, invalid=96777
- 0416: dt=4.800000, rms=0.540 (0.061%), neg=0, invalid=96777
- 0417: dt=4.800000, rms=0.539 (0.058%), neg=0, invalid=96777
- 0418: dt=4.800000, rms=0.539 (0.060%), neg=0, invalid=96777
- 0419: dt=4.800000, rms=0.539 (0.064%), neg=0, invalid=96777
- 0420: dt=4.800000, rms=0.538 (0.059%), neg=0, invalid=96777
- 0421: dt=4.800000, rms=0.538 (0.056%), neg=0, invalid=96777
- 0422: dt=4.800000, rms=0.538 (0.048%), neg=0, invalid=96777
- 0423: dt=4.800000, rms=0.537 (0.050%), neg=0, invalid=96777
- 0424: dt=4.800000, rms=0.537 (0.044%), neg=0, invalid=96777
- 0425: dt=4.800000, rms=0.537 (0.047%), neg=0, invalid=96777
- 0426: dt=4.800000, rms=0.537 (0.045%), neg=0, invalid=96777
- 0427: dt=4.800000, rms=0.536 (0.044%), neg=0, invalid=96777
- 0428: dt=4.800000, rms=0.536 (0.043%), neg=0, invalid=96777
- 0429: dt=4.800000, rms=0.536 (0.035%), neg=0, invalid=96777
- 0430: dt=4.800000, rms=0.536 (0.037%), neg=0, invalid=96777
- 0431: dt=4.800000, rms=0.536 (0.036%), neg=0, invalid=96777
- 0432: dt=4.800000, rms=0.535 (0.036%), neg=0, invalid=96777
- 0433: dt=4.800000, rms=0.535 (0.034%), neg=0, invalid=96777
- 0434: dt=4.800000, rms=0.535 (0.035%), neg=0, invalid=96777
- 0435: dt=4.800000, rms=0.535 (0.027%), neg=0, invalid=96777
- 0436: dt=4.800000, rms=0.535 (0.040%), neg=0, invalid=96777
- 0437: dt=4.800000, rms=0.534 (0.038%), neg=0, invalid=96777
- 0438: dt=4.800000, rms=0.534 (0.039%), neg=0, invalid=96777
- 0439: dt=4.800000, rms=0.534 (0.037%), neg=0, invalid=96777
- 0440: dt=4.800000, rms=0.534 (0.037%), neg=0, invalid=96777
- 0441: dt=4.800000, rms=0.534 (0.026%), neg=0, invalid=96777
- 0442: dt=4.800000, rms=0.534 (0.029%), neg=0, invalid=96777
- 0443: dt=4.800000, rms=0.533 (0.028%), neg=0, invalid=96777
- 0444: dt=4.800000, rms=0.533 (0.032%), neg=0, invalid=96777
- 0445: dt=4.800000, rms=0.533 (0.034%), neg=0, invalid=96777
- 0446: dt=4.800000, rms=0.533 (0.028%), neg=0, invalid=96777
- 0447: dt=4.800000, rms=0.533 (0.033%), neg=0, invalid=96777
- 0448: dt=4.800000, rms=0.533 (0.030%), neg=0, invalid=96777
- 0449: dt=4.800000, rms=0.532 (0.029%), neg=0, invalid=96777
- 0450: dt=4.800000, rms=0.532 (0.026%), neg=0, invalid=96777
- 0451: dt=4.800000, rms=0.532 (0.028%), neg=0, invalid=96777
- 0452: dt=4.800000, rms=0.532 (0.033%), neg=0, invalid=96777
- 0453: dt=4.800000, rms=0.532 (0.032%), neg=0, invalid=96777
- 0454: dt=4.800000, rms=0.532 (0.026%), neg=0, invalid=96777
- 0455: dt=4.800000, rms=0.532 (0.026%), neg=0, invalid=96777
- 0456: dt=4.800000, rms=0.531 (0.024%), neg=0, invalid=96777
- 0457: dt=4.800000, rms=0.531 (0.022%), neg=0, invalid=96777
- 0458: dt=44.800000, rms=0.531 (0.040%), neg=0, invalid=96777
- 0459: dt=0.000000, rms=0.531 (0.006%), neg=0, invalid=96777
- 0460: dt=0.250000, rms=0.531 (-0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.531, neg=0, invalid=96777
- 0461: dt=32.000000, rms=0.530 (0.258%), neg=0, invalid=96777
- 0462: dt=10.133333, rms=0.529 (0.214%), neg=0, invalid=96777
- 0463: dt=6.400000, rms=0.528 (0.033%), neg=0, invalid=96777
- 0464: dt=6.400000, rms=0.528 (0.030%), neg=0, invalid=96777
- 0465: dt=6.400000, rms=0.528 (0.052%), neg=0, invalid=96777
- 0466: dt=6.400000, rms=0.528 (0.056%), neg=0, invalid=96777
- 0467: dt=6.400000, rms=0.527 (0.055%), neg=0, invalid=96777
- 0468: dt=6.400000, rms=0.527 (0.062%), neg=0, invalid=96777
- 0469: dt=6.400000, rms=0.527 (0.044%), neg=0, invalid=96777
- 0470: dt=6.400000, rms=0.527 (0.032%), neg=0, invalid=96777
- 0471: dt=6.400000, rms=0.526 (0.027%), neg=0, invalid=96777
- 0472: dt=6.400000, rms=0.526 (0.015%), neg=0, invalid=96777
- 0473: dt=6.400000, rms=0.526 (0.011%), neg=0, invalid=96777
- 0474: dt=44.800000, rms=0.526 (0.048%), neg=0, invalid=96777
- 0475: dt=9.600000, rms=0.526 (0.043%), neg=0, invalid=96777
- 0476: dt=9.600000, rms=0.526 (0.013%), neg=0, invalid=96777
- 0477: dt=9.600000, rms=0.526 (0.011%), neg=0, invalid=96777
- 0478: dt=9.600000, rms=0.526 (0.038%), neg=0, invalid=96777
- 0479: dt=9.600000, rms=0.525 (0.035%), neg=0, invalid=96777
- 0480: dt=9.600000, rms=0.525 (0.033%), neg=0, invalid=96777
- 0481: dt=9.600000, rms=0.525 (0.043%), neg=0, invalid=96777
- 0482: dt=9.600000, rms=0.525 (0.049%), neg=0, invalid=96777
- 0483: dt=9.600000, rms=0.524 (0.040%), neg=0, invalid=96777
- 0484: dt=9.600000, rms=0.524 (0.031%), neg=0, invalid=96777
- 0485: dt=9.600000, rms=0.524 (0.030%), neg=0, invalid=96777
- 0486: dt=9.600000, rms=0.524 (0.038%), neg=0, invalid=96777
- 0487: dt=9.600000, rms=0.524 (0.034%), neg=0, invalid=96777
- 0488: dt=9.600000, rms=0.524 (0.032%), neg=0, invalid=96777
- 0489: dt=9.600000, rms=0.523 (0.028%), neg=0, invalid=96777
- 0490: dt=9.600000, rms=0.523 (0.029%), neg=0, invalid=96777
- 0491: dt=9.600000, rms=0.523 (0.027%), neg=0, invalid=96777
- 0492: dt=9.600000, rms=0.523 (0.034%), neg=0, invalid=96777
- 0493: dt=9.600000, rms=0.523 (0.024%), neg=0, invalid=96777
- 0494: dt=9.600000, rms=0.523 (0.018%), neg=0, invalid=96777
- 0495: dt=44.800000, rms=0.523 (0.040%), neg=0, invalid=96777
- 0496: dt=2.800000, rms=0.523 (0.002%), neg=0, invalid=96777
- 0497: dt=2.800000, rms=0.523 (0.003%), neg=0, invalid=96777
- 0498: dt=2.800000, rms=0.523 (0.004%), neg=0, invalid=96777
- 0499: dt=2.800000, rms=0.523 (0.001%), neg=0, invalid=96777
- 0500: dt=2.800000, rms=0.523 (-0.000%), neg=0, invalid=96777
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.542, neg=0, invalid=96777
- 0501: dt=0.000000, rms=0.542 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.542, neg=0, invalid=96777
- 0502: dt=0.000000, rms=0.542 (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=0.582, neg=0, invalid=96777
- 0503: dt=0.892351, rms=0.580 (0.388%), neg=0, invalid=96777
- 0504: dt=0.112000, rms=0.580 (0.005%), neg=0, invalid=96777
- 0505: dt=0.112000, rms=0.580 (-0.002%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.580, neg=0, invalid=96777
- 0506: dt=0.448000, rms=0.580 (0.074%), neg=0, invalid=96777
- 0507: dt=0.112000, rms=0.580 (0.006%), neg=0, invalid=96777
- 0508: dt=0.112000, rms=0.580 (0.000%), neg=0, invalid=96777
- 0509: dt=0.112000, rms=0.580 (-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=0.530, neg=0, invalid=96777
- 0510: dt=0.096000, rms=0.526 (0.836%), neg=0, invalid=96777
- 0511: dt=0.020000, rms=0.525 (0.144%), neg=0, invalid=96777
- 0512: dt=0.028000, rms=0.524 (0.190%), neg=0, invalid=96777
- 0513: dt=0.150826, rms=0.519 (0.971%), neg=0, invalid=96777
- 0514: dt=0.080000, rms=0.517 (0.374%), neg=0, invalid=96777
- 0515: dt=0.006000, rms=0.517 (0.023%), neg=0, invalid=96777
- 0516: dt=0.006000, rms=0.517 (0.024%), neg=0, invalid=96777
- 0517: dt=0.006000, rms=0.517 (0.046%), neg=0, invalid=96777
- 0518: dt=0.006000, rms=0.516 (0.063%), neg=0, invalid=96777
- 0519: dt=0.006000, rms=0.516 (0.080%), neg=0, invalid=96777
- 0520: dt=0.006000, rms=0.515 (0.094%), neg=0, invalid=96777
- 0521: dt=0.006000, rms=0.515 (0.104%), neg=0, invalid=96777
- 0522: dt=0.006000, rms=0.514 (0.114%), neg=0, invalid=96777
- 0523: dt=0.006000, rms=0.514 (0.120%), neg=0, invalid=96777
- 0524: dt=0.006000, rms=0.513 (0.126%), neg=0, invalid=96777
- 0525: dt=0.006000, rms=0.512 (0.128%), neg=0, invalid=96777
- 0526: dt=0.006000, rms=0.512 (0.130%), neg=0, invalid=96777
- 0527: dt=0.006000, rms=0.512 (0.012%), neg=0, invalid=96777
- 0528: dt=0.006000, rms=0.511 (0.027%), neg=0, invalid=96777
- 0529: dt=0.006000, rms=0.511 (0.035%), neg=0, invalid=96777
- 0530: dt=0.006000, rms=0.511 (0.046%), neg=0, invalid=96777
- 0531: dt=0.006000, rms=0.511 (0.055%), neg=0, invalid=96777
- 0532: dt=0.006000, rms=0.510 (0.061%), neg=0, invalid=96777
- 0533: dt=0.006000, rms=0.510 (0.064%), neg=0, invalid=96777
- 0534: dt=0.006000, rms=0.510 (0.068%), neg=0, invalid=96777
- 0535: dt=0.006000, rms=0.509 (0.072%), neg=0, invalid=96777
- 0536: dt=0.006000, rms=0.509 (0.073%), neg=0, invalid=96777
- 0537: dt=0.006000, rms=0.509 (0.079%), neg=0, invalid=96777
- 0538: dt=0.006000, rms=0.508 (0.076%), neg=0, invalid=96777
- 0539: dt=0.006000, rms=0.508 (0.077%), neg=0, invalid=96777
- 0540: dt=0.006000, rms=0.507 (0.077%), neg=0, invalid=96777
- 0541: dt=0.006000, rms=0.507 (0.077%), neg=0, invalid=96777
- 0542: dt=0.006000, rms=0.507 (0.073%), neg=0, invalid=96777
- 0543: dt=0.006000, rms=0.506 (0.072%), neg=0, invalid=96777
- 0544: dt=0.006000, rms=0.506 (0.070%), neg=0, invalid=96777
- 0545: dt=0.006000, rms=0.506 (0.067%), neg=0, invalid=96777
- 0546: dt=0.006000, rms=0.505 (0.062%), neg=0, invalid=96777
- 0547: dt=0.006000, rms=0.505 (0.063%), neg=0, invalid=96777
- 0548: dt=0.006000, rms=0.505 (0.056%), neg=0, invalid=96777
- 0549: dt=0.006000, rms=0.504 (0.054%), neg=0, invalid=96777
- 0550: dt=0.006000, rms=0.504 (0.051%), neg=0, invalid=96777
- 0551: dt=0.006000, rms=0.504 (0.046%), neg=0, invalid=96777
- 0552: dt=0.006000, rms=0.504 (0.045%), neg=0, invalid=96777
- 0553: dt=0.006000, rms=0.503 (0.040%), neg=0, invalid=96777
- 0554: dt=0.006000, rms=0.503 (0.037%), neg=0, invalid=96777
- 0555: dt=0.006000, rms=0.503 (0.037%), neg=0, invalid=96777
- 0556: dt=0.006000, rms=0.503 (0.030%), neg=0, invalid=96777
- 0557: dt=0.006000, rms=0.503 (0.028%), neg=0, invalid=96777
- 0558: dt=0.006000, rms=0.503 (0.028%), neg=0, invalid=96777
- 0559: dt=0.006000, rms=0.503 (0.024%), neg=0, invalid=96777
- 0560: dt=0.006000, rms=0.502 (0.022%), neg=0, invalid=96777
- 0561: dt=0.007000, rms=0.502 (0.002%), neg=0, invalid=96777
- 0562: dt=0.007000, rms=0.502 (0.000%), neg=0, invalid=96777
- 0563: dt=0.007000, rms=0.502 (0.001%), neg=0, invalid=96777
- 0564: dt=0.007000, rms=0.502 (-0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.502, neg=0, invalid=96777
- 0565: dt=0.028000, rms=0.502 (0.081%), neg=0, invalid=96777
- 0566: dt=0.112000, rms=0.500 (0.302%), neg=0, invalid=96777
- 0567: dt=0.001750, rms=0.500 (0.003%), neg=0, invalid=96777
- 0568: dt=0.001750, rms=0.500 (0.004%), neg=0, invalid=96777
- 0569: dt=0.001750, rms=0.500 (0.007%), neg=0, invalid=96777
- 0570: dt=0.001750, rms=0.500 (0.010%), neg=0, invalid=96777
- 0571: dt=0.001750, rms=0.500 (0.012%), neg=0, invalid=96777
- 0572: dt=0.001750, rms=0.500 (0.016%), neg=0, invalid=96777
- 0573: dt=0.001750, rms=0.500 (0.018%), neg=0, invalid=96777
- 0574: dt=0.001750, rms=0.500 (0.018%), neg=0, invalid=96777
- 0575: dt=0.001750, rms=0.500 (0.019%), neg=0, invalid=96777
- 0576: dt=0.001750, rms=0.500 (0.021%), neg=0, invalid=96777
- 0577: dt=0.001750, rms=0.500 (0.020%), neg=0, invalid=96777
- 0578: dt=0.001750, rms=0.500 (0.024%), neg=0, invalid=96777
- 0579: dt=0.001750, rms=0.500 (0.024%), neg=0, invalid=96777
- 0580: dt=0.001750, rms=0.499 (0.025%), neg=0, invalid=96777
- 0581: dt=0.001750, rms=0.499 (0.025%), neg=0, invalid=96777
- 0582: dt=0.097039, rms=0.499 (0.153%), neg=0, invalid=96777
- 0583: dt=0.007000, rms=0.498 (0.009%), neg=0, invalid=96777
- 0584: dt=0.007000, rms=0.498 (0.009%), neg=0, invalid=96777
- 0585: dt=0.007000, rms=0.498 (0.015%), neg=0, invalid=96777
- 0586: dt=0.007000, rms=0.498 (0.024%), neg=0, invalid=96777
- 0587: dt=0.007000, rms=0.498 (0.029%), neg=0, invalid=96777
- 0588: dt=0.007000, rms=0.498 (0.032%), neg=0, invalid=96777
- 0589: dt=0.007000, rms=0.498 (0.036%), neg=0, invalid=96777
- 0590: dt=0.007000, rms=0.498 (0.041%), neg=0, invalid=96777
- 0591: dt=0.007000, rms=0.497 (0.043%), neg=0, invalid=96777
- 0592: dt=0.007000, rms=0.497 (0.045%), neg=0, invalid=96777
- 0593: dt=0.007000, rms=0.497 (0.045%), neg=0, invalid=96777
- 0594: dt=0.007000, rms=0.497 (0.006%), neg=0, invalid=96777
- 0595: dt=0.007000, rms=0.497 (0.006%), neg=0, invalid=96777
- 0596: dt=0.112000, rms=0.496 (0.067%), neg=0, invalid=96777
- 0597: dt=0.028000, rms=0.496 (0.017%), neg=0, invalid=96777
- 0598: dt=0.028000, rms=0.496 (0.012%), neg=0, invalid=96777
- 0599: dt=0.028000, rms=0.496 (0.022%), neg=0, invalid=96777
- 0600: dt=0.028000, rms=0.496 (0.035%), neg=0, invalid=96777
- 0601: dt=0.007000, rms=0.496 (0.003%), neg=0, invalid=96777
- 0602: dt=0.007000, rms=0.496 (0.005%), neg=0, invalid=96777
- 0603: dt=0.007000, rms=0.496 (0.008%), neg=0, invalid=96777
- 0604: dt=0.007000, rms=0.496 (0.001%), neg=0, invalid=96777
- 0605: dt=0.001750, rms=0.496 (0.001%), neg=0, invalid=96777
- 0606: dt=0.001750, rms=0.496 (-0.000%), neg=0, invalid=96777
- label assignment complete, 0 changed (0.00%)
- *********************************************************************************************
- *********************************************************************************************
- *********************************************************************************************
- ********************* ALLOWING NEGATIVE NODES IN DEFORMATION ********************************
- *********************************************************************************************
- *********************************************************************************************
- *********************************************************************************************
- **************** pass 1 of 1 ************************
- setting smoothness coefficient to 0.008
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.494, neg=0, invalid=96777
- 0607: dt=0.003613, rms=0.494 (0.000%), neg=0, invalid=96777
- 0608: dt=0.003613, rms=0.494 (-0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.494, neg=0, invalid=96777
- 0609: dt=129.472000, rms=0.494 (0.029%), neg=0, invalid=96777
- 0610: dt=73.984000, rms=0.494 (0.022%), neg=0, invalid=96777
- 0611: dt=73.984000, rms=0.494 (0.014%), neg=0, invalid=96777
- 0612: dt=73.984000, rms=0.494 (0.019%), neg=0, invalid=96777
- 0613: dt=73.984000, rms=0.494 (0.022%), neg=0, invalid=96777
- 0614: dt=73.984000, rms=0.493 (0.025%), neg=0, invalid=96777
- 0615: dt=73.984000, rms=0.493 (0.013%), neg=0, invalid=96777
- 0616: dt=73.984000, rms=0.493 (0.013%), neg=0, invalid=96777
- 0617: dt=73.984000, rms=0.493 (0.020%), neg=0, invalid=96777
- 0618: dt=73.984000, rms=0.493 (0.007%), neg=0, invalid=96777
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.493, neg=0, invalid=96777
- 0619: dt=25.920000, rms=0.493 (0.043%), neg=0, invalid=96777
- 0620: dt=9.072000, rms=0.493 (0.010%), neg=0, invalid=96777
- 0621: dt=9.072000, rms=0.493 (0.002%), neg=0, invalid=96777
- 0622: dt=9.072000, rms=0.493 (-0.004%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.493, neg=0, invalid=96777
- 0623: dt=103.680000, rms=0.491 (0.318%), neg=0, invalid=96777
- 0624: dt=36.288000, rms=0.491 (0.137%), neg=0, invalid=96777
- 0625: dt=36.288000, rms=0.490 (0.056%), neg=0, invalid=96777
- 0626: dt=36.288000, rms=0.490 (0.091%), neg=0, invalid=96777
- 0627: dt=36.288000, rms=0.489 (0.107%), neg=0, invalid=96777
- 0628: dt=36.288000, rms=0.489 (0.150%), neg=0, invalid=96777
- 0629: dt=36.288000, rms=0.488 (0.084%), neg=0, invalid=96777
- 0630: dt=36.288000, rms=0.488 (0.092%), neg=0, invalid=96777
- 0631: dt=36.288000, rms=0.488 (0.061%), neg=0, invalid=96777
- 0632: dt=25.920000, rms=0.487 (0.039%), neg=0, invalid=96777
- 0633: dt=25.920000, rms=0.487 (0.009%), neg=0, invalid=96777
- 0634: dt=25.920000, rms=0.487 (0.022%), neg=0, invalid=96777
- 0635: dt=25.920000, rms=0.487 (0.028%), neg=0, invalid=96777
- 0636: dt=25.920000, rms=0.487 (0.025%), neg=0, invalid=96777
- 0637: dt=25.920000, rms=0.487 (0.027%), neg=0, invalid=96777
- 0638: dt=25.920000, rms=0.487 (0.034%), neg=0, invalid=96777
- 0639: dt=25.920000, rms=0.486 (0.042%), neg=0, invalid=96777
- 0640: dt=25.920000, rms=0.486 (0.040%), neg=0, invalid=96777
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.487, neg=0, invalid=96777
- iter 0, gcam->neg = 3
- after 3 iterations, nbhd size=0, neg = 0
- 0641: dt=32.000000, rms=0.485 (0.404%), neg=0, invalid=96777
- iter 0, gcam->neg = 6
- after 7 iterations, nbhd size=1, neg = 0
- 0642: dt=44.800000, rms=0.483 (0.366%), neg=0, invalid=96777
- 0643: dt=9.600000, rms=0.482 (0.153%), neg=0, invalid=96777
- 0644: dt=9.600000, rms=0.482 (0.098%), neg=0, invalid=96777
- 0645: dt=9.600000, rms=0.481 (0.118%), neg=0, invalid=96777
- iter 0, gcam->neg = 3
- after 7 iterations, nbhd size=1, neg = 0
- 0646: dt=9.600000, rms=0.480 (0.177%), neg=0, invalid=96777
- iter 0, gcam->neg = 6
- after 8 iterations, nbhd size=1, neg = 0
- 0647: dt=9.600000, rms=0.479 (0.168%), neg=0, invalid=96777
- iter 0, gcam->neg = 2
- after 6 iterations, nbhd size=1, neg = 0
- 0648: dt=9.600000, rms=0.479 (0.178%), neg=0, invalid=96777
- 0649: dt=9.600000, rms=0.478 (0.132%), neg=0, invalid=96777
- 0650: dt=9.600000, rms=0.477 (0.130%), neg=0, invalid=96777
- 0651: dt=9.600000, rms=0.477 (0.125%), neg=0, invalid=96777
- 0652: dt=9.600000, rms=0.476 (0.146%), neg=0, invalid=96777
- 0653: dt=9.600000, rms=0.475 (0.134%), neg=0, invalid=96777
- 0654: dt=9.600000, rms=0.475 (0.112%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0655: dt=9.600000, rms=0.474 (0.114%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0656: dt=9.600000, rms=0.474 (0.125%), neg=0, invalid=96777
- 0657: dt=9.600000, rms=0.473 (0.133%), neg=0, invalid=96777
- 0658: dt=9.600000, rms=0.473 (0.113%), neg=0, invalid=96777
- 0659: dt=9.600000, rms=0.472 (0.106%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0660: dt=32.000000, rms=0.472 (0.031%), neg=0, invalid=96777
- 0661: dt=32.000000, rms=0.472 (0.015%), neg=0, invalid=96777
- iter 0, gcam->neg = 44
- after 41 iterations, nbhd size=4, neg = 0
- 0662: dt=32.000000, rms=0.472 (-0.641%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.472, neg=0, invalid=96777
- 0663: dt=10.074074, rms=0.470 (0.289%), neg=0, invalid=96777
- 0664: dt=11.200000, rms=0.469 (0.291%), neg=0, invalid=96777
- 0665: dt=9.600000, rms=0.468 (0.149%), neg=0, invalid=96777
- 0666: dt=9.600000, rms=0.468 (0.177%), neg=0, invalid=96777
- 0667: dt=9.600000, rms=0.467 (0.209%), neg=0, invalid=96777
- 0668: dt=9.600000, rms=0.465 (0.228%), neg=0, invalid=96777
- 0669: dt=9.600000, rms=0.465 (0.185%), neg=0, invalid=96777
- 0670: dt=9.600000, rms=0.464 (0.199%), neg=0, invalid=96777
- 0671: dt=9.600000, rms=0.463 (0.116%), neg=0, invalid=96777
- 0672: dt=9.600000, rms=0.463 (0.085%), neg=0, invalid=96777
- 0673: dt=38.400000, rms=0.463 (0.052%), neg=0, invalid=96777
- iter 0, gcam->neg = 6
- after 8 iterations, nbhd size=1, neg = 0
- 0674: dt=38.400000, rms=0.462 (-0.250%), neg=0, invalid=96777
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.467, neg=0, invalid=96777
- 0675: dt=4.129032, rms=0.467 (0.119%), neg=0, invalid=96777
- iter 0, gcam->neg = 2
- after 0 iterations, nbhd size=0, neg = 0
- 0676: dt=1.008000, rms=0.467 (0.020%), neg=0, invalid=96777
- 0677: dt=1.008000, rms=0.467 (0.010%), neg=0, invalid=96777
- 0678: dt=1.008000, rms=0.466 (0.025%), neg=0, invalid=96777
- 0679: dt=1.008000, rms=0.466 (0.019%), neg=0, invalid=96777
- iter 0, gcam->neg = 2
- after 1 iterations, nbhd size=0, neg = 0
- 0680: dt=1.008000, rms=0.466 (-0.013%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.466, neg=0, invalid=96777
- iter 0, gcam->neg = 21
- after 18 iterations, nbhd size=2, neg = 0
- 0681: dt=9.216000, rms=0.465 (0.250%), neg=0, invalid=96777
- iter 0, gcam->neg = 41
- after 10 iterations, nbhd size=1, neg = 0
- 0682: dt=8.590164, rms=0.464 (0.231%), neg=0, invalid=96777
- iter 0, gcam->neg = 82
- after 11 iterations, nbhd size=1, neg = 0
- 0683: dt=8.590164, rms=0.464 (-0.067%), 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
- 0684: 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
- 0685: 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=0.461, neg=0, invalid=96777
- iter 0, gcam->neg = 1039
- after 35 iterations, nbhd size=3, neg = 0
- 0686: dt=1.792000, rms=0.419 (8.997%), neg=0, invalid=96777
- 0687: dt=0.000094, rms=0.419 (-0.005%), neg=0, invalid=96777
- 0688: dt=0.000094, rms=0.419 (0.001%), neg=0, invalid=96777
- 0689: dt=0.000094, rms=0.419 (-0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.419, neg=0, invalid=96777
- 0690: dt=0.000250, rms=0.419 (0.001%), neg=0, invalid=96777
- 0691: dt=0.000020, rms=0.419 (0.002%), neg=0, invalid=96777
- 0692: dt=0.000000, rms=0.419 (0.000%), neg=0, invalid=96777
- iter 0, gcam->neg = 127
- after 10 iterations, nbhd size=1, neg = 0
- 0693: dt=0.050000, rms=0.419 (-0.275%), neg=0, invalid=96777
- label assignment complete, 0 changed (0.00%)
- label assignment complete, 0 changed (0.00%)
- ***************** morphing with label term set to 0 *******************************
- **************** pass 1 of 1 ************************
- setting smoothness coefficient to 0.008
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.404, neg=0, invalid=96777
- 0694: dt=0.000000, rms=0.406 (-0.433%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.406, neg=0, invalid=96777
- 0695: dt=32.368000, rms=0.406 (0.019%), neg=0, invalid=96777
- 0696: dt=32.368000, rms=0.406 (0.004%), neg=0, invalid=96777
- 0697: dt=32.368000, rms=0.406 (0.001%), neg=0, invalid=96777
- 0698: dt=32.368000, rms=0.406 (-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=0.406, neg=0, invalid=96777
- 0699: dt=0.000000, rms=0.406 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.406, neg=0, invalid=96777
- 0700: dt=36.288000, rms=0.406 (0.032%), neg=0, invalid=96777
- 0701: dt=15.552000, rms=0.406 (0.004%), neg=0, invalid=96777
- 0702: dt=15.552000, rms=0.406 (0.006%), neg=0, invalid=96777
- 0703: dt=15.552000, rms=0.406 (0.007%), neg=0, invalid=96777
- 0704: dt=15.552000, rms=0.406 (0.004%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0705: dt=15.552000, rms=0.406 (-0.004%), neg=0, invalid=96777
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.407, neg=0, invalid=96777
- 0706: dt=2.800000, rms=0.407 (0.012%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0707: dt=1.600000, rms=0.406 (0.002%), neg=0, invalid=96777
- 0708: dt=1.600000, rms=0.406 (0.007%), neg=0, invalid=96777
- 0709: dt=1.600000, rms=0.406 (0.008%), neg=0, invalid=96777
- 0710: dt=1.600000, rms=0.406 (0.001%), neg=0, invalid=96777
- 0711: dt=1.600000, rms=0.406 (-0.013%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.406, neg=0, invalid=96777
- iter 0, gcam->neg = 5
- after 8 iterations, nbhd size=1, neg = 0
- 0712: dt=9.600000, rms=0.406 (0.059%), neg=0, invalid=96777
- iter 0, gcam->neg = 13
- after 200 iterations, nbhd size=3, neg = 1
- starting rms=0.003, neg=1, removing folds in lattice....
- iter 1, dt=0.000100: new neg 0, old_neg 1, delta 1, rms=0.003 (11.435%)
- 0713: dt=32.000000, rms=0.406 (0.013%), neg=0, invalid=96777
- iter 0, gcam->neg = 4
- after 22 iterations, nbhd size=3, neg = 0
- 0714: dt=32.000000, rms=0.405 (0.234%), neg=0, invalid=96777
- iter 0, gcam->neg = 71
- after 200 iterations, nbhd size=4, neg = 2
- starting rms=0.006, neg=2, removing folds in lattice....
- iter 1, dt=0.000039: new neg 0, old_neg 2, delta 2, rms=0.003 (50.130%)
- 0715: dt=32.000000, rms=0.405 (-0.351%), neg=0, invalid=96777
- 0716: dt=6.400000, rms=0.405 (0.018%), neg=0, invalid=96777
- iter 0, gcam->neg = 16
- after 200 iterations, nbhd size=2, neg = 1
- starting rms=0.004, neg=1, removing folds in lattice....
- iter 1, dt=0.000080: new neg 0, old_neg 1, delta 1, rms=0.003 (22.335%)
- 0717: dt=38.400000, rms=0.405 (0.059%), neg=0, invalid=96777
- iter 0, gcam->neg = 10
- after 38 iterations, nbhd size=4, neg = 0
- 0718: dt=38.400000, rms=0.405 (0.069%), neg=0, invalid=96777
- 0719: dt=11.200000, rms=0.404 (0.026%), neg=0, invalid=96777
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.407, neg=0, invalid=96777
- iter 0, gcam->neg = 34
- after 35 iterations, nbhd size=3, neg = 0
- 0720: dt=4.270270, rms=0.406 (0.173%), neg=0, invalid=96777
- 0721: dt=0.001688, rms=0.406 (0.000%), neg=0, invalid=96777
- 0722: dt=0.001688, rms=0.406 (0.000%), neg=0, invalid=96777
- 0723: dt=0.001688, rms=0.406 (0.000%), neg=0, invalid=96777
- 0724: dt=0.001688, rms=0.406 (0.000%), neg=0, invalid=96777
- 0725: dt=0.001688, rms=0.406 (0.000%), neg=0, invalid=96777
- 0726: dt=0.001688, rms=0.406 (0.000%), neg=0, invalid=96777
- 0727: dt=0.001688, rms=0.406 (0.000%), neg=0, invalid=96777
- 0728: dt=0.001688, rms=0.406 (0.000%), neg=0, invalid=96777
- 0729: dt=0.001688, rms=0.406 (0.000%), neg=0, invalid=96777
- 0730: dt=0.001688, rms=0.406 (0.000%), neg=0, invalid=96777
- 0731: dt=0.001688, rms=0.406 (0.000%), neg=0, invalid=96777
- 0732: dt=0.001688, rms=0.406 (0.000%), neg=0, invalid=96777
- 0733: dt=0.001688, rms=0.406 (0.000%), neg=0, invalid=96777
- 0734: dt=0.001688, rms=0.406 (0.000%), neg=0, invalid=96777
- 0735: dt=0.001688, rms=0.406 (0.000%), neg=0, invalid=96777
- 0736: dt=0.001688, rms=0.406 (0.000%), neg=0, invalid=96777
- 0737: dt=0.001688, rms=0.406 (0.001%), neg=0, invalid=96777
- 0738: dt=0.001688, rms=0.406 (0.001%), neg=0, invalid=96777
- 0739: dt=0.001688, rms=0.406 (0.001%), neg=0, invalid=96777
- 0740: dt=0.001688, rms=0.406 (0.001%), neg=0, invalid=96777
- 0741: dt=0.001688, rms=0.406 (0.001%), neg=0, invalid=96777
- 0742: dt=0.001688, rms=0.406 (0.001%), neg=0, invalid=96777
- 0743: dt=0.001688, rms=0.406 (0.001%), neg=0, invalid=96777
- 0744: dt=0.001688, rms=0.406 (0.001%), neg=0, invalid=96777
- 0745: dt=0.001688, rms=0.406 (0.001%), neg=0, invalid=96777
- 0746: dt=0.001688, rms=0.406 (0.001%), neg=0, invalid=96777
- 0747: dt=0.001688, rms=0.406 (0.001%), neg=0, invalid=96777
- 0748: dt=0.001688, rms=0.406 (0.001%), neg=0, invalid=96777
- 0749: dt=0.001688, rms=0.406 (0.001%), neg=0, invalid=96777
- 0750: dt=0.001688, rms=0.406 (0.001%), neg=0, invalid=96777
- 0751: dt=0.001688, rms=0.406 (0.001%), neg=0, invalid=96777
- 0752: dt=0.001688, rms=0.406 (0.001%), neg=0, invalid=96777
- 0753: dt=0.001688, rms=0.406 (0.001%), neg=0, invalid=96777
- 0754: dt=0.001688, rms=0.406 (0.001%), neg=0, invalid=96777
- 0755: dt=0.001688, rms=0.406 (0.001%), neg=0, invalid=96777
- 0756: dt=0.001688, rms=0.406 (0.001%), neg=0, invalid=96777
- 0757: dt=0.001688, rms=0.406 (0.001%), neg=0, invalid=96777
- 0758: dt=0.001688, rms=0.406 (0.001%), neg=0, invalid=96777
- 0759: dt=0.001688, rms=0.406 (0.001%), neg=0, invalid=96777
- 0760: dt=0.001688, rms=0.406 (0.001%), neg=0, invalid=96777
- 0761: dt=0.001688, rms=0.406 (0.001%), neg=0, invalid=96777
- 0762: dt=0.001688, rms=0.406 (0.001%), neg=0, invalid=96777
- 0763: dt=0.001688, rms=0.406 (0.001%), neg=0, invalid=96777
- 0764: dt=0.001688, rms=0.406 (0.001%), neg=0, invalid=96777
- 0765: dt=0.001688, rms=0.406 (0.001%), neg=0, invalid=96777
- 0766: dt=0.001688, rms=0.406 (0.001%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.406, neg=0, invalid=96777
- iter 0, gcam->neg = 128
- after 37 iterations, nbhd size=3, neg = 0
- 0767: dt=13.824000, rms=0.404 (0.604%), neg=0, invalid=96777
- 0768: dt=0.002812, rms=0.404 (0.000%), neg=0, invalid=96777
- 0769: dt=0.002812, rms=0.404 (0.000%), neg=0, invalid=96777
- 0770: dt=0.002812, rms=0.404 (0.000%), neg=0, invalid=96777
- 0771: dt=0.002812, rms=0.404 (0.000%), neg=0, invalid=96777
- 0772: dt=0.144000, rms=0.404 (0.001%), neg=0, invalid=96777
- iter 0, gcam->neg = 28
- after 40 iterations, nbhd size=1, neg = 0
- 0773: dt=4.266667, rms=0.403 (0.041%), neg=0, invalid=96777
- 0774: dt=0.001688, rms=0.403 (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=0.409, neg=0, invalid=96777
- 0775: dt=0.000160, rms=0.409 (0.000%), neg=0, invalid=96777
- 0776: dt=0.000000, rms=0.409 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.409, neg=0, invalid=96777
- 0777: dt=0.000000, rms=0.409 (0.000%), neg=0, invalid=96777
- resetting metric properties...
- setting smoothness coefficient to 2.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.400, neg=0, invalid=96777
- iter 0, gcam->neg = 580
- after 41 iterations, nbhd size=3, neg = 0
- 0778: dt=0.849079, rms=0.386 (3.573%), neg=0, invalid=96777
- 0779: dt=0.000000, rms=0.386 (0.000%), neg=0, invalid=96777
- iter 0, gcam->neg = 944
- after 10 iterations, nbhd size=1, neg = 0
- 0780: dt=0.050000, rms=0.386 (-0.291%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.386, neg=0, invalid=96777
- 0781: dt=0.000000, rms=0.386 (0.000%), neg=0, invalid=96777
- writing output transformation to transforms/talairach.m3z...
- GCAMwrite
- registration took 5 hours, 31 minutes and 20 seconds.
- #--------------------------------------
- #@# CA Reg Inv Thu Aug 8 17:38:27 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 17:40:01 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...
- 11861212 nonbrain voxels erased
- writing output to nu_noneck.mgz...
- nonbrain removal took 1 minutes and 35 seconds.
- #--------------------------------------
- #@# SkullLTA Thu Aug 8 17:41:36 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=7.0
- skull bounding box = (59, 25, 29) --> (200, 196, 216)
- using (106, 82, 123) as brain centroid...
- mean wm in atlas = 126, using box (89,61,100) --> (123, 103,146) to find MRI wm
- before smoothing, mri peak at 108
- after smoothing, mri peak at 109, scaling input intensities by 1.156
- scaling channel 0 by 1.15596
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.1 (thresh=-4.1)
- 1.235 0.028 0.013 -37.558;
- -0.054 1.169 0.187 -10.321;
- -0.005 -0.159 1.083 -4.156;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.143 0.026 0.012 -25.309;
- -0.054 1.169 0.187 -10.321;
- -0.005 -0.159 1.083 -4.156;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 2 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.143 0.026 0.012 -25.309;
- -0.054 1.169 0.187 -10.321;
- -0.005 -0.159 1.083 -4.156;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.2500
- ****************************************
- Nine parameter search. iteration 3 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-4.0 (thresh=-4.0)
- 1.161 0.065 0.018 -32.331;
- -0.093 1.188 0.189 -7.589;
- -0.005 -0.168 1.145 -12.307;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 4 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 1.161 0.065 0.018 -32.331;
- -0.093 1.188 0.189 -7.589;
- -0.005 -0.168 1.145 -12.307;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.0625
- ****************************************
- Nine parameter search. iteration 5 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 1.158 0.055 0.017 -30.273;
- -0.084 1.187 0.208 -10.957;
- -0.004 -0.187 1.144 -10.415;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 6 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 1.153 0.055 0.017 -29.725;
- -0.084 1.186 0.208 -10.802;
- -0.004 -0.187 1.144 -10.415;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 7 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 1.153 0.055 0.017 -29.725;
- -0.084 1.186 0.208 -10.802;
- -0.004 -0.187 1.144 -10.415;
- 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
- 1.15348 0.05516 0.01660 -29.72474;
- -0.08357 1.18606 0.20823 -10.80184;
- -0.00423 -0.18747 1.14435 -10.41545;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 3481
- Quasinewton: input matrix
- 1.15348 0.05516 0.01660 -29.72474;
- -0.08357 1.18606 0.20823 -10.80184;
- -0.00423 -0.18747 1.14435 -10.41545;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 1.153 0.055 0.017 -29.725;
- -0.084 1.186 0.208 -10.802;
- -0.004 -0.187 1.144 -10.415;
- 0.000 0.000 0.000 1.000;
- pass 1, spacing 8: log(p) = -3.9 (old=-4.1)
- transform before final EM align:
- 1.153 0.055 0.017 -29.725;
- -0.084 1.186 0.208 -10.802;
- -0.004 -0.187 1.144 -10.415;
- 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
- 1.15348 0.05516 0.01660 -29.72474;
- -0.08357 1.18606 0.20823 -10.80184;
- -0.00423 -0.18747 1.14435 -10.41545;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 382743
- Quasinewton: input matrix
- 1.15348 0.05516 0.01660 -29.72474;
- -0.08357 1.18606 0.20823 -10.80184;
- -0.00423 -0.18747 1.14435 -10.41545;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = 4.4 tol 0.000000
- final transform:
- 1.153 0.055 0.017 -29.725;
- -0.084 1.186 0.208 -10.802;
- -0.004 -0.187 1.144 -10.415;
- 0.000 0.000 0.000 1.000;
- writing output transformation to transforms/talairach_with_skull_2.lta...
- registration took 43 minutes and 22 seconds.
- #--------------------------------------
- #@# SubCort Seg Thu Aug 8 18:24:59 CEST 2013
- mri_ca_label -align norm.mgz transforms/talairach.m3z /opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz
- sysname Linux
- hostname snake5
- machine x86_64
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 = 0.13737 ( 9)
- Left_Lateral_Ventricle (4): linear fit = 0.29 x + 0.0 (475 voxels, overlap=0.005)
- Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (475 voxels, peak = 8), gca=10.8
- gca peak = 0.14982 (20)
- mri peak = 0.11470 (10)
- Right_Lateral_Ventricle (43): linear fit = 0.31 x + 0.0 (471 voxels, overlap=0.007)
- Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (471 voxels, peak = 6), gca=8.0
- gca peak = 0.28003 (97)
- mri peak = 0.10218 (89)
- Right_Pallidum (52): linear fit = 0.90 x + 0.0 (247 voxels, overlap=0.042)
- Right_Pallidum (52): linear fit = 0.90 x + 0.0 (247 voxels, peak = 88), gca=87.8
- gca peak = 0.18160 (96)
- mri peak = 0.08750 (89)
- Left_Pallidum (13): linear fit = 0.88 x + 0.0 (242 voxels, overlap=0.051)
- Left_Pallidum (13): linear fit = 0.88 x + 0.0 (242 voxels, peak = 84), gca=84.0
- gca peak = 0.27536 (62)
- mri peak = 0.09256 (54)
- Right_Hippocampus (53): linear fit = 0.83 x + 0.0 (602 voxels, overlap=0.021)
- Right_Hippocampus (53): linear fit = 0.83 x + 0.0 (602 voxels, peak = 52), gca=51.8
- gca peak = 0.32745 (63)
- mri peak = 0.09905 (56)
- Left_Hippocampus (17): linear fit = 0.88 x + 0.0 (678 voxels, overlap=0.386)
- Left_Hippocampus (17): linear fit = 0.88 x + 0.0 (678 voxels, peak = 55), gca=55.1
- gca peak = 0.08597 (105)
- mri peak = 0.09341 (110)
- Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (22467 voxels, overlap=0.608)
- Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (22467 voxels, peak = 109), gca=108.7
- gca peak = 0.09209 (106)
- mri peak = 0.09578 (112)
- Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (21390 voxels, overlap=0.504)
- Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (21390 voxels, peak = 111), gca=110.8
- gca peak = 0.07826 (63)
- mri peak = 0.05662 (51)
- Left_Cerebral_Cortex (3): linear fit = 0.80 x + 0.0 (11036 voxels, overlap=0.241)
- Left_Cerebral_Cortex (3): linear fit = 0.80 x + 0.0 (11036 voxels, peak = 50), gca=50.1
- gca peak = 0.08598 (64)
- mri peak = 0.04978 (54)
- Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (9897 voxels, overlap=0.266)
- Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (9897 voxels, peak = 53), gca=52.8
- gca peak = 0.24164 (71)
- mri peak = 0.11545 (65)
- Right_Caudate (50): linear fit = 0.90 x + 0.0 (584 voxels, overlap=0.428)
- Right_Caudate (50): linear fit = 0.90 x + 0.0 (584 voxels, peak = 64), gca=64.3
- gca peak = 0.18227 (75)
- mri peak = 0.10143 (72)
- Left_Caudate (11): linear fit = 0.82 x + 0.0 (903 voxels, overlap=0.021)
- Left_Caudate (11): linear fit = 0.82 x + 0.0 (903 voxels, peak = 62), gca=61.9
- gca peak = 0.10629 (62)
- mri peak = 0.05341 (57)
- Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (7110 voxels, overlap=1.000)
- Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (7110 voxels, peak = 60), gca=59.8
- gca peak = 0.11668 (59)
- mri peak = 0.05407 (56)
- Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (7148 voxels, overlap=0.999)
- Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (7148 voxels, peak = 57), gca=56.9
- gca peak = 0.17849 (88)
- mri peak = 0.08327 (91)
- Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (3812 voxels, overlap=0.875)
- Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (3812 voxels, peak = 92), gca=92.0
- gca peak = 0.16819 (86)
- mri peak = 0.09446 (91)
- Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (3648 voxels, overlap=0.944)
- Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (3648 voxels, peak = 89), gca=89.0
- gca peak = 0.41688 (64)
- mri peak = 0.14786 (56)
- Left_Amygdala (18): linear fit = 0.86 x + 0.0 (267 voxels, overlap=0.623)
- Left_Amygdala (18): linear fit = 0.86 x + 0.0 (267 voxels, peak = 55), gca=54.7
- gca peak = 0.42394 (62)
- mri peak = 0.10117 (60)
- Right_Amygdala (54): linear fit = 0.94 x + 0.0 (255 voxels, overlap=1.046)
- Right_Amygdala (54): linear fit = 0.94 x + 0.0 (255 voxels, peak = 58), gca=58.0
- gca peak = 0.10041 (96)
- mri peak = 0.06482 (91)
- Left_Thalamus_Proper (10): linear fit = 0.96 x + 0.0 (2599 voxels, overlap=0.963)
- Left_Thalamus_Proper (10): linear fit = 0.96 x + 0.0 (2599 voxels, peak = 93), gca=92.6
- gca peak = 0.13978 (88)
- mri peak = 0.06612 (85)
- Right_Thalamus_Proper (49): linear fit = 0.95 x + 0.0 (2988 voxels, overlap=0.887)
- Right_Thalamus_Proper (49): linear fit = 0.95 x + 0.0 (2988 voxels, peak = 84), gca=84.0
- gca peak = 0.08514 (81)
- mri peak = 0.11843 (72)
- Left_Putamen (12): linear fit = 0.88 x + 0.0 (1204 voxels, overlap=0.537)
- Left_Putamen (12): linear fit = 0.88 x + 0.0 (1204 voxels, peak = 71), gca=70.9
- gca peak = 0.09624 (82)
- mri peak = 0.10036 (71)
- Right_Putamen (51): linear fit = 0.90 x + 0.0 (1112 voxels, overlap=0.477)
- Right_Putamen (51): linear fit = 0.90 x + 0.0 (1112 voxels, peak = 74), gca=74.2
- gca peak = 0.07543 (88)
- mri peak = 0.07778 (84)
- Brain_Stem (16): linear fit = 1.00 x + 0.0 (8137 voxels, overlap=0.765)
- Brain_Stem (16): linear fit = 1.00 x + 0.0 (8137 voxels, peak = 88), gca=87.6
- gca peak = 0.12757 (95)
- mri peak = 0.06006 (97)
- Right_VentralDC (60): linear fit = 1.03 x + 0.0 (747 voxels, overlap=0.878)
- Right_VentralDC (60): linear fit = 1.03 x + 0.0 (747 voxels, peak = 98), gca=98.3
- gca peak = 0.17004 (92)
- mri peak = 0.06868 (98)
- Left_VentralDC (28): linear fit = 1.04 x + 0.0 (765 voxels, overlap=0.912)
- Left_VentralDC (28): linear fit = 1.04 x + 0.0 (765 voxels, peak = 96), gca=96.1
- gca peak = 0.21361 (36)
- uniform distribution in MR - rejecting arbitrary fit
- gca peak = 0.26069 (23)
- mri peak = 0.18723 ( 8)
- Fourth_Ventricle (15): linear fit = 0.26 x + 0.0 (232 voxels, overlap=0.027)
- Fourth_Ventricle (15): linear fit = 0.26 x + 0.0 (232 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 0.85 x + 0.0
- estimating mean wm scale to be 1.04 x + 0.0
- estimating mean csf scale to be 0.40 x + 0.0
- saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
- renormalizing by structure alignment....
- renormalizing input #0
- gca peak = 0.31600 (11)
- mri peak = 0.13737 ( 9)
- Left_Lateral_Ventricle (4): linear fit = 0.81 x + 0.0 (475 voxels, overlap=0.872)
- Left_Lateral_Ventricle (4): linear fit = 0.81 x + 0.0 (475 voxels, peak = 9), gca=8.9
- gca peak = 0.29325 ( 9)
- mri peak = 0.11470 (10)
- Right_Lateral_Ventricle (43): linear fit = 0.79 x + 0.0 (471 voxels, overlap=0.886)
- Right_Lateral_Ventricle (43): linear fit = 0.79 x + 0.0 (471 voxels, peak = 7), gca=7.1
- gca peak = 0.32314 (88)
- mri peak = 0.10218 (89)
- Right_Pallidum (52): linear fit = 1.00 x + 0.0 (247 voxels, overlap=1.011)
- Right_Pallidum (52): linear fit = 1.00 x + 0.0 (247 voxels, peak = 88), gca=87.6
- gca peak = 0.18877 (84)
- mri peak = 0.08750 (89)
- Left_Pallidum (13): linear fit = 0.99 x + 0.0 (242 voxels, overlap=1.005)
- Left_Pallidum (13): linear fit = 0.99 x + 0.0 (242 voxels, peak = 83), gca=82.7
- gca peak = 0.30642 (52)
- mri peak = 0.09256 (54)
- Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (602 voxels, overlap=1.007)
- Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (602 voxels, peak = 52), gca=52.0
- gca peak = 0.33227 (55)
- mri peak = 0.09905 (56)
- Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (678 voxels, overlap=1.005)
- Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (678 voxels, peak = 55), gca=55.0
- gca peak = 0.08268 (109)
- mri peak = 0.09341 (110)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (22467 voxels, overlap=0.736)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (22467 voxels, peak = 109), gca=109.0
- gca peak = 0.08584 (111)
- mri peak = 0.09578 (112)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (21390 voxels, overlap=0.706)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (21390 voxels, peak = 112), gca=111.6
- gca peak = 0.09726 (50)
- mri peak = 0.05662 (51)
- Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (11036 voxels, overlap=0.997)
- Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (11036 voxels, peak = 49), gca=49.2
- gca peak = 0.10559 (53)
- mri peak = 0.04978 (54)
- Right_Cerebral_Cortex (42): linear fit = 0.96 x + 0.0 (9897 voxels, overlap=0.993)
- Right_Cerebral_Cortex (42): linear fit = 0.96 x + 0.0 (9897 voxels, peak = 51), gca=51.1
- gca peak = 0.24090 (64)
- mri peak = 0.11545 (65)
- Right_Caudate (50): linear fit = 1.00 x + 0.0 (584 voxels, overlap=1.004)
- Right_Caudate (50): linear fit = 1.00 x + 0.0 (584 voxels, peak = 64), gca=64.0
- gca peak = 0.16489 (62)
- mri peak = 0.10143 (72)
- Left_Caudate (11): linear fit = 1.01 x + 0.0 (903 voxels, overlap=0.990)
- Left_Caudate (11): linear fit = 1.01 x + 0.0 (903 voxels, peak = 63), gca=62.9
- gca peak = 0.10996 (60)
- mri peak = 0.05341 (57)
- Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (7110 voxels, overlap=0.997)
- Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (7110 voxels, peak = 62), gca=61.5
- gca peak = 0.12346 (58)
- mri peak = 0.05407 (56)
- Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (7148 voxels, overlap=0.999)
- Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (7148 voxels, peak = 59), gca=59.4
- gca peak = 0.17369 (92)
- mri peak = 0.08327 (91)
- Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (3812 voxels, overlap=0.986)
- Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (3812 voxels, peak = 92), gca=91.5
- gca peak = 0.16437 (89)
- mri peak = 0.09446 (91)
- Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (3648 voxels, overlap=0.995)
- Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (3648 voxels, peak = 89), gca=88.6
- gca peak = 0.35645 (54)
- mri peak = 0.14786 (56)
- Left_Amygdala (18): linear fit = 1.02 x + 0.0 (267 voxels, overlap=1.032)
- Left_Amygdala (18): linear fit = 1.02 x + 0.0 (267 voxels, peak = 55), gca=55.3
- gca peak = 0.43413 (58)
- mri peak = 0.10117 (60)
- Right_Amygdala (54): linear fit = 1.01 x + 0.0 (255 voxels, overlap=1.023)
- Right_Amygdala (54): linear fit = 1.01 x + 0.0 (255 voxels, peak = 59), gca=58.9
- gca peak = 0.10681 (93)
- mri peak = 0.06482 (91)
- Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (2599 voxels, overlap=0.961)
- Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (2599 voxels, peak = 93), gca=92.5
- gca peak = 0.14353 (84)
- mri peak = 0.06612 (85)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (2988 voxels, overlap=0.995)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (2988 voxels, peak = 84), gca=83.6
- gca peak = 0.09324 (72)
- mri peak = 0.11843 (72)
- Left_Putamen (12): linear fit = 1.00 x + 0.0 (1204 voxels, overlap=0.952)
- Left_Putamen (12): linear fit = 1.00 x + 0.0 (1204 voxels, peak = 72), gca=72.0
- gca peak = 0.10505 (69)
- mri peak = 0.10036 (71)
- Right_Putamen (51): linear fit = 0.96 x + 0.0 (1112 voxels, overlap=0.988)
- Right_Putamen (51): linear fit = 0.96 x + 0.0 (1112 voxels, peak = 67), gca=66.6
- gca peak = 0.07757 (88)
- mri peak = 0.07778 (84)
- Brain_Stem (16): linear fit = 1.01 x + 0.0 (8137 voxels, overlap=0.756)
- Brain_Stem (16): linear fit = 1.01 x + 0.0 (8137 voxels, peak = 89), gca=89.3
- gca peak = 0.13022 (98)
- mri peak = 0.06006 (97)
- Right_VentralDC (60): linear fit = 1.00 x + 0.0 (747 voxels, overlap=0.897)
- Right_VentralDC (60): linear fit = 1.00 x + 0.0 (747 voxels, peak = 98), gca=98.5
- gca peak = 0.13679 (96)
- mri peak = 0.06868 (98)
- Left_VentralDC (28): linear fit = 1.00 x + 0.0 (765 voxels, overlap=0.902)
- Left_VentralDC (28): linear fit = 1.00 x + 0.0 (765 voxels, peak = 96), gca=96.5
- gca peak = 0.35640 (14)
- uniform distribution in MR - rejecting arbitrary fit
- gca peak = 0.33827 ( 9)
- mri peak = 0.18723 ( 8)
- Fourth_Ventricle (15): linear fit = 0.68 x + 0.0 (232 voxels, overlap=0.870)
- Fourth_Ventricle (15): linear fit = 0.68 x + 0.0 (232 voxels, peak = 6), gca=6.1
- gca peak Unknown = 0.94427 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.27467 (31)
- gca peak Third_Ventricle = 0.35640 (14)
- gca peak CSF = 0.30128 (18)
- gca peak Left_Accumbens_area = 0.51409 (58)
- gca peak Left_undetermined = 1.00000 (35)
- gca peak Left_vessel = 0.44864 (61)
- gca peak Left_choroid_plexus = 0.09084 (48)
- gca peak Right_Inf_Lat_Vent = 0.30433 (27)
- gca peak Right_Accumbens_area = 0.38912 (65)
- gca peak Right_vessel = 0.58297 (60)
- gca peak Right_choroid_plexus = 0.10381 (48)
- gca peak Fifth_Ventricle = 0.45329 (19)
- gca peak WM_hypointensities = 0.16968 (85)
- gca peak non_WM_hypointensities = 0.11242 (55)
- gca peak Optic_Chiasm = 0.34840 (76)
- not using caudate to estimate GM means
- estimating mean gm scale to be 1.00 x + 0.0
- estimating mean wm scale to be 1.00 x + 0.0
- estimating mean csf scale to be 0.76 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
- 9927 gm and wm labels changed (%10 to gray, %90 to white out of all changed labels)
- 194 hippocampal voxels changed.
- 3 amygdala voxels changed.
- pass 1: 74185 changed. image ll: -2.146, PF=1.000
- pass 2: 13563 changed. image ll: -2.143, PF=1.000
- pass 3: 4833 changed.
- writing labeled volume to aseg.auto_noCCseg.mgz...
- auto-labeling took 19 minutes and 29 seconds.
- mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/cc_up.lta sub014
- 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/sub014/mri/transforms/cc_up.lta
- reading aseg from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/aseg.auto_noCCseg.mgz
- reading norm from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/norm.mgz
- 18340 voxels in left wm, 30462 in right wm, xrange [125, 133]
- searching rotation angles z=[-9 5], y=[-6 8]
-
searching scale 1 Z rot -9.4
searching scale 1 Z rot -9.1
searching scale 1 Z rot -8.9
searching scale 1 Z rot -8.6
searching scale 1 Z rot -8.4
searching scale 1 Z rot -8.1
searching scale 1 Z rot -7.9
searching scale 1 Z rot -7.6
searching scale 1 Z rot -7.4
searching scale 1 Z rot -7.1
searching scale 1 Z rot -6.9
searching scale 1 Z rot -6.6
searching scale 1 Z rot -6.4
searching scale 1 Z rot -6.1
searching scale 1 Z rot -5.9
searching scale 1 Z rot -5.6
searching scale 1 Z rot -5.4
searching scale 1 Z rot -5.1
searching scale 1 Z rot -4.9
searching scale 1 Z rot -4.6
searching scale 1 Z rot -4.4
searching scale 1 Z rot -4.1
searching scale 1 Z rot -3.9
searching scale 1 Z rot -3.6
searching scale 1 Z rot -3.4
searching scale 1 Z rot -3.1
searching scale 1 Z rot -2.9
searching scale 1 Z rot -2.6
searching scale 1 Z rot -2.4
searching scale 1 Z rot -2.1
searching scale 1 Z rot -1.9
searching scale 1 Z rot -1.6
searching scale 1 Z rot -1.4
searching scale 1 Z rot -1.1
searching scale 1 Z rot -0.9
searching scale 1 Z rot -0.6
searching scale 1 Z rot -0.4
searching scale 1 Z rot -0.1
searching scale 1 Z rot 0.1
searching scale 1 Z rot 0.4
searching scale 1 Z rot 0.6
searching scale 1 Z rot 0.9
searching scale 1 Z rot 1.1
searching scale 1 Z rot 1.4
searching scale 1 Z rot 1.6
searching scale 1 Z rot 1.9
searching scale 1 Z rot 2.1
searching scale 1 Z rot 2.4
searching scale 1 Z rot 2.6
searching scale 1 Z rot 2.9
searching scale 1 Z rot 3.1
searching scale 1 Z rot 3.4
searching scale 1 Z rot 3.6
searching scale 1 Z rot 3.9
searching scale 1 Z rot 4.1
searching scale 1 Z rot 4.4 global minimum found at slice 129.2, rotations (0.51, -2.38)
- final transformation (x=129.2, yr=0.514, zr=-2.377):
- 0.999 0.041 0.009 -5.552;
- -0.041 0.999 -0.000 49.472;
- -0.009 0.000 1.000 19.164;
- 0.000 0.000 0.000 1.000;
- updating x range to be [127, 131] in xformed coordinates
- best xformed slice 129
- cc center is found at 129 144 120
- eigenvectors:
- -0.001 0.001 1.000;
- -0.014 -1.000 0.001;
- 1.000 -0.014 0.001;
- writing aseg with callosum to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/aseg.auto.mgz...
- corpus callosum matter segmentation took 0.7 minutes
- #--------------------------------------
- #@# Merge ASeg Thu Aug 8 18:45:13 CEST 2013
- cp aseg.auto.mgz aseg.mgz
- #--------------------------------------------
- #@# Intensity Normalization2 Thu Aug 8 18:45:13 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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...
- 2360 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 29 (29)
- csf peak at 28, setting threshold to 46
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- ---------------------------------
- 3d normalization pass 2 of 2
- white matter peak found at 111
- white matter peak found at 110
- gm peak at 57 (57), valley at 25 (25)
- csf peak at 28, setting threshold to 47
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Done iterating ---------------------------------
- writing output to brain.mgz
- 3D bias adjustment took 4 minutes and 36 seconds.
- #--------------------------------------------
- #@# Mask BFS Thu Aug 8 18:49:52 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri
- mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
- threshold mask volume at 5
- DoAbs = 0
- Found 1312472 voxels in mask (pct= 7.82)
- Writing masked volume to brain.finalsurfs.mgz...done.
- #--------------------------------------------
- #@# WM Segmentation Thu Aug 8 18:49:55 CEST 2013
- mri_segment brain.mgz wm.seg.mgz
- doing initial intensity segmentation...
- using local statistics to label ambiguous voxels...
- computing class statistics for intensity windows...
- WM (107.0): 106.9 +- 5.2 [80.0 --> 125.0]
- GM (67.0) : 66.2 +- 9.8 [30.0 --> 96.0]
- setting bottom of white matter range to 76.0
- setting top of gray matter range to 85.8
- 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...
- 5810 sparsely connected voxels removed...
- thickening thin strands....
- 20 segments, 5323 filled
- 429 bright non-wm voxels segmented.
- 3261 diagonally connected voxels added...
- white matter segmentation took 1.7 minutes
- writing output to wm.seg.mgz...
- mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz
- preserving editing changes in input volume...
- auto filling took 0.72 minutes
- reading wm segmentation from wm.seg.mgz...
- 42 voxels added to wm to prevent paths from MTL structures to cortex
- 988 additional wm voxels added
- 0 additional wm voxels added
- SEG EDIT: 38813 voxels turned on, 31140 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+): 10 found - 10 modified | TOTAL: 10
- pass 2 (xy+): 0 found - 10 modified | TOTAL: 10
- pass 1 (xy-): 8 found - 8 modified | TOTAL: 18
- pass 2 (xy-): 0 found - 8 modified | TOTAL: 18
- pass 1 (yz+): 17 found - 17 modified | TOTAL: 35
- pass 2 (yz+): 0 found - 17 modified | TOTAL: 35
- pass 1 (yz-): 8 found - 8 modified | TOTAL: 43
- pass 2 (yz-): 0 found - 8 modified | TOTAL: 43
- pass 1 (xz+): 16 found - 16 modified | TOTAL: 59
- pass 2 (xz+): 0 found - 16 modified | TOTAL: 59
- pass 1 (xz-): 14 found - 14 modified | TOTAL: 73
- pass 2 (xz-): 0 found - 14 modified | TOTAL: 73
- Iteration Number : 1
- pass 1 (+++): 6 found - 6 modified | TOTAL: 6
- pass 2 (+++): 0 found - 6 modified | TOTAL: 6
- pass 1 (+++): 12 found - 12 modified | TOTAL: 18
- pass 2 (+++): 0 found - 12 modified | TOTAL: 18
- pass 1 (+++): 6 found - 6 modified | TOTAL: 24
- pass 2 (+++): 0 found - 6 modified | TOTAL: 24
- pass 1 (+++): 9 found - 9 modified | TOTAL: 33
- pass 2 (+++): 0 found - 9 modified | TOTAL: 33
- Iteration Number : 1
- pass 1 (++): 178 found - 178 modified | TOTAL: 178
- pass 2 (++): 0 found - 178 modified | TOTAL: 178
- pass 1 (+-): 180 found - 180 modified | TOTAL: 358
- pass 2 (+-): 0 found - 180 modified | TOTAL: 358
- pass 1 (--): 133 found - 133 modified | TOTAL: 491
- pass 2 (--): 0 found - 133 modified | TOTAL: 491
- pass 1 (-+): 186 found - 186 modified | TOTAL: 677
- pass 2 (-+): 0 found - 186 modified | TOTAL: 677
- Iteration Number : 2
- pass 1 (xy+): 3 found - 3 modified | TOTAL: 3
- pass 2 (xy+): 0 found - 3 modified | TOTAL: 3
- pass 1 (xy-): 4 found - 4 modified | TOTAL: 7
- pass 2 (xy-): 0 found - 4 modified | TOTAL: 7
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 7
- pass 1 (yz-): 3 found - 3 modified | TOTAL: 10
- pass 2 (yz-): 0 found - 3 modified | TOTAL: 10
- pass 1 (xz+): 1 found - 1 modified | TOTAL: 11
- pass 2 (xz+): 0 found - 1 modified | TOTAL: 11
- pass 1 (xz-): 1 found - 1 modified | TOTAL: 12
- pass 2 (xz-): 0 found - 1 modified | TOTAL: 12
- Iteration Number : 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (++): 2 found - 2 modified | TOTAL: 2
- pass 2 (++): 0 found - 2 modified | TOTAL: 2
- pass 1 (+-): 0 found - 0 modified | TOTAL: 2
- pass 1 (--): 0 found - 0 modified | TOTAL: 2
- pass 1 (-+): 0 found - 0 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 = 797 (out of 433992: 0.183644)
- binarizing input wm segmentation...
- Ambiguous edge configurations...
- mri_pretess done
- #--------------------------------------------
- #@# Fill Thu Aug 8 18:52:25 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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
- 1.149 0.026 0.012 -26.163;
- -0.054 1.169 0.187 -10.321;
- -0.005 -0.159 1.083 -4.156;
- 0.000 0.000 0.000 1.000;
- voxel to talairach voxel transform
- 1.149 0.026 0.012 -26.163;
- -0.054 1.169 0.187 -10.321;
- -0.005 -0.159 1.083 -4.156;
- 0.000 0.000 0.000 1.000;
- reading segmented volume aseg.auto_noCCseg.mgz...
- Looking for area (min, max) = (350, 1400)
- area[0] = 1225 (min = 350, max = 1400), aspect = 0.43 (min = 0.10, max = 0.75)
- no need to search
- using seed (126, 111, 89), TAL = (2.0, -39.0, 17.0)
- talairach voxel to voxel transform
- 0.869 -0.020 -0.006 22.509;
- 0.039 0.835 -0.144 9.030;
- 0.010 0.122 0.902 5.265;
- 0.000 0.000 0.000 1.000;
- segmentation indicates cc at (126, 111, 89) --> (2.0, -39.0, 17.0)
- done.
- writing output to filled.mgz...
- filling took 1.0 minutes
- talairach cc position changed to (2.00, -39.00, 17.00)
- Erasing brainstem...done.
- seed_search_size = 9, min_neighbors = 5
- search rh wm seed point around talairach space:(20.00, -39.00, 17.00) SRC: (113.62, 93.06, 100.16)
- search lh wm seed point around talairach space (-16.00, -39.00, 17.00), SRC: (144.91, 94.45, 100.51)
- 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 18:53:24 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/scripts
- mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz
- Iteration Number : 1
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 4 found - 4 modified | TOTAL: 4
- pass 2 (xy-): 0 found - 4 modified | TOTAL: 4
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 4
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 4
- pass 1 (xz+): 3 found - 3 modified | TOTAL: 7
- pass 2 (xz+): 0 found - 3 modified | TOTAL: 7
- pass 1 (xz-): 3 found - 3 modified | TOTAL: 10
- pass 2 (xz-): 0 found - 3 modified | TOTAL: 10
- 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 (++): 2 found - 2 modified | TOTAL: 2
- pass 2 (++): 0 found - 2 modified | TOTAL: 2
- pass 1 (+-): 2 found - 2 modified | TOTAL: 4
- pass 2 (+-): 0 found - 2 modified | TOTAL: 4
- pass 1 (--): 0 found - 0 modified | TOTAL: 4
- pass 1 (-+): 0 found - 0 modified | TOTAL: 4
- Iteration Number : 2
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Total Number of Modified Voxels = 14 (out of 208028: 0.006730)
- Ambiguous edge configurations...
- mri_pretess done
- mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix
- $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- slice 50: 2369 vertices, 2531 faces
- slice 60: 8482 vertices, 8724 faces
- slice 70: 16932 vertices, 17295 faces
- slice 80: 26715 vertices, 27039 faces
- slice 90: 36646 vertices, 36969 faces
- slice 100: 46611 vertices, 46994 faces
- slice 110: 57937 vertices, 58319 faces
- slice 120: 68286 vertices, 68649 faces
- slice 130: 78703 vertices, 79052 faces
- slice 140: 88758 vertices, 89144 faces
- slice 150: 97409 vertices, 97707 faces
- slice 160: 104924 vertices, 105192 faces
- slice 170: 111621 vertices, 111843 faces
- slice 180: 117586 vertices, 117803 faces
- slice 190: 122339 vertices, 122490 faces
- slice 200: 123866 vertices, 123882 faces
- slice 210: 123866 vertices, 123882 faces
- slice 220: 123866 vertices, 123882 faces
- slice 230: 123866 vertices, 123882 faces
- slice 240: 123866 vertices, 123882 faces
- slice 250: 123866 vertices, 123882 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...
- 123866 voxel in cpt #1: X=-16 [v=123866,e=371646,f=247764] located at (-26.791243, -13.523129, 35.785511)
- For the whole surface: X=-16 [v=123866,e=371646,f=247764]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Smooth1 lh Thu Aug 8 18:53:33 CEST 2013
- mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 18:53:37 CEST 2013
- mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/scripts
- avg radius = 44.4 mm, total surface area = 64323 mm^2
- writing inflated surface to ../surf/lh.inflated.nofix
- inflation took 0.6 minutes
- Not saving sulc
-
step 000: RMS=0.101 (target=0.015)
step 005: RMS=0.073 (target=0.015)
step 010: RMS=0.054 (target=0.015)
step 015: RMS=0.044 (target=0.015)
step 020: RMS=0.036 (target=0.015)
step 025: RMS=0.031 (target=0.015)
step 030: RMS=0.027 (target=0.015)
step 035: RMS=0.024 (target=0.015)
step 040: RMS=0.022 (target=0.015)
step 045: RMS=0.021 (target=0.015)
step 050: RMS=0.020 (target=0.015)
step 055: RMS=0.020 (target=0.015)
step 060: RMS=0.019 (target=0.015)
- inflation complete.
- Not saving sulc
- #--------------------------------------------
- #@# QSphere lh Thu Aug 8 18:54:16 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/scripts
- mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix
- doing quick spherical unfolding.
- setting seed for random number genererator to 1234
- $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading original vertex positions...
- unfolding cortex into spherical form...
- surface projected - minimizing metric distortion...
- vertex spacing 1.03 +- 0.60 (0.00-->6.93) (max @ vno 90411 --> 91375)
- face area 0.03 +- 0.03 (-0.17-->0.69)
- scaling brain by 0.322...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=176.932, avgs=0
- 005/300: dt: 0.9000, rms radial error=176.673, avgs=0
- 010/300: dt: 0.9000, rms radial error=176.118, avgs=0
- 015/300: dt: 0.9000, rms radial error=175.390, avgs=0
- 020/300: dt: 0.9000, rms radial error=174.561, avgs=0
- 025/300: dt: 0.9000, rms radial error=173.674, avgs=0
- 030/300: dt: 0.9000, rms radial error=172.755, avgs=0
- 035/300: dt: 0.9000, rms radial error=171.818, avgs=0
- 040/300: dt: 0.9000, rms radial error=170.875, avgs=0
- 045/300: dt: 0.9000, rms radial error=169.928, avgs=0
- 050/300: dt: 0.9000, rms radial error=168.983, avgs=0
- 055/300: dt: 0.9000, rms radial error=168.040, avgs=0
- 060/300: dt: 0.9000, rms radial error=167.101, avgs=0
- 065/300: dt: 0.9000, rms radial error=166.165, avgs=0
- 070/300: dt: 0.9000, rms radial error=165.235, avgs=0
- 075/300: dt: 0.9000, rms radial error=164.309, avgs=0
- 080/300: dt: 0.9000, rms radial error=163.389, avgs=0
- 085/300: dt: 0.9000, rms radial error=162.473, avgs=0
- 090/300: dt: 0.9000, rms radial error=161.562, avgs=0
- 095/300: dt: 0.9000, rms radial error=160.656, avgs=0
- 100/300: dt: 0.9000, rms radial error=159.755, avgs=0
- 105/300: dt: 0.9000, rms radial error=158.858, avgs=0
- 110/300: dt: 0.9000, rms radial error=157.967, avgs=0
- 115/300: dt: 0.9000, rms radial error=157.080, avgs=0
- 120/300: dt: 0.9000, rms radial error=156.198, avgs=0
- 125/300: dt: 0.9000, rms radial error=155.321, avgs=0
- 130/300: dt: 0.9000, rms radial error=154.448, avgs=0
- 135/300: dt: 0.9000, rms radial error=153.580, avgs=0
- 140/300: dt: 0.9000, rms radial error=152.717, avgs=0
- 145/300: dt: 0.9000, rms radial error=151.859, avgs=0
- 150/300: dt: 0.9000, rms radial error=151.005, avgs=0
- 155/300: dt: 0.9000, rms radial error=150.156, avgs=0
- 160/300: dt: 0.9000, rms radial error=149.311, avgs=0
- 165/300: dt: 0.9000, rms radial error=148.472, avgs=0
- 170/300: dt: 0.9000, rms radial error=147.636, avgs=0
- 175/300: dt: 0.9000, rms radial error=146.805, avgs=0
- 180/300: dt: 0.9000, rms radial error=145.979, avgs=0
- 185/300: dt: 0.9000, rms radial error=145.158, avgs=0
- 190/300: dt: 0.9000, rms radial error=144.341, avgs=0
- 195/300: dt: 0.9000, rms radial error=143.528, avgs=0
- 200/300: dt: 0.9000, rms radial error=142.721, avgs=0
- 205/300: dt: 0.9000, rms radial error=141.917, avgs=0
- 210/300: dt: 0.9000, rms radial error=141.118, avgs=0
- 215/300: dt: 0.9000, rms radial error=140.323, avgs=0
- 220/300: dt: 0.9000, rms radial error=139.533, avgs=0
- 225/300: dt: 0.9000, rms radial error=138.748, avgs=0
- 230/300: dt: 0.9000, rms radial error=137.966, avgs=0
- 235/300: dt: 0.9000, rms radial error=137.189, avgs=0
- 240/300: dt: 0.9000, rms radial error=136.417, avgs=0
- 245/300: dt: 0.9000, rms radial error=135.648, avgs=0
- 250/300: dt: 0.9000, rms radial error=134.884, avgs=0
- 255/300: dt: 0.9000, rms radial error=134.124, avgs=0
- 260/300: dt: 0.9000, rms radial error=133.369, avgs=0
- 265/300: dt: 0.9000, rms radial error=132.618, avgs=0
- 270/300: dt: 0.9000, rms radial error=131.870, avgs=0
- 275/300: dt: 0.9000, rms radial error=131.127, avgs=0
- 280/300: dt: 0.9000, rms radial error=130.388, avgs=0
- 285/300: dt: 0.9000, rms radial error=129.654, avgs=0
- 290/300: dt: 0.9000, rms radial error=128.923, avgs=0
- 295/300: dt: 0.9000, rms radial error=128.196, avgs=0
- 300/300: dt: 0.9000, rms radial error=127.474, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 14359.37
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00017
- epoch 2 (K=40.0), pass 1, starting sse = 2352.35
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00012
- epoch 3 (K=160.0), pass 1, starting sse = 239.14
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.09/11 = 0.00847
- epoch 4 (K=640.0), pass 1, starting sse = 12.72
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.10/13 = 0.00775
- 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 18:59:09 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/sub014/scripts
- mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub014 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=-16 (nv=123866, nf=247764, ne=371646, g=9)
- using quasi-homeomorphic spherical map to tessellate cortical surface...
- Correction of the Topology
- Finding true center and radius of Spherical Surface...done
- Surface centered at (0,0,0) with radius 100.0 in 8 iterations
- marking ambiguous vertices...
- 1328 ambiguous faces found in tessellation
- segmenting defects...
- 18 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- -merging segment 7 into 4
- 17 defects to be corrected
- 0 vertices coincident
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/lh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -9.8413 (-4.9207)
- -vertex loglikelihood: -6.7568 (-3.3784)
- -normal dot loglikelihood: -3.6710 (-3.6710)
- -quad curv loglikelihood: -6.4456 (-3.2228)
- Total Loglikelihood : -26.7147
- CORRECTING DEFECT 0 (vertices=60, convex hull=93)
- After retessellation of defect 0, euler #=-14 (123057,368821,245750) : difference with theory (-14) = 0
- CORRECTING DEFECT 1 (vertices=98, convex hull=97)
- After retessellation of defect 1, euler #=-13 (123088,368957,245856) : difference with theory (-13) = 0
- CORRECTING DEFECT 2 (vertices=25, convex hull=39)
- After retessellation of defect 2, euler #=-12 (123098,368999,245889) : difference with theory (-12) = 0
- CORRECTING DEFECT 3 (vertices=5, convex hull=24)
- After retessellation of defect 3, euler #=-11 (123098,369007,245898) : difference with theory (-11) = 0
- CORRECTING DEFECT 4 (vertices=133, convex hull=151)
- After retessellation of defect 4, euler #=-9 (123164,369273,246100) : difference with theory (-10) = -1
- CORRECTING DEFECT 5 (vertices=35, convex hull=67)
- After retessellation of defect 5, euler #=-8 (123180,369349,246161) : difference with theory (-9) = -1
- CORRECTING DEFECT 6 (vertices=13, convex hull=22)
- After retessellation of defect 6, euler #=-7 (123184,369368,246177) : difference with theory (-8) = -1
- CORRECTING DEFECT 7 (vertices=25, convex hull=49)
- After retessellation of defect 7, euler #=-6 (123200,369435,246229) : difference with theory (-7) = -1
- CORRECTING DEFECT 8 (vertices=6, convex hull=14)
- After retessellation of defect 8, euler #=-5 (123201,369441,246235) : difference with theory (-6) = -1
- CORRECTING DEFECT 9 (vertices=19, convex hull=54)
- After retessellation of defect 9, euler #=-4 (123211,369492,246277) : difference with theory (-5) = -1
- CORRECTING DEFECT 10 (vertices=25, convex hull=57)
- After retessellation of defect 10, euler #=-3 (123225,369557,246329) : difference with theory (-4) = -1
- CORRECTING DEFECT 11 (vertices=36, convex hull=57)
- After retessellation of defect 11, euler #=-2 (123242,369631,246387) : difference with theory (-3) = -1
- CORRECTING DEFECT 12 (vertices=34, convex hull=34)
- After retessellation of defect 12, euler #=-1 (123248,369663,246414) : difference with theory (-2) = -1
- CORRECTING DEFECT 13 (vertices=207, convex hull=45)
- After retessellation of defect 13, euler #=0 (123262,369727,246465) : difference with theory (-1) = -1
- CORRECTING DEFECT 14 (vertices=14, convex hull=24)
- After retessellation of defect 14, euler #=0 (123265,369747,246482) : difference with theory (0) = 0
- CORRECTING DEFECT 15 (vertices=61, convex hull=34)
- After retessellation of defect 15, euler #=1 (123274,369786,246513) : difference with theory (1) = 0
- CORRECTING DEFECT 16 (vertices=37, convex hull=71)
- After retessellation of defect 16, euler #=2 (123287,369855,246570) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.88 +- 0.21 (0.10-->6.51) (max @ vno 19436 --> 25232)
- 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 (0.10-->6.51) (max @ vno 19436 --> 25232)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 51 mutations (31.5%), 111 crossovers (68.5%), 20 vertices were eliminated
- building final representation...
- 579 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=123287, nf=246570, ne=369855, g=0)
- writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/lh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 8.6 minutes
- 0 defective edges
- removing intersecting faces
- 000: 98 intersecting
- 001: 4 intersecting
- expanding nbhd size to 2
- 002: 5 intersecting
- 003: 2 intersecting
- mris_euler_number ../surf/lh.orig
- euler # = v-e+f = 2g-2: 123287 - 369855 + 246570 = 2 --> 0 holes
- F =2V-4: 246570 = 246574-4 (0)
- 2E=3F: 739710 = 739710 (0)
- total defect index = 0
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/scripts
- mris_remove_intersection ../surf/lh.orig ../surf/lh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 26 intersecting
- writing corrected surface to ../surf/lh.orig
- rm ../surf/lh.inflated
- #--------------------------------------------
- #@# Make White Surf lh Thu Aug 8 19:07:48 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/scripts
- mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub014 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/sub014/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/wm.mgz...
- 15343 bright wm thresholded.
- 473 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/lh.orig...
- computing class statistics...
- border white: 218506 voxels (1.30%)
- border gray 254901 voxels (1.52%)
- WM (92.0): 93.3 +- 10.4 [70.0 --> 110.0]
- GM (75.0) : 73.0 +- 13.3 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 46.7 (was 70)
- setting MAX_BORDER_WHITE to 116.4 (was 105)
- setting MIN_BORDER_WHITE to 60.0 (was 85)
- setting MAX_CSF to 33.5 (was 40)
- setting MAX_GRAY to 95.6 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 53.4 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 20.2 (was 40)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.81 +- 0.22 (0.03-->2.73) (max @ vno 51677 --> 123119)
- face area 0.27 +- 0.12 (0.00-->1.99)
- mean absolute distance = 0.65 +- 0.80
- 3025 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=106, GM=60
- mean inside = 93.0, mean outside = 68.0
- smoothing surface for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- mean border=72.6, 42 (42) missing vertices, mean dist 0.3 [0.5 (%32.5)->0.7 (%67.5))]
- %64 local maxima, %31 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 (0.12-->3.50) (max @ vno 50539 --> 52810)
- face area 0.27 +- 0.13 (0.00-->1.58)
- mean absolute distance = 0.29 +- 0.47
- 2014 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=6636346.0, rms=13.61
- 001: dt: 0.5000, sse=6779423.0, rms=9.808 (0.000%)
- 002: dt: 0.5000, sse=7040670.0, rms=7.666 (0.000%)
- 003: dt: 0.5000, sse=7140933.0, rms=6.325 (0.000%)
- 004: dt: 0.5000, sse=7426491.5, rms=5.528 (0.000%)
- 005: dt: 0.5000, sse=7447426.0, rms=5.090 (0.000%)
- 006: dt: 0.5000, sse=7617420.0, rms=4.856 (0.000%)
- 007: dt: 0.5000, sse=7536988.0, rms=4.730 (0.000%)
- 008: dt: 0.5000, sse=7602783.5, rms=4.638 (0.000%)
- rms = 4.59, time step reduction 1 of 3 to 0.250...
- 009: dt: 0.5000, sse=7513749.0, rms=4.592 (0.000%)
- 010: dt: 0.2500, sse=4925945.5, rms=3.238 (0.000%)
- 011: dt: 0.2500, sse=4523146.5, rms=2.791 (0.000%)
- 012: dt: 0.2500, sse=4269880.0, rms=2.692 (0.000%)
- 013: dt: 0.2500, sse=4201672.0, rms=2.604 (0.000%)
- rms = 2.57, time step reduction 2 of 3 to 0.125...
- 014: dt: 0.2500, sse=4111730.5, rms=2.572 (0.000%)
- 015: dt: 0.1250, sse=3843435.0, rms=2.249 (0.000%)
- rms = 2.20, time step reduction 3 of 3 to 0.062...
- 016: dt: 0.1250, sse=3792642.2, rms=2.204 (0.000%)
- positioning took 1.8 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 4 vertex label from ripped group
- mean border=76.8, 63 (9) missing vertices, mean dist -0.2 [0.3 (%76.4)->0.2 (%23.6))]
- %78 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 (0.07-->3.53) (max @ vno 51676 --> 123131)
- face area 0.35 +- 0.16 (0.00-->2.13)
- mean absolute distance = 0.21 +- 0.28
- 2029 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4569868.0, rms=5.76
- 017: dt: 0.5000, sse=4912598.0, rms=4.219 (0.000%)
- rms = 4.63, time step reduction 1 of 3 to 0.250...
- 018: dt: 0.2500, sse=4432057.5, rms=2.980 (0.000%)
- 019: dt: 0.2500, sse=4254629.0, rms=2.456 (0.000%)
- 020: dt: 0.2500, sse=4189434.2, rms=2.065 (0.000%)
- rms = 2.06, time step reduction 2 of 3 to 0.125...
- 021: dt: 0.2500, sse=4175122.0, rms=2.057 (0.000%)
- 022: dt: 0.1250, sse=4011607.2, rms=1.776 (0.000%)
- rms = 1.74, time step reduction 3 of 3 to 0.062...
- 023: dt: 0.1250, sse=3963969.0, rms=1.737 (0.000%)
- positioning took 0.8 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 1 vertex label from ripped group
- removing 1 vertex label from ripped group
- removing 3 vertex label from ripped group
- mean border=80.4, 32 (0) missing vertices, mean dist -0.1 [0.2 (%77.9)->0.2 (%22.1))]
- %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.25 (0.11-->3.69) (max @ vno 51678 --> 51677)
- face area 0.34 +- 0.16 (0.00-->2.21)
- mean absolute distance = 0.15 +- 0.23
- 2120 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4358882.0, rms=4.57
- 024: dt: 0.5000, sse=4647241.0, rms=4.321 (0.000%)
- rms = 4.44, time step reduction 1 of 3 to 0.250...
- 025: dt: 0.2500, sse=4210103.5, rms=2.729 (0.000%)
- 026: dt: 0.2500, sse=4073894.8, rms=2.280 (0.000%)
- 027: dt: 0.2500, sse=4148962.5, rms=1.909 (0.000%)
- rms = 1.97, time step reduction 2 of 3 to 0.125...
- 028: dt: 0.1250, sse=4083041.5, rms=1.748 (0.000%)
- 029: dt: 0.1250, sse=3992689.5, rms=1.519 (0.000%)
- rms = 1.49, time step reduction 3 of 3 to 0.062...
- 030: dt: 0.1250, sse=3955613.8, rms=1.493 (0.000%)
- positioning took 0.9 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 1 vertex label from ripped group
- removing 4 vertex label from ripped group
- mean border=81.6, 33 (0) missing vertices, mean dist -0.0 [0.2 (%59.5)->0.2 (%40.5))]
- %90 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- writing white matter surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/lh.white...
- writing smoothed curvature to lh.curv
- 000: dt: 0.0000, sse=3981738.0, rms=1.92
- rms = 3.00, time step reduction 1 of 3 to 0.250...
- 031: dt: 0.2500, sse=4058089.8, rms=1.234 (0.000%)
- 032: dt: 0.2500, sse=4204565.5, rms=1.109 (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...
- 033: dt: 0.1250, sse=4207593.5, rms=1.095 (0.000%)
- positioning took 0.5 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 3 vertex label from ripped group
- generating cortex label...
- 9 non-cortical segments detected
- only using segment with 1918 vertices
- erasing segment 1 (vno[0] = 70682)
- erasing segment 2 (vno[0] = 76976)
- erasing segment 3 (vno[0] = 88797)
- erasing segment 4 (vno[0] = 88836)
- erasing segment 5 (vno[0] = 89708)
- erasing segment 6 (vno[0] = 93084)
- erasing segment 7 (vno[0] = 93955)
- erasing segment 8 (vno[0] = 97128)
- writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/label/lh.cortex.label...
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/lh.curv
- writing smoothed area to lh.area
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/lh.area
- vertex spacing 0.90 +- 0.25 (0.05-->3.75) (max @ vno 51676 --> 123131)
- face area 0.33 +- 0.16 (0.00-->2.25)
- refinement took 6.0 minutes
- #--------------------------------------------
- #@# Smooth2 lh Thu Aug 8 19:13:48 CEST 2013
- mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 19:13:53 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/scripts
- mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated
- avg radius = 44.6 mm, total surface area = 74901 mm^2
- writing inflated surface to ../surf/lh.inflated
- writing sulcal depths to ../surf/lh.sulc
-
step 000: RMS=0.119 (target=0.015)
step 005: RMS=0.081 (target=0.015)
step 010: RMS=0.059 (target=0.015)
step 015: RMS=0.048 (target=0.015)
step 020: RMS=0.039 (target=0.015)
step 025: RMS=0.032 (target=0.015)
step 030: RMS=0.026 (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/lh.inflated
- normalizing curvature values.
- averaging curvature patterns 5 times.
- sampling 10 neighbors out to a distance of 10 mm
- 132 vertices thresholded to be in k1 ~ [-0.23 0.33], k2 ~ [-0.10 0.08]
- total integrated curvature = 0.615*4pi (7.724) --> 0 handles
- ICI = 1.6, FI = 10.5, variation=178.516
- 99 vertices thresholded to be in [-0.01 0.02]
- writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level
- curvature mean = 0.000, std = 0.001
- 122 vertices thresholded to be in [-0.15 0.16]
- done.
- writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.018, std = 0.024
- done.
- #-----------------------------------------
- #@# Curvature Stats lh Thu Aug 8 19:16:02 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub014 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 [ sub014/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 [ 228 ]
- Gb_filter = 0
- WARN: S lookup min: -0.288928
- WARN: S explicit min: 0.000000 vertex = 2221
- WARN: C lookup max: 130.038651
- WARN: C explicit max: 128.068314 vertex = 88696
- #--------------------------------------------
- #@# Sphere lh Thu Aug 8 19:16:06 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 0.298...
- 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 %19.25
- pass 1: epoch 2 of 3 starting distance error %19.24
- unfolding complete - removing small folds...
- starting distance error %19.22
- removing remaining folds...
- final distance error %19.24
- MRISunfold() return, current seed 1234
- writing spherical brain to ../surf/lh.sphere
- spherical transformation took 0.90 hours
- #--------------------------------------------
- #@# Surf Reg lh Thu Aug 8 20:10:06 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 = 0.566
- curvature mean = 0.032, std = 0.939
- curvature mean = 0.023, std = 0.861
- Starting MRISrigidBodyAlignGlobal()
- d=64.00 min @ (0.00, -16.00, 0.00) sse = 224750.2, tmin=1.1705
- d=32.00 min @ (0.00, 8.00, 0.00) sse = 224687.2, tmin=2.3689
- d=16.00 min @ (0.00, -4.00, 0.00) sse = 195730.5, tmin=3.5724
- d=8.00 min @ (2.00, 0.00, 2.00) sse = 191249.0, tmin=4.7625
- d=4.00 min @ (-1.00, 0.00, 0.00) sse = 189699.8, tmin=5.9573
- d=1.00 min @ (0.00, 0.25, -0.25) sse = 189603.0, tmin=8.3897
- d=0.50 min @ (0.00, 0.00, 0.12) sse = 189584.0, tmin=9.5996
- 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 9.60 min
- curvature mean = 0.019, std = 0.960
- curvature mean = 0.012, std = 0.940
- curvature mean = 0.018, std = 0.973
- curvature mean = 0.006, std = 0.972
- curvature mean = 0.017, std = 0.976
- curvature mean = 0.002, std = 0.987
- 2 Reading smoothwm
- curvature mean = -0.023, std = 0.316
- curvature mean = 0.003, std = 0.067
- curvature mean = 0.072, std = 0.324
- curvature mean = 0.003, std = 0.079
- curvature mean = 0.030, std = 0.514
- curvature mean = 0.003, std = 0.086
- curvature mean = 0.018, std = 0.648
- curvature mean = 0.004, std = 0.089
- curvature mean = 0.006, std = 0.760
- MRISregister() return, current seed 0
- writing registered surface to ../surf/lh.sphere.reg...
- expanding nbhd size to 1
- #--------------------------------------------
- #@# Jacobian white lh Thu Aug 8 20:38:31 CEST 2013
- mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white
- reading surface from ../surf/lh.white...
- writing curvature file ../surf/lh.jacobian_white
- #--------------------------------------------
- #@# AvgCurv lh Thu Aug 8 20:38:34 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/scripts
- mrisp_paint -a 5 /opt/freesurfer/5.3.0/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv
- averaging curvature patterns 5 times...
- reading surface from ../surf/lh.sphere.reg...
- reading template parameterization from /opt/freesurfer/5.3.0/average/lh.average.curvature.filled.buckner40.tif...
- writing curvature file to ../surf/lh.avg_curv...
- #-----------------------------------------
- #@# Cortical Parc lh Thu Aug 8 20:38:36 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub014 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...
- 994 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2883 changed, 123287 examined...
- 001: 648 changed, 12292 examined...
- 002: 144 changed, 3578 examined...
- 003: 58 changed, 870 examined...
- 004: 24 changed, 345 examined...
- 005: 4 changed, 141 examined...
- 006: 0 changed, 25 examined...
- 221 labels changed using aseg
- 000: 108 total segments, 65 labels (206 vertices) changed
- 001: 43 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 73 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 984 vertices marked for relabeling...
- 984 labels changed in reclassification.
- writing output to ../label/lh.aparc.annot...
- classification took 0 minutes and 58 seconds.
- #--------------------------------------------
- #@# Make Pial Surf lh Thu Aug 8 20:39:34 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/scripts
- mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub014 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/sub014/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/wm.mgz...
- 15343 bright wm thresholded.
- 473 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/lh.orig...
- computing class statistics...
- border white: 218506 voxels (1.30%)
- border gray 254901 voxels (1.52%)
- WM (92.0): 93.3 +- 10.4 [70.0 --> 110.0]
- GM (75.0) : 73.0 +- 13.3 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 46.7 (was 70)
- setting MAX_BORDER_WHITE to 116.4 (was 105)
- setting MIN_BORDER_WHITE to 60.0 (was 85)
- setting MAX_CSF to 33.5 (was 40)
- setting MAX_GRAY to 95.6 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 53.4 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 20.2 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=106, GM=60
- mean inside = 93.0, mean outside = 68.0
- smoothing surface for 5 iterations...
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.81 +- 0.22 (0.03-->2.73) (max @ vno 51677 --> 123119)
- face area 0.27 +- 0.12 (0.00-->1.99)
- mean absolute distance = 0.66 +- 0.81
- 2506 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 69 points - only 0.00% unknown
- deleting segment 2 with 822 points - only 0.00% unknown
- deleting segment 3 with 11 points - only 0.00% unknown
- deleting segment 4 with 6 points - only 0.00% unknown
- mean border=72.6, 42 (42) missing vertices, mean dist 0.3 [0.5 (%32.6)->0.7 (%67.4))]
- %64 local maxima, %31 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 (0.12-->3.50) (max @ vno 50539 --> 52810)
- face area 0.27 +- 0.13 (0.00-->1.57)
- mean absolute distance = 0.29 +- 0.47
- 2061 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=6662300.0, rms=13.58
- 001: dt: 0.5000, sse=6822475.0, rms=9.787 (0.000%)
- 002: dt: 0.5000, sse=7084183.0, rms=7.650 (0.000%)
- 003: dt: 0.5000, sse=7194250.5, rms=6.312 (0.000%)
- 004: dt: 0.5000, sse=7476645.5, rms=5.517 (0.000%)
- 005: dt: 0.5000, sse=7501845.5, rms=5.081 (0.000%)
- 006: dt: 0.5000, sse=7671475.0, rms=4.848 (0.000%)
- 007: dt: 0.5000, sse=7592306.5, rms=4.723 (0.000%)
- 008: dt: 0.5000, sse=7660467.0, rms=4.630 (0.000%)
- rms = 4.59, time step reduction 1 of 3 to 0.250...
- 009: dt: 0.5000, sse=7572285.0, rms=4.586 (0.000%)
- 010: dt: 0.2500, sse=4962039.0, rms=3.233 (0.000%)
- 011: dt: 0.2500, sse=4557340.0, rms=2.787 (0.000%)
- 012: dt: 0.2500, sse=4301658.5, rms=2.688 (0.000%)
- 013: dt: 0.2500, sse=4232614.5, rms=2.600 (0.000%)
- rms = 2.57, time step reduction 2 of 3 to 0.125...
- 014: dt: 0.2500, sse=4141787.2, rms=2.569 (0.000%)
- 015: dt: 0.1250, sse=3873802.0, rms=2.248 (0.000%)
- rms = 2.20, time step reduction 3 of 3 to 0.062...
- 016: dt: 0.1250, sse=3823957.8, rms=2.203 (0.000%)
- positioning took 1.9 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 78 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 4 with 661 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 8 with 3 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 9 with 2 points - only 0.00% unknown
- deleting segment 11 with 6 points - only 0.00% unknown
- deleting segment 12 with 5 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 13 with 4 points - only 0.00% unknown
- mean border=76.8, 64 (9) missing vertices, mean dist -0.2 [0.3 (%76.3)->0.2 (%23.7))]
- %79 local maxima, %16 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.90 +- 0.25 (0.07-->3.53) (max @ vno 51676 --> 123131)
- face area 0.35 +- 0.16 (0.00-->2.13)
- mean absolute distance = 0.21 +- 0.29
- 2081 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4604919.5, rms=5.75
- 017: dt: 0.5000, sse=4953723.5, rms=4.211 (0.000%)
- rms = 4.62, time step reduction 1 of 3 to 0.250...
- 018: dt: 0.2500, sse=4469111.5, rms=2.975 (0.000%)
- 019: dt: 0.2500, sse=4291499.5, rms=2.452 (0.000%)
- 020: dt: 0.2500, sse=4225615.0, rms=2.063 (0.000%)
- rms = 2.05, time step reduction 2 of 3 to 0.125...
- 021: dt: 0.2500, sse=4211784.0, rms=2.053 (0.000%)
- 022: dt: 0.1250, sse=4047053.5, rms=1.775 (0.000%)
- rms = 1.74, time step reduction 3 of 3 to 0.062...
- 023: dt: 0.1250, sse=3998996.2, rms=1.737 (0.000%)
- positioning took 0.9 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 79 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 3 with 697 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 4 with 2 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- 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 7 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 10 with 1 points - only 0.00% unknown
- deleting segment 11 with 5 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 12 with 3 points - only 0.00% unknown
- mean border=80.4, 32 (0) missing vertices, mean dist -0.1 [0.2 (%77.7)->0.2 (%22.3))]
- %89 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.25 (0.11-->3.69) (max @ vno 51678 --> 51677)
- face area 0.34 +- 0.16 (0.00-->2.21)
- mean absolute distance = 0.15 +- 0.23
- 2195 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4396728.0, rms=4.56
- 024: dt: 0.5000, sse=4685896.0, rms=4.310 (0.000%)
- rms = 4.43, time step reduction 1 of 3 to 0.250...
- 025: dt: 0.2500, sse=4247462.0, rms=2.723 (0.000%)
- 026: dt: 0.2500, sse=4110278.2, rms=2.276 (0.000%)
- 027: dt: 0.2500, sse=4184906.8, rms=1.908 (0.000%)
- rms = 1.97, time step reduction 2 of 3 to 0.125...
- 028: dt: 0.1250, sse=4118771.8, rms=1.747 (0.000%)
- 029: dt: 0.1250, sse=4028150.0, rms=1.520 (0.000%)
- rms = 1.49, time step reduction 3 of 3 to 0.062...
- 030: dt: 0.1250, sse=3990906.5, rms=1.494 (0.000%)
- positioning took 0.9 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 85 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 2 with 707 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- removing 3 vertex label from ripped group
- deleting segment 4 with 3 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 5 with 2 points - only 0.00% unknown
- deleting segment 6 with 7 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 7 with 1 points - only 0.00% unknown
- deleting segment 8 with 5 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 9 with 4 points - only 0.00% unknown
- mean border=81.5, 33 (0) missing vertices, mean dist -0.0 [0.2 (%59.5)->0.2 (%40.5))]
- %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=4017185.2, rms=1.92
- rms = 2.99, time step reduction 1 of 3 to 0.250...
- 031: dt: 0.2500, sse=4094921.2, rms=1.235 (0.000%)
- 032: dt: 0.2500, sse=4244434.0, rms=1.110 (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...
- 033: dt: 0.1250, sse=4247241.0, rms=1.097 (0.000%)
- positioning took 0.5 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
- smoothing surface for 5 iterations...
- mean border=49.2, 30 (30) missing vertices, mean dist 1.7 [0.4 (%0.0)->2.2 (%100.0))]
- %18 local maxima, %57 large gradients and %20 min vals, 1449 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=26218740.0, rms=31.68
- 001: dt: 0.5000, sse=18673266.0, rms=26.109 (0.000%)
- 002: dt: 0.5000, sse=13531623.0, rms=21.525 (0.000%)
- 003: dt: 0.5000, sse=10206217.0, rms=17.853 (0.000%)
- 004: dt: 0.5000, sse=8318194.0, rms=14.952 (0.000%)
- 005: dt: 0.5000, sse=7219393.5, rms=12.691 (0.000%)
- 006: dt: 0.5000, sse=6576040.5, rms=10.974 (0.000%)
- 007: dt: 0.5000, sse=6154145.0, rms=9.516 (0.000%)
- 008: dt: 0.5000, sse=5885543.5, rms=8.211 (0.000%)
- 009: dt: 0.5000, sse=5733540.5, rms=7.034 (0.000%)
- 010: dt: 0.5000, sse=5732020.5, rms=6.091 (0.000%)
- 011: dt: 0.5000, sse=5828343.0, rms=5.404 (0.000%)
- 012: dt: 0.5000, sse=5889546.5, rms=4.945 (0.000%)
- 013: dt: 0.5000, sse=6017770.5, rms=4.622 (0.000%)
- 014: dt: 0.5000, sse=6051846.5, rms=4.413 (0.000%)
- 015: dt: 0.5000, sse=6183539.5, rms=4.261 (0.000%)
- 016: dt: 0.5000, sse=6159990.5, rms=4.173 (0.000%)
- 017: dt: 0.5000, sse=6232402.5, rms=4.091 (0.000%)
- rms = 4.06, time step reduction 1 of 3 to 0.250...
- 018: dt: 0.5000, sse=6202295.0, rms=4.060 (0.000%)
- 019: dt: 0.2500, sse=4424597.5, rms=3.287 (0.000%)
- 020: dt: 0.2500, sse=4239709.5, rms=3.069 (0.000%)
- rms = 3.04, time step reduction 2 of 3 to 0.125...
- 021: dt: 0.2500, sse=4119901.5, rms=3.037 (0.000%)
- 022: dt: 0.1250, sse=3945067.2, rms=2.890 (0.000%)
- rms = 2.87, time step reduction 3 of 3 to 0.062...
- 023: dt: 0.1250, sse=3917260.8, rms=2.870 (0.000%)
- positioning took 2.6 minutes
- mean border=46.5, 690 (2) missing vertices, mean dist 0.2 [0.2 (%46.5)->0.6 (%53.5))]
- %33 local maxima, %47 large gradients and %15 min vals, 413 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=4586206.5, rms=5.27
- 024: dt: 0.5000, sse=4819447.5, rms=4.452 (0.000%)
- 025: dt: 0.5000, sse=6104067.0, rms=4.335 (0.000%)
- rms = 4.31, time step reduction 1 of 3 to 0.250...
- 026: dt: 0.5000, sse=6029977.0, rms=4.311 (0.000%)
- 027: dt: 0.2500, sse=4808690.5, rms=3.318 (0.000%)
- 028: dt: 0.2500, sse=4667444.0, rms=3.001 (0.000%)
- rms = 2.97, time step reduction 2 of 3 to 0.125...
- 029: dt: 0.2500, sse=4565772.5, rms=2.970 (0.000%)
- 030: dt: 0.1250, sse=4378018.0, rms=2.768 (0.000%)
- rms = 2.73, time step reduction 3 of 3 to 0.062...
- 031: dt: 0.1250, sse=4354511.0, rms=2.735 (0.000%)
- positioning took 0.9 minutes
- mean border=43.7, 779 (2) missing vertices, mean dist 0.2 [0.2 (%36.0)->0.4 (%64.0))]
- %54 local maxima, %26 large gradients and %15 min vals, 514 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=4693039.5, rms=4.54
- 032: dt: 0.5000, sse=4799318.5, rms=4.208 (0.000%)
- rms = 4.19, time step reduction 1 of 3 to 0.250...
- 033: dt: 0.5000, sse=6268396.5, rms=4.195 (0.000%)
- 034: dt: 0.2500, sse=4717322.0, rms=3.159 (0.000%)
- 035: dt: 0.2500, sse=4819958.5, rms=2.825 (0.000%)
- rms = 2.83, time step reduction 2 of 3 to 0.125...
- 036: dt: 0.1250, sse=4704136.5, rms=2.715 (0.000%)
- 037: dt: 0.1250, sse=4512445.5, rms=2.558 (0.000%)
- rms = 2.53, time step reduction 3 of 3 to 0.062...
- 038: dt: 0.1250, sse=4456741.5, rms=2.534 (0.000%)
- positioning took 0.9 minutes
- mean border=42.4, 1493 (2) missing vertices, mean dist 0.1 [0.2 (%44.1)->0.3 (%55.9))]
- %58 local maxima, %21 large gradients and %15 min vals, 391 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/sub014/surf/lh.pial...
- writing smoothed curvature to lh.curv.pial
- 000: dt: 0.0000, sse=4522218.0, rms=3.03
- rms = 3.88, time step reduction 1 of 3 to 0.250...
- 039: dt: 0.2500, sse=4385979.0, rms=2.672 (0.000%)
- 040: dt: 0.2500, sse=4496000.0, rms=2.566 (0.000%)
- rms = 2.54, time step reduction 2 of 3 to 0.125...
- 041: dt: 0.2500, sse=4546474.5, rms=2.538 (0.000%)
- 042: dt: 0.1250, sse=4450844.0, rms=2.402 (0.000%)
- rms = 2.38, time step reduction 3 of 3 to 0.062...
- 043: dt: 0.1250, sse=4440818.5, rms=2.383 (0.000%)
- positioning took 0.6 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/lh.curv.pial
- writing smoothed area to lh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/lh.area.pial
- vertex spacing 1.02 +- 0.42 (0.08-->7.94) (max @ vno 86058 --> 85075)
- face area 0.41 +- 0.30 (0.00-->7.77)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 123287 vertices processed
- 25000 of 123287 vertices processed
- 50000 of 123287 vertices processed
- 75000 of 123287 vertices processed
- 100000 of 123287 vertices processed
- 0 of 123287 vertices processed
- 25000 of 123287 vertices processed
- 50000 of 123287 vertices processed
- 75000 of 123287 vertices processed
- 100000 of 123287 vertices processed
- thickness calculation complete, 482:823 truncations.
- 28265 vertices at 0 distance
- 82705 vertices at 1 distance
- 80211 vertices at 2 distance
- 32059 vertices at 3 distance
- 8794 vertices at 4 distance
- 2266 vertices at 5 distance
- 705 vertices at 6 distance
- 284 vertices at 7 distance
- 110 vertices at 8 distance
- 78 vertices at 9 distance
- 43 vertices at 10 distance
- 30 vertices at 11 distance
- 20 vertices at 12 distance
- 14 vertices at 13 distance
- 18 vertices at 14 distance
- 19 vertices at 15 distance
- 16 vertices at 16 distance
- 23 vertices at 17 distance
- 9 vertices at 18 distance
- 8 vertices at 19 distance
- 15 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/lh.thickness
- positioning took 12.7 minutes
- #--------------------------------------------
- #@# Surf Volume lh Thu Aug 8 20:52:15 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 20:52:15 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/scripts
- pctsurfcon --s sub014 --lh-only
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/scripts/pctsurfcon.log
- Thu Aug 8 20:52:15 CEST 2013
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/scripts
- /opt/freesurfer/5.3.0/bin/pctsurfcon
- $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $
- Linux snake5 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
- FREESURFER_HOME /opt/freesurfer/5.3.0
- mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/tmp.pctsurfcon.4959/lh.wm.mgh --regheader sub014 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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/sub014/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/label/lh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 = 95541
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/label/lh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/tmp.pctsurfcon.4959/lh.wm.mgh
- Dim: 123287 1 1
- mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/tmp.pctsurfcon.4959/lh.gm.mgh --projfrac 0.3 --regheader sub014 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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/sub014/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/label/lh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/lh.white
- Done reading source surface
- Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 = 109667
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/label/lh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/tmp.pctsurfcon.4959/lh.gm.mgh
- Dim: 123287 1 1
- mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/tmp.pctsurfcon.4959/lh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/tmp.pctsurfcon.4959/lh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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/sub014/surf/lh.w-g.pct.mgh
- mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/lh.w-g.pct.mgh --annot sub014 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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/sub014/surf/lh.w-g.pct.mgh --annot sub014 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/stats/lh.w-g.pct.stats --snr
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- UseRobust 0
- Constructing seg from annotation
- Reading annotation
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
- Seg base 1000
- Loading /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/lh.w-g.pct.mgh
- Vertex Area is 0.66671 mm^3
- Generating list of segmentation ids
- Found 36 segmentations
- Computing statistics for each segmentation
- 0 1000 unknown 0 0.000
- 1 1001 bankssts 1251 880.165
- 2 1002 caudalanteriorcingulate 928 631.022
- 3 1003 caudalmiddlefrontal 3469 2419.246
- 4 1004 corpuscallosum 0 0.000
- 5 1005 cuneus 2433 1528.919
- 6 1006 entorhinal 486 364.532
- 7 1007 fusiform 4317 2862.214
- 8 1008 inferiorparietal 5620 3816.278
- 9 1009 inferiortemporal 4547 3090.878
- 10 1010 isthmuscingulate 1569 1023.362
- 11 1011 lateraloccipital 5831 3749.242
- 12 1012 lateralorbitofrontal 3464 2278.681
- 13 1013 lingual 4119 2720.615
- 14 1014 medialorbitofrontal 2081 1362.094
- 15 1015 middletemporal 3956 2755.838
- 16 1016 parahippocampal 923 620.767
- 17 1017 paracentral 1754 1136.984
- 18 1018 parsopercularis 2083 1444.400
- 19 1019 parsorbitalis 807 552.355
- 20 1020 parstriangularis 1827 1238.910
- 21 1021 pericalcarine 2043 1370.216
- 22 1022 postcentral 6433 4254.462
- 23 1023 posteriorcingulate 1818 1232.357
- 24 1024 precentral 6631 4306.972
- 25 1025 precuneus 5709 3877.615
- 26 1026 rostralanteriorcingulate 1079 735.606
- 27 1027 rostralmiddlefrontal 7684 5225.198
- 28 1028 superiorfrontal 9524 6535.985
- 29 1029 superiorparietal 8514 5485.941
- 30 1030 superiortemporal 5450 3696.233
- 31 1031 supramarginal 4589 3149.923
- 32 1032 frontalpole 290 184.265
- 33 1033 temporalpole 827 540.157
- 34 1034 transversetemporal 628 393.950
- 35 1035 insula 2945 1890.359
- Reporting on 34 segmentations
- mri_segstats done
- Cleaning up
- #-----------------------------------------
- #@# Parcellation Stats lh Thu Aug 8 20:52:28 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 sub014 lh white
- computing statistics for each annotation in ../label/lh.aparc.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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
- 1251 880 1975 2.281 0.433 0.122 0.030 11 1.6 bankssts
- 928 631 1881 2.886 0.489 0.170 0.050 22 2.0 caudalanteriorcingulate
- 3469 2419 6208 2.312 0.413 0.134 0.048 80 5.6 caudalmiddlefrontal
- 2433 1529 3705 2.098 0.388 0.167 0.079 64 6.4 cuneus
- 486 365 1797 3.381 0.786 0.138 0.039 5 0.8 entorhinal
- 4317 2862 8891 2.737 0.638 0.159 0.066 94 11.5 fusiform
- 5620 3816 10818 2.524 0.505 0.153 0.057 170 13.8 inferiorparietal
- 4547 3091 9397 2.510 0.669 0.162 0.073 118 12.6 inferiortemporal
- 1569 1023 2682 2.481 0.745 0.157 0.066 35 3.7 isthmuscingulate
- 5831 3749 9222 2.217 0.440 0.157 0.056 107 13.0 lateraloccipital
- 3464 2279 6554 2.509 0.607 0.152 0.060 71 8.5 lateralorbitofrontal
- 4119 2721 6548 2.177 0.458 0.164 0.161 217 11.2 lingual
- 2081 1362 3539 2.130 0.798 0.160 0.092 78 7.5 medialorbitofrontal
- 3956 2756 8745 2.608 0.586 0.171 0.082 119 11.9 middletemporal
- 923 621 2372 3.168 0.751 0.142 0.062 17 2.2 parahippocampal
- 1754 1137 2772 2.210 0.495 0.127 0.041 19 2.8 paracentral
- 2083 1444 4402 2.543 0.470 0.140 0.044 34 3.7 parsopercularis
- 807 552 2065 3.064 0.619 0.197 0.200 55 5.8 parsorbitalis
- 1827 1239 3273 2.281 0.507 0.153 0.055 41 4.3 parstriangularis
- 2043 1370 2573 1.902 0.430 0.140 0.065 55 5.4 pericalcarine
- 6433 4254 9663 2.003 0.535 0.137 0.049 125 13.2 postcentral
- 1818 1232 3625 2.590 0.725 0.174 0.072 42 5.8 posteriorcingulate
- 6631 4307 11656 2.482 0.482 0.132 0.044 92 12.0 precentral
- 5709 3878 9698 2.307 0.517 0.150 0.059 105 12.7 precuneus
- 1079 736 2321 2.564 0.868 0.162 0.074 27 3.3 rostralanteriorcingulate
- 7684 5225 13941 2.293 0.523 0.165 0.070 198 21.7 rostralmiddlefrontal
- 9524 6536 19367 2.605 0.510 0.144 0.048 153 18.0 superiorfrontal
- 8514 5486 12521 2.075 0.386 0.137 0.047 140 16.1 superiorparietal
- 5450 3696 11133 2.594 0.619 0.135 0.044 90 10.0 superiortemporal
- 4589 3150 8733 2.437 0.527 0.151 0.055 87 9.2 supramarginal
- 290 184 631 2.483 0.495 0.171 0.071 11 0.6 frontalpole
- 827 540 2878 3.755 0.535 0.147 0.069 17 2.4 temporalpole
- 628 394 1081 2.403 0.371 0.129 0.039 8 0.9 transversetemporal
- 2945 1890 6096 2.994 0.821 0.120 0.046 34 5.4 insula
- #-----------------------------------------
- #@# Cortical Parc 2 lh Thu Aug 8 20:52:43 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub014 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...
- 21 labels changed using aseg
- relabeling using gibbs priors...
- 000: 8506 changed, 123287 examined...
- 001: 2128 changed, 32675 examined...
- 002: 641 changed, 10800 examined...
- 003: 271 changed, 3582 examined...
- 004: 132 changed, 1569 examined...
- 005: 68 changed, 756 examined...
- 006: 36 changed, 368 examined...
- 007: 24 changed, 229 examined...
- 008: 12 changed, 128 examined...
- 009: 4 changed, 73 examined...
- 010: 3 changed, 21 examined...
- 011: 5 changed, 17 examined...
- 012: 2 changed, 23 examined...
- 013: 0 changed, 18 examined...
- 9 labels changed using aseg
- 000: 276 total segments, 190 labels (2000 vertices) changed
- 001: 106 total segments, 21 labels (61 vertices) changed
- 002: 85 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 170 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 444 vertices marked for relabeling...
- 444 labels changed in reclassification.
- writing output to ../label/lh.aparc.a2009s.annot...
- classification took 1 minutes and 4 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 2 lh Thu Aug 8 20:53:47 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 sub014 lh white
- computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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
- 1041 710 1780 2.143 0.495 0.181 0.074 31 3.2 G_and_S_frontomargin
- 1339 876 2480 2.479 0.410 0.172 0.065 29 3.5 G_and_S_occipital_inf
- 1322 836 2155 2.158 0.533 0.140 0.048 20 2.6 G_and_S_paracentral
- 1364 926 2662 2.475 0.520 0.163 0.063 33 3.3 G_and_S_subcentral
- 693 462 1508 2.492 0.439 0.196 0.099 28 2.3 G_and_S_transv_frontopol
- 2097 1432 4212 2.626 0.757 0.163 0.073 54 5.9 G_and_S_cingul-Ant
- 1390 963 2596 2.668 0.507 0.141 0.043 20 2.5 G_and_S_cingul-Mid-Ant
- 1291 867 2439 2.578 0.500 0.147 0.054 18 2.9 G_and_S_cingul-Mid-Post
- 624 397 1510 2.967 0.581 0.196 0.096 21 2.6 G_cingul-Post-dorsal
- 290 176 520 2.468 0.788 0.173 0.089 10 0.7 G_cingul-Post-ventral
- 2210 1369 3441 2.102 0.393 0.176 0.095 71 7.5 G_cuneus
- 1163 801 2977 2.808 0.427 0.163 0.064 27 2.7 G_front_inf-Opercular
- 370 252 973 2.898 0.411 0.203 0.106 14 1.3 G_front_inf-Orbital
- 1204 820 2743 2.545 0.381 0.177 0.068 38 3.6 G_front_inf-Triangul
- 4412 3065 9529 2.435 0.482 0.174 0.086 165 13.9 G_front_middle
- 5855 3976 13243 2.695 0.483 0.155 0.055 110 12.7 G_front_sup
- 463 288 1054 3.192 0.746 0.128 0.056 6 0.9 G_Ins_lg_and_S_cent_ins
- 658 401 2100 3.851 0.756 0.138 0.075 14 2.1 G_insular_short
- 1920 1235 3957 2.501 0.390 0.179 0.086 98 6.7 G_occipital_middle
- 1499 955 2249 2.097 0.400 0.163 0.064 35 3.9 G_occipital_sup
- 1789 1148 3861 2.878 0.620 0.164 0.072 46 5.3 G_oc-temp_lat-fusifor
- 2588 1660 4564 2.259 0.487 0.180 0.227 198 8.1 G_oc-temp_med-Lingual
- 1086 745 3549 3.434 0.719 0.153 0.072 21 2.9 G_oc-temp_med-Parahip
- 2317 1513 5582 2.781 0.697 0.183 0.120 103 10.9 G_orbital
- 2033 1326 4797 2.760 0.540 0.176 0.078 75 6.2 G_pariet_inf-Angular
- 2275 1629 5318 2.588 0.498 0.165 0.062 56 5.4 G_pariet_inf-Supramar
- 3434 2220 5789 2.145 0.403 0.145 0.050 66 6.8 G_parietal_sup
- 2610 1704 4250 2.063 0.435 0.156 0.058 62 6.4 G_postcentral
- 2446 1564 5434 2.696 0.367 0.143 0.054 47 5.7 G_precentral
- 2998 2004 6110 2.449 0.523 0.177 0.076 84 8.6 G_precuneus
- 820 507 1683 2.336 0.665 0.194 0.132 50 5.2 G_rectus
- 307 206 622 2.706 0.825 0.110 0.051 4 0.4 G_subcallosal
- 483 293 915 2.398 0.349 0.127 0.037 7 0.7 G_temp_sup-G_T_transv
- 1909 1327 5269 2.865 0.525 0.170 0.063 52 5.1 G_temp_sup-Lateral
- 618 428 1558 3.350 0.796 0.116 0.053 7 0.9 G_temp_sup-Plan_polar
- 978 677 1854 2.444 0.476 0.129 0.035 13 1.5 G_temp_sup-Plan_tempo
- 2445 1683 5787 2.588 0.691 0.188 0.095 87 9.0 G_temporal_inf
- 2541 1788 6511 2.698 0.578 0.196 0.108 103 10.2 G_temporal_middle
- 287 202 335 1.664 0.362 0.114 0.024 2 0.3 Lat_Fis-ant-Horizont
- 202 151 322 2.101 0.280 0.109 0.023 1 0.2 Lat_Fis-ant-Vertical
- 1207 799 1591 2.421 0.515 0.135 0.041 12 2.0 Lat_Fis-post
- 1829 1150 2706 2.125 0.392 0.164 0.055 34 4.2 Pole_occipital
- 1912 1285 5881 3.186 0.785 0.164 0.072 45 5.8 Pole_temporal
- 2733 1877 3623 1.997 0.514 0.135 0.057 56 6.0 S_calcarine
- 2959 1957 3338 1.870 0.558 0.110 0.029 21 3.6 S_central
- 919 642 1261 2.012 0.403 0.103 0.022 5 0.9 S_cingul-Marginalis
- 438 289 749 2.881 0.529 0.099 0.021 2 0.4 S_circular_insula_ant
- 1294 827 1729 2.254 0.422 0.092 0.020 7 1.1 S_circular_insula_inf
- 1739 1146 2599 2.504 0.471 0.111 0.030 11 2.2 S_circular_insula_sup
- 812 569 1264 2.530 0.602 0.136 0.036 9 1.3 S_collat_transv_ant
- 409 260 515 2.128 0.326 0.154 0.066 6 1.1 S_collat_transv_post
- 2030 1365 2795 2.141 0.389 0.131 0.040 25 3.3 S_front_inf
- 1516 1034 2282 2.137 0.593 0.141 0.046 23 2.8 S_front_middle
- 3059 2141 5072 2.305 0.399 0.114 0.027 26 3.6 S_front_sup
- 158 105 202 1.811 0.397 0.129 0.028 1 0.2 S_interm_prim-Jensen
- 3039 2019 3959 2.083 0.377 0.123 0.041 31 4.5 S_intrapariet_and_P_trans
- 796 539 897 1.788 0.329 0.118 0.027 5 1.0 S_oc_middle_and_Lunatus
- 1233 841 1770 2.166 0.369 0.118 0.031 10 1.6 S_oc_sup_and_transversal
- 664 421 1050 2.309 0.458 0.134 0.043 11 1.1 S_occipital_ant
- 807 537 1278 2.303 0.554 0.136 0.070 15 1.6 S_oc-temp_lat
- 1825 1258 2912 2.439 0.512 0.137 0.040 23 3.1 S_oc-temp_med_and_Lingual
- 215 160 399 2.271 0.431 0.181 0.073 5 0.6 S_orbital_lateral
- 529 354 661 1.972 0.681 0.117 0.025 4 0.5 S_orbital_med-olfact
- 1215 840 1984 2.367 0.480 0.145 0.050 17 2.5 S_orbital-H_Shaped
- 2143 1421 2906 2.165 0.480 0.124 0.041 26 3.7 S_parieto_occipital
- 1173 769 1426 2.181 0.913 0.167 0.066 28 2.6 S_pericallosal
- 2989 1936 4025 2.076 0.409 0.124 0.039 46 5.1 S_postcentral
- 1297 863 1933 2.343 0.393 0.111 0.029 9 1.5 S_precentral-inf-part
- 1325 891 1747 2.285 0.368 0.118 0.030 10 1.7 S_precentral-sup-part
- 647 419 764 1.748 0.786 0.142 0.061 16 1.4 S_suborbital
- 1040 711 1565 2.375 0.466 0.134 0.041 11 1.6 S_subparietal
- 1261 862 1716 2.229 0.596 0.116 0.027 9 1.5 S_temporal_inf
- 4713 3259 7448 2.382 0.502 0.124 0.034 53 6.6 S_temporal_sup
- 333 228 475 2.422 0.525 0.129 0.029 3 0.4 S_temporal_transverse
- #-----------------------------------------
- #@# Cortical Parc 3 lh Thu Aug 8 20:54:04 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub014 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...
- 900 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2613 changed, 123287 examined...
- 001: 623 changed, 11077 examined...
- 002: 145 changed, 3305 examined...
- 003: 46 changed, 863 examined...
- 004: 23 changed, 277 examined...
- 005: 11 changed, 136 examined...
- 006: 12 changed, 64 examined...
- 007: 11 changed, 58 examined...
- 008: 6 changed, 57 examined...
- 009: 2 changed, 35 examined...
- 010: 1 changed, 13 examined...
- 011: 0 changed, 7 examined...
- 96 labels changed using aseg
- 000: 64 total segments, 31 labels (183 vertices) changed
- 001: 34 total segments, 1 labels (3 vertices) changed
- 002: 33 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 43 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 534 vertices marked for relabeling...
- 534 labels changed in reclassification.
- writing output to ../label/lh.aparc.DKTatlas40.annot...
- classification took 0 minutes and 57 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 3 lh Thu Aug 8 20:55:00 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 sub014 lh white
- computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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
- 1473 1001 2783 2.891 0.471 0.156 0.052 28 3.0 caudalanteriorcingulate
- 3659 2549 6584 2.323 0.411 0.134 0.048 83 5.9 caudalmiddlefrontal
- 3253 2064 4764 2.090 0.393 0.159 0.071 75 8.0 cuneus
- 470 352 1735 3.413 0.801 0.141 0.039 5 0.8 entorhinal
- 3913 2589 7704 2.714 0.610 0.156 0.062 81 9.6 fusiform
- 5371 3617 10232 2.520 0.516 0.153 0.057 162 13.2 inferiorparietal
- 4622 3178 9792 2.526 0.675 0.163 0.075 120 13.5 inferiortemporal
- 1556 1014 2679 2.499 0.738 0.158 0.067 35 3.7 isthmuscingulate
- 6020 3849 9565 2.218 0.437 0.158 0.058 115 14.1 lateraloccipital
- 3544 2334 6773 2.454 0.620 0.161 0.065 84 9.4 lateralorbitofrontal
- 4124 2726 6561 2.177 0.461 0.164 0.161 218 11.4 lingual
- 1774 1141 3025 2.127 0.819 0.156 0.081 63 6.5 medialorbitofrontal
- 5324 3685 11281 2.556 0.612 0.164 0.073 145 14.7 middletemporal
- 930 624 2390 3.171 0.745 0.143 0.066 17 2.3 parahippocampal
- 1974 1289 3164 2.237 0.483 0.125 0.039 20 3.1 paracentral
- 1919 1307 3962 2.545 0.458 0.142 0.048 34 3.8 parsopercularis
- 1037 711 2283 2.702 0.666 0.159 0.067 23 2.8 parsorbitalis
- 2059 1409 3802 2.341 0.477 0.152 0.053 41 4.4 parstriangularis
- 2043 1371 2576 1.903 0.429 0.139 0.065 55 5.4 pericalcarine
- 7321 4847 10965 2.017 0.528 0.136 0.048 137 14.5 postcentral
- 1947 1310 3759 2.568 0.721 0.173 0.071 44 6.0 posteriorcingulate
- 6578 4265 11525 2.484 0.485 0.131 0.043 90 11.9 precentral
- 5619 3805 9915 2.337 0.512 0.151 0.060 107 12.7 precuneus
- 1473 1006 3062 2.519 0.832 0.166 0.087 44 4.6 rostralanteriorcingulate
- 5182 3509 9612 2.343 0.564 0.166 0.088 158 18.0 rostralmiddlefrontal
- 10822 7444 21844 2.522 0.534 0.150 0.053 209 22.4 superiorfrontal
- 6794 4383 9859 2.061 0.376 0.136 0.046 111 12.1 superiorparietal
- 7271 4936 15759 2.706 0.704 0.136 0.046 120 13.8 superiortemporal
- 4353 2989 8226 2.446 0.526 0.151 0.055 80 8.8 supramarginal
- 596 375 1044 2.422 0.362 0.132 0.039 8 0.8 transversetemporal
- 2608 1675 5540 3.038 0.824 0.117 0.044 29 4.7 insula
- #--------------------------------------------
- #@# Tessellate rh Thu Aug 8 20:55:18 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/scripts
- mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz
- Iteration Number : 1
- pass 1 (xy+): 1 found - 1 modified | TOTAL: 1
- pass 2 (xy+): 0 found - 1 modified | TOTAL: 1
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 1
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 1
- pass 1 (yz-): 1 found - 1 modified | TOTAL: 2
- pass 2 (yz-): 0 found - 1 modified | TOTAL: 2
- pass 1 (xz+): 2 found - 2 modified | TOTAL: 4
- pass 2 (xz+): 0 found - 2 modified | TOTAL: 4
- pass 1 (xz-): 2 found - 2 modified | TOTAL: 6
- pass 2 (xz-): 0 found - 2 modified | TOTAL: 6
- Iteration Number : 1
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 2 found - 2 modified | TOTAL: 2
- pass 2 (+++): 0 found - 2 modified | TOTAL: 2
- Iteration Number : 1
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 1 found - 1 modified | TOTAL: 1
- pass 2 (--): 0 found - 1 modified | TOTAL: 1
- pass 1 (-+): 1 found - 1 modified | TOTAL: 2
- pass 2 (-+): 0 found - 1 modified | TOTAL: 2
- Iteration Number : 2
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz-): 1 found - 1 modified | TOTAL: 1
- pass 2 (yz-): 0 found - 1 modified | TOTAL: 1
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 1
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 1
- Iteration Number : 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 3
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 3
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 3
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Total Number of Modified Voxels = 11 (out of 208069: 0.005287)
- 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 50: 1249 vertices, 1350 faces
- slice 60: 6811 vertices, 7053 faces
- slice 70: 15375 vertices, 15731 faces
- slice 80: 25360 vertices, 25698 faces
- slice 90: 35812 vertices, 36178 faces
- slice 100: 46149 vertices, 46468 faces
- slice 110: 57412 vertices, 57745 faces
- slice 120: 67901 vertices, 68258 faces
- slice 130: 78356 vertices, 78717 faces
- slice 140: 88351 vertices, 88684 faces
- slice 150: 96801 vertices, 97105 faces
- slice 160: 104473 vertices, 104753 faces
- slice 170: 111317 vertices, 111537 faces
- slice 180: 117023 vertices, 117215 faces
- slice 190: 121842 vertices, 121992 faces
- slice 200: 123528 vertices, 123546 faces
- slice 210: 123528 vertices, 123546 faces
- slice 220: 123528 vertices, 123546 faces
- slice 230: 123528 vertices, 123546 faces
- slice 240: 123528 vertices, 123546 faces
- slice 250: 123528 vertices, 123546 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...
- 123528 voxel in cpt #1: X=-18 [v=123528,e=370638,f=247092] located at (24.870646, -12.918326, 38.348251)
- For the whole surface: X=-18 [v=123528,e=370638,f=247092]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Smooth1 rh Thu Aug 8 20:55:26 CEST 2013
- mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 20:55:31 CEST 2013
- mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/scripts
- avg radius = 44.1 mm, total surface area = 64308 mm^2
- writing inflated surface to ../surf/rh.inflated.nofix
- inflation took 0.5 minutes
- Not saving sulc
-
step 000: RMS=0.101 (target=0.015)
step 005: RMS=0.073 (target=0.015)
step 010: RMS=0.053 (target=0.015)
step 015: RMS=0.043 (target=0.015)
step 020: RMS=0.037 (target=0.015)
step 025: RMS=0.032 (target=0.015)
step 030: RMS=0.028 (target=0.015)
step 035: RMS=0.025 (target=0.015)
step 040: RMS=0.024 (target=0.015)
step 045: RMS=0.022 (target=0.015)
step 050: RMS=0.021 (target=0.015)
step 055: RMS=0.021 (target=0.015)
step 060: RMS=0.021 (target=0.015)
- inflation complete.
- Not saving sulc
- #--------------------------------------------
- #@# QSphere rh Thu Aug 8 20:56:03 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/scripts
- mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix
- doing quick spherical unfolding.
- setting seed for random number genererator to 1234
- $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading original vertex positions...
- unfolding cortex into spherical form...
- surface projected - minimizing metric distortion...
- vertex spacing 1.03 +- 0.59 (0.00-->6.84) (max @ vno 90833 --> 91791)
- face area 0.03 +- 0.03 (-0.13-->0.61)
- scaling brain by 0.326...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=176.670, avgs=0
- 005/300: dt: 0.9000, rms radial error=176.409, avgs=0
- 010/300: dt: 0.9000, rms radial error=175.849, avgs=0
- 015/300: dt: 0.9000, rms radial error=175.114, avgs=0
- 020/300: dt: 0.9000, rms radial error=174.278, avgs=0
- 025/300: dt: 0.9000, rms radial error=173.387, avgs=0
- 030/300: dt: 0.9000, rms radial error=172.469, avgs=0
- 035/300: dt: 0.9000, rms radial error=171.534, avgs=0
- 040/300: dt: 0.9000, rms radial error=170.592, avgs=0
- 045/300: dt: 0.9000, rms radial error=169.647, avgs=0
- 050/300: dt: 0.9000, rms radial error=168.703, avgs=0
- 055/300: dt: 0.9000, rms radial error=167.761, avgs=0
- 060/300: dt: 0.9000, rms radial error=166.823, avgs=0
- 065/300: dt: 0.9000, rms radial error=165.889, avgs=0
- 070/300: dt: 0.9000, rms radial error=164.960, avgs=0
- 075/300: dt: 0.9000, rms radial error=164.035, avgs=0
- 080/300: dt: 0.9000, rms radial error=163.115, avgs=0
- 085/300: dt: 0.9000, rms radial error=162.200, avgs=0
- 090/300: dt: 0.9000, rms radial error=161.290, avgs=0
- 095/300: dt: 0.9000, rms radial error=160.384, avgs=0
- 100/300: dt: 0.9000, rms radial error=159.484, avgs=0
- 105/300: dt: 0.9000, rms radial error=158.589, avgs=0
- 110/300: dt: 0.9000, rms radial error=157.698, avgs=0
- 115/300: dt: 0.9000, rms radial error=156.813, avgs=0
- 120/300: dt: 0.9000, rms radial error=155.932, avgs=0
- 125/300: dt: 0.9000, rms radial error=155.056, avgs=0
- 130/300: dt: 0.9000, rms radial error=154.185, avgs=0
- 135/300: dt: 0.9000, rms radial error=153.318, avgs=0
- 140/300: dt: 0.9000, rms radial error=152.457, avgs=0
- 145/300: dt: 0.9000, rms radial error=151.600, avgs=0
- 150/300: dt: 0.9000, rms radial error=150.748, avgs=0
- 155/300: dt: 0.9000, rms radial error=149.901, avgs=0
- 160/300: dt: 0.9000, rms radial error=149.058, avgs=0
- 165/300: dt: 0.9000, rms radial error=148.221, avgs=0
- 170/300: dt: 0.9000, rms radial error=147.387, avgs=0
- 175/300: dt: 0.9000, rms radial error=146.559, avgs=0
- 180/300: dt: 0.9000, rms radial error=145.735, avgs=0
- 185/300: dt: 0.9000, rms radial error=144.915, avgs=0
- 190/300: dt: 0.9000, rms radial error=144.100, avgs=0
- 195/300: dt: 0.9000, rms radial error=143.289, avgs=0
- 200/300: dt: 0.9000, rms radial error=142.483, avgs=0
- 205/300: dt: 0.9000, rms radial error=141.681, avgs=0
- 210/300: dt: 0.9000, rms radial error=140.884, avgs=0
- 215/300: dt: 0.9000, rms radial error=140.091, avgs=0
- 220/300: dt: 0.9000, rms radial error=139.302, avgs=0
- 225/300: dt: 0.9000, rms radial error=138.518, avgs=0
- 230/300: dt: 0.9000, rms radial error=137.738, avgs=0
- 235/300: dt: 0.9000, rms radial error=136.963, avgs=0
- 240/300: dt: 0.9000, rms radial error=136.192, avgs=0
- 245/300: dt: 0.9000, rms radial error=135.425, avgs=0
- 250/300: dt: 0.9000, rms radial error=134.662, avgs=0
- 255/300: dt: 0.9000, rms radial error=133.904, avgs=0
- 260/300: dt: 0.9000, rms radial error=133.150, avgs=0
- 265/300: dt: 0.9000, rms radial error=132.401, avgs=0
- 270/300: dt: 0.9000, rms radial error=131.655, avgs=0
- 275/300: dt: 0.9000, rms radial error=130.914, avgs=0
- 280/300: dt: 0.9000, rms radial error=130.177, avgs=0
- 285/300: dt: 0.9000, rms radial error=129.444, avgs=0
- 290/300: dt: 0.9000, rms radial error=128.715, avgs=0
- 295/300: dt: 0.9000, rms radial error=127.991, avgs=0
- 300/300: dt: 0.9000, rms radial error=127.270, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 14249.33
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00018
- epoch 2 (K=40.0), pass 1, starting sse = 2311.98
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00011
- epoch 3 (K=160.0), pass 1, starting sse = 231.12
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.10/11 = 0.00949
- epoch 4 (K=640.0), pass 1, starting sse = 11.57
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.14/15 = 0.00911
- final writing spherical brain to ../surf/rh.qsphere.nofix
- spherical transformation took 0.07 hours
- distance error %100000.00
- #--------------------------------------------
- #@# Fix Topology rh Thu Aug 8 21:00:23 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/sub014/scripts
- mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub014 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=-18 (nv=123528, nf=247092, ne=370638, g=10)
- 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...
- 1195 ambiguous faces found in tessellation
- segmenting defects...
- 16 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- -merging segment 7 into 8
- 15 defects to be corrected
- 0 vertices coincident
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/rh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -9.8329 (-4.9165)
- -vertex loglikelihood: -6.7303 (-3.3651)
- -normal dot loglikelihood: -3.5950 (-3.5950)
- -quad curv loglikelihood: -6.5416 (-3.2708)
- Total Loglikelihood : -26.6998
- CORRECTING DEFECT 0 (vertices=43, convex hull=83)
- After retessellation of defect 0, euler #=-13 (122801,368075,245261) : difference with theory (-12) = 1
- CORRECTING DEFECT 1 (vertices=6, convex hull=25)
- After retessellation of defect 1, euler #=-12 (122804,368090,245274) : difference with theory (-11) = 1
- CORRECTING DEFECT 2 (vertices=167, convex hull=139)
- After retessellation of defect 2, euler #=-11 (122876,368369,245482) : difference with theory (-10) = 1
- CORRECTING DEFECT 3 (vertices=19, convex hull=26)
- After retessellation of defect 3, euler #=-10 (122880,368391,245501) : difference with theory (-9) = 1
- CORRECTING DEFECT 4 (vertices=16, convex hull=26)
- After retessellation of defect 4, euler #=-9 (122882,368404,245513) : difference with theory (-8) = 1
- CORRECTING DEFECT 5 (vertices=81, convex hull=58)
- After retessellation of defect 5, euler #=-8 (122895,368467,245564) : difference with theory (-7) = 1
- CORRECTING DEFECT 6 (vertices=41, convex hull=33)
- After retessellation of defect 6, euler #=-7 (122901,368495,245587) : difference with theory (-6) = 1
- CORRECTING DEFECT 7 (vertices=39, convex hull=44)
- After retessellation of defect 7, euler #=-5 (122908,368533,245620) : difference with theory (-5) = 0
- CORRECTING DEFECT 8 (vertices=15, convex hull=21)
- After retessellation of defect 8, euler #=-4 (122912,368550,245634) : difference with theory (-4) = 0
- CORRECTING DEFECT 9 (vertices=109, convex hull=49)
- After retessellation of defect 9, euler #=-3 (122924,368611,245684) : difference with theory (-3) = 0
- CORRECTING DEFECT 10 (vertices=57, convex hull=98)
- After retessellation of defect 10, euler #=-2 (122965,368776,245809) : difference with theory (-2) = 0
- CORRECTING DEFECT 11 (vertices=38, convex hull=64)
- After retessellation of defect 11, euler #=-1 (122982,368854,245871) : difference with theory (-1) = 0
- CORRECTING DEFECT 12 (vertices=69, convex hull=66)
- After retessellation of defect 12, euler #=0 (122999,368929,245930) : difference with theory (0) = 0
- CORRECTING DEFECT 13 (vertices=35, convex hull=77)
- After retessellation of defect 13, euler #=1 (123016,369015,246000) : difference with theory (1) = 0
- CORRECTING DEFECT 14 (vertices=21, convex hull=73)
- After retessellation of defect 14, euler #=2 (123027,369075,246050) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.88 +- 0.21 (0.15-->9.00) (max @ vno 50303 --> 53862)
- 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 (0.15-->9.00) (max @ vno 50303 --> 53862)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 49 mutations (35.5%), 89 crossovers (64.5%), 19 vertices were eliminated
- building final representation...
- 501 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=123027, nf=246050, ne=369075, g=0)
- writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/rh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 9.0 minutes
- 0 defective edges
- removing intersecting faces
- 000: 72 intersecting
- mris_euler_number ../surf/rh.orig
- euler # = v-e+f = 2g-2: 123027 - 369075 + 246050 = 2 --> 0 holes
- F =2V-4: 246050 = 246054-4 (0)
- 2E=3F: 738150 = 738150 (0)
- total defect index = 0
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/scripts
- mris_remove_intersection ../surf/rh.orig ../surf/rh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 7 intersecting
- writing corrected surface to ../surf/rh.orig
- rm ../surf/rh.inflated
- #--------------------------------------------
- #@# Make White Surf rh Thu Aug 8 21:09:29 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/scripts
- mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub014 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/sub014/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/wm.mgz...
- 15389 bright wm thresholded.
- 474 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/rh.orig...
- computing class statistics...
- border white: 218506 voxels (1.30%)
- border gray 254901 voxels (1.52%)
- WM (92.0): 93.3 +- 10.4 [70.0 --> 110.0]
- GM (75.0) : 73.0 +- 13.1 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 44.9 (was 70)
- setting MAX_BORDER_WHITE to 116.4 (was 105)
- setting MIN_BORDER_WHITE to 58.0 (was 85)
- setting MAX_CSF to 31.8 (was 40)
- setting MAX_GRAY to 95.6 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 51.5 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 18.8 (was 40)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.81 +- 0.22 (0.05-->3.25) (max @ vno 113767 --> 117357)
- face area 0.28 +- 0.12 (0.00-->1.51)
- mean absolute distance = 0.67 +- 0.76
- 3538 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=106, GM=58
- mean inside = 93.2, mean outside = 68.1
- smoothing surface for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- mean border=71.9, 16 (16) missing vertices, mean dist 0.4 [0.5 (%29.7)->0.8 (%70.3))]
- %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 (0.10-->4.57) (max @ vno 50303 --> 53862)
- face area 0.28 +- 0.13 (0.00-->3.04)
- mean absolute distance = 0.31 +- 0.46
- 2579 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=6985250.5, rms=14.16
- 001: dt: 0.5000, sse=6896132.5, rms=10.305 (0.000%)
- 002: dt: 0.5000, sse=7030071.0, rms=8.023 (0.000%)
- 003: dt: 0.5000, sse=7105792.0, rms=6.525 (0.000%)
- 004: dt: 0.5000, sse=7271625.0, rms=5.608 (0.000%)
- 005: dt: 0.5000, sse=7381769.5, rms=5.088 (0.000%)
- 006: dt: 0.5000, sse=7478702.5, rms=4.803 (0.000%)
- 007: dt: 0.5000, sse=7498999.0, rms=4.654 (0.000%)
- 008: dt: 0.5000, sse=7494016.5, rms=4.550 (0.000%)
- 009: dt: 0.5000, sse=7486466.5, rms=4.491 (0.000%)
- 010: dt: 0.5000, sse=7450045.0, rms=4.439 (0.000%)
- rms = 4.41, time step reduction 1 of 3 to 0.250...
- 011: dt: 0.5000, sse=7447176.5, rms=4.407 (0.000%)
- 012: dt: 0.2500, sse=4771758.5, rms=3.053 (0.000%)
- 013: dt: 0.2500, sse=4368855.0, rms=2.587 (0.000%)
- 014: dt: 0.2500, sse=4133257.0, rms=2.493 (0.000%)
- 015: dt: 0.2500, sse=4055258.5, rms=2.399 (0.000%)
- rms = 2.37, time step reduction 2 of 3 to 0.125...
- 016: dt: 0.2500, sse=3972836.0, rms=2.371 (0.000%)
- 017: dt: 0.1250, sse=3752413.2, rms=2.093 (0.000%)
- rms = 2.06, time step reduction 3 of 3 to 0.062...
- 018: dt: 0.1250, sse=3714163.0, rms=2.056 (0.000%)
- positioning took 2.1 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 1 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 1 vertex label from ripped group
- mean border=76.6, 27 (4) missing vertices, mean dist -0.2 [0.3 (%78.8)->0.2 (%21.2))]
- %82 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.91 +- 0.26 (0.12-->4.73) (max @ vno 50303 --> 53862)
- face area 0.35 +- 0.17 (0.00-->4.19)
- mean absolute distance = 0.21 +- 0.28
- 2083 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4660162.5, rms=6.24
- 019: dt: 0.5000, sse=4830315.0, rms=4.261 (0.000%)
- rms = 4.63, time step reduction 1 of 3 to 0.250...
- 020: dt: 0.2500, sse=4381808.5, rms=3.094 (0.000%)
- 021: dt: 0.2500, sse=4200995.5, rms=2.500 (0.000%)
- 022: dt: 0.2500, sse=4131826.5, rms=2.057 (0.000%)
- 023: dt: 0.2500, sse=4116746.2, rms=2.003 (0.000%)
- 024: dt: 0.2500, sse=4058189.0, rms=1.895 (0.000%)
- rms = 1.93, time step reduction 2 of 3 to 0.125...
- 025: dt: 0.1250, sse=4001284.5, rms=1.802 (0.000%)
- 026: dt: 0.1250, sse=3924953.5, rms=1.679 (0.000%)
- rms = 1.67, time step reduction 3 of 3 to 0.062...
- 027: dt: 0.1250, sse=3886832.2, rms=1.671 (0.000%)
- positioning took 1.2 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 1 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 1 vertex label from ripped group
- removing 1 vertex label from ripped group
- removing 4 vertex label from ripped group
- mean border=80.2, 24 (2) missing vertices, mean dist -0.1 [0.2 (%78.1)->0.2 (%21.9))]
- %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 (0.11-->4.82) (max @ vno 50303 --> 53862)
- face area 0.34 +- 0.16 (0.00-->3.86)
- mean absolute distance = 0.15 +- 0.23
- 2156 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4292956.0, rms=4.59
- 028: dt: 0.5000, sse=4581467.5, rms=4.234 (0.000%)
- rms = 4.42, time step reduction 1 of 3 to 0.250...
- 029: dt: 0.2500, sse=4138985.2, rms=2.660 (0.000%)
- 030: dt: 0.2500, sse=4020812.5, rms=2.217 (0.000%)
- 031: dt: 0.2500, sse=4085542.0, rms=1.843 (0.000%)
- rms = 1.90, time step reduction 2 of 3 to 0.125...
- 032: dt: 0.1250, sse=4015388.5, rms=1.688 (0.000%)
- 033: dt: 0.1250, sse=3934286.2, rms=1.472 (0.000%)
- rms = 1.45, time step reduction 3 of 3 to 0.062...
- 034: dt: 0.1250, sse=3900540.5, rms=1.450 (0.000%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 1 vertex label from ripped group
- removing 1 vertex label from ripped group
- removing 4 vertex label from ripped group
- mean border=81.3, 26 (1) missing vertices, mean dist -0.0 [0.2 (%59.5)->0.2 (%40.5))]
- %91 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/sub014/surf/rh.white...
- writing smoothed curvature to rh.curv
- 000: dt: 0.0000, sse=3922955.2, rms=1.89
- rms = 2.90, time step reduction 1 of 3 to 0.250...
- 035: dt: 0.2500, sse=4003927.2, rms=1.211 (0.000%)
- 036: dt: 0.2500, sse=4151907.8, rms=1.083 (0.000%)
- rms = 1.10, time step reduction 2 of 3 to 0.125...
- rms = 1.07, time step reduction 3 of 3 to 0.062...
- 037: dt: 0.1250, sse=4152130.0, rms=1.071 (0.000%)
- positioning took 0.5 minutes
- inhibiting deformation at non-cortical midline structures...
- generating cortex label...
- 9 non-cortical segments detected
- only using segment with 2117 vertices
- erasing segment 1 (vno[0] = 74488)
- erasing segment 2 (vno[0] = 76579)
- erasing segment 3 (vno[0] = 84004)
- erasing segment 4 (vno[0] = 85641)
- erasing segment 5 (vno[0] = 86678)
- erasing segment 6 (vno[0] = 88438)
- erasing segment 7 (vno[0] = 93700)
- erasing segment 8 (vno[0] = 93740)
- writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/label/rh.cortex.label...
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/rh.curv
- writing smoothed area to rh.area
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/rh.area
- vertex spacing 0.90 +- 0.25 (0.05-->4.85) (max @ vno 50303 --> 53862)
- face area 0.34 +- 0.16 (0.00-->3.83)
- refinement took 6.9 minutes
- #--------------------------------------------
- #@# Smooth2 rh Thu Aug 8 21:16:23 CEST 2013
- mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/scripts
- smoothing for 3 iterations
- setting seed for random number generator to 1234
- smoothing surface tessellation for 3 iterations...
- smoothing complete - recomputing first and second fundamental forms...
- #--------------------------------------------
- #@# Inflation2 rh Thu Aug 8 21:16:27 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/scripts
- mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated
- avg radius = 44.3 mm, total surface area = 75468 mm^2
- writing inflated surface to ../surf/rh.inflated
- writing sulcal depths to ../surf/rh.sulc
-
step 000: RMS=0.119 (target=0.015)
step 005: RMS=0.081 (target=0.015)
step 010: RMS=0.058 (target=0.015)
step 015: RMS=0.047 (target=0.015)
step 020: RMS=0.039 (target=0.015)
step 025: RMS=0.032 (target=0.015)
step 030: RMS=0.026 (target=0.015)
step 035: RMS=0.022 (target=0.015)
step 040: RMS=0.019 (target=0.015)
step 045: RMS=0.017 (target=0.015)
step 050: RMS=0.015 (target=0.015)
- inflation complete.
- inflation took 0.5 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
- 218 vertices thresholded to be in k1 ~ [-0.23 0.31], k2 ~ [-0.10 0.07]
- total integrated curvature = 0.571*4pi (7.179) --> 0 handles
- ICI = 1.7, FI = 10.3, variation=178.047
- 107 vertices thresholded to be in [-0.01 0.01]
- writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level
- curvature mean = 0.000, std = 0.001
- 119 vertices thresholded to be in [-0.14 0.16]
- done.
- writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.018, std = 0.025
- done.
- #-----------------------------------------
- #@# Curvature Stats rh Thu Aug 8 21:18:38 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub014 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 [ sub014/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 [ 284 ]
- Gb_filter = 0
- WARN: S lookup min: -0.151465
- WARN: S explicit min: 0.000000 vertex = 1446
- #--------------------------------------------
- #@# Sphere rh Thu Aug 8 21:18:43 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 0.300...
- 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 %19.79
- pass 1: epoch 2 of 3 starting distance error %19.77
- unfolding complete - removing small folds...
- starting distance error %19.72
- removing remaining folds...
- final distance error %19.75
- MRISunfold() return, current seed 1234
- writing spherical brain to ../surf/rh.sphere
- spherical transformation took 0.84 hours
- #--------------------------------------------
- #@# Surf Reg rh Thu Aug 8 22:08:50 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 = 0.574
- curvature mean = 0.029, std = 0.935
- curvature mean = 0.022, std = 0.857
- Starting MRISrigidBodyAlignGlobal()
- d=64.00 min @ (0.00, -16.00, 0.00) sse = 356592.2, tmin=1.3111
- d=32.00 min @ (8.00, 8.00, 8.00) sse = 265544.1, tmin=2.4103
- d=16.00 min @ (4.00, 0.00, 0.00) sse = 250922.8, tmin=3.5252
- d=8.00 min @ (-2.00, -2.00, -2.00) sse = 242983.3, tmin=4.6480
- d=4.00 min @ (1.00, 1.00, 0.00) sse = 242661.5, tmin=5.7747
- d=2.00 min @ (-0.50, -0.50, 0.00) sse = 242135.4, tmin=6.8939
- d=0.50 min @ (0.00, 0.12, 0.12) sse = 242101.4, tmin=9.0677
- 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 9.07 min
- curvature mean = 0.014, std = 0.948
- curvature mean = 0.011, std = 0.940
- curvature mean = 0.011, std = 0.959
- curvature mean = 0.005, std = 0.973
- curvature mean = 0.010, std = 0.961
- curvature mean = 0.001, std = 0.988
- 2 Reading smoothwm
- curvature mean = -0.022, std = 0.295
- curvature mean = 0.006, std = 0.070
- curvature mean = 0.070, std = 0.352
- curvature mean = 0.006, std = 0.083
- curvature mean = 0.032, std = 0.545
- curvature mean = 0.007, std = 0.090
- curvature mean = 0.017, std = 0.688
- curvature mean = 0.007, std = 0.093
- curvature mean = 0.005, std = 0.801
- MRISregister() return, current seed 0
- writing registered surface to ../surf/rh.sphere.reg...
- expanding nbhd size to 1
- #--------------------------------------------
- #@# Jacobian white rh Thu Aug 8 22:34:59 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 22:35:01 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 22:35:03 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub014 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...
- 1027 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2796 changed, 123027 examined...
- 001: 623 changed, 11957 examined...
- 002: 143 changed, 3512 examined...
- 003: 51 changed, 897 examined...
- 004: 27 changed, 280 examined...
- 005: 12 changed, 154 examined...
- 006: 3 changed, 74 examined...
- 007: 0 changed, 15 examined...
- 188 labels changed using aseg
- 000: 101 total segments, 62 labels (303 vertices) changed
- 001: 39 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...
- 796 vertices marked for relabeling...
- 796 labels changed in reclassification.
- writing output to ../label/rh.aparc.annot...
- classification took 1 minutes and 2 seconds.
- #--------------------------------------------
- #@# Make Pial Surf rh Thu Aug 8 22:36:05 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/scripts
- mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub014 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/sub014/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/wm.mgz...
- 15389 bright wm thresholded.
- 474 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/rh.orig...
- computing class statistics...
- border white: 218506 voxels (1.30%)
- border gray 254901 voxels (1.52%)
- WM (92.0): 93.3 +- 10.4 [70.0 --> 110.0]
- GM (75.0) : 73.0 +- 13.1 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 44.9 (was 70)
- setting MAX_BORDER_WHITE to 116.4 (was 105)
- setting MIN_BORDER_WHITE to 58.0 (was 85)
- setting MAX_CSF to 31.8 (was 40)
- setting MAX_GRAY to 95.6 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 51.5 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 18.8 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=106, GM=58
- mean inside = 93.2, mean outside = 68.1
- 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/sub014/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.81 +- 0.22 (0.05-->3.25) (max @ vno 113767 --> 117357)
- face area 0.28 +- 0.12 (0.00-->1.51)
- mean absolute distance = 0.67 +- 0.76
- 3601 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 23 points - only 0.00% unknown
- deleting segment 2 with 357 points - only 0.00% unknown
- deleting segment 5 with 55 points - only 0.00% unknown
- deleting segment 6 with 13 points - only 0.00% unknown
- mean border=71.9, 17 (17) missing vertices, mean dist 0.4 [0.5 (%29.7)->0.8 (%70.3))]
- %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 (0.10-->4.57) (max @ vno 50303 --> 53862)
- face area 0.28 +- 0.13 (0.00-->3.04)
- mean absolute distance = 0.31 +- 0.46
- 2612 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=6998481.5, rms=14.14
- 001: dt: 0.5000, sse=6912692.0, rms=10.292 (0.000%)
- 002: dt: 0.5000, sse=7052703.0, rms=8.014 (0.000%)
- 003: dt: 0.5000, sse=7134615.5, rms=6.517 (0.000%)
- 004: dt: 0.5000, sse=7299368.0, rms=5.603 (0.000%)
- 005: dt: 0.5000, sse=7415254.0, rms=5.083 (0.000%)
- 006: dt: 0.5000, sse=7507749.0, rms=4.799 (0.000%)
- 007: dt: 0.5000, sse=7531378.0, rms=4.650 (0.000%)
- 008: dt: 0.5000, sse=7525885.0, rms=4.547 (0.000%)
- 009: dt: 0.5000, sse=7516926.5, rms=4.487 (0.000%)
- 010: dt: 0.5000, sse=7480897.5, rms=4.436 (0.000%)
- rms = 4.40, time step reduction 1 of 3 to 0.250...
- 011: dt: 0.5000, sse=7476975.5, rms=4.404 (0.000%)
- 012: dt: 0.2500, sse=4791525.5, rms=3.051 (0.000%)
- 013: dt: 0.2500, sse=4385472.5, rms=2.585 (0.000%)
- 014: dt: 0.2500, sse=4146337.0, rms=2.492 (0.000%)
- 015: dt: 0.2500, sse=4068522.2, rms=2.397 (0.000%)
- rms = 2.37, time step reduction 2 of 3 to 0.125...
- 016: dt: 0.2500, sse=3987556.5, rms=2.370 (0.000%)
- 017: dt: 0.1250, sse=3767156.0, rms=2.093 (0.000%)
- rms = 2.06, time step reduction 3 of 3 to 0.062...
- 018: dt: 0.1250, sse=3728723.8, rms=2.056 (0.000%)
- positioning took 2.1 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- deleting segment 0 with 2 points - only 0.00% unknown
- deleting segment 1 with 28 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 3 with 309 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 4 with 1 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 7 with 35 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 17 points - only 0.00% unknown
- mean border=76.5, 27 (5) missing vertices, mean dist -0.2 [0.3 (%78.7)->0.2 (%21.3))]
- %82 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.91 +- 0.25 (0.12-->4.73) (max @ vno 50303 --> 53862)
- face area 0.35 +- 0.17 (0.00-->4.19)
- mean absolute distance = 0.21 +- 0.29
- 2107 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4676044.0, rms=6.24
- 019: dt: 0.5000, sse=4850651.0, rms=4.256 (0.000%)
- rms = 4.62, time step reduction 1 of 3 to 0.250...
- 020: dt: 0.2500, sse=4399218.0, rms=3.091 (0.000%)
- 021: dt: 0.2500, sse=4219496.0, rms=2.498 (0.000%)
- 022: dt: 0.2500, sse=4149236.5, rms=2.056 (0.000%)
- 023: dt: 0.2500, sse=4132728.0, rms=2.001 (0.000%)
- 024: dt: 0.2500, sse=4072907.0, rms=1.893 (0.000%)
- rms = 1.92, time step reduction 2 of 3 to 0.125...
- 025: dt: 0.1250, sse=4016019.8, rms=1.801 (0.000%)
- 026: dt: 0.1250, sse=3940913.2, rms=1.679 (0.000%)
- rms = 1.67, time step reduction 3 of 3 to 0.062...
- 027: dt: 0.1250, sse=3903378.8, rms=1.672 (0.000%)
- positioning took 1.2 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- deleting segment 0 with 3 points - only 0.00% unknown
- deleting segment 1 with 41 points - only 7.32% unknown
- deleting segment 2 with 323 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 3 with 1 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 6 with 32 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 7 with 1 points - only 0.00% unknown
- deleting segment 8 with 20 points - only 0.00% unknown
- mean border=80.2, 26 (4) missing vertices, mean dist -0.1 [0.2 (%78.1)->0.2 (%21.9))]
- %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 (0.11-->4.82) (max @ vno 50303 --> 53862)
- face area 0.34 +- 0.16 (0.00-->3.86)
- mean absolute distance = 0.15 +- 0.23
- 2200 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4313592.0, rms=4.59
- 028: dt: 0.5000, sse=4601494.5, rms=4.229 (0.000%)
- rms = 4.41, time step reduction 1 of 3 to 0.250...
- 029: dt: 0.2500, sse=4158098.0, rms=2.658 (0.000%)
- 030: dt: 0.2500, sse=4039340.5, rms=2.216 (0.000%)
- 031: dt: 0.2500, sse=4104406.0, rms=1.843 (0.000%)
- rms = 1.90, time step reduction 2 of 3 to 0.125...
- 032: dt: 0.1250, sse=4033981.0, rms=1.689 (0.000%)
- 033: dt: 0.1250, sse=3953255.2, rms=1.473 (0.000%)
- rms = 1.45, time step reduction 3 of 3 to 0.062...
- 034: dt: 0.1250, sse=3919485.0, rms=1.452 (0.000%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- deleting segment 0 with 3 points - only 0.00% unknown
- deleting segment 1 with 46 points - only 19.57% unknown
- deleting segment 3 with 342 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 4 with 1 points - only 0.00% unknown
- deleting segment 6 with 38 points - only 0.00% unknown
- deleting segment 7 with 21 points - only 0.00% unknown
- deleting segment 8 with 20 points - only 0.00% unknown
- mean border=81.3, 32 (2) missing vertices, mean dist -0.0 [0.2 (%59.5)->0.2 (%40.5))]
- %92 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- repositioning cortical surface to gray/csf boundary.
- smoothing T1 volume with sigma = 2.000
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=3941719.2, rms=1.88
- rms = 2.89, time step reduction 1 of 3 to 0.250...
- 035: dt: 0.2500, sse=4024351.0, rms=1.209 (0.000%)
- 036: dt: 0.2500, sse=4173889.2, rms=1.085 (0.000%)
- rms = 1.10, time step reduction 2 of 3 to 0.125...
- rms = 1.07, time step reduction 3 of 3 to 0.062...
- 037: dt: 0.1250, sse=4173977.0, rms=1.073 (0.000%)
- positioning took 0.5 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- deleting segment 0 with 3 points - only 33.33% unknown
- smoothing surface for 5 iterations...
- mean border=47.6, 32 (32) missing vertices, mean dist 1.7 [2.6 (%0.0)->2.3 (%100.0))]
- %16 local maxima, %55 large gradients and %25 min vals, 1297 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=28242134.0, rms=33.02
- 001: dt: 0.5000, sse=20230816.0, rms=27.358 (0.000%)
- 002: dt: 0.5000, sse=14685759.0, rms=22.653 (0.000%)
- 003: dt: 0.5000, sse=10988190.0, rms=18.871 (0.000%)
- 004: dt: 0.5000, sse=8732321.0, rms=15.888 (0.000%)
- 005: dt: 0.5000, sse=7445387.0, rms=13.551 (0.000%)
- 006: dt: 0.5000, sse=6723859.5, rms=11.759 (0.000%)
- 007: dt: 0.5000, sse=6297987.0, rms=10.234 (0.000%)
- 008: dt: 0.5000, sse=6002012.5, rms=8.874 (0.000%)
- 009: dt: 0.5000, sse=5863830.0, rms=7.618 (0.000%)
- 010: dt: 0.5000, sse=5777709.5, rms=6.561 (0.000%)
- 011: dt: 0.5000, sse=5857119.0, rms=5.728 (0.000%)
- 012: dt: 0.5000, sse=5918205.5, rms=5.149 (0.000%)
- 013: dt: 0.5000, sse=6104452.0, rms=4.762 (0.000%)
- 014: dt: 0.5000, sse=6178183.5, rms=4.540 (0.000%)
- 015: dt: 0.5000, sse=6318538.5, rms=4.390 (0.000%)
- 016: dt: 0.5000, sse=6285598.0, rms=4.304 (0.000%)
- 017: dt: 0.5000, sse=6386846.0, rms=4.234 (0.000%)
- rms = 4.20, time step reduction 1 of 3 to 0.250...
- 018: dt: 0.5000, sse=6367448.5, rms=4.200 (0.000%)
- 019: dt: 0.2500, sse=4491861.5, rms=3.410 (0.000%)
- 020: dt: 0.2500, sse=4297746.5, rms=3.188 (0.000%)
- rms = 3.16, time step reduction 2 of 3 to 0.125...
- 021: dt: 0.2500, sse=4165817.2, rms=3.162 (0.000%)
- 022: dt: 0.1250, sse=3967252.2, rms=3.001 (0.000%)
- rms = 2.98, time step reduction 3 of 3 to 0.062...
- 023: dt: 0.1250, sse=3936385.8, rms=2.980 (0.000%)
- positioning took 2.7 minutes
- mean border=45.3, 740 (1) missing vertices, mean dist 0.2 [0.2 (%49.1)->0.6 (%50.9))]
- %31 local maxima, %44 large gradients and %20 min vals, 294 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=4501635.0, rms=4.93
- 024: dt: 0.5000, sse=4821877.5, rms=4.317 (0.000%)
- rms = 4.31, time step reduction 1 of 3 to 0.250...
- 025: dt: 0.5000, sse=6197797.5, rms=4.313 (0.000%)
- 026: dt: 0.2500, sse=4634065.0, rms=3.373 (0.000%)
- 027: dt: 0.2500, sse=4658152.0, rms=3.116 (0.000%)
- rms = 3.08, time step reduction 2 of 3 to 0.125...
- 028: dt: 0.2500, sse=4532998.0, rms=3.085 (0.000%)
- 029: dt: 0.1250, sse=4348195.0, rms=2.868 (0.000%)
- rms = 2.83, time step reduction 3 of 3 to 0.062...
- 030: dt: 0.1250, sse=4327055.5, rms=2.830 (0.000%)
- positioning took 0.8 minutes
- mean border=42.9, 827 (1) missing vertices, mean dist 0.1 [0.2 (%39.0)->0.4 (%61.0))]
- %51 local maxima, %24 large gradients and %20 min vals, 417 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=4596051.0, rms=4.29
- 031: dt: 0.5000, sse=4851039.5, rms=4.200 (0.000%)
- rms = 4.21, time step reduction 1 of 3 to 0.250...
- 032: dt: 0.2500, sse=4522805.0, rms=3.356 (0.000%)
- 033: dt: 0.2500, sse=4670929.0, rms=3.009 (0.000%)
- 034: dt: 0.2500, sse=4633195.5, rms=2.940 (0.000%)
- 035: dt: 0.2500, sse=4687632.5, rms=2.888 (0.000%)
- rms = 2.90, time step reduction 2 of 3 to 0.125...
- 036: dt: 0.1250, sse=4609061.0, rms=2.807 (0.000%)
- 037: dt: 0.1250, sse=4501050.5, rms=2.694 (0.000%)
- rms = 2.67, time step reduction 3 of 3 to 0.062...
- 038: dt: 0.1250, sse=4474719.0, rms=2.672 (0.000%)
- positioning took 1.1 minutes
- mean border=41.8, 1687 (1) missing vertices, mean dist 0.1 [0.2 (%46.2)->0.3 (%53.8))]
- %55 local maxima, %19 large gradients and %20 min vals, 354 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/sub014/surf/rh.pial...
- writing smoothed curvature to rh.curv.pial
- 000: dt: 0.0000, sse=4534292.0, rms=3.09
- rms = 3.89, time step reduction 1 of 3 to 0.250...
- 039: dt: 0.2500, sse=4417121.5, rms=2.783 (0.000%)
- 040: dt: 0.2500, sse=4572324.5, rms=2.702 (0.000%)
- rms = 2.69, time step reduction 2 of 3 to 0.125...
- 041: dt: 0.2500, sse=4640240.0, rms=2.693 (0.000%)
- 042: dt: 0.1250, sse=4549322.0, rms=2.558 (0.000%)
- rms = 2.54, time step reduction 3 of 3 to 0.062...
- 043: dt: 0.1250, sse=4557541.0, rms=2.537 (0.000%)
- positioning took 0.7 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/rh.curv.pial
- writing smoothed area to rh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/rh.area.pial
- vertex spacing 1.02 +- 0.42 (0.05-->6.47) (max @ vno 84746 --> 84726)
- face area 0.41 +- 0.31 (0.00-->10.23)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 123027 vertices processed
- 25000 of 123027 vertices processed
- 50000 of 123027 vertices processed
- 75000 of 123027 vertices processed
- 100000 of 123027 vertices processed
- 0 of 123027 vertices processed
- 25000 of 123027 vertices processed
- 50000 of 123027 vertices processed
- 75000 of 123027 vertices processed
- 100000 of 123027 vertices processed
- thickness calculation complete, 217:560 truncations.
- 26798 vertices at 0 distance
- 83158 vertices at 1 distance
- 80085 vertices at 2 distance
- 32300 vertices at 3 distance
- 9165 vertices at 4 distance
- 2437 vertices at 5 distance
- 765 vertices at 6 distance
- 271 vertices at 7 distance
- 143 vertices at 8 distance
- 44 vertices at 9 distance
- 44 vertices at 10 distance
- 39 vertices at 11 distance
- 22 vertices at 12 distance
- 6 vertices at 13 distance
- 12 vertices at 14 distance
- 6 vertices at 15 distance
- 5 vertices at 16 distance
- 10 vertices at 17 distance
- 14 vertices at 18 distance
- 8 vertices at 19 distance
- 4 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/rh.thickness
- positioning took 14.2 minutes
- #--------------------------------------------
- #@# Surf Volume rh Thu Aug 8 22:50:16 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 22:50:21 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/scripts
- pctsurfcon --s sub014 --rh-only
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/scripts/pctsurfcon.log
- Thu Aug 8 22:50:21 CEST 2013
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/scripts
- /opt/freesurfer/5.3.0/bin/pctsurfcon
- $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $
- Linux snake5 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
- FREESURFER_HOME /opt/freesurfer/5.3.0
- mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/tmp.pctsurfcon.15796/rh.wm.mgh --regheader sub014 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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/sub014/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/label/rh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 = 95723
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/label/rh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/tmp.pctsurfcon.15796/rh.wm.mgh
- Dim: 123027 1 1
- mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/tmp.pctsurfcon.15796/rh.gm.mgh --projfrac 0.3 --regheader sub014 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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/sub014/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/label/rh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/rh.white
- Done reading source surface
- Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 = 109627
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/label/rh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/tmp.pctsurfcon.15796/rh.gm.mgh
- Dim: 123027 1 1
- mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/tmp.pctsurfcon.15796/rh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/tmp.pctsurfcon.15796/rh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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/sub014/surf/rh.w-g.pct.mgh
- mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/rh.w-g.pct.mgh --annot sub014 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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/sub014/surf/rh.w-g.pct.mgh --annot sub014 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/stats/rh.w-g.pct.stats --snr
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- UseRobust 0
- Constructing seg from annotation
- Reading annotation
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
- Seg base 2000
- Loading /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/rh.w-g.pct.mgh
- Vertex Area is 0.672142 mm^3
- Generating list of segmentation ids
- Found 36 segmentations
- Computing statistics for each segmentation
- 0 2000 unknown 0 0.000
- 1 2001 bankssts 1197 846.033
- 2 2002 caudalanteriorcingulate 1111 731.025
- 3 2003 caudalmiddlefrontal 3037 2081.212
- 4 2004 corpuscallosum 0 0.000
- 5 2005 cuneus 2174 1423.973
- 6 2006 entorhinal 332 220.836
- 7 2007 fusiform 3577 2438.580
- 8 2008 inferiorparietal 7563 5088.471
- 9 2009 inferiortemporal 3913 2649.240
- 10 2010 isthmuscingulate 1638 1077.020
- 11 2011 lateraloccipital 6315 4089.263
- 12 2012 lateralorbitofrontal 3175 2121.831
- 13 2013 lingual 4385 2940.760
- 14 2014 medialorbitofrontal 1815 1258.495
- 15 2015 middletemporal 4785 3347.731
- 16 2016 parahippocampal 857 570.738
- 17 2017 paracentral 2084 1351.224
- 18 2018 parsopercularis 1832 1244.166
- 19 2019 parsorbitalis 1006 697.096
- 20 2020 parstriangularis 1815 1263.648
- 21 2021 pericalcarine 2141 1426.040
- 22 2022 postcentral 5220 3523.962
- 23 2023 posteriorcingulate 1661 1107.496
- 24 2024 precentral 6110 4129.170
- 25 2025 precuneus 6102 4137.942
- 26 2026 rostralanteriorcingulate 852 600.274
- 27 2027 rostralmiddlefrontal 8383 5741.095
- 28 2028 superiorfrontal 9397 6407.274
- 29 2029 superiorparietal 8356 5442.966
- 30 2030 superiortemporal 5256 3644.782
- 31 2031 supramarginal 4837 3345.102
- 32 2032 frontalpole 349 209.946
- 33 2033 temporalpole 520 358.388
- 34 2034 transversetemporal 453 284.481
- 35 2035 insula 2797 1848.760
- Reporting on 34 segmentations
- mri_segstats done
- Cleaning up
- #-----------------------------------------
- #@# Parcellation Stats rh Thu Aug 8 22:50:41 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 sub014 rh white
- computing statistics for each annotation in ../label/rh.aparc.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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
- 1197 846 2026 2.426 0.324 0.117 0.030 10 1.5 bankssts
- 1111 731 2170 2.961 0.636 0.174 0.075 30 3.2 caudalanteriorcingulate
- 3037 2081 5652 2.474 0.467 0.136 0.042 41 5.5 caudalmiddlefrontal
- 2174 1424 3389 2.140 0.392 0.175 0.067 48 5.9 cuneus
- 332 221 1258 3.761 0.603 0.127 0.044 4 0.5 entorhinal
- 3577 2439 6954 2.557 0.496 0.154 0.072 97 7.7 fusiform
- 7563 5088 13450 2.364 0.477 0.148 0.055 144 16.3 inferiorparietal
- 3913 2649 7479 2.306 0.704 0.155 0.066 89 10.2 inferiortemporal
- 1638 1077 3117 2.547 0.737 0.165 0.079 41 4.8 isthmuscingulate
- 6315 4089 10381 2.275 0.440 0.164 0.059 130 14.6 lateraloccipital
- 3175 2122 6556 2.727 0.547 0.157 0.063 69 8.0 lateralorbitofrontal
- 4385 2941 6875 2.127 0.551 0.166 0.065 98 12.0 lingual
- 1815 1258 3412 2.379 0.581 0.177 0.085 97 6.3 medialorbitofrontal
- 4785 3348 11543 2.698 0.627 0.153 0.069 142 11.0 middletemporal
- 857 571 2075 2.879 0.618 0.136 0.120 43 1.7 parahippocampal
- 2084 1351 3425 2.379 0.482 0.120 0.036 22 3.3 paracentral
- 1832 1244 3508 2.476 0.421 0.151 0.058 55 4.0 parsopercularis
- 1006 697 2501 2.842 0.475 0.188 0.084 30 3.2 parsorbitalis
- 1815 1264 3527 2.479 0.409 0.150 0.054 38 3.6 parstriangularis
- 2141 1426 2721 1.949 0.464 0.148 0.072 33 4.9 pericalcarine
- 5220 3524 7553 1.922 0.544 0.145 0.053 87 11.5 postcentral
- 1661 1107 3352 2.697 0.671 0.162 0.064 35 4.2 posteriorcingulate
- 6110 4129 10975 2.423 0.480 0.123 0.034 64 8.8 precentral
- 6102 4138 10593 2.369 0.481 0.150 0.068 136 14.9 precuneus
- 852 600 2176 3.177 0.477 0.169 0.069 20 2.2 rostralanteriorcingulate
- 8383 5741 16014 2.414 0.468 0.154 0.063 176 18.9 rostralmiddlefrontal
- 9397 6407 19953 2.746 0.491 0.142 0.046 142 17.2 superiorfrontal
- 8356 5443 13080 2.145 0.410 0.135 0.044 132 15.5 superiorparietal
- 5256 3645 11688 2.819 0.565 0.136 0.069 101 8.9 superiortemporal
- 4837 3345 8897 2.334 0.528 0.141 0.045 82 8.9 supramarginal
- 349 210 798 2.594 0.578 0.212 0.128 16 1.9 frontalpole
- 520 358 1802 3.822 0.794 0.158 0.095 11 2.4 temporalpole
- 453 284 845 2.665 0.392 0.154 0.060 9 0.9 transversetemporal
- 2797 1849 5891 3.000 0.747 0.139 0.103 79 12.9 insula
- #-----------------------------------------
- #@# Cortical Parc 2 rh Thu Aug 8 22:51:00 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub014 rh ../surf/rh.sphere.reg /opt/freesurfer/5.3.0/average/rh.destrieux.simple.2009-07-29.gcs ../label/rh.aparc.a2009s.annot
- setting seed for random number generator to 1234
- using ../mri/aseg.mgz aseg volume to correct midline
- $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading atlas from /opt/freesurfer/5.3.0/average/rh.destrieux.simple.2009-07-29.gcs...
- reading color table from GCSA file....
- average std = 1.9 0.2 using min determinant for regularization = 0.000
- 0 singular and 851 ill-conditioned covariance matrices regularized
- input 1: CURVATURE FILE, flags 0, avgs 0, name sulc
- input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
- labeling surface...
- 20 labels changed using aseg
- relabeling using gibbs priors...
- 000: 8871 changed, 123027 examined...
- 001: 2070 changed, 34235 examined...
- 002: 662 changed, 10712 examined...
- 003: 289 changed, 3677 examined...
- 004: 135 changed, 1671 examined...
- 005: 84 changed, 784 examined...
- 006: 41 changed, 445 examined...
- 007: 19 changed, 245 examined...
- 008: 16 changed, 105 examined...
- 009: 13 changed, 87 examined...
- 010: 7 changed, 59 examined...
- 011: 4 changed, 42 examined...
- 012: 4 changed, 29 examined...
- 013: 1 changed, 20 examined...
- 014: 0 changed, 6 examined...
- 2 labels changed using aseg
- 000: 240 total segments, 158 labels (1836 vertices) changed
- 001: 87 total segments, 5 labels (10 vertices) changed
- 002: 82 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 110 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 524 vertices marked for relabeling...
- 524 labels changed in reclassification.
- writing output to ../label/rh.aparc.a2009s.annot...
- classification took 1 minutes and 9 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 2 rh Thu Aug 8 22:52:09 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 sub014 rh white
- computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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
- 950 617 1551 2.210 0.402 0.153 0.063 23 2.6 G_and_S_frontomargin
- 991 660 1934 2.486 0.404 0.153 0.049 18 1.8 G_and_S_occipital_inf
- 1252 773 2183 2.367 0.541 0.142 0.069 25 3.9 G_and_S_paracentral
- 1594 1084 2977 2.394 0.525 0.147 0.041 25 2.9 G_and_S_subcentral
- 860 606 1978 2.597 0.479 0.197 0.102 32 3.1 G_and_S_transv_frontopol
- 2215 1565 4550 2.731 0.560 0.148 0.062 38 4.8 G_and_S_cingul-Ant
- 1836 1232 3699 2.828 0.543 0.148 0.051 33 4.0 G_and_S_cingul-Mid-Ant
- 1136 801 2230 2.662 0.545 0.132 0.043 14 1.9 G_and_S_cingul-Mid-Post
- 698 439 1788 3.153 0.510 0.202 0.115 25 2.9 G_cingul-Post-dorsal
- 271 169 644 2.954 0.737 0.188 0.080 8 0.9 G_cingul-Post-ventral
- 2016 1336 3177 2.103 0.412 0.178 0.074 47 5.8 G_cuneus
- 1074 756 2764 2.738 0.351 0.166 0.069 46 2.7 G_front_inf-Opercular
- 255 178 570 2.530 0.420 0.195 0.097 9 1.0 G_front_inf-Orbital
- 782 525 1895 2.725 0.338 0.179 0.070 25 2.0 G_front_inf-Triangul
- 4072 2813 9676 2.623 0.451 0.170 0.077 110 10.4 G_front_middle
- 5733 3851 13912 2.864 0.474 0.154 0.054 110 13.0 G_front_sup
- 450 311 1127 2.970 0.655 0.122 0.035 6 0.6 G_Ins_lg_and_S_cent_ins
- 579 375 1925 3.689 0.755 0.205 0.326 53 9.4 G_insular_short
- 1989 1294 4254 2.598 0.454 0.176 0.081 55 6.1 G_occipital_middle
- 1548 937 2663 2.261 0.386 0.139 0.049 30 2.9 G_occipital_sup
- 1520 1011 3076 2.593 0.513 0.160 0.106 61 3.8 G_oc-temp_lat-fusifor
- 2739 1808 4709 2.225 0.610 0.179 0.072 73 8.6 G_oc-temp_med-Lingual
- 1021 663 2896 3.292 0.696 0.153 0.124 48 2.4 G_oc-temp_med-Parahip
- 2331 1563 6127 2.898 0.556 0.182 0.083 78 7.3 G_orbital
- 2901 2031 6727 2.550 0.546 0.180 0.075 89 8.2 G_pariet_inf-Angular
- 2068 1466 4487 2.447 0.519 0.157 0.058 49 4.7 G_pariet_inf-Supramar
- 2763 1873 5207 2.216 0.403 0.147 0.051 57 6.3 G_parietal_sup
- 1815 1218 2789 1.883 0.423 0.158 0.065 37 4.4 G_postcentral
- 2079 1389 4816 2.655 0.423 0.144 0.045 35 3.9 G_precentral
- 3214 2123 6508 2.416 0.481 0.173 0.089 108 11.0 G_precuneus
- 487 344 1042 2.332 0.575 0.227 0.129 65 2.5 G_rectus
- 223 135 471 3.092 0.461 0.165 0.096 8 1.0 G_subcallosal
- 374 229 730 2.625 0.363 0.145 0.061 8 0.7 G_temp_sup-G_T_transv
- 1754 1244 4713 2.967 0.510 0.170 0.145 65 4.1 G_temp_sup-Lateral
- 678 482 1844 3.422 0.709 0.105 0.028 4 0.7 G_temp_sup-Plan_polar
- 769 557 1519 2.496 0.413 0.129 0.042 12 1.5 G_temp_sup-Plan_tempo
- 2245 1488 4787 2.357 0.706 0.173 0.084 70 7.6 G_temporal_inf
- 2876 2053 8162 2.836 0.593 0.178 0.094 121 8.6 G_temporal_middle
- 421 290 715 2.377 0.237 0.122 0.038 5 0.7 Lat_Fis-ant-Horizont
- 167 126 226 1.978 0.368 0.111 0.019 1 0.1 Lat_Fis-ant-Vertical
- 1376 913 1921 2.516 0.450 0.123 0.038 11 2.1 Lat_Fis-post
- 3272 2093 4848 2.068 0.445 0.170 0.071 72 8.6 Pole_occipital
- 1664 1135 5130 3.251 0.693 0.170 0.084 42 5.8 Pole_temporal
- 2440 1680 3373 2.086 0.531 0.141 0.066 40 4.9 S_calcarine
- 2540 1732 2939 1.866 0.547 0.110 0.027 15 3.1 S_central
- 1110 780 1626 2.121 0.338 0.103 0.025 6 1.1 S_cingul-Marginalis
- 573 382 945 2.734 0.462 0.110 0.032 4 0.8 S_circular_insula_ant
- 1190 757 1759 2.608 0.551 0.091 0.026 6 1.3 S_circular_insula_inf
- 1167 804 1756 2.492 0.496 0.124 0.037 12 1.7 S_circular_insula_sup
- 610 435 827 2.042 0.544 0.131 0.031 6 0.8 S_collat_transv_ant
- 679 447 924 2.099 0.314 0.149 0.051 11 1.4 S_collat_transv_post
- 2029 1337 2782 2.249 0.364 0.136 0.046 28 3.9 S_front_inf
- 2294 1564 3416 2.248 0.405 0.134 0.039 27 3.6 S_front_middle
- 2806 1930 4454 2.350 0.440 0.126 0.039 28 4.0 S_front_sup
- 470 301 507 1.858 0.241 0.101 0.020 2 0.5 S_interm_prim-Jensen
- 3431 2238 4347 2.032 0.376 0.125 0.036 36 5.2 S_intrapariet_and_P_trans
- 1042 700 1275 2.039 0.382 0.144 0.043 13 1.8 S_oc_middle_and_Lunatus
- 1584 1052 2177 2.156 0.347 0.126 0.036 16 2.4 S_oc_sup_and_transversal
- 482 323 647 2.211 0.389 0.124 0.034 5 0.7 S_occipital_ant
- 536 368 884 2.300 0.444 0.149 0.040 11 0.8 S_oc-temp_lat
- 1829 1244 3065 2.418 0.469 0.134 0.037 24 2.9 S_oc-temp_med_and_Lingual
- 367 282 741 2.541 0.393 0.192 0.080 9 1.0 S_orbital_lateral
- 497 352 717 2.127 0.567 0.132 0.031 4 0.7 S_orbital_med-olfact
- 1255 833 2174 2.655 0.437 0.144 0.054 17 2.9 S_orbital-H_Shaped
- 2091 1411 3030 2.338 0.459 0.127 0.037 22 3.1 S_parieto_occipital
- 1425 921 1966 2.506 0.830 0.158 0.055 30 3.0 S_pericallosal
- 2024 1330 2290 1.913 0.392 0.132 0.039 22 3.3 S_postcentral
- 1476 1022 2468 2.492 0.379 0.120 0.037 14 2.1 S_precentral-inf-part
- 1332 916 1850 2.217 0.386 0.103 0.023 8 1.4 S_precentral-sup-part
- 177 128 330 2.521 0.439 0.165 0.048 3 0.4 S_suborbital
- 1295 877 2034 2.396 0.411 0.137 0.044 14 2.3 S_subparietal
- 1336 931 1741 2.038 0.394 0.117 0.028 9 1.6 S_temporal_inf
- 5621 3819 9147 2.424 0.472 0.119 0.031 52 7.2 S_temporal_sup
- 279 196 498 2.741 0.555 0.153 0.036 4 0.5 S_temporal_transverse
- #-----------------------------------------
- #@# Cortical Parc 3 rh Thu Aug 8 22:52:34 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub014 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...
- 949 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2497 changed, 123027 examined...
- 001: 593 changed, 10771 examined...
- 002: 157 changed, 3215 examined...
- 003: 53 changed, 904 examined...
- 004: 20 changed, 283 examined...
- 005: 20 changed, 111 examined...
- 006: 18 changed, 112 examined...
- 007: 11 changed, 78 examined...
- 008: 8 changed, 48 examined...
- 009: 5 changed, 38 examined...
- 010: 1 changed, 27 examined...
- 011: 0 changed, 7 examined...
- 149 labels changed using aseg
- 000: 55 total segments, 22 labels (267 vertices) changed
- 001: 33 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 40 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 419 vertices marked for relabeling...
- 419 labels changed in reclassification.
- writing output to ../label/rh.aparc.DKTatlas40.annot...
- classification took 1 minutes and 14 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 3 rh Thu Aug 8 22:53:49 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 sub014 rh white
- computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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
- 1111 736 2180 2.969 0.632 0.169 0.069 28 2.7 caudalanteriorcingulate
- 3121 2128 5729 2.471 0.476 0.136 0.042 42 5.6 caudalmiddlefrontal
- 2676 1762 4117 2.149 0.371 0.165 0.060 52 6.5 cuneus
- 363 247 1278 3.628 0.664 0.139 0.049 4 0.6 entorhinal
- 3148 2145 6003 2.531 0.485 0.155 0.074 91 6.7 fusiform
- 7114 4778 12719 2.369 0.482 0.149 0.057 139 15.7 inferiorparietal
- 4256 2878 8273 2.346 0.710 0.155 0.066 94 11.1 inferiortemporal
- 1605 1054 3067 2.549 0.738 0.165 0.080 40 4.8 isthmuscingulate
- 6628 4292 10838 2.269 0.436 0.162 0.057 133 15.0 lateraloccipital
- 3537 2346 7423 2.694 0.575 0.165 0.072 91 10.2 lateralorbitofrontal
- 4363 2917 6862 2.132 0.550 0.165 0.065 97 11.8 lingual
- 1293 900 2598 2.427 0.644 0.185 0.093 85 5.0 medialorbitofrontal
- 5686 3980 13096 2.655 0.606 0.147 0.063 150 12.1 middletemporal
- 834 560 2021 2.870 0.617 0.134 0.121 42 1.6 parahippocampal
- 2182 1419 3750 2.421 0.501 0.120 0.036 23 3.4 paracentral
- 1819 1239 3385 2.452 0.425 0.149 0.059 55 3.9 parsopercularis
- 1048 715 2334 2.690 0.463 0.160 0.063 22 2.7 parsorbitalis
- 2021 1389 3953 2.504 0.408 0.153 0.056 42 4.2 parstriangularis
- 2166 1450 2744 1.941 0.469 0.149 0.073 34 5.2 pericalcarine
- 5617 3794 8153 1.930 0.552 0.145 0.053 94 12.1 postcentral
- 1754 1178 3518 2.689 0.662 0.164 0.067 39 4.7 posteriorcingulate
- 6022 4062 10931 2.436 0.476 0.124 0.034 65 9.0 precentral
- 6190 4182 10907 2.374 0.482 0.149 0.068 138 15.1 precuneus
- 996 692 2399 3.081 0.541 0.170 0.069 23 2.6 rostralanteriorcingulate
- 5711 3891 11032 2.426 0.485 0.152 0.064 115 12.6 rostralmiddlefrontal
- 12136 8327 24999 2.657 0.504 0.147 0.051 209 24.2 superiorfrontal
- 7274 4752 11381 2.146 0.407 0.136 0.045 119 13.8 superiorparietal
- 6728 4674 15387 2.871 0.660 0.139 0.068 127 12.9 superiortemporal
- 4582 3153 8115 2.310 0.501 0.137 0.043 72 8.2 supramarginal
- 449 281 835 2.671 0.392 0.155 0.060 9 0.9 transversetemporal
- 2615 1727 5610 3.005 0.712 0.138 0.102 75 12.5 insula
- #--------------------------------------------
- #@# Refine Pial Surfs w/ T2/FLAIR Thu Aug 8 22:54:13 CEST 2013
- bbregister --s sub014 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/T2raw.lta --init-fsl --T2
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/T2raw.dat.log
- Thu Aug 8 22:54:13 CEST 2013
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/scripts
- /opt/freesurfer/5.3.0/bin/bbregister --s sub014 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/T2raw.lta --init-fsl --T2
- $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $
- Linux snake5 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
- FREESURFER_HOME /opt/freesurfer/5.3.0
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/template.nii
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/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/sub014/mri/orig/T2raw.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.999671, 0.0251903, -0.0048728)
- j_ras = (0.0252193, 0.999664, -0.00597949)
- k_ras = (-0.00472054, 0.00610041, 0.99997)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/template.nii...
- fslregister --s sub014 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/fslregister --dof 6 --fsvol brainmask.mgz
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/reg.init.dat.fslregister.log
- Thu Aug 8 22:54:19 CEST 2013
- --s sub014 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/fslregister --dof 6 --fsvol brainmask.mgz
- $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $
- snake5
- Linux snake5 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
- nIters 1
- --------------------------------------
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/scripts
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/fslregister/refvol.fslregister.nii
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/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/sub014/mri/brainmask.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, -4.89672e-09, 4.65661e-10)
- j_ras = (0, 0, -1)
- k_ras = (1.16779e-09, 1, -9.31323e-10)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/fslregister/refvol.fslregister.nii...
- --------------------------------------
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/scripts
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/fslregister/movvol.fslregister.nii --frame 0
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/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/sub014/mri/transforms/tmp.bbregister.16273/template.nii...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.999671, 0.0251903, -0.0048728)
- j_ras = (0.0252193, 0.999664, -0.00597949)
- k_ras = (-0.00472054, 0.00610041, 0.99997)
- keeping frame 0
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/fslregister/movvol.fslregister.nii...
- Mov determinant is -0.3111
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/scripts
- tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/fslregister/movvol.fslregister.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/fslregister/reg0.16313.dat --regheader --fslregout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/reg.init.dat.fsl.mat0 --s sub014 --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/sub014/mri/transforms/tmp.bbregister.16273/fslregister/movvol.fslregister.nii
- reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/fslregister/reg0.16313.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/sub014/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/sub014/mri/transforms/tmp.bbregister.16273/fslregister/movvol.fslregister.nii
- Tmov: --------------------
- -0.700 0.000 0.000 95.896;
- 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) --------
- 1.000 -0.025 0.005 0.000;
- -0.005 0.006 1.000 0.000;
- -0.025 -1.000 0.006 -0.000;
- 0.000 0.000 0.000 1.000;
- ---------------------------------------
- ---- Input registration matrix --------
- 1.000 -0.025 0.005 0.000;
- -0.005 0.006 1.000 0.000;
- -0.025 -1.000 0.006 -0.000;
- 0.000 0.000 0.000 1.000;
- Determinant 1
- subject = sub014
- RegMat ---------------------------
- 1.000 -0.025 0.005 0.000;
- -0.005 0.006 1.000 0.000;
- -0.025 -1.000 0.006 -0.000;
- 0.000 0.000 0.000 1.000;
- FSLOUTPUTTYPE NIFTI
- tkreg2FSL: mov det = -0.3111, ref det = -1
- Thu Aug 8 22:54:31 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/scripts
- flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/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/sub014/mri/transforms/tmp.bbregister.16273/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/reg.init.dat.fsl.mat0
- Thu Aug 8 22:59:26 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/scripts
- flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/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/sub014/mri/transforms/tmp.bbregister.16273/reg.init.dat.fsl.mat -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/fslregister/fslmat0.trans.mat -schedule /opt/freesurfer/5.3.0/bin/flirt.newdefault.20080811.sch
- tkregister2_cmdl --s sub014 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/reg.init.dat --fslreg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/reg.init.dat.fsl.mat --noedit
- tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl
- ---- FSL registration matrix --------
- 0.999 -0.017 0.038 28.742;
- 0.038 -0.002 -0.999 255.609;
- 0.017 1.000 -0.001 -2.635;
- 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/sub014/mri/transforms/tmp.bbregister.16273/template.nii
- reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/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/sub014/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/sub014/mri/transforms/tmp.bbregister.16273/template.nii
- Tmov: --------------------
- -0.700 0.000 0.000 95.896;
- 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 = -0.3111, ref det = -1
- ---- Input registration matrix (computed) --------
- 0.999 -0.017 0.038 -0.640;
- -0.038 -0.001 0.999 3.103;
- -0.017 -1.000 -0.002 -1.207;
- 0.000 0.000 0.000 1.000;
- ---------------------------------------
- ---- Input registration matrix --------
- 0.999 -0.017 0.038 -0.640;
- -0.038 -0.001 0.999 3.103;
- -0.017 -1.000 -0.002 -1.207;
- 0.000 0.000 0.000 1.000;
- Determinant 1
- subject = sub014
- RegMat ---------------------------
- 0.999 -0.017 0.038 -0.640;
- -0.038 -0.001 0.999 3.103;
- -0.017 -1.000 -0.002 -1.207;
- 0.000 0.000 0.000 1.000;
-
- Started at Thu Aug 8 22:54:19 CEST 2013
- Ended at Thu Aug 8 23:05:15 CEST 2013
-
- fslregister Done
-
- To check results, run:
- tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/reg.init.dat --surf orig
-
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/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/sub014/scripts
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/template.nii
- regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/reg.init.dat
- subject sub014
- dof 6
- outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/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 1376461260
- TransRandMax 0.000000
- RotRandMax 0.000000
- Translations 0.000000 0.000000 0.000000
- Rotations 0.000000 0.000000 0.000000
- Input reg
- 0.999 -0.017 0.038 -0.640;
- -0.038 -0.001 0.999 3.103;
- -0.017 -1.000 -0.002 -1.207;
- 0.000 0.000 0.000 1.000;
- Loading mov
- Projecting LH Surfs
- Loading lh.white surf
- Loading lh.thickness for GM
- GM Proj: 1 0.500000 2.000000
- WM Proj: 0 0.500000 2.000000
- Projecting RH Surfs
- Loading rh.white surf
- Loading rh.thickness
- Projecting RH Surfs
- Computing relative cost
- 0 -25.0 -25.0 -25.0 0.986752
- 1 -25.0 -25.0 25.0 1.002092
- 2 -25.0 25.0 -25.0 0.990588
- 3 -25.0 25.0 25.0 0.978944
- 4 25.0 -25.0 -25.0 1.009483
- 5 25.0 -25.0 25.0 1.038056
- 6 25.0 25.0 -25.0 1.035361
- 7 25.0 25.0 25.0 1.043742
- REL: 8 0.900028 8.085019 1.010627 rel = 0.890563
- Initial costs ----------------
- Number of surface hits 2294
- WM Intensity 63.2230 +/- 16.6547
- Ctx Intensity 67.4687 +/- 21.8448
- Pct Contrast 4.9138 +/- 30.3109
- Cost 0.9000
- RelCost 0.8906
- ------------------------------------
- Brute force preopt -4 4 4, n = 729
- 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9121 0.9121 0.0
- 19 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.0000 0.8636 0.8636 0.0
- 21 -4.0000 -4.0000 -4.0000 4.0000 0.0000 -4.0000 0.8472 0.8472 0.0
- 39 -4.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.8438 0.8438 0.0
- 42 -4.0000 -4.0000 0.0000 0.0000 4.0000 -4.0000 0.8318 0.8318 0.0
- 43 -4.0000 -4.0000 0.0000 0.0000 4.0000 0.0000 0.7828 0.7828 0.0
- 265 0.0000 -4.0000 -4.0000 4.0000 0.0000 0.0000 0.6949 0.6949 0.0
- 283 0.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.4784 0.4784 0.0
- Brute Force --------------------------
- Min cost was 0.478408
- Number of iterations 729
- Search time 1.954000 sec
- Parameters at best (transmm, rotdeg)
- 0.000 -4.000 0.000 0.000 0.000 0.000
- --------------------------------------------
- Starting Powell Minimization
- Init Powel Params dof = 6
- 0 0
- 1 -4
- 2 0
- 3 0
- 4 0
- 5 0
- 9 -0.090 -4.000 0.000 0.000 0.000 0.000 0.4783318782
- 10 -0.052 -4.000 0.000 0.000 0.000 0.000 0.4779906850
- 12 -0.062 -4.000 0.000 0.000 0.000 0.000 0.4779337422
- 13 -0.064 -4.000 0.000 0.000 0.000 0.000 0.4779336111
- 20 -0.064 -3.618 0.000 0.000 0.000 0.000 0.4692872480
- 23 -0.064 -3.617 0.000 0.000 0.000 0.000 0.4692847807
- 25 -0.064 -3.616 0.000 0.000 0.000 0.000 0.4692836165
- 27 -0.064 -3.616 1.000 0.000 0.000 0.000 0.2951205999
- 30 -0.064 -3.616 1.618 0.000 0.000 0.000 0.2382767933
- 34 -0.064 -3.616 1.619 0.000 0.000 0.000 0.2382719202
- 35 -0.064 -3.616 1.628 0.000 0.000 0.000 0.2382554089
- 37 -0.064 -3.616 1.626 0.000 0.000 0.000 0.2382540536
- 44 -0.064 -3.616 1.626 0.382 0.000 0.000 0.2086442006
- 49 -0.064 -3.616 1.626 0.378 0.000 0.000 0.2086356021
- 52 -0.064 -3.616 1.626 0.377 0.000 0.000 0.2086350000
- 63 -0.064 -3.616 1.626 0.377 0.020 0.000 0.2084471240
- 68 -0.064 -3.616 1.626 0.377 0.020 1.000 0.2030106289
- 72 -0.064 -3.616 1.626 0.377 0.020 0.618 0.1709380935
- 73 -0.064 -3.616 1.626 0.377 0.020 0.483 0.1683528079
- 74 -0.064 -3.616 1.626 0.377 0.020 0.474 0.1682443152
- 78 -0.064 -3.616 1.626 0.377 0.020 0.470 0.1682313475
- 79 -0.064 -3.616 1.626 0.377 0.020 0.469 0.1682311997
- 87 0.318 -3.616 1.626 0.377 0.020 0.469 0.1645247877
- 88 0.171 -3.616 1.626 0.377 0.020 0.469 0.1570430992
- 90 0.163 -3.616 1.626 0.377 0.020 0.469 0.1570034986
- 99 0.163 -3.482 1.626 0.377 0.020 0.469 0.1531713886
- 100 0.163 -3.473 1.626 0.377 0.020 0.469 0.1531098361
- 111 0.163 -3.473 1.603 0.377 0.020 0.469 0.1527427783
- 113 0.163 -3.473 1.596 0.377 0.020 0.469 0.1527163810
- 122 0.163 -3.473 1.596 0.525 0.020 0.469 0.1447793822
- 123 0.163 -3.473 1.596 0.540 0.020 0.469 0.1447316420
- 124 0.163 -3.473 1.596 0.537 0.020 0.469 0.1447207893
- 133 0.163 -3.473 1.596 0.537 -0.013 0.469 0.1446372607
- 134 0.163 -3.473 1.596 0.537 -0.008 0.469 0.1446313075
- 135 0.163 -3.473 1.596 0.537 -0.006 0.469 0.1446299267
- 146 0.163 -3.473 1.596 0.537 -0.006 0.582 0.1444223367
- 147 0.163 -3.473 1.596 0.537 -0.006 0.534 0.1439491560
- 148 0.163 -3.473 1.596 0.537 -0.006 0.531 0.1439401099
- 149 0.163 -3.473 1.596 0.537 -0.006 0.523 0.1439128925
- 151 0.163 -3.473 1.596 0.537 -0.006 0.517 0.1439003024
- 156 0.390 -3.331 1.565 0.698 -0.031 0.565 0.1359593906
- 162 0.303 -3.386 1.577 0.637 -0.021 0.546 0.1351754334
- 163 0.326 -3.371 1.573 0.653 -0.024 0.551 0.1351399000
- 165 0.351 -3.356 1.570 0.670 -0.027 0.556 0.1349389288
- 168 0.351 -3.355 1.570 0.671 -0.027 0.557 0.1349379317
- 170 0.353 -3.354 1.570 0.672 -0.027 0.557 0.1349363417
- 171 0.355 -3.353 1.570 0.673 -0.027 0.557 0.1349345705
- 173 0.355 -3.353 1.570 0.673 -0.027 0.557 0.1349345013
- 181 0.355 -3.353 1.570 0.673 -0.027 0.693 0.1338980484
- 182 0.355 -3.353 1.570 0.673 -0.027 0.662 0.1334638298
- 183 0.355 -3.353 1.570 0.673 -0.027 0.644 0.1332582195
- 184 0.355 -3.353 1.570 0.673 -0.027 0.611 0.1331272357
- 185 0.355 -3.353 1.570 0.673 -0.027 0.614 0.1331081966
- 186 0.355 -3.353 1.570 0.673 -0.027 0.621 0.1330992368
- 188 0.355 -3.353 1.570 0.673 -0.027 0.619 0.1330973869
- 189 0.355 -3.353 1.570 0.673 -0.027 0.620 0.1330972848
- 196 0.355 -3.273 1.570 0.673 -0.027 0.620 0.1314136237
- 198 0.355 -3.293 1.570 0.673 -0.027 0.620 0.1312442943
- 200 0.355 -3.292 1.570 0.673 -0.027 0.620 0.1312441423
- 208 0.355 -3.292 1.321 0.673 -0.027 0.620 0.1249550417
- 209 0.355 -3.292 1.345 0.673 -0.027 0.620 0.1246001406
- 210 0.355 -3.292 1.374 0.673 -0.027 0.620 0.1239649641
- 212 0.355 -3.292 1.402 0.673 -0.027 0.620 0.1237298032
- 213 0.355 -3.292 1.403 0.673 -0.027 0.620 0.1237290083
- 222 0.355 -3.292 1.403 0.725 -0.027 0.620 0.1229477132
- 225 0.355 -3.292 1.403 0.773 -0.027 0.620 0.1225203345
- 228 0.355 -3.292 1.403 0.769 -0.027 0.620 0.1225137724
- 229 0.355 -3.292 1.403 0.770 -0.027 0.620 0.1225117835
- 230 0.355 -3.292 1.403 0.771 -0.027 0.620 0.1225112393
- 239 0.355 -3.292 1.403 0.771 -0.044 0.620 0.1224102040
- 247 0.441 -3.238 1.391 0.832 -0.054 0.638 0.1223575197
- 248 0.400 -3.264 1.396 0.803 -0.049 0.630 0.1217148605
- 250 0.401 -3.263 1.396 0.804 -0.049 0.630 0.1217111139
- 253 0.404 -3.261 1.396 0.805 -0.049 0.630 0.1217092478
- 254 0.403 -3.262 1.396 0.805 -0.049 0.630 0.1217092091
- 263 0.403 -3.262 1.396 0.805 -0.049 0.721 0.1203724297
- 264 0.403 -3.262 1.396 0.805 -0.049 0.716 0.1202262294
- 265 0.403 -3.262 1.396 0.805 -0.049 0.689 0.1199872847
- 268 0.403 -3.262 1.396 0.805 -0.049 0.687 0.1199845214
- 270 0.403 -3.262 1.396 0.805 -0.049 0.685 0.1199837585
- 278 0.403 -3.217 1.396 0.805 -0.049 0.685 0.1185900177
- 281 0.403 -3.219 1.396 0.805 -0.049 0.685 0.1185879503
- 289 0.403 -3.219 1.207 0.805 -0.049 0.685 0.1182555060
- 290 0.403 -3.219 1.293 0.805 -0.049 0.685 0.1171410312
- 291 0.403 -3.219 1.295 0.805 -0.049 0.685 0.1171095932
- 292 0.403 -3.219 1.334 0.805 -0.049 0.685 0.1169789739
- 293 0.403 -3.219 1.321 0.805 -0.049 0.685 0.1169075832
- 295 0.403 -3.219 1.322 0.805 -0.049 0.685 0.1169074812
- 305 0.403 -3.219 1.322 0.811 -0.049 0.685 0.1169052328
- 306 0.403 -3.219 1.322 0.809 -0.049 0.685 0.1169035521
- 308 0.403 -3.219 1.322 0.810 -0.049 0.685 0.1169028510
- 315 0.403 -3.219 1.322 0.810 -0.094 0.685 0.1168989821
- 316 0.403 -3.219 1.322 0.810 -0.072 0.685 0.1167708612
- 317 0.403 -3.219 1.322 0.810 -0.071 0.685 0.1167690868
- 327 0.350 -3.253 1.329 0.772 -0.065 0.674 0.1160915877
- 329 0.369 -3.241 1.326 0.786 -0.067 0.678 0.1158896702
- 338 0.334 -3.220 1.256 0.766 -0.085 0.726 0.1152588601
- 375 0.369 -3.227 1.279 0.786 -0.067 0.704 0.1150847833
- 376 0.369 -3.227 1.296 0.786 -0.067 0.704 0.1149927504
- 378 0.369 -3.227 1.298 0.786 -0.067 0.704 0.1149843094
- 380 0.369 -3.227 1.302 0.786 -0.067 0.704 0.1149822754
- 381 0.369 -3.227 1.301 0.786 -0.067 0.704 0.1149809297
- 390 0.369 -3.227 1.301 0.780 -0.067 0.704 0.1149124844
- 391 0.369 -3.227 1.301 0.772 -0.067 0.704 0.1148219403
- 393 0.369 -3.227 1.301 0.767 -0.067 0.704 0.1148020374
- 394 0.369 -3.227 1.301 0.766 -0.067 0.704 0.1148018888
- 404 0.369 -3.227 1.301 0.766 -0.062 0.704 0.1147794300
- 405 0.369 -3.227 1.301 0.766 -0.060 0.704 0.1147777970
- 415 0.355 -3.236 1.303 0.756 -0.059 0.701 0.1144934537
- 420 0.355 -3.235 1.303 0.756 -0.059 0.701 0.1144932723
- 432 0.355 -3.235 1.303 0.756 -0.059 0.713 0.1143062356
- 433 0.355 -3.235 1.303 0.756 -0.059 0.717 0.1143047062
- 434 0.355 -3.235 1.303 0.756 -0.059 0.715 0.1142997976
- 445 0.355 -3.229 1.303 0.756 -0.059 0.715 0.1142576359
- 458 0.355 -3.229 1.306 0.756 -0.059 0.715 0.1142561167
- 459 0.355 -3.229 1.305 0.756 -0.059 0.715 0.1142559662
- 469 0.355 -3.229 1.305 0.766 -0.059 0.715 0.1142360703
- 470 0.355 -3.229 1.305 0.762 -0.059 0.715 0.1142188278
- 481 0.355 -3.229 1.305 0.762 -0.047 0.715 0.1141424320
- 482 0.355 -3.229 1.305 0.762 -0.046 0.715 0.1141412866
- 493 0.347 -3.234 1.306 0.757 -0.045 0.713 0.1140424156
- 494 0.347 -3.234 1.306 0.756 -0.045 0.713 0.1140423071
- 507 0.347 -3.234 1.306 0.756 -0.045 0.712 0.1140398837
- 515 0.347 -3.233 1.306 0.756 -0.045 0.712 0.1140274174
- 518 0.347 -3.229 1.306 0.756 -0.045 0.712 0.1140065955
- 531 0.347 -3.229 1.305 0.756 -0.045 0.712 0.1140044828
- 533 0.347 -3.229 1.304 0.756 -0.045 0.712 0.1140038221
- 542 0.347 -3.229 1.304 0.766 -0.045 0.712 0.1140007136
- 543 0.347 -3.229 1.304 0.762 -0.045 0.712 0.1139759719
- 554 0.347 -3.229 1.304 0.762 -0.042 0.712 0.1139685659
- 555 0.347 -3.229 1.304 0.762 -0.041 0.712 0.1139682147
- 566 0.342 -3.232 1.305 0.758 -0.040 0.711 0.1139141260
- 567 0.341 -3.233 1.305 0.757 -0.040 0.711 0.1139134784
- 569 0.335 -3.231 1.304 0.758 -0.035 0.708 0.1138320663
- 572 0.326 -3.229 1.301 0.760 -0.027 0.704 0.1138114781
- 573 0.329 -3.229 1.302 0.759 -0.030 0.706 0.1138057067
- 576 0.328 -3.229 1.302 0.759 -0.029 0.705 0.1138056025
- 577 0.328 -3.229 1.302 0.759 -0.029 0.705 0.1138054942
- 595 0.328 -3.229 1.302 0.759 -0.029 0.704 0.1138033988
- 617 0.328 -3.229 1.303 0.759 -0.029 0.704 0.1138024710
- 618 0.328 -3.229 1.304 0.759 -0.029 0.704 0.1138023060
- 631 0.328 -3.229 1.304 0.760 -0.029 0.704 0.1138021776
- 642 0.328 -3.229 1.304 0.760 -0.031 0.704 0.1138016983
- 649 0.326 -3.229 1.304 0.761 -0.030 0.703 0.1138013340
- 650 0.327 -3.229 1.304 0.761 -0.030 0.704 0.1138010738
- 651 0.327 -3.229 1.304 0.761 -0.030 0.704 0.1138009397
- 653 0.327 -3.229 1.304 0.761 -0.030 0.703 0.1138009141
- 659 0.327 -3.229 1.304 0.761 -0.030 0.703 0.1138008941
- Powell done niters = 7
- Computing relative cost
- 0 -25.0 -25.0 -25.0 1.042397
- 1 -25.0 -25.0 25.0 1.010680
- 2 -25.0 25.0 -25.0 0.986969
- 3 -25.0 25.0 25.0 0.988324
- 4 25.0 -25.0 -25.0 1.024644
- 5 25.0 -25.0 25.0 1.038656
- 6 25.0 25.0 -25.0 1.004267
- 7 25.0 25.0 25.0 1.033285
- REL: 8 0.113801 8.129221 1.016153 rel = 0.111992
- Number of iterations 7
- Min cost was 0.113801
- Number of FunctionCalls 661
- TolPowell 0.000100
- nMaxItersPowell 36
- OptimizationTime 1.868000 sec
- Parameters at optimum (transmm) 0.32679 -3.22888 1.30372
- Parameters at optimum (rotdeg) 0.76064 -0.03011 0.70344
- Final costs ----------------
- Number of surface hits 2294
- WM Intensity 53.9992 +/- 8.5046
- Ctx Intensity 68.0198 +/- 9.0261
- Pct Contrast 23.1340 +/- 14.7873
- Cost 0.1138
- RelCost 0.8906
- Reg at min cost was
- 1.000 -0.017 0.026 -0.351;
- -0.026 0.012 1.000 -0.118;
- -0.017 -1.000 0.011 0.137;
- 0.000 0.000 0.000 1.000;
- Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/bbr.pass1.dat, type = 14
- Original Reg
- 0.999 -0.017 0.038 -0.640;
- -0.038 -0.001 0.999 3.103;
- -0.017 -1.000 -0.002 -1.207;
- 0.000 0.000 0.000 1.000;
- Original Reg - Optimal Reg
- -0.000 -0.000 0.012 -0.289;
- -0.012 -0.013 -0.000 3.221;
- -0.000 -0.000 -0.013 -1.345;
- 0.000 0.000 0.000 0.000;
- Computing change in lh position
- LH rmsDiffMean 4.174227
- Computing change in rh position
- Surface RMS Diff (mm) 3.896964 4.940328
- mri_segreg done
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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/sub014/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/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/sub014/scripts
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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/sub014/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/template.nii
- regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/tmp.bbregister.16273/bbr.pass1.dat
- subject sub014
- dof 6
- outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 1376178620
- TransRandMax 0.000000
- RotRandMax 0.000000
- Translations 0.000000 0.000000 0.000000
- Rotations 0.000000 0.000000 0.000000
- Input reg
- 1.000 -0.017 0.026 -0.351;
- -0.026 0.012 1.000 -0.118;
- -0.017 -1.000 0.011 0.137;
- 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 1.010880
- 1 -25.0 -25.0 25.0 1.001435
- 2 -25.0 25.0 -25.0 1.009779
- 3 -25.0 25.0 25.0 1.002560
- 4 25.0 -25.0 -25.0 1.027779
- 5 25.0 -25.0 25.0 1.021593
- 6 25.0 25.0 -25.0 1.020105
- 7 25.0 25.0 25.0 1.025094
- REL: 8 0.126927 8.119226 1.014903 rel = 0.125063
- Initial costs ----------------
- Number of surface hits 230674
- WM Intensity 54.0431 +/- 8.8999
- Ctx Intensity 67.8838 +/- 8.9533
- Pct Contrast 22.9525 +/- 14.9910
- Cost 0.1269
- RelCost 0.1251
- ------------------------------------
- Brute force preopt -0.1 0.1 0.1, n = 729
- 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1330 0.1330 0.0
- 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1288 0.1288 0.0
- 2 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.1276 0.1276 0.0
- 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.1240 0.1240 0.0
- 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.1229 0.1229 0.0
- 13 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.1207 0.1207 0.0
- 93 -0.1000 0.0000 -0.1000 0.0000 0.0000 -0.1000 0.1191 0.1191 0.0
- 94 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.0000 0.1178 0.1178 0.0
- 102 -0.1000 0.0000 -0.1000 0.1000 0.0000 -0.1000 0.1174 0.1174 0.0
- 184 -0.1000 0.1000 -0.1000 0.1000 0.0000 0.0000 0.1169 0.1169 0.0
- 337 0.0000 0.0000 -0.1000 0.0000 0.0000 0.0000 0.1166 0.1166 0.0
- 346 0.0000 0.0000 -0.1000 0.1000 0.0000 0.0000 0.1161 0.1161 0.0
- 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1138 0.1138 0.0
- 674 0.1000 0.1000 -0.1000 0.1000 0.1000 0.1000 0.1134 0.1134 0.0
- Brute Force --------------------------
- Min cost was 0.113423
- Number of iterations 729
- Search time 2.043000 sec
- Parameters at best (transmm, rotdeg)
- 0.100 0.100 -0.100 0.100 0.100 0.100
- --------------------------------------------
- Starting Powell Minimization
- Init Powel Params dof = 6
- 0 0.1
- 1 0.1
- 2 -0.1
- 3 0.1
- 4 0.1
- 5 0.1
- 7 0.034 0.100 -0.100 0.100 0.100 0.100 0.1209569181
- 9 0.033 0.100 -0.100 0.100 0.100 0.100 0.1209567854
- 27 0.033 0.100 -0.243 0.100 0.100 0.100 0.1172754385
- 28 0.033 0.100 -0.266 0.100 0.100 0.100 0.1172663217
- 29 0.033 0.100 -0.256 0.100 0.100 0.100 0.1172481612
- 30 0.033 0.100 -0.255 0.100 0.100 0.100 0.1172478789
- 38 0.033 0.100 -0.255 0.149 0.100 0.100 0.1168529527
- 39 0.033 0.100 -0.255 0.146 0.100 0.100 0.1168472014
- 40 0.033 0.100 -0.255 0.143 0.100 0.100 0.1168456765
- 49 0.033 0.100 -0.255 0.143 0.037 0.100 0.1167484557
- 50 0.033 0.100 -0.255 0.143 0.062 0.100 0.1166621064
- 52 0.033 0.100 -0.255 0.143 0.065 0.100 0.1166614152
- 62 0.033 0.100 -0.255 0.143 0.065 0.144 0.1162169473
- 63 0.033 0.100 -0.255 0.143 0.065 0.159 0.1162070196
- 64 0.033 0.100 -0.255 0.143 0.065 0.153 0.1162017613
- 65 0.033 0.100 -0.255 0.143 0.065 0.154 0.1162017390
- 74 0.073 0.100 -0.255 0.143 0.065 0.154 0.1160241063
- 75 0.072 0.100 -0.255 0.143 0.065 0.154 0.1160228127
- 76 0.070 0.100 -0.255 0.143 0.065 0.154 0.1160226169
- 84 0.070 0.126 -0.255 0.143 0.065 0.154 0.1160084222
- 85 0.070 0.115 -0.255 0.143 0.065 0.154 0.1159997555
- 86 0.070 0.116 -0.255 0.143 0.065 0.154 0.1159996304
- 94 0.070 0.116 -0.281 0.143 0.065 0.154 0.1157860000
- 95 0.070 0.116 -0.303 0.143 0.065 0.154 0.1157716747
- 96 0.070 0.116 -0.294 0.143 0.065 0.154 0.1157593353
- 97 0.070 0.116 -0.293 0.143 0.065 0.154 0.1157592172
- 105 0.070 0.116 -0.293 0.172 0.065 0.154 0.1156371057
- 106 0.070 0.116 -0.293 0.169 0.065 0.154 0.1156364461
- 107 0.070 0.116 -0.293 0.170 0.065 0.154 0.1156361582
- 116 0.070 0.116 -0.293 0.170 0.058 0.154 0.1156288862
- 118 0.070 0.116 -0.293 0.170 0.059 0.154 0.1156288589
- 127 0.070 0.116 -0.293 0.170 0.059 0.164 0.1155757933
- 128 0.070 0.116 -0.293 0.170 0.059 0.180 0.1155512182
- 129 0.070 0.116 -0.293 0.170 0.059 0.177 0.1155501252
- 132 0.107 0.133 -0.332 0.197 0.054 0.199 0.1153706279
- 139 0.103 0.131 -0.328 0.194 0.054 0.197 0.1153687550
- 140 0.103 0.131 -0.328 0.194 0.054 0.197 0.1153685717
- 142 0.104 0.131 -0.329 0.194 0.054 0.197 0.1153684932
- 154 0.091 0.131 -0.329 0.194 0.054 0.197 0.1153580260
- 156 0.095 0.131 -0.329 0.194 0.054 0.197 0.1153556017
- 166 0.095 0.133 -0.329 0.194 0.054 0.197 0.1153554408
- 175 0.095 0.133 -0.329 0.194 0.054 0.195 0.1153541620
- 184 0.095 0.133 -0.329 0.193 0.054 0.195 0.1153539683
- 194 0.095 0.133 -0.329 0.193 0.050 0.195 0.1153474111
- 195 0.095 0.133 -0.329 0.193 0.048 0.195 0.1153469081
- 203 0.099 0.135 -0.333 0.197 0.047 0.198 0.1153430672
- 206 0.099 0.135 -0.333 0.196 0.047 0.198 0.1153429918
- 210 0.099 0.135 -0.333 0.196 0.047 0.198 0.1153429763
- 229 0.099 0.133 -0.333 0.196 0.047 0.198 0.1153417625
- 239 0.099 0.133 -0.333 0.196 0.047 0.197 0.1153412469
- 240 0.099 0.133 -0.333 0.196 0.047 0.196 0.1153411410
- 258 0.099 0.133 -0.333 0.196 0.046 0.196 0.1153407991
- 266 0.100 0.133 -0.334 0.197 0.046 0.196 0.1153407972
- 267 0.099 0.133 -0.333 0.197 0.046 0.196 0.1153407194
- 268 0.099 0.133 -0.333 0.197 0.046 0.196 0.1153406845
- 280 0.098 0.133 -0.333 0.197 0.046 0.196 0.1153405005
- 289 0.098 0.132 -0.333 0.197 0.046 0.196 0.1153404106
- 299 0.098 0.132 -0.333 0.197 0.046 0.195 0.1153402948
- 326 0.099 0.133 -0.335 0.198 0.045 0.195 0.1153401488
- 327 0.099 0.133 -0.334 0.197 0.046 0.195 0.1153401011
- 329 0.099 0.133 -0.334 0.197 0.046 0.195 0.1153400820
- 331 0.099 0.133 -0.334 0.197 0.046 0.195 0.1153400756
- 332 0.099 0.132 -0.336 0.198 0.045 0.194 0.1153397664
- 337 0.099 0.132 -0.336 0.199 0.045 0.194 0.1153396371
- 343 0.099 0.132 -0.336 0.199 0.045 0.194 0.1153395969
- 357 0.097 0.132 -0.336 0.199 0.045 0.194 0.1153386248
- 383 0.097 0.132 -0.336 0.198 0.045 0.194 0.1153385619
- 404 0.097 0.132 -0.336 0.198 0.045 0.194 0.1153385331
- 442 0.097 0.132 -0.336 0.198 0.045 0.194 0.1153385172
- 514 0.097 0.132 -0.336 0.198 0.045 0.194 0.1153385019
- Powell done niters = 8
- Computing relative cost
- 0 -25.0 -25.0 -25.0 1.009676
- 1 -25.0 -25.0 25.0 1.002688
- 2 -25.0 25.0 -25.0 1.012445
- 3 -25.0 25.0 25.0 1.002504
- 4 25.0 -25.0 -25.0 1.027067
- 5 25.0 -25.0 25.0 1.020760
- 6 25.0 25.0 -25.0 1.022105
- 7 25.0 25.0 25.0 1.025591
- REL: 8 0.115339 8.122836 1.015354 rel = 0.113594
- Number of iterations 8
- Min cost was 0.115339
- Number of FunctionCalls 638
- TolPowell 0.000000
- nMaxItersPowell 36
- OptimizationTime 62.577000 sec
- Parameters at optimum (transmm) 0.09717 0.13175 -0.33615
- Parameters at optimum (rotdeg) 0.19756 0.04529 0.19402
- Final costs ----------------
- Number of surface hits 230674
- WM Intensity 54.0491 +/- 8.9047
- Ctx Intensity 67.8323 +/- 8.8661
- Pct Contrast 22.8816 +/- 14.8108
- Cost 0.1153
- RelCost 0.1251
- Reg at min cost was
- 1.000 -0.017 0.022 -0.253;
- -0.022 0.015 1.000 0.012;
- -0.018 -1.000 0.015 -0.199;
- 0.000 0.000 0.000 1.000;
- Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/T2raw.dat, type = 14
- Original Reg
- 1.000 -0.017 0.026 -0.351;
- -0.026 0.012 1.000 -0.118;
- -0.017 -1.000 0.011 0.137;
- 0.000 0.000 0.000 1.000;
- Original Reg - Optimal Reg
- -0.000 0.001 0.003 -0.098;
- -0.003 -0.003 -0.000 -0.130;
- 0.001 -0.000 -0.003 0.336;
- 0.000 0.000 0.000 0.000;
- Computing change in lh position
- LH rmsDiffMean 0.252247
- Computing change in rh position
- Surface RMS Diff (mm) 0.289352 0.536197
- mri_segreg done
- tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/T2raw.dat --noedit --ltaout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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/sub014/mri/orig/T2raw.mgz
- reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 --------
- 1.000 -0.017 0.022 -0.253;
- -0.022 0.015 1.000 0.012;
- -0.018 -1.000 0.015 -0.199;
- 0.000 0.000 0.000 1.000;
- float2int = 0
- ---------------------------------------
- INFO: loading target /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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/sub014/mri/orig/T2raw.mgz
- Tmov: --------------------
- -0.700 0.000 0.000 95.896;
- 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 --------
- 1.000 -0.017 0.022 -0.253;
- -0.022 0.015 1.000 0.012;
- -0.018 -1.000 0.015 -0.199;
- 0.000 0.000 0.000 1.000;
- Determinant 1
- subject = sub014
- RegMat ---------------------------
- 1.000 -0.017 0.022 -0.253;
- -0.022 0.015 1.000 0.012;
- -0.018 -1.000 0.015 -0.199;
- 0.000 0.000 0.000 1.000;
- transformed matrix:
- 1.000 -0.008 -0.017 -0.155;
- 0.008 1.000 0.009 0.113;
- 0.017 -0.009 1.000 0.236;
- 0.000 0.000 0.000 1.000;
- transformed matrix:
- 0.700 -0.012 0.015 31.335;
- 0.016 0.010 -0.666 251.942;
- 0.012 0.666 0.010 -3.761;
- 0.000 0.000 0.000 1.000;
- Cleaning up
-
- Started at Thu Aug 8 22:54:13 CEST 2013
- Ended at Thu Aug 8 23:07:13 CEST 2013
- BBR-Run-Time-Sec 780
-
- bbregister Done
- To check results, run:
- tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/T2raw.dat --surf
-
- mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/T2.mgz
- mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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/sub014/mri/orig/T2raw.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.999671, 0.0251903, -0.0048728)
- j_ras = (0.0252193, 0.999664, -0.00597949)
- k_ras = (-0.00472054, 0.00610041, 0.99997)
- INFO: Reading transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/T2raw.lta...
- Reading transform with LTAreadEx()
- reading extra input line subject sub014
- reading extra input line fscale 0.150000
- reading template info from volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/orig.mgz...
- INFO: Applying transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/transforms/T2raw.lta...
- ---------------------------------
- INFO: Transform Matrix (linear_ras_to_ras)
- 1.000 -0.008 -0.017 -0.155;
- 0.008 1.000 0.009 0.113;
- 0.017 -0.009 1.000 0.236;
- 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/sub014/mri/T2.mgz...
- mri_normalize -aseg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/aseg.mgz -sigma 4 -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/rh.white identity.nofile -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/lh.white identity.nofile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/T2.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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/sub014/mri/T2.mgz...
- computing distance transform
- computing distance transform
- computing nonmaximum suppression
- 6724 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/sub014/mri/T2.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/scripts
- cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/lh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/lh.woT2.pial
- `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/lh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/lh.woT2.pial'
- mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub014 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/sub014/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/wm.mgz...
- 15343 bright wm thresholded.
- 473 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/lh.orig...
- computing class statistics...
- border white: 218506 voxels (1.30%)
- border gray 254901 voxels (1.52%)
- WM (92.0): 93.3 +- 10.4 [70.0 --> 110.0]
- GM (75.0) : 73.0 +- 13.3 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 46.7 (was 70)
- setting MAX_BORDER_WHITE to 116.4 (was 105)
- setting MIN_BORDER_WHITE to 60.0 (was 85)
- setting MAX_CSF to 33.5 (was 40)
- setting MAX_GRAY to 95.6 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 53.4 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 20.2 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=106, GM=60
- mean inside = 93.0, mean outside = 68.0
- smoothing surface for 5 iterations...
- reading initial white vertex positions from white...
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.90 +- 0.26 (0.03-->3.75) (max @ vno 51676 --> 123131)
- face area 0.33 +- 0.16 (0.00-->2.24)
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 76 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 816 points - only 0.00% unknown
- deleting segment 4 with 11 points - only 0.00% unknown
- deleting segment 5 with 9 points - only 0.00% unknown
- deleting segment 6 with 6 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 7 with 1 points - only 0.00% unknown
- deleting segment 8 with 6 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 9 with 1 points - only 0.00% unknown
- tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.90 +- 0.25 (0.07-->3.75) (max @ vno 51676 --> 123131)
- face area 0.33 +- 0.16 (0.00-->2.24)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4199632.0, rms=0.00
- rms = 1.29, time step reduction 1 of 3 to 0.250...
- rms = 0.33, time step reduction 2 of 3 to 0.125...
- rms = 0.04, time step reduction 3 of 3 to 0.062...
- 001: dt: 0.1250, sse=4199632.0, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 76 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 816 points - only 0.00% unknown
- deleting segment 3 with 11 points - only 0.00% unknown
- deleting segment 4 with 9 points - only 0.00% unknown
- deleting segment 5 with 6 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 6 with 1 points - only 0.00% unknown
- deleting segment 7 with 6 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 8 with 1 points - only 0.00% unknown
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.90 +- 0.25 (0.07-->3.75) (max @ vno 51676 --> 123131)
- face area 0.33 +- 0.16 (0.00-->2.24)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4199632.0, rms=0.00
- rms = 1.30, time step reduction 1 of 3 to 0.250...
- rms = 0.33, time step reduction 2 of 3 to 0.125...
- rms = 0.04, time step reduction 3 of 3 to 0.062...
- 002: dt: 0.1250, sse=4199632.0, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 76 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 816 points - only 0.00% unknown
- deleting segment 3 with 11 points - only 0.00% unknown
- deleting segment 4 with 9 points - only 0.00% unknown
- deleting segment 5 with 6 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 6 with 1 points - only 0.00% unknown
- deleting segment 7 with 6 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 8 with 1 points - only 0.00% unknown
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.25 (0.07-->3.75) (max @ vno 51676 --> 123131)
- face area 0.33 +- 0.16 (0.00-->2.24)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4199632.0, rms=0.00
- rms = 1.29, time step reduction 1 of 3 to 0.250...
- rms = 0.33, time step reduction 2 of 3 to 0.125...
- rms = 0.04, time step reduction 3 of 3 to 0.062...
- 003: dt: 0.1250, sse=4199632.0, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 76 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 816 points - only 0.00% unknown
- deleting segment 3 with 11 points - only 0.00% unknown
- deleting segment 4 with 9 points - only 0.00% unknown
- deleting segment 5 with 6 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 6 with 1 points - only 0.00% unknown
- deleting segment 7 with 6 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 8 with 1 points - only 0.00% unknown
- tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- repositioning cortical surface to gray/csf boundary.
- smoothing T1 volume with sigma = 2.000
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4199632.0, rms=0.00
- rms = 1.30, time step reduction 1 of 3 to 0.250...
- rms = 0.33, time step reduction 2 of 3 to 0.125...
- rms = 0.04, time step reduction 3 of 3 to 0.062...
- 004: dt: 0.1250, sse=4199632.0, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- deleting segment 0 with 4 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- smoothing surface for 5 iterations...
- reading initial pial vertex positions from woT2.pial...
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [108.20 213.80], gm=161.00+-17.60, and vertices in regions > 152.2
- 47495 surface locations found to contain inconsistent values (6369 in, 41126 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=439031.9, rms=0.27
- 001: dt: 0.5000, sse=414246.6, rms=0.258 (0.000%)
- 002: dt: 0.5000, sse=398963.2, rms=0.243 (0.000%)
- 003: dt: 0.5000, sse=390096.4, rms=0.232 (0.000%)
- 004: dt: 0.5000, sse=382754.5, rms=0.222 (0.000%)
- 005: dt: 0.5000, sse=377472.7, rms=0.213 (0.000%)
- 006: dt: 0.5000, sse=373623.0, rms=0.205 (0.000%)
- 007: dt: 0.5000, sse=370636.1, rms=0.199 (0.000%)
- 008: dt: 0.5000, sse=368160.9, rms=0.193 (0.000%)
- 009: dt: 0.5000, sse=366396.9, rms=0.188 (0.000%)
- 010: dt: 0.5000, sse=364753.8, rms=0.183 (0.000%)
- 011: dt: 0.5000, sse=363223.9, rms=0.179 (0.000%)
- 012: dt: 0.5000, sse=362059.6, rms=0.176 (0.000%)
- 013: dt: 0.5000, sse=360809.4, rms=0.173 (0.000%)
- 014: dt: 0.5000, sse=359880.3, rms=0.170 (0.000%)
- 015: dt: 0.5000, sse=358903.8, rms=0.168 (0.000%)
- 016: dt: 0.5000, sse=358049.3, rms=0.166 (0.000%)
- 017: dt: 0.5000, sse=357063.8, rms=0.165 (0.000%)
- 018: dt: 0.5000, sse=356193.9, rms=0.163 (0.000%)
- 019: dt: 0.5000, sse=355229.5, rms=0.162 (0.000%)
- 020: dt: 0.5000, sse=354331.6, rms=0.161 (0.000%)
- 021: dt: 0.5000, sse=353493.8, rms=0.160 (0.000%)
- 022: dt: 0.5000, sse=352634.8, rms=0.159 (0.000%)
- 023: dt: 0.5000, sse=351918.6, rms=0.158 (0.000%)
- 024: dt: 0.5000, sse=351137.4, rms=0.158 (0.000%)
- 025: dt: 0.5000, sse=350481.8, rms=0.157 (0.000%)
- 026: dt: 0.5000, sse=349635.4, rms=0.157 (0.000%)
- 027: dt: 0.5000, sse=349672.5, rms=0.157 (0.000%)
- 028: dt: 0.5000, sse=348859.7, rms=0.157 (0.000%)
- 029: dt: 0.5000, sse=347820.7, rms=0.157 (0.000%)
- 030: dt: 0.5000, sse=347039.0, rms=0.157 (0.000%)
- positioning took 3.4 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [53.80 266.20], gm=160.00+-35.40, and vertices in regions > 142.3
- 32416 surface locations found to contain inconsistent values (6 in, 32410 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=41143.5, rms=0.24
- 031: dt: 0.5000, sse=40262.7, rms=0.229 (0.000%)
- 032: dt: 0.5000, sse=39239.6, rms=0.209 (0.000%)
- 033: dt: 0.5000, sse=38748.5, rms=0.191 (0.000%)
- 034: dt: 0.5000, sse=38674.8, rms=0.174 (0.000%)
- 035: dt: 0.5000, sse=38871.2, rms=0.159 (0.000%)
- 036: dt: 0.5000, sse=39185.7, rms=0.146 (0.000%)
- 037: dt: 0.5000, sse=39636.8, rms=0.135 (0.000%)
- 038: dt: 0.5000, sse=40160.0, rms=0.125 (0.000%)
- 039: dt: 0.5000, sse=40819.5, rms=0.116 (0.000%)
- 040: dt: 0.5000, sse=41558.2, rms=0.108 (0.000%)
- 041: dt: 0.5000, sse=42303.1, rms=0.102 (0.000%)
- 042: dt: 0.5000, sse=43073.6, rms=0.096 (0.000%)
- 043: dt: 0.5000, sse=43802.4, rms=0.091 (0.000%)
- 044: dt: 0.5000, sse=44515.8, rms=0.086 (0.000%)
- 045: dt: 0.5000, sse=45226.0, rms=0.082 (0.000%)
- 046: dt: 0.5000, sse=45870.4, rms=0.078 (0.000%)
- 047: dt: 0.5000, sse=46497.4, rms=0.075 (0.000%)
- 048: dt: 0.5000, sse=47087.2, rms=0.072 (0.000%)
- 049: dt: 0.5000, sse=47642.1, rms=0.069 (0.000%)
- 050: dt: 0.5000, sse=48175.0, rms=0.067 (0.000%)
- 051: dt: 0.5000, sse=48653.8, rms=0.064 (0.000%)
- 052: dt: 0.5000, sse=49123.4, rms=0.062 (0.000%)
- 053: dt: 0.5000, sse=49573.6, rms=0.060 (0.000%)
- 054: dt: 0.5000, sse=49970.9, rms=0.058 (0.000%)
- 055: dt: 0.5000, sse=50329.0, rms=0.056 (0.000%)
- 056: dt: 0.5000, sse=50684.1, rms=0.055 (0.000%)
- 057: dt: 0.5000, sse=51025.0, rms=0.053 (0.000%)
- 058: dt: 0.5000, sse=51347.7, rms=0.052 (0.000%)
- 059: dt: 0.5000, sse=51635.6, rms=0.050 (0.000%)
- 060: dt: 0.5000, sse=51905.9, rms=0.049 (0.000%)
- positioning took 3.3 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [111.00 213.00], gm=162.00+-17.00, and vertices in regions > 153.5
- 50949 surface locations found to contain inconsistent values (33081 in, 17868 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=10996.9, rms=0.22
- 061: dt: 0.5000, sse=10295.1, rms=0.209 (0.000%)
- 062: dt: 0.5000, sse=9256.7, rms=0.191 (0.000%)
- 063: dt: 0.5000, sse=8530.8, rms=0.176 (0.000%)
- 064: dt: 0.5000, sse=8020.9, rms=0.163 (0.000%)
- 065: dt: 0.5000, sse=7635.2, rms=0.153 (0.000%)
- 066: dt: 0.5000, sse=7364.9, rms=0.145 (0.000%)
- 067: dt: 0.5000, sse=7148.1, rms=0.138 (0.000%)
- 068: dt: 0.5000, sse=6977.1, rms=0.131 (0.000%)
- 069: dt: 0.5000, sse=6841.1, rms=0.125 (0.000%)
- 070: dt: 0.5000, sse=6739.6, rms=0.119 (0.000%)
- 071: dt: 0.5000, sse=6668.0, rms=0.114 (0.000%)
- 072: dt: 0.5000, sse=6604.0, rms=0.110 (0.000%)
- 073: dt: 0.5000, sse=6556.3, rms=0.105 (0.000%)
- 074: dt: 0.5000, sse=6523.1, rms=0.101 (0.000%)
- 075: dt: 0.5000, sse=6494.5, rms=0.097 (0.000%)
- 076: dt: 0.5000, sse=6474.4, rms=0.093 (0.000%)
- 077: dt: 0.5000, sse=6462.0, rms=0.089 (0.000%)
- 078: dt: 0.5000, sse=6456.3, rms=0.085 (0.000%)
- 079: dt: 0.5000, sse=6452.4, rms=0.082 (0.000%)
- 080: dt: 0.5000, sse=6457.8, rms=0.079 (0.000%)
- 081: dt: 0.5000, sse=6461.9, rms=0.076 (0.000%)
- 082: dt: 0.5000, sse=6469.5, rms=0.073 (0.000%)
- 083: dt: 0.5000, sse=6480.3, rms=0.071 (0.000%)
- 084: dt: 0.5000, sse=6493.3, rms=0.068 (0.000%)
- 085: dt: 0.5000, sse=6504.5, rms=0.066 (0.000%)
- 086: dt: 0.5000, sse=6517.0, rms=0.063 (0.000%)
- 087: dt: 0.5000, sse=6534.4, rms=0.061 (0.000%)
- 088: dt: 0.5000, sse=6547.5, rms=0.059 (0.000%)
- 089: dt: 0.5000, sse=6560.0, rms=0.057 (0.000%)
- 090: dt: 0.5000, sse=6578.8, rms=0.056 (0.000%)
- positioning took 3.2 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [99.50 222.50], gm=161.00+-20.50, and vertices in regions > 150.7
- 19149 surface locations found to contain inconsistent values (160 in, 18989 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/sub014/surf/lh.pial...
- writing smoothed curvature to lh.curv.pial
- 000: dt: 0.0000, sse=1315.4, rms=0.08
- 091: dt: 0.5000, sse=1241.1, rms=0.072 (0.000%)
- 092: dt: 0.5000, sse=1108.5, rms=0.064 (0.000%)
- 093: dt: 0.5000, sse=1036.5, rms=0.058 (0.000%)
- 094: dt: 0.5000, sse=992.5, rms=0.054 (0.000%)
- 095: dt: 0.5000, sse=957.0, rms=0.050 (0.000%)
- 096: dt: 0.5000, sse=934.9, rms=0.048 (0.000%)
- 097: dt: 0.5000, sse=917.8, rms=0.046 (0.000%)
- 098: dt: 0.5000, sse=905.6, rms=0.044 (0.000%)
- 099: dt: 0.5000, sse=892.6, rms=0.043 (0.000%)
- 100: dt: 0.5000, sse=881.0, rms=0.041 (0.000%)
- 101: dt: 0.5000, sse=871.2, rms=0.040 (0.000%)
- 102: dt: 0.5000, sse=863.4, rms=0.039 (0.000%)
- 103: dt: 0.5000, sse=856.9, rms=0.038 (0.000%)
- 104: dt: 0.5000, sse=851.5, rms=0.037 (0.000%)
- 105: dt: 0.5000, sse=846.2, rms=0.037 (0.000%)
- 106: dt: 0.5000, sse=841.9, rms=0.036 (0.000%)
- 107: dt: 0.5000, sse=839.8, rms=0.036 (0.000%)
- 108: dt: 0.5000, sse=836.6, rms=0.035 (0.000%)
- 109: dt: 0.5000, sse=837.2, rms=0.035 (0.000%)
- 110: dt: 0.5000, sse=833.6, rms=0.034 (0.000%)
- 111: dt: 0.5000, sse=831.3, rms=0.034 (0.000%)
- 112: dt: 0.5000, sse=829.5, rms=0.034 (0.000%)
- 113: dt: 0.5000, sse=827.4, rms=0.034 (0.000%)
- 114: dt: 0.5000, sse=826.7, rms=0.033 (0.000%)
- 115: dt: 0.5000, sse=827.4, rms=0.033 (0.000%)
- 116: dt: 0.5000, sse=826.1, rms=0.033 (0.000%)
- 117: dt: 0.5000, sse=825.1, rms=0.033 (0.000%)
- 118: dt: 0.5000, sse=823.3, rms=0.033 (0.000%)
- 119: dt: 0.5000, sse=822.0, rms=0.033 (0.000%)
- 120: dt: 0.5000, sse=822.4, rms=0.033 (0.000%)
- positioning took 3.1 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/lh.curv.pial
- writing smoothed area to lh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/lh.area.pial
- vertex spacing 1.04 +- 0.45 (0.06-->7.85) (max @ vno 86058 --> 85075)
- face area 0.42 +- 0.32 (0.00-->7.39)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 123287 vertices processed
- 25000 of 123287 vertices processed
- 50000 of 123287 vertices processed
- 75000 of 123287 vertices processed
- 100000 of 123287 vertices processed
- 0 of 123287 vertices processed
- 25000 of 123287 vertices processed
- 50000 of 123287 vertices processed
- 75000 of 123287 vertices processed
- 100000 of 123287 vertices processed
- thickness calculation complete, 456:915 truncations.
- 28084 vertices at 0 distance
- 83200 vertices at 1 distance
- 79238 vertices at 2 distance
- 32159 vertices at 3 distance
- 9050 vertices at 4 distance
- 2533 vertices at 5 distance
- 764 vertices at 6 distance
- 289 vertices at 7 distance
- 126 vertices at 8 distance
- 83 vertices at 9 distance
- 42 vertices at 10 distance
- 28 vertices at 11 distance
- 22 vertices at 12 distance
- 15 vertices at 13 distance
- 21 vertices at 14 distance
- 19 vertices at 15 distance
- 18 vertices at 16 distance
- 20 vertices at 17 distance
- 15 vertices at 18 distance
- 5 vertices at 19 distance
- 9 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/lh.thickness
- positioning took 17.1 minutes
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/scripts
- cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/rh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/rh.woT2.pial
- `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/rh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/rh.woT2.pial'
- mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub014 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/sub014/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/wm.mgz...
- 15389 bright wm thresholded.
- 474 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/rh.orig...
- computing class statistics...
- border white: 218506 voxels (1.30%)
- border gray 254901 voxels (1.52%)
- WM (92.0): 93.3 +- 10.4 [70.0 --> 110.0]
- GM (75.0) : 73.0 +- 13.1 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 44.9 (was 70)
- setting MAX_BORDER_WHITE to 116.4 (was 105)
- setting MIN_BORDER_WHITE to 58.0 (was 85)
- setting MAX_CSF to 31.8 (was 40)
- setting MAX_GRAY to 95.6 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 51.5 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 18.8 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=106, GM=58
- mean inside = 93.2, mean outside = 68.1
- 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/sub014/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.90 +- 0.26 (0.05-->4.85) (max @ vno 50303 --> 53862)
- face area 0.34 +- 0.16 (0.00-->3.81)
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 7 points - only 0.00% unknown
- deleting segment 1 with 49 points - only 28.57% unknown
- removing 1 vertex label from ripped group
- deleting segment 4 with 11 points - only 0.00% unknown
- deleting segment 5 with 337 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 6 with 1 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- removing 2 vertex label from ripped group
- deleting segment 9 with 2 points - only 0.00% unknown
- deleting segment 11 with 47 points - only 0.00% unknown
- deleting segment 12 with 17 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 13 with 2 points - only 0.00% unknown
- tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.90 +- 0.25 (0.05-->4.85) (max @ vno 50303 --> 53862)
- face area 0.34 +- 0.16 (0.00-->3.81)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4140533.5, rms=0.00
- rms = 1.84, time step reduction 1 of 3 to 0.250...
- rms = 0.49, time step reduction 2 of 3 to 0.125...
- rms = 0.06, time step reduction 3 of 3 to 0.062...
- 001: dt: 0.1250, sse=4140533.5, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 7 points - only 0.00% unknown
- deleting segment 1 with 49 points - only 28.57% unknown
- removing 1 vertex label from ripped group
- deleting segment 3 with 11 points - only 0.00% unknown
- deleting segment 4 with 337 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 5 with 1 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- removing 2 vertex label from ripped group
- deleting segment 7 with 2 points - only 0.00% unknown
- deleting segment 8 with 47 points - only 0.00% unknown
- deleting segment 9 with 17 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 10 with 2 points - only 0.00% unknown
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.90 +- 0.25 (0.05-->4.85) (max @ vno 50303 --> 53862)
- face area 0.34 +- 0.16 (0.00-->3.81)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4140533.5, rms=0.00
- rms = 1.84, time step reduction 1 of 3 to 0.250...
- rms = 0.49, time step reduction 2 of 3 to 0.125...
- rms = 0.06, time step reduction 3 of 3 to 0.062...
- 002: dt: 0.1250, sse=4140533.5, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 7 points - only 0.00% unknown
- deleting segment 1 with 49 points - only 28.57% unknown
- removing 1 vertex label from ripped group
- deleting segment 3 with 11 points - only 0.00% unknown
- deleting segment 4 with 337 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 5 with 1 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- removing 2 vertex label from ripped group
- deleting segment 7 with 2 points - only 0.00% unknown
- deleting segment 8 with 47 points - only 0.00% unknown
- deleting segment 9 with 17 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 10 with 2 points - only 0.00% unknown
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.25 (0.05-->4.85) (max @ vno 50303 --> 53862)
- face area 0.34 +- 0.16 (0.00-->3.81)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4140533.5, rms=0.00
- rms = 1.84, time step reduction 1 of 3 to 0.250...
- rms = 0.49, time step reduction 2 of 3 to 0.125...
- rms = 0.06, time step reduction 3 of 3 to 0.062...
- 003: dt: 0.1250, sse=4140533.5, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 7 points - only 0.00% unknown
- deleting segment 1 with 49 points - only 28.57% unknown
- removing 1 vertex label from ripped group
- deleting segment 3 with 11 points - only 0.00% unknown
- deleting segment 4 with 337 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 5 with 1 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- removing 2 vertex label from ripped group
- deleting segment 7 with 2 points - only 0.00% unknown
- deleting segment 8 with 47 points - only 0.00% unknown
- deleting segment 9 with 17 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 10 with 2 points - only 0.00% unknown
- tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- repositioning cortical surface to gray/csf boundary.
- smoothing T1 volume with sigma = 2.000
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4140533.5, rms=0.00
- rms = 1.84, time step reduction 1 of 3 to 0.250...
- rms = 0.49, time step reduction 2 of 3 to 0.125...
- rms = 0.06, time step reduction 3 of 3 to 0.062...
- 004: dt: 0.1250, sse=4140533.5, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 1 vertex label from ripped group
- removing 1 vertex label from ripped group
- smoothing surface for 5 iterations...
- reading initial pial vertex positions from woT2.pial...
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [-80.20 396.20], gm=158.00+-79.40, and vertices in regions > 118.3
- 0 surface locations found to contain inconsistent values (0 in, 0 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=442435.5, rms=0.00
- 001: dt: 0.5000, sse=415069.0, rms=0.013 (0.000%)
- 002: dt: 0.5000, sse=396779.0, rms=0.021 (0.000%)
- 003: dt: 0.5000, sse=384333.8, rms=0.027 (0.000%)
- 004: dt: 0.5000, sse=375233.9, rms=0.031 (0.000%)
- 005: dt: 0.5000, sse=368542.8, rms=0.034 (0.000%)
- 006: dt: 0.5000, sse=363203.3, rms=0.038 (0.000%)
- 007: dt: 0.5000, sse=358800.8, rms=0.040 (0.000%)
- 008: dt: 0.5000, sse=354949.0, rms=0.043 (0.000%)
- 009: dt: 0.5000, sse=351492.9, rms=0.045 (0.000%)
- 010: dt: 0.5000, sse=348471.3, rms=0.047 (0.000%)
- 011: dt: 0.5000, sse=346094.7, rms=0.049 (0.000%)
- 012: dt: 0.5000, sse=343566.2, rms=0.051 (0.000%)
- 013: dt: 0.5000, sse=341205.3, rms=0.053 (0.000%)
- 014: dt: 0.5000, sse=339158.3, rms=0.055 (0.000%)
- 015: dt: 0.5000, sse=337192.0, rms=0.056 (0.000%)
- 016: dt: 0.5000, sse=335249.8, rms=0.058 (0.000%)
- 017: dt: 0.5000, sse=333386.9, rms=0.059 (0.000%)
- 018: dt: 0.5000, sse=331639.1, rms=0.061 (0.000%)
- 019: dt: 0.5000, sse=330133.1, rms=0.062 (0.000%)
- 020: dt: 0.5000, sse=328631.0, rms=0.064 (0.000%)
- 021: dt: 0.5000, sse=327345.5, rms=0.065 (0.000%)
- 022: dt: 0.5000, sse=326020.2, rms=0.066 (0.000%)
- 023: dt: 0.5000, sse=324713.1, rms=0.067 (0.000%)
- 024: dt: 0.5000, sse=323697.3, rms=0.069 (0.000%)
- 025: dt: 0.5000, sse=322595.1, rms=0.070 (0.000%)
- 026: dt: 0.5000, sse=321540.3, rms=0.071 (0.000%)
- 027: dt: 0.5000, sse=320492.6, rms=0.072 (0.000%)
- 028: dt: 0.5000, sse=319547.2, rms=0.073 (0.000%)
- 029: dt: 0.5000, sse=318543.4, rms=0.074 (0.000%)
- 030: dt: 0.5000, sse=317652.0, rms=0.075 (0.000%)
- positioning took 3.3 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [92.50 233.50], gm=163.00+-23.50, and vertices in regions > 151.2
- 39021 surface locations found to contain inconsistent values (2173 in, 36848 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=38624.7, rms=0.25
- 031: dt: 0.5000, sse=37833.1, rms=0.234 (0.000%)
- 032: dt: 0.5000, sse=37023.0, rms=0.216 (0.000%)
- 033: dt: 0.5000, sse=36777.0, rms=0.200 (0.000%)
- 034: dt: 0.5000, sse=36836.5, rms=0.185 (0.000%)
- 035: dt: 0.5000, sse=37123.9, rms=0.172 (0.000%)
- 036: dt: 0.5000, sse=37518.7, rms=0.161 (0.000%)
- 037: dt: 0.5000, sse=38043.7, rms=0.150 (0.000%)
- 038: dt: 0.5000, sse=38619.0, rms=0.140 (0.000%)
- 039: dt: 0.5000, sse=39307.9, rms=0.131 (0.000%)
- 040: dt: 0.5000, sse=40048.5, rms=0.123 (0.000%)
- 041: dt: 0.5000, sse=40845.0, rms=0.116 (0.000%)
- 042: dt: 0.5000, sse=41655.6, rms=0.109 (0.000%)
- 043: dt: 0.5000, sse=42482.4, rms=0.103 (0.000%)
- 044: dt: 0.5000, sse=43287.3, rms=0.098 (0.000%)
- 045: dt: 0.5000, sse=44091.5, rms=0.093 (0.000%)
- 046: dt: 0.5000, sse=44856.5, rms=0.089 (0.000%)
- 047: dt: 0.5000, sse=45583.5, rms=0.085 (0.000%)
- 048: dt: 0.5000, sse=46313.2, rms=0.081 (0.000%)
- 049: dt: 0.5000, sse=46973.2, rms=0.078 (0.000%)
- 050: dt: 0.5000, sse=47642.8, rms=0.075 (0.000%)
- 051: dt: 0.5000, sse=48249.9, rms=0.072 (0.000%)
- 052: dt: 0.5000, sse=48812.2, rms=0.069 (0.000%)
- 053: dt: 0.5000, sse=49315.3, rms=0.067 (0.000%)
- 054: dt: 0.5000, sse=49790.1, rms=0.064 (0.000%)
- 055: dt: 0.5000, sse=50245.5, rms=0.062 (0.000%)
- 056: dt: 0.5000, sse=50656.9, rms=0.060 (0.000%)
- 057: dt: 0.5000, sse=51014.7, rms=0.058 (0.000%)
- 058: dt: 0.5000, sse=51366.7, rms=0.057 (0.000%)
- 059: dt: 0.5000, sse=51666.1, rms=0.055 (0.000%)
- 060: dt: 0.5000, sse=51982.1, rms=0.054 (0.000%)
- positioning took 3.2 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [89.00 239.00], gm=164.00+-25.00, and vertices in regions > 151.5
- 35317 surface locations found to contain inconsistent values (172 in, 35145 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=5889.1, rms=0.08
- 061: dt: 0.5000, sse=5803.8, rms=0.072 (0.000%)
- 062: dt: 0.5000, sse=5862.7, rms=0.062 (0.000%)
- 063: dt: 0.5000, sse=5960.6, rms=0.056 (0.000%)
- 064: dt: 0.5000, sse=6046.5, rms=0.052 (0.000%)
- 065: dt: 0.5000, sse=6111.9, rms=0.049 (0.000%)
- 066: dt: 0.5000, sse=6153.0, rms=0.047 (0.000%)
- 067: dt: 0.5000, sse=6180.7, rms=0.044 (0.000%)
- 068: dt: 0.5000, sse=6207.7, rms=0.043 (0.000%)
- 069: dt: 0.5000, sse=6235.5, rms=0.041 (0.000%)
- 070: dt: 0.5000, sse=6259.0, rms=0.039 (0.000%)
- 071: dt: 0.5000, sse=6282.2, rms=0.037 (0.000%)
- 072: dt: 0.5000, sse=6302.5, rms=0.036 (0.000%)
- 073: dt: 0.5000, sse=6321.0, rms=0.034 (0.000%)
- 074: dt: 0.5000, sse=6336.2, rms=0.033 (0.000%)
- 075: dt: 0.5000, sse=6351.0, rms=0.032 (0.000%)
- 076: dt: 0.5000, sse=6364.0, rms=0.031 (0.000%)
- 077: dt: 0.5000, sse=6376.6, rms=0.030 (0.000%)
- 078: dt: 0.5000, sse=6387.4, rms=0.029 (0.000%)
- 079: dt: 0.5000, sse=6397.4, rms=0.029 (0.000%)
- 080: dt: 0.5000, sse=6406.6, rms=0.028 (0.000%)
- 081: dt: 0.5000, sse=6413.4, rms=0.027 (0.000%)
- 082: dt: 0.5000, sse=6420.5, rms=0.027 (0.000%)
- 083: dt: 0.5000, sse=6427.0, rms=0.026 (0.000%)
- 084: dt: 0.5000, sse=6432.9, rms=0.026 (0.000%)
- 085: dt: 0.5000, sse=6437.4, rms=0.026 (0.000%)
- 086: dt: 0.5000, sse=6440.9, rms=0.025 (0.000%)
- 087: dt: 0.5000, sse=6444.6, rms=0.025 (0.000%)
- 088: dt: 0.5000, sse=6448.1, rms=0.025 (0.000%)
- 089: dt: 0.5000, sse=6451.5, rms=0.025 (0.000%)
- 090: dt: 0.5000, sse=6454.5, rms=0.024 (0.000%)
- positioning took 3.2 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [93.80 234.20], gm=164.00+-23.40, and vertices in regions > 152.3
- 19484 surface locations found to contain inconsistent values (636 in, 18848 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/sub014/surf/rh.pial...
- writing smoothed curvature to rh.curv.pial
- 000: dt: 0.0000, sse=865.9, rms=0.04
- 091: dt: 0.5000, sse=859.4, rms=0.043 (0.000%)
- 092: dt: 0.5000, sse=834.6, rms=0.040 (0.000%)
- 093: dt: 0.5000, sse=816.8, rms=0.038 (0.000%)
- 094: dt: 0.5000, sse=802.1, rms=0.036 (0.000%)
- 095: dt: 0.5000, sse=789.9, rms=0.035 (0.000%)
- 096: dt: 0.5000, sse=780.4, rms=0.034 (0.000%)
- 097: dt: 0.5000, sse=773.8, rms=0.033 (0.000%)
- 098: dt: 0.5000, sse=767.2, rms=0.032 (0.000%)
- 099: dt: 0.5000, sse=761.9, rms=0.031 (0.000%)
- 100: dt: 0.5000, sse=756.0, rms=0.030 (0.000%)
- 101: dt: 0.5000, sse=750.4, rms=0.029 (0.000%)
- 102: dt: 0.5000, sse=745.3, rms=0.029 (0.000%)
- 103: dt: 0.5000, sse=740.6, rms=0.028 (0.000%)
- 104: dt: 0.5000, sse=736.7, rms=0.027 (0.000%)
- 105: dt: 0.5000, sse=733.0, rms=0.027 (0.000%)
- 106: dt: 0.5000, sse=729.8, rms=0.026 (0.000%)
- 107: dt: 0.5000, sse=727.4, rms=0.026 (0.000%)
- 108: dt: 0.5000, sse=725.0, rms=0.025 (0.000%)
- 109: dt: 0.5000, sse=722.7, rms=0.025 (0.000%)
- 110: dt: 0.5000, sse=720.5, rms=0.024 (0.000%)
- 111: dt: 0.5000, sse=718.6, rms=0.024 (0.000%)
- 112: dt: 0.5000, sse=717.1, rms=0.024 (0.000%)
- 113: dt: 0.5000, sse=715.7, rms=0.023 (0.000%)
- 114: dt: 0.5000, sse=714.4, rms=0.023 (0.000%)
- 115: dt: 0.5000, sse=713.4, rms=0.023 (0.000%)
- 116: dt: 0.5000, sse=712.5, rms=0.023 (0.000%)
- 117: dt: 0.5000, sse=711.8, rms=0.022 (0.000%)
- 118: dt: 0.5000, sse=711.1, rms=0.022 (0.000%)
- 119: dt: 0.5000, sse=710.5, rms=0.022 (0.000%)
- 120: dt: 0.5000, sse=710.0, rms=0.022 (0.000%)
- positioning took 3.1 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/rh.curv.pial
- writing smoothed area to rh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/rh.area.pial
- vertex spacing 1.04 +- 0.44 (0.07-->6.42) (max @ vno 76658 --> 75608)
- face area 0.42 +- 0.32 (0.00-->10.05)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 123027 vertices processed
- 25000 of 123027 vertices processed
- 50000 of 123027 vertices processed
- 75000 of 123027 vertices processed
- 100000 of 123027 vertices processed
- 0 of 123027 vertices processed
- 25000 of 123027 vertices processed
- 50000 of 123027 vertices processed
- 75000 of 123027 vertices processed
- 100000 of 123027 vertices processed
- thickness calculation complete, 254:618 truncations.
- 26097 vertices at 0 distance
- 82338 vertices at 1 distance
- 80113 vertices at 2 distance
- 33128 vertices at 3 distance
- 9586 vertices at 4 distance
- 2623 vertices at 5 distance
- 820 vertices at 6 distance
- 266 vertices at 7 distance
- 131 vertices at 8 distance
- 59 vertices at 9 distance
- 39 vertices at 10 distance
- 36 vertices at 11 distance
- 29 vertices at 12 distance
- 11 vertices at 13 distance
- 14 vertices at 14 distance
- 4 vertices at 15 distance
- 2 vertices at 16 distance
- 15 vertices at 17 distance
- 10 vertices at 18 distance
- 12 vertices at 19 distance
- 5 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/rh.thickness
- positioning took 16.6 minutes
- #--------------------------------------------
- #@# Surf Volume lh Thu Aug 8 23:42:44 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 23:42:45 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 23:42:46 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri
- mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon sub014
- 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 = 3
- writing volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/ribbon.mgz
- writing ribbon files
- #--------------------------------------------
- #@# ASeg Stats Thu Aug 8 23:58:03 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014
- 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 sub014
- $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 sub014
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- UseRobust 0
- atlas_icv (eTIV) = 1041856 mm^3 (det: 1.869841 )
- Computing euler number
- orig.nofix lheno = -16, rheno = -18
- orig.nofix lhholes = 9, rhholes = 10
- Loading mri/aseg.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 225009.030 223758.000 diff= 1251.0 pctdiff= 0.556
- rhCtxGM: 226318.401 225226.000 diff= 1092.4 pctdiff= 0.483
- lhCtxWM: 178818.697 178471.000 diff= 347.7 pctdiff= 0.194
- rhCtxWM: 180365.304 180313.000 diff= 52.3 pctdiff= 0.029
- SubCortGMVol 54932.000
- SupraTentVol 878905.432 (875493.000) diff=3412.432 pctdiff=0.388
- SupraTentVolNotVent 866225.432 (862813.000) diff=3412.432 pctdiff=0.394
- BrainSegVol 980324.000 (978044.000) diff=2280.000 pctdiff=0.233
- BrainSegVolNotVent 964414.000 (966930.432) diff=-2516.432 pctdiff=-0.261
- BrainSegVolNotVent 964414.000
- CerebellumVol 101374.000
- VentChorVol 12680.000
- 3rd4th5thCSF 3230.000
- CSFVol 965.000, OptChiasmVol 212.000
- MaskVol 1401220.000
- 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 4664 4664.335
- 4 5 Left-Inf-Lat-Vent 364 363.856
- 5 7 Left-Cerebellum-White-Matter 11686 11685.915
- 6 8 Left-Cerebellum-Cortex 39826 39826.406
- 7 10 Left-Thalamus-Proper 6214 6213.961
- 8 11 Left-Caudate 3553 3553.366
- 9 12 Left-Putamen 5445 5444.709
- 10 13 Left-Pallidum 1861 1860.783
- 11 14 3rd-Ventricle 669 668.647
- 12 15 4th-Ventricle 1748 1748.456
- 13 16 Brain-Stem 18512 18512.117
- 14 17 Left-Hippocampus 3996 3996.132
- 15 18 Left-Amygdala 1581 1581.346
- 16 24 CSF 962 962.138
- 17 26 Left-Accumbens-area 797 797.434
- 18 28 Left-VentralDC 3309 3308.761
- 19 30 Left-vessel 42 42.200
- 20 31 Left-choroid-plexus 1022 1021.937
- 23 43 Right-Lateral-Ventricle 4733 4732.998
- 24 44 Right-Inf-Lat-Vent 559 558.569
- 25 46 Right-Cerebellum-White-Matter 11877 11876.548
- 26 47 Right-Cerebellum-Cortex 41025 41024.664
- 27 49 Right-Thalamus-Proper 6317 6316.685
- 28 50 Right-Caudate 3841 3841.311
- 29 51 Right-Putamen 5123 5123.420
- 30 52 Right-Pallidum 1473 1473.032
- 31 53 Right-Hippocampus 3811 3810.586
- 32 54 Right-Amygdala 1812 1812.055
- 33 58 Right-Accumbens-area 643 642.997
- 34 60 Right-VentralDC 3504 3504.205
- 35 62 Right-vessel 63 62.704
- 36 63 Right-choroid-plexus 1388 1387.951
- 37 72 5th-Ventricle 0 0.000
- 38 77 WM-hypointensities 791 791.334
- 39 78 Left-WM-hypointensities 0 0.000
- 40 79 Right-WM-hypointensities 0 0.000
- 41 80 non-WM-hypointensities 14 14.417
- 42 81 Left-non-WM-hypointensities 0 0.000
- 43 82 Right-non-WM-hypointensities 0 0.000
- 44 85 Optic-Chiasm 216 216.135
- 45 251 CC_Posterior 728 728.276
- 46 252 CC_Mid_Posterior 310 310.403
- 47 253 CC_Central 332 332.345
- 48 254 CC_Mid_Anterior 328 327.838
- 49 255 CC_Anterior 719 718.572
- Reporting on 45 segmentations
- mri_segstats done
- #-----------------------------------------
- #@# AParc-to-ASeg Fri Aug 9 00:03:07 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014
- mri_aparc2aseg --s sub014 --volmask
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- subject sub014
- outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/aparc+aseg.mgz
- useribbon 0
- baseoffset 0
- RipUnknown 0
- Reading lh white surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/lh.white
- Reading lh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/lh.pial
- Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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/sub014/surf/rh.white
- Reading rh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/rh.pial
- Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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/sub014/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/sub014/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 = 446119
- Used brute-force search on 0 voxels
- Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/aparc+aseg.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014
- mri_aparc2aseg --s sub014 --volmask --a2009s
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- subject sub014
- outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/aparc.a2009s+aseg.mgz
- useribbon 0
- baseoffset 10100
- RipUnknown 0
- Reading lh white surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/lh.white
- Reading lh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/lh.pial
- Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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/sub014/surf/rh.white
- Reading rh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/rh.pial
- Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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/sub014/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/sub014/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 = 446119
- Used brute-force search on 0 voxels
- Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/aparc.a2009s+aseg.mgz
- #-----------------------------------------
- #@# WMParc Fri Aug 9 00:08:22 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014
- mri_aparc2aseg --s sub014 --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 sub014
- 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/sub014/mri/aparc+aseg.mgz
- Reading lh white surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/lh.white
- Reading lh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/lh.pial
- Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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/sub014/surf/rh.white
- Reading rh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/rh.pial
- Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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/sub014/mri/ribbon.mgz
- Loading filled from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/filled.mgz
- Ripping vertices labeled as unkown
- Ripped 7658 vertices from left hemi
- Ripped 7982 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/sub014/mri/aseg.mgz
- Loading Ctx Seg File /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 = 805270
- Used brute-force search on 252 voxels
- Fixing Parahip LH WM
- Found 8 clusters
- 0 k 1.000000
- 1 k 1244.000000
- 2 k 14.000000
- 3 k 1.000000
- 4 k 1.000000
- 5 k 1.000000
- 6 k 1.000000
- 7 k 8.000000
- Fixing Parahip RH WM
- Found 4 clusters
- 0 k 1.000000
- 1 k 1230.000000
- 2 k 2.000000
- 3 k 3.000000
- Writing output aseg to mri/wmparc.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014
- 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 sub014 --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 sub014 --surf-wm-vol --ctab /opt/freesurfer/5.3.0/WMParcStatsLUT.txt --etiv
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- UseRobust 0
- atlas_icv (eTIV) = 1041856 mm^3 (det: 1.869841 )
- Loading mri/wmparc.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 225009.030 223758.000 diff= 1251.0 pctdiff= 0.556
- rhCtxGM: 226318.401 225226.000 diff= 1092.4 pctdiff= 0.483
- lhCtxWM: 178818.697 178471.000 diff= 347.7 pctdiff= 0.194
- rhCtxWM: 180365.304 180313.000 diff= 52.3 pctdiff= 0.029
- SubCortGMVol 54932.000
- SupraTentVol 878905.432 (875493.000) diff=3412.432 pctdiff=0.388
- SupraTentVolNotVent 866225.432 (862813.000) diff=3412.432 pctdiff=0.394
- BrainSegVol 980324.000 (978044.000) diff=2280.000 pctdiff=0.233
- BrainSegVolNotVent 964414.000 (966930.432) diff=-2516.432 pctdiff=-0.261
- BrainSegVolNotVent 964414.000
- CerebellumVol 101374.000
- VentChorVol 12680.000
- 3rd4th5thCSF 3230.000
- CSFVol 965.000, OptChiasmVol 212.000
- MaskVol 1401220.000
- 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 2704 2704.029
- 2 3002 wm-lh-caudalanteriorcingulate 2403 2403.292
- 3 3003 wm-lh-caudalmiddlefrontal 5674 5673.860
- 4 3004 wm-lh-corpuscallosum 0 0.000
- 5 3005 wm-lh-cuneus 2109 2109.320
- 6 3006 wm-lh-entorhinal 759 758.553
- 7 3007 wm-lh-fusiform 5605 5605.311
- 8 3008 wm-lh-inferiorparietal 7394 7393.808
- 9 3009 wm-lh-inferiortemporal 5176 5175.997
- 10 3010 wm-lh-isthmuscingulate 3513 3512.532
- 11 3011 wm-lh-lateraloccipital 5851 5850.543
- 12 3012 wm-lh-lateralorbitofrontal 5275 5274.825
- 13 3013 wm-lh-lingual 4250 4249.600
- 14 3014 wm-lh-medialorbitofrontal 2281 2280.826
- 15 3015 wm-lh-middletemporal 4364 4363.567
- 16 3016 wm-lh-parahippocampal 1312 1311.689
- 17 3017 wm-lh-paracentral 2759 2758.823
- 18 3018 wm-lh-parsopercularis 2789 2788.542
- 19 3019 wm-lh-parsorbitalis 663 662.594
- 20 3020 wm-lh-parstriangularis 2688 2687.592
- 21 3021 wm-lh-pericalcarine 2648 2647.635
- 22 3022 wm-lh-postcentral 6510 6510.271
- 23 3023 wm-lh-posteriorcingulate 4101 4100.679
- 24 3024 wm-lh-precentral 10902 10902.067
- 25 3025 wm-lh-precuneus 7758 7758.364
- 26 3026 wm-lh-rostralanteriorcingulate 2511 2510.979
- 27 3027 wm-lh-rostralmiddlefrontal 10752 10751.928
- 28 3028 wm-lh-superiorfrontal 14636 14635.643
- 29 3029 wm-lh-superiorparietal 11120 11120.426
- 30 3030 wm-lh-superiortemporal 6690 6690.204
- 31 3031 wm-lh-supramarginal 6091 6091.223
- 32 3032 wm-lh-frontalpole 156 155.602
- 33 3033 wm-lh-temporalpole 610 609.686
- 34 3034 wm-lh-transversetemporal 620 619.821
- 35 3035 wm-lh-insula 7252 7252.088
- 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 2337 2337.415
- 120 4002 wm-rh-caudalanteriorcingulate 3052 3052.461
- 121 4003 wm-rh-caudalmiddlefrontal 5402 5401.894
- 122 4004 wm-rh-corpuscallosum 0 0.000
- 123 4005 wm-rh-cuneus 1902 1901.741
- 124 4006 wm-rh-entorhinal 412 411.741
- 125 4007 wm-rh-fusiform 4897 4897.083
- 126 4008 wm-rh-inferiorparietal 9892 9891.718
- 127 4009 wm-rh-inferiortemporal 4176 4175.974
- 128 4010 wm-rh-isthmuscingulate 3487 3487.032
- 129 4011 wm-rh-lateraloccipital 6536 6535.720
- 130 4012 wm-rh-lateralorbitofrontal 4995 4994.706
- 131 4013 wm-rh-lingual 4633 4633.011
- 132 4014 wm-rh-medialorbitofrontal 2793 2792.814
- 133 4015 wm-rh-middletemporal 5521 5520.691
- 134 4016 wm-rh-parahippocampal 1299 1299.159
- 135 4017 wm-rh-paracentral 3882 3881.924
- 136 4018 wm-rh-parsopercularis 2816 2815.789
- 137 4019 wm-rh-parsorbitalis 850 850.077
- 138 4020 wm-rh-parstriangularis 2538 2537.989
- 139 4021 wm-rh-pericalcarine 2447 2447.356
- 140 4022 wm-rh-postcentral 5723 5722.869
- 141 4023 wm-rh-posteriorcingulate 3659 3658.729
- 142 4024 wm-rh-precentral 10382 10382.087
- 143 4025 wm-rh-precuneus 8710 8710.278
- 144 4026 wm-rh-rostralanteriorcingulate 1491 1490.617
- 145 4027 wm-rh-rostralmiddlefrontal 10595 10594.635
- 146 4028 wm-rh-superiorfrontal 14544 14543.719
- 147 4029 wm-rh-superiorparietal 10505 10505.142
- 148 4030 wm-rh-superiortemporal 5880 5879.782
- 149 4031 wm-rh-supramarginal 6707 6706.989
- 150 4032 wm-rh-frontalpole 150 150.029
- 151 4033 wm-rh-temporalpole 603 603.019
- 152 4034 wm-rh-transversetemporal 523 522.682
- 153 4035 wm-rh-insula 7013 7013.457
- 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 20416 20415.676
- 237 5002 Right-UnsegmentedWhiteMatter 19641 19641.248
- 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/sub014/label
- #--------------------------------------------
- #@# BA Labels lh Fri Aug 9 00:19:44 CEST 2013
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123287
- Number of reverse mapping hits = 272
- Checking for and removing duplicates
- Writing label file ./lh.BA1.label 4401
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123287
- Number of reverse mapping hits = 620
- Checking for and removing duplicates
- Writing label file ./lh.BA2.label 8529
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123287
- Number of reverse mapping hits = 116
- Checking for and removing duplicates
- Writing label file ./lh.BA3a.label 4193
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123287
- Number of reverse mapping hits = 269
- Checking for and removing duplicates
- Writing label file ./lh.BA3b.label 6252
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123287
- Number of reverse mapping hits = 185
- Checking for and removing duplicates
- Writing label file ./lh.BA4a.label 5969
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123287
- Number of reverse mapping hits = 134
- Checking for and removing duplicates
- Writing label file ./lh.BA4p.label 4204
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123287
- Number of reverse mapping hits = 917
- Checking for and removing duplicates
- Writing label file ./lh.BA6.label 14506
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123287
- Number of reverse mapping hits = 210
- Checking for and removing duplicates
- Writing label file ./lh.BA44.label 4391
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123287
- Number of reverse mapping hits = 589
- Checking for and removing duplicates
- Writing label file ./lh.BA45.label 4011
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123287
- Number of reverse mapping hits = 1119
- Checking for and removing duplicates
- Writing label file ./lh.V1.label 5760
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123287
- Number of reverse mapping hits = 2470
- Checking for and removing duplicates
- Writing label file ./lh.V2.label 10584
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123287
- Number of reverse mapping hits = 140
- Checking for and removing duplicates
- Writing label file ./lh.MT.label 2158
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.perirhinal.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123287
- Number of reverse mapping hits = 64
- Checking for and removing duplicates
- Writing label file ./lh.perirhinal.label 1263
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.thresh.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123287
- Number of reverse mapping hits = 81
- Checking for and removing duplicates
- Writing label file ./lh.BA1.thresh.label 1095
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.thresh.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123287
- Number of reverse mapping hits = 288
- Checking for and removing duplicates
- Writing label file ./lh.BA2.thresh.label 2380
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.thresh.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123287
- Number of reverse mapping hits = 16
- Checking for and removing duplicates
- Writing label file ./lh.BA3a.thresh.label 1520
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.thresh.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123287
- Number of reverse mapping hits = 150
- Checking for and removing duplicates
- Writing label file ./lh.BA3b.thresh.label 2146
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.thresh.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123287
- Number of reverse mapping hits = 63
- Checking for and removing duplicates
- Writing label file ./lh.BA4a.thresh.label 2382
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.thresh.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123287
- Number of reverse mapping hits = 66
- Checking for and removing duplicates
- Writing label file ./lh.BA4p.thresh.label 1615
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.thresh.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123287
- Number of reverse mapping hits = 257
- Checking for and removing duplicates
- Writing label file ./lh.BA6.thresh.label 7292
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.thresh.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123287
- Number of reverse mapping hits = 101
- Checking for and removing duplicates
- Writing label file ./lh.BA44.thresh.label 2013
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.thresh.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123287
- Number of reverse mapping hits = 233
- Checking for and removing duplicates
- Writing label file ./lh.BA45.thresh.label 1384
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.thresh.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123287
- Number of reverse mapping hits = 761
- Checking for and removing duplicates
- Writing label file ./lh.V1.thresh.label 4166
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.thresh.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123287
- Number of reverse mapping hits = 1221
- Checking for and removing duplicates
- Writing label file ./lh.V2.thresh.label 4555
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.thresh.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123287
- Number of reverse mapping hits = 24
- Checking for and removing duplicates
- Writing label file ./lh.MT.thresh.label 537
- mri_label2label: Done
- mris_label2annot --s sub014 --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/sub014/label
- cmdline mris_label2annot --s sub014 --hemi lh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --l lh.perirhinal.label --a BA --maxstatwinner --noverbose
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- subject sub014
- 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/sub014/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 85577 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/label/lh.BA.annot
- mris_label2annot --s sub014 --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/sub014/label
- cmdline mris_label2annot --s sub014 --hemi lh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l lh.BA1.thresh.label --l lh.BA2.thresh.label --l lh.BA3a.thresh.label --l lh.BA3b.thresh.label --l lh.BA4a.thresh.label --l lh.BA4p.thresh.label --l lh.BA6.thresh.label --l lh.BA44.thresh.label --l lh.BA45.thresh.label --l lh.V1.thresh.label --l lh.V2.thresh.label --l lh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- subject sub014
- 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/sub014/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 101532 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/label/lh.BA.thresh.annot
- mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab sub014 lh white
- computing statistics for each annotation in ./lh.BA.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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
- 1078 681 1841 1.892 0.744 0.168 0.072 27 3.3 BA1
- 4059 2671 7107 2.328 0.505 0.129 0.039 69 6.7 BA2
- 866 596 821 1.885 0.379 0.140 0.040 8 1.4 BA3a
- 2324 1556 3442 1.961 0.457 0.132 0.044 41 4.4 BA3b
- 1402 858 2952 2.698 0.517 0.123 0.042 16 2.4 BA4a
- 1223 780 2131 2.687 0.355 0.105 0.024 8 1.3 BA4p
- 8462 5730 19608 2.754 0.575 0.137 0.048 155 15.6 BA6
- 1968 1353 4346 2.713 0.515 0.140 0.048 33 3.6 BA44
- 2892 2011 6226 2.507 0.465 0.166 0.074 79 8.9 BA45
- 3347 2196 4876 2.054 0.443 0.153 0.075 94 9.4 V1
- 7911 5085 12671 2.236 0.426 0.169 0.069 180 21.0 V2
- 1355 875 2344 2.384 0.459 0.150 0.048 25 2.7 MT
- 823 583 2753 3.418 0.673 0.149 0.061 13 2.1 perirhinal
- mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab sub014 lh white
- computing statistics for each annotation in ./lh.BA.thresh.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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
- 697 423 1022 1.649 0.744 0.182 0.067 19 1.9 BA1
- 1808 1182 3364 2.309 0.544 0.129 0.047 41 3.4 BA2
- 706 479 640 1.889 0.399 0.142 0.041 7 1.2 BA3a
- 1515 1025 2051 1.816 0.308 0.113 0.030 17 2.0 BA3b
- 1313 831 2825 2.755 0.494 0.111 0.038 11 1.9 BA4a
- 1033 662 1725 2.664 0.366 0.107 0.026 7 1.2 BA4p
- 4223 2787 10052 2.819 0.594 0.135 0.045 57 7.8 BA6
- 1309 899 3034 2.737 0.472 0.151 0.052 25 2.6 BA44
- 1180 813 2871 2.624 0.425 0.168 0.060 32 3.0 BA45
- 3507 2315 5140 2.048 0.441 0.153 0.075 96 9.4 V1
- 4123 2644 6405 2.209 0.413 0.176 0.070 103 11.9 V2
- 341 236 542 2.261 0.414 0.148 0.038 4 0.6 MT
- #--------------------------------------------
- #@# BA Labels rh Fri Aug 9 00:25:11 CEST 2013
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123027
- Number of reverse mapping hits = 151
- Checking for and removing duplicates
- Writing label file ./rh.BA1.label 4113
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123027
- Number of reverse mapping hits = 213
- Checking for and removing duplicates
- Writing label file ./rh.BA2.label 6900
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123027
- Number of reverse mapping hits = 55
- Checking for and removing duplicates
- Writing label file ./rh.BA3a.label 4035
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123027
- Number of reverse mapping hits = 127
- Checking for and removing duplicates
- Writing label file ./rh.BA3b.label 4649
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123027
- Number of reverse mapping hits = 116
- Checking for and removing duplicates
- Writing label file ./rh.BA4a.label 5863
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123027
- Number of reverse mapping hits = 56
- Checking for and removing duplicates
- Writing label file ./rh.BA4p.label 4529
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123027
- Number of reverse mapping hits = 566
- Checking for and removing duplicates
- Writing label file ./rh.BA6.label 12822
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123027
- Number of reverse mapping hits = 497
- Checking for and removing duplicates
- Writing label file ./rh.BA44.label 7409
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123027
- Number of reverse mapping hits = 690
- Checking for and removing duplicates
- Writing label file ./rh.BA45.label 6045
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123027
- Number of reverse mapping hits = 1336
- Checking for and removing duplicates
- Writing label file ./rh.V1.label 6063
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123027
- Number of reverse mapping hits = 2584
- Checking for and removing duplicates
- Writing label file ./rh.V2.label 10600
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123027
- Number of reverse mapping hits = 276
- Checking for and removing duplicates
- Writing label file ./rh.MT.label 2208
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.perirhinal.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123027
- Number of reverse mapping hits = 26
- Checking for and removing duplicates
- Writing label file ./rh.perirhinal.label 778
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.thresh.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123027
- Number of reverse mapping hits = 51
- Checking for and removing duplicates
- Writing label file ./rh.BA1.thresh.label 927
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.thresh.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123027
- Number of reverse mapping hits = 73
- Checking for and removing duplicates
- Writing label file ./rh.BA2.thresh.label 2761
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.thresh.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123027
- Number of reverse mapping hits = 20
- Checking for and removing duplicates
- Writing label file ./rh.BA3a.thresh.label 1718
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.thresh.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123027
- Number of reverse mapping hits = 70
- Checking for and removing duplicates
- Writing label file ./rh.BA3b.thresh.label 2253
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.thresh.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123027
- Number of reverse mapping hits = 41
- Checking for and removing duplicates
- Writing label file ./rh.BA4a.thresh.label 1429
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.thresh.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123027
- Number of reverse mapping hits = 24
- Checking for and removing duplicates
- Writing label file ./rh.BA4p.thresh.label 1513
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.thresh.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123027
- Number of reverse mapping hits = 225
- Checking for and removing duplicates
- Writing label file ./rh.BA6.thresh.label 7184
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.thresh.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123027
- Number of reverse mapping hits = 83
- Checking for and removing duplicates
- Writing label file ./rh.BA44.thresh.label 1095
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.thresh.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123027
- Number of reverse mapping hits = 89
- Checking for and removing duplicates
- Writing label file ./rh.BA45.thresh.label 1267
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.thresh.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123027
- Number of reverse mapping hits = 852
- Checking for and removing duplicates
- Writing label file ./rh.V1.thresh.label 4084
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.thresh.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123027
- Number of reverse mapping hits = 1311
- Checking for and removing duplicates
- Writing label file ./rh.V2.thresh.label 4748
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.thresh.label --trgsubject sub014 --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 = sub014
- 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/sub014/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 123027
- Number of reverse mapping hits = 24
- Checking for and removing duplicates
- Writing label file ./rh.MT.thresh.label 292
- mri_label2label: Done
- mris_label2annot --s sub014 --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/sub014/label
- cmdline mris_label2annot --s sub014 --hemi rh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --l rh.perirhinal.label --a BA --maxstatwinner --noverbose
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- subject sub014
- 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/sub014/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 86767 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/label/rh.BA.annot
- mris_label2annot --s sub014 --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/sub014/label
- cmdline mris_label2annot --s sub014 --hemi rh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l rh.BA1.thresh.label --l rh.BA2.thresh.label --l rh.BA3a.thresh.label --l rh.BA3b.thresh.label --l rh.BA4a.thresh.label --l rh.BA4p.thresh.label --l rh.BA6.thresh.label --l rh.BA44.thresh.label --l rh.BA45.thresh.label --l rh.V1.thresh.label --l rh.V2.thresh.label --l rh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- subject sub014
- 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/sub014/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 103350 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/label/rh.BA.thresh.annot
- mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab sub014 rh white
- computing statistics for each annotation in ./rh.BA.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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
- 803 497 1701 2.380 0.481 0.171 0.074 20 2.1 BA1
- 2701 1830 4259 2.165 0.464 0.139 0.044 37 4.8 BA2
- 931 626 919 1.849 0.378 0.132 0.037 9 1.5 BA3a
- 1636 1131 2428 1.778 0.438 0.133 0.056 27 4.2 BA3b
- 1240 763 2759 2.884 0.488 0.110 0.031 11 1.7 BA4a
- 1003 670 1843 2.677 0.397 0.108 0.027 6 1.2 BA4p
- 6796 4558 15648 2.795 0.547 0.129 0.037 80 10.7 BA6
- 3357 2337 6908 2.580 0.478 0.141 0.047 73 6.2 BA44
- 3673 2523 8155 2.659 0.466 0.159 0.059 79 8.4 BA45
- 3759 2512 5239 1.971 0.468 0.159 0.069 71 10.1 V1
- 8094 5293 13076 2.250 0.486 0.169 0.069 185 20.8 V2
- 1769 1184 2800 2.331 0.403 0.146 0.050 28 3.5 MT
- 498 332 1732 3.505 0.656 0.140 0.052 7 1.0 perirhinal
- mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab sub014 rh white
- computing statistics for each annotation in ./rh.BA.thresh.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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
- 531 309 1043 2.282 0.485 0.195 0.102 18 2.0 BA1
- 1538 1061 2567 2.162 0.512 0.137 0.043 20 2.6 BA2
- 817 548 750 1.857 0.363 0.133 0.035 6 1.4 BA3a
- 1316 934 1675 1.610 0.297 0.113 0.029 11 1.5 BA3b
- 796 466 1700 2.989 0.460 0.114 0.037 6 1.4 BA4a
- 834 562 1575 2.766 0.369 0.098 0.024 4 0.8 BA4p
- 4046 2752 9723 2.776 0.568 0.132 0.039 51 6.6 BA6
- 799 570 1877 2.616 0.439 0.173 0.082 42 2.2 BA44
- 833 579 2142 2.782 0.488 0.151 0.050 14 1.6 BA45
- 3592 2416 4958 1.973 0.474 0.156 0.066 63 9.2 V1
- 4358 2818 6673 2.166 0.491 0.177 0.076 108 13.1 V2
- 217 142 380 2.485 0.267 0.162 0.064 5 0.5 MT
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/label
- #--------------------------------------------
- #@# Ex-vivo Entorhinal Cortex Label lh Fri Aug 9 00:30:59 CEST 2013
- mris_spherical_average -erode 1 -orig white -t 0.4 -o sub014 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label
- painting output onto subject sub014.
- processing subject lh.EC_average...
- reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 863 points to lh.entorhinal_exvivo.label...
- mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label sub014 lh white
- limiting computations to label ./lh.entorhinal_exvivo.label.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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
- 284 187 1143 3.452 0.529 0.113 0.035 2 0.5 ./lh.entorhinal_exvivo.label
- #--------------------------------------------
- #@# Ex-vivo Entorhinal Cortex Label rh Fri Aug 9 00:31:21 CEST 2013
- mris_spherical_average -erode 1 -orig white -t 0.4 -o sub014 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label
- painting output onto subject sub014.
- processing subject rh.EC_average...
- reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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 655 points to rh.entorhinal_exvivo.label...
- mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label sub014 rh white
- limiting computations to label ./rh.entorhinal_exvivo.label.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub014/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
- 221 136 863 3.531 0.521 0.119 0.034 2 0.3 ./rh.entorhinal_exvivo.label
- #------------------------------------------
- Started at Thu Aug 8 10:54:17 CEST 2013
- Ended at Fri Aug 9 00:31:37 CEST 2013
- #@#%# recon-all-run-time-hours 13.622
- recon-all -s sub014 finished without error at Fri Aug 9 00:31:37 CEST 2013
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