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- Thu Aug 8 10:53:55 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003
- /opt/freesurfer/5.3.0/bin/recon-all
- -i /home/data/exppsy/forrest_gump/openfmri.org/sub003/anatomy/highres001.nii.gz -cw256 -all -T2 /home/data/exppsy/forrest_gump/openfmri.org/sub003/anatomy/other/t2w001.nii.gz -T2pial -subjid sub003 -sd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- subjid sub003
- 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 96468108 2733584 0 177872 94401912
- -/+ buffers/cache: 1888324 97313368
- Swap: 25165780 3620 25162160
- ########################################
- program versions used
- $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
- $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
- mri_convert -all-info
- ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:56-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- FLIRT version 5.5
- $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
- mri_convert --version
- stable5
- ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:56-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- Program nu_correct, built from:
- Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
- ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:56-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:56-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:56-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:56-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:56-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:56-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ======= NUMBER OF OPENMP THREADS = 1 =======
- ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:58-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:58-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:58-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:58-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:58-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:58-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:58-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:58-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:58-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:58-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:59-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:59-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:59-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:59-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $
- ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:59-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $
- ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:59-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:59-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:59-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:59-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:59-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- #######################################
- GCADIR /opt/freesurfer/5.3.0/average
- GCA RB_all_2008-03-26.gca
- GCASkull RB_all_withskull_2008-03-26.gca
- AvgCurvTif average.curvature.filled.buckner40.tif
- GCSDIR /opt/freesurfer/5.3.0/average
- GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
- #######################################
- -cw256 option is now persistent (remove with -clean-cw256)
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub003/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/orig/001.mgz
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub003/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/anatomy/highres001.nii.gz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.99822, -0.0508489, 0.0311494)
- j_ras = (-0.0512259, 0.998622, -0.0114243)
- k_ras = (0.0305256, 0.0129996, 0.999449)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/orig/001.mgz...
- #--------------------------------------------
- #@# T2/FLAIR Input Thu Aug 8 10:54:14 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub003/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/orig/T2raw.mgz
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub003/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/anatomy/other/t2w001.nii.gz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.99822, -0.0508489, 0.0311494)
- j_ras = (-0.0512259, 0.998622, -0.0114243)
- k_ras = (0.0305256, 0.0129996, 0.999449)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/orig/T2raw.mgz...
- #--------------------------------------------
- #@# MotionCor Thu Aug 8 10:54:27 CEST 2013
- Found 1 runs
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/mri/orig/001.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/rawavg.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/orig.mgz --conform --cw256
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/mri/rawavg.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.99822, -0.0508489, 0.0311494)
- j_ras = (-0.0512259, 0.998622, -0.0114243)
- k_ras = (0.0305256, 0.0129996, 0.999449)
- Original Data has (0.699959, 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/sub003/mri/orig.mgz...
- mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/talairach.xfm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/orig.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Talairach Thu Aug 8 10:55:06 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri
- mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
- talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
- cp transforms/talairach.auto.xfm transforms/talairach.xfm
- #--------------------------------------------
- #@# Talairach Failure Detection Thu Aug 8 10:57:51 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri
- talairach_afd -T 0.005 -xfm transforms/talairach.xfm
- talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7490, 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/sub003/mri/transforms/talairach_avi.log
- tal_QC_AZS /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/talairach_avi.log
- TalAviQA: 0.96561
- z-score: -2
- #--------------------------------------------
- #@# Nu Intensity Correction Thu Aug 8 10:57:51 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/sub003/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 10:57:51 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.12223
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.12223/nu0.mnc -odt float
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.12223/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, 4.65661e-09, -1.86265e-09)
- j_ras = (1.86265e-09, 2.79397e-09, -1)
- k_ras = (-8.3528e-09, 1, -9.31323e-10)
- changing data type from uchar to float (noscale = 0)...
- writing to ./tmp.mri_nu_correct.mni.12223/nu0.mnc...
-
- --------------------------------------------------------
- Iteration 1 Thu Aug 8 10:57:56 CEST 2013
- nu_correct -clobber ./tmp.mri_nu_correct.mni.12223/nu0.mnc ./tmp.mri_nu_correct.mni.12223/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.12223/0/
- [fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/] [2013-08-08 10:57:56] 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.12223/0/ ./tmp.mri_nu_correct.mni.12223/nu0.mnc ./tmp.mri_nu_correct.mni.12223/nu1.imp
- Processing:.................................................................Done
- Processing:.................................................................Done
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- Processing:.................................................................Done
- Processing:.................................................................Done
- Number of iterations: 31
- CV of field change: 0.000976255
- [fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/] [2013-08-08 10:58:35] running:
- /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.12223/nu0.mnc ./tmp.mri_nu_correct.mni.12223/0//template.mnc
- Transforming slices:......................................................................................Done
- Transforming slices:................................................................................................................................................................................................................................................................Done
-
-
- --------------------------------------------------------
- Iteration 2 Thu Aug 8 10:58:43 CEST 2013
- nu_correct -clobber ./tmp.mri_nu_correct.mni.12223/nu1.mnc ./tmp.mri_nu_correct.mni.12223/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.12223/1/
- [fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/] [2013-08-08 10:58:43] 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.12223/1/ ./tmp.mri_nu_correct.mni.12223/nu1.mnc ./tmp.mri_nu_correct.mni.12223/nu2.imp
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
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- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Number of iterations: 23
- CV of field change: 0.000975575
- [fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/] [2013-08-08 10:59:19] running:
- /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.12223/nu1.mnc ./tmp.mri_nu_correct.mni.12223/1//template.mnc
- Transforming slices:......................................................................................Done
- Transforming slices:................................................................................................................................................................................................................................................................Done
-
-
-
- mri_binarize --i ./tmp.mri_nu_correct.mni.12223/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.12223/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/sub003/mri
- cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.12223/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.12223/ones.mgz
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- input ./tmp.mri_nu_correct.mni.12223/nu2.mnc
- frame 0
- nErode3d 0
- nErode2d 0
- output ./tmp.mri_nu_correct.mni.12223/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.12223/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.12223/sum.junk --avgwf ./tmp.mri_nu_correct.mni.12223/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.12223/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.12223/sum.junk --avgwf ./tmp.mri_nu_correct.mni.12223/input.mean.dat
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.12223/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.12223/input.mean.dat
- mri_segstats done
- mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.12223/ones.mgz --i ./tmp.mri_nu_correct.mni.12223/nu2.mnc --sum ./tmp.mri_nu_correct.mni.12223/sum.junk --avgwf ./tmp.mri_nu_correct.mni.12223/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.12223/ones.mgz --i ./tmp.mri_nu_correct.mni.12223/nu2.mnc --sum ./tmp.mri_nu_correct.mni.12223/sum.junk --avgwf ./tmp.mri_nu_correct.mni.12223/output.mean.dat
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.12223/ones.mgz
- Loading ./tmp.mri_nu_correct.mni.12223/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.12223/output.mean.dat
- mri_segstats done
- mris_calc -o ./tmp.mri_nu_correct.mni.12223/nu2.mnc ./tmp.mri_nu_correct.mni.12223/nu2.mnc mul .96234187965292691773
- Saving result to './tmp.mri_nu_correct.mni.12223/nu2.mnc' (type = MINC ) [ ok ]
- mri_convert ./tmp.mri_nu_correct.mni.12223/nu2.mnc nu.mgz --like orig.mgz
- mri_convert ./tmp.mri_nu_correct.mni.12223/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.12223/nu2.mnc...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, 4.65661e-09, -1.86265e-09)
- j_ras = (1.86265e-09, 2.79397e-09, -1)
- k_ras = (-8.3528e-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 (12, 204) to ( 3, 110)
-
-
- Thu Aug 8 11:00:10 CEST 2013
- mri_nu_correct.mni done
- mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/talairach.xfm nu.mgz nu.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Intensity Normalization Thu Aug 8 11:00:12 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri
- mri_normalize -g 1 nu.mgz T1.mgz
- using max gradient = 1.000
- reading from nu.mgz...
- normalizing image...
- talairach transform
- 1.180 0.077 -0.031 -0.003;
- -0.080 1.219 0.135 -38.645;
- 0.045 -0.260 1.294 -20.863;
- 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 = 15
- Starting OpenSpline(): npoints = 15
- 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 50 (50), valley at 32 (32)
- csf peak at 25, setting threshold to 41
- 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 51 (51), valley at 32 (32)
- csf peak at 15, setting threshold to 39
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Done iterating ---------------------------------
- writing output to T1.mgz
- 3D bias adjustment took 2 minutes and 53 seconds.
- #--------------------------------------------
- #@# Skull Stripping Thu Aug 8 11:03:07 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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=34.4
- skull bounding box = (62, 39, 43) --> (188, 211, 179)
- using (104, 96, 111) as brain centroid...
- mean wm in atlas = 126, using box (89,75,94) --> (119, 117,127) to find MRI wm
- before smoothing, mri peak at 113
- after smoothing, mri peak at 112, scaling input intensities by 1.125
- scaling channel 0 by 1.125
- initial log_p = -5.0
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -4.747513 @ (-9.091, 27.273, -9.091)
- max log p = -4.604891 @ (4.545, -13.636, -4.545)
- max log p = -4.542052 @ (6.818, 2.273, 2.273)
- max log p = -4.533968 @ (-3.409, -1.136, -1.136)
- max log p = -4.520561 @ (1.705, 1.705, 1.705)
- max log p = -4.520561 @ (0.000, 0.000, 0.000)
- Found translation: (0.6, 16.5, -10.8): log p = -4.521
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.5 (thresh=-4.5)
- 1.064 0.000 0.000 -7.413;
- 0.000 1.226 0.161 -17.501;
- 0.000 -0.150 1.140 -9.507;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1)
- 1.064 0.000 0.000 -7.413;
- 0.000 1.226 0.161 -17.501;
- 0.000 -0.150 1.140 -9.507;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.2500
- ****************************************
- Nine parameter search. iteration 2 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.1 (thresh=-4.1)
- 1.083 -0.037 -0.043 -3.155;
- 0.036 1.197 0.195 -23.161;
- 0.038 -0.199 1.198 -21.787;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 3 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.078 0.013 -0.117 3.144;
- -0.000 1.225 0.162 -17.451;
- 0.108 -0.159 1.176 -30.076;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 4 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.061 0.007 -0.077 1.138;
- -0.000 1.225 0.162 -17.451;
- 0.074 -0.162 1.201 -28.466;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.0625
- ****************************************
- Nine parameter search. iteration 5 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.061 0.019 -0.086 0.502;
- -0.009 1.221 0.163 -15.941;
- 0.082 -0.162 1.197 -29.460;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 6 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.061 0.017 -0.076 -0.451;
- -0.009 1.225 0.163 -16.423;
- 0.073 -0.162 1.196 -27.802;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 7 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.061 0.017 -0.076 -0.451;
- -0.009 1.225 0.163 -16.423;
- 0.073 -0.162 1.196 -27.802;
- 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
- 1.06086 0.01736 -0.07570 -0.45149;
- -0.00881 1.22506 0.16318 -16.42283;
- 0.07348 -0.16174 1.19586 -27.80207;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 3481
- Quasinewton: input matrix
- 1.06086 0.01736 -0.07570 -0.45149;
- -0.00881 1.22506 0.16318 -16.42283;
- 0.07348 -0.16174 1.19586 -27.80207;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 1.061 0.017 -0.076 -0.451;
- -0.009 1.225 0.163 -16.423;
- 0.073 -0.162 1.196 -27.802;
- 0.000 0.000 0.000 1.000;
- pass 1, spacing 8: log(p) = -4.0 (old=-5.0)
- transform before final EM align:
- 1.061 0.017 -0.076 -0.451;
- -0.009 1.225 0.163 -16.423;
- 0.073 -0.162 1.196 -27.802;
- 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
- 1.06086 0.01736 -0.07570 -0.45149;
- -0.00881 1.22506 0.16318 -16.42283;
- 0.07348 -0.16174 1.19586 -27.80207;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 382743
- Quasinewton: input matrix
- 1.06086 0.01736 -0.07570 -0.45149;
- -0.00881 1.22506 0.16318 -16.42283;
- 0.07348 -0.16174 1.19586 -27.80207;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 012: -log(p) = 4.4 tol 0.000000
- final transform:
- 1.061 0.017 -0.076 -0.451;
- -0.009 1.225 0.163 -16.423;
- 0.073 -0.162 1.196 -27.802;
- 0.000 0.000 0.000 1.000;
- writing output transformation to transforms/talairach_with_skull.lta...
- registration took 39 minutes and 19 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=125 y=86 z=122 r=86
- first estimation of the main basin volume: 2692528 voxels
- Looking for seedpoints
- 2 found in the cerebellum
- 15 found in the rest of the brain
- global maximum in x=152, y=86, z=87, 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=19354074114 voxels, voxel volume =1.000
- = 19354074114 mmm3 = 19354075.136 cm3
- done.
- PostAnalyze...Basin Prior
- 162 basins merged thanks to atlas
- ***** 0 basin(s) merged in 1 iteration(s)
- ***** 0 voxel(s) added to the main basin
- done.
- Weighting the input with prior template
- ****************TEMPLATE DEFORMATION****************
- second estimation of the COG coord: x=126,y=97, z=115, r=9457 iterations
- ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^
- GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=7 , nb = 45566
- RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=9 , nb = -1037164009
- LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=12 , nb = 1094733289
- RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=7 , nb = 1059422609
- LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1079664476
- OTHER CSF_MIN=0, CSF_intensity=6, CSF_MAX=36 , nb = -1112638672
- Problem with the least square interpolation in GM_MIN calculation.
-
- CSF_MAX TRANSITION GM_MIN GM
- GLOBAL
- before analyzing : 7, 11, 29, 49
- after analyzing : 7, 23, 29, 29
- RIGHT_CER
- before analyzing : 9, 11, 23, 59
- after analyzing : 9, 20, 25, 29
- LEFT_CER
- before analyzing : 12, 14, 24, 60
- after analyzing : 12, 21, 25, 30
- RIGHT_BRAIN
- before analyzing : 7, 10, 27, 49
- after analyzing : 7, 21, 27, 28
- LEFT_BRAIN
- before analyzing : 4, 6, 29, 49
- after analyzing : 4, 21, 29, 28
- OTHER
- before analyzing : 36, 78, 89, 96
- after analyzing : 36, 85, 89, 87
- mri_strip_skull: done peeling brain
- highly tesselated surface with 10242 vertices
- matching...69 iterations
- *********************VALIDATION*********************
- curvature mean = -0.013, std = 0.012
- curvature mean = 67.488, std = 7.941
- No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
- before rotation: sse = 2.30, sigma = 4.07
- after rotation: sse = 2.30, sigma = 4.07
- Localization of inacurate regions: Erosion-Dilation steps
- the sse mean is 2.35, its var is 3.31
- before Erosion-Dilatation 0.32% 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...46 iterations
- mri_strip_skull: done peeling brain
- Brain Size = 1519485 voxels, voxel volume = 1.000 mm3
- = 1519485 mmm3 = 1519.485 cm3
- ******************************
- Saving brainmask.auto.mgz
- done
- cp brainmask.auto.mgz brainmask.mgz
- #-------------------------------------
- #@# EM Registration Thu Aug 8 11:42:55 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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=21.0
- skull bounding box = (60, 39, 40) --> (189, 160, 204)
- using (103, 79, 122) as brain centroid...
- mean wm in atlas = 107, using box (87,64,102) --> (118, 93,142) to find MRI wm
- before smoothing, mri peak at 109
- after smoothing, mri peak at 109, scaling input intensities by 0.982
- scaling channel 0 by 0.981651
- initial log_p = -4.6
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -4.050945 @ (-9.091, 27.273, -9.091)
- max log p = -3.907736 @ (4.545, -4.545, -4.545)
- max log p = -3.852608 @ (2.273, -2.273, -2.273)
- max log p = -3.845421 @ (-1.136, -1.136, -1.136)
- max log p = -3.822341 @ (2.841, 0.568, 2.841)
- max log p = -3.822341 @ (0.000, 0.000, 0.000)
- Found translation: (-0.6, 19.9, -14.2): log p = -3.822
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p =-3.8 (thresh=-3.8)
- 1.150 0.000 0.000 -19.675;
- 0.000 1.150 0.000 5.040;
- 0.000 0.000 1.000 -14.205;
- 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)
- 1.150 0.000 0.000 -19.675;
- 0.000 1.150 0.000 5.040;
- 0.000 0.000 1.000 -14.205;
- 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=-3.3, old_max_log_p =-3.5 (thresh=-3.5)
- 1.126 -0.028 -0.067 -5.862;
- 0.034 1.165 0.098 -8.804;
- 0.079 -0.119 1.050 -18.373;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 3 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3)
- 1.100 -0.062 -0.102 4.833;
- 0.072 1.185 0.096 -15.413;
- 0.118 -0.122 1.067 -23.172;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 4 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3)
- 1.100 -0.062 -0.102 4.833;
- 0.072 1.185 0.096 -15.413;
- 0.118 -0.122 1.067 -23.172;
- 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=-3.2, old_max_log_p =-3.3 (thresh=-3.3)
- 1.103 -0.027 -0.064 -3.969;
- 0.036 1.185 0.099 -12.067;
- 0.082 -0.120 1.068 -19.353;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 6 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2)
- 1.105 -0.027 -0.064 -4.123;
- 0.036 1.188 0.090 -11.195;
- 0.083 -0.111 1.069 -20.889;
- 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)
- 1.106 -0.027 -0.064 -4.276;
- 0.036 1.189 0.090 -11.347;
- 0.083 -0.111 1.069 -20.889;
- 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
- 1.10592 -0.02670 -0.06425 -4.27603;
- 0.03566 1.18895 0.09021 -11.34732;
- 0.08259 -0.11063 1.06874 -20.88874;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 2772
- Quasinewton: input matrix
- 1.10592 -0.02670 -0.06425 -4.27603;
- 0.03566 1.18895 0.09021 -11.34732;
- 0.08259 -0.11063 1.06874 -20.88874;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 1.106 -0.027 -0.064 -4.276;
- 0.036 1.189 0.090 -11.347;
- 0.083 -0.111 1.069 -20.889;
- 0.000 0.000 0.000 1.000;
- pass 1, spacing 8: log(p) = -3.2 (old=-4.6)
- transform before final EM align:
- 1.106 -0.027 -0.064 -4.276;
- 0.036 1.189 0.090 -11.347;
- 0.083 -0.111 1.069 -20.889;
- 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
- 1.10592 -0.02670 -0.06425 -4.27603;
- 0.03566 1.18895 0.09021 -11.34732;
- 0.08259 -0.11063 1.06874 -20.88874;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 312841
- Quasinewton: input matrix
- 1.10592 -0.02670 -0.06425 -4.27603;
- 0.03566 1.18895 0.09021 -11.34732;
- 0.08259 -0.11063 1.06874 -20.88874;
- 0.00000 0.00000 0.00000 1.00000;
- dfp_em_step_func: 011: -log(p) = 3.8
- after pass:transform: ( 1.11, -0.03, -0.06, -4.28)
- ( 0.04, 1.19, 0.09, -11.35)
- ( 0.08, -0.11, 1.07, -20.89)
- dfp_em_step_func: 012: -log(p) = 3.8
- after pass:transform: ( 1.11, -0.03, -0.06, -4.28)
- ( 0.04, 1.19, 0.09, -11.35)
- ( 0.08, -0.11, 1.07, -20.89)
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization...
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 014: -log(p) = 3.8 tol 0.000000
- final transform:
- 1.106 -0.027 -0.064 -4.276;
- 0.036 1.189 0.090 -11.347;
- 0.083 -0.111 1.069 -20.889;
- 0.000 0.000 0.000 1.000;
- writing output transformation to transforms/talairach.lta...
- registration took 32 minutes and 13 seconds.
- #--------------------------------------
- #@# CA Normalize Thu Aug 8 12:15:08 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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=21.0
- skull bounding box = (60, 39, 40) --> (189, 161, 204)
- using (103, 80, 122) as brain centroid...
- mean wm in atlas = 107, using box (87,65,102) --> (118, 94,142) to find MRI wm
- before smoothing, mri peak at 109
- after smoothing, mri peak at 109, scaling input intensities by 0.982
- scaling channel 0 by 0.981651
- using 244171 sample points...
- INFO: compute sample coordinates transform
- 1.106 -0.027 -0.064 -4.276;
- 0.036 1.189 0.090 -11.347;
- 0.083 -0.111 1.069 -20.889;
- 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 (122, 40, 45) --> (186, 137, 200)
- Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 133.0
- 0 of 78 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 40735 control points for structure...
- bounding box (68, 42, 46) --> (130, 139, 202)
- Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 133.0
- 0 of 57 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3012 control points for structure...
- bounding box (127, 112, 67) --> (172, 148, 118)
- Left_Cerebellum_White_Matter: limiting intensities to 89.0 --> 133.0
- 0 of 8 (0.0%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2764 control points for structure...
- bounding box (85, 112, 68) --> (127, 149, 120)
- Right_Cerebellum_White_Matter: limiting intensities to 82.0 --> 133.0
- 0 of 9 (0.0%) samples deleted
- finding control points in Brain_Stem....
- found 3520 control points for structure...
- bounding box (113, 106, 100) --> (142, 164, 130)
- Brain_Stem: limiting intensities to 74.0 --> 133.0
- 0 of 12 (0.0%) samples deleted
- using 164 total control points for intensity normalization...
- bias field = 1.005 +- 0.050
- 0 of 164 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 41584 control points for structure...
- bounding box (122, 40, 45) --> (186, 137, 200)
- Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 130.0
- 0 of 130 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 40735 control points for structure...
- bounding box (68, 42, 46) --> (130, 139, 202)
- Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 130.0
- 0 of 134 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3012 control points for structure...
- bounding box (127, 112, 67) --> (172, 148, 118)
- Left_Cerebellum_White_Matter: limiting intensities to 78.0 --> 130.0
- 0 of 33 (0.0%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2764 control points for structure...
- bounding box (85, 112, 68) --> (127, 149, 120)
- Right_Cerebellum_White_Matter: limiting intensities to 83.0 --> 130.0
- 0 of 32 (0.0%) samples deleted
- finding control points in Brain_Stem....
- found 3520 control points for structure...
- bounding box (113, 106, 100) --> (142, 164, 130)
- Brain_Stem: limiting intensities to 72.0 --> 130.0
- 0 of 64 (0.0%) samples deleted
- using 393 total control points for intensity normalization...
- bias field = 1.001 +- 0.058
- 0 of 393 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 41584 control points for structure...
- bounding box (122, 40, 45) --> (186, 137, 200)
- Left_Cerebral_White_Matter: limiting intensities to 90.0 --> 128.0
- 0 of 249 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 40735 control points for structure...
- bounding box (68, 42, 46) --> (130, 139, 202)
- Right_Cerebral_White_Matter: limiting intensities to 94.0 --> 128.0
- 0 of 183 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3012 control points for structure...
- bounding box (127, 112, 67) --> (172, 148, 118)
- Left_Cerebellum_White_Matter: limiting intensities to 83.0 --> 128.0
- 3 of 31 (9.7%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2764 control points for structure...
- bounding box (85, 112, 68) --> (127, 149, 120)
- Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 128.0
- 9 of 40 (22.5%) samples deleted
- finding control points in Brain_Stem....
- found 3520 control points for structure...
- bounding box (113, 106, 100) --> (142, 164, 130)
- Brain_Stem: limiting intensities to 69.0 --> 128.0
- 0 of 93 (0.0%) samples deleted
- using 596 total control points for intensity normalization...
- bias field = 1.015 +- 0.048
- 0 of 584 control points discarded
- writing normalized volume to norm.mgz...
- writing control points to ctrl_pts.mgz
- freeing GCA...done.
- normalization took 2 minutes and 4 seconds.
- #--------------------------------------
- #@# CA Reg Thu Aug 8 12:17:12 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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) = 1.42 (predicted orig area = 5.6)
- 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=0.904, neg=0, invalid=96777
- 0001: dt=129.472000, rms=0.802 (11.269%), neg=0, invalid=96777
- 0002: dt=129.472000, rms=0.783 (2.392%), neg=0, invalid=96777
- 0003: dt=129.472000, rms=0.770 (1.636%), neg=0, invalid=96777
- 0004: dt=110.976000, rms=0.765 (0.593%), neg=0, invalid=96777
- 0005: dt=129.472000, rms=0.759 (0.815%), neg=0, invalid=96777
- 0006: dt=110.976000, rms=0.757 (0.337%), neg=0, invalid=96777
- 0007: dt=295.936000, rms=0.751 (0.740%), neg=0, invalid=96777
- 0008: dt=55.488000, rms=0.748 (0.412%), neg=0, invalid=96777
- 0009: dt=369.920000, rms=0.745 (0.435%), neg=0, invalid=96777
- 0010: dt=110.976000, rms=0.740 (0.570%), neg=0, invalid=96777
- 0011: dt=73.984000, rms=0.740 (0.076%), neg=0, invalid=96777
- 0012: dt=73.984000, rms=0.739 (0.147%), neg=0, invalid=96777
- 0013: dt=73.984000, rms=0.737 (0.230%), neg=0, invalid=96777
- 0014: dt=73.984000, rms=0.735 (0.291%), neg=0, invalid=96777
- 0015: dt=73.984000, rms=0.733 (0.315%), neg=0, invalid=96777
- 0016: dt=73.984000, rms=0.730 (0.333%), neg=0, invalid=96777
- 0017: dt=73.984000, rms=0.728 (0.359%), neg=0, invalid=96777
- 0018: dt=73.984000, rms=0.725 (0.382%), neg=0, invalid=96777
- 0019: dt=73.984000, rms=0.722 (0.340%), neg=0, invalid=96777
- 0020: dt=73.984000, rms=0.720 (0.286%), neg=0, invalid=96777
- 0021: dt=73.984000, rms=0.719 (0.247%), neg=0, invalid=96777
- 0022: dt=73.984000, rms=0.717 (0.247%), neg=0, invalid=96777
- 0023: dt=73.984000, rms=0.715 (0.273%), neg=0, invalid=96777
- 0024: dt=73.984000, rms=0.713 (0.279%), neg=0, invalid=96777
- 0025: dt=73.984000, rms=0.711 (0.235%), neg=0, invalid=96777
- 0026: dt=73.984000, rms=0.710 (0.180%), neg=0, invalid=96777
- 0027: dt=73.984000, rms=0.709 (0.158%), neg=0, invalid=96777
- 0028: dt=73.984000, rms=0.707 (0.199%), neg=0, invalid=96777
- 0029: dt=73.984000, rms=0.706 (0.210%), neg=0, invalid=96777
- 0030: dt=73.984000, rms=0.705 (0.175%), neg=0, invalid=96777
- 0031: dt=73.984000, rms=0.704 (0.148%), neg=0, invalid=96777
- 0032: dt=73.984000, rms=0.703 (0.127%), neg=0, invalid=96777
- 0033: dt=73.984000, rms=0.702 (0.131%), neg=0, invalid=96777
- 0034: dt=73.984000, rms=0.701 (0.154%), neg=0, invalid=96777
- 0035: dt=73.984000, rms=0.700 (0.140%), neg=0, invalid=96777
- 0036: dt=73.984000, rms=0.699 (0.113%), neg=0, invalid=96777
- 0037: dt=73.984000, rms=0.698 (0.104%), neg=0, invalid=96777
- 0038: dt=1183.744000, rms=0.697 (0.167%), neg=0, invalid=96777
- 0039: dt=27.744000, rms=0.697 (0.020%), neg=0, invalid=96777
- 0040: dt=27.744000, rms=0.697 (0.011%), neg=0, invalid=96777
- 0041: dt=27.744000, rms=0.697 (-0.029%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.697, neg=0, invalid=96777
- 0042: dt=73.984000, rms=0.696 (0.053%), neg=0, invalid=96777
- 0043: dt=92.480000, rms=0.696 (0.040%), neg=0, invalid=96777
- 0044: dt=92.480000, rms=0.696 (0.038%), neg=0, invalid=96777
- 0045: dt=92.480000, rms=0.696 (0.043%), neg=0, invalid=96777
- 0046: dt=92.480000, rms=0.695 (0.015%), neg=0, invalid=96777
- 0047: dt=92.480000, rms=0.695 (0.020%), neg=0, invalid=96777
- 0048: dt=92.480000, rms=0.695 (0.075%), neg=0, invalid=96777
- 0049: dt=92.480000, rms=0.694 (0.086%), neg=0, invalid=96777
- 0050: dt=92.480000, rms=0.694 (0.030%), neg=0, invalid=96777
- setting smoothness coefficient to 0.154
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.700, neg=0, invalid=96777
- 0051: dt=145.152000, rms=0.689 (1.620%), neg=0, invalid=96777
- 0052: dt=62.208000, rms=0.683 (0.846%), neg=0, invalid=96777
- 0053: dt=62.208000, rms=0.677 (0.856%), neg=0, invalid=96777
- 0054: dt=9.072000, rms=0.676 (0.166%), neg=0, invalid=96777
- 0055: dt=9.072000, rms=0.675 (0.109%), neg=0, invalid=96777
- 0056: dt=9.072000, rms=0.674 (0.099%), neg=0, invalid=96777
- 0057: dt=9.072000, rms=0.674 (0.119%), neg=0, invalid=96777
- 0058: dt=9.072000, rms=0.672 (0.196%), neg=0, invalid=96777
- 0059: dt=9.072000, rms=0.670 (0.318%), neg=0, invalid=96777
- 0060: dt=9.072000, rms=0.667 (0.410%), neg=0, invalid=96777
- 0061: dt=9.072000, rms=0.665 (0.409%), neg=0, invalid=96777
- 0062: dt=9.072000, rms=0.662 (0.381%), neg=0, invalid=96777
- 0063: dt=9.072000, rms=0.660 (0.339%), neg=0, invalid=96777
- 0064: dt=9.072000, rms=0.658 (0.320%), neg=0, invalid=96777
- 0065: dt=9.072000, rms=0.656 (0.291%), neg=0, invalid=96777
- 0066: dt=9.072000, rms=0.654 (0.258%), neg=0, invalid=96777
- 0067: dt=9.072000, rms=0.652 (0.251%), neg=0, invalid=96777
- 0068: dt=9.072000, rms=0.651 (0.283%), neg=0, invalid=96777
- 0069: dt=9.072000, rms=0.649 (0.315%), neg=0, invalid=96777
- 0070: dt=9.072000, rms=0.647 (0.311%), neg=0, invalid=96777
- 0071: dt=9.072000, rms=0.645 (0.276%), neg=0, invalid=96777
- 0072: dt=9.072000, rms=0.643 (0.239%), neg=0, invalid=96777
- 0073: dt=9.072000, rms=0.642 (0.213%), neg=0, invalid=96777
- 0074: dt=9.072000, rms=0.641 (0.193%), neg=0, invalid=96777
- 0075: dt=9.072000, rms=0.640 (0.169%), neg=0, invalid=96777
- 0076: dt=9.072000, rms=0.639 (0.158%), neg=0, invalid=96777
- 0077: dt=9.072000, rms=0.637 (0.164%), neg=0, invalid=96777
- 0078: dt=9.072000, rms=0.636 (0.175%), neg=0, invalid=96777
- 0079: dt=9.072000, rms=0.635 (0.189%), neg=0, invalid=96777
- 0080: dt=9.072000, rms=0.634 (0.176%), neg=0, invalid=96777
- 0081: dt=9.072000, rms=0.633 (0.160%), neg=0, invalid=96777
- 0082: dt=9.072000, rms=0.632 (0.137%), neg=0, invalid=96777
- 0083: dt=9.072000, rms=0.631 (0.114%), neg=0, invalid=96777
- 0084: dt=9.072000, rms=0.631 (0.100%), neg=0, invalid=96777
- 0085: dt=145.152000, rms=0.631 (0.035%), neg=0, invalid=96777
- 0086: dt=145.152000, rms=0.631 (-0.007%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.631, neg=0, invalid=96777
- 0087: dt=36.288000, rms=0.629 (0.199%), neg=0, invalid=96777
- 0088: dt=20.736000, rms=0.629 (0.010%), neg=0, invalid=96777
- 0089: dt=20.736000, rms=0.629 (0.013%), neg=0, invalid=96777
- 0090: dt=20.736000, rms=0.629 (0.004%), neg=0, invalid=96777
- 0091: dt=20.736000, rms=0.629 (-0.033%), neg=0, invalid=96777
- setting smoothness coefficient to 0.588
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.653, neg=0, invalid=96777
- 0092: dt=11.636364, rms=0.651 (0.215%), neg=0, invalid=96777
- 0093: dt=9.600000, rms=0.651 (0.052%), neg=0, invalid=96777
- 0094: dt=9.600000, rms=0.651 (0.054%), neg=0, invalid=96777
- 0095: dt=9.600000, rms=0.651 (-0.017%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.651, neg=0, invalid=96777
- 0096: dt=0.000000, rms=0.651 (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
- 0097: dt=4.198895, rms=0.699 (0.862%), neg=0, invalid=96777
- 0098: dt=1.008000, rms=0.699 (0.026%), neg=0, invalid=96777
- 0099: dt=1.008000, rms=0.699 (0.007%), neg=0, invalid=96777
- 0100: dt=1.008000, rms=0.699 (-0.026%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.699, neg=0, invalid=96777
- 0101: dt=0.000000, rms=0.699 (0.000%), neg=0, invalid=96777
- setting smoothness coefficient to 5.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.771, neg=0, invalid=96777
- 0102: dt=0.848718, rms=0.768 (0.294%), neg=0, invalid=96777
- 0103: dt=1.659722, rms=0.765 (0.404%), neg=0, invalid=96777
- 0104: dt=1.792000, rms=0.764 (0.227%), neg=0, invalid=96777
- 0105: dt=1.792000, rms=0.763 (0.074%), neg=0, invalid=96777
- 0106: dt=1.792000, rms=0.763 (-0.138%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.763, neg=0, invalid=96777
- 0107: dt=0.882006, rms=0.761 (0.256%), neg=0, invalid=96777
- 0108: dt=0.256000, rms=0.761 (0.005%), neg=0, invalid=96777
- 0109: dt=0.256000, rms=0.761 (-0.000%), 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=0.706, neg=0, invalid=96777
- 0110: dt=0.320000, rms=0.690 (2.279%), neg=0, invalid=96777
- 0111: dt=0.000000, rms=0.690 (0.006%), neg=0, invalid=96777
- 0112: dt=0.050000, rms=0.690 (-0.329%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.690, neg=0, invalid=96777
- 0113: dt=0.000000, rms=0.690 (0.000%), neg=0, invalid=96777
- renormalizing by structure alignment....
- renormalizing input #0
- gca peak = 0.11725 (24)
- mri peak = 0.08748 ( 5)
- Left_Lateral_Ventricle (4): linear fit = 0.17 x + 0.0 (1345 voxels, overlap=0.137)
- Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (1345 voxels, peak = 4), gca=9.6
- gca peak = 0.14022 (22)
- mri peak = 0.13408 (55)
- Right_Lateral_Ventricle (43): linear fit = 0.20 x + 0.0 (755 voxels, overlap=0.004)
- Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (755 voxels, peak = 5), gca=8.8
- gca peak = 0.24234 (100)
- mri peak = 0.07578 (75)
- Right_Pallidum (52): linear fit = 0.82 x + 0.0 (280 voxels, overlap=0.045)
- Right_Pallidum (52): linear fit = 0.82 x + 0.0 (280 voxels, peak = 82), gca=82.5
- gca peak = 0.19192 (97)
- mri peak = 0.10324 (80)
- Left_Pallidum (13): linear fit = 0.79 x + 0.0 (154 voxels, overlap=0.034)
- Left_Pallidum (13): linear fit = 0.79 x + 0.0 (154 voxels, peak = 76), gca=76.1
- gca peak = 0.24007 (63)
- mri peak = 0.09007 (53)
- Right_Hippocampus (53): linear fit = 0.85 x + 0.0 (442 voxels, overlap=0.537)
- Right_Hippocampus (53): linear fit = 0.85 x + 0.0 (442 voxels, peak = 53), gca=53.2
- gca peak = 0.29892 (64)
- mri peak = 0.08799 (54)
- Left_Hippocampus (17): linear fit = 0.88 x + 0.0 (498 voxels, overlap=0.429)
- Left_Hippocampus (17): linear fit = 0.88 x + 0.0 (498 voxels, peak = 56), gca=56.0
- gca peak = 0.12541 (104)
- mri peak = 0.08176 (107)
- Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (49751 voxels, overlap=0.696)
- Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (49751 voxels, peak = 109), gca=108.7
- gca peak = 0.13686 (104)
- mri peak = 0.08587 (108)
- Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (54124 voxels, overlap=0.651)
- Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (54124 voxels, peak = 110), gca=109.7
- gca peak = 0.11691 (63)
- mri peak = 0.06253 (52)
- Left_Cerebral_Cortex (3): linear fit = 0.77 x + 0.0 (13695 voxels, overlap=0.013)
- Left_Cerebral_Cortex (3): linear fit = 0.77 x + 0.0 (13695 voxels, peak = 49), gca=48.8
- gca peak = 0.13270 (63)
- mri peak = 0.07149 (51)
- Right_Cerebral_Cortex (42): linear fit = 0.80 x + 0.0 (13348 voxels, overlap=0.014)
- Right_Cerebral_Cortex (42): linear fit = 0.80 x + 0.0 (13348 voxels, peak = 50), gca=50.1
- gca peak = 0.15182 (70)
- mri peak = 0.08434 (64)
- Right_Caudate (50): linear fit = 0.90 x + 0.0 (433 voxels, overlap=0.471)
- Right_Caudate (50): linear fit = 0.90 x + 0.0 (433 voxels, peak = 63), gca=63.3
- gca peak = 0.14251 (76)
- mri peak = 0.07703 (63)
- Left_Caudate (11): linear fit = 0.82 x + 0.0 (446 voxels, overlap=0.061)
- Left_Caudate (11): linear fit = 0.82 x + 0.0 (446 voxels, peak = 63), gca=62.7
- gca peak = 0.12116 (60)
- mri peak = 0.04763 (59)
- Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (9930 voxels, overlap=0.983)
- Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (9930 voxels, peak = 59), gca=59.1
- gca peak = 0.12723 (61)
- mri peak = 0.05089 (57)
- Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (10376 voxels, overlap=0.974)
- Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (10376 voxels, peak = 59), gca=58.9
- gca peak = 0.22684 (88)
- mri peak = 0.07078 (91)
- Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (5273 voxels, overlap=0.904)
- Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (5273 voxels, peak = 92), gca=92.0
- gca peak = 0.21067 (87)
- mri peak = 0.07103 (88)
- Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (4739 voxels, overlap=0.965)
- Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (4739 voxels, peak = 90), gca=90.0
- gca peak = 0.25455 (62)
- mri peak = 0.13688 (53)
- Left_Amygdala (18): linear fit = 0.83 x + 0.0 (280 voxels, overlap=0.315)
- Left_Amygdala (18): linear fit = 0.83 x + 0.0 (280 voxels, peak = 52), gca=51.8
- gca peak = 0.39668 (62)
- mri peak = 0.11325 (54)
- Right_Amygdala (54): linear fit = 0.86 x + 0.0 (233 voxels, overlap=0.684)
- Right_Amygdala (54): linear fit = 0.86 x + 0.0 (233 voxels, peak = 53), gca=53.0
- gca peak = 0.10129 (93)
- mri peak = 0.04470 (96)
- Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4274 voxels, overlap=0.970)
- Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4274 voxels, peak = 93), gca=93.5
- gca peak = 0.12071 (89)
- mri peak = 0.05443 (82)
- Right_Thalamus_Proper (49): linear fit = 0.94 x + 0.0 (3020 voxels, overlap=0.942)
- Right_Thalamus_Proper (49): linear fit = 0.94 x + 0.0 (3020 voxels, peak = 83), gca=83.2
- gca peak = 0.13716 (82)
- mri peak = 0.05156 (70)
- Left_Putamen (12): linear fit = 0.92 x + 0.0 (1505 voxels, overlap=0.755)
- Left_Putamen (12): linear fit = 0.92 x + 0.0 (1505 voxels, peak = 75), gca=75.0
- gca peak = 0.15214 (84)
- mri peak = 0.06922 (72)
- Right_Putamen (51): linear fit = 0.88 x + 0.0 (1590 voxels, overlap=0.415)
- Right_Putamen (51): linear fit = 0.88 x + 0.0 (1590 voxels, peak = 74), gca=74.3
- gca peak = 0.08983 (85)
- mri peak = 0.07526 (89)
- Brain_Stem (16): linear fit = 1.03 x + 0.0 (8419 voxels, overlap=0.777)
- Brain_Stem (16): linear fit = 1.03 x + 0.0 (8419 voxels, peak = 88), gca=88.0
- gca peak = 0.11809 (92)
- mri peak = 0.07792 (87)
- Right_VentralDC (60): linear fit = 1.02 x + 0.0 (544 voxels, overlap=0.898)
- Right_VentralDC (60): linear fit = 1.02 x + 0.0 (544 voxels, peak = 94), gca=94.3
- gca peak = 0.12914 (94)
- mri peak = 0.07407 (85)
- Left_VentralDC (28): linear fit = 1.00 x + 0.0 (632 voxels, overlap=0.856)
- Left_VentralDC (28): linear fit = 1.00 x + 0.0 (632 voxels, peak = 94), gca=94.0
- gca peak = 0.21100 (36)
- mri peak = 0.02731 ( 7)
- gca peak = 0.13542 (27)
- mri peak = 0.11213 ( 9)
- Fourth_Ventricle (15): linear fit = 0.28 x + 0.0 (173 voxels, overlap=0.022)
- Fourth_Ventricle (15): linear fit = 0.28 x + 0.0 (173 voxels, peak = 7), gca=7.4
- gca peak Unknown = 0.94427 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.21802 (40)
- gca peak Third_Ventricle = 0.21100 (36)
- gca peak Fourth_Ventricle = 0.13542 (27)
- gca peak CSF = 0.17123 (45)
- gca peak Left_Accumbens_area = 0.25875 (69)
- gca peak Left_undetermined = 0.96240 (36)
- gca peak Left_vessel = 0.33262 (65)
- gca peak Left_choroid_plexus = 0.09846 (46)
- gca peak Right_Inf_Lat_Vent = 0.28113 (34)
- gca peak Right_Accumbens_area = 0.27120 (72)
- gca peak Right_vessel = 0.61915 (60)
- gca peak Right_choroid_plexus = 0.12775 (51)
- gca peak Fifth_Ventricle = 0.45329 (44)
- gca peak WM_hypointensities = 0.11729 (81)
- gca peak non_WM_hypointensities = 0.10912 (56)
- gca peak Optic_Chiasm = 0.33287 (75)
- label assignment complete, 0 changed (0.00%)
- not using caudate to estimate GM means
- estimating mean gm scale to be 0.83 x + 0.0
- estimating mean wm scale to be 1.05 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=0.732, neg=0, invalid=96777
- 0114: dt=129.472000, rms=0.725 (1.009%), neg=0, invalid=96777
- 0115: dt=129.472000, rms=0.722 (0.411%), neg=0, invalid=96777
- 0116: dt=92.480000, rms=0.721 (0.135%), neg=0, invalid=96777
- 0117: dt=129.472000, rms=0.719 (0.276%), neg=0, invalid=96777
- 0118: dt=55.488000, rms=0.718 (0.068%), neg=0, invalid=96777
- 0119: dt=1183.744000, rms=0.713 (0.749%), neg=0, invalid=96777
- 0120: dt=32.368000, rms=0.712 (0.106%), neg=0, invalid=96777
- 0121: dt=55.488000, rms=0.712 (0.045%), neg=0, invalid=96777
- 0122: dt=55.488000, rms=0.711 (0.056%), neg=0, invalid=96777
- 0123: dt=55.488000, rms=0.711 (0.087%), neg=0, invalid=96777
- 0124: dt=55.488000, rms=0.710 (0.099%), neg=0, invalid=96777
- 0125: dt=55.488000, rms=0.709 (0.103%), neg=0, invalid=96777
- 0126: dt=55.488000, rms=0.709 (0.106%), neg=0, invalid=96777
- 0127: dt=55.488000, rms=0.708 (0.107%), neg=0, invalid=96777
- 0128: dt=55.488000, rms=0.707 (0.106%), neg=0, invalid=96777
- 0129: dt=55.488000, rms=0.706 (0.098%), neg=0, invalid=96777
- 0130: dt=55.488000, rms=0.706 (0.090%), neg=0, invalid=96777
- 0131: dt=55.488000, rms=0.705 (0.083%), neg=0, invalid=96777
- 0132: dt=55.488000, rms=0.705 (0.085%), neg=0, invalid=96777
- 0133: dt=55.488000, rms=0.704 (0.087%), neg=0, invalid=96777
- 0134: dt=55.488000, rms=0.703 (0.077%), neg=0, invalid=96777
- 0135: dt=55.488000, rms=0.703 (0.070%), neg=0, invalid=96777
- 0136: dt=55.488000, rms=0.702 (0.063%), neg=0, invalid=96777
- 0137: dt=55.488000, rms=0.702 (0.059%), neg=0, invalid=96777
- 0138: dt=55.488000, rms=0.702 (0.065%), neg=0, invalid=96777
- 0139: dt=55.488000, rms=0.701 (0.067%), neg=0, invalid=96777
- 0140: dt=55.488000, rms=0.701 (0.061%), neg=0, invalid=96777
- 0141: dt=55.488000, rms=0.700 (0.057%), neg=0, invalid=96777
- 0142: dt=55.488000, rms=0.700 (0.054%), neg=0, invalid=96777
- 0143: dt=55.488000, rms=0.700 (0.054%), neg=0, invalid=96777
- 0144: dt=55.488000, rms=0.699 (0.060%), neg=0, invalid=96777
- 0145: dt=55.488000, rms=0.699 (0.055%), neg=0, invalid=96777
- 0146: dt=55.488000, rms=0.698 (0.055%), neg=0, invalid=96777
- 0147: dt=55.488000, rms=0.698 (0.051%), neg=0, invalid=96777
- 0148: dt=55.488000, rms=0.698 (0.043%), neg=0, invalid=96777
- 0149: dt=55.488000, rms=0.697 (0.041%), neg=0, invalid=96777
- 0150: dt=55.488000, rms=0.697 (0.050%), neg=0, invalid=96777
- 0151: dt=55.488000, rms=0.697 (0.048%), neg=0, invalid=96777
- 0152: dt=55.488000, rms=0.696 (0.047%), neg=0, invalid=96777
- 0153: dt=55.488000, rms=0.696 (0.044%), neg=0, invalid=96777
- 0154: dt=55.488000, rms=0.696 (0.043%), neg=0, invalid=96777
- 0155: dt=55.488000, rms=0.696 (0.043%), neg=0, invalid=96777
- 0156: dt=55.488000, rms=0.695 (0.044%), neg=0, invalid=96777
- 0157: dt=55.488000, rms=0.695 (0.044%), neg=0, invalid=96777
- 0158: dt=55.488000, rms=0.695 (0.042%), neg=0, invalid=96777
- 0159: dt=55.488000, rms=0.694 (0.038%), neg=0, invalid=96777
- 0160: dt=55.488000, rms=0.694 (0.034%), neg=0, invalid=96777
- 0161: dt=55.488000, rms=0.694 (0.032%), neg=0, invalid=96777
- 0162: dt=55.488000, rms=0.694 (0.032%), neg=0, invalid=96777
- 0163: dt=55.488000, rms=0.693 (0.039%), neg=0, invalid=96777
- 0164: dt=55.488000, rms=0.693 (0.040%), neg=0, invalid=96777
- 0165: dt=55.488000, rms=0.693 (0.036%), neg=0, invalid=96777
- 0166: dt=55.488000, rms=0.693 (0.029%), neg=0, invalid=96777
- 0167: dt=55.488000, rms=0.692 (0.030%), neg=0, invalid=96777
- 0168: dt=55.488000, rms=0.692 (0.034%), neg=0, invalid=96777
- 0169: dt=55.488000, rms=0.692 (0.034%), neg=0, invalid=96777
- 0170: dt=55.488000, rms=0.692 (0.027%), neg=0, invalid=96777
- 0171: dt=55.488000, rms=0.692 (0.023%), neg=0, invalid=96777
- 0172: dt=55.488000, rms=0.691 (0.023%), neg=0, invalid=96777
- 0173: dt=517.888000, rms=0.691 (0.064%), neg=0, invalid=96777
- 0174: dt=0.000903, rms=0.691 (-0.004%), neg=0, invalid=96777
- 0175: dt=0.000903, rms=0.691 (0.000%), neg=0, invalid=96777
- 0176: dt=0.000903, rms=0.691 (-0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.691, neg=0, invalid=96777
- 0177: dt=32.368000, rms=0.691 (0.021%), neg=0, invalid=96777
- 0178: dt=32.368000, rms=0.691 (0.014%), neg=0, invalid=96777
- 0179: dt=32.368000, rms=0.691 (0.009%), neg=0, invalid=96777
- 0180: dt=32.368000, rms=0.691 (0.008%), neg=0, invalid=96777
- 0181: dt=32.368000, rms=0.691 (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=0.691, neg=0, invalid=96777
- 0182: dt=103.680000, rms=0.685 (0.929%), neg=0, invalid=96777
- 0183: dt=36.288000, rms=0.679 (0.823%), neg=0, invalid=96777
- 0184: dt=124.416000, rms=0.674 (0.826%), neg=0, invalid=96777
- 0185: dt=9.072000, rms=0.671 (0.335%), neg=0, invalid=96777
- 0186: dt=9.072000, rms=0.670 (0.163%), neg=0, invalid=96777
- 0187: dt=9.072000, rms=0.670 (0.088%), neg=0, invalid=96777
- 0188: dt=6.480000, rms=0.669 (0.046%), neg=0, invalid=96777
- 0189: dt=0.405000, rms=0.669 (0.007%), neg=0, invalid=96777
- 0190: dt=0.012656, rms=0.669 (-0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.669, neg=0, invalid=96777
- 0191: dt=0.008859, rms=0.669 (0.000%), neg=0, invalid=96777
- 0192: dt=0.008859, rms=0.669 (0.000%), neg=0, invalid=96777
- 0193: dt=0.002215, rms=0.669 (0.000%), neg=0, invalid=96777
- 0194: dt=0.001107, rms=0.669 (0.000%), neg=0, invalid=96777
- 0195: dt=0.000554, rms=0.669 (0.000%), neg=0, invalid=96777
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.672, neg=0, invalid=96777
- 0196: dt=0.000000, rms=0.672 (0.000%), neg=0, invalid=96777
- 0197: dt=0.000031, rms=0.672 (0.000%), neg=0, invalid=96777
- 0198: dt=0.000031, rms=0.672 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.672, neg=0, invalid=96777
- 0199: dt=0.000000, rms=0.672 (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=0.680, neg=0, invalid=96777
- 0200: dt=11.520000, rms=0.612 (10.080%), neg=0, invalid=96777
- 0201: dt=4.032000, rms=0.604 (1.237%), neg=0, invalid=96777
- 0202: dt=4.032000, rms=0.598 (0.953%), neg=0, invalid=96777
- 0203: dt=4.032000, rms=0.593 (0.805%), neg=0, invalid=96777
- 0204: dt=4.032000, rms=0.590 (0.651%), neg=0, invalid=96777
- 0205: dt=11.520000, rms=0.580 (1.542%), neg=0, invalid=96777
- 0206: dt=4.032000, rms=0.579 (0.281%), neg=0, invalid=96777
- 0207: dt=4.032000, rms=0.577 (0.269%), neg=0, invalid=96777
- 0208: dt=4.032000, rms=0.576 (0.221%), neg=0, invalid=96777
- 0209: dt=16.128000, rms=0.571 (0.792%), neg=0, invalid=96777
- 0210: dt=2.880000, rms=0.571 (0.080%), neg=0, invalid=96777
- 0211: dt=16.128000, rms=0.569 (0.368%), neg=0, invalid=96777
- 0212: dt=3.456000, rms=0.568 (0.097%), neg=0, invalid=96777
- 0213: dt=5.473684, rms=0.568 (0.130%), neg=0, invalid=96777
- 0214: dt=4.032000, rms=0.567 (0.059%), neg=0, invalid=96777
- 0215: dt=6.000000, rms=0.567 (0.108%), neg=0, invalid=96777
- 0216: dt=3.456000, rms=0.566 (0.055%), neg=0, invalid=96777
- 0217: dt=6.000000, rms=0.566 (0.102%), neg=0, invalid=96777
- 0218: dt=3.456000, rms=0.566 (0.036%), neg=0, invalid=96777
- 0219: dt=3.456000, rms=0.565 (0.070%), neg=0, invalid=96777
- 0220: dt=3.456000, rms=0.565 (0.079%), neg=0, invalid=96777
- 0221: dt=3.456000, rms=0.564 (0.115%), neg=0, invalid=96777
- 0222: dt=3.456000, rms=0.563 (0.130%), neg=0, invalid=96777
- 0223: dt=3.456000, rms=0.562 (0.171%), neg=0, invalid=96777
- 0224: dt=3.456000, rms=0.561 (0.167%), neg=0, invalid=96777
- 0225: dt=3.456000, rms=0.560 (0.162%), neg=0, invalid=96777
- 0226: dt=3.456000, rms=0.560 (0.153%), neg=0, invalid=96777
- 0227: dt=3.456000, rms=0.559 (0.148%), neg=0, invalid=96777
- 0228: dt=3.456000, rms=0.558 (0.142%), neg=0, invalid=96777
- 0229: dt=3.456000, rms=0.557 (0.127%), neg=0, invalid=96777
- 0230: dt=3.456000, rms=0.557 (0.109%), neg=0, invalid=96777
- 0231: dt=3.456000, rms=0.556 (0.087%), neg=0, invalid=96777
- 0232: dt=3.456000, rms=0.556 (0.084%), neg=0, invalid=96777
- 0233: dt=3.456000, rms=0.555 (0.078%), neg=0, invalid=96777
- 0234: dt=3.456000, rms=0.555 (0.066%), neg=0, invalid=96777
- 0235: dt=3.456000, rms=0.555 (0.053%), neg=0, invalid=96777
- 0236: dt=3.456000, rms=0.554 (0.042%), neg=0, invalid=96777
- 0237: dt=3.456000, rms=0.554 (0.043%), neg=0, invalid=96777
- 0238: dt=3.456000, rms=0.554 (0.046%), neg=0, invalid=96777
- 0239: dt=3.456000, rms=0.554 (0.043%), neg=0, invalid=96777
- 0240: dt=3.456000, rms=0.554 (0.030%), neg=0, invalid=96777
- 0241: dt=3.456000, rms=0.553 (0.029%), neg=0, invalid=96777
- 0242: dt=3.456000, rms=0.553 (0.040%), neg=0, invalid=96777
- 0243: dt=3.456000, rms=0.553 (0.032%), neg=0, invalid=96777
- 0244: dt=3.456000, rms=0.553 (0.025%), neg=0, invalid=96777
- 0245: dt=3.456000, rms=0.553 (0.032%), neg=0, invalid=96777
- 0246: dt=3.456000, rms=0.552 (0.028%), neg=0, invalid=96777
- 0247: dt=3.456000, rms=0.552 (0.019%), neg=0, invalid=96777
- 0248: dt=3.456000, rms=0.552 (0.023%), neg=0, invalid=96777
- 0249: dt=3.456000, rms=0.552 (0.019%), neg=0, invalid=96777
- 0250: dt=11.520000, rms=0.552 (0.012%), neg=0, invalid=96777
- 0251: dt=11.520000, rms=0.552 (-0.030%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.552, neg=0, invalid=96777
- 0252: dt=4.032000, rms=0.552 (0.061%), neg=0, invalid=96777
- 0253: dt=0.063000, rms=0.552 (0.002%), neg=0, invalid=96777
- 0254: dt=0.063000, rms=0.552 (-0.000%), neg=0, invalid=96777
- setting smoothness coefficient to 1.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.572, neg=0, invalid=96777
- 0255: dt=0.000000, rms=0.572 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.572, neg=0, invalid=96777
- 0256: dt=0.000000, rms=0.572 (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=0.538, neg=0, invalid=96777
- 0257: dt=0.112000, rms=0.532 (0.967%), neg=0, invalid=96777
- 0258: dt=0.028000, rms=0.531 (0.193%), neg=0, invalid=96777
- 0259: dt=0.153646, rms=0.526 (0.992%), neg=0, invalid=96777
- 0260: dt=0.131198, rms=0.523 (0.616%), neg=0, invalid=96777
- 0261: dt=0.121324, rms=0.521 (0.443%), neg=0, invalid=96777
- 0262: dt=0.114316, rms=0.519 (0.340%), neg=0, invalid=96777
- 0263: dt=0.028000, rms=0.518 (0.066%), neg=0, invalid=96777
- 0264: dt=0.080000, rms=0.517 (0.190%), neg=0, invalid=96777
- 0265: dt=0.112000, rms=0.516 (0.234%), neg=0, invalid=96777
- 0266: dt=0.112000, rms=0.515 (0.200%), neg=0, invalid=96777
- 0267: dt=0.028000, rms=0.515 (0.041%), neg=0, invalid=96777
- 0268: dt=0.028000, rms=0.515 (0.043%), neg=0, invalid=96777
- 0269: dt=0.028000, rms=0.514 (0.074%), neg=0, invalid=96777
- 0270: dt=0.028000, rms=0.514 (0.110%), neg=0, invalid=96777
- 0271: dt=0.028000, rms=0.513 (0.128%), neg=0, invalid=96777
- 0272: dt=0.028000, rms=0.512 (0.144%), neg=0, invalid=96777
- 0273: dt=0.028000, rms=0.512 (0.157%), neg=0, invalid=96777
- 0274: dt=0.028000, rms=0.511 (0.156%), neg=0, invalid=96777
- 0275: dt=0.028000, rms=0.510 (0.158%), neg=0, invalid=96777
- 0276: dt=0.007000, rms=0.510 (0.003%), neg=0, invalid=96777
- 0277: dt=0.007000, rms=0.510 (0.007%), neg=0, invalid=96777
- 0278: dt=0.007000, rms=0.510 (0.006%), neg=0, invalid=96777
- 0279: dt=0.112000, rms=0.510 (0.045%), neg=0, invalid=96777
- 0280: dt=0.096000, rms=0.510 (0.037%), neg=0, invalid=96777
- 0281: dt=0.006000, rms=0.510 (-0.001%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.510, neg=0, invalid=96777
- 0282: dt=0.007000, rms=0.509 (0.022%), neg=0, invalid=96777
- 0283: dt=0.001750, rms=0.509 (0.005%), neg=0, invalid=96777
- 0284: dt=0.001750, rms=0.509 (0.005%), neg=0, invalid=96777
- 0285: dt=0.001750, rms=0.509 (0.010%), neg=0, invalid=96777
- 0286: dt=0.001750, rms=0.509 (0.018%), neg=0, invalid=96777
- 0287: dt=0.001750, rms=0.509 (0.019%), neg=0, invalid=96777
- 0288: dt=0.001750, rms=0.509 (0.021%), neg=0, invalid=96777
- 0289: dt=0.001750, rms=0.509 (0.025%), neg=0, invalid=96777
- 0290: dt=0.001750, rms=0.509 (0.027%), neg=0, invalid=96777
- 0291: dt=0.001750, rms=0.509 (0.030%), neg=0, invalid=96777
- 0292: dt=0.001750, rms=0.508 (0.032%), neg=0, invalid=96777
- 0293: dt=0.001750, rms=0.508 (0.034%), neg=0, invalid=96777
- 0294: dt=0.001750, rms=0.508 (0.036%), neg=0, invalid=96777
- 0295: dt=0.001750, rms=0.508 (0.037%), neg=0, invalid=96777
- 0296: dt=0.001750, rms=0.508 (0.037%), neg=0, invalid=96777
- 0297: dt=0.001750, rms=0.508 (0.037%), neg=0, invalid=96777
- 0298: dt=0.001750, rms=0.507 (0.036%), neg=0, invalid=96777
- 0299: dt=0.001750, rms=0.507 (0.038%), neg=0, invalid=96777
- 0300: dt=0.001750, rms=0.507 (0.038%), neg=0, invalid=96777
- 0301: dt=0.001750, rms=0.507 (0.038%), neg=0, invalid=96777
- 0302: dt=0.001750, rms=0.507 (0.039%), neg=0, invalid=96777
- 0303: dt=0.001750, rms=0.506 (0.039%), neg=0, invalid=96777
- 0304: dt=0.001750, rms=0.506 (0.037%), neg=0, invalid=96777
- 0305: dt=0.001750, rms=0.506 (0.037%), neg=0, invalid=96777
- 0306: dt=0.001750, rms=0.506 (0.035%), neg=0, invalid=96777
- 0307: dt=0.001750, rms=0.506 (0.037%), neg=0, invalid=96777
- 0308: dt=0.001750, rms=0.505 (0.034%), neg=0, invalid=96777
- 0309: dt=0.001750, rms=0.505 (0.032%), neg=0, invalid=96777
- 0310: dt=0.001750, rms=0.505 (0.031%), neg=0, invalid=96777
- 0311: dt=0.001750, rms=0.505 (0.035%), neg=0, invalid=96777
- 0312: dt=0.001750, rms=0.505 (0.033%), neg=0, invalid=96777
- 0313: dt=0.001750, rms=0.505 (0.029%), neg=0, invalid=96777
- 0314: dt=0.001750, rms=0.505 (0.030%), neg=0, invalid=96777
- 0315: dt=0.001750, rms=0.504 (0.028%), neg=0, invalid=96777
- 0316: dt=0.001750, rms=0.504 (0.029%), neg=0, invalid=96777
- 0317: dt=0.001750, rms=0.504 (0.028%), neg=0, invalid=96777
- 0318: dt=0.001750, rms=0.504 (0.025%), neg=0, invalid=96777
- 0319: dt=0.001750, rms=0.504 (0.025%), neg=0, invalid=96777
- 0320: dt=0.001750, rms=0.504 (0.026%), neg=0, invalid=96777
- 0321: dt=0.001750, rms=0.504 (0.025%), neg=0, invalid=96777
- 0322: dt=0.001750, rms=0.503 (0.023%), neg=0, invalid=96777
- 0323: dt=0.448000, rms=0.502 (0.370%), neg=0, invalid=96777
- 0324: dt=0.096000, rms=0.502 (0.020%), neg=0, invalid=96777
- 0325: dt=0.006000, rms=0.502 (0.001%), neg=0, invalid=96777
- 0326: dt=0.006000, rms=0.502 (0.001%), neg=0, invalid=96777
- 0327: dt=0.006000, rms=0.501 (0.003%), neg=0, invalid=96777
- 0328: dt=0.006000, rms=0.501 (0.004%), neg=0, invalid=96777
- 0329: dt=0.006000, rms=0.501 (0.005%), neg=0, invalid=96777
- 0330: dt=0.006000, rms=0.501 (0.007%), neg=0, invalid=96777
- 0331: dt=0.006000, rms=0.501 (0.008%), neg=0, invalid=96777
- 0332: dt=0.006000, rms=0.501 (0.008%), neg=0, invalid=96777
- 0333: dt=0.006000, rms=0.501 (0.009%), neg=0, invalid=96777
- 0334: dt=0.006000, rms=0.501 (0.008%), neg=0, invalid=96777
- 0335: dt=0.112000, rms=0.501 (0.024%), neg=0, invalid=96777
- 0336: dt=0.028000, rms=0.501 (0.007%), 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=0.499, neg=0, invalid=96777
- 0337: dt=8.092000, rms=0.499 (-0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.499, neg=0, invalid=96777
- 0338: dt=73.984000, rms=0.499 (0.047%), neg=0, invalid=96777
- 0339: dt=92.480000, rms=0.499 (0.030%), neg=0, invalid=96777
- 0340: dt=92.480000, rms=0.499 (0.023%), neg=0, invalid=96777
- 0341: dt=92.480000, rms=0.498 (0.056%), neg=0, invalid=96777
- 0342: dt=92.480000, rms=0.498 (0.029%), neg=0, invalid=96777
- 0343: dt=92.480000, rms=0.498 (0.037%), neg=0, invalid=96777
- 0344: dt=92.480000, rms=0.498 (0.021%), neg=0, invalid=96777
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.498, neg=0, invalid=96777
- 0345: dt=25.920000, rms=0.497 (0.137%), neg=0, invalid=96777
- 0346: dt=36.288000, rms=0.497 (0.057%), neg=0, invalid=96777
- 0347: dt=36.288000, rms=0.497 (0.036%), neg=0, invalid=96777
- 0348: dt=36.288000, rms=0.497 (-0.008%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.497, neg=0, invalid=96777
- 0349: dt=36.288000, rms=0.495 (0.300%), neg=0, invalid=96777
- 0350: dt=124.416000, rms=0.494 (0.318%), neg=0, invalid=96777
- 0351: dt=25.920000, rms=0.493 (0.177%), neg=0, invalid=96777
- 0352: dt=25.920000, rms=0.493 (0.029%), neg=0, invalid=96777
- 0353: dt=25.920000, rms=0.493 (0.057%), neg=0, invalid=96777
- 0354: dt=25.920000, rms=0.492 (0.116%), neg=0, invalid=96777
- 0355: dt=25.920000, rms=0.491 (0.111%), neg=0, invalid=96777
- 0356: dt=25.920000, rms=0.491 (0.107%), neg=0, invalid=96777
- 0357: dt=145.152000, rms=0.491 (0.067%), neg=0, invalid=96777
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.491, neg=0, invalid=96777
- iter 0, gcam->neg = 4
- after 9 iterations, nbhd size=1, neg = 0
- 0358: dt=19.200000, rms=0.488 (0.551%), neg=0, invalid=96777
- 0359: dt=8.744186, rms=0.487 (0.148%), neg=0, invalid=96777
- 0360: dt=8.744186, rms=0.486 (0.229%), neg=0, invalid=96777
- iter 0, gcam->neg = 2
- after 5 iterations, nbhd size=1, neg = 0
- 0361: dt=8.744186, rms=0.485 (0.259%), neg=0, invalid=96777
- 0362: dt=8.744186, rms=0.484 (0.277%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0363: dt=8.744186, rms=0.483 (0.206%), neg=0, invalid=96777
- 0364: dt=8.744186, rms=0.482 (0.225%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 1 iterations, nbhd size=0, neg = 0
- 0365: dt=8.744186, rms=0.481 (0.195%), neg=0, invalid=96777
- iter 0, gcam->neg = 6
- after 2 iterations, nbhd size=0, neg = 0
- 0366: dt=8.744186, rms=0.480 (0.185%), neg=0, invalid=96777
- iter 0, gcam->neg = 4
- after 2 iterations, nbhd size=0, neg = 0
- 0367: dt=8.744186, rms=0.479 (0.218%), neg=0, invalid=96777
- 0368: dt=8.744186, rms=0.478 (0.216%), neg=0, invalid=96777
- 0369: dt=8.744186, rms=0.476 (0.253%), neg=0, invalid=96777
- 0370: dt=8.744186, rms=0.475 (0.230%), neg=0, invalid=96777
- iter 0, gcam->neg = 2
- after 6 iterations, nbhd size=1, neg = 0
- 0371: dt=8.744186, rms=0.474 (0.211%), neg=0, invalid=96777
- 0372: dt=8.744186, rms=0.474 (0.174%), neg=0, invalid=96777
- 0373: dt=8.744186, rms=0.473 (0.165%), neg=0, invalid=96777
- 0374: dt=8.744186, rms=0.472 (0.152%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0375: dt=8.744186, rms=0.471 (0.146%), neg=0, invalid=96777
- 0376: dt=8.744186, rms=0.471 (0.137%), neg=0, invalid=96777
- 0377: dt=8.744186, rms=0.470 (0.109%), neg=0, invalid=96777
- 0378: dt=8.744186, rms=0.470 (0.120%), neg=0, invalid=96777
- 0379: dt=8.744186, rms=0.469 (0.110%), neg=0, invalid=96777
- iter 0, gcam->neg = 3
- after 8 iterations, nbhd size=1, neg = 0
- 0380: dt=25.600000, rms=0.469 (0.052%), neg=0, invalid=96777
- iter 0, gcam->neg = 2
- after 0 iterations, nbhd size=0, neg = 0
- 0381: dt=25.600000, rms=0.469 (-0.138%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.469, neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 5 iterations, nbhd size=1, neg = 0
- 0382: dt=25.600000, rms=0.467 (0.501%), neg=0, invalid=96777
- 0383: dt=7.265700, rms=0.465 (0.268%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 5 iterations, nbhd size=1, neg = 0
- 0384: dt=19.200000, rms=0.464 (0.238%), neg=0, invalid=96777
- iter 0, gcam->neg = 6
- after 1 iterations, nbhd size=0, neg = 0
- 0385: dt=19.200000, rms=0.464 (-0.152%), neg=0, invalid=96777
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.473, neg=0, invalid=96777
- iter 0, gcam->neg = 23
- after 8 iterations, nbhd size=1, neg = 0
- 0386: dt=4.521739, rms=0.471 (0.296%), neg=0, invalid=96777
- iter 0, gcam->neg = 11
- after 8 iterations, nbhd size=1, neg = 0
- 0387: dt=1.500000, rms=0.471 (0.036%), neg=0, invalid=96777
- 0388: dt=1.500000, rms=0.471 (0.057%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0389: dt=1.500000, rms=0.470 (0.080%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 6 iterations, nbhd size=1, neg = 0
- 0390: dt=1.500000, rms=0.470 (0.019%), neg=0, invalid=96777
- iter 0, gcam->neg = 2
- after 0 iterations, nbhd size=0, neg = 0
- 0391: dt=1.500000, rms=0.470 (-0.009%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.470, neg=0, invalid=96777
- iter 0, gcam->neg = 57
- after 34 iterations, nbhd size=3, neg = 0
- 0392: dt=8.356506, rms=0.468 (0.417%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 5 iterations, nbhd size=1, neg = 0
- 0393: dt=2.133333, rms=0.468 (0.050%), neg=0, invalid=96777
- 0394: dt=2.133333, rms=0.467 (0.146%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 5 iterations, nbhd size=1, neg = 0
- 0395: dt=2.133333, rms=0.466 (0.195%), neg=0, invalid=96777
- iter 0, gcam->neg = 18
- after 7 iterations, nbhd size=1, neg = 0
- 0396: dt=2.133333, rms=0.466 (0.183%), neg=0, invalid=96777
- iter 0, gcam->neg = 16
- after 18 iterations, nbhd size=2, neg = 0
- 0397: dt=2.133333, rms=0.465 (0.101%), neg=0, invalid=96777
- iter 0, gcam->neg = 22
- after 9 iterations, nbhd size=1, neg = 0
- 0398: dt=2.133333, rms=0.465 (0.026%), neg=0, invalid=96777
- iter 0, gcam->neg = 10
- after 7 iterations, nbhd size=1, neg = 0
- 0399: dt=5.600000, rms=0.464 (0.121%), neg=0, invalid=96777
- iter 0, gcam->neg = 85
- after 20 iterations, nbhd size=2, neg = 0
- 0400: dt=13.824000, rms=0.463 (0.328%), neg=0, invalid=96777
- 0401: dt=0.036000, rms=0.463 (0.000%), neg=0, invalid=96777
- 0402: dt=0.036000, rms=0.463 (0.001%), neg=0, invalid=96777
- 0403: dt=0.036000, rms=0.463 (0.002%), neg=0, invalid=96777
- 0404: dt=0.036000, rms=0.463 (-0.002%), neg=0, invalid=96777
- setting smoothness coefficient to 1.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.468, neg=0, invalid=96777
- 0405: dt=0.000000, rms=0.468 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.468, neg=0, invalid=96777
- 0406: dt=0.000000, rms=0.468 (0.000%), neg=0, invalid=96777
- resetting metric properties...
- setting smoothness coefficient to 2.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.460, neg=0, invalid=96777
- iter 0, gcam->neg = 929
- after 24 iterations, nbhd size=2, neg = 0
- 0407: dt=1.497678, rms=0.424 (7.722%), neg=0, invalid=96777
- 0408: dt=0.000047, rms=0.424 (0.007%), neg=0, invalid=96777
- 0409: dt=0.000047, rms=0.424 (0.000%), neg=0, invalid=96777
- 0410: dt=0.000047, rms=0.424 (-0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.424, neg=0, invalid=96777
- 0411: dt=0.000188, rms=0.424 (0.000%), neg=0, invalid=96777
- 0412: dt=0.000000, rms=0.424 (-0.000%), neg=0, invalid=96777
- label assignment complete, 0 changed (0.00%)
- label assignment complete, 0 changed (0.00%)
- ***************** morphing with label term set to 0 *******************************
- **************** pass 1 of 1 ************************
- setting smoothness coefficient to 0.008
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.414, neg=0, invalid=96777
- 0413: dt=0.000000, rms=0.416 (-0.304%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.416, neg=0, invalid=96777
- 0414: dt=32.368000, rms=0.416 (0.023%), neg=0, invalid=96777
- 0415: dt=55.488000, rms=0.415 (0.007%), neg=0, invalid=96777
- 0416: dt=55.488000, rms=0.415 (0.001%), neg=0, invalid=96777
- 0417: dt=55.488000, rms=0.415 (-0.001%), neg=0, invalid=96777
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.416, neg=0, invalid=96777
- 0418: dt=0.000000, rms=0.416 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.416, neg=0, invalid=96777
- 0419: dt=62.208000, rms=0.415 (0.050%), neg=0, invalid=96777
- 0420: dt=124.416000, rms=0.415 (0.046%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 5 iterations, nbhd size=1, neg = 0
- 0421: dt=124.416000, rms=0.415 (-0.046%), neg=0, invalid=96777
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.416, neg=0, invalid=96777
- iter 0, gcam->neg = 9
- after 23 iterations, nbhd size=3, neg = 0
- 0422: dt=9.600000, rms=0.415 (0.052%), neg=0, invalid=96777
- 0423: dt=0.010937, rms=0.415 (0.000%), neg=0, invalid=96777
- 0424: dt=0.010937, rms=0.415 (0.000%), neg=0, invalid=96777
- 0425: dt=0.010937, rms=0.415 (0.000%), neg=0, invalid=96777
- 0426: dt=0.010937, rms=0.415 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.415, neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0427: dt=11.200000, rms=0.415 (0.131%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 14 iterations, nbhd size=2, neg = 0
- 0428: dt=2.800000, rms=0.415 (0.019%), neg=0, invalid=96777
- 0429: dt=2.800000, rms=0.415 (0.045%), neg=0, invalid=96777
- 0430: dt=2.800000, rms=0.414 (0.081%), neg=0, invalid=96777
- 0431: dt=2.800000, rms=0.414 (0.105%), neg=0, invalid=96777
- iter 0, gcam->neg = 3
- after 8 iterations, nbhd size=1, neg = 0
- 0432: dt=2.800000, rms=0.413 (0.112%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0433: dt=2.800000, rms=0.413 (0.091%), neg=0, invalid=96777
- iter 0, gcam->neg = 8
- after 50 iterations, nbhd size=3, neg = 0
- 0434: dt=2.800000, rms=0.413 (0.014%), neg=0, invalid=96777
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.415, neg=0, invalid=96777
- 0435: dt=0.002813, rms=0.415 (0.000%), neg=0, invalid=96777
- iter 0, gcam->neg = 65
- after 31 iterations, nbhd size=3, neg = 0
- 0436: dt=5.361702, rms=0.413 (0.302%), neg=0, invalid=96777
- 0437: dt=0.002250, rms=0.413 (0.000%), neg=0, invalid=96777
- 0438: dt=0.002250, rms=0.413 (0.000%), neg=0, invalid=96777
- 0439: dt=0.002250, rms=0.413 (0.000%), neg=0, invalid=96777
- 0440: dt=0.002250, rms=0.413 (0.000%), neg=0, invalid=96777
- 0441: dt=0.002250, rms=0.413 (0.000%), neg=0, invalid=96777
- 0442: dt=0.002250, rms=0.413 (0.000%), neg=0, invalid=96777
- 0443: dt=0.002250, rms=0.413 (0.000%), neg=0, invalid=96777
- 0444: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777
- 0445: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777
- 0446: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777
- 0447: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777
- 0448: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777
- 0449: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777
- 0450: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777
- 0451: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777
- 0452: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777
- 0453: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777
- 0454: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777
- 0455: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777
- 0456: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777
- 0457: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777
- 0458: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777
- 0459: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777
- 0460: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777
- 0461: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777
- 0462: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777
- 0463: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777
- 0464: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777
- 0465: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777
- 0466: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777
- 0467: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777
- 0468: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777
- 0469: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777
- 0470: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777
- 0471: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777
- 0472: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777
- 0473: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777
- 0474: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777
- 0475: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777
- 0476: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777
- 0477: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777
- 0478: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777
- 0479: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777
- 0480: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777
- 0481: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777
- 0482: dt=0.002250, rms=0.413 (0.001%), neg=0, invalid=96777
- iter 0, gcam->neg = 84
- after 200 iterations, nbhd size=2, neg = 1
- starting rms=0.004, neg=1, removing folds in lattice....
- iter 1, dt=0.000094: new neg 1, old_neg 1, delta 0, rms=0.003 (29.848%)
- iter 2, dt=0.000143: new neg 0, old_neg 1, delta 1, rms=0.002 (14.394%)
- 0483: dt=6.583333, rms=0.412 (0.174%), neg=0, invalid=96777
- iter 0, gcam->neg = 10
- after 15 iterations, nbhd size=2, neg = 0
- 0484: dt=1.728000, rms=0.412 (0.016%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.412, neg=0, invalid=96777
- 0485: dt=0.002250, rms=0.412 (0.000%), neg=0, invalid=96777
- iter 0, gcam->neg = 26
- after 27 iterations, nbhd size=3, neg = 0
- 0486: dt=1.728000, rms=0.412 (0.099%), neg=0, invalid=96777
- iter 0, gcam->neg = 16
- after 11 iterations, nbhd size=1, neg = 0
- 0487: dt=2.304000, rms=0.411 (0.141%), neg=0, invalid=96777
- iter 0, gcam->neg = 34
- after 43 iterations, nbhd size=2, neg = 0
- 0488: dt=4.032000, rms=0.411 (0.121%), neg=0, invalid=96777
- iter 0, gcam->neg = 206
- after 27 iterations, nbhd size=2, neg = 0
- 0489: dt=4.032000, rms=0.411 (-0.036%), neg=0, invalid=96777
- setting smoothness coefficient to 1.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.415, neg=0, invalid=96777
- 0490: dt=0.000050, rms=0.415 (0.000%), neg=0, invalid=96777
- 0491: dt=0.000000, rms=0.415 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.415, neg=0, invalid=96777
- 0492: dt=0.000250, rms=0.415 (0.000%), neg=0, invalid=96777
- 0493: dt=0.000000, rms=0.415 (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=0.408, neg=0, invalid=96777
- iter 0, gcam->neg = 651
- after 34 iterations, nbhd size=4, neg = 0
- 0494: dt=0.737864, rms=0.395 (3.217%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0495: dt=0.000063, rms=0.395 (0.003%), neg=0, invalid=96777
- 0496: dt=0.000063, rms=0.395 (0.000%), neg=0, invalid=96777
- 0497: dt=0.000063, rms=0.395 (0.000%), neg=0, invalid=96777
- 0498: dt=0.000063, rms=0.395 (-0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.395, neg=0, invalid=96777
- 0499: dt=0.001750, rms=0.395 (0.001%), neg=0, invalid=96777
- iter 0, gcam->neg = 5
- after 7 iterations, nbhd size=1, neg = 0
- 0500: dt=0.028000, rms=0.395 (0.028%), neg=0, invalid=96777
- 0501: dt=0.000003, rms=0.395 (0.000%), neg=0, invalid=96777
- 0502: dt=0.000003, rms=0.395 (0.000%), neg=0, invalid=96777
- 0503: dt=0.000003, rms=0.395 (0.000%), neg=0, invalid=96777
- 0504: dt=0.000003, rms=0.395 (0.000%), neg=0, invalid=96777
- 0505: dt=0.000003, rms=0.395 (0.000%), neg=0, invalid=96777
- 0506: dt=0.000003, rms=0.395 (0.000%), neg=0, invalid=96777
- writing output transformation to transforms/talairach.m3z...
- GCAMwrite
- registration took 3 hours, 47 minutes and 8 seconds.
- #--------------------------------------
- #@# CA Reg Inv Thu Aug 8 16:04:20 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri
- mri_ca_register -invert-and-save transforms/talairach.m3z
- Loading, Inverting, Saving, Exiting ...
- Reading transforms/talairach.m3z
- Inverting GCAM
- Saving inverse
- #--------------------------------------
- #@# Remove Neck Thu Aug 8 16:06:02 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...
- 11654984 nonbrain voxels erased
- writing output to nu_noneck.mgz...
- nonbrain removal took 1 minutes and 43 seconds.
- #--------------------------------------
- #@# SkullLTA Thu Aug 8 16:07:46 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=15.0
- skull bounding box = (52, 23, 26) --> (200, 194, 218)
- using (101, 80, 122) as brain centroid...
- mean wm in atlas = 126, using box (83,59,98) --> (119, 101,145) to find MRI wm
- before smoothing, mri peak at 109
- after smoothing, mri peak at 109, scaling input intensities by 1.156
- scaling channel 0 by 1.15596
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.2 (thresh=-4.2)
- 1.189 -0.029 -0.069 -14.029;
- 0.036 1.189 0.090 -11.347;
- 0.089 -0.119 1.149 -30.408;
- 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)
- 1.189 -0.029 -0.069 -14.029;
- 0.036 1.189 0.090 -11.347;
- 0.089 -0.119 1.149 -30.408;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.2500
- ****************************************
- Nine parameter search. iteration 2 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.212 -0.034 -0.035 -20.437;
- 0.039 1.206 0.132 -16.648;
- 0.043 -0.147 1.084 -10.317;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 3 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.146 0.006 -0.028 -16.785;
- 0.003 1.201 0.168 -15.701;
- 0.043 -0.189 1.099 -7.844;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 4 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.146 0.006 -0.028 -16.785;
- 0.003 1.201 0.168 -15.701;
- 0.043 -0.189 1.099 -7.844;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.0625
- ****************************************
- Nine parameter search. iteration 5 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.144 -0.012 -0.039 -13.427;
- 0.021 1.209 0.150 -16.126;
- 0.052 -0.170 1.101 -10.763;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 6 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.142 0.001 -0.056 -11.985;
- 0.011 1.210 0.151 -14.689;
- 0.071 -0.170 1.101 -13.494;
- 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
- 1.14160 0.00070 -0.05573 -11.98465;
- 0.01126 1.20996 0.15055 -14.68894;
- 0.07067 -0.16981 1.10053 -13.49355;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 3481
- Quasinewton: input matrix
- 1.14160 0.00070 -0.05573 -11.98465;
- 0.01126 1.20996 0.15055 -14.68894;
- 0.07067 -0.16981 1.10053 -13.49355;
- 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:
- 1.142 0.001 -0.056 -11.985;
- 0.011 1.210 0.151 -14.689;
- 0.071 -0.170 1.101 -13.494;
- 0.000 0.000 0.000 1.000;
- pass 1, spacing 8: log(p) = -4.0 (old=-4.2)
- transform before final EM align:
- 1.142 0.001 -0.056 -11.985;
- 0.011 1.210 0.151 -14.689;
- 0.071 -0.170 1.101 -13.494;
- 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
- 1.14160 0.00070 -0.05573 -11.98465;
- 0.01126 1.20996 0.15055 -14.68894;
- 0.07067 -0.16981 1.10053 -13.49355;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 382743
- Quasinewton: input matrix
- 1.14160 0.00070 -0.05573 -11.98465;
- 0.01126 1.20996 0.15055 -14.68894;
- 0.07067 -0.16981 1.10053 -13.49355;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = 4.4 tol 0.000000
- final transform:
- 1.142 0.001 -0.056 -11.985;
- 0.011 1.210 0.151 -14.689;
- 0.071 -0.170 1.101 -13.494;
- 0.000 0.000 0.000 1.000;
- writing output transformation to transforms/talairach_with_skull_2.lta...
- registration took 39 minutes and 41 seconds.
- #--------------------------------------
- #@# SubCort Seg Thu Aug 8 16:47:27 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/sub003/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 = 0.09295 ( 4)
- Left_Lateral_Ventricle (4): linear fit = 0.12 x + 0.0 (160 voxels, overlap=0.007)
- Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (160 voxels, peak = 3), gca=10.8
- gca peak = 0.14982 (20)
- mri peak = 0.09989 ( 6)
- Right_Lateral_Ventricle (43): linear fit = 0.14 x + 0.0 (99 voxels, overlap=0.057)
- Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (99 voxels, peak = 3), gca=8.0
- gca peak = 0.28003 (97)
- mri peak = 0.11307 (88)
- Right_Pallidum (52): linear fit = 0.88 x + 0.0 (282 voxels, overlap=0.042)
- Right_Pallidum (52): linear fit = 0.88 x + 0.0 (282 voxels, peak = 85), gca=84.9
- gca peak = 0.18160 (96)
- mri peak = 0.14844 (88)
- Left_Pallidum (13): linear fit = 0.88 x + 0.0 (251 voxels, overlap=0.041)
- Left_Pallidum (13): linear fit = 0.88 x + 0.0 (251 voxels, peak = 85), gca=85.0
- gca peak = 0.27536 (62)
- mri peak = 0.14191 (56)
- Right_Hippocampus (53): linear fit = 0.86 x + 0.0 (451 voxels, overlap=0.457)
- Right_Hippocampus (53): linear fit = 0.86 x + 0.0 (451 voxels, peak = 53), gca=53.0
- gca peak = 0.32745 (63)
- mri peak = 0.10251 (54)
- Left_Hippocampus (17): linear fit = 0.85 x + 0.0 (514 voxels, overlap=0.347)
- Left_Hippocampus (17): linear fit = 0.85 x + 0.0 (514 voxels, peak = 53), gca=53.2
- gca peak = 0.08597 (105)
- mri peak = 0.07945 (107)
- Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (24517 voxels, overlap=0.608)
- Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (24517 voxels, peak = 110), gca=109.7
- gca peak = 0.09209 (106)
- mri peak = 0.09088 (108)
- Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (23723 voxels, overlap=0.564)
- Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (23723 voxels, peak = 111), gca=110.8
- gca peak = 0.07826 (63)
- mri peak = 0.06574 (52)
- Left_Cerebral_Cortex (3): linear fit = 0.80 x + 0.0 (11644 voxels, overlap=0.170)
- Left_Cerebral_Cortex (3): linear fit = 0.80 x + 0.0 (11644 voxels, peak = 50), gca=50.1
- gca peak = 0.08598 (64)
- mri peak = 0.06639 (53)
- Right_Cerebral_Cortex (42): linear fit = 0.80 x + 0.0 (9724 voxels, overlap=0.067)
- Right_Cerebral_Cortex (42): linear fit = 0.80 x + 0.0 (9724 voxels, peak = 51), gca=50.9
- gca peak = 0.24164 (71)
- mri peak = 0.09369 (67)
- Right_Caudate (50): linear fit = 0.94 x + 0.0 (274 voxels, overlap=0.583)
- Right_Caudate (50): linear fit = 0.94 x + 0.0 (274 voxels, peak = 67), gca=67.1
- gca peak = 0.18227 (75)
- mri peak = 0.09580 (66)
- Left_Caudate (11): linear fit = 0.86 x + 0.0 (595 voxels, overlap=0.031)
- Left_Caudate (11): linear fit = 0.86 x + 0.0 (595 voxels, peak = 64), gca=64.1
- gca peak = 0.10629 (62)
- mri peak = 0.05526 (61)
- Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (9316 voxels, overlap=0.999)
- Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (9316 voxels, peak = 61), gca=61.1
- gca peak = 0.11668 (59)
- mri peak = 0.05718 (57)
- Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (8907 voxels, overlap=0.959)
- Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (8907 voxels, peak = 57), gca=56.9
- gca peak = 0.17849 (88)
- mri peak = 0.07904 (91)
- Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (3949 voxels, overlap=0.980)
- Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (3949 voxels, peak = 91), gca=91.1
- gca peak = 0.16819 (86)
- mri peak = 0.08305 (89)
- Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (3771 voxels, overlap=0.984)
- Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (3771 voxels, peak = 89), gca=89.0
- gca peak = 0.41688 (64)
- mri peak = 0.13552 (54)
- Left_Amygdala (18): linear fit = 0.82 x + 0.0 (250 voxels, overlap=0.831)
- Left_Amygdala (18): linear fit = 0.82 x + 0.0 (250 voxels, peak = 53), gca=52.8
- gca peak = 0.42394 (62)
- mri peak = 0.11791 (56)
- Right_Amygdala (54): linear fit = 0.88 x + 0.0 (219 voxels, overlap=0.622)
- Right_Amygdala (54): linear fit = 0.88 x + 0.0 (219 voxels, peak = 55), gca=54.9
- gca peak = 0.10041 (96)
- mri peak = 0.06043 (85)
- Left_Thalamus_Proper (10): linear fit = 0.94 x + 0.0 (2887 voxels, overlap=0.769)
- Left_Thalamus_Proper (10): linear fit = 0.94 x + 0.0 (2887 voxels, peak = 91), gca=90.7
- gca peak = 0.13978 (88)
- mri peak = 0.07904 (82)
- Right_Thalamus_Proper (49): linear fit = 0.93 x + 0.0 (3127 voxels, overlap=0.754)
- Right_Thalamus_Proper (49): linear fit = 0.93 x + 0.0 (3127 voxels, peak = 81), gca=81.4
- gca peak = 0.08514 (81)
- mri peak = 0.06416 (70)
- Left_Putamen (12): linear fit = 0.88 x + 0.0 (1674 voxels, overlap=0.610)
- Left_Putamen (12): linear fit = 0.88 x + 0.0 (1674 voxels, peak = 71), gca=70.9
- gca peak = 0.09624 (82)
- mri peak = 0.08647 (72)
- Right_Putamen (51): linear fit = 0.90 x + 0.0 (1432 voxels, overlap=0.475)
- Right_Putamen (51): linear fit = 0.90 x + 0.0 (1432 voxels, peak = 74), gca=74.2
- gca peak = 0.07543 (88)
- mri peak = 0.07404 (89)
- Brain_Stem (16): linear fit = 1.01 x + 0.0 (7608 voxels, overlap=0.765)
- Brain_Stem (16): linear fit = 1.01 x + 0.0 (7608 voxels, peak = 89), gca=89.3
- gca peak = 0.12757 (95)
- mri peak = 0.08062 (93)
- Right_VentralDC (60): linear fit = 0.99 x + 0.0 (715 voxels, overlap=0.837)
- Right_VentralDC (60): linear fit = 0.99 x + 0.0 (715 voxels, peak = 94), gca=93.6
- gca peak = 0.17004 (92)
- mri peak = 0.07068 (96)
- Left_VentralDC (28): linear fit = 0.99 x + 0.0 (731 voxels, overlap=0.933)
- Left_VentralDC (28): linear fit = 0.99 x + 0.0 (731 voxels, peak = 91), gca=90.6
- gca peak = 0.21361 (36)
- mri peak = 0.25018 ( 3)
- gca peak = 0.26069 (23)
- mri peak = 0.11236 ( 4)
- Fourth_Ventricle (15): linear fit = 0.26 x + 0.0 (83 voxels, overlap=0.029)
- Fourth_Ventricle (15): linear fit = 0.26 x + 0.0 (83 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 0.83 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 = 0.09295 ( 4)
- Left_Lateral_Ventricle (4): linear fit = 0.52 x + 0.0 (160 voxels, overlap=0.761)
- Left_Lateral_Ventricle (4): linear fit = 0.52 x + 0.0 (160 voxels, peak = 6), gca=5.8
- gca peak = 0.29325 ( 9)
- mri peak = 0.09989 ( 6)
- Right_Lateral_Ventricle (43): linear fit = 0.38 x + 0.0 (99 voxels, overlap=0.260)
- Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (99 voxels, peak = 3), gca=3.6
- gca peak = 0.26184 (85)
- mri peak = 0.11307 (88)
- Right_Pallidum (52): linear fit = 1.00 x + 0.0 (282 voxels, overlap=1.005)
- Right_Pallidum (52): linear fit = 1.00 x + 0.0 (282 voxels, peak = 85), gca=85.0
- gca peak = 0.18578 (85)
- mri peak = 0.14844 (88)
- Left_Pallidum (13): linear fit = 1.01 x + 0.0 (251 voxels, overlap=1.003)
- Left_Pallidum (13): linear fit = 1.01 x + 0.0 (251 voxels, peak = 86), gca=86.3
- gca peak = 0.33434 (53)
- mri peak = 0.14191 (56)
- Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (451 voxels, overlap=1.008)
- Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (451 voxels, peak = 53), gca=53.0
- gca peak = 0.29127 (53)
- mri peak = 0.10251 (54)
- Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (514 voxels, overlap=1.001)
- Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (514 voxels, peak = 53), gca=53.0
- gca peak = 0.08168 (110)
- mri peak = 0.07945 (107)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (24517 voxels, overlap=0.771)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (24517 voxels, peak = 110), gca=110.0
- gca peak = 0.08583 (111)
- mri peak = 0.09088 (108)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (23723 voxels, overlap=0.719)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (23723 voxels, peak = 111), gca=111.0
- gca peak = 0.09719 (50)
- mri peak = 0.06574 (52)
- Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (11644 voxels, overlap=0.988)
- Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (11644 voxels, peak = 50), gca=50.0
- gca peak = 0.11022 (51)
- mri peak = 0.06639 (53)
- Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (9724 voxels, overlap=0.936)
- Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (9724 voxels, peak = 50), gca=50.2
- gca peak = 0.23446 (69)
- mri peak = 0.09369 (67)
- Right_Caudate (50): linear fit = 1.00 x + 0.0 (274 voxels, overlap=1.010)
- Right_Caudate (50): linear fit = 1.00 x + 0.0 (274 voxels, peak = 69), gca=69.0
- gca peak = 0.18422 (64)
- mri peak = 0.09580 (66)
- Left_Caudate (11): linear fit = 0.99 x + 0.0 (595 voxels, overlap=0.975)
- Left_Caudate (11): linear fit = 0.99 x + 0.0 (595 voxels, peak = 63), gca=63.0
- gca peak = 0.11091 (61)
- mri peak = 0.05526 (61)
- Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (9316 voxels, overlap=0.997)
- Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (9316 voxels, peak = 63), gca=62.5
- gca peak = 0.12326 (57)
- mri peak = 0.05718 (57)
- Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (8907 voxels, overlap=1.000)
- Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (8907 voxels, peak = 56), gca=56.1
- gca peak = 0.16819 (91)
- mri peak = 0.07904 (91)
- Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (3949 voxels, overlap=1.000)
- Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (3949 voxels, peak = 91), gca=90.5
- gca peak = 0.16430 (89)
- mri peak = 0.08305 (89)
- Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (3771 voxels, overlap=1.000)
- Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (3771 voxels, peak = 89), gca=88.6
- gca peak = 0.34863 (52)
- mri peak = 0.13552 (54)
- Left_Amygdala (18): linear fit = 1.00 x + 0.0 (250 voxels, overlap=1.031)
- Left_Amygdala (18): linear fit = 1.00 x + 0.0 (250 voxels, peak = 52), gca=52.0
- gca peak = 0.54141 (55)
- mri peak = 0.11791 (56)
- Right_Amygdala (54): linear fit = 1.00 x + 0.0 (219 voxels, overlap=1.023)
- Right_Amygdala (54): linear fit = 1.00 x + 0.0 (219 voxels, peak = 55), gca=55.0
- gca peak = 0.10948 (89)
- mri peak = 0.06043 (85)
- Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (2887 voxels, overlap=0.894)
- Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (2887 voxels, peak = 89), gca=88.6
- gca peak = 0.11263 (81)
- mri peak = 0.07904 (82)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3127 voxels, overlap=0.987)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3127 voxels, peak = 81), gca=80.6
- gca peak = 0.09324 (72)
- mri peak = 0.06416 (70)
- Left_Putamen (12): linear fit = 1.03 x + 0.0 (1674 voxels, overlap=1.000)
- Left_Putamen (12): linear fit = 1.03 x + 0.0 (1674 voxels, peak = 75), gca=74.5
- gca peak = 0.10809 (69)
- mri peak = 0.08647 (72)
- Right_Putamen (51): linear fit = 1.01 x + 0.0 (1432 voxels, overlap=0.985)
- Right_Putamen (51): linear fit = 1.01 x + 0.0 (1432 voxels, peak = 70), gca=70.0
- gca peak = 0.07498 (87)
- mri peak = 0.07404 (89)
- Brain_Stem (16): linear fit = 1.00 x + 0.0 (7608 voxels, overlap=0.797)
- Brain_Stem (16): linear fit = 1.00 x + 0.0 (7608 voxels, peak = 87), gca=86.6
- gca peak = 0.13759 (93)
- mri peak = 0.08062 (93)
- Right_VentralDC (60): linear fit = 1.01 x + 0.0 (715 voxels, overlap=0.816)
- Right_VentralDC (60): linear fit = 1.01 x + 0.0 (715 voxels, peak = 94), gca=94.4
- gca peak = 0.16758 (91)
- mri peak = 0.07068 (96)
- Left_VentralDC (28): linear fit = 1.00 x + 0.0 (731 voxels, overlap=0.912)
- Left_VentralDC (28): linear fit = 1.00 x + 0.0 (731 voxels, peak = 91), gca=90.5
- gca peak = 0.35640 (14)
- mri peak = 0.25018 ( 3)
- gca peak = 0.33827 ( 9)
- mri peak = 0.11236 ( 4)
- Fourth_Ventricle (15): linear fit = 0.70 x + 0.0 (83 voxels, overlap=0.845)
- Fourth_Ventricle (15): linear fit = 0.70 x + 0.0 (83 voxels, peak = 6), gca=6.3
- gca peak Unknown = 0.94427 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.27462 (30)
- gca peak Third_Ventricle = 0.35640 (14)
- gca peak CSF = 0.30128 (18)
- gca peak Left_Accumbens_area = 0.51723 (60)
- gca peak Left_undetermined = 1.00000 (35)
- gca peak Left_vessel = 0.43860 (61)
- gca peak Left_choroid_plexus = 0.09084 (48)
- gca peak Right_Inf_Lat_Vent = 0.31195 (27)
- gca peak Right_Accumbens_area = 0.31042 (68)
- gca peak Right_vessel = 0.53014 (60)
- gca peak Right_choroid_plexus = 0.10423 (48)
- gca peak Fifth_Ventricle = 0.45329 (19)
- gca peak WM_hypointensities = 0.16060 (85)
- gca peak non_WM_hypointensities = 0.11646 (55)
- gca peak Optic_Chiasm = 0.34849 (76)
- not using caudate to estimate GM means
- estimating mean gm scale to be 1.00 x + 0.0
- estimating mean wm scale to be 1.00 x + 0.0
- estimating mean csf scale to be 0.54 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
- 10266 gm and wm labels changed (%10 to gray, %90 to white out of all changed labels)
- 241 hippocampal voxels changed.
- 0 amygdala voxels changed.
- pass 1: 83197 changed. image ll: -2.166, PF=1.000
- pass 2: 16100 changed. image ll: -2.164, PF=1.000
- pass 3: 6390 changed.
- pass 4: 3087 changed.
- writing labeled volume to aseg.auto_noCCseg.mgz...
- auto-labeling took 21 minutes and 16 seconds.
- mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/cc_up.lta sub003
- 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/sub003/mri/transforms/cc_up.lta
- reading aseg from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/aseg.auto_noCCseg.mgz
- reading norm from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/norm.mgz
- 28093 voxels in left wm, 39898 in right wm, xrange [121, 131]
- searching rotation angles z=[-6 8], y=[-11 3]
-
searching scale 1 Z rot -6.0
searching scale 1 Z rot -5.8
searching scale 1 Z rot -5.5
searching scale 1 Z rot -5.3
searching scale 1 Z rot -5.0
searching scale 1 Z rot -4.8
searching scale 1 Z rot -4.5
searching scale 1 Z rot -4.3
searching scale 1 Z rot -4.0
searching scale 1 Z rot -3.8
searching scale 1 Z rot -3.5
searching scale 1 Z rot -3.3
searching scale 1 Z rot -3.0
searching scale 1 Z rot -2.8
searching scale 1 Z rot -2.5
searching scale 1 Z rot -2.3
searching scale 1 Z rot -2.0
searching scale 1 Z rot -1.8
searching scale 1 Z rot -1.5
searching scale 1 Z rot -1.3
searching scale 1 Z rot -1.0
searching scale 1 Z rot -0.8
searching scale 1 Z rot -0.5
searching scale 1 Z rot -0.3
searching scale 1 Z rot -0.0
searching scale 1 Z rot 0.2
searching scale 1 Z rot 0.5
searching scale 1 Z rot 0.7
searching scale 1 Z rot 1.0
searching scale 1 Z rot 1.2
searching scale 1 Z rot 1.5
searching scale 1 Z rot 1.7
searching scale 1 Z rot 2.0
searching scale 1 Z rot 2.2
searching scale 1 Z rot 2.5
searching scale 1 Z rot 2.7
searching scale 1 Z rot 3.0
searching scale 1 Z rot 3.2
searching scale 1 Z rot 3.5
searching scale 1 Z rot 3.7
searching scale 1 Z rot 4.0
searching scale 1 Z rot 4.2
searching scale 1 Z rot 4.5
searching scale 1 Z rot 4.7
searching scale 1 Z rot 5.0
searching scale 1 Z rot 5.2
searching scale 1 Z rot 5.5
searching scale 1 Z rot 5.7
searching scale 1 Z rot 6.0
searching scale 1 Z rot 6.2
searching scale 1 Z rot 6.5
searching scale 1 Z rot 6.7
searching scale 1 Z rot 7.0
searching scale 1 Z rot 7.2
searching scale 1 Z rot 7.5
searching scale 1 Z rot 7.7 global minimum found at slice 126.1, rotations (-3.60, 0.99)
- final transformation (x=126.1, yr=-3.601, zr=0.994):
- 0.998 -0.017 -0.063 10.978;
- 0.017 1.000 -0.001 45.958;
- 0.063 -0.000 0.998 2.314;
- 0.000 0.000 0.000 1.000;
- updating x range to be [126, 130] in xformed coordinates
- best xformed slice 128
- cc center is found at 128 147 160
- eigenvectors:
- -0.002 0.001 1.000;
- 0.022 -1.000 0.001;
- 1.000 0.022 0.001;
- error in mid anterior detected - correcting...
- writing aseg with callosum to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/aseg.auto.mgz...
- corpus callosum matter segmentation took 1.0 minutes
- #--------------------------------------
- #@# Merge ASeg Thu Aug 8 17:09:40 CEST 2013
- cp aseg.auto.mgz aseg.mgz
- #--------------------------------------------
- #@# Intensity Normalization2 Thu Aug 8 17:09:40 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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...
- 2558 control points removed
- Building bias image
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 0...
- Smoothing with sigma 8
- Applying bias correction
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Iterating 2 times
- ---------------------------------
- 3d normalization pass 1 of 2
- white matter peak found at 111
- white matter peak found at 109
- gm peak at 55 (55), valley at 30 (30)
- csf peak at 27, setting threshold to 45
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- ---------------------------------
- 3d normalization pass 2 of 2
- white matter peak found at 111
- white matter peak found at 110
- gm peak at 56 (56), valley at 24 (24)
- csf peak at 28, setting threshold to 46
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Done iterating ---------------------------------
- writing output to brain.mgz
- 3D bias adjustment took 4 minutes and 40 seconds.
- #--------------------------------------------
- #@# Mask BFS Thu Aug 8 17:14:22 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri
- mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
- threshold mask volume at 5
- DoAbs = 0
- Found 1383897 voxels in mask (pct= 8.25)
- Writing masked volume to brain.finalsurfs.mgz...done.
- #--------------------------------------------
- #@# WM Segmentation Thu Aug 8 17:14:25 CEST 2013
- mri_segment brain.mgz wm.seg.mgz
- doing initial intensity segmentation...
- using local statistics to label ambiguous voxels...
- computing class statistics for intensity windows...
- WM (107.0): 107.0 +- 4.9 [80.0 --> 125.0]
- GM (66.0) : 65.3 +- 9.9 [30.0 --> 96.0]
- setting bottom of white matter range to 75.1
- setting top of gray matter range to 85.0
- 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...
- 6982 sparsely connected voxels removed...
- thickening thin strands....
- 20 segments, 6893 filled
- 187 bright non-wm voxels segmented.
- 3746 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 0.67 minutes
- reading wm segmentation from wm.seg.mgz...
- 58 voxels added to wm to prevent paths from MTL structures to cortex
- 1127 additional wm voxels added
- 0 additional wm voxels added
- SEG EDIT: 34372 voxels turned on, 37121 voxels turned off.
- propagating editing to output volume from wm.seg.mgz
- 115,126,128 old 0 new 0
- 115,126,128 old 0 new 0
- writing edited volume to wm.asegedit.mgz....
- mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz
- Iteration Number : 1
- pass 1 (xy+): 23 found - 23 modified | TOTAL: 23
- pass 2 (xy+): 0 found - 23 modified | TOTAL: 23
- pass 1 (xy-): 25 found - 25 modified | TOTAL: 48
- pass 2 (xy-): 0 found - 25 modified | TOTAL: 48
- pass 1 (yz+): 27 found - 27 modified | TOTAL: 75
- pass 2 (yz+): 0 found - 27 modified | TOTAL: 75
- pass 1 (yz-): 16 found - 16 modified | TOTAL: 91
- pass 2 (yz-): 0 found - 16 modified | TOTAL: 91
- pass 1 (xz+): 24 found - 24 modified | TOTAL: 115
- pass 2 (xz+): 0 found - 24 modified | TOTAL: 115
- pass 1 (xz-): 24 found - 24 modified | TOTAL: 139
- pass 2 (xz-): 0 found - 24 modified | TOTAL: 139
- Iteration Number : 1
- pass 1 (+++): 18 found - 18 modified | TOTAL: 18
- pass 2 (+++): 0 found - 18 modified | TOTAL: 18
- pass 1 (+++): 8 found - 8 modified | TOTAL: 26
- pass 2 (+++): 0 found - 8 modified | TOTAL: 26
- pass 1 (+++): 6 found - 6 modified | TOTAL: 32
- pass 2 (+++): 0 found - 6 modified | TOTAL: 32
- pass 1 (+++): 13 found - 13 modified | TOTAL: 45
- pass 2 (+++): 0 found - 13 modified | TOTAL: 45
- Iteration Number : 1
- pass 1 (++): 162 found - 162 modified | TOTAL: 162
- pass 2 (++): 0 found - 162 modified | TOTAL: 162
- pass 1 (+-): 238 found - 238 modified | TOTAL: 400
- pass 2 (+-): 1 found - 239 modified | TOTAL: 401
- pass 3 (+-): 0 found - 239 modified | TOTAL: 401
- pass 1 (--): 144 found - 144 modified | TOTAL: 545
- pass 2 (--): 0 found - 144 modified | TOTAL: 545
- pass 1 (-+): 190 found - 190 modified | TOTAL: 735
- pass 2 (-+): 0 found - 190 modified | TOTAL: 735
- Iteration Number : 2
- pass 1 (xy+): 7 found - 7 modified | TOTAL: 7
- pass 2 (xy+): 0 found - 7 modified | TOTAL: 7
- pass 1 (xy-): 2 found - 2 modified | TOTAL: 9
- pass 2 (xy-): 0 found - 2 modified | TOTAL: 9
- pass 1 (yz+): 2 found - 2 modified | TOTAL: 11
- pass 2 (yz+): 0 found - 2 modified | TOTAL: 11
- pass 1 (yz-): 6 found - 6 modified | TOTAL: 17
- pass 2 (yz-): 0 found - 6 modified | TOTAL: 17
- pass 1 (xz+): 5 found - 5 modified | TOTAL: 22
- pass 2 (xz+): 0 found - 5 modified | TOTAL: 22
- pass 1 (xz-): 3 found - 3 modified | TOTAL: 25
- pass 2 (xz-): 0 found - 3 modified | TOTAL: 25
- 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 (-+): 1 found - 1 modified | TOTAL: 1
- pass 2 (-+): 0 found - 1 modified | TOTAL: 1
- 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 = 945 (out of 449892: 0.210050)
- binarizing input wm segmentation...
- Ambiguous edge configurations...
- mri_pretess done
- #--------------------------------------------
- #@# Fill Thu Aug 8 17:16:53 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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
- 1.106 -0.027 -0.064 -4.276;
- 0.036 1.189 0.090 -11.347;
- 0.083 -0.111 1.069 -20.889;
- 0.000 0.000 0.000 1.000;
- voxel to talairach voxel transform
- 1.106 -0.027 -0.064 -4.276;
- 0.036 1.189 0.090 -11.347;
- 0.083 -0.111 1.069 -20.889;
- 0.000 0.000 0.000 1.000;
- reading segmented volume aseg.auto_noCCseg.mgz...
- Looking for area (min, max) = (350, 1400)
- area[0] = 1194 (min = 350, max = 1400), aspect = 0.52 (min = 0.10, max = 0.75)
- no need to search
- using seed (126, 115, 145), TAL = (2.0, 17.0, 13.0)
- talairach voxel to voxel transform
- 0.900 0.025 0.052 5.216;
- -0.022 0.834 -0.072 7.873;
- -0.072 0.084 0.924 19.957;
- 0.000 0.000 0.000 1.000;
- segmentation indicates cc at (126, 115, 145) --> (2.0, 17.0, 13.0)
- done.
- writing output to filled.mgz...
- filling took 1.0 minutes
- talairach cc position changed to (2.00, 17.00, 13.00)
- Erasing brainstem...done.
- seed_search_size = 9, min_neighbors = 5
- search rh wm seed point around talairach space:(20.00, 17.00, 13.00) SRC: (112.78, 91.05, 155.93)
- search lh wm seed point around talairach space (-16.00, 17.00, 13.00), SRC: (145.16, 90.28, 153.35)
- compute mri_fill using aseg
- Erasing Brain Stem and Cerebellum ...
- Define left and right masks using aseg:
- Building Voronoi diagram ...
- Using the Voronoi diagram to separate WM into two hemispheres ...
- Find the largest connected component for each hemisphere ...
- #--------------------------------------------
- #@# Tessellate lh Thu Aug 8 17:17:56 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts
- mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz
- Iteration Number : 1
- pass 1 (xy+): 2 found - 2 modified | TOTAL: 2
- pass 2 (xy+): 0 found - 2 modified | TOTAL: 2
- pass 1 (xy-): 1 found - 1 modified | TOTAL: 3
- pass 2 (xy-): 0 found - 1 modified | TOTAL: 3
- pass 1 (yz+): 1 found - 1 modified | TOTAL: 4
- pass 2 (yz+): 0 found - 1 modified | TOTAL: 4
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 4
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 4
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 4
- Iteration Number : 1
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 1
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- 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 = 4 (out of 216070: 0.001851)
- Ambiguous edge configurations...
- mri_pretess done
- mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix
- $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- slice 40: 16 vertices, 22 faces
- slice 50: 3802 vertices, 3997 faces
- slice 60: 10981 vertices, 11263 faces
- slice 70: 20573 vertices, 20908 faces
- slice 80: 31321 vertices, 31695 faces
- slice 90: 41789 vertices, 42139 faces
- slice 100: 52568 vertices, 52941 faces
- slice 110: 64298 vertices, 64702 faces
- slice 120: 75278 vertices, 75667 faces
- slice 130: 86018 vertices, 86379 faces
- slice 140: 96250 vertices, 96551 faces
- slice 150: 104805 vertices, 105079 faces
- slice 160: 111797 vertices, 112055 faces
- slice 170: 118318 vertices, 118529 faces
- slice 180: 124034 vertices, 124223 faces
- slice 190: 128211 vertices, 128332 faces
- slice 200: 129694 vertices, 129710 faces
- slice 210: 129694 vertices, 129710 faces
- slice 220: 129694 vertices, 129710 faces
- slice 230: 129694 vertices, 129710 faces
- slice 240: 129694 vertices, 129710 faces
- slice 250: 129694 vertices, 129710 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...
- 129694 voxel in cpt #1: X=-16 [v=129694,e=389130,f=259420] located at (-24.568037, -16.476614, 38.646660)
- For the whole surface: X=-16 [v=129694,e=389130,f=259420]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Smooth1 lh Thu Aug 8 17:18:04 CEST 2013
- mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts
- setting seed for random number generator to 1234
- smoothing surface tessellation for 10 iterations...
- smoothing complete - recomputing first and second fundamental forms...
- #--------------------------------------------
- #@# Inflation1 lh Thu Aug 8 17:18:09 CEST 2013
- mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts
- avg radius = 45.2 mm, total surface area = 67371 mm^2
- writing inflated surface to ../surf/lh.inflated.nofix
- inflation took 0.7 minutes
- Not saving sulc
-
step 000: RMS=0.103 (target=0.015)
step 005: RMS=0.075 (target=0.015)
step 010: RMS=0.055 (target=0.015)
step 015: RMS=0.046 (target=0.015)
step 020: RMS=0.039 (target=0.015)
step 025: RMS=0.035 (target=0.015)
step 030: RMS=0.031 (target=0.015)
step 035: RMS=0.028 (target=0.015)
step 040: RMS=0.027 (target=0.015)
step 045: RMS=0.025 (target=0.015)
step 050: RMS=0.024 (target=0.015)
step 055: RMS=0.024 (target=0.015)
step 060: RMS=0.023 (target=0.015)
- inflation complete.
- Not saving sulc
- #--------------------------------------------
- #@# QSphere lh Thu Aug 8 17:18:51 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 1.00 +- 0.59 (0.00-->8.39) (max @ vno 91160 --> 92232)
- face area 0.03 +- 0.03 (-0.13-->1.03)
- scaling brain by 0.316...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=176.813, avgs=0
- 005/300: dt: 0.9000, rms radial error=176.555, avgs=0
- 010/300: dt: 0.9000, rms radial error=176.000, avgs=0
- 015/300: dt: 0.9000, rms radial error=175.271, avgs=0
- 020/300: dt: 0.9000, rms radial error=174.442, avgs=0
- 025/300: dt: 0.9000, rms radial error=173.556, avgs=0
- 030/300: dt: 0.9000, rms radial error=172.637, avgs=0
- 035/300: dt: 0.9000, rms radial error=171.701, avgs=0
- 040/300: dt: 0.9000, rms radial error=170.758, avgs=0
- 045/300: dt: 0.9000, rms radial error=169.811, avgs=0
- 050/300: dt: 0.9000, rms radial error=168.864, avgs=0
- 055/300: dt: 0.9000, rms radial error=167.920, avgs=0
- 060/300: dt: 0.9000, rms radial error=166.979, avgs=0
- 065/300: dt: 0.9000, rms radial error=166.041, avgs=0
- 070/300: dt: 0.9000, rms radial error=165.109, avgs=0
- 075/300: dt: 0.9000, rms radial error=164.180, avgs=0
- 080/300: dt: 0.9000, rms radial error=163.257, avgs=0
- 085/300: dt: 0.9000, rms radial error=162.338, avgs=0
- 090/300: dt: 0.9000, rms radial error=161.424, avgs=0
- 095/300: dt: 0.9000, rms radial error=160.515, avgs=0
- 100/300: dt: 0.9000, rms radial error=159.611, avgs=0
- 105/300: dt: 0.9000, rms radial error=158.711, avgs=0
- 110/300: dt: 0.9000, rms radial error=157.817, avgs=0
- 115/300: dt: 0.9000, rms radial error=156.927, avgs=0
- 120/300: dt: 0.9000, rms radial error=156.044, avgs=0
- 125/300: dt: 0.9000, rms radial error=155.166, avgs=0
- 130/300: dt: 0.9000, rms radial error=154.293, avgs=0
- 135/300: dt: 0.9000, rms radial error=153.425, avgs=0
- 140/300: dt: 0.9000, rms radial error=152.562, avgs=0
- 145/300: dt: 0.9000, rms radial error=151.704, avgs=0
- 150/300: dt: 0.9000, rms radial error=150.850, avgs=0
- 155/300: dt: 0.9000, rms radial error=150.000, avgs=0
- 160/300: dt: 0.9000, rms radial error=149.155, avgs=0
- 165/300: dt: 0.9000, rms radial error=148.315, avgs=0
- 170/300: dt: 0.9000, rms radial error=147.480, avgs=0
- 175/300: dt: 0.9000, rms radial error=146.649, avgs=0
- 180/300: dt: 0.9000, rms radial error=145.823, avgs=0
- 185/300: dt: 0.9000, rms radial error=145.001, avgs=0
- 190/300: dt: 0.9000, rms radial error=144.184, avgs=0
- 195/300: dt: 0.9000, rms radial error=143.371, avgs=0
- 200/300: dt: 0.9000, rms radial error=142.563, avgs=0
- 205/300: dt: 0.9000, rms radial error=141.759, avgs=0
- 210/300: dt: 0.9000, rms radial error=140.959, avgs=0
- 215/300: dt: 0.9000, rms radial error=140.165, avgs=0
- 220/300: dt: 0.9000, rms radial error=139.374, avgs=0
- 225/300: dt: 0.9000, rms radial error=138.589, avgs=0
- 230/300: dt: 0.9000, rms radial error=137.807, avgs=0
- 235/300: dt: 0.9000, rms radial error=137.030, avgs=0
- 240/300: dt: 0.9000, rms radial error=136.257, avgs=0
- 245/300: dt: 0.9000, rms radial error=135.489, avgs=0
- 250/300: dt: 0.9000, rms radial error=134.725, avgs=0
- 255/300: dt: 0.9000, rms radial error=133.965, avgs=0
- 260/300: dt: 0.9000, rms radial error=133.209, avgs=0
- 265/300: dt: 0.9000, rms radial error=132.458, avgs=0
- 270/300: dt: 0.9000, rms radial error=131.710, avgs=0
- 275/300: dt: 0.9000, rms radial error=130.968, avgs=0
- 280/300: dt: 0.9000, rms radial error=130.229, avgs=0
- 285/300: dt: 0.9000, rms radial error=129.495, avgs=0
- 290/300: dt: 0.9000, rms radial error=128.764, avgs=0
- 295/300: dt: 0.9000, rms radial error=128.038, avgs=0
- 300/300: dt: 0.9000, rms radial error=127.316, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 15148.56
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00015
- epoch 2 (K=40.0), pass 1, starting sse = 2533.04
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00009
- epoch 3 (K=160.0), pass 1, starting sse = 264.64
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.09/11 = 0.00857
- epoch 4 (K=640.0), pass 1, starting sse = 14.98
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.14/16 = 0.00905
- final writing spherical brain to ../surf/lh.qsphere.nofix
- spherical transformation took 0.08 hours
- distance error %100000.00
- #--------------------------------------------
- #@# Fix Topology lh Thu Aug 8 17:23:35 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/sub003/scripts
- mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub003 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=129694, nf=259420, ne=389130, 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...
- 1837 ambiguous faces found in tessellation
- segmenting defects...
- 19 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- 19 defects to be corrected
- 0 vertices coincident
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -9.8374 (-4.9187)
- -vertex loglikelihood: -6.7649 (-3.3824)
- -normal dot loglikelihood: -3.6152 (-3.6152)
- -quad curv loglikelihood: -6.5526 (-3.2763)
- Total Loglikelihood : -26.7701
- CORRECTING DEFECT 0 (vertices=20, convex hull=76)
- After retessellation of defect 0, euler #=-16 (128575,385286,256695) : difference with theory (-16) = 0
- CORRECTING DEFECT 1 (vertices=60, convex hull=97)
- After retessellation of defect 1, euler #=-15 (128590,385373,256768) : difference with theory (-15) = 0
- CORRECTING DEFECT 2 (vertices=224, convex hull=194)
- After retessellation of defect 2, euler #=-14 (128647,385632,256971) : difference with theory (-14) = 0
- CORRECTING DEFECT 3 (vertices=11, convex hull=24)
- After retessellation of defect 3, euler #=-13 (128651,385650,256986) : difference with theory (-13) = 0
- CORRECTING DEFECT 4 (vertices=89, convex hull=42)
- After retessellation of defect 4, euler #=-12 (128658,385696,257026) : difference with theory (-12) = 0
- CORRECTING DEFECT 5 (vertices=120, convex hull=73)
- After retessellation of defect 5, euler #=-11 (128683,385803,257109) : difference with theory (-11) = 0
- CORRECTING DEFECT 6 (vertices=59, convex hull=29)
- After retessellation of defect 6, euler #=-10 (128691,385837,257136) : difference with theory (-10) = 0
- CORRECTING DEFECT 7 (vertices=10, convex hull=26)
- After retessellation of defect 7, euler #=-9 (128695,385857,257153) : difference with theory (-9) = 0
- CORRECTING DEFECT 8 (vertices=161, convex hull=64)
- After retessellation of defect 8, euler #=-8 (128704,385915,257203) : difference with theory (-8) = 0
- CORRECTING DEFECT 9 (vertices=12, convex hull=29)
- After retessellation of defect 9, euler #=-7 (128709,385941,257225) : difference with theory (-7) = 0
- CORRECTING DEFECT 10 (vertices=22, convex hull=28)
- After retessellation of defect 10, euler #=-6 (128712,385961,257243) : difference with theory (-6) = 0
- CORRECTING DEFECT 11 (vertices=6, convex hull=23)
- After retessellation of defect 11, euler #=-5 (128714,385974,257255) : difference with theory (-5) = 0
- CORRECTING DEFECT 12 (vertices=46, convex hull=86)
- After retessellation of defect 12, euler #=-4 (128740,386083,257339) : difference with theory (-4) = 0
- CORRECTING DEFECT 13 (vertices=18, convex hull=25)
- After retessellation of defect 13, euler #=-3 (128743,386098,257352) : difference with theory (-3) = 0
- CORRECTING DEFECT 14 (vertices=28, convex hull=49)
- After retessellation of defect 14, euler #=-2 (128755,386156,257399) : difference with theory (-2) = 0
- CORRECTING DEFECT 15 (vertices=28, convex hull=75)
- After retessellation of defect 15, euler #=-1 (128772,386237,257464) : difference with theory (-1) = 0
- CORRECTING DEFECT 16 (vertices=9, convex hull=18)
- After retessellation of defect 16, euler #=0 (128773,386245,257472) : difference with theory (0) = 0
- CORRECTING DEFECT 17 (vertices=174, convex hull=102)
- After retessellation of defect 17, euler #=1 (128805,386384,257580) : difference with theory (1) = 0
- CORRECTING DEFECT 18 (vertices=33, convex hull=66)
- After retessellation of defect 18, euler #=2 (128814,386436,257624) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.88 +- 0.22 (0.07-->7.78) (max @ vno 125265 --> 127336)
- face area 0.00 +- 0.00 (0.00-->0.00)
- performing soap bubble on retessellated vertices for 0 iterations...
- vertex spacing 0.88 +- 0.22 (0.07-->7.78) (max @ vno 125265 --> 127336)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 69 mutations (34.0%), 134 crossovers (66.0%), 71 vertices were eliminated
- building final representation...
- 880 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=128814, nf=257624, ne=386436, g=0)
- writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 11.9 minutes
- 0 defective edges
- removing intersecting faces
- 000: 104 intersecting
- 001: 8 intersecting
- mris_euler_number ../surf/lh.orig
- euler # = v-e+f = 2g-2: 128814 - 386436 + 257624 = 2 --> 0 holes
- F =2V-4: 257624 = 257628-4 (0)
- 2E=3F: 772872 = 772872 (0)
- total defect index = 0
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts
- mris_remove_intersection ../surf/lh.orig ../surf/lh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 14 intersecting
- writing corrected surface to ../surf/lh.orig
- rm ../surf/lh.inflated
- #--------------------------------------------
- #@# Make White Surf lh Thu Aug 8 17:35:36 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts
- mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub003 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/sub003/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/wm.mgz...
- 15061 bright wm thresholded.
- 302 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.orig...
- computing class statistics...
- border white: 229356 voxels (1.37%)
- border gray 266114 voxels (1.59%)
- WM (92.0): 92.8 +- 10.6 [70.0 --> 110.0]
- GM (74.0) : 72.1 +- 13.1 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 43.9 (was 70)
- setting MAX_BORDER_WHITE to 115.6 (was 105)
- setting MIN_BORDER_WHITE to 57.0 (was 85)
- setting MAX_CSF to 30.8 (was 40)
- setting MAX_GRAY to 94.4 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 50.4 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 17.6 (was 40)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.81 +- 0.22 (0.00-->3.59) (max @ vno 56572 --> 128641)
- face area 0.27 +- 0.12 (0.00-->1.50)
- mean absolute distance = 0.66 +- 0.75
- 3216 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=105, GM=57
- mean inside = 92.8, mean outside = 67.3
- smoothing surface for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 4 vertex label from ripped group
- mean border=70.6, 37 (37) missing vertices, mean dist 0.4 [0.4 (%29.2)->0.8 (%70.8))]
- %70 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.92 +- 0.27 (0.07-->4.54) (max @ vno 128641 --> 61076)
- face area 0.27 +- 0.13 (0.00-->2.13)
- mean absolute distance = 0.31 +- 0.46
- 2364 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=7465953.0, rms=14.40
- 001: dt: 0.5000, sse=7262134.0, rms=10.477 (0.000%)
- 002: dt: 0.5000, sse=7351785.0, rms=8.228 (0.000%)
- 003: dt: 0.5000, sse=7413903.5, rms=6.769 (0.000%)
- 004: dt: 0.5000, sse=7597030.0, rms=5.886 (0.000%)
- 005: dt: 0.5000, sse=7659898.0, rms=5.350 (0.000%)
- 006: dt: 0.5000, sse=7772073.5, rms=5.077 (0.000%)
- 007: dt: 0.5000, sse=7755777.5, rms=4.889 (0.000%)
- 008: dt: 0.5000, sse=7801354.0, rms=4.794 (0.000%)
- 009: dt: 0.5000, sse=7751140.0, rms=4.702 (0.000%)
- rms = 4.66, time step reduction 1 of 3 to 0.250...
- 010: dt: 0.5000, sse=7755212.5, rms=4.664 (0.000%)
- 011: dt: 0.2500, sse=4943071.0, rms=3.317 (0.000%)
- 012: dt: 0.2500, sse=4577469.5, rms=2.876 (0.000%)
- 013: dt: 0.2500, sse=4314085.0, rms=2.788 (0.000%)
- 014: dt: 0.2500, sse=4268909.5, rms=2.701 (0.000%)
- rms = 2.68, time step reduction 2 of 3 to 0.125...
- 015: dt: 0.2500, sse=4162221.5, rms=2.675 (0.000%)
- 016: dt: 0.1250, sse=3871362.5, rms=2.326 (0.000%)
- 017: dt: 0.1250, sse=3831868.2, rms=2.273 (0.000%)
- rms = 2.26, time step reduction 3 of 3 to 0.062...
- 018: dt: 0.1250, sse=3800823.0, rms=2.263 (0.000%)
- positioning took 2.1 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 1 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 4 vertex label from ripped group
- mean border=75.5, 19 (3) missing vertices, mean dist -0.2 [0.3 (%78.8)->0.2 (%21.2))]
- %81 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 (0.10-->4.77) (max @ vno 128641 --> 61076)
- face area 0.35 +- 0.17 (0.00-->2.79)
- mean absolute distance = 0.21 +- 0.29
- 2665 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4803874.0, rms=6.41
- 019: dt: 0.5000, sse=4962588.0, rms=4.328 (0.000%)
- rms = 4.76, time step reduction 1 of 3 to 0.250...
- 020: dt: 0.2500, sse=4493959.0, rms=3.071 (0.000%)
- 021: dt: 0.2500, sse=4333171.0, rms=2.534 (0.000%)
- 022: dt: 0.2500, sse=4261336.5, rms=2.121 (0.000%)
- rms = 2.12, time step reduction 2 of 3 to 0.125...
- 023: dt: 0.2500, sse=4262324.0, rms=2.116 (0.000%)
- 024: dt: 0.1250, sse=4062707.8, rms=1.769 (0.000%)
- 025: dt: 0.1250, sse=4015600.2, rms=1.716 (0.000%)
- rms = 1.72, time step reduction 3 of 3 to 0.062...
- 026: dt: 0.1250, sse=4015600.2, rms=1.716 (0.000%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 4 vertex label from ripped group
- mean border=79.3, 22 (2) missing vertices, mean dist -0.1 [0.2 (%78.9)->0.2 (%21.1))]
- %89 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.25 (0.11-->4.90) (max @ vno 128641 --> 61076)
- face area 0.34 +- 0.16 (0.00-->2.77)
- mean absolute distance = 0.15 +- 0.23
- 2784 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4474704.0, rms=4.76
- 027: dt: 0.5000, sse=4776922.5, rms=4.468 (0.000%)
- rms = 4.55, time step reduction 1 of 3 to 0.250...
- 028: dt: 0.2500, sse=4306562.0, rms=2.805 (0.000%)
- 029: dt: 0.2500, sse=4177830.8, rms=2.405 (0.000%)
- 030: dt: 0.2500, sse=4245258.0, rms=2.000 (0.000%)
- rms = 2.10, time step reduction 2 of 3 to 0.125...
- 031: dt: 0.1250, sse=4171524.5, rms=1.801 (0.000%)
- 032: dt: 0.1250, sse=4077918.5, rms=1.518 (0.000%)
- rms = 1.47, time step reduction 3 of 3 to 0.062...
- 033: dt: 0.1250, sse=4045932.8, rms=1.475 (0.000%)
- positioning took 0.9 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 3 vertex label from ripped group
- mean border=80.5, 30 (1) missing vertices, mean dist -0.0 [0.2 (%59.7)->0.1 (%40.3))]
- %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/sub003/surf/lh.white...
- writing smoothed curvature to lh.curv
- 000: dt: 0.0000, sse=4080045.0, rms=1.97
- rms = 3.07, time step reduction 1 of 3 to 0.250...
- 034: dt: 0.2500, sse=4151119.0, rms=1.280 (0.000%)
- 035: dt: 0.2500, sse=4290692.0, rms=1.100 (0.000%)
- rms = 1.10, time step reduction 2 of 3 to 0.125...
- 036: dt: 0.2500, sse=4374876.0, rms=1.096 (0.000%)
- rms = 1.07, time step reduction 3 of 3 to 0.062...
- 037: dt: 0.1250, sse=4403312.5, rms=1.070 (0.000%)
- positioning took 0.5 minutes
- inhibiting deformation at non-cortical midline structures...
- generating cortex label...
- 14 non-cortical segments detected
- only using segment with 1770 vertices
- erasing segment 1 (vno[0] = 74553)
- erasing segment 2 (vno[0] = 76852)
- erasing segment 3 (vno[0] = 77980)
- erasing segment 4 (vno[0] = 83191)
- erasing segment 5 (vno[0] = 87211)
- erasing segment 6 (vno[0] = 87222)
- erasing segment 7 (vno[0] = 91656)
- erasing segment 8 (vno[0] = 94452)
- erasing segment 9 (vno[0] = 96138)
- erasing segment 10 (vno[0] = 96140)
- erasing segment 11 (vno[0] = 100554)
- erasing segment 12 (vno[0] = 101378)
- erasing segment 13 (vno[0] = 102157)
- writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/label/lh.cortex.label...
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.curv
- writing smoothed area to lh.area
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.area
- vertex spacing 0.90 +- 0.25 (0.03-->4.88) (max @ vno 128641 --> 61076)
- face area 0.34 +- 0.16 (0.00-->2.78)
- refinement took 6.6 minutes
- #--------------------------------------------
- #@# Smooth2 lh Thu Aug 8 17:42:15 CEST 2013
- mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts
- smoothing for 3 iterations
- setting seed for random number generator to 1234
- smoothing surface tessellation for 3 iterations...
- smoothing complete - recomputing first and second fundamental forms...
- #--------------------------------------------
- #@# Inflation2 lh Thu Aug 8 17:42:19 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts
- mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated
- avg radius = 45.4 mm, total surface area = 78610 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=0.082 (target=0.015)
step 010: RMS=0.059 (target=0.015)
step 015: RMS=0.048 (target=0.015)
step 020: RMS=0.040 (target=0.015)
step 025: RMS=0.034 (target=0.015)
step 030: RMS=0.028 (target=0.015)
step 035: RMS=0.024 (target=0.015)
step 040: RMS=0.021 (target=0.015)
step 045: RMS=0.019 (target=0.015)
step 050: RMS=0.017 (target=0.015)
step 055: RMS=0.016 (target=0.015)
step 060: 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/lh.inflated
- normalizing curvature values.
- averaging curvature patterns 5 times.
- sampling 10 neighbors out to a distance of 10 mm
- 111 vertices thresholded to be in k1 ~ [-0.23 0.79], k2 ~ [-0.14 0.08]
- total integrated curvature = 0.588*4pi (7.387) --> 0 handles
- ICI = 1.5, FI = 8.0, variation=145.885
- 116 vertices thresholded to be in [-0.04 0.02]
- writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level
- curvature mean = 0.000, std = 0.001
- 95 vertices thresholded to be in [-0.15 0.15]
- done.
- writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.017, std = 0.021
- done.
- #-----------------------------------------
- #@# Curvature Stats lh Thu Aug 8 17:44:29 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub003 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 [ sub003/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 [ 211 ]
- Gb_filter = 0
- WARN: S lookup min: -1.156500
- WARN: S explicit min: 0.000000 vertex = 678
- #--------------------------------------------
- #@# Sphere lh Thu Aug 8 17:44:33 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 0.292...
- MRISunfold() max_passes = 1 -------
- tol=5.0e-01, sigma=0.0, host=snake, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
- using quadratic fit line minimization
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 1.000000
- desired_rms_height -1.000000
- momentum 0.900000
- nbhd_size 7
- max_nbrs 8
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 1234
- --------------------
- mrisRemoveNegativeArea()
- pass 1: epoch 1 of 3 starting distance error %20.77
- pass 1: epoch 2 of 3 starting distance error %20.75
- unfolding complete - removing small folds...
- starting distance error %20.68
- removing remaining folds...
- final distance error %20.69
- MRISunfold() return, current seed 1234
- writing spherical brain to ../surf/lh.sphere
- spherical transformation took 0.90 hours
- #--------------------------------------------
- #@# Surf Reg lh Thu Aug 8 18:38:41 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 = 0.596
- curvature mean = 0.030, std = 0.936
- curvature mean = 0.023, std = 0.864
- Starting MRISrigidBodyAlignGlobal()
- d=64.00 min @ (0.00, -16.00, 0.00) sse = 321607.3, tmin=1.0430
- d=32.00 min @ (0.00, 8.00, 0.00) sse = 270092.5, tmin=2.0947
- d=16.00 min @ (4.00, 0.00, 0.00) sse = 248718.9, tmin=3.1583
- d=4.00 min @ (0.00, 1.00, 1.00) sse = 247261.0, tmin=5.3649
- d=0.50 min @ (-0.12, 0.00, 0.12) sse = 247231.8, tmin=8.5913
- 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 8.59 min
- curvature mean = 0.018, std = 0.961
- curvature mean = 0.012, std = 0.941
- curvature mean = 0.018, std = 0.973
- curvature mean = 0.006, std = 0.973
- curvature mean = 0.016, std = 0.975
- curvature mean = 0.002, std = 0.988
- 2 Reading smoothwm
- curvature mean = -0.026, std = 0.313
- curvature mean = 0.004, std = 0.067
- curvature mean = 0.076, std = 0.326
- curvature mean = 0.004, std = 0.080
- curvature mean = 0.036, std = 0.517
- curvature mean = 0.004, std = 0.086
- curvature mean = 0.020, std = 0.657
- curvature mean = 0.004, std = 0.089
- curvature mean = 0.008, std = 0.769
- MRISregister() return, current seed 0
- writing registered surface to ../surf/lh.sphere.reg...
- expanding nbhd size to 1
- #--------------------------------------------
- #@# Jacobian white lh Thu Aug 8 19:04:44 CEST 2013
- mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white
- reading surface from ../surf/lh.white...
- writing curvature file ../surf/lh.jacobian_white
- #--------------------------------------------
- #@# AvgCurv lh Thu Aug 8 19:04:47 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts
- mrisp_paint -a 5 /opt/freesurfer/5.3.0/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv
- averaging curvature patterns 5 times...
- reading surface from ../surf/lh.sphere.reg...
- reading template parameterization from /opt/freesurfer/5.3.0/average/lh.average.curvature.filled.buckner40.tif...
- writing curvature file to ../surf/lh.avg_curv...
- #-----------------------------------------
- #@# Cortical Parc lh Thu Aug 8 19:04:49 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub003 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...
- 1095 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2699 changed, 128814 examined...
- 001: 578 changed, 11878 examined...
- 002: 132 changed, 3273 examined...
- 003: 47 changed, 791 examined...
- 004: 21 changed, 291 examined...
- 005: 5 changed, 122 examined...
- 006: 3 changed, 36 examined...
- 007: 2 changed, 19 examined...
- 008: 1 changed, 10 examined...
- 009: 0 changed, 7 examined...
- 212 labels changed using aseg
- 000: 120 total segments, 80 labels (246 vertices) changed
- 001: 41 total segments, 1 labels (1 vertices) changed
- 002: 40 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 51 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 1129 vertices marked for relabeling...
- 1129 labels changed in reclassification.
- writing output to ../label/lh.aparc.annot...
- classification took 0 minutes and 59 seconds.
- #--------------------------------------------
- #@# Make Pial Surf lh Thu Aug 8 19:05:48 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts
- mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub003 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/sub003/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/wm.mgz...
- 15061 bright wm thresholded.
- 302 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.orig...
- computing class statistics...
- border white: 229356 voxels (1.37%)
- border gray 266114 voxels (1.59%)
- WM (92.0): 92.8 +- 10.6 [70.0 --> 110.0]
- GM (74.0) : 72.1 +- 13.1 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 43.9 (was 70)
- setting MAX_BORDER_WHITE to 115.6 (was 105)
- setting MIN_BORDER_WHITE to 57.0 (was 85)
- setting MAX_CSF to 30.8 (was 40)
- setting MAX_GRAY to 94.4 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 50.4 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 17.6 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=105, GM=57
- mean inside = 92.8, mean outside = 67.3
- 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/sub003/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.81 +- 0.22 (0.00-->3.59) (max @ vno 56572 --> 128641)
- face area 0.27 +- 0.12 (0.00-->1.50)
- mean absolute distance = 0.66 +- 0.75
- 3216 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 94 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 1 with 2 points - only 0.00% unknown
- deleting segment 4 with 5 points - only 0.00% unknown
- deleting segment 5 with 10 points - only 0.00% unknown
- deleting segment 7 with 7 points - only 0.00% unknown
- deleting segment 8 with 14 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 9 with 4 points - only 0.00% unknown
- deleting segment 10 with 21 points - only 0.00% unknown
- deleting segment 11 with 7 points - only 0.00% unknown
- mean border=70.6, 37 (37) missing vertices, mean dist 0.4 [0.4 (%29.2)->0.8 (%70.8))]
- %70 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.92 +- 0.27 (0.07-->4.54) (max @ vno 128641 --> 61076)
- face area 0.27 +- 0.13 (0.00-->2.13)
- mean absolute distance = 0.31 +- 0.46
- 2365 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=7473539.0, rms=14.40
- 001: dt: 0.5000, sse=7271485.5, rms=10.476 (0.000%)
- 002: dt: 0.5000, sse=7357718.5, rms=8.228 (0.000%)
- 003: dt: 0.5000, sse=7421993.5, rms=6.769 (0.000%)
- 004: dt: 0.5000, sse=7602813.5, rms=5.887 (0.000%)
- 005: dt: 0.5000, sse=7667546.0, rms=5.351 (0.000%)
- 006: dt: 0.5000, sse=7780513.5, rms=5.078 (0.000%)
- 007: dt: 0.5000, sse=7763787.0, rms=4.890 (0.000%)
- 008: dt: 0.5000, sse=7811158.0, rms=4.794 (0.000%)
- 009: dt: 0.5000, sse=7760282.0, rms=4.702 (0.000%)
- rms = 4.66, time step reduction 1 of 3 to 0.250...
- 010: dt: 0.5000, sse=7765007.5, rms=4.663 (0.000%)
- 011: dt: 0.2500, sse=4947214.5, rms=3.316 (0.000%)
- 012: dt: 0.2500, sse=4581080.5, rms=2.875 (0.000%)
- 013: dt: 0.2500, sse=4317435.0, rms=2.787 (0.000%)
- 014: dt: 0.2500, sse=4272544.5, rms=2.701 (0.000%)
- rms = 2.67, time step reduction 2 of 3 to 0.125...
- 015: dt: 0.2500, sse=4165785.5, rms=2.675 (0.000%)
- 016: dt: 0.1250, sse=3874189.8, rms=2.325 (0.000%)
- 017: dt: 0.1250, sse=3834696.5, rms=2.273 (0.000%)
- rms = 2.26, time step reduction 3 of 3 to 0.062...
- 018: dt: 0.1250, sse=3803987.5, rms=2.262 (0.000%)
- positioning took 2.2 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 91 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 1 with 2 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 2 with 3 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 3 with 3 points - only 0.00% unknown
- deleting segment 5 with 6 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- removing 3 vertex label from ripped group
- deleting segment 8 with 5 points - only 0.00% unknown
- deleting segment 10 with 11 points - only 0.00% unknown
- deleting segment 11 with 40 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 12 with 3 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 13 with 2 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 14 with 4 points - only 0.00% unknown
- mean border=75.5, 19 (3) missing vertices, mean dist -0.2 [0.3 (%78.8)->0.2 (%21.2))]
- %81 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.91 +- 0.26 (0.10-->4.77) (max @ vno 128641 --> 61076)
- face area 0.35 +- 0.17 (0.00-->2.79)
- mean absolute distance = 0.21 +- 0.29
- 2679 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4809469.5, rms=6.41
- 019: dt: 0.5000, sse=4968671.0, rms=4.324 (0.000%)
- rms = 4.76, time step reduction 1 of 3 to 0.250...
- 020: dt: 0.2500, sse=4499053.0, rms=3.068 (0.000%)
- 021: dt: 0.2500, sse=4337635.0, rms=2.532 (0.000%)
- 022: dt: 0.2500, sse=4267446.5, rms=2.120 (0.000%)
- rms = 2.11, time step reduction 2 of 3 to 0.125...
- 023: dt: 0.2500, sse=4267548.0, rms=2.115 (0.000%)
- 024: dt: 0.1250, sse=4067736.2, rms=1.768 (0.000%)
- 025: dt: 0.1250, sse=4020981.5, rms=1.715 (0.000%)
- rms = 1.72, time step reduction 3 of 3 to 0.062...
- 026: dt: 0.1250, sse=4020981.5, rms=1.715 (0.000%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 80 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 1 with 2 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 2 with 3 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 3 with 2 points - only 0.00% unknown
- deleting segment 5 with 6 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 6 with 2 points - only 0.00% unknown
- deleting segment 7 with 11 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 10 with 11 points - only 0.00% unknown
- deleting segment 11 with 14 points - only 0.00% unknown
- deleting segment 12 with 40 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 13 with 3 points - only 0.00% unknown
- deleting segment 14 with 8 points - only 0.00% unknown
- deleting segment 15 with 9 points - only 0.00% unknown
- deleting segment 16 with 5 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 17 with 4 points - only 0.00% unknown
- mean border=79.3, 22 (2) missing vertices, mean dist -0.1 [0.2 (%79.0)->0.2 (%21.0))]
- %89 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.25 (0.11-->4.90) (max @ vno 128641 --> 61076)
- face area 0.34 +- 0.16 (0.00-->2.77)
- mean absolute distance = 0.15 +- 0.24
- 2805 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4481905.0, rms=4.77
- 027: dt: 0.5000, sse=4780509.0, rms=4.467 (0.000%)
- rms = 4.54, time step reduction 1 of 3 to 0.250...
- 028: dt: 0.2500, sse=4309538.5, rms=2.804 (0.000%)
- 029: dt: 0.2500, sse=4180369.0, rms=2.402 (0.000%)
- 030: dt: 0.2500, sse=4248919.5, rms=1.999 (0.000%)
- rms = 2.09, time step reduction 2 of 3 to 0.125...
- 031: dt: 0.1250, sse=4175122.8, rms=1.801 (0.000%)
- 032: dt: 0.1250, sse=4081150.5, rms=1.517 (0.000%)
- rms = 1.47, time step reduction 3 of 3 to 0.062...
- 033: dt: 0.1250, sse=4049539.2, rms=1.474 (0.000%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 72 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 1 with 2 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 2 with 3 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 3 with 3 points - only 0.00% unknown
- deleting segment 4 with 6 points - only 0.00% unknown
- deleting segment 5 with 7 points - only 0.00% unknown
- deleting segment 6 with 11 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 8 with 9 points - only 0.00% unknown
- deleting segment 9 with 15 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 10 with 4 points - only 0.00% unknown
- deleting segment 11 with 40 points - only 0.00% unknown
- deleting segment 12 with 8 points - only 0.00% unknown
- deleting segment 13 with 15 points - only 0.00% unknown
- deleting segment 14 with 5 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 15 with 3 points - only 0.00% unknown
- mean border=80.5, 30 (1) missing vertices, mean dist -0.0 [0.2 (%59.7)->0.2 (%40.3))]
- %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
- 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=4083266.5, rms=1.96
- rms = 3.06, time step reduction 1 of 3 to 0.250...
- 034: dt: 0.2500, sse=4155235.5, rms=1.276 (0.000%)
- 035: dt: 0.2500, sse=4295353.5, rms=1.099 (0.000%)
- rms = 1.10, time step reduction 2 of 3 to 0.125...
- 036: dt: 0.2500, sse=4380404.5, rms=1.096 (0.000%)
- rms = 1.07, time step reduction 3 of 3 to 0.062...
- 037: dt: 0.1250, sse=4409607.5, rms=1.070 (0.000%)
- positioning took 0.6 minutes
- inhibiting deformation at non-cortical midline structures...
- smoothing surface for 5 iterations...
- mean border=46.8, 24 (24) missing vertices, mean dist 1.7 [0.4 (%0.0)->2.2 (%100.0))]
- %15 local maxima, %60 large gradients and %21 min vals, 1201 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=29363298.0, rms=32.90
- 001: dt: 0.5000, sse=20971844.0, rms=27.211 (0.000%)
- 002: dt: 0.5000, sse=15249326.0, rms=22.545 (0.000%)
- 003: dt: 0.5000, sse=11478462.0, rms=18.803 (0.000%)
- 004: dt: 0.5000, sse=9214643.0, rms=15.820 (0.000%)
- 005: dt: 0.5000, sse=7897537.5, rms=13.450 (0.000%)
- 006: dt: 0.5000, sse=7129650.0, rms=11.618 (0.000%)
- 007: dt: 0.5000, sse=6673061.5, rms=10.072 (0.000%)
- 008: dt: 0.5000, sse=6358933.0, rms=8.702 (0.000%)
- 009: dt: 0.5000, sse=6158782.5, rms=7.503 (0.000%)
- 010: dt: 0.5000, sse=6165566.5, rms=6.532 (0.000%)
- 011: dt: 0.5000, sse=6199794.5, rms=5.790 (0.000%)
- 012: dt: 0.5000, sse=6300519.5, rms=5.234 (0.000%)
- 013: dt: 0.5000, sse=6415731.0, rms=4.880 (0.000%)
- 014: dt: 0.5000, sse=6515793.5, rms=4.658 (0.000%)
- 015: dt: 0.5000, sse=6607865.5, rms=4.524 (0.000%)
- 016: dt: 0.5000, sse=6635672.5, rms=4.422 (0.000%)
- 017: dt: 0.5000, sse=6702909.0, rms=4.355 (0.000%)
- 018: dt: 0.5000, sse=6709572.5, rms=4.295 (0.000%)
- rms = 4.26, time step reduction 1 of 3 to 0.250...
- 019: dt: 0.5000, sse=6738862.0, rms=4.262 (0.000%)
- 020: dt: 0.2500, sse=4781606.5, rms=3.500 (0.000%)
- 021: dt: 0.2500, sse=4594213.5, rms=3.283 (0.000%)
- rms = 3.25, time step reduction 2 of 3 to 0.125...
- 022: dt: 0.2500, sse=4463428.5, rms=3.252 (0.000%)
- 023: dt: 0.1250, sse=4246123.0, rms=3.096 (0.000%)
- rms = 3.07, time step reduction 3 of 3 to 0.062...
- 024: dt: 0.1250, sse=4218790.0, rms=3.075 (0.000%)
- positioning took 3.0 minutes
- mean border=44.4, 720 (4) missing vertices, mean dist 0.2 [0.2 (%49.8)->0.6 (%50.2))]
- %32 local maxima, %46 large gradients and %17 min vals, 415 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=4865797.0, rms=5.11
- 025: dt: 0.5000, sse=5170906.5, rms=4.379 (0.000%)
- rms = 4.39, time step reduction 1 of 3 to 0.250...
- 026: dt: 0.2500, sse=4789324.5, rms=3.738 (0.000%)
- 027: dt: 0.2500, sse=4849623.0, rms=3.427 (0.000%)
- 028: dt: 0.2500, sse=4790957.5, rms=3.294 (0.000%)
- 029: dt: 0.2500, sse=4861055.0, rms=3.214 (0.000%)
- rms = 3.18, time step reduction 2 of 3 to 0.125...
- 030: dt: 0.2500, sse=4867138.5, rms=3.176 (0.000%)
- 031: dt: 0.1250, sse=4687796.0, rms=3.000 (0.000%)
- rms = 2.96, time step reduction 3 of 3 to 0.062...
- 032: dt: 0.1250, sse=4680468.5, rms=2.962 (0.000%)
- positioning took 1.1 minutes
- mean border=41.6, 891 (3) missing vertices, mean dist 0.1 [0.2 (%36.1)->0.4 (%63.9))]
- %55 local maxima, %23 large gradients and %17 min vals, 509 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=5026844.0, rms=4.66
- 033: dt: 0.5000, sse=5225649.5, rms=4.280 (0.000%)
- rms = 4.33, time step reduction 1 of 3 to 0.250...
- 034: dt: 0.2500, sse=4863804.5, rms=3.401 (0.000%)
- 035: dt: 0.2500, sse=5017575.5, rms=3.058 (0.000%)
- 036: dt: 0.2500, sse=4992551.0, rms=2.982 (0.000%)
- rms = 2.94, time step reduction 2 of 3 to 0.125...
- 037: dt: 0.2500, sse=5046519.0, rms=2.939 (0.000%)
- 038: dt: 0.1250, sse=4847981.0, rms=2.742 (0.000%)
- rms = 2.71, time step reduction 3 of 3 to 0.062...
- 039: dt: 0.1250, sse=4834373.5, rms=2.711 (0.000%)
- positioning took 0.9 minutes
- mean border=40.2, 1678 (2) missing vertices, mean dist 0.1 [0.2 (%43.6)->0.3 (%56.4))]
- %60 local maxima, %17 large gradients and %17 min vals, 371 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/sub003/surf/lh.pial...
- writing smoothed curvature to lh.curv.pial
- 000: dt: 0.0000, sse=4912659.0, rms=3.24
- rms = 4.20, time step reduction 1 of 3 to 0.250...
- 040: dt: 0.2500, sse=4756649.5, rms=2.849 (0.000%)
- 041: dt: 0.2500, sse=4882015.5, rms=2.749 (0.000%)
- rms = 2.72, time step reduction 2 of 3 to 0.125...
- 042: dt: 0.2500, sse=4955121.5, rms=2.717 (0.000%)
- 043: dt: 0.1250, sse=4865108.5, rms=2.585 (0.000%)
- rms = 2.57, time step reduction 3 of 3 to 0.062...
- 044: dt: 0.1250, sse=4866558.0, rms=2.568 (0.000%)
- positioning took 0.7 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.curv.pial
- writing smoothed area to lh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.area.pial
- vertex spacing 1.03 +- 0.43 (0.11-->8.33) (max @ vno 102151 --> 101354)
- face area 0.42 +- 0.31 (0.00-->6.35)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 128814 vertices processed
- 25000 of 128814 vertices processed
- 50000 of 128814 vertices processed
- 75000 of 128814 vertices processed
- 100000 of 128814 vertices processed
- 125000 of 128814 vertices processed
- 0 of 128814 vertices processed
- 25000 of 128814 vertices processed
- 50000 of 128814 vertices processed
- 75000 of 128814 vertices processed
- 100000 of 128814 vertices processed
- 125000 of 128814 vertices processed
- thickness calculation complete, 344:1057 truncations.
- 29578 vertices at 0 distance
- 87298 vertices at 1 distance
- 83046 vertices at 2 distance
- 34244 vertices at 3 distance
- 9081 vertices at 4 distance
- 2194 vertices at 5 distance
- 679 vertices at 6 distance
- 224 vertices at 7 distance
- 59 vertices at 8 distance
- 32 vertices at 9 distance
- 39 vertices at 10 distance
- 30 vertices at 11 distance
- 16 vertices at 12 distance
- 20 vertices at 13 distance
- 12 vertices at 14 distance
- 7 vertices at 15 distance
- 17 vertices at 16 distance
- 14 vertices at 17 distance
- 6 vertices at 18 distance
- 4 vertices at 19 distance
- 16 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.thickness
- positioning took 13.9 minutes
- #--------------------------------------------
- #@# Surf Volume lh Thu Aug 8 19:19:44 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf
- mris_calc -o lh.area.mid lh.area add lh.area.pial
- Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o lh.area.mid lh.area.mid div 2
- Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o lh.volume lh.area.mid mul lh.thickness
- Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ]
- #-----------------------------------------
- #@# WM/GM Contrast lh Thu Aug 8 19:19:45 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts
- pctsurfcon --s sub003 --lh-only
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts/pctsurfcon.log
- Thu Aug 8 19:19:45 CEST 2013
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/tmp.pctsurfcon.1521/lh.wm.mgh --regheader sub003 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/label/lh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 = 99517
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/label/lh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/tmp.pctsurfcon.1521/lh.wm.mgh
- Dim: 128814 1 1
- mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/tmp.pctsurfcon.1521/lh.gm.mgh --projfrac 0.3 --regheader sub003 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/label/lh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.white
- Done reading source surface
- Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 = 114982
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/label/lh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/tmp.pctsurfcon.1521/lh.gm.mgh
- Dim: 128814 1 1
- mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/tmp.pctsurfcon.1521/lh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/tmp.pctsurfcon.1521/lh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/surf/lh.w-g.pct.mgh
- mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.w-g.pct.mgh --annot sub003 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/surf/lh.w-g.pct.mgh --annot sub003 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/surf/lh.w-g.pct.mgh
- Vertex Area is 0.668935 mm^3
- Generating list of segmentation ids
- Found 36 segmentations
- Computing statistics for each segmentation
- 0 1000 unknown 0 0.000
- 1 1001 bankssts 1313 912.526
- 2 1002 caudalanteriorcingulate 1207 797.752
- 3 1003 caudalmiddlefrontal 3048 2076.126
- 4 1004 corpuscallosum 0 0.000
- 5 1005 cuneus 2385 1534.899
- 6 1006 entorhinal 642 439.147
- 7 1007 fusiform 4680 3118.398
- 8 1008 inferiorparietal 8019 5422.172
- 9 1009 inferiortemporal 4652 3183.842
- 10 1010 isthmuscingulate 1397 920.880
- 11 1011 lateraloccipital 7688 4947.458
- 12 1012 lateralorbitofrontal 3472 2351.095
- 13 1013 lingual 4989 3368.609
- 14 1014 medialorbitofrontal 2458 1637.896
- 15 1015 middletemporal 4026 2802.262
- 16 1016 parahippocampal 943 632.615
- 17 1017 paracentral 1806 1199.072
- 18 1018 parsopercularis 2289 1564.207
- 19 1019 parsorbitalis 861 574.945
- 20 1020 parstriangularis 1942 1297.889
- 21 1021 pericalcarine 2546 1710.734
- 22 1022 postcentral 5594 3713.786
- 23 1023 posteriorcingulate 1802 1215.047
- 24 1024 precentral 6059 4011.424
- 25 1025 precuneus 5795 3903.047
- 26 1026 rostralanteriorcingulate 1151 752.602
- 27 1027 rostralmiddlefrontal 7838 5340.084
- 28 1028 superiorfrontal 9528 6568.189
- 29 1029 superiorparietal 8197 5422.492
- 30 1030 superiortemporal 4968 3300.387
- 31 1031 supramarginal 5392 3678.488
- 32 1032 frontalpole 336 229.860
- 33 1033 temporalpole 610 421.463
- 34 1034 transversetemporal 701 449.925
- 35 1035 insula 3025 1921.944
- Reporting on 34 segmentations
- mri_segstats done
- Cleaning up
- #-----------------------------------------
- #@# Parcellation Stats lh Thu Aug 8 19:19:58 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 sub003 lh white
- computing statistics for each annotation in ../label/lh.aparc.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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
- 1313 913 2183 2.297 0.409 0.121 0.031 13 1.6 bankssts
- 1207 798 2356 2.720 0.709 0.175 0.068 31 3.4 caudalanteriorcingulate
- 3048 2076 5891 2.507 0.452 0.133 0.038 40 4.8 caudalmiddlefrontal
- 2385 1535 3593 1.999 0.562 0.164 0.071 48 7.5 cuneus
- 642 439 1862 2.952 0.902 0.159 0.068 18 2.0 entorhinal
- 4680 3118 10090 2.782 0.570 0.159 0.076 123 13.0 fusiform
- 8019 5422 15214 2.473 0.473 0.143 0.046 132 15.2 inferiorparietal
- 4652 3184 9405 2.452 0.618 0.144 0.060 94 10.5 inferiortemporal
- 1397 921 2659 2.629 0.845 0.161 0.066 32 3.1 isthmuscingulate
- 7688 4947 11816 2.150 0.442 0.155 0.059 143 18.1 lateraloccipital
- 3472 2351 6651 2.490 0.603 0.164 0.078 103 10.5 lateralorbitofrontal
- 4989 3369 8147 2.189 0.563 0.170 0.075 106 15.0 lingual
- 2458 1638 4697 2.393 0.745 0.162 0.091 83 8.7 medialorbitofrontal
- 4026 2802 9497 2.683 0.601 0.153 0.055 87 8.2 middletemporal
- 943 633 2299 3.027 0.681 0.129 0.052 13 2.2 parahippocampal
- 1806 1199 3117 2.288 0.520 0.118 0.029 18 2.2 paracentral
- 2289 1564 4977 2.676 0.504 0.131 0.041 34 3.7 parsopercularis
- 861 575 1979 2.662 0.571 0.158 0.055 17 1.7 parsorbitalis
- 1942 1298 3766 2.470 0.441 0.152 0.056 42 4.0 parstriangularis
- 2546 1711 3160 1.914 0.471 0.136 0.058 34 4.6 pericalcarine
- 5594 3714 8680 2.060 0.558 0.136 0.048 91 10.3 postcentral
- 1802 1215 3319 2.474 0.639 0.168 0.051 42 3.9 posteriorcingulate
- 6059 4011 11803 2.567 0.517 0.121 0.032 63 8.1 precentral
- 5795 3903 10220 2.342 0.455 0.159 0.065 122 14.2 precuneus
- 1151 753 2653 2.890 0.797 0.158 0.066 27 2.8 rostralanteriorcingulate
- 7838 5340 14208 2.277 0.542 0.171 0.083 222 22.6 rostralmiddlefrontal
- 9528 6568 21005 2.659 0.551 0.147 0.055 182 20.6 superiorfrontal
- 8197 5422 12474 2.077 0.407 0.135 0.043 130 14.5 superiorparietal
- 4968 3300 10547 2.647 0.630 0.144 0.060 190 14.4 superiortemporal
- 5392 3678 10196 2.409 0.472 0.149 0.049 97 10.5 supramarginal
- 336 230 693 2.333 0.480 0.255 0.158 18 2.4 frontalpole
- 610 421 2332 3.637 0.960 0.182 0.084 15 2.3 temporalpole
- 701 450 1347 2.485 0.322 0.113 0.042 6 1.1 transversetemporal
- 3025 1922 6705 3.230 0.903 0.119 0.066 60 7.5 insula
- #-----------------------------------------
- #@# Cortical Parc 2 lh Thu Aug 8 19:20:16 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub003 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...
- 34 labels changed using aseg
- relabeling using gibbs priors...
- 000: 9137 changed, 128814 examined...
- 001: 2210 changed, 34529 examined...
- 002: 682 changed, 11259 examined...
- 003: 321 changed, 3790 examined...
- 004: 164 changed, 1763 examined...
- 005: 74 changed, 913 examined...
- 006: 32 changed, 409 examined...
- 007: 14 changed, 175 examined...
- 008: 8 changed, 85 examined...
- 009: 4 changed, 33 examined...
- 010: 3 changed, 24 examined...
- 011: 1 changed, 16 examined...
- 012: 0 changed, 6 examined...
- 8 labels changed using aseg
- 000: 275 total segments, 194 labels (2471 vertices) changed
- 001: 99 total segments, 19 labels (44 vertices) changed
- 002: 80 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 109 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 698 vertices marked for relabeling...
- 698 labels changed in reclassification.
- writing output to ../label/lh.aparc.a2009s.annot...
- classification took 1 minutes and 8 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 2 lh Thu Aug 8 19:21:24 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 sub003 lh white
- computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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
- 1283 876 2219 2.152 0.591 0.174 0.081 33 3.8 G_and_S_frontomargin
- 1722 1148 3448 2.506 0.479 0.167 0.060 35 3.9 G_and_S_occipital_inf
- 1509 973 2744 2.334 0.524 0.126 0.033 19 2.1 G_and_S_paracentral
- 1323 902 2836 2.655 0.483 0.154 0.056 25 2.9 G_and_S_subcentral
- 851 591 1821 2.395 0.469 0.227 0.112 38 3.9 G_and_S_transv_frontopol
- 2248 1539 4781 2.708 0.695 0.157 0.066 49 5.8 G_and_S_cingul-Ant
- 1733 1184 3348 2.617 0.583 0.148 0.062 28 3.3 G_and_S_cingul-Mid-Ant
- 1375 942 2573 2.495 0.478 0.145 0.043 23 2.5 G_and_S_cingul-Mid-Post
- 490 325 1204 2.878 0.561 0.217 0.094 19 1.8 G_cingul-Post-dorsal
- 361 221 760 2.874 0.993 0.166 0.079 11 0.9 G_cingul-Post-ventral
- 2163 1400 3365 1.931 0.556 0.166 0.084 47 7.1 G_cuneus
- 1256 882 3590 2.927 0.399 0.170 0.060 34 3.1 G_front_inf-Opercular
- 291 198 696 2.670 0.553 0.228 0.133 16 1.1 G_front_inf-Orbital
- 1102 715 2524 2.643 0.433 0.137 0.041 19 1.9 G_front_inf-Triangul
- 4358 3011 9617 2.498 0.525 0.176 0.093 144 13.3 G_front_middle
- 6152 4245 15510 2.809 0.557 0.164 0.062 148 15.6 G_front_sup
- 439 267 1093 3.545 0.670 0.125 0.082 9 1.1 G_Ins_lg_and_S_cent_ins
- 630 369 2126 4.092 0.730 0.129 0.129 28 3.5 G_insular_short
- 2194 1443 4532 2.504 0.465 0.174 0.067 53 5.9 G_occipital_middle
- 1622 1062 2501 2.019 0.455 0.150 0.047 28 3.2 G_occipital_sup
- 1478 921 3679 3.063 0.480 0.173 0.077 45 4.7 G_oc-temp_lat-fusifor
- 3359 2224 5807 2.166 0.572 0.184 0.084 81 11.5 G_oc-temp_med-Lingual
- 1133 772 3384 3.154 0.821 0.149 0.064 22 3.0 G_oc-temp_med-Parahip
- 2252 1516 5406 2.686 0.646 0.181 0.094 90 8.1 G_orbital
- 2624 1741 5368 2.497 0.421 0.143 0.043 47 4.8 G_pariet_inf-Angular
- 3002 2049 6580 2.589 0.435 0.166 0.061 69 6.9 G_pariet_inf-Supramar
- 2955 1982 5554 2.214 0.434 0.153 0.053 72 6.7 G_parietal_sup
- 1995 1278 3380 2.118 0.513 0.148 0.066 45 4.6 G_postcentral
- 2371 1525 5689 2.804 0.435 0.136 0.039 34 3.9 G_precentral
- 2924 1947 6143 2.458 0.493 0.183 0.086 88 9.1 G_precuneus
- 929 642 2188 2.421 0.705 0.226 0.161 64 6.3 G_rectus
- 244 143 402 2.791 0.501 0.089 0.043 2 0.4 G_subcallosal
- 552 336 1149 2.582 0.284 0.119 0.047 6 0.9 G_temp_sup-G_T_transv
- 1960 1319 5560 2.910 0.652 0.193 0.096 166 9.0 G_temp_sup-Lateral
- 451 335 1562 3.703 0.805 0.160 0.060 9 1.2 G_temp_sup-Plan_polar
- 730 510 1425 2.398 0.445 0.109 0.027 6 0.8 G_temp_sup-Plan_tempo
- 2628 1770 6096 2.556 0.649 0.162 0.074 76 8.1 G_temporal_inf
- 2437 1725 6895 2.882 0.581 0.167 0.061 64 5.6 G_temporal_middle
- 375 255 582 2.213 0.353 0.157 0.055 7 0.9 Lat_Fis-ant-Horizont
- 329 221 522 2.481 0.609 0.104 0.027 2 0.3 Lat_Fis-ant-Vertical
- 1407 930 1778 2.216 0.408 0.123 0.033 12 2.0 Lat_Fis-post
- 2513 1537 3348 1.939 0.463 0.163 0.080 62 7.9 Pole_occipital
- 1811 1271 5452 2.993 0.865 0.189 0.117 72 8.0 Pole_temporal
- 2997 2058 3919 2.047 0.534 0.133 0.051 39 5.4 S_calcarine
- 2701 1827 3323 1.983 0.558 0.101 0.023 14 2.7 S_central
- 1011 676 1412 2.195 0.459 0.109 0.026 7 1.0 S_cingul-Marginalis
- 460 308 818 2.880 0.515 0.111 0.029 3 0.6 S_circular_insula_ant
- 1341 874 2267 2.794 0.720 0.087 0.027 10 1.2 S_circular_insula_inf
- 1696 1139 2570 2.535 0.461 0.116 0.030 13 2.1 S_circular_insula_sup
- 1133 779 2064 2.510 0.570 0.133 0.074 19 2.0 S_collat_transv_ant
- 565 375 751 2.163 0.376 0.124 0.035 5 0.8 S_collat_transv_post
- 2113 1422 3247 2.208 0.462 0.139 0.041 29 3.5 S_front_inf
- 1138 763 1562 2.004 0.444 0.152 0.061 20 2.5 S_front_middle
- 2165 1482 3353 2.342 0.333 0.099 0.023 12 2.1 S_front_sup
- 248 164 465 2.358 0.353 0.099 0.034 3 0.4 S_interm_prim-Jensen
- 3488 2317 4596 2.069 0.377 0.118 0.031 30 4.5 S_intrapariet_and_P_trans
- 1651 1092 2163 2.116 0.360 0.146 0.047 21 3.1 S_oc_middle_and_Lunatus
- 1407 935 1967 2.150 0.405 0.116 0.030 12 1.7 S_oc_sup_and_transversal
- 687 460 881 2.291 0.376 0.127 0.042 6 1.1 S_occipital_ant
- 972 668 1490 2.451 0.393 0.122 0.031 8 1.3 S_oc-temp_lat
- 2177 1494 3517 2.540 0.440 0.130 0.045 25 3.6 S_oc-temp_med_and_Lingual
- 480 318 708 2.295 0.380 0.150 0.055 7 1.1 S_orbital_lateral
- 752 507 1087 2.019 0.805 0.109 0.048 8 0.8 S_orbital_med-olfact
- 1349 902 2261 2.367 0.486 0.155 0.065 25 3.2 S_orbital-H_Shaped
- 2204 1481 3186 2.254 0.414 0.141 0.047 31 4.3 S_parieto_occipital
- 1187 739 1250 2.079 0.860 0.148 0.043 21 2.0 S_pericallosal
- 2641 1773 3454 1.957 0.395 0.131 0.038 31 3.8 S_postcentral
- 1540 1029 2435 2.458 0.387 0.108 0.027 12 1.7 S_precentral-inf-part
- 806 566 1097 2.108 0.363 0.099 0.018 4 0.7 S_precentral-sup-part
- 664 433 1363 2.780 0.659 0.175 0.084 19 2.2 S_suborbital
- 1078 741 1690 2.262 0.438 0.145 0.053 15 2.1 S_subparietal
- 1406 951 1822 2.128 0.436 0.123 0.033 14 2.0 S_temporal_inf
- 5364 3661 9133 2.396 0.469 0.129 0.041 68 9.7 S_temporal_sup
- 377 244 453 2.096 0.265 0.096 0.022 2 0.4 S_temporal_transverse
- #-----------------------------------------
- #@# Cortical Parc 3 lh Thu Aug 8 19:21:43 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub003 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...
- 917 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2665 changed, 128814 examined...
- 001: 605 changed, 11425 examined...
- 002: 169 changed, 3300 examined...
- 003: 63 changed, 995 examined...
- 004: 30 changed, 385 examined...
- 005: 8 changed, 158 examined...
- 006: 4 changed, 45 examined...
- 007: 3 changed, 25 examined...
- 008: 1 changed, 17 examined...
- 009: 1 changed, 9 examined...
- 010: 1 changed, 7 examined...
- 011: 1 changed, 7 examined...
- 012: 2 changed, 6 examined...
- 013: 2 changed, 12 examined...
- 014: 2 changed, 12 examined...
- 015: 2 changed, 15 examined...
- 016: 4 changed, 13 examined...
- 017: 5 changed, 18 examined...
- 018: 5 changed, 23 examined...
- 019: 2 changed, 28 examined...
- 020: 5 changed, 13 examined...
- 021: 3 changed, 21 examined...
- 022: 2 changed, 17 examined...
- 023: 0 changed, 14 examined...
- 124 labels changed using aseg
- 000: 61 total segments, 28 labels (160 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...
- 504 vertices marked for relabeling...
- 504 labels changed in reclassification.
- writing output to ../label/lh.aparc.DKTatlas40.annot...
- classification took 1 minutes and 0 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 3 lh Thu Aug 8 19:22:42 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 sub003 lh white
- computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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
- 1727 1161 3341 2.648 0.680 0.168 0.076 39 4.3 caudalanteriorcingulate
- 3077 2087 5894 2.502 0.452 0.132 0.038 40 4.9 caudalmiddlefrontal
- 3280 2135 4940 2.042 0.519 0.155 0.063 59 8.8 cuneus
- 570 384 1513 2.835 0.902 0.132 0.038 5 0.9 entorhinal
- 4154 2757 8674 2.771 0.549 0.149 0.058 86 9.4 fusiform
- 7518 5070 14114 2.461 0.468 0.141 0.044 121 13.7 inferiorparietal
- 4907 3361 10333 2.491 0.636 0.155 0.080 134 14.3 inferiortemporal
- 1344 883 2577 2.638 0.831 0.163 0.067 32 3.0 isthmuscingulate
- 7882 5068 12119 2.145 0.459 0.156 0.060 149 18.6 lateraloccipital
- 3841 2598 7497 2.456 0.657 0.173 0.085 128 12.8 lateralorbitofrontal
- 5004 3382 8171 2.183 0.557 0.169 0.074 104 14.6 lingual
- 2174 1442 4253 2.402 0.753 0.173 0.105 84 8.9 medialorbitofrontal
- 5701 3978 12799 2.618 0.597 0.149 0.052 113 11.3 middletemporal
- 961 642 2334 3.053 0.691 0.132 0.060 16 2.7 parahippocampal
- 2079 1381 3637 2.318 0.530 0.118 0.029 20 2.5 paracentral
- 1976 1353 4389 2.740 0.466 0.131 0.042 30 3.3 parsopercularis
- 933 637 1915 2.504 0.538 0.152 0.065 22 2.0 parsorbitalis
- 2421 1601 4543 2.453 0.444 0.146 0.047 42 4.5 parstriangularis
- 2537 1698 3144 1.917 0.471 0.136 0.058 34 4.7 pericalcarine
- 6427 4267 10016 2.085 0.549 0.137 0.048 105 12.2 postcentral
- 2026 1358 3591 2.447 0.621 0.160 0.049 43 4.1 posteriorcingulate
- 6105 4038 11845 2.575 0.519 0.121 0.032 64 8.2 precentral
- 5624 3808 10117 2.333 0.464 0.161 0.067 122 14.2 precuneus
- 1433 948 3185 2.857 0.765 0.154 0.063 31 3.3 rostralanteriorcingulate
- 5558 3774 10227 2.287 0.558 0.160 0.071 137 14.2 rostralmiddlefrontal
- 10530 7277 22903 2.602 0.559 0.159 0.066 244 26.3 superiorfrontal
- 6501 4295 9810 2.079 0.398 0.133 0.042 105 11.0 superiorparietal
- 6515 4367 14464 2.716 0.736 0.148 0.061 220 18.4 superiortemporal
- 5205 3554 9820 2.409 0.476 0.150 0.050 92 10.1 supramarginal
- 697 449 1342 2.485 0.320 0.114 0.042 6 1.1 transversetemporal
- 2652 1670 6037 3.282 0.889 0.112 0.064 51 6.4 insula
- #--------------------------------------------
- #@# Tessellate rh Thu Aug 8 19:22:59 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts
- mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz
- Iteration Number : 1
- pass 1 (xy+): 3 found - 3 modified | TOTAL: 3
- pass 2 (xy+): 0 found - 3 modified | TOTAL: 3
- pass 1 (xy-): 1 found - 1 modified | TOTAL: 4
- pass 2 (xy-): 0 found - 1 modified | TOTAL: 4
- pass 1 (yz+): 1 found - 1 modified | TOTAL: 5
- pass 2 (yz+): 0 found - 1 modified | TOTAL: 5
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 5
- pass 1 (xz+): 1 found - 1 modified | TOTAL: 6
- pass 2 (xz+): 0 found - 1 modified | TOTAL: 6
- pass 1 (xz-): 1 found - 1 modified | TOTAL: 7
- pass 2 (xz-): 0 found - 1 modified | TOTAL: 7
- Iteration Number : 1
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 1
- pass 1 (++): 1 found - 1 modified | TOTAL: 1
- pass 2 (++): 0 found - 1 modified | TOTAL: 1
- pass 1 (+-): 0 found - 0 modified | TOTAL: 1
- pass 1 (--): 1 found - 1 modified | TOTAL: 2
- pass 2 (--): 0 found - 1 modified | TOTAL: 2
- pass 1 (-+): 0 found - 0 modified | TOTAL: 2
- Iteration Number : 2
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Total Number of Modified Voxels = 9 (out of 216437: 0.004158)
- 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: 1381 vertices, 1487 faces
- slice 60: 6522 vertices, 6713 faces
- slice 70: 14552 vertices, 14911 faces
- slice 80: 24424 vertices, 24790 faces
- slice 90: 34974 vertices, 35317 faces
- slice 100: 45064 vertices, 45394 faces
- slice 110: 56376 vertices, 56740 faces
- slice 120: 67383 vertices, 67766 faces
- slice 130: 78824 vertices, 79204 faces
- slice 140: 89653 vertices, 90034 faces
- slice 150: 99678 vertices, 99995 faces
- slice 160: 107250 vertices, 107518 faces
- slice 170: 114617 vertices, 114868 faces
- slice 180: 120756 vertices, 120997 faces
- slice 190: 125574 vertices, 125731 faces
- slice 200: 128227 vertices, 128278 faces
- slice 210: 128276 vertices, 128300 faces
- slice 220: 128276 vertices, 128300 faces
- slice 230: 128276 vertices, 128300 faces
- slice 240: 128276 vertices, 128300 faces
- slice 250: 128276 vertices, 128300 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...
- 128276 voxel in cpt #1: X=-24 [v=128276,e=384900,f=256600] located at (28.519100, -10.943598, 38.935242)
- For the whole surface: X=-24 [v=128276,e=384900,f=256600]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Smooth1 rh Thu Aug 8 19:23:07 CEST 2013
- mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts
- setting seed for random number generator to 1234
- smoothing surface tessellation for 10 iterations...
- smoothing complete - recomputing first and second fundamental forms...
- #--------------------------------------------
- #@# Inflation1 rh Thu Aug 8 19:23:11 CEST 2013
- mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts
- avg radius = 44.3 mm, total surface area = 66756 mm^2
- writing inflated surface to ../surf/rh.inflated.nofix
- inflation took 0.5 minutes
- Not saving sulc
-
step 000: RMS=0.103 (target=0.015)
step 005: RMS=0.075 (target=0.015)
step 010: RMS=0.054 (target=0.015)
step 015: RMS=0.045 (target=0.015)
step 020: RMS=0.039 (target=0.015)
step 025: RMS=0.034 (target=0.015)
step 030: RMS=0.031 (target=0.015)
step 035: RMS=0.028 (target=0.015)
step 040: RMS=0.026 (target=0.015)
step 045: RMS=0.024 (target=0.015)
step 050: RMS=0.023 (target=0.015)
step 055: RMS=0.023 (target=0.015)
step 060: RMS=0.022 (target=0.015)
- inflation complete.
- Not saving sulc
- #--------------------------------------------
- #@# QSphere rh Thu Aug 8 19:23:43 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 1.01 +- 0.59 (0.00-->7.25) (max @ vno 46638 --> 47748)
- face area 0.03 +- 0.03 (-0.03-->0.82)
- scaling brain by 0.318...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=176.937, avgs=0
- 005/300: dt: 0.9000, rms radial error=176.678, avgs=0
- 010/300: dt: 0.9000, rms radial error=176.121, avgs=0
- 015/300: dt: 0.9000, rms radial error=175.390, avgs=0
- 020/300: dt: 0.9000, rms radial error=174.559, avgs=0
- 025/300: dt: 0.9000, rms radial error=173.669, avgs=0
- 030/300: dt: 0.9000, rms radial error=172.747, avgs=0
- 035/300: dt: 0.9000, rms radial error=171.808, avgs=0
- 040/300: dt: 0.9000, rms radial error=170.864, avgs=0
- 045/300: dt: 0.9000, rms radial error=169.916, avgs=0
- 050/300: dt: 0.9000, rms radial error=168.969, avgs=0
- 055/300: dt: 0.9000, rms radial error=168.025, avgs=0
- 060/300: dt: 0.9000, rms radial error=167.083, avgs=0
- 065/300: dt: 0.9000, rms radial error=166.146, avgs=0
- 070/300: dt: 0.9000, rms radial error=165.214, avgs=0
- 075/300: dt: 0.9000, rms radial error=164.286, avgs=0
- 080/300: dt: 0.9000, rms radial error=163.362, avgs=0
- 085/300: dt: 0.9000, rms radial error=162.444, avgs=0
- 090/300: dt: 0.9000, rms radial error=161.530, avgs=0
- 095/300: dt: 0.9000, rms radial error=160.622, avgs=0
- 100/300: dt: 0.9000, rms radial error=159.718, avgs=0
- 105/300: dt: 0.9000, rms radial error=158.820, avgs=0
- 110/300: dt: 0.9000, rms radial error=157.926, avgs=0
- 115/300: dt: 0.9000, rms radial error=157.037, avgs=0
- 120/300: dt: 0.9000, rms radial error=156.154, avgs=0
- 125/300: dt: 0.9000, rms radial error=155.275, avgs=0
- 130/300: dt: 0.9000, rms radial error=154.400, avgs=0
- 135/300: dt: 0.9000, rms radial error=153.531, avgs=0
- 140/300: dt: 0.9000, rms radial error=152.666, avgs=0
- 145/300: dt: 0.9000, rms radial error=151.807, avgs=0
- 150/300: dt: 0.9000, rms radial error=150.951, avgs=0
- 155/300: dt: 0.9000, rms radial error=150.101, avgs=0
- 160/300: dt: 0.9000, rms radial error=149.255, avgs=0
- 165/300: dt: 0.9000, rms radial error=148.414, avgs=0
- 170/300: dt: 0.9000, rms radial error=147.578, avgs=0
- 175/300: dt: 0.9000, rms radial error=146.746, avgs=0
- 180/300: dt: 0.9000, rms radial error=145.920, avgs=0
- 185/300: dt: 0.9000, rms radial error=145.097, avgs=0
- 190/300: dt: 0.9000, rms radial error=144.280, avgs=0
- 195/300: dt: 0.9000, rms radial error=143.467, avgs=0
- 200/300: dt: 0.9000, rms radial error=142.658, avgs=0
- 205/300: dt: 0.9000, rms radial error=141.854, avgs=0
- 210/300: dt: 0.9000, rms radial error=141.055, avgs=0
- 215/300: dt: 0.9000, rms radial error=140.259, avgs=0
- 220/300: dt: 0.9000, rms radial error=139.469, avgs=0
- 225/300: dt: 0.9000, rms radial error=138.683, avgs=0
- 230/300: dt: 0.9000, rms radial error=137.901, avgs=0
- 235/300: dt: 0.9000, rms radial error=137.123, avgs=0
- 240/300: dt: 0.9000, rms radial error=136.350, avgs=0
- 245/300: dt: 0.9000, rms radial error=135.581, avgs=0
- 250/300: dt: 0.9000, rms radial error=134.817, avgs=0
- 255/300: dt: 0.9000, rms radial error=134.056, avgs=0
- 260/300: dt: 0.9000, rms radial error=133.300, avgs=0
- 265/300: dt: 0.9000, rms radial error=132.549, avgs=0
- 270/300: dt: 0.9000, rms radial error=131.801, avgs=0
- 275/300: dt: 0.9000, rms radial error=131.057, avgs=0
- 280/300: dt: 0.9000, rms radial error=130.318, avgs=0
- 285/300: dt: 0.9000, rms radial error=129.583, avgs=0
- 290/300: dt: 0.9000, rms radial error=128.852, avgs=0
- 295/300: dt: 0.9000, rms radial error=128.125, avgs=0
- 300/300: dt: 0.9000, rms radial error=127.402, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 14934.66
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00015
- epoch 2 (K=40.0), pass 1, starting sse = 2467.32
- 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 = 252.81
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.15/13 = 0.01180
- epoch 4 (K=640.0), pass 1, starting sse = 12.93
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.36/27 = 0.01348
- final writing spherical brain to ../surf/rh.qsphere.nofix
- spherical transformation took 0.09 hours
- distance error %100000.00
- #--------------------------------------------
- #@# Fix Topology rh Thu Aug 8 19:29:11 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/sub003/scripts
- mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub003 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=-24 (nv=128276, nf=256600, ne=384900, g=13)
- using quasi-homeomorphic spherical map to tessellate cortical surface...
- Correction of the Topology
- Finding true center and radius of Spherical Surface...done
- Surface centered at (0,0,0) with radius 100.0 in 9 iterations
- marking ambiguous vertices...
- 1864 ambiguous faces found in tessellation
- segmenting defects...
- 23 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- -merging segment 3 into 2
- -merging segment 10 into 9
- -merging segment 21 into 20
- 20 defects to be corrected
- 0 vertices coincident
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -9.9022 (-4.9511)
- -vertex loglikelihood: -6.7965 (-3.3982)
- -normal dot loglikelihood: -3.6210 (-3.6210)
- -quad curv loglikelihood: -6.5603 (-3.2802)
- Total Loglikelihood : -26.8800
- CORRECTING DEFECT 0 (vertices=18, convex hull=26)
- After retessellation of defect 0, euler #=-20 (127094,380724,253610) : difference with theory (-17) = 3
- CORRECTING DEFECT 1 (vertices=127, convex hull=118)
- After retessellation of defect 1, euler #=-19 (127134,380894,253741) : difference with theory (-16) = 3
- CORRECTING DEFECT 2 (vertices=97, convex hull=88)
- After retessellation of defect 2, euler #=-17 (127155,380994,253822) : difference with theory (-15) = 2
- CORRECTING DEFECT 3 (vertices=20, convex hull=58)
- After retessellation of defect 3, euler #=-16 (127168,381054,253870) : difference with theory (-14) = 2
- CORRECTING DEFECT 4 (vertices=6, convex hull=27)
- After retessellation of defect 4, euler #=-15 (127169,381065,253881) : difference with theory (-13) = 2
- CORRECTING DEFECT 5 (vertices=26, convex hull=35)
- After retessellation of defect 5, euler #=-14 (127173,381095,253908) : difference with theory (-12) = 2
- CORRECTING DEFECT 6 (vertices=41, convex hull=68)
- After retessellation of defect 6, euler #=-13 (127191,381175,253971) : difference with theory (-11) = 2
- CORRECTING DEFECT 7 (vertices=72, convex hull=73)
- After retessellation of defect 7, euler #=-12 (127221,381297,254064) : difference with theory (-10) = 2
- CORRECTING DEFECT 8 (vertices=32, convex hull=67)
- After retessellation of defect 8, euler #=-10 (127227,381345,254108) : difference with theory (-9) = 1
- CORRECTING DEFECT 9 (vertices=5, convex hull=15)
- After retessellation of defect 9, euler #=-9 (127228,381352,254115) : difference with theory (-8) = 1
- CORRECTING DEFECT 10 (vertices=11, convex hull=29)
- After retessellation of defect 10, euler #=-8 (127232,381373,254133) : difference with theory (-7) = 1
- CORRECTING DEFECT 11 (vertices=39, convex hull=30)
- After retessellation of defect 11, euler #=-7 (127237,381399,254155) : difference with theory (-6) = 1
- CORRECTING DEFECT 12 (vertices=12, convex hull=42)
- After retessellation of defect 12, euler #=-6 (127238,381415,254171) : difference with theory (-5) = 1
- CORRECTING DEFECT 13 (vertices=85, convex hull=99)
- After retessellation of defect 13, euler #=-5 (127275,381567,254287) : difference with theory (-4) = 1
- CORRECTING DEFECT 14 (vertices=203, convex hull=71)
- After retessellation of defect 14, euler #=-4 (127294,381657,254359) : difference with theory (-3) = 1
- CORRECTING DEFECT 15 (vertices=14, convex hull=16)
- After retessellation of defect 15, euler #=-3 (127296,381666,254367) : difference with theory (-2) = 1
- CORRECTING DEFECT 16 (vertices=187, convex hull=185)
- After retessellation of defect 16, euler #=-2 (127375,381993,254616) : difference with theory (-1) = 1
- CORRECTING DEFECT 17 (vertices=50, convex hull=91)
- After retessellation of defect 17, euler #=-1 (127396,382097,254700) : difference with theory (0) = 1
- CORRECTING DEFECT 18 (vertices=78, convex hull=114)
- After retessellation of defect 18, euler #=1 (127430,382250,254821) : difference with theory (1) = 0
- CORRECTING DEFECT 19 (vertices=61, convex hull=87)
- After retessellation of defect 19, euler #=2 (127449,382341,254894) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.88 +- 0.22 (0.05-->9.06) (max @ vno 41533 --> 51218)
- face area 0.00 +- 0.00 (0.00-->0.00)
- performing soap bubble on retessellated vertices for 0 iterations...
- vertex spacing 0.88 +- 0.22 (0.05-->9.06) (max @ vno 41533 --> 51218)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 75 mutations (35.9%), 134 crossovers (64.1%), 39 vertices were eliminated
- building final representation...
- 827 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=127449, nf=254894, ne=382341, g=0)
- writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 12.6 minutes
- 0 defective edges
- removing intersecting faces
- 000: 115 intersecting
- 001: 4 intersecting
- mris_euler_number ../surf/rh.orig
- euler # = v-e+f = 2g-2: 127449 - 382341 + 254894 = 2 --> 0 holes
- F =2V-4: 254894 = 254898-4 (0)
- 2E=3F: 764682 = 764682 (0)
- total defect index = 0
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts
- mris_remove_intersection ../surf/rh.orig ../surf/rh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 15 intersecting
- writing corrected surface to ../surf/rh.orig
- rm ../surf/rh.inflated
- #--------------------------------------------
- #@# Make White Surf rh Thu Aug 8 19:41:56 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts
- mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub003 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/sub003/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/wm.mgz...
- 14678 bright wm thresholded.
- 302 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.orig...
- computing class statistics...
- border white: 229356 voxels (1.37%)
- border gray 266114 voxels (1.59%)
- WM (92.0): 92.8 +- 10.5 [70.0 --> 110.0]
- GM (74.0) : 72.0 +- 13.3 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 42.7 (was 70)
- setting MAX_BORDER_WHITE to 115.5 (was 105)
- setting MIN_BORDER_WHITE to 56.0 (was 85)
- setting MAX_CSF to 29.3 (was 40)
- setting MAX_GRAY to 94.5 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 49.3 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 16.0 (was 40)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.81 +- 0.22 (0.02-->3.76) (max @ vno 41533 --> 51218)
- face area 0.28 +- 0.12 (0.00-->2.00)
- mean absolute distance = 0.65 +- 0.74
- 4220 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=105, GM=56
- mean inside = 92.5, mean outside = 66.6
- smoothing surface for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- mean border=70.2, 21 (21) missing vertices, mean dist 0.4 [0.4 (%29.6)->0.8 (%70.4))]
- %73 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.92 +- 0.27 (0.11-->3.96) (max @ vno 96770 --> 127334)
- face area 0.28 +- 0.13 (0.00-->2.35)
- mean absolute distance = 0.30 +- 0.46
- 2092 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=7453672.0, rms=14.48
- 001: dt: 0.5000, sse=7266450.0, rms=10.620 (0.000%)
- 002: dt: 0.5000, sse=7384190.5, rms=8.387 (0.000%)
- 003: dt: 0.5000, sse=7452752.5, rms=6.883 (0.000%)
- 004: dt: 0.5000, sse=7611918.0, rms=5.946 (0.000%)
- 005: dt: 0.5000, sse=7699602.0, rms=5.375 (0.000%)
- 006: dt: 0.5000, sse=7802816.0, rms=5.080 (0.000%)
- 007: dt: 0.5000, sse=7835676.5, rms=4.899 (0.000%)
- 008: dt: 0.5000, sse=7859050.0, rms=4.804 (0.000%)
- 009: dt: 0.5000, sse=7816631.0, rms=4.720 (0.000%)
- rms = 4.68, time step reduction 1 of 3 to 0.250...
- 010: dt: 0.5000, sse=7805371.0, rms=4.679 (0.000%)
- 011: dt: 0.2500, sse=5051549.5, rms=3.290 (0.000%)
- 012: dt: 0.2500, sse=4662302.0, rms=2.825 (0.000%)
- 013: dt: 0.2500, sse=4407076.0, rms=2.735 (0.000%)
- 014: dt: 0.2500, sse=4338599.5, rms=2.650 (0.000%)
- rms = 2.62, time step reduction 2 of 3 to 0.125...
- 015: dt: 0.2500, sse=4240810.5, rms=2.619 (0.000%)
- 016: dt: 0.1250, sse=3950006.2, rms=2.266 (0.000%)
- 017: dt: 0.1250, sse=3901774.2, rms=2.215 (0.000%)
- rms = 2.21, time step reduction 3 of 3 to 0.062...
- 018: dt: 0.1250, sse=3869343.0, rms=2.206 (0.000%)
- positioning took 2.1 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- mean border=75.0, 31 (2) missing vertices, mean dist -0.2 [0.3 (%78.3)->0.2 (%21.7))]
- %82 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.91 +- 0.26 (0.10-->3.84) (max @ vno 96770 --> 127334)
- face area 0.35 +- 0.17 (0.00-->2.85)
- mean absolute distance = 0.21 +- 0.29
- 2502 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4856976.5, rms=6.35
- 019: dt: 0.5000, sse=5106578.0, rms=4.306 (0.000%)
- rms = 4.80, time step reduction 1 of 3 to 0.250...
- 020: dt: 0.2500, sse=4610242.0, rms=3.023 (0.000%)
- 021: dt: 0.2500, sse=4436322.0, rms=2.517 (0.000%)
- 022: dt: 0.2500, sse=4377291.5, rms=2.127 (0.000%)
- rms = 2.14, time step reduction 2 of 3 to 0.125...
- 023: dt: 0.1250, sse=4301798.5, rms=1.991 (0.000%)
- 024: dt: 0.1250, sse=4192281.2, rms=1.793 (0.000%)
- rms = 1.76, time step reduction 3 of 3 to 0.062...
- 025: dt: 0.1250, sse=4143849.2, rms=1.761 (0.000%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 1 vertex label from ripped group
- mean border=78.6, 35 (1) missing vertices, mean dist -0.1 [0.2 (%78.2)->0.2 (%21.8))]
- %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 0.91 +- 0.25 (0.05-->4.00) (max @ vno 96851 --> 95998)
- face area 0.34 +- 0.16 (0.00-->2.73)
- mean absolute distance = 0.15 +- 0.22
- 2514 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4570445.0, rms=4.64
- 026: dt: 0.5000, sse=4903614.0, rms=4.524 (0.000%)
- rms = 4.60, time step reduction 1 of 3 to 0.250...
- 027: dt: 0.2500, sse=4414154.5, rms=2.841 (0.000%)
- 028: dt: 0.2500, sse=4273651.0, rms=2.455 (0.000%)
- 029: dt: 0.2500, sse=4337364.0, rms=2.036 (0.000%)
- rms = 2.14, time step reduction 2 of 3 to 0.125...
- 030: dt: 0.1250, sse=4262148.5, rms=1.834 (0.000%)
- 031: dt: 0.1250, sse=4165483.2, rms=1.547 (0.000%)
- rms = 1.50, time step reduction 3 of 3 to 0.062...
- 032: dt: 0.1250, sse=4131703.0, rms=1.503 (0.000%)
- positioning took 0.9 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 1 vertex label from ripped group
- mean border=79.8, 33 (1) missing vertices, mean dist -0.0 [0.2 (%59.4)->0.2 (%40.6))]
- %92 local maxima, % 2 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- writing white matter surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.white...
- writing smoothed curvature to rh.curv
- 000: dt: 0.0000, sse=4160251.8, rms=1.96
- rms = 3.14, time step reduction 1 of 3 to 0.250...
- 033: dt: 0.2500, sse=4243662.5, rms=1.257 (0.000%)
- 034: dt: 0.2500, sse=4395133.0, rms=1.123 (0.000%)
- rms = 1.13, time step reduction 2 of 3 to 0.125...
- rms = 1.11, time step reduction 3 of 3 to 0.062...
- 035: dt: 0.1250, sse=4400362.0, rms=1.106 (0.000%)
- positioning took 0.5 minutes
- inhibiting deformation at non-cortical midline structures...
- generating cortex label...
- 15 non-cortical segments detected
- only using segment with 2136 vertices
- erasing segment 1 (vno[0] = 74662)
- erasing segment 2 (vno[0] = 80162)
- erasing segment 3 (vno[0] = 81298)
- erasing segment 4 (vno[0] = 81312)
- erasing segment 5 (vno[0] = 85521)
- erasing segment 6 (vno[0] = 88554)
- erasing segment 7 (vno[0] = 88589)
- erasing segment 8 (vno[0] = 88598)
- erasing segment 9 (vno[0] = 88669)
- erasing segment 10 (vno[0] = 89652)
- erasing segment 11 (vno[0] = 89754)
- erasing segment 12 (vno[0] = 98381)
- erasing segment 13 (vno[0] = 98436)
- erasing segment 14 (vno[0] = 99160)
- writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/label/rh.cortex.label...
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.curv
- writing smoothed area to rh.area
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.area
- vertex spacing 0.90 +- 0.26 (0.04-->4.00) (max @ vno 95998 --> 96851)
- face area 0.34 +- 0.16 (0.00-->2.74)
- refinement took 6.7 minutes
- #--------------------------------------------
- #@# Smooth2 rh Thu Aug 8 19:48:36 CEST 2013
- mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts
- smoothing for 3 iterations
- setting seed for random number generator to 1234
- smoothing surface tessellation for 3 iterations...
- smoothing complete - recomputing first and second fundamental forms...
- #--------------------------------------------
- #@# Inflation2 rh Thu Aug 8 19:48:40 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts
- mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated
- avg radius = 44.5 mm, total surface area = 78549 mm^2
- writing inflated surface to ../surf/rh.inflated
- writing sulcal depths to ../surf/rh.sulc
-
step 000: RMS=0.120 (target=0.015)
step 005: RMS=0.082 (target=0.015)
step 010: RMS=0.060 (target=0.015)
step 015: RMS=0.049 (target=0.015)
step 020: RMS=0.040 (target=0.015)
step 025: RMS=0.034 (target=0.015)
step 030: RMS=0.029 (target=0.015)
step 035: RMS=0.024 (target=0.015)
step 040: RMS=0.021 (target=0.015)
step 045: RMS=0.018 (target=0.015)
step 050: RMS=0.017 (target=0.015)
step 055: RMS=0.016 (target=0.015)
step 060: RMS=0.015 (target=0.015)
- inflation complete.
- inflation took 0.6 minutes
- mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated
- normalizing curvature values.
- averaging curvature patterns 5 times.
- sampling 10 neighbors out to a distance of 10 mm
- 134 vertices thresholded to be in k1 ~ [-0.14 1.18], k2 ~ [-0.10 0.07]
- total integrated curvature = 0.603*4pi (7.578) --> 0 handles
- ICI = 1.5, FI = 7.9, variation=142.226
- 96 vertices thresholded to be in [-0.03 0.01]
- writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level
- curvature mean = 0.000, std = 0.001
- 81 vertices thresholded to be in [-0.11 0.22]
- done.
- writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.017, std = 0.021
- done.
- #-----------------------------------------
- #@# Curvature Stats rh Thu Aug 8 19:50:58 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub003 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 [ sub003/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 [ 235 ]
- Gb_filter = 0
- WARN: S lookup min: -0.673576
- WARN: S explicit min: 0.000000 vertex = 120
- #--------------------------------------------
- #@# Sphere rh Thu Aug 8 19:51:03 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 0.292...
- MRISunfold() max_passes = 1 -------
- tol=5.0e-01, sigma=0.0, host=snake, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
- using quadratic fit line minimization
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 1.000000
- desired_rms_height -1.000000
- momentum 0.900000
- nbhd_size 7
- max_nbrs 8
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 1234
- --------------------
- mrisRemoveNegativeArea()
- pass 1: epoch 1 of 3 starting distance error %20.93
- pass 1: epoch 2 of 3 starting distance error %20.88
- unfolding complete - removing small folds...
- starting distance error %20.73
- removing remaining folds...
- final distance error %20.75
- MRISunfold() return, current seed 1234
- writing spherical brain to ../surf/rh.sphere
- spherical transformation took 1.01 hours
- #--------------------------------------------
- #@# Surf Reg rh Thu Aug 8 20:51:48 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 = 0.603
- curvature mean = 0.029, std = 0.923
- curvature mean = 0.020, std = 0.864
- Starting MRISrigidBodyAlignGlobal()
- d=64.00 min @ (16.00, 0.00, 0.00) sse = 358105.3, tmin=1.0184
- d=32.00 min @ (0.00, -8.00, 8.00) sse = 294718.3, tmin=2.0409
- d=16.00 min @ (-4.00, 4.00, 0.00) sse = 260841.7, tmin=3.0736
- d=8.00 min @ (2.00, -2.00, 2.00) sse = 248670.1, tmin=4.1391
- d=4.00 min @ (0.00, 1.00, 0.00) sse = 248486.3, tmin=5.2322
- d=2.00 min @ (0.00, -0.50, 0.00) sse = 247984.5, tmin=6.3537
- d=1.00 min @ (-0.25, 0.00, -0.25) sse = 247894.1, tmin=7.4741
- 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 8.61 min
- curvature mean = 0.022, std = 0.949
- curvature mean = 0.011, std = 0.943
- curvature mean = 0.020, std = 0.961
- curvature mean = 0.005, std = 0.974
- curvature mean = 0.019, std = 0.963
- curvature mean = 0.001, std = 0.989
- 2 Reading smoothwm
- curvature mean = -0.020, std = 0.311
- curvature mean = 0.006, std = 0.070
- curvature mean = 0.065, std = 0.328
- curvature mean = 0.006, std = 0.084
- curvature mean = 0.028, std = 0.514
- curvature mean = 0.007, std = 0.090
- curvature mean = 0.016, std = 0.650
- curvature mean = 0.007, std = 0.093
- curvature mean = 0.005, std = 0.762
- MRISregister() return, current seed 0
- writing registered surface to ../surf/rh.sphere.reg...
- expanding nbhd size to 1
- #--------------------------------------------
- #@# Jacobian white rh Thu Aug 8 21:17:53 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 21:17:55 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 21:17:57 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub003 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...
- 1189 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2829 changed, 127449 examined...
- 001: 676 changed, 11956 examined...
- 002: 172 changed, 3793 examined...
- 003: 75 changed, 1036 examined...
- 004: 25 changed, 411 examined...
- 005: 12 changed, 146 examined...
- 006: 7 changed, 61 examined...
- 007: 1 changed, 33 examined...
- 008: 2 changed, 8 examined...
- 009: 2 changed, 12 examined...
- 010: 0 changed, 12 examined...
- 260 labels changed using aseg
- 000: 92 total segments, 55 labels (419 vertices) changed
- 001: 41 total segments, 4 labels (10 vertices) changed
- 002: 37 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 44 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 664 vertices marked for relabeling...
- 664 labels changed in reclassification.
- writing output to ../label/rh.aparc.annot...
- classification took 1 minutes and 0 seconds.
- #--------------------------------------------
- #@# Make Pial Surf rh Thu Aug 8 21:18:58 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts
- mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub003 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/sub003/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/wm.mgz...
- 14678 bright wm thresholded.
- 302 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.orig...
- computing class statistics...
- border white: 229356 voxels (1.37%)
- border gray 266114 voxels (1.59%)
- WM (92.0): 92.8 +- 10.5 [70.0 --> 110.0]
- GM (74.0) : 72.0 +- 13.3 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 42.7 (was 70)
- setting MAX_BORDER_WHITE to 115.5 (was 105)
- setting MIN_BORDER_WHITE to 56.0 (was 85)
- setting MAX_CSF to 29.3 (was 40)
- setting MAX_GRAY to 94.5 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 49.3 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 16.0 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=105, GM=56
- mean inside = 92.5, mean outside = 66.6
- smoothing surface for 5 iterations...
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.81 +- 0.22 (0.02-->3.76) (max @ vno 41533 --> 51218)
- face area 0.28 +- 0.12 (0.00-->2.00)
- mean absolute distance = 0.66 +- 0.75
- 3563 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- deleting segment 1 with 2 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 4 with 2 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 5 with 3 points - only 0.00% unknown
- deleting segment 7 with 469 points - only 2.56% unknown
- removing 2 vertex label from ripped group
- deleting segment 9 with 13 points - only 0.00% unknown
- deleting segment 10 with 72 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 11 with 2 points - only 0.00% unknown
- mean border=70.2, 27 (23) missing vertices, mean dist 0.4 [0.4 (%29.6)->0.8 (%70.4))]
- %73 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.92 +- 0.27 (0.11-->3.65) (max @ vno 103328 --> 127415)
- face area 0.28 +- 0.13 (0.00-->2.35)
- mean absolute distance = 0.30 +- 0.47
- 2173 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=7474115.0, rms=14.45
- 001: dt: 0.5000, sse=7295226.5, rms=10.605 (0.000%)
- 002: dt: 0.5000, sse=7421282.5, rms=8.377 (0.000%)
- 003: dt: 0.5000, sse=7495878.0, rms=6.876 (0.000%)
- 004: dt: 0.5000, sse=7654546.0, rms=5.941 (0.000%)
- 005: dt: 0.5000, sse=7742302.0, rms=5.372 (0.000%)
- 006: dt: 0.5000, sse=7848051.0, rms=5.077 (0.000%)
- 007: dt: 0.5000, sse=7878429.5, rms=4.896 (0.000%)
- 008: dt: 0.5000, sse=7900173.0, rms=4.800 (0.000%)
- 009: dt: 0.5000, sse=7862075.0, rms=4.717 (0.000%)
- rms = 4.67, time step reduction 1 of 3 to 0.250...
- 010: dt: 0.5000, sse=7849494.0, rms=4.675 (0.000%)
- 011: dt: 0.2500, sse=5083620.5, rms=3.290 (0.000%)
- 012: dt: 0.2500, sse=4693034.5, rms=2.826 (0.000%)
- 013: dt: 0.2500, sse=4436248.0, rms=2.736 (0.000%)
- 014: dt: 0.2500, sse=4368500.5, rms=2.651 (0.000%)
- rms = 2.62, time step reduction 2 of 3 to 0.125...
- 015: dt: 0.2500, sse=4270207.0, rms=2.620 (0.000%)
- 016: dt: 0.1250, sse=3979691.8, rms=2.269 (0.000%)
- 017: dt: 0.1250, sse=3929857.2, rms=2.219 (0.000%)
- rms = 2.21, time step reduction 3 of 3 to 0.062...
- 018: dt: 0.1250, sse=3897658.2, rms=2.210 (0.000%)
- positioning took 2.1 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- deleting segment 2 with 4 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 6 with 2 points - only 0.00% unknown
- deleting segment 8 with 12 points - only 0.00% unknown
- deleting segment 10 with 368 points - only 3.26% unknown
- removing 2 vertex label from ripped group
- deleting segment 12 with 17 points - only 0.00% unknown
- deleting segment 13 with 36 points - only 0.00% unknown
- mean border=74.9, 40 (3) missing vertices, mean dist -0.2 [0.3 (%78.3)->0.2 (%21.7))]
- %83 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.91 +- 0.26 (0.10-->3.81) (max @ vno 96851 --> 95998)
- face area 0.35 +- 0.17 (0.00-->2.85)
- mean absolute distance = 0.21 +- 0.29
- 2583 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4887542.5, rms=6.34
- 019: dt: 0.5000, sse=5136694.5, rms=4.305 (0.000%)
- rms = 4.80, time step reduction 1 of 3 to 0.250...
- 020: dt: 0.2500, sse=4640588.0, rms=3.026 (0.000%)
- 021: dt: 0.2500, sse=4466881.5, rms=2.522 (0.000%)
- 022: dt: 0.2500, sse=4408578.5, rms=2.134 (0.000%)
- rms = 2.15, time step reduction 2 of 3 to 0.125...
- 023: dt: 0.1250, sse=4332940.5, rms=1.999 (0.000%)
- 024: dt: 0.1250, sse=4223839.0, rms=1.802 (0.000%)
- rms = 1.77, time step reduction 3 of 3 to 0.062...
- 025: dt: 0.1250, sse=4175795.8, rms=1.771 (0.000%)
- positioning took 0.9 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- deleting segment 2 with 4 points - only 0.00% unknown
- deleting segment 3 with 13 points - only 0.00% unknown
- deleting segment 4 with 395 points - only 3.04% unknown
- deleting segment 5 with 24 points - only 0.00% unknown
- deleting segment 6 with 41 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 7 with 3 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 8 with 1 points - only 0.00% unknown
- mean border=78.6, 43 (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 0.91 +- 0.25 (0.10-->4.00) (max @ vno 96851 --> 95998)
- face area 0.34 +- 0.16 (0.00-->2.62)
- mean absolute distance = 0.15 +- 0.23
- 2617 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4603211.5, rms=4.64
- 026: dt: 0.5000, sse=4940450.5, rms=4.521 (0.000%)
- rms = 4.59, time step reduction 1 of 3 to 0.250...
- 027: dt: 0.2500, sse=4449440.0, rms=2.843 (0.000%)
- 028: dt: 0.2500, sse=4309617.0, rms=2.459 (0.000%)
- 029: dt: 0.2500, sse=4373618.5, rms=2.041 (0.000%)
- rms = 2.15, time step reduction 2 of 3 to 0.125...
- 030: dt: 0.1250, sse=4298228.5, rms=1.840 (0.000%)
- 031: dt: 0.1250, sse=4201184.0, rms=1.556 (0.000%)
- rms = 1.51, time step reduction 3 of 3 to 0.062...
- 032: dt: 0.1250, sse=4166465.8, rms=1.512 (0.000%)
- positioning took 0.9 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- deleting segment 1 with 4 points - only 0.00% unknown
- deleting segment 2 with 14 points - only 0.00% unknown
- deleting segment 3 with 391 points - only 3.07% unknown
- deleting segment 5 with 24 points - only 0.00% unknown
- deleting segment 6 with 41 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 7 with 3 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 8 with 1 points - only 0.00% unknown
- mean border=79.8, 44 (2) missing vertices, mean dist -0.0 [0.2 (%59.4)->0.2 (%40.6))]
- %92 local maxima, % 2 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- repositioning cortical surface to gray/csf boundary.
- smoothing T1 volume with sigma = 2.000
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4196169.0, rms=1.96
- rms = 3.14, time step reduction 1 of 3 to 0.250...
- 033: dt: 0.2500, sse=4281657.5, rms=1.266 (0.000%)
- 034: dt: 0.2500, sse=4438970.0, rms=1.132 (0.000%)
- rms = 1.14, time step reduction 2 of 3 to 0.125...
- rms = 1.12, time step reduction 3 of 3 to 0.062...
- 035: dt: 0.1250, sse=4444141.5, rms=1.116 (0.000%)
- positioning took 0.5 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 5 with 28 points - only 42.86% unknown
- smoothing surface for 5 iterations...
- mean border=45.8, 58 (58) missing vertices, mean dist 1.7 [0.1 (%0.0)->2.2 (%100.0))]
- %13 local maxima, %60 large gradients and %22 min vals, 1243 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=29410856.0, rms=33.14
- 001: dt: 0.5000, sse=20951966.0, rms=27.374 (0.000%)
- 002: dt: 0.5000, sse=15182975.0, rms=22.647 (0.000%)
- 003: dt: 0.5000, sse=11382203.0, rms=18.876 (0.000%)
- 004: dt: 0.5000, sse=9104711.0, rms=15.903 (0.000%)
- 005: dt: 0.5000, sse=7896732.5, rms=13.591 (0.000%)
- 006: dt: 0.5000, sse=7130652.5, rms=11.796 (0.000%)
- 007: dt: 0.5000, sse=6644975.0, rms=10.244 (0.000%)
- 008: dt: 0.5000, sse=6305187.0, rms=8.853 (0.000%)
- 009: dt: 0.5000, sse=6140117.5, rms=7.620 (0.000%)
- 010: dt: 0.5000, sse=6092370.5, rms=6.639 (0.000%)
- 011: dt: 0.5000, sse=6168638.0, rms=5.882 (0.000%)
- 012: dt: 0.5000, sse=6215960.0, rms=5.294 (0.000%)
- 013: dt: 0.5000, sse=6383658.0, rms=4.901 (0.000%)
- 014: dt: 0.5000, sse=6485862.0, rms=4.643 (0.000%)
- 015: dt: 0.5000, sse=6604944.0, rms=4.485 (0.000%)
- 016: dt: 0.5000, sse=6663277.0, rms=4.375 (0.000%)
- 017: dt: 0.5000, sse=6727157.0, rms=4.286 (0.000%)
- 018: dt: 0.5000, sse=6710818.5, rms=4.227 (0.000%)
- rms = 4.19, time step reduction 1 of 3 to 0.250...
- 019: dt: 0.5000, sse=6764291.0, rms=4.186 (0.000%)
- 020: dt: 0.2500, sse=4741081.5, rms=3.422 (0.000%)
- 021: dt: 0.2500, sse=4537224.5, rms=3.206 (0.000%)
- rms = 3.18, time step reduction 2 of 3 to 0.125...
- 022: dt: 0.2500, sse=4421609.5, rms=3.180 (0.000%)
- 023: dt: 0.1250, sse=4215136.0, rms=3.047 (0.000%)
- rms = 3.03, time step reduction 3 of 3 to 0.062...
- 024: dt: 0.1250, sse=4182074.2, rms=3.031 (0.000%)
- positioning took 2.7 minutes
- mean border=43.5, 703 (4) missing vertices, mean dist 0.2 [0.2 (%49.8)->0.5 (%50.2))]
- %31 local maxima, %46 large gradients and %18 min vals, 303 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=4780434.5, rms=4.91
- 025: dt: 0.5000, sse=5050464.0, rms=4.208 (0.000%)
- rms = 4.30, time step reduction 1 of 3 to 0.250...
- 026: dt: 0.2500, sse=4701266.5, rms=3.589 (0.000%)
- 027: dt: 0.2500, sse=4782997.0, rms=3.318 (0.000%)
- 028: dt: 0.2500, sse=4728798.0, rms=3.201 (0.000%)
- 029: dt: 0.2500, sse=4782871.0, rms=3.148 (0.000%)
- rms = 3.12, time step reduction 2 of 3 to 0.125...
- 030: dt: 0.2500, sse=4783259.5, rms=3.119 (0.000%)
- 031: dt: 0.1250, sse=4631725.0, rms=2.979 (0.000%)
- rms = 2.95, time step reduction 3 of 3 to 0.062...
- 032: dt: 0.1250, sse=4627159.5, rms=2.953 (0.000%)
- positioning took 1.0 minutes
- mean border=40.8, 847 (1) missing vertices, mean dist 0.1 [0.2 (%36.9)->0.4 (%63.1))]
- %54 local maxima, %22 large gradients and %18 min vals, 406 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=4955397.0, rms=4.60
- 033: dt: 0.5000, sse=5138247.0, rms=4.200 (0.000%)
- rms = 4.32, time step reduction 1 of 3 to 0.250...
- 034: dt: 0.2500, sse=4822962.0, rms=3.363 (0.000%)
- 035: dt: 0.2500, sse=5020140.0, rms=3.046 (0.000%)
- 036: dt: 0.2500, sse=4977545.5, rms=2.977 (0.000%)
- rms = 2.94, time step reduction 2 of 3 to 0.125...
- 037: dt: 0.2500, sse=5045740.5, rms=2.945 (0.000%)
- 038: dt: 0.1250, sse=4856544.5, rms=2.782 (0.000%)
- rms = 2.76, time step reduction 3 of 3 to 0.062...
- 039: dt: 0.1250, sse=4844206.5, rms=2.760 (0.000%)
- positioning took 0.9 minutes
- mean border=39.3, 1701 (0) missing vertices, mean dist 0.1 [0.2 (%44.3)->0.3 (%55.7))]
- %59 local maxima, %17 large gradients and %18 min vals, 326 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/sub003/surf/rh.pial...
- writing smoothed curvature to rh.curv.pial
- 000: dt: 0.0000, sse=4916712.5, rms=3.24
- rms = 4.16, time step reduction 1 of 3 to 0.250...
- 040: dt: 0.2500, sse=4767624.0, rms=2.852 (0.000%)
- 041: dt: 0.2500, sse=4913418.0, rms=2.766 (0.000%)
- rms = 2.72, time step reduction 2 of 3 to 0.125...
- 042: dt: 0.2500, sse=4985712.5, rms=2.720 (0.000%)
- 043: dt: 0.1250, sse=4899711.5, rms=2.591 (0.000%)
- rms = 2.57, time step reduction 3 of 3 to 0.062...
- 044: dt: 0.1250, sse=4897560.0, rms=2.572 (0.000%)
- positioning took 0.6 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.curv.pial
- writing smoothed area to rh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.area.pial
- vertex spacing 1.03 +- 0.43 (0.08-->6.12) (max @ vno 83570 --> 83557)
- face area 0.42 +- 0.31 (0.00-->4.77)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 127449 vertices processed
- 25000 of 127449 vertices processed
- 50000 of 127449 vertices processed
- 75000 of 127449 vertices processed
- 100000 of 127449 vertices processed
- 125000 of 127449 vertices processed
- 0 of 127449 vertices processed
- 25000 of 127449 vertices processed
- 50000 of 127449 vertices processed
- 75000 of 127449 vertices processed
- 100000 of 127449 vertices processed
- 125000 of 127449 vertices processed
- thickness calculation complete, 398:665 truncations.
- 29618 vertices at 0 distance
- 83784 vertices at 1 distance
- 83372 vertices at 2 distance
- 34131 vertices at 3 distance
- 8808 vertices at 4 distance
- 2301 vertices at 5 distance
- 629 vertices at 6 distance
- 239 vertices at 7 distance
- 113 vertices at 8 distance
- 60 vertices at 9 distance
- 36 vertices at 10 distance
- 54 vertices at 11 distance
- 49 vertices at 12 distance
- 35 vertices at 13 distance
- 29 vertices at 14 distance
- 20 vertices at 15 distance
- 10 vertices at 16 distance
- 13 vertices at 17 distance
- 15 vertices at 18 distance
- 12 vertices at 19 distance
- 6 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.thickness
- positioning took 13.1 minutes
- #--------------------------------------------
- #@# Surf Volume rh Thu Aug 8 21:32:06 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 21:32:07 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts
- pctsurfcon --s sub003 --rh-only
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts/pctsurfcon.log
- Thu Aug 8 21:32:07 CEST 2013
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/tmp.pctsurfcon.7121/rh.wm.mgh --regheader sub003 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/label/rh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 = 99332
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/label/rh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/tmp.pctsurfcon.7121/rh.wm.mgh
- Dim: 127449 1 1
- mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/tmp.pctsurfcon.7121/rh.gm.mgh --projfrac 0.3 --regheader sub003 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/label/rh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.white
- Done reading source surface
- Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 = 113777
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/label/rh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/tmp.pctsurfcon.7121/rh.gm.mgh
- Dim: 127449 1 1
- mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/tmp.pctsurfcon.7121/rh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/tmp.pctsurfcon.7121/rh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/surf/rh.w-g.pct.mgh
- mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.w-g.pct.mgh --annot sub003 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/surf/rh.w-g.pct.mgh --annot sub003 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/surf/rh.w-g.pct.mgh
- Vertex Area is 0.676693 mm^3
- Generating list of segmentation ids
- Found 36 segmentations
- Computing statistics for each segmentation
- 0 2000 unknown 0 0.000
- 1 2001 bankssts 1331 939.548
- 2 2002 caudalanteriorcingulate 1036 681.329
- 3 2003 caudalmiddlefrontal 2272 1530.222
- 4 2004 corpuscallosum 0 0.000
- 5 2005 cuneus 2425 1607.873
- 6 2006 entorhinal 448 309.408
- 7 2007 fusiform 4200 2877.131
- 8 2008 inferiorparietal 8944 6206.092
- 9 2009 inferiortemporal 4353 3039.652
- 10 2010 isthmuscingulate 1357 906.082
- 11 2011 lateraloccipital 6960 4565.230
- 12 2012 lateralorbitofrontal 3815 2582.281
- 13 2013 lingual 4639 3196.726
- 14 2014 medialorbitofrontal 2210 1547.753
- 15 2015 middletemporal 4284 3010.956
- 16 2016 parahippocampal 1040 706.010
- 17 2017 paracentral 2081 1378.797
- 18 2018 parsopercularis 1724 1200.683
- 19 2019 parsorbitalis 1150 769.446
- 20 2020 parstriangularis 2205 1527.890
- 21 2021 pericalcarine 2356 1639.314
- 22 2022 postcentral 5115 3459.484
- 23 2023 posteriorcingulate 1711 1180.435
- 24 2024 precentral 6288 4162.129
- 25 2025 precuneus 6136 4148.881
- 26 2026 rostralanteriorcingulate 835 551.488
- 27 2027 rostralmiddlefrontal 8318 5772.868
- 28 2028 superiorfrontal 9184 6405.801
- 29 2029 superiorparietal 8255 5460.278
- 30 2030 superiortemporal 4572 3057.099
- 31 2031 supramarginal 5507 3739.162
- 32 2032 frontalpole 425 298.237
- 33 2033 temporalpole 516 368.095
- 34 2034 transversetemporal 499 305.694
- 35 2035 insula 2873 1900.918
- Reporting on 34 segmentations
- mri_segstats done
- Cleaning up
- #-----------------------------------------
- #@# Parcellation Stats rh Thu Aug 8 21:32:23 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 sub003 rh white
- computing statistics for each annotation in ../label/rh.aparc.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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
- 1331 940 2400 2.449 0.420 0.131 0.038 14 1.8 bankssts
- 1036 681 1939 2.412 0.724 0.139 0.037 16 1.5 caudalanteriorcingulate
- 2272 1530 4074 2.426 0.456 0.129 0.040 28 3.5 caudalmiddlefrontal
- 2425 1608 3740 2.054 0.396 0.186 0.087 63 7.7 cuneus
- 448 309 1494 3.344 0.801 0.170 0.094 14 1.5 entorhinal
- 4200 2877 8339 2.467 0.592 0.159 0.063 114 10.4 fusiform
- 8944 6206 17221 2.375 0.517 0.150 0.071 751 31.8 inferiorparietal
- 4353 3040 8827 2.356 0.700 0.156 0.074 114 15.0 inferiortemporal
- 1357 906 2654 2.455 0.780 0.165 0.140 157 7.3 isthmuscingulate
- 6960 4565 10937 2.113 0.493 0.160 0.086 181 16.1 lateraloccipital
- 3815 2582 7673 2.731 0.622 0.164 0.082 129 11.9 lateralorbitofrontal
- 4639 3197 7320 2.095 0.505 0.171 0.073 112 12.7 lingual
- 2210 1548 4498 2.532 0.657 0.175 0.098 97 8.4 medialorbitofrontal
- 4284 3011 10626 2.807 0.632 0.159 0.060 97 10.4 middletemporal
- 1040 706 2286 2.752 0.711 0.130 0.045 13 1.7 parahippocampal
- 2081 1379 3486 2.265 0.523 0.120 0.029 21 2.6 paracentral
- 1724 1201 3368 2.544 0.359 0.127 0.041 24 2.8 parsopercularis
- 1150 769 2765 2.809 0.578 0.172 0.081 27 2.9 parsorbitalis
- 2205 1528 4561 2.509 0.479 0.154 0.049 46 4.2 parstriangularis
- 2356 1639 3093 1.931 0.427 0.148 0.056 35 5.1 pericalcarine
- 5115 3459 7961 2.033 0.594 0.125 0.041 68 8.3 postcentral
- 1711 1180 3380 2.486 0.785 0.168 0.159 46 4.4 posteriorcingulate
- 6288 4162 12009 2.551 0.510 0.128 0.035 72 9.5 precentral
- 6136 4149 10373 2.296 0.465 0.153 0.059 133 14.7 precuneus
- 835 551 2074 3.163 0.698 0.165 0.061 19 2.0 rostralanteriorcingulate
- 8318 5773 16683 2.421 0.520 0.166 0.082 213 33.1 rostralmiddlefrontal
- 9184 6406 20741 2.760 0.553 0.146 0.047 148 17.8 superiorfrontal
- 8255 5460 12778 2.057 0.427 0.141 0.046 147 15.7 superiorparietal
- 4572 3057 10532 2.911 0.637 0.127 0.041 55 8.0 superiortemporal
- 5507 3739 9971 2.381 0.553 0.146 0.048 101 10.2 supramarginal
- 425 298 1170 2.836 0.445 0.231 0.102 19 2.0 frontalpole
- 516 368 1814 3.595 0.767 0.164 0.071 10 1.4 temporalpole
- 499 306 867 2.505 0.325 0.143 0.044 7 0.9 transversetemporal
- 2873 1901 6519 3.099 0.831 0.138 0.083 79 7.5 insula
- #-----------------------------------------
- #@# Cortical Parc 2 rh Thu Aug 8 21:32:43 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub003 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...
- 69 labels changed using aseg
- relabeling using gibbs priors...
- 000: 9200 changed, 127449 examined...
- 001: 2120 changed, 35285 examined...
- 002: 673 changed, 10882 examined...
- 003: 309 changed, 3770 examined...
- 004: 131 changed, 1729 examined...
- 005: 71 changed, 775 examined...
- 006: 35 changed, 381 examined...
- 007: 11 changed, 188 examined...
- 008: 8 changed, 73 examined...
- 009: 3 changed, 46 examined...
- 010: 6 changed, 22 examined...
- 011: 3 changed, 25 examined...
- 012: 3 changed, 18 examined...
- 013: 1 changed, 15 examined...
- 014: 2 changed, 7 examined...
- 015: 2 changed, 10 examined...
- 016: 0 changed, 8 examined...
- 3 labels changed using aseg
- 000: 242 total segments, 156 labels (1981 vertices) changed
- 001: 94 total segments, 9 labels (94 vertices) changed
- 002: 85 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 106 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 436 vertices marked for relabeling...
- 436 labels changed in reclassification.
- writing output to ../label/rh.aparc.a2009s.annot...
- classification took 1 minutes and 11 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 2 rh Thu Aug 8 21:33:53 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 sub003 rh white
- computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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
- 1208 839 2507 2.489 0.608 0.188 0.076 35 3.9 G_and_S_frontomargin
- 1233 846 2450 2.320 0.501 0.156 0.054 25 2.5 G_and_S_occipital_inf
- 1194 783 2204 2.305 0.491 0.135 0.037 17 1.9 G_and_S_paracentral
- 1151 801 2560 2.851 0.435 0.145 0.045 18 2.1 G_and_S_subcentral
- 1030 741 2207 2.396 0.482 0.191 0.209 42 14.1 G_and_S_transv_frontopol
- 2337 1626 5089 2.845 0.557 0.149 0.062 44 5.0 G_and_S_cingul-Ant
- 1415 978 2974 2.779 0.504 0.139 0.040 21 2.2 G_and_S_cingul-Mid-Ant
- 1195 839 2405 2.572 0.522 0.160 0.055 23 2.7 G_and_S_cingul-Mid-Post
- 537 360 1597 3.282 0.522 0.218 0.419 29 2.0 G_cingul-Post-dorsal
- 241 152 570 2.737 0.658 0.178 0.096 9 0.9 G_cingul-Post-ventral
- 2168 1493 3394 1.976 0.442 0.196 0.094 61 7.4 G_cuneus
- 1089 777 2814 2.738 0.335 0.156 0.059 27 2.7 G_front_inf-Opercular
- 348 236 938 2.818 0.342 0.182 0.072 11 1.0 G_front_inf-Orbital
- 1021 708 2539 2.658 0.422 0.179 0.067 30 2.6 G_front_inf-Triangul
- 3591 2499 9253 2.702 0.464 0.178 0.074 109 10.6 G_front_middle
- 6449 4485 16580 2.867 0.555 0.159 0.055 129 14.4 G_front_sup
- 490 314 1188 3.226 0.891 0.140 0.133 27 2.0 G_Ins_lg_and_S_cent_ins
- 578 389 2124 3.885 0.721 0.207 0.178 32 3.1 G_insular_short
- 2283 1519 4824 2.471 0.474 0.183 0.075 67 7.0 G_occipital_middle
- 1641 1088 2807 2.149 0.377 0.162 0.056 33 3.8 G_occipital_sup
- 1575 1001 3598 2.745 0.451 0.168 0.073 55 4.6 G_oc-temp_lat-fusifor
- 2931 1998 5095 2.133 0.545 0.188 0.091 92 9.6 G_oc-temp_med-Lingual
- 806 534 2481 3.200 0.763 0.148 0.062 12 1.8 G_oc-temp_med-Parahip
- 2576 1739 6702 2.891 0.657 0.198 0.122 132 11.2 G_orbital
- 3399 2387 8059 2.575 0.522 0.180 0.124 681 22.7 G_pariet_inf-Angular
- 2648 1800 5949 2.600 0.530 0.163 0.057 66 5.8 G_pariet_inf-Supramar
- 2450 1635 4572 2.223 0.441 0.165 0.064 64 6.3 G_parietal_sup
- 2007 1343 3613 2.156 0.450 0.144 0.057 38 4.4 G_postcentral
- 2373 1556 5957 2.858 0.431 0.138 0.039 34 3.9 G_precentral
- 2790 1868 5820 2.431 0.473 0.173 0.073 77 8.1 G_precuneus
- 604 414 1361 2.509 0.689 0.207 0.142 57 4.2 G_rectus
- 112 71 261 3.226 0.436 0.133 0.126 2 0.4 G_subcallosal
- 358 211 679 2.503 0.271 0.145 0.046 6 0.7 G_temp_sup-G_T_transv
- 1564 1061 4895 3.243 0.599 0.161 0.063 32 4.3 G_temp_sup-Lateral
- 448 309 1335 3.609 0.712 0.123 0.042 4 0.6 G_temp_sup-Plan_polar
- 779 547 1596 2.621 0.328 0.106 0.025 6 0.8 G_temp_sup-Plan_tempo
- 2345 1642 5469 2.487 0.697 0.181 0.110 92 12.2 G_temporal_inf
- 2535 1838 7398 2.942 0.619 0.178 0.076 74 7.5 G_temporal_middle
- 375 268 663 2.360 0.510 0.118 0.024 3 0.3 Lat_Fis-ant-Horizont
- 183 135 279 2.239 0.384 0.093 0.017 1 0.1 Lat_Fis-ant-Vertical
- 1376 922 1946 2.394 0.381 0.128 0.039 15 2.1 Lat_Fis-post
- 3600 2322 5228 2.043 0.527 0.169 0.067 76 9.7 Pole_occipital
- 1792 1291 5628 3.103 0.720 0.181 0.080 60 5.8 Pole_temporal
- 2505 1725 3465 2.073 0.494 0.145 0.055 41 5.3 S_calcarine
- 2487 1652 2847 1.899 0.585 0.099 0.023 12 2.6 S_central
- 1333 889 1794 2.026 0.448 0.106 0.026 9 1.4 S_cingul-Marginalis
- 733 480 1270 2.853 0.535 0.122 0.032 6 1.0 S_circular_insula_ant
- 1220 768 2079 2.824 0.659 0.079 0.020 5 1.0 S_circular_insula_inf
- 1197 813 1812 2.553 0.437 0.113 0.029 8 1.5 S_circular_insula_sup
- 854 598 1486 2.190 0.632 0.119 0.034 11 1.2 S_collat_transv_ant
- 447 300 544 2.132 0.390 0.174 0.061 7 1.1 S_collat_transv_post
- 2335 1562 3406 2.225 0.392 0.123 0.035 24 3.1 S_front_inf
- 1791 1251 2728 2.184 0.439 0.149 0.060 32 4.5 S_front_middle
- 1857 1298 2822 2.289 0.385 0.119 0.030 15 2.4 S_front_sup
- 807 540 966 2.133 0.388 0.124 0.037 8 1.2 S_interm_prim-Jensen
- 3351 2188 4186 1.953 0.374 0.114 0.028 33 3.9 S_intrapariet_and_P_trans
- 1232 856 1530 1.881 0.322 0.130 0.035 13 1.8 S_oc_middle_and_Lunatus
- 1684 1154 2226 1.980 0.358 0.130 0.034 17 2.3 S_oc_sup_and_transversal
- 667 465 938 2.030 0.332 0.142 0.337 56 1.0 S_occipital_ant
- 1042 713 1274 1.838 0.431 0.140 0.050 18 1.7 S_oc-temp_lat
- 2239 1571 3425 2.338 0.516 0.124 0.031 19 2.9 S_oc-temp_med_and_Lingual
- 523 353 776 2.332 0.416 0.147 0.049 7 1.0 S_orbital_lateral
- 526 386 759 2.270 0.541 0.125 0.027 4 0.6 S_orbital_med-olfact
- 1628 1097 2830 2.641 0.605 0.142 0.050 26 3.3 S_orbital-H_Shaped
- 2292 1538 3128 2.160 0.351 0.139 0.051 46 5.3 S_parieto_occipital
- 1652 1041 1714 1.952 0.711 0.140 0.096 148 6.5 S_pericallosal
- 2408 1598 2760 1.787 0.368 0.121 0.033 24 3.1 S_postcentral
- 1538 1021 2212 2.369 0.311 0.112 0.029 13 1.8 S_precentral-inf-part
- 951 640 1285 2.261 0.397 0.126 0.034 8 1.3 S_precentral-sup-part
- 384 265 682 2.419 0.898 0.163 0.069 7 1.1 S_suborbital
- 1357 939 2007 2.172 0.368 0.134 0.039 17 2.1 S_subparietal
- 1100 741 1529 2.281 0.575 0.115 0.026 8 1.4 S_temporal_inf
- 5859 4049 9697 2.364 0.482 0.123 0.034 57 8.3 S_temporal_sup
- 240 175 389 3.015 0.546 0.146 0.030 2 0.3 S_temporal_transverse
- #-----------------------------------------
- #@# Cortical Parc 3 rh Thu Aug 8 21:34:14 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub003 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...
- 1033 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2644 changed, 127449 examined...
- 001: 574 changed, 11321 examined...
- 002: 154 changed, 3158 examined...
- 003: 51 changed, 922 examined...
- 004: 24 changed, 291 examined...
- 005: 20 changed, 135 examined...
- 006: 14 changed, 117 examined...
- 007: 10 changed, 65 examined...
- 008: 10 changed, 50 examined...
- 009: 15 changed, 55 examined...
- 010: 8 changed, 63 examined...
- 011: 6 changed, 39 examined...
- 012: 4 changed, 26 examined...
- 013: 1 changed, 18 examined...
- 014: 0 changed, 5 examined...
- 190 labels changed using aseg
- 000: 65 total segments, 32 labels (362 vertices) changed
- 001: 34 total segments, 1 labels (2 vertices) changed
- 002: 33 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 35 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 495 vertices marked for relabeling...
- 495 labels changed in reclassification.
- writing output to ../label/rh.aparc.DKTatlas40.annot...
- classification took 1 minutes and 1 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 3 rh Thu Aug 8 21:35:15 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 sub003 rh white
- computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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
- 1107 725 2134 2.471 0.726 0.143 0.039 18 1.8 caudalanteriorcingulate
- 2332 1575 4244 2.441 0.459 0.132 0.039 30 3.8 caudalmiddlefrontal
- 2976 1982 4491 2.042 0.377 0.176 0.078 68 8.6 cuneus
- 428 306 1465 3.342 0.778 0.166 0.094 13 1.3 entorhinal
- 3603 2448 6762 2.433 0.577 0.149 0.055 81 7.6 fusiform
- 8563 5937 16372 2.367 0.525 0.150 0.096 792 31.3 inferiorparietal
- 4839 3379 10123 2.397 0.710 0.161 0.078 142 17.6 inferiortemporal
- 1364 912 2664 2.452 0.779 0.165 0.139 157 7.3 isthmuscingulate
- 7323 4810 11504 2.108 0.494 0.159 0.057 141 17.0 lateraloccipital
- 4171 2858 9086 2.764 0.629 0.178 0.089 159 14.3 lateralorbitofrontal
- 4664 3213 7370 2.096 0.503 0.170 0.072 111 12.6 lingual
- 1722 1192 3468 2.499 0.699 0.183 0.109 85 7.3 medialorbitofrontal
- 5384 3764 12480 2.718 0.619 0.154 0.057 112 11.9 middletemporal
- 1026 700 2256 2.754 0.714 0.130 0.045 13 1.6 parahippocampal
- 2160 1438 3663 2.272 0.521 0.119 0.028 22 2.7 paracentral
- 1766 1217 3404 2.549 0.363 0.130 0.042 26 2.9 parsopercularis
- 1260 843 2822 2.719 0.524 0.156 0.068 23 2.8 parsorbitalis
- 2387 1658 4815 2.450 0.470 0.152 0.049 50 4.6 parstriangularis
- 2339 1630 3068 1.930 0.422 0.149 0.057 35 5.2 pericalcarine
- 5697 3830 8875 2.051 0.595 0.128 0.042 78 9.5 postcentral
- 1750 1206 3411 2.478 0.775 0.168 0.157 47 4.5 posteriorcingulate
- 6104 4046 11851 2.564 0.512 0.127 0.035 70 9.2 precentral
- 6157 4168 10586 2.305 0.463 0.153 0.059 135 14.7 precuneus
- 986 651 2349 3.120 0.676 0.161 0.062 21 2.3 rostralanteriorcingulate
- 5340 3670 10751 2.447 0.527 0.164 0.068 129 14.4 rostralmiddlefrontal
- 12079 8448 26332 2.666 0.565 0.150 0.062 226 36.0 superiorfrontal
- 6947 4591 10815 2.061 0.433 0.143 0.047 127 13.2 superiorparietal
- 6152 4215 14531 2.895 0.680 0.135 0.046 86 11.3 superiortemporal
- 5035 3398 9103 2.393 0.545 0.144 0.046 90 9.2 supramarginal
- 498 304 858 2.500 0.323 0.142 0.044 7 0.9 transversetemporal
- 2905 1918 6518 3.093 0.822 0.137 0.080 77 7.6 insula
- #--------------------------------------------
- #@# Refine Pial Surfs w/ T2/FLAIR Thu Aug 8 21:35:33 CEST 2013
- bbregister --s sub003 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/T2raw.lta --init-fsl --T2
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/T2raw.dat.log
- Thu Aug 8 21:35:33 CEST 2013
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts
- /opt/freesurfer/5.3.0/bin/bbregister --s sub003 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/template.nii
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/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/sub003/mri/orig/T2raw.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.99822, -0.0508489, 0.0311494)
- j_ras = (-0.0512259, 0.998622, -0.0114243)
- k_ras = (0.0305256, 0.0129996, 0.999449)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/template.nii...
- fslregister --s sub003 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/fslregister --dof 6 --fsvol brainmask.mgz
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/reg.init.dat.fslregister.log
- Thu Aug 8 21:35:38 CEST 2013
- --s sub003 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/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/sub003/scripts
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/fslregister/refvol.fslregister.nii
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/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/sub003/mri/brainmask.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, 4.65661e-09, -1.86265e-09)
- j_ras = (1.86265e-09, 2.79397e-09, -1)
- k_ras = (-8.3528e-09, 1, -9.31323e-10)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/fslregister/refvol.fslregister.nii...
- --------------------------------------
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/fslregister/movvol.fslregister.nii --frame 0
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/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/sub003/mri/transforms/tmp.bbregister.7576/template.nii...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.99822, -0.0508489, 0.0311494)
- j_ras = (-0.0512259, 0.998622, -0.0114243)
- k_ras = (0.0305256, 0.0129996, 0.999449)
- keeping frame 0
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/fslregister/movvol.fslregister.nii...
- Mov determinant is -0.311093
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts
- tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/fslregister/movvol.fslregister.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/fslregister/reg0.7616.dat --regheader --fslregout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/reg.init.dat.fsl.mat0 --s sub003 --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/sub003/mri/transforms/tmp.bbregister.7576/fslregister/movvol.fslregister.nii
- reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/fslregister/reg0.7616.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/sub003/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/sub003/mri/transforms/tmp.bbregister.7576/fslregister/movvol.fslregister.nii
- Tmov: --------------------
- -0.700 0.000 0.000 95.894;
- 0.000 0.000 0.667 -128.000;
- 0.000 -0.667 0.000 128.000;
- 0.000 0.000 0.000 1.000;
- mkheaderreg = 1, float2int = 0
- Computing reg from header (and possibly input matrix)
- ---- Input registration matrix (computed) --------
- 0.998 0.051 -0.031 -0.000;
- 0.031 0.013 0.999 0.000;
- 0.051 -0.999 0.011 0.000;
- 0.000 0.000 0.000 1.000;
- ---------------------------------------
- ---- Input registration matrix --------
- 0.998 0.051 -0.031 -0.000;
- 0.031 0.013 0.999 0.000;
- 0.051 -0.999 0.011 0.000;
- 0.000 0.000 0.000 1.000;
- Determinant 1
- subject = sub003
- RegMat ---------------------------
- 0.998 0.051 -0.031 -0.000;
- 0.031 0.013 0.999 0.000;
- 0.051 -0.999 0.011 0.000;
- 0.000 0.000 0.000 1.000;
- FSLOUTPUTTYPE NIFTI
- tkreg2FSL: mov det = -0.311093, ref det = -1
- Thu Aug 8 21:35:47 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts
- flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/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/sub003/mri/transforms/tmp.bbregister.7576/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/reg.init.dat.fsl.mat0
- Thu Aug 8 21:40:24 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts
- flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/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/sub003/mri/transforms/tmp.bbregister.7576/reg.init.dat.fsl.mat -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/fslregister/fslmat0.trans.mat -schedule /opt/freesurfer/5.3.0/bin/flirt.newdefault.20080811.sch
- tkregister2_cmdl --s sub003 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/reg.init.dat --fslreg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/reg.init.dat.fsl.mat --noedit
- tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl
- ---- FSL registration matrix --------
- 0.998 0.051 -0.033 30.148;
- -0.033 -0.006 -0.999 260.830;
- -0.051 0.999 -0.004 5.216;
- 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/sub003/mri/transforms/tmp.bbregister.7576/template.nii
- reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/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/sub003/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/sub003/mri/transforms/tmp.bbregister.7576/template.nii
- Tmov: --------------------
- -0.700 0.000 0.000 95.894;
- 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 = -0.311093, ref det = -1
- ---- Input registration matrix (computed) --------
- 0.998 0.051 -0.033 0.150;
- 0.033 -0.004 0.999 1.026;
- 0.051 -0.999 -0.006 -0.374;
- 0.000 0.000 0.000 1.000;
- ---------------------------------------
- ---- Input registration matrix --------
- 0.998 0.051 -0.033 0.150;
- 0.033 -0.004 0.999 1.026;
- 0.051 -0.999 -0.006 -0.374;
- 0.000 0.000 0.000 1.000;
- Determinant 1
- subject = sub003
- RegMat ---------------------------
- 0.998 0.051 -0.033 0.150;
- 0.033 -0.004 0.999 1.026;
- 0.051 -0.999 -0.006 -0.374;
- 0.000 0.000 0.000 1.000;
-
- Started at Thu Aug 8 21:35:38 CEST 2013
- Ended at Thu Aug 8 21:47:22 CEST 2013
-
- fslregister Done
-
- To check results, run:
- tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/reg.init.dat --surf orig
-
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/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/sub003/scripts
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/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/sub003/mri/transforms/tmp.bbregister.7576/template.nii
- regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/reg.init.dat
- subject sub003
- dof 6
- outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/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 1376059224
- TransRandMax 0.000000
- RotRandMax 0.000000
- Translations 0.000000 0.000000 0.000000
- Rotations 0.000000 0.000000 0.000000
- Input reg
- 0.998 0.051 -0.033 0.150;
- 0.033 -0.004 0.999 1.026;
- 0.051 -0.999 -0.006 -0.374;
- 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 0.986576
- 1 -25.0 -25.0 25.0 0.983247
- 2 -25.0 25.0 -25.0 1.007463
- 3 -25.0 25.0 25.0 1.044004
- 4 25.0 -25.0 -25.0 1.036276
- 5 25.0 -25.0 25.0 1.040975
- 6 25.0 25.0 -25.0 1.013110
- 7 25.0 25.0 25.0 1.034280
- REL: 8 0.467633 8.145932 1.018241 rel = 0.459255
- Initial costs ----------------
- Number of surface hits 2411
- WM Intensity 67.2941 +/- 13.0305
- Ctx Intensity 80.6970 +/- 18.9236
- Pct Contrast 17.0092 +/- 23.6115
- Cost 0.4676
- RelCost 0.4593
- ------------------------------------
- Brute force preopt -4 4 4, n = 729
- 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9902 0.9902 0.0
- 3 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 -4.0000 0.9857 0.9857 0.0
- 4 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.0000 0.9724 0.9724 0.0
- 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.8944 0.8944 0.0
- 21 -4.0000 -4.0000 -4.0000 4.0000 0.0000 -4.0000 0.8910 0.8910 0.0
- 39 -4.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.8550 0.8550 0.0
- 102 -4.0000 0.0000 -4.0000 4.0000 0.0000 -4.0000 0.7523 0.7523 0.0
- 120 -4.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.7029 0.7029 0.0
- 346 0.0000 0.0000 -4.0000 4.0000 0.0000 0.0000 0.5969 0.5969 0.0
- 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.4676 0.4676 0.0
- Brute Force --------------------------
- Min cost was 0.467633
- Number of iterations 729
- Search time 2.660000 sec
- Parameters at best (transmm, rotdeg)
- 0.000 0.000 0.000 0.000 0.000 0.000
- --------------------------------------------
- Starting Powell Minimization
- Init Powel Params dof = 6
- 0 0
- 1 0
- 2 0
- 3 0
- 4 0
- 5 0
- 11 0.019 0.000 0.000 0.000 0.000 0.000 0.4675131428
- 12 0.025 0.000 0.000 0.000 0.000 0.000 0.4674809813
- 13 0.036 0.000 0.000 0.000 0.000 0.000 0.4674561091
- 14 0.035 0.000 0.000 0.000 0.000 0.000 0.4674542680
- 15 0.033 0.000 0.000 0.000 0.000 0.000 0.4674534706
- 21 0.033 -1.618 0.000 0.000 0.000 0.000 0.4053029209
- 22 0.033 -1.331 0.000 0.000 0.000 0.000 0.3953529608
- 24 0.033 -0.823 0.000 0.000 0.000 0.000 0.3941499489
- 26 0.033 -1.058 0.000 0.000 0.000 0.000 0.3931425806
- 30 0.033 -1.069 0.000 0.000 0.000 0.000 0.3930436256
- 31 0.033 -1.073 0.000 0.000 0.000 0.000 0.3930194551
- 33 0.033 -1.075 0.000 0.000 0.000 0.000 0.3930114613
- 35 0.033 -1.076 0.000 0.000 0.000 0.000 0.3930113406
- 37 0.033 -1.076 1.000 0.000 0.000 0.000 0.2670190595
- 40 0.033 -1.076 1.618 0.000 0.000 0.000 0.2610119080
- 42 0.033 -1.076 1.345 0.000 0.000 0.000 0.2531224902
- 43 0.033 -1.076 1.352 0.000 0.000 0.000 0.2528559976
- 44 0.033 -1.076 1.423 0.000 0.000 0.000 0.2525060895
- 46 0.033 -1.076 1.394 0.000 0.000 0.000 0.2522172948
- 56 0.033 -1.076 1.394 0.382 0.000 0.000 0.2357375372
- 57 0.033 -1.076 1.394 0.336 0.000 0.000 0.2341538128
- 58 0.033 -1.076 1.394 0.284 0.000 0.000 0.2328213725
- 60 0.033 -1.076 1.394 0.243 0.000 0.000 0.2326645563
- 61 0.033 -1.076 1.394 0.255 0.000 0.000 0.2323784493
- 62 0.033 -1.076 1.394 0.261 0.000 0.000 0.2323630026
- 63 0.033 -1.076 1.394 0.260 0.000 0.000 0.2323600515
- 71 0.033 -1.076 1.394 0.260 0.046 0.000 0.2321164858
- 73 0.033 -1.076 1.394 0.260 0.039 0.000 0.2320909955
- 76 0.033 -1.076 1.394 0.260 0.038 0.000 0.2320871752
- 84 0.033 -1.076 1.394 0.260 0.038 -0.255 0.2288025977
- 85 0.033 -1.076 1.394 0.260 0.038 -0.226 0.2286803540
- 86 0.033 -1.076 1.394 0.260 0.038 -0.213 0.2286702508
- 88 0.033 -1.076 1.394 0.260 0.038 -0.131 0.2283463921
- 90 0.033 -1.076 1.394 0.260 0.038 -0.163 0.2283462069
- 91 0.033 -1.076 1.394 0.260 0.038 -0.147 0.2282822144
- 92 0.033 -1.076 1.394 0.260 0.038 -0.146 0.2282811641
- 93 0.033 -1.076 1.394 0.260 0.038 -0.144 0.2282744338
- 107 0.015 -1.076 1.394 0.260 0.038 -0.144 0.2280284491
- 108 0.016 -1.076 1.394 0.260 0.038 -0.144 0.2280243147
- 109 0.017 -1.076 1.394 0.260 0.038 -0.144 0.2280232614
- 117 0.017 -0.694 1.394 0.260 0.038 -0.144 0.2050094028
- 119 0.017 -0.730 1.394 0.260 0.038 -0.144 0.2047954990
- 120 0.017 -0.727 1.394 0.260 0.038 -0.144 0.2047353044
- 121 0.017 -0.715 1.394 0.260 0.038 -0.144 0.2046219815
- 123 0.017 -0.716 1.394 0.260 0.038 -0.144 0.2046207957
- 132 0.017 -0.716 1.155 0.260 0.038 -0.144 0.2001881173
- 133 0.017 -0.716 1.177 0.260 0.038 -0.144 0.2000120596
- 134 0.017 -0.716 1.199 0.260 0.038 -0.144 0.1999988262
- 135 0.017 -0.716 1.189 0.260 0.038 -0.144 0.1999617517
- 143 0.017 -0.716 1.189 0.642 0.038 -0.144 0.1836026879
- 144 0.017 -0.716 1.189 0.571 0.038 -0.144 0.1826210799
- 145 0.017 -0.716 1.189 0.568 0.038 -0.144 0.1825894435
- 146 0.017 -0.716 1.189 0.450 0.038 -0.144 0.1817752020
- 148 0.017 -0.716 1.189 0.495 0.038 -0.144 0.1817290746
- 149 0.017 -0.716 1.189 0.478 0.038 -0.144 0.1816493584
- 151 0.017 -0.716 1.189 0.481 0.038 -0.144 0.1816467865
- 153 0.017 -0.716 1.189 0.480 0.038 -0.144 0.1816464746
- 162 0.017 -0.716 1.189 0.480 0.066 -0.144 0.1816448783
- 163 0.017 -0.716 1.189 0.480 0.052 -0.144 0.1816346052
- 165 0.017 -0.716 1.189 0.480 0.047 -0.144 0.1816325051
- 166 0.017 -0.716 1.189 0.480 0.049 -0.144 0.1816295590
- 175 0.017 -0.716 1.189 0.480 0.049 -0.258 0.1812482422
- 176 0.017 -0.716 1.189 0.480 0.049 -0.211 0.1808579081
- 177 0.017 -0.716 1.189 0.480 0.049 -0.210 0.1808553024
- 178 0.017 -0.716 1.189 0.480 0.049 -0.200 0.1808404900
- 180 0.017 -0.716 1.189 0.480 0.049 -0.198 0.1808404695
- 181 0.017 -0.716 1.189 0.480 0.049 -0.197 0.1808401222
- 182 0.017 -0.716 1.189 0.480 0.049 -0.190 0.1808362096
- 186 0.017 -0.716 1.189 0.480 0.049 -0.191 0.1808355393
- 187 0.001 -0.357 0.985 0.700 0.061 -0.238 0.1722128821
- 194 0.003 -0.391 1.004 0.679 0.060 -0.233 0.1718116350
- 196 0.003 -0.383 1.000 0.684 0.060 -0.234 0.1717705390
- 206 -0.109 -0.383 1.000 0.684 0.060 -0.234 0.1709969041
- 221 -0.109 -0.383 1.000 0.684 0.060 -0.211 0.1702856055
- 222 -0.109 -0.383 1.000 0.684 0.060 -0.139 0.1688426579
- 225 -0.109 -0.383 1.000 0.684 0.060 -0.133 0.1687721311
- 226 -0.109 -0.383 1.000 0.684 0.060 -0.123 0.1687097224
- 236 -0.109 -0.383 0.737 0.684 0.060 -0.123 0.1573634780
- 239 -0.109 -0.383 0.734 0.684 0.060 -0.123 0.1573594472
- 249 -0.109 -0.383 0.734 0.860 0.060 -0.123 0.1490910204
- 251 -0.109 -0.383 0.734 0.840 0.060 -0.123 0.1490776266
- 253 -0.109 -0.383 0.734 0.849 0.060 -0.123 0.1490195326
- 254 -0.109 -0.383 0.734 0.848 0.060 -0.123 0.1490181004
- 263 -0.109 -0.383 0.734 0.848 0.033 -0.123 0.1486217550
- 264 -0.109 -0.383 0.734 0.848 0.024 -0.123 0.1486186896
- 265 -0.109 -0.383 0.734 0.848 0.028 -0.123 0.1486107347
- 267 -0.109 -0.383 0.734 0.848 0.029 -0.123 0.1486103046
- 275 -0.106 -0.453 0.774 0.806 0.027 -0.114 0.1481831611
- 289 -0.064 -0.453 0.774 0.806 0.027 -0.114 0.1481664275
- 290 -0.084 -0.453 0.774 0.806 0.027 -0.114 0.1480575169
- 301 -0.084 -0.453 0.774 0.806 0.027 -0.153 0.1477852686
- 302 -0.084 -0.453 0.774 0.806 0.027 -0.145 0.1477742506
- 303 -0.084 -0.453 0.774 0.806 0.027 -0.147 0.1477712237
- 304 -0.084 -0.453 0.774 0.806 0.027 -0.148 0.1477709643
- 312 -0.084 -0.453 0.586 0.806 0.027 -0.148 0.1405570570
- 314 -0.084 -0.453 0.592 0.806 0.027 -0.148 0.1405391024
- 315 -0.084 -0.453 0.599 0.806 0.027 -0.148 0.1405186979
- 320 -0.084 -0.453 0.598 0.806 0.027 -0.148 0.1405164413
- 322 -0.084 -0.453 0.597 0.806 0.027 -0.148 0.1405156542
- 329 -0.084 -0.453 0.597 0.938 0.027 -0.148 0.1372059596
- 332 -0.084 -0.453 0.597 0.953 0.027 -0.148 0.1372033284
- 333 -0.084 -0.453 0.597 0.945 0.027 -0.148 0.1371705124
- 336 -0.084 -0.453 0.597 0.944 0.027 -0.148 0.1371703173
- 346 -0.084 -0.453 0.597 0.944 0.055 -0.148 0.1363851946
- 347 -0.084 -0.453 0.597 0.944 0.062 -0.148 0.1363652232
- 348 -0.084 -0.453 0.597 0.944 0.061 -0.148 0.1363640171
- 356 -0.080 -0.533 0.643 0.895 0.058 -0.137 0.1347476246
- 357 -0.080 -0.533 0.643 0.895 0.058 -0.137 0.1347362534
- 358 -0.081 -0.516 0.633 0.906 0.059 -0.139 0.1346805271
- 360 -0.081 -0.522 0.637 0.902 0.059 -0.139 0.1346635519
- 361 -0.081 -0.521 0.636 0.902 0.059 -0.139 0.1346634868
- 363 -0.055 -0.590 0.498 0.999 0.091 -0.163 0.1306214095
- 370 -0.058 -0.581 0.516 0.987 0.087 -0.160 0.1305123469
- 371 -0.058 -0.581 0.516 0.987 0.087 -0.160 0.1305109192
- 372 -0.058 -0.583 0.512 0.989 0.087 -0.161 0.1305000663
- 374 -0.057 -0.583 0.511 0.990 0.088 -0.161 0.1304990943
- 384 -0.094 -0.583 0.511 0.990 0.088 -0.161 0.1303908439
- 385 -0.085 -0.583 0.511 0.990 0.088 -0.161 0.1303653723
- 386 -0.082 -0.583 0.511 0.990 0.088 -0.161 0.1303601038
- 388 -0.080 -0.583 0.511 0.990 0.088 -0.161 0.1303589313
- 389 -0.081 -0.583 0.511 0.990 0.088 -0.161 0.1303587661
- 397 -0.081 -0.583 0.511 0.990 0.088 -0.189 0.1302129309
- 398 -0.081 -0.583 0.511 0.990 0.088 -0.188 0.1302124721
- 399 -0.081 -0.583 0.511 0.990 0.088 -0.187 0.1302111751
- 409 -0.080 -0.590 0.515 0.986 0.087 -0.186 0.1300492376
- 411 -0.079 -0.617 0.530 0.970 0.087 -0.182 0.1298577719
- 412 -0.079 -0.610 0.526 0.974 0.087 -0.183 0.1298386809
- 415 -0.080 -0.607 0.524 0.976 0.087 -0.184 0.1298362414
- 416 -0.079 -0.607 0.525 0.975 0.087 -0.184 0.1298354730
- 417 -0.079 -0.608 0.525 0.975 0.087 -0.184 0.1298353065
- 425 -0.079 -0.608 0.525 0.948 0.087 -0.184 0.1294352107
- 427 -0.079 -0.608 0.525 0.951 0.087 -0.184 0.1294232040
- 430 -0.079 -0.608 0.525 0.952 0.087 -0.184 0.1294205362
- 438 -0.079 -0.608 0.525 0.952 0.063 -0.184 0.1290539386
- 439 -0.079 -0.608 0.525 0.952 0.054 -0.184 0.1289878445
- 440 -0.079 -0.608 0.525 0.952 0.037 -0.184 0.1289744422
- 441 -0.079 -0.608 0.525 0.952 0.044 -0.184 0.1289537906
- 442 -0.079 -0.608 0.525 0.952 0.045 -0.184 0.1289526990
- 449 -0.070 -0.634 0.472 0.989 0.057 -0.193 0.1289489272
- 450 -0.075 -0.621 0.498 0.970 0.051 -0.188 0.1284704510
- 452 -0.074 -0.621 0.498 0.971 0.051 -0.188 0.1284703164
- 465 -0.077 -0.621 0.498 0.971 0.051 -0.188 0.1284661953
- 466 -0.078 -0.621 0.498 0.971 0.051 -0.188 0.1284656516
- 475 -0.078 -0.621 0.498 0.971 0.051 -0.203 0.1283631135
- 476 -0.078 -0.621 0.498 0.971 0.051 -0.208 0.1283598454
- 480 -0.078 -0.621 0.498 0.971 0.051 -0.212 0.1283589260
- 481 -0.078 -0.621 0.498 0.971 0.051 -0.211 0.1283587004
- 482 -0.078 -0.621 0.498 0.971 0.051 -0.210 0.1283582946
- 491 -0.078 -0.619 0.497 0.972 0.051 -0.210 0.1283545845
- 492 -0.078 -0.619 0.497 0.972 0.051 -0.210 0.1283536503
- 502 -0.078 -0.619 0.497 0.963 0.051 -0.210 0.1282398325
- 505 -0.078 -0.619 0.497 0.958 0.051 -0.210 0.1282233966
- 516 -0.078 -0.619 0.497 0.958 0.043 -0.210 0.1281501180
- 518 -0.078 -0.619 0.497 0.958 0.039 -0.210 0.1281414781
- 519 -0.078 -0.619 0.497 0.958 0.038 -0.210 0.1281369757
- 520 -0.078 -0.619 0.497 0.958 0.034 -0.210 0.1281365397
- 522 -0.078 -0.619 0.497 0.958 0.035 -0.210 0.1281323452
- 530 -0.076 -0.624 0.486 0.966 0.038 -0.212 0.1280227170
- 531 -0.076 -0.626 0.482 0.968 0.039 -0.213 0.1280155175
- 532 -0.076 -0.626 0.483 0.968 0.039 -0.213 0.1280147430
- 533 -0.076 -0.626 0.484 0.968 0.038 -0.212 0.1280140471
- 537 -0.076 -0.626 0.483 0.968 0.038 -0.212 0.1280139666
- 548 -0.079 -0.626 0.483 0.968 0.038 -0.212 0.1280115701
- 549 -0.078 -0.626 0.483 0.968 0.038 -0.212 0.1280099384
- 550 -0.077 -0.626 0.483 0.968 0.038 -0.212 0.1280093167
- 559 -0.077 -0.626 0.483 0.968 0.038 -0.211 0.1280093009
- 569 -0.077 -0.619 0.480 0.972 0.039 -0.211 0.1279943915
- 571 -0.077 -0.620 0.480 0.971 0.039 -0.211 0.1279942885
- 581 -0.077 -0.620 0.480 0.966 0.039 -0.211 0.1279674828
- 582 -0.077 -0.620 0.480 0.967 0.039 -0.211 0.1279674502
- 592 -0.077 -0.620 0.480 0.967 0.038 -0.211 0.1279614525
- 593 -0.077 -0.620 0.480 0.967 0.034 -0.211 0.1279500962
- 595 -0.077 -0.620 0.480 0.967 0.033 -0.211 0.1279493426
- 603 -0.076 -0.623 0.473 0.972 0.034 -0.213 0.1279196292
- 605 -0.076 -0.623 0.474 0.971 0.034 -0.212 0.1279175584
- 606 -0.076 -0.623 0.474 0.970 0.034 -0.212 0.1279173460
- 610 -0.077 -0.620 0.465 0.973 0.029 -0.212 0.1278815070
- 617 -0.077 -0.620 0.466 0.973 0.030 -0.212 0.1278798259
- 623 -0.077 -0.620 0.466 0.973 0.030 -0.212 0.1278796220
- 636 -0.079 -0.620 0.466 0.973 0.030 -0.212 0.1278790959
- 638 -0.078 -0.620 0.466 0.973 0.030 -0.212 0.1278787608
- 646 -0.078 -0.620 0.466 0.973 0.030 -0.207 0.1278720852
- 657 -0.078 -0.621 0.467 0.972 0.030 -0.207 0.1278699518
- 680 -0.078 -0.621 0.467 0.972 0.031 -0.207 0.1278692602
- 688 -0.078 -0.620 0.466 0.973 0.031 -0.206 0.1278674976
- 694 -0.078 -0.620 0.466 0.973 0.031 -0.206 0.1278673395
- Powell done niters = 7
- Computing relative cost
- 0 -25.0 -25.0 -25.0 0.968830
- 1 -25.0 -25.0 25.0 1.022399
- 2 -25.0 25.0 -25.0 1.010376
- 3 -25.0 25.0 25.0 1.027400
- 4 25.0 -25.0 -25.0 1.051955
- 5 25.0 -25.0 25.0 1.018903
- 6 25.0 25.0 -25.0 1.019751
- 7 25.0 25.0 25.0 1.046903
- REL: 8 0.127867 8.166515 1.020814 rel = 0.12526
- Number of iterations 7
- Min cost was 0.127867
- Number of FunctionCalls 696
- TolPowell 0.000100
- nMaxItersPowell 36
- OptimizationTime 2.516000 sec
- Parameters at optimum (transmm) -0.07808 -0.62048 0.46589
- Parameters at optimum (rotdeg) 0.97265 0.03053 -0.20650
- Final costs ----------------
- Number of surface hits 2411
- WM Intensity 65.1866 +/- 11.3468
- Ctx Intensity 79.9800 +/- 13.1774
- Pct Contrast 20.3501 +/- 13.6723
- Cost 0.1279
- RelCost 0.4593
- Reg at min cost was
- 0.998 0.051 -0.029 0.075;
- 0.029 0.013 1.000 0.411;
- 0.051 -0.999 0.011 0.109;
- 0.000 0.000 0.000 1.000;
- Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/bbr.pass1.dat, type = 14
- Original Reg
- 0.998 0.051 -0.033 0.150;
- 0.033 -0.004 0.999 1.026;
- 0.051 -0.999 -0.006 -0.374;
- 0.000 0.000 0.000 1.000;
- Original Reg - Optimal Reg
- -0.000 0.000 -0.004 0.075;
- 0.004 -0.017 -0.000 0.615;
- -0.000 -0.000 -0.017 -0.483;
- 0.000 0.000 0.000 0.000;
- Computing change in lh position
- LH rmsDiffMean 1.517281
- Computing change in rh position
- Surface RMS Diff (mm) 1.555715 2.412896
- mri_segreg done
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/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/sub003/scripts
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/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/sub003/mri/transforms/tmp.bbregister.7576/template.nii
- regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/tmp.bbregister.7576/bbr.pass1.dat
- subject sub003
- dof 6
- outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 1376293067
- TransRandMax 0.000000
- RotRandMax 0.000000
- Translations 0.000000 0.000000 0.000000
- Rotations 0.000000 0.000000 0.000000
- Input reg
- 0.998 0.051 -0.029 0.075;
- 0.029 0.013 1.000 0.411;
- 0.051 -0.999 0.011 0.109;
- 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 1.012628
- 1 -25.0 -25.0 25.0 1.010317
- 2 -25.0 25.0 -25.0 1.013781
- 3 -25.0 25.0 25.0 1.026243
- 4 25.0 -25.0 -25.0 1.035852
- 5 25.0 -25.0 25.0 1.031547
- 6 25.0 25.0 -25.0 1.028321
- 7 25.0 25.0 25.0 1.031602
- REL: 8 0.133532 8.190292 1.023786 rel = 0.130429
- Initial costs ----------------
- Number of surface hits 240423
- WM Intensity 64.9359 +/- 11.1877
- Ctx Intensity 79.7729 +/- 12.9062
- Pct Contrast 20.4782 +/- 13.8817
- Cost 0.1335
- RelCost 0.1304
- ------------------------------------
- Brute force preopt -0.1 0.1 0.1, n = 729
- 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1323 0.1323 0.0
- 9 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 -0.1000 0.1284 0.1284 0.0
- 21 -0.1000 -0.1000 -0.1000 0.1000 0.0000 -0.1000 0.1280 0.1280 0.0
- 99 -0.1000 0.0000 -0.1000 0.1000 -0.1000 -0.1000 0.1271 0.1271 0.0
- Brute Force --------------------------
- Min cost was 0.127104
- Number of iterations 729
- Search time 2.645000 sec
- Parameters at best (transmm, rotdeg)
- -0.100 0.000 -0.100 0.100 -0.100 -0.100
- --------------------------------------------
- Starting Powell Minimization
- Init Powel Params dof = 6
- 0 -0.1
- 1 0
- 2 -0.1
- 3 0.1
- 4 -0.1
- 5 -0.1
- 7 -0.042 0.000 -0.100 0.100 -0.100 -0.100 0.1307987305
- 8 -0.030 0.000 -0.100 0.100 -0.100 -0.100 0.1307770674
- 9 -0.029 0.000 -0.100 0.100 -0.100 -0.100 0.1307765224
- 10 -0.027 0.000 -0.100 0.100 -0.100 -0.100 0.1307761312
- 11 -0.026 0.000 -0.100 0.100 -0.100 -0.100 0.1307759415
- 14 -0.025 0.000 -0.100 0.100 -0.100 -0.100 0.1307759274
- 22 -0.025 0.075 -0.100 0.100 -0.100 -0.100 0.1300930603
- 23 -0.025 0.070 -0.100 0.100 -0.100 -0.100 0.1300780848
- 24 -0.025 0.063 -0.100 0.100 -0.100 -0.100 0.1300697692
- 25 -0.025 0.064 -0.100 0.100 -0.100 -0.100 0.1300695851
- 33 -0.025 0.064 -0.191 0.100 -0.100 -0.100 0.1288568820
- 34 -0.025 0.064 -0.201 0.100 -0.100 -0.100 0.1288540792
- 35 -0.025 0.064 -0.197 0.100 -0.100 -0.100 0.1288519871
- 44 -0.025 0.064 -0.197 0.160 -0.100 -0.100 0.1282988494
- 45 -0.025 0.064 -0.197 0.152 -0.100 -0.100 0.1282747727
- 46 -0.025 0.064 -0.197 0.149 -0.100 -0.100 0.1282723798
- 47 -0.025 0.064 -0.197 0.148 -0.100 -0.100 0.1282721881
- 55 -0.025 0.064 -0.197 0.148 -0.038 -0.100 0.1277993515
- 57 -0.025 0.064 -0.197 0.148 -0.042 -0.100 0.1277987802
- 59 -0.025 0.064 -0.197 0.148 -0.040 -0.100 0.1277982290
- 67 -0.025 0.064 -0.197 0.148 -0.040 -0.034 0.1275387248
- 68 -0.025 0.064 -0.197 0.148 -0.040 -0.051 0.1274734378
- 69 -0.025 0.064 -0.197 0.148 -0.040 -0.055 0.1274698060
- 70 -0.025 0.064 -0.197 0.148 -0.040 -0.056 0.1274694474
- 80 -0.012 0.064 -0.197 0.148 -0.040 -0.056 0.1274541905
- 82 -0.014 0.064 -0.197 0.148 -0.040 -0.056 0.1274531144
- 91 -0.014 0.087 -0.197 0.148 -0.040 -0.056 0.1274297659
- 92 -0.014 0.079 -0.197 0.148 -0.040 -0.056 0.1274225386
- 93 -0.014 0.080 -0.197 0.148 -0.040 -0.056 0.1274222259
- 94 -0.014 0.081 -0.197 0.148 -0.040 -0.056 0.1274222185
- 103 -0.014 0.081 -0.231 0.148 -0.040 -0.056 0.1272575196
- 113 -0.014 0.081 -0.231 0.185 -0.040 -0.056 0.1271104372
- 114 -0.014 0.081 -0.231 0.176 -0.040 -0.056 0.1270789392
- 115 -0.014 0.081 -0.231 0.174 -0.040 -0.056 0.1270777567
- 124 -0.014 0.081 -0.231 0.174 -0.038 -0.056 0.1270736522
- 126 -0.014 0.081 -0.231 0.174 -0.036 -0.056 0.1270728425
- 135 -0.014 0.081 -0.231 0.174 -0.036 -0.045 0.1270528137
- 138 -0.004 0.099 -0.266 0.200 -0.031 -0.033 0.1269067538
- 145 -0.003 0.101 -0.270 0.204 -0.031 -0.032 0.1269045210
- 146 -0.003 0.101 -0.271 0.204 -0.031 -0.032 0.1269043616
- 148 -0.002 0.102 -0.272 0.205 -0.030 -0.031 0.1269041834
- 171 -0.002 0.106 -0.272 0.205 -0.030 -0.031 0.1269024512
- 173 -0.002 0.107 -0.272 0.205 -0.030 -0.031 0.1269023307
- 182 -0.002 0.107 -0.279 0.205 -0.030 -0.031 0.1268956505
- 183 -0.002 0.107 -0.280 0.205 -0.030 -0.031 0.1268956258
- 200 -0.002 0.107 -0.280 0.205 -0.039 -0.031 0.1268924465
- 201 -0.002 0.107 -0.280 0.205 -0.036 -0.031 0.1268905816
- 210 -0.004 0.104 -0.274 0.201 -0.037 -0.033 0.1268869372
- 216 -0.004 0.104 -0.273 0.200 -0.037 -0.033 0.1268869206
- 231 -0.002 0.104 -0.273 0.200 -0.037 -0.033 0.1268861339
- 247 -0.002 0.104 -0.275 0.200 -0.037 -0.033 0.1268854410
- 248 -0.002 0.104 -0.276 0.200 -0.037 -0.033 0.1268853028
- 274 -0.002 0.103 -0.275 0.200 -0.037 -0.034 0.1268852642
- 275 -0.002 0.103 -0.275 0.200 -0.037 -0.034 0.1268852221
- 331 -0.002 0.103 -0.275 0.200 -0.037 -0.034 0.1268851593
- 344 -0.003 0.103 -0.275 0.199 -0.037 -0.034 0.1268851469
- 350 -0.003 0.103 -0.275 0.199 -0.037 -0.034 0.1268851387
- 355 -0.003 0.103 -0.275 0.199 -0.037 -0.034 0.1268851321
- 356 -0.003 0.103 -0.275 0.199 -0.037 -0.034 0.1268851311
- 402 -0.003 0.103 -0.275 0.199 -0.036 -0.034 0.1268851099
- 404 -0.003 0.103 -0.275 0.199 -0.036 -0.034 0.1268850452
- 413 -0.003 0.103 -0.275 0.199 -0.036 -0.034 0.1268850423
- 414 -0.003 0.103 -0.275 0.199 -0.036 -0.034 0.1268850316
- 418 -0.003 0.103 -0.275 0.199 -0.036 -0.034 0.1268850312
- 474 -0.003 0.103 -0.275 0.199 -0.036 -0.034 0.1268850109
- 530 -0.003 0.103 -0.275 0.199 -0.036 -0.034 0.1268850104
- 531 -0.003 0.103 -0.275 0.199 -0.036 -0.034 0.1268850093
- Powell done niters = 7
- Computing relative cost
- 0 -25.0 -25.0 -25.0 1.012531
- 1 -25.0 -25.0 25.0 1.011168
- 2 -25.0 25.0 -25.0 1.013170
- 3 -25.0 25.0 25.0 1.026299
- 4 25.0 -25.0 -25.0 1.036595
- 5 25.0 -25.0 25.0 1.032410
- 6 25.0 25.0 -25.0 1.028059
- 7 25.0 25.0 25.0 1.032638
- REL: 8 0.126885 8.192870 1.024109 rel = 0.123898
- Number of iterations 7
- Min cost was 0.126885
- Number of FunctionCalls 534
- TolPowell 0.000000
- nMaxItersPowell 36
- OptimizationTime 62.002000 sec
- Parameters at optimum (transmm) -0.00261 0.10287 -0.27464
- Parameters at optimum (rotdeg) 0.19921 -0.03618 -0.03386
- Final costs ----------------
- Number of surface hits 240423
- WM Intensity 64.9338 +/- 11.2144
- Ctx Intensity 79.7146 +/- 12.8242
- Pct Contrast 20.4261 +/- 13.7529
- Cost 0.1269
- RelCost 0.1304
- Reg at min cost was
- 0.998 0.052 -0.029 0.073;
- 0.028 0.016 0.999 0.513;
- 0.052 -0.999 0.015 -0.164;
- 0.000 0.000 0.000 1.000;
- Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/T2raw.dat, type = 14
- Original Reg
- 0.998 0.051 -0.029 0.075;
- 0.029 0.013 1.000 0.411;
- 0.051 -0.999 0.011 0.109;
- 0.000 0.000 0.000 1.000;
- Original Reg - Optimal Reg
- 0.000 -0.001 -0.001 0.002;
- 0.001 -0.003 0.000 -0.102;
- -0.001 -0.000 -0.003 0.273;
- 0.000 0.000 0.000 0.000;
- Computing change in lh position
- LH rmsDiffMean 0.217297
- Computing change in rh position
- Surface RMS Diff (mm) 0.199717 0.396121
- mri_segreg done
- tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/T2raw.dat --noedit --ltaout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/mri/orig/T2raw.mgz
- reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/T2raw.dat
- LoadVol 0
- ZeroCRAS 0
- $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
- Diagnostic Level -1
- ---- Input registration matrix --------
- 0.998 0.052 -0.029 0.073;
- 0.028 0.016 0.999 0.513;
- 0.052 -0.999 0.015 -0.164;
- 0.000 0.000 0.000 1.000;
- float2int = 0
- ---------------------------------------
- INFO: loading target /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/mri/orig/T2raw.mgz
- Tmov: --------------------
- -0.700 0.000 0.000 95.894;
- 0.000 0.000 0.667 -128.000;
- 0.000 -0.667 0.000 128.000;
- 0.000 0.000 0.000 1.000;
- mkheaderreg = 0, float2int = 0
- ---- Input registration matrix --------
- 0.998 0.052 -0.029 0.073;
- 0.028 0.016 0.999 0.513;
- 0.052 -0.999 0.015 -0.164;
- 0.000 0.000 0.000 1.000;
- Determinant 1
- subject = sub003
- RegMat ---------------------------
- 0.998 0.052 -0.029 0.073;
- 0.028 0.016 0.999 0.513;
- 0.052 -0.999 0.015 -0.164;
- 0.000 0.000 0.000 1.000;
- transformed matrix:
- 1.000 -0.001 -0.002 -0.083;
- 0.001 1.000 0.003 -0.144;
- 0.002 -0.003 1.000 -0.430;
- 0.000 0.000 0.000 1.000;
- transformed matrix:
- 0.699 0.035 -0.019 29.283;
- -0.020 0.010 -0.666 257.303;
- -0.036 0.666 0.011 2.863;
- 0.000 0.000 0.000 1.000;
- Cleaning up
-
- Started at Thu Aug 8 21:35:33 CEST 2013
- Ended at Thu Aug 8 21:49:20 CEST 2013
- BBR-Run-Time-Sec 827
-
- bbregister Done
- To check results, run:
- tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/T2raw.dat --surf
-
- mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/T2.mgz
- mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/mri/orig/T2raw.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.99822, -0.0508489, 0.0311494)
- j_ras = (-0.0512259, 0.998622, -0.0114243)
- k_ras = (0.0305256, 0.0129996, 0.999449)
- INFO: Reading transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/T2raw.lta...
- Reading transform with LTAreadEx()
- reading extra input line subject sub003
- reading extra input line fscale 0.150000
- reading template info from volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/orig.mgz...
- INFO: Applying transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/transforms/T2raw.lta...
- ---------------------------------
- INFO: Transform Matrix (linear_ras_to_ras)
- 1.000 -0.001 -0.002 -0.083;
- 0.001 1.000 0.003 -0.144;
- 0.002 -0.003 1.000 -0.430;
- 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/sub003/mri/T2.mgz...
- mri_normalize -aseg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/aseg.mgz -sigma 4 -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.white identity.nofile -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.white identity.nofile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/T2.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/mri/T2.mgz...
- computing distance transform
- computing distance transform
- computing nonmaximum suppression
- 7298 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/sub003/mri/T2.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts
- cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.woT2.pial
- `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.woT2.pial'
- mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub003 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/sub003/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/wm.mgz...
- 15061 bright wm thresholded.
- 302 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.orig...
- computing class statistics...
- border white: 229356 voxels (1.37%)
- border gray 266114 voxels (1.59%)
- WM (92.0): 92.8 +- 10.6 [70.0 --> 110.0]
- GM (74.0) : 72.1 +- 13.1 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 43.9 (was 70)
- setting MAX_BORDER_WHITE to 115.6 (was 105)
- setting MIN_BORDER_WHITE to 57.0 (was 85)
- setting MAX_CSF to 30.8 (was 40)
- setting MAX_GRAY to 94.4 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 50.4 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 17.6 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=105, GM=57
- mean inside = 92.8, mean outside = 67.3
- 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/sub003/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.90 +- 0.26 (0.03-->4.88) (max @ vno 61076 --> 128641)
- face area 0.33 +- 0.16 (0.00-->2.76)
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 82 points - only 0.00% unknown
- deleting segment 1 with 6 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 2 with 2 points - only 0.00% unknown
- deleting segment 5 with 5 points - only 0.00% unknown
- deleting segment 6 with 10 points - only 0.00% unknown
- deleting segment 8 with 7 points - only 0.00% unknown
- deleting segment 9 with 14 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 10 with 4 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 11 with 2 points - only 0.00% unknown
- deleting segment 12 with 21 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 13 with 2 points - only 0.00% unknown
- deleting segment 14 with 7 points - only 0.00% unknown
- deleting segment 15 with 7 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 (0.03-->4.88) (max @ vno 128641 --> 61076)
- face area 0.33 +- 0.16 (0.00-->2.76)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4386998.0, rms=0.00
- rms = 2.14, time step reduction 1 of 3 to 0.250...
- rms = 0.53, time step reduction 2 of 3 to 0.125...
- rms = 0.07, time step reduction 3 of 3 to 0.062...
- 001: dt: 0.1250, sse=4386998.0, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 82 points - only 0.00% unknown
- deleting segment 1 with 6 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 2 with 2 points - only 0.00% unknown
- deleting segment 3 with 5 points - only 0.00% unknown
- deleting segment 4 with 10 points - only 0.00% unknown
- deleting segment 5 with 7 points - only 0.00% unknown
- deleting segment 6 with 14 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 7 with 4 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 21 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 10 with 2 points - only 0.00% unknown
- deleting segment 11 with 7 points - only 0.00% unknown
- deleting segment 12 with 7 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 (0.03-->4.88) (max @ vno 128641 --> 61076)
- face area 0.33 +- 0.16 (0.00-->2.76)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4386998.0, rms=0.00
- rms = 2.14, time step reduction 1 of 3 to 0.250...
- rms = 0.53, time step reduction 2 of 3 to 0.125...
- rms = 0.07, time step reduction 3 of 3 to 0.062...
- 002: dt: 0.1250, sse=4386998.0, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 82 points - only 0.00% unknown
- deleting segment 1 with 6 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 2 with 2 points - only 0.00% unknown
- deleting segment 3 with 5 points - only 0.00% unknown
- deleting segment 4 with 10 points - only 0.00% unknown
- deleting segment 5 with 7 points - only 0.00% unknown
- deleting segment 6 with 14 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 7 with 4 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 21 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 10 with 2 points - only 0.00% unknown
- deleting segment 11 with 7 points - only 0.00% unknown
- deleting segment 12 with 7 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 (0.03-->4.88) (max @ vno 128641 --> 61076)
- face area 0.33 +- 0.16 (0.00-->2.76)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4386998.0, rms=0.00
- rms = 2.14, time step reduction 1 of 3 to 0.250...
- rms = 0.53, time step reduction 2 of 3 to 0.125...
- rms = 0.07, time step reduction 3 of 3 to 0.062...
- 003: dt: 0.1250, sse=4386998.0, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 82 points - only 0.00% unknown
- deleting segment 1 with 6 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 2 with 2 points - only 0.00% unknown
- deleting segment 3 with 5 points - only 0.00% unknown
- deleting segment 4 with 10 points - only 0.00% unknown
- deleting segment 5 with 7 points - only 0.00% unknown
- deleting segment 6 with 14 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 7 with 4 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 21 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 10 with 2 points - only 0.00% unknown
- deleting segment 11 with 7 points - only 0.00% unknown
- deleting segment 12 with 7 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=4386998.0, rms=0.00
- rms = 2.14, time step reduction 1 of 3 to 0.250...
- rms = 0.53, time step reduction 2 of 3 to 0.125...
- rms = 0.07, time step reduction 3 of 3 to 0.062...
- 004: dt: 0.1250, sse=4386998.0, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- smoothing surface for 5 iterations...
- reading initial pial vertex positions from woT2.pial...
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [90.30 215.70], gm=153.00+-20.90, and vertices in regions > 142.5
- 32807 surface locations found to contain inconsistent values (2310 in, 30497 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=477812.7, rms=0.22
- 001: dt: 0.5000, sse=449355.5, rms=0.218 (0.000%)
- 002: dt: 0.5000, sse=432252.6, rms=0.205 (0.000%)
- 003: dt: 0.5000, sse=421216.9, rms=0.196 (0.000%)
- 004: dt: 0.5000, sse=412802.5, rms=0.187 (0.000%)
- 005: dt: 0.5000, sse=406688.1, rms=0.180 (0.000%)
- 006: dt: 0.5000, sse=402262.4, rms=0.174 (0.000%)
- 007: dt: 0.5000, sse=398851.8, rms=0.168 (0.000%)
- 008: dt: 0.5000, sse=396372.0, rms=0.164 (0.000%)
- 009: dt: 0.5000, sse=394094.9, rms=0.160 (0.000%)
- 010: dt: 0.5000, sse=392314.0, rms=0.157 (0.000%)
- 011: dt: 0.5000, sse=390760.2, rms=0.154 (0.000%)
- 012: dt: 0.5000, sse=389267.7, rms=0.151 (0.000%)
- 013: dt: 0.5000, sse=387842.2, rms=0.150 (0.000%)
- 014: dt: 0.5000, sse=386798.8, rms=0.148 (0.000%)
- 015: dt: 0.5000, sse=385312.5, rms=0.147 (0.000%)
- 016: dt: 0.5000, sse=384137.6, rms=0.146 (0.000%)
- 017: dt: 0.5000, sse=383178.7, rms=0.145 (0.000%)
- 018: dt: 0.5000, sse=381952.5, rms=0.144 (0.000%)
- 019: dt: 0.5000, sse=380576.8, rms=0.144 (0.000%)
- 020: dt: 0.5000, sse=379593.5, rms=0.143 (0.000%)
- 021: dt: 0.5000, sse=378391.9, rms=0.143 (0.000%)
- 022: dt: 0.5000, sse=377621.7, rms=0.143 (0.000%)
- 023: dt: 0.5000, sse=376297.8, rms=0.143 (0.000%)
- 024: dt: 0.5000, sse=375100.4, rms=0.143 (0.000%)
- 025: dt: 0.5000, sse=374101.6, rms=0.144 (0.000%)
- 026: dt: 0.5000, sse=373066.3, rms=0.144 (0.000%)
- 027: dt: 0.5000, sse=372314.5, rms=0.144 (0.000%)
- 028: dt: 0.5000, sse=371561.9, rms=0.144 (0.000%)
- 029: dt: 0.5000, sse=370353.1, rms=0.145 (0.000%)
- 030: dt: 0.5000, sse=369477.8, rms=0.145 (0.000%)
- positioning took 3.5 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [89.50 218.50], gm=154.00+-21.50, and vertices in regions > 143.2
- 27943 surface locations found to contain inconsistent values (809 in, 27134 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=38378.2, rms=0.12
- 031: dt: 0.5000, sse=38135.8, rms=0.120 (0.000%)
- 032: dt: 0.5000, sse=39009.0, rms=0.110 (0.000%)
- 033: dt: 0.5000, sse=40026.8, rms=0.102 (0.000%)
- 034: dt: 0.5000, sse=40911.9, rms=0.097 (0.000%)
- 035: dt: 0.5000, sse=41665.4, rms=0.091 (0.000%)
- 036: dt: 0.5000, sse=42385.6, rms=0.087 (0.000%)
- 037: dt: 0.5000, sse=43072.5, rms=0.082 (0.000%)
- 038: dt: 0.5000, sse=43729.2, rms=0.078 (0.000%)
- 039: dt: 0.5000, sse=44369.7, rms=0.075 (0.000%)
- 040: dt: 0.5000, sse=44999.9, rms=0.071 (0.000%)
- 041: dt: 0.5000, sse=45601.4, rms=0.068 (0.000%)
- 042: dt: 0.5000, sse=46167.7, rms=0.065 (0.000%)
- 043: dt: 0.5000, sse=46702.2, rms=0.062 (0.000%)
- 044: dt: 0.5000, sse=47200.3, rms=0.060 (0.000%)
- 045: dt: 0.5000, sse=47676.0, rms=0.057 (0.000%)
- 046: dt: 0.5000, sse=48146.5, rms=0.055 (0.000%)
- 047: dt: 0.5000, sse=48575.5, rms=0.053 (0.000%)
- 048: dt: 0.5000, sse=48998.5, rms=0.051 (0.000%)
- 049: dt: 0.5000, sse=49365.2, rms=0.050 (0.000%)
- 050: dt: 0.5000, sse=49735.8, rms=0.048 (0.000%)
- 051: dt: 0.5000, sse=50066.8, rms=0.047 (0.000%)
- 052: dt: 0.5000, sse=50379.9, rms=0.046 (0.000%)
- 053: dt: 0.5000, sse=50670.9, rms=0.045 (0.000%)
- 054: dt: 0.5000, sse=50904.4, rms=0.044 (0.000%)
- 055: dt: 0.5000, sse=51164.3, rms=0.043 (0.000%)
- 056: dt: 0.5000, sse=51377.6, rms=0.042 (0.000%)
- 057: dt: 0.5000, sse=51585.4, rms=0.041 (0.000%)
- 058: dt: 0.5000, sse=51787.5, rms=0.040 (0.000%)
- 059: dt: 0.5000, sse=51969.9, rms=0.040 (0.000%)
- 060: dt: 0.5000, sse=52121.2, rms=0.039 (0.000%)
- positioning took 3.4 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [108.70 199.30], gm=154.00+-15.10, and vertices in regions > 146.4
- 19570 surface locations found to contain inconsistent values (9132 in, 10438 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=11476.4, rms=0.23
- 061: dt: 0.5000, sse=11187.8, rms=0.220 (0.000%)
- 062: dt: 0.5000, sse=10539.7, rms=0.209 (0.000%)
- 063: dt: 0.5000, sse=10026.6, rms=0.198 (0.000%)
- 064: dt: 0.5000, sse=9615.5, rms=0.189 (0.000%)
- 065: dt: 0.5000, sse=9293.1, rms=0.180 (0.000%)
- 066: dt: 0.5000, sse=9042.6, rms=0.173 (0.000%)
- 067: dt: 0.5000, sse=8818.6, rms=0.166 (0.000%)
- 068: dt: 0.5000, sse=8612.3, rms=0.160 (0.000%)
- 069: dt: 0.5000, sse=8428.4, rms=0.153 (0.000%)
- 070: dt: 0.5000, sse=8277.6, rms=0.147 (0.000%)
- 071: dt: 0.5000, sse=8152.2, rms=0.141 (0.000%)
- 072: dt: 0.5000, sse=8046.2, rms=0.135 (0.000%)
- 073: dt: 0.5000, sse=7952.0, rms=0.130 (0.000%)
- 074: dt: 0.5000, sse=7872.8, rms=0.124 (0.000%)
- 075: dt: 0.5000, sse=7806.1, rms=0.119 (0.000%)
- 076: dt: 0.5000, sse=7751.3, rms=0.114 (0.000%)
- 077: dt: 0.5000, sse=7706.8, rms=0.110 (0.000%)
- 078: dt: 0.5000, sse=7672.5, rms=0.105 (0.000%)
- 079: dt: 0.5000, sse=7645.5, rms=0.100 (0.000%)
- 080: dt: 0.5000, sse=7627.4, rms=0.096 (0.000%)
- 081: dt: 0.5000, sse=7613.3, rms=0.092 (0.000%)
- 082: dt: 0.5000, sse=7607.2, rms=0.088 (0.000%)
- 083: dt: 0.5000, sse=7605.6, rms=0.084 (0.000%)
- 084: dt: 0.5000, sse=7604.2, rms=0.080 (0.000%)
- 085: dt: 0.5000, sse=7608.4, rms=0.077 (0.000%)
- 086: dt: 0.5000, sse=7614.9, rms=0.073 (0.000%)
- 087: dt: 0.5000, sse=7622.4, rms=0.070 (0.000%)
- 088: dt: 0.5000, sse=7628.2, rms=0.067 (0.000%)
- 089: dt: 0.5000, sse=7640.1, rms=0.064 (0.000%)
- 090: dt: 0.5000, sse=7649.8, rms=0.062 (0.000%)
- positioning took 3.5 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [87.40 220.60], gm=154.00+-22.20, and vertices in regions > 142.9
- 29719 surface locations found to contain inconsistent values (21 in, 29698 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/sub003/surf/lh.pial...
- writing smoothed curvature to lh.curv.pial
- 000: dt: 0.0000, sse=1238.4, rms=0.06
- 091: dt: 0.5000, sse=1204.5, rms=0.063 (0.000%)
- 092: dt: 0.5000, sse=1125.0, rms=0.056 (0.000%)
- 093: dt: 0.5000, sse=1081.8, rms=0.052 (0.000%)
- 094: dt: 0.5000, sse=1051.0, rms=0.048 (0.000%)
- 095: dt: 0.5000, sse=1025.0, rms=0.045 (0.000%)
- 096: dt: 0.5000, sse=1007.5, rms=0.043 (0.000%)
- 097: dt: 0.5000, sse=993.6, rms=0.041 (0.000%)
- 098: dt: 0.5000, sse=982.4, rms=0.039 (0.000%)
- 099: dt: 0.5000, sse=971.8, rms=0.038 (0.000%)
- 100: dt: 0.5000, sse=963.0, rms=0.036 (0.000%)
- 101: dt: 0.5000, sse=955.3, rms=0.035 (0.000%)
- 102: dt: 0.5000, sse=948.3, rms=0.034 (0.000%)
- 103: dt: 0.5000, sse=943.1, rms=0.033 (0.000%)
- 104: dt: 0.5000, sse=938.0, rms=0.032 (0.000%)
- 105: dt: 0.5000, sse=934.2, rms=0.031 (0.000%)
- 106: dt: 0.5000, sse=930.5, rms=0.030 (0.000%)
- 107: dt: 0.5000, sse=927.6, rms=0.030 (0.000%)
- 108: dt: 0.5000, sse=924.8, rms=0.029 (0.000%)
- 109: dt: 0.5000, sse=923.0, rms=0.029 (0.000%)
- 110: dt: 0.5000, sse=921.2, rms=0.028 (0.000%)
- 111: dt: 0.5000, sse=919.6, rms=0.028 (0.000%)
- 112: dt: 0.5000, sse=918.5, rms=0.028 (0.000%)
- 113: dt: 0.5000, sse=917.8, rms=0.027 (0.000%)
- 114: dt: 0.5000, sse=917.3, rms=0.027 (0.000%)
- 115: dt: 0.5000, sse=916.8, rms=0.027 (0.000%)
- 116: dt: 0.5000, sse=916.2, rms=0.027 (0.000%)
- 117: dt: 0.5000, sse=915.7, rms=0.027 (0.000%)
- 118: dt: 0.5000, sse=915.5, rms=0.027 (0.000%)
- 119: dt: 0.5000, sse=915.3, rms=0.026 (0.000%)
- 120: dt: 0.5000, sse=915.3, rms=0.026 (0.000%)
- positioning took 3.4 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.curv.pial
- writing smoothed area to lh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.area.pial
- vertex spacing 1.05 +- 0.45 (0.05-->8.33) (max @ vno 102151 --> 101354)
- face area 0.43 +- 0.33 (0.00-->6.26)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 128814 vertices processed
- 25000 of 128814 vertices processed
- 50000 of 128814 vertices processed
- 75000 of 128814 vertices processed
- 100000 of 128814 vertices processed
- 125000 of 128814 vertices processed
- 0 of 128814 vertices processed
- 25000 of 128814 vertices processed
- 50000 of 128814 vertices processed
- 75000 of 128814 vertices processed
- 100000 of 128814 vertices processed
- 125000 of 128814 vertices processed
- thickness calculation complete, 399:1099 truncations.
- 29395 vertices at 0 distance
- 87072 vertices at 1 distance
- 83101 vertices at 2 distance
- 34346 vertices at 3 distance
- 9174 vertices at 4 distance
- 2323 vertices at 5 distance
- 761 vertices at 6 distance
- 211 vertices at 7 distance
- 75 vertices at 8 distance
- 40 vertices at 9 distance
- 32 vertices at 10 distance
- 22 vertices at 11 distance
- 19 vertices at 12 distance
- 14 vertices at 13 distance
- 7 vertices at 14 distance
- 12 vertices at 15 distance
- 16 vertices at 16 distance
- 8 vertices at 17 distance
- 5 vertices at 18 distance
- 4 vertices at 19 distance
- 21 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.thickness
- positioning took 17.7 minutes
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/scripts
- cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.woT2.pial
- `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.woT2.pial'
- mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub003 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/sub003/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/wm.mgz...
- 14678 bright wm thresholded.
- 302 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.orig...
- computing class statistics...
- border white: 229356 voxels (1.37%)
- border gray 266114 voxels (1.59%)
- WM (92.0): 92.8 +- 10.5 [70.0 --> 110.0]
- GM (74.0) : 72.0 +- 13.3 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 42.7 (was 70)
- setting MAX_BORDER_WHITE to 115.5 (was 105)
- setting MIN_BORDER_WHITE to 56.0 (was 85)
- setting MAX_CSF to 29.3 (was 40)
- setting MAX_GRAY to 94.5 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 49.3 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 16.0 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=105, GM=56
- mean inside = 92.5, mean outside = 66.6
- smoothing surface for 5 iterations...
- reading initial white vertex positions from white...
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.90 +- 0.26 (0.02-->4.00) (max @ vno 95998 --> 96851)
- face area 0.34 +- 0.16 (0.00-->2.73)
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- deleting segment 1 with 4 points - only 0.00% unknown
- deleting segment 4 with 12 points - only 0.00% unknown
- deleting segment 6 with 460 points - only 2.61% unknown
- deleting segment 7 with 13 points - only 0.00% unknown
- deleting segment 8 with 64 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 10 with 11 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 11 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 (0.04-->4.00) (max @ vno 96851 --> 95998)
- face area 0.34 +- 0.16 (0.00-->2.73)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4397407.0, rms=0.00
- rms = 1.10, time step reduction 1 of 3 to 0.250...
- rms = 0.29, time step reduction 2 of 3 to 0.125...
- rms = 0.04, time step reduction 3 of 3 to 0.062...
- 001: dt: 0.1250, sse=4397407.0, 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
- deleting segment 1 with 12 points - only 0.00% unknown
- deleting segment 2 with 460 points - only 2.61% unknown
- deleting segment 3 with 13 points - only 0.00% unknown
- deleting segment 4 with 64 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 6 with 11 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 7 with 2 points - only 0.00% unknown
- 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 (0.04-->4.00) (max @ vno 96851 --> 95998)
- face area 0.34 +- 0.16 (0.00-->2.73)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4397407.0, rms=0.00
- rms = 1.13, time step reduction 1 of 3 to 0.250...
- rms = 0.29, time step reduction 2 of 3 to 0.125...
- rms = 0.04, time step reduction 3 of 3 to 0.062...
- 002: dt: 0.1250, sse=4397407.0, 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
- deleting segment 1 with 12 points - only 0.00% unknown
- deleting segment 2 with 460 points - only 2.61% unknown
- deleting segment 3 with 13 points - only 0.00% unknown
- deleting segment 4 with 64 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 6 with 11 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 7 with 2 points - only 0.00% unknown
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.25 (0.04-->4.00) (max @ vno 96851 --> 95998)
- face area 0.34 +- 0.16 (0.00-->2.73)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4397407.0, rms=0.00
- rms = 1.10, time step reduction 1 of 3 to 0.250...
- rms = 0.29, time step reduction 2 of 3 to 0.125...
- rms = 0.04, time step reduction 3 of 3 to 0.062...
- 003: dt: 0.1250, sse=4397407.0, 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
- deleting segment 1 with 12 points - only 0.00% unknown
- deleting segment 2 with 460 points - only 2.61% unknown
- deleting segment 3 with 13 points - only 0.00% unknown
- deleting segment 4 with 64 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 6 with 11 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 7 with 2 points - only 0.00% unknown
- 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=4397407.0, rms=0.00
- rms = 1.13, time step reduction 1 of 3 to 0.250...
- rms = 0.29, time step reduction 2 of 3 to 0.125...
- rms = 0.04, time step reduction 3 of 3 to 0.062...
- 004: dt: 0.1250, sse=4397407.0, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 1 vertex label from ripped group
- smoothing surface for 5 iterations...
- reading initial pial vertex positions from woT2.pial...
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [88.60 219.40], gm=154.00+-21.80, and vertices in regions > 143.1
- 34217 surface locations found to contain inconsistent values (2516 in, 31701 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=482860.4, rms=0.22
- 001: dt: 0.5000, sse=453568.3, rms=0.213 (0.000%)
- 002: dt: 0.5000, sse=435436.9, rms=0.201 (0.000%)
- 003: dt: 0.5000, sse=424307.9, rms=0.191 (0.000%)
- 004: dt: 0.5000, sse=415493.0, rms=0.182 (0.000%)
- 005: dt: 0.5000, sse=409468.9, rms=0.175 (0.000%)
- 006: dt: 0.5000, sse=404844.1, rms=0.169 (0.000%)
- 007: dt: 0.5000, sse=401477.8, rms=0.164 (0.000%)
- 008: dt: 0.5000, sse=398681.3, rms=0.160 (0.000%)
- 009: dt: 0.5000, sse=396681.0, rms=0.156 (0.000%)
- 010: dt: 0.5000, sse=394722.8, rms=0.153 (0.000%)
- 011: dt: 0.5000, sse=393133.6, rms=0.151 (0.000%)
- 012: dt: 0.5000, sse=391517.3, rms=0.149 (0.000%)
- 013: dt: 0.5000, sse=389977.8, rms=0.147 (0.000%)
- 014: dt: 0.5000, sse=388417.8, rms=0.146 (0.000%)
- 015: dt: 0.5000, sse=387054.7, rms=0.145 (0.000%)
- 016: dt: 0.5000, sse=385886.7, rms=0.145 (0.000%)
- 017: dt: 0.5000, sse=384518.3, rms=0.144 (0.000%)
- 018: dt: 0.5000, sse=383164.8, rms=0.144 (0.000%)
- 019: dt: 0.5000, sse=381827.3, rms=0.144 (0.000%)
- 020: dt: 0.5000, sse=380372.8, rms=0.144 (0.000%)
- 021: dt: 0.5000, sse=379264.2, rms=0.144 (0.000%)
- 022: dt: 0.5000, sse=377852.0, rms=0.144 (0.000%)
- 023: dt: 0.5000, sse=376810.3, rms=0.144 (0.000%)
- 024: dt: 0.5000, sse=375525.6, rms=0.144 (0.000%)
- 025: dt: 0.5000, sse=374336.8, rms=0.144 (0.000%)
- 026: dt: 0.5000, sse=373390.2, rms=0.145 (0.000%)
- 027: dt: 0.5000, sse=372069.3, rms=0.145 (0.000%)
- 028: dt: 0.5000, sse=371236.5, rms=0.146 (0.000%)
- 029: dt: 0.5000, sse=370461.8, rms=0.146 (0.000%)
- 030: dt: 0.5000, sse=369661.6, rms=0.146 (0.000%)
- positioning took 3.7 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [105.50 204.50], gm=155.00+-16.50, and vertices in regions > 146.7
- 25355 surface locations found to contain inconsistent values (7809 in, 17546 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=42535.0, rms=0.22
- 031: dt: 0.5000, sse=42114.6, rms=0.217 (0.000%)
- 032: dt: 0.5000, sse=41659.8, rms=0.205 (0.000%)
- 033: dt: 0.5000, sse=41729.4, rms=0.194 (0.000%)
- 034: dt: 0.5000, sse=42056.3, rms=0.186 (0.000%)
- 035: dt: 0.5000, sse=42418.2, rms=0.179 (0.000%)
- 036: dt: 0.5000, sse=42838.1, rms=0.171 (0.000%)
- 037: dt: 0.5000, sse=43298.3, rms=0.165 (0.000%)
- 038: dt: 0.5000, sse=43806.6, rms=0.158 (0.000%)
- 039: dt: 0.5000, sse=44370.1, rms=0.152 (0.000%)
- 040: dt: 0.5000, sse=44980.9, rms=0.146 (0.000%)
- 041: dt: 0.5000, sse=45632.4, rms=0.141 (0.000%)
- 042: dt: 0.5000, sse=46265.5, rms=0.136 (0.000%)
- 043: dt: 0.5000, sse=46913.8, rms=0.131 (0.000%)
- 044: dt: 0.5000, sse=47565.2, rms=0.126 (0.000%)
- 045: dt: 0.5000, sse=48197.7, rms=0.122 (0.000%)
- 046: dt: 0.5000, sse=48805.5, rms=0.117 (0.000%)
- 047: dt: 0.5000, sse=49411.1, rms=0.113 (0.000%)
- 048: dt: 0.5000, sse=49999.7, rms=0.109 (0.000%)
- 049: dt: 0.5000, sse=50571.0, rms=0.106 (0.000%)
- 050: dt: 0.5000, sse=51117.0, rms=0.102 (0.000%)
- 051: dt: 0.5000, sse=51633.1, rms=0.099 (0.000%)
- 052: dt: 0.5000, sse=52135.4, rms=0.095 (0.000%)
- 053: dt: 0.5000, sse=52612.7, rms=0.092 (0.000%)
- 054: dt: 0.5000, sse=53058.0, rms=0.089 (0.000%)
- 055: dt: 0.5000, sse=53490.7, rms=0.086 (0.000%)
- 056: dt: 0.5000, sse=53917.7, rms=0.083 (0.000%)
- 057: dt: 0.5000, sse=54323.5, rms=0.080 (0.000%)
- 058: dt: 0.5000, sse=54708.8, rms=0.077 (0.000%)
- 059: dt: 0.5000, sse=55063.3, rms=0.074 (0.000%)
- 060: dt: 0.5000, sse=55436.0, rms=0.072 (0.000%)
- positioning took 3.5 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [108.90 197.10], gm=153.00+-14.70, and vertices in regions > 145.6
- 21451 surface locations found to contain inconsistent values (12924 in, 8527 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=10524.7, rms=0.20
- 061: dt: 0.5000, sse=10284.0, rms=0.198 (0.000%)
- 062: dt: 0.5000, sse=9826.4, rms=0.188 (0.000%)
- 063: dt: 0.5000, sse=9480.1, rms=0.179 (0.000%)
- 064: dt: 0.5000, sse=9200.0, rms=0.171 (0.000%)
- 065: dt: 0.5000, sse=8970.0, rms=0.164 (0.000%)
- 066: dt: 0.5000, sse=8783.6, rms=0.158 (0.000%)
- 067: dt: 0.5000, sse=8611.4, rms=0.152 (0.000%)
- 068: dt: 0.5000, sse=8447.4, rms=0.146 (0.000%)
- 069: dt: 0.5000, sse=8299.6, rms=0.141 (0.000%)
- 070: dt: 0.5000, sse=8167.2, rms=0.135 (0.000%)
- 071: dt: 0.5000, sse=8054.4, rms=0.130 (0.000%)
- 072: dt: 0.5000, sse=7957.4, rms=0.125 (0.000%)
- 073: dt: 0.5000, sse=7872.5, rms=0.120 (0.000%)
- 074: dt: 0.5000, sse=7797.2, rms=0.115 (0.000%)
- 075: dt: 0.5000, sse=7731.2, rms=0.110 (0.000%)
- 076: dt: 0.5000, sse=7674.8, rms=0.106 (0.000%)
- 077: dt: 0.5000, sse=7625.3, rms=0.102 (0.000%)
- 078: dt: 0.5000, sse=7585.4, rms=0.097 (0.000%)
- 079: dt: 0.5000, sse=7550.1, rms=0.093 (0.000%)
- 080: dt: 0.5000, sse=7529.5, rms=0.090 (0.000%)
- 081: dt: 0.5000, sse=7506.7, rms=0.086 (0.000%)
- 082: dt: 0.5000, sse=7489.7, rms=0.083 (0.000%)
- 083: dt: 0.5000, sse=7478.4, rms=0.079 (0.000%)
- 084: dt: 0.5000, sse=7473.8, rms=0.076 (0.000%)
- 085: dt: 0.5000, sse=7465.4, rms=0.073 (0.000%)
- 086: dt: 0.5000, sse=7462.3, rms=0.070 (0.000%)
- 087: dt: 0.5000, sse=7465.9, rms=0.068 (0.000%)
- 088: dt: 0.5000, sse=7467.3, rms=0.065 (0.000%)
- 089: dt: 0.5000, sse=7472.5, rms=0.063 (0.000%)
- 090: dt: 0.5000, sse=7471.7, rms=0.061 (0.000%)
- positioning took 3.4 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [85.00 223.00], gm=154.00+-23.00, and vertices in regions > 142.5
- 37706 surface locations found to contain inconsistent values (8 in, 37698 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/sub003/surf/rh.pial...
- writing smoothed curvature to rh.curv.pial
- 000: dt: 0.0000, sse=1885.8, rms=0.10
- 091: dt: 0.5000, sse=1749.3, rms=0.093 (0.000%)
- 092: dt: 0.5000, sse=1521.6, rms=0.081 (0.000%)
- 093: dt: 0.5000, sse=1384.6, rms=0.073 (0.000%)
- 094: dt: 0.5000, sse=1291.3, rms=0.066 (0.000%)
- 095: dt: 0.5000, sse=1221.4, rms=0.060 (0.000%)
- 096: dt: 0.5000, sse=1178.9, rms=0.057 (0.000%)
- 097: dt: 0.5000, sse=1145.6, rms=0.053 (0.000%)
- 098: dt: 0.5000, sse=1118.7, rms=0.051 (0.000%)
- 099: dt: 0.5000, sse=1095.2, rms=0.048 (0.000%)
- 100: dt: 0.5000, sse=1077.4, rms=0.045 (0.000%)
- 101: dt: 0.5000, sse=1062.5, rms=0.043 (0.000%)
- 102: dt: 0.5000, sse=1050.8, rms=0.042 (0.000%)
- 103: dt: 0.5000, sse=1040.5, rms=0.040 (0.000%)
- 104: dt: 0.5000, sse=1032.4, rms=0.038 (0.000%)
- 105: dt: 0.5000, sse=1026.7, rms=0.037 (0.000%)
- 106: dt: 0.5000, sse=1021.3, rms=0.036 (0.000%)
- 107: dt: 0.5000, sse=1017.7, rms=0.035 (0.000%)
- 108: dt: 0.5000, sse=1014.3, rms=0.035 (0.000%)
- 109: dt: 0.5000, sse=1011.2, rms=0.034 (0.000%)
- 110: dt: 0.5000, sse=1008.9, rms=0.034 (0.000%)
- 111: dt: 0.5000, sse=1006.8, rms=0.033 (0.000%)
- 112: dt: 0.5000, sse=1005.6, rms=0.033 (0.000%)
- 113: dt: 0.5000, sse=1005.0, rms=0.032 (0.000%)
- 114: dt: 0.5000, sse=1004.1, rms=0.032 (0.000%)
- 115: dt: 0.5000, sse=1004.1, rms=0.032 (0.000%)
- 116: dt: 0.5000, sse=1003.4, rms=0.032 (0.000%)
- 117: dt: 0.5000, sse=1002.9, rms=0.032 (0.000%)
- 118: dt: 0.5000, sse=1002.3, rms=0.031 (0.000%)
- 119: dt: 0.5000, sse=1001.9, rms=0.031 (0.000%)
- 120: dt: 0.5000, sse=1001.3, rms=0.031 (0.000%)
- positioning took 3.4 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.curv.pial
- writing smoothed area to rh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.area.pial
- vertex spacing 1.06 +- 0.46 (0.09-->6.06) (max @ vno 83570 --> 83557)
- face area 0.43 +- 0.33 (0.00-->5.92)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 127449 vertices processed
- 25000 of 127449 vertices processed
- 50000 of 127449 vertices processed
- 75000 of 127449 vertices processed
- 100000 of 127449 vertices processed
- 125000 of 127449 vertices processed
- 0 of 127449 vertices processed
- 25000 of 127449 vertices processed
- 50000 of 127449 vertices processed
- 75000 of 127449 vertices processed
- 100000 of 127449 vertices processed
- 125000 of 127449 vertices processed
- thickness calculation complete, 367:766 truncations.
- 29366 vertices at 0 distance
- 84591 vertices at 1 distance
- 82829 vertices at 2 distance
- 33888 vertices at 3 distance
- 8892 vertices at 4 distance
- 2439 vertices at 5 distance
- 696 vertices at 6 distance
- 252 vertices at 7 distance
- 125 vertices at 8 distance
- 62 vertices at 9 distance
- 36 vertices at 10 distance
- 49 vertices at 11 distance
- 43 vertices at 12 distance
- 37 vertices at 13 distance
- 21 vertices at 14 distance
- 16 vertices at 15 distance
- 8 vertices at 16 distance
- 10 vertices at 17 distance
- 15 vertices at 18 distance
- 16 vertices at 19 distance
- 7 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.thickness
- positioning took 18.2 minutes
- #--------------------------------------------
- #@# Surf Volume lh Thu Aug 8 22:26:50 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 22:26:50 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 22:26:51 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri
- mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon sub003
- 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 = 19
- writing volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/ribbon.mgz
- writing ribbon files
- #--------------------------------------------
- #@# ASeg Stats Thu Aug 8 22:50:35 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003
- 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 sub003
- $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 sub003
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- UseRobust 0
- atlas_icv (eTIV) = 1018934 mm^3 (det: 1.911905 )
- Computing euler number
- orig.nofix lheno = -16, rheno = -24
- orig.nofix lhholes = 9, rhholes = 13
- Loading mri/aseg.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 236673.500 235684.000 diff= 989.5 pctdiff= 0.418
- rhCtxGM: 236677.165 235302.000 diff= 1375.2 pctdiff= 0.581
- lhCtxWM: 188062.518 188277.500 diff= -215.0 pctdiff=-0.114
- rhCtxWM: 190680.655 190057.500 diff= 623.2 pctdiff= 0.327
- SubCortGMVol 59365.000
- SupraTentVol 920678.838 (917222.000) diff=3456.838 pctdiff=0.375
- SupraTentVolNotVent 912477.838 (909021.000) diff=3456.838 pctdiff=0.379
- BrainSegVol 1042313.000 (1040328.000) diff=1985.000 pctdiff=0.190
- BrainSegVolNotVent 1031549.000 (1034086.838) diff=-2537.838 pctdiff=-0.246
- BrainSegVolNotVent 1031549.000
- CerebellumVol 122293.000
- VentChorVol 8201.000
- 3rd4th5thCSF 2563.000
- CSFVol 597.000, OptChiasmVol 216.000
- MaskVol 1465683.000
- 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 3174 3174.281
- 4 5 Left-Inf-Lat-Vent 341 340.772
- 5 7 Left-Cerebellum-White-Matter 12687 12687.178
- 6 8 Left-Cerebellum-Cortex 48130 48129.738
- 7 10 Left-Thalamus-Proper 7080 7079.920
- 8 11 Left-Caudate 3482 3482.067
- 9 12 Left-Putamen 6615 6615.351
- 10 13 Left-Pallidum 1985 1984.917
- 11 14 3rd-Ventricle 858 858.224
- 12 15 4th-Ventricle 1310 1309.628
- 13 16 Brain-Stem 18583 18583.396
- 14 17 Left-Hippocampus 3974 3974.137
- 15 18 Left-Amygdala 1426 1426.304
- 16 24 CSF 600 600.095
- 17 26 Left-Accumbens-area 727 726.984
- 18 28 Left-VentralDC 3496 3495.827
- 19 30 Left-vessel 198 197.954
- 20 31 Left-choroid-plexus 964 964.113
- 23 43 Right-Lateral-Ventricle 2276 2276.475
- 24 44 Right-Inf-Lat-Vent 215 214.511
- 25 46 Right-Cerebellum-White-Matter 13616 13616.034
- 26 47 Right-Cerebellum-Cortex 50097 50096.945
- 27 49 Right-Thalamus-Proper 7254 7254.009
- 28 50 Right-Caudate 3359 3359.181
- 29 51 Right-Putamen 6317 6317.163
- 30 52 Right-Pallidum 1790 1790.350
- 31 53 Right-Hippocampus 3896 3895.694
- 32 54 Right-Amygdala 1726 1726.466
- 33 58 Right-Accumbens-area 761 760.781
- 34 60 Right-VentralDC 3476 3476.094
- 35 62 Right-vessel 111 110.917
- 36 63 Right-choroid-plexus 1384 1384.161
- 37 72 5th-Ventricle 0 0.000
- 38 77 WM-hypointensities 1460 1460.332
- 39 78 Left-WM-hypointensities 0 0.000
- 40 79 Right-WM-hypointensities 0 0.000
- 41 80 non-WM-hypointensities 13 12.577
- 42 81 Left-non-WM-hypointensities 0 0.000
- 43 82 Right-non-WM-hypointensities 0 0.000
- 44 85 Optic-Chiasm 227 226.940
- 45 251 CC_Posterior 717 717.405
- 46 252 CC_Mid_Posterior 331 331.448
- 47 253 CC_Central 360 359.750
- 48 254 CC_Mid_Anterior 392 392.465
- 49 255 CC_Anterior 752 752.399
- Reporting on 45 segmentations
- mri_segstats done
- #-----------------------------------------
- #@# AParc-to-ASeg Thu Aug 8 22:56:05 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003
- mri_aparc2aseg --s sub003 --volmask
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- subject sub003
- outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/aparc+aseg.mgz
- useribbon 0
- baseoffset 0
- RipUnknown 0
- Reading lh white surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.white
- Reading lh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.pial
- Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/surf/rh.white
- Reading rh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.pial
- Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/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/sub003/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 = 468608
- Used brute-force search on 0 voxels
- Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/aparc+aseg.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003
- mri_aparc2aseg --s sub003 --volmask --a2009s
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- subject sub003
- outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/aparc.a2009s+aseg.mgz
- useribbon 0
- baseoffset 10100
- RipUnknown 0
- Reading lh white surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.white
- Reading lh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.pial
- Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/surf/rh.white
- Reading rh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.pial
- Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/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/sub003/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 = 468608
- Used brute-force search on 0 voxels
- Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/aparc.a2009s+aseg.mgz
- #-----------------------------------------
- #@# WMParc Thu Aug 8 23:01:38 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003
- mri_aparc2aseg --s sub003 --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 sub003
- 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/sub003/mri/aparc+aseg.mgz
- Reading lh white surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.white
- Reading lh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.pial
- Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/surf/rh.white
- Reading rh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.pial
- Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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/sub003/mri/ribbon.mgz
- Loading filled from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/filled.mgz
- Ripping vertices labeled as unkown
- Ripped 7455 vertices from left hemi
- Ripped 8385 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/sub003/mri/aseg.mgz
- Loading Ctx Seg File /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 = 846670
- Used brute-force search on 382 voxels
- Fixing Parahip LH WM
- Found 11 clusters
- 0 k 1.000000
- 1 k 6.000000
- 2 k 1322.000000
- 3 k 1.000000
- 4 k 1.000000
- 5 k 1.000000
- 6 k 1.000000
- 7 k 1.000000
- 8 k 2.000000
- 9 k 2.000000
- 10 k 1.000000
- Fixing Parahip RH WM
- Found 14 clusters
- 0 k 1589.000000
- 1 k 1.000000
- 2 k 2.000000
- 3 k 1.000000
- 4 k 2.000000
- 5 k 1.000000
- 6 k 2.000000
- 7 k 1.000000
- 8 k 1.000000
- 9 k 11.000000
- 10 k 1.000000
- 11 k 1.000000
- 12 k 1.000000
- 13 k 1.000000
- Writing output aseg to mri/wmparc.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003
- 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 sub003 --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 sub003 --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) = 1018934 mm^3 (det: 1.911905 )
- Loading mri/wmparc.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 236673.500 235684.000 diff= 989.5 pctdiff= 0.418
- rhCtxGM: 236677.165 235302.000 diff= 1375.2 pctdiff= 0.581
- lhCtxWM: 188062.518 188277.500 diff= -215.0 pctdiff=-0.114
- rhCtxWM: 190680.655 190057.500 diff= 623.2 pctdiff= 0.327
- SubCortGMVol 59365.000
- SupraTentVol 920678.838 (917222.000) diff=3456.838 pctdiff=0.375
- SupraTentVolNotVent 912477.838 (909021.000) diff=3456.838 pctdiff=0.379
- BrainSegVol 1042313.000 (1040328.000) diff=1985.000 pctdiff=0.190
- BrainSegVolNotVent 1031549.000 (1034086.838) diff=-2537.838 pctdiff=-0.246
- BrainSegVolNotVent 1031549.000
- CerebellumVol 122293.000
- VentChorVol 8201.000
- 3rd4th5thCSF 2563.000
- CSFVol 597.000, OptChiasmVol 216.000
- MaskVol 1465683.000
- 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 2144 2143.738
- 2 3002 wm-lh-caudalanteriorcingulate 2810 2809.829
- 3 3003 wm-lh-caudalmiddlefrontal 5684 5684.414
- 4 3004 wm-lh-corpuscallosum 0 0.000
- 5 3005 wm-lh-cuneus 2013 2013.271
- 6 3006 wm-lh-entorhinal 916 916.275
- 7 3007 wm-lh-fusiform 5595 5594.664
- 8 3008 wm-lh-inferiorparietal 10709 10708.769
- 9 3009 wm-lh-inferiortemporal 5080 5079.736
- 10 3010 wm-lh-isthmuscingulate 3211 3210.994
- 11 3011 wm-lh-lateraloccipital 8140 8140.225
- 12 3012 wm-lh-lateralorbitofrontal 5232 5231.973
- 13 3013 wm-lh-lingual 5275 5275.343
- 14 3014 wm-lh-medialorbitofrontal 3112 3112.314
- 15 3015 wm-lh-middletemporal 4170 4169.850
- 16 3016 wm-lh-parahippocampal 1356 1355.829
- 17 3017 wm-lh-paracentral 2891 2890.717
- 18 3018 wm-lh-parsopercularis 3151 3150.771
- 19 3019 wm-lh-parsorbitalis 755 754.968
- 20 3020 wm-lh-parstriangularis 2848 2848.275
- 21 3021 wm-lh-pericalcarine 3337 3336.769
- 22 3022 wm-lh-postcentral 6306 6305.770
- 23 3023 wm-lh-posteriorcingulate 4348 4348.173
- 24 3024 wm-lh-precentral 9854 9853.964
- 25 3025 wm-lh-precuneus 8168 8168.355
- 26 3026 wm-lh-rostralanteriorcingulate 2574 2573.539
- 27 3027 wm-lh-rostralmiddlefrontal 10352 10351.646
- 28 3028 wm-lh-superiorfrontal 14322 14321.698
- 29 3029 wm-lh-superiorparietal 11486 11485.747
- 30 3030 wm-lh-superiortemporal 6842 6842.421
- 31 3031 wm-lh-supramarginal 6737 6737.016
- 32 3032 wm-lh-frontalpole 185 185.201
- 33 3033 wm-lh-temporalpole 533 532.920
- 34 3034 wm-lh-transversetemporal 564 563.637
- 35 3035 wm-lh-insula 6653 6652.805
- 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 2840 2840.422
- 120 4002 wm-rh-caudalanteriorcingulate 2610 2609.644
- 121 4003 wm-rh-caudalmiddlefrontal 4047 4046.623
- 122 4004 wm-rh-corpuscallosum 0 0.000
- 123 4005 wm-rh-cuneus 2033 2033.063
- 124 4006 wm-rh-entorhinal 551 550.972
- 125 4007 wm-rh-fusiform 5449 5448.645
- 126 4008 wm-rh-inferiorparietal 12357 12357.479
- 127 4009 wm-rh-inferiortemporal 4950 4949.798
- 128 4010 wm-rh-isthmuscingulate 2789 2788.676
- 129 4011 wm-rh-lateraloccipital 7763 7762.572
- 130 4012 wm-rh-lateralorbitofrontal 6147 6146.587
- 131 4013 wm-rh-lingual 5198 5197.819
- 132 4014 wm-rh-medialorbitofrontal 3322 3321.590
- 133 4015 wm-rh-middletemporal 4994 4993.922
- 134 4016 wm-rh-parahippocampal 1632 1632.081
- 135 4017 wm-rh-paracentral 4249 4248.789
- 136 4018 wm-rh-parsopercularis 2588 2588.202
- 137 4019 wm-rh-parsorbitalis 1054 1053.704
- 138 4020 wm-rh-parstriangularis 3209 3209.153
- 139 4021 wm-rh-pericalcarine 3090 3090.221
- 140 4022 wm-rh-postcentral 5844 5843.754
- 141 4023 wm-rh-posteriorcingulate 3819 3818.954
- 142 4024 wm-rh-precentral 10313 10313.099
- 143 4025 wm-rh-precuneus 9477 9477.032
- 144 4026 wm-rh-rostralanteriorcingulate 1585 1585.142
- 145 4027 wm-rh-rostralmiddlefrontal 10613 10613.044
- 146 4028 wm-rh-superiorfrontal 14713 14712.778
- 147 4029 wm-rh-superiorparietal 10255 10255.189
- 148 4030 wm-rh-superiortemporal 5277 5277.438
- 149 4031 wm-rh-supramarginal 7641 7640.863
- 150 4032 wm-rh-frontalpole 295 294.753
- 151 4033 wm-rh-temporalpole 524 523.643
- 152 4034 wm-rh-transversetemporal 399 399.371
- 153 4035 wm-rh-insula 6709 6709.368
- 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 21614 21613.861
- 237 5002 Right-UnsegmentedWhiteMatter 21556 21555.986
- 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/sub003/label
- #--------------------------------------------
- #@# BA Labels lh Thu Aug 8 23:13:13 CEST 2013
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814
- Number of reverse mapping hits = 208
- Checking for and removing duplicates
- Writing label file ./lh.BA1.label 4337
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814
- Number of reverse mapping hits = 390
- Checking for and removing duplicates
- Writing label file ./lh.BA2.label 8299
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814
- Number of reverse mapping hits = 61
- Checking for and removing duplicates
- Writing label file ./lh.BA3a.label 4138
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814
- Number of reverse mapping hits = 199
- Checking for and removing duplicates
- Writing label file ./lh.BA3b.label 6182
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814
- Number of reverse mapping hits = 147
- Checking for and removing duplicates
- Writing label file ./lh.BA4a.label 5931
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814
- Number of reverse mapping hits = 89
- Checking for and removing duplicates
- Writing label file ./lh.BA4p.label 4159
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814
- Number of reverse mapping hits = 679
- Checking for and removing duplicates
- Writing label file ./lh.BA6.label 14268
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814
- 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 sub003 --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 = sub003
- 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/sub003/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814
- Number of reverse mapping hits = 793
- Checking for and removing duplicates
- Writing label file ./lh.BA45.label 4215
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814
- Number of reverse mapping hits = 1884
- Checking for and removing duplicates
- Writing label file ./lh.V1.label 6525
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814
- Number of reverse mapping hits = 3494
- Checking for and removing duplicates
- Writing label file ./lh.V2.label 11608
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814
- Number of reverse mapping hits = 371
- Checking for and removing duplicates
- Writing label file ./lh.MT.label 2389
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.perirhinal.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814
- Number of reverse mapping hits = 154
- Checking for and removing duplicates
- Writing label file ./lh.perirhinal.label 1353
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.thresh.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814
- Number of reverse mapping hits = 21
- Checking for and removing duplicates
- Writing label file ./lh.BA1.thresh.label 1035
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.thresh.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814
- Number of reverse mapping hits = 165
- Checking for and removing duplicates
- Writing label file ./lh.BA2.thresh.label 2257
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.thresh.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814
- Number of reverse mapping hits = 13
- Checking for and removing duplicates
- Writing label file ./lh.BA3a.thresh.label 1517
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.thresh.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814
- Number of reverse mapping hits = 41
- Checking for and removing duplicates
- Writing label file ./lh.BA3b.thresh.label 2037
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.thresh.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814
- Number of reverse mapping hits = 90
- Checking for and removing duplicates
- Writing label file ./lh.BA4a.thresh.label 2409
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.thresh.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814
- Number of reverse mapping hits = 50
- Checking for and removing duplicates
- Writing label file ./lh.BA4p.thresh.label 1599
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.thresh.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814
- Number of reverse mapping hits = 200
- Checking for and removing duplicates
- Writing label file ./lh.BA6.thresh.label 7235
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.thresh.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814
- Number of reverse mapping hits = 100
- Checking for and removing duplicates
- Writing label file ./lh.BA44.thresh.label 2012
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.thresh.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814
- Number of reverse mapping hits = 268
- Checking for and removing duplicates
- Writing label file ./lh.BA45.thresh.label 1419
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.thresh.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814
- Number of reverse mapping hits = 1378
- Checking for and removing duplicates
- Writing label file ./lh.V1.thresh.label 4783
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.thresh.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814
- Number of reverse mapping hits = 1676
- Checking for and removing duplicates
- Writing label file ./lh.V2.thresh.label 5010
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.thresh.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 128814
- Number of reverse mapping hits = 74
- Checking for and removing duplicates
- Writing label file ./lh.MT.thresh.label 587
- mri_label2label: Done
- mris_label2annot --s sub003 --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/sub003/label
- cmdline mris_label2annot --s sub003 --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 sub003
- 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/sub003/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 89823 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/label/lh.BA.annot
- mris_label2annot --s sub003 --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/sub003/label
- cmdline mris_label2annot --s sub003 --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 sub003
- 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/sub003/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 106666 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/label/lh.BA.thresh.annot
- mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab sub003 lh white
- computing statistics for each annotation in ./lh.BA.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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
- 952 575 1632 1.886 0.639 0.172 0.094 29 3.0 BA1
- 3592 2423 6069 2.241 0.499 0.135 0.043 51 6.0 BA2
- 856 570 860 1.905 0.375 0.125 0.030 6 1.1 BA3a
- 2063 1404 3567 2.104 0.624 0.125 0.036 23 2.9 BA3b
- 1361 880 3200 2.694 0.520 0.120 0.030 15 1.7 BA4a
- 1133 756 2245 2.728 0.498 0.099 0.021 6 1.0 BA4p
- 7559 5146 18810 2.770 0.577 0.143 0.046 133 14.4 BA6
- 2101 1463 5099 2.879 0.453 0.131 0.040 33 3.4 BA44
- 3195 2137 6468 2.490 0.520 0.145 0.045 52 5.9 BA45
- 4154 2757 5619 1.936 0.496 0.144 0.069 72 11.5 V1
- 9099 5935 13860 2.093 0.511 0.167 0.069 187 23.7 V2
- 1926 1292 3502 2.450 0.426 0.152 0.049 31 3.9 MT
- 1000 672 2594 3.029 0.773 0.158 0.071 27 3.2 perirhinal
- mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab sub003 lh white
- computing statistics for each annotation in ./lh.BA.thresh.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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
- 543 298 823 1.690 0.552 0.187 0.118 21 2.1 BA1
- 1445 945 2354 2.154 0.481 0.124 0.034 16 2.2 BA2
- 690 460 677 1.902 0.383 0.132 0.033 5 0.9 BA3a
- 1195 846 1749 1.816 0.480 0.097 0.023 8 1.1 BA3b
- 1379 898 3151 2.710 0.555 0.107 0.024 9 1.5 BA4a
- 931 623 1784 2.690 0.487 0.100 0.022 5 0.8 BA4p
- 3793 2541 9540 2.788 0.634 0.142 0.047 73 7.7 BA6
- 1334 932 3366 2.924 0.407 0.137 0.046 26 2.4 BA44
- 1220 819 3107 2.696 0.521 0.159 0.049 26 2.5 BA45
- 4425 2925 5993 1.934 0.498 0.146 0.067 79 11.6 V1
- 4693 3059 6728 1.943 0.501 0.173 0.082 102 15.0 V2
- 500 338 774 2.291 0.381 0.132 0.037 5 0.8 MT
- #--------------------------------------------
- #@# BA Labels rh Thu Aug 8 23:18:12 CEST 2013
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg
- Rescaling ... original radius = 99.9999
- 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 127449
- Number of reverse mapping hits = 157
- Checking for and removing duplicates
- Writing label file ./rh.BA1.label 4119
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg
- Rescaling ... original radius = 99.9999
- 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 127449
- Number of reverse mapping hits = 313
- Checking for and removing duplicates
- Writing label file ./rh.BA2.label 7000
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg
- Rescaling ... original radius = 99.9999
- 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 127449
- Number of reverse mapping hits = 57
- Checking for and removing duplicates
- Writing label file ./rh.BA3a.label 4037
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg
- Rescaling ... original radius = 99.9999
- 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 127449
- Number of reverse mapping hits = 109
- Checking for and removing duplicates
- Writing label file ./rh.BA3b.label 4631
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg
- Rescaling ... original radius = 99.9999
- 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 127449
- Number of reverse mapping hits = 184
- Checking for and removing duplicates
- Writing label file ./rh.BA4a.label 5931
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg
- Rescaling ... original radius = 99.9999
- 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 127449
- Number of reverse mapping hits = 107
- Checking for and removing duplicates
- Writing label file ./rh.BA4p.label 4580
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg
- Rescaling ... original radius = 99.9999
- 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 127449
- Number of reverse mapping hits = 620
- Checking for and removing duplicates
- Writing label file ./rh.BA6.label 12876
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg
- Rescaling ... original radius = 99.9999
- 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 127449
- Number of reverse mapping hits = 758
- Checking for and removing duplicates
- Writing label file ./rh.BA44.label 7670
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg
- Rescaling ... original radius = 99.9999
- 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 127449
- Number of reverse mapping hits = 1058
- Checking for and removing duplicates
- Writing label file ./rh.BA45.label 6413
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg
- Rescaling ... original radius = 99.9999
- 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 127449
- Number of reverse mapping hits = 1888
- Checking for and removing duplicates
- Writing label file ./rh.V1.label 6615
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg
- Rescaling ... original radius = 99.9999
- 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 127449
- Number of reverse mapping hits = 3220
- Checking for and removing duplicates
- Writing label file ./rh.V2.label 11236
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg
- Rescaling ... original radius = 99.9999
- 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 127449
- Number of reverse mapping hits = 303
- Checking for and removing duplicates
- Writing label file ./rh.MT.label 2235
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.perirhinal.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg
- Rescaling ... original radius = 99.9999
- 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 127449
- Number of reverse mapping hits = 41
- Checking for and removing duplicates
- Writing label file ./rh.perirhinal.label 793
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.thresh.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg
- Rescaling ... original radius = 99.9999
- 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 127449
- Number of reverse mapping hits = 49
- Checking for and removing duplicates
- Writing label file ./rh.BA1.thresh.label 925
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.thresh.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg
- Rescaling ... original radius = 99.9999
- 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 127449
- Number of reverse mapping hits = 88
- Checking for and removing duplicates
- Writing label file ./rh.BA2.thresh.label 2776
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.thresh.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg
- Rescaling ... original radius = 99.9999
- 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 127449
- Number of reverse mapping hits = 21
- Checking for and removing duplicates
- Writing label file ./rh.BA3a.thresh.label 1719
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.thresh.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg
- Rescaling ... original radius = 99.9999
- 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 127449
- Number of reverse mapping hits = 71
- Checking for and removing duplicates
- Writing label file ./rh.BA3b.thresh.label 2254
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.thresh.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg
- Rescaling ... original radius = 99.9999
- 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 127449
- Number of reverse mapping hits = 18
- Checking for and removing duplicates
- Writing label file ./rh.BA4a.thresh.label 1406
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.thresh.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg
- Rescaling ... original radius = 99.9999
- 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 127449
- Number of reverse mapping hits = 65
- Checking for and removing duplicates
- Writing label file ./rh.BA4p.thresh.label 1554
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.thresh.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg
- Rescaling ... original radius = 99.9999
- 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 127449
- Number of reverse mapping hits = 339
- Checking for and removing duplicates
- Writing label file ./rh.BA6.thresh.label 7298
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.thresh.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg
- Rescaling ... original radius = 99.9999
- 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 127449
- Number of reverse mapping hits = 58
- Checking for and removing duplicates
- Writing label file ./rh.BA44.thresh.label 1070
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.thresh.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg
- Rescaling ... original radius = 99.9999
- 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 127449
- Number of reverse mapping hits = 204
- Checking for and removing duplicates
- Writing label file ./rh.BA45.thresh.label 1382
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.thresh.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg
- Rescaling ... original radius = 99.9999
- 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 127449
- Number of reverse mapping hits = 1244
- Checking for and removing duplicates
- Writing label file ./rh.V1.thresh.label 4476
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.thresh.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg
- Rescaling ... original radius = 99.9999
- 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 127449
- Number of reverse mapping hits = 1639
- Checking for and removing duplicates
- Writing label file ./rh.V2.thresh.label 5076
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.thresh.label --trgsubject sub003 --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 = sub003
- 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/sub003/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.sphere.reg
- Rescaling ... original radius = 99.9999
- 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 127449
- Number of reverse mapping hits = 21
- Checking for and removing duplicates
- Writing label file ./rh.MT.thresh.label 289
- mri_label2label: Done
- mris_label2annot --s sub003 --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/sub003/label
- cmdline mris_label2annot --s sub003 --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 sub003
- 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/sub003/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 88818 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/label/rh.BA.annot
- mris_label2annot --s sub003 --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/sub003/label
- cmdline mris_label2annot --s sub003 --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 sub003
- 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/sub003/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 106521 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/label/rh.BA.thresh.annot
- mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab sub003 rh white
- computing statistics for each annotation in ./rh.BA.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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
- 812 500 1581 2.048 0.676 0.171 0.059 20 2.0 BA1
- 3056 2077 4963 2.102 0.532 0.126 0.040 37 4.2 BA2
- 852 553 882 1.985 0.480 0.122 0.032 6 1.1 BA3a
- 1641 1125 2735 1.919 0.563 0.114 0.037 19 2.8 BA3b
- 1165 778 2563 2.606 0.594 0.117 0.028 11 1.4 BA4a
- 1050 681 1916 2.595 0.495 0.112 0.028 8 1.3 BA4p
- 6867 4714 17154 2.800 0.589 0.137 0.042 91 11.5 BA6
- 3307 2273 6666 2.615 0.392 0.122 0.034 41 4.6 BA44
- 4552 3085 10200 2.641 0.492 0.156 0.058 95 9.6 BA45
- 4286 3014 6239 1.921 0.581 0.166 0.081 105 13.3 V1
- 8716 5752 13223 2.091 0.510 0.175 0.070 200 23.6 V2
- 1817 1259 2863 2.108 0.383 0.140 0.150 72 2.9 MT
- 510 352 1660 3.308 0.706 0.161 0.083 14 1.5 perirhinal
- mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab sub003 rh white
- computing statistics for each annotation in ./rh.BA.thresh.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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
- 518 314 1029 2.054 0.654 0.182 0.067 13 1.3 BA1
- 1571 1080 2530 2.070 0.521 0.111 0.038 17 1.9 BA2
- 734 468 659 1.908 0.387 0.120 0.033 5 1.0 BA3a
- 1352 943 1998 1.815 0.459 0.102 0.030 12 2.1 BA3b
- 631 424 1408 2.480 0.704 0.125 0.030 7 0.8 BA4a
- 878 585 1682 2.616 0.461 0.108 0.026 5 1.1 BA4p
- 4361 2981 11297 2.816 0.596 0.141 0.043 63 7.5 BA6
- 719 529 1806 2.718 0.369 0.139 0.043 13 1.2 BA44
- 1108 778 2918 2.754 0.473 0.172 0.067 31 2.8 BA45
- 4109 2884 5847 1.905 0.605 0.164 0.078 98 12.6 V1
- 4724 3108 6777 1.985 0.489 0.183 0.078 118 14.1 V2
- 223 169 547 2.335 0.390 0.132 0.036 2 0.4 MT
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/label
- #--------------------------------------------
- #@# Ex-vivo Entorhinal Cortex Label lh Thu Aug 8 23:22:46 CEST 2013
- mris_spherical_average -erode 1 -orig white -t 0.4 -o sub003 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label
- painting output onto subject sub003.
- processing subject lh.EC_average...
- reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 929 points to lh.entorhinal_exvivo.label...
- mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label sub003 lh white
- limiting computations to label ./lh.entorhinal_exvivo.label.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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
- 343 214 902 2.738 0.688 0.126 0.038 3 0.6 ./lh.entorhinal_exvivo.label
- #--------------------------------------------
- #@# Ex-vivo Entorhinal Cortex Label rh Thu Aug 8 23:23:02 CEST 2013
- mris_spherical_average -erode 1 -orig white -t 0.4 -o sub003 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label
- painting output onto subject sub003.
- processing subject rh.EC_average...
- reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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 667 points to rh.entorhinal_exvivo.label...
- mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label sub003 rh white
- limiting computations to label ./rh.entorhinal_exvivo.label.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/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
- 280 175 891 3.051 0.725 0.141 0.053 3 0.7 ./rh.entorhinal_exvivo.label
- #------------------------------------------
- Started at Thu Aug 8 10:53:55 CEST 2013
- Ended at Thu Aug 8 23:23:17 CEST 2013
- #@#%# recon-all-run-time-hours 12.489
- recon-all -s sub003 finished without error at Thu Aug 8 23:23:17 CEST 2013
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