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- Thu Aug 8 10:53:42 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005
- /opt/freesurfer/5.3.0/bin/recon-all
- -i /home/data/exppsy/forrest_gump/openfmri.org/sub005/anatomy/highres001.nii.gz -cw256 -all -T2 /home/data/exppsy/forrest_gump/openfmri.org/sub005/anatomy/other/t2w001.nii.gz -T2pial -subjid sub005 -sd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- subjid sub005
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Actual FREESURFER_HOME /opt/freesurfer/5.3.0
- build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
- Linux snake4 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
- cputime unlimited
- filesize unlimited
- datasize unlimited
- stacksize unlimited
- coredumpsize 0 kbytes
- memoryuse unlimited
- vmemoryuse unlimited
- descriptors 1024
- memorylocked 64 kbytes
- maxproc unlimited
- maxlocks unlimited
- maxsignal 16382
- maxmessage 819200
- maxnice 0
- maxrtprio 0
- maxrttime unlimited
- total used free shared buffers cached
- Mem: 99201692 96396048 2805644 0 188520 94505440
- -/+ buffers/cache: 1702088 97499604
- Swap: 25165780 532 25165248
- ########################################
- program versions used
- $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
- $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
- mri_convert -all-info
- ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:42-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- FLIRT version 5.5
- $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
- mri_convert --version
- stable5
- ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- Program nu_correct, built from:
- Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
- ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:44-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:44-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:44-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ======= NUMBER OF OPENMP THREADS = 1 =======
- ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:44-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:44-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:45-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:45-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:45-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:45-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:45-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:45-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:45-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:45-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:45-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $
- ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $
- ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- #######################################
- GCADIR /opt/freesurfer/5.3.0/average
- GCA RB_all_2008-03-26.gca
- GCASkull RB_all_withskull_2008-03-26.gca
- AvgCurvTif average.curvature.filled.buckner40.tif
- GCSDIR /opt/freesurfer/5.3.0/average
- GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
- #######################################
- -cw256 option is now persistent (remove with -clean-cw256)
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub005/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/001.mgz
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub005/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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/sub005/anatomy/highres001.nii.gz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.998148, -0.0400878, -0.0457496)
- j_ras = (-0.0459461, 0.989757, 0.135168)
- k_ras = (-0.0398624, -0.13702, 0.989766)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/001.mgz...
- #--------------------------------------------
- #@# T2/FLAIR Input Thu Aug 8 10:54:07 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub005/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/T2raw.mgz
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub005/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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/sub005/anatomy/other/t2w001.nii.gz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.998148, -0.0400878, -0.0457496)
- j_ras = (-0.0459461, 0.989757, 0.135168)
- k_ras = (-0.0398624, -0.13702, 0.989766)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/T2raw.mgz...
- #--------------------------------------------
- #@# MotionCor Thu Aug 8 10:54:24 CEST 2013
- Found 1 runs
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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/sub005/mri/orig/001.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/rawavg.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig.mgz --conform --cw256
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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/sub005/mri/rawavg.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.998148, -0.0400878, -0.0457496)
- j_ras = (-0.0459461, 0.989757, 0.135168)
- k_ras = (-0.0398624, -0.13702, 0.989766)
- Original Data has (0.699913, 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/sub005/mri/orig.mgz...
- mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/talairach.xfm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Talairach Thu Aug 8 10:55:05 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri
- mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
- talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
- cp transforms/talairach.auto.xfm transforms/talairach.xfm
- #--------------------------------------------
- #@# Talairach Failure Detection Thu Aug 8 10:58:01 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri
- talairach_afd -T 0.005 -xfm transforms/talairach.xfm
- talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.5432, pval=0.2115 >= threshold=0.0050)
- awk -f /opt/freesurfer/5.3.0/bin/extract_talairach_avi_QA.awk /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/talairach_avi.log
- tal_QC_AZS /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/talairach_avi.log
- TalAviQA: 0.96657
- z-score: -2
- #--------------------------------------------
- #@# Nu Intensity Correction Thu Aug 8 10:58:01 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/sub005/mri
- /opt/freesurfer/5.3.0/bin/mri_nu_correct.mni
- --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
- nIters 2
- $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $
- Linux snake4 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
- Thu Aug 8 10:58:01 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.20260
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.20260/nu0.mnc -odt float
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.20260/nu0.mnc -odt float
- $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
- reading from orig.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, 4.19095e-09, 3.72529e-09)
- j_ras = (7.45058e-09, 1.49012e-08, -1)
- k_ras = (-6.0536e-09, 1, -1.49012e-08)
- changing data type from uchar to float (noscale = 0)...
- writing to ./tmp.mri_nu_correct.mni.20260/nu0.mnc...
-
- --------------------------------------------------------
- Iteration 1 Thu Aug 8 10:58:04 CEST 2013
- nu_correct -clobber ./tmp.mri_nu_correct.mni.20260/nu0.mnc ./tmp.mri_nu_correct.mni.20260/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.20260/0/
- [fkaule@snake4:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/] [2013-08-08 10:58:04] 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.20260/0/ ./tmp.mri_nu_correct.mni.20260/nu0.mnc ./tmp.mri_nu_correct.mni.20260/nu1.imp
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Number of iterations: 50
- CV of field change: 0.00140342
- [fkaule@snake4:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/] [2013-08-08 10:59:11] running:
- /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.20260/nu0.mnc ./tmp.mri_nu_correct.mni.20260/0//template.mnc
- Transforming slices:......................................................................................Done
- Transforming slices:................................................................................................................................................................................................................................................................Done
-
-
- --------------------------------------------------------
- Iteration 2 Thu Aug 8 10:59:18 CEST 2013
- nu_correct -clobber ./tmp.mri_nu_correct.mni.20260/nu1.mnc ./tmp.mri_nu_correct.mni.20260/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.20260/1/
- [fkaule@snake4:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/] [2013-08-08 10:59:18] running:
- /opt/freesurfer/5.3.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.20260/1/ ./tmp.mri_nu_correct.mni.20260/nu1.mnc ./tmp.mri_nu_correct.mni.20260/nu2.imp
- Processing:.................................................................Done
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- Processing:.................................................................Done
- Number of iterations: 50
- CV of field change: 0.00110121
- [fkaule@snake4:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/] [2013-08-08 11:00:10] running:
- /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.20260/nu1.mnc ./tmp.mri_nu_correct.mni.20260/1//template.mnc
- Transforming slices:......................................................................................Done
- Transforming slices:................................................................................................................................................................................................................................................................Done
-
-
-
- mri_binarize --i ./tmp.mri_nu_correct.mni.20260/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.20260/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/sub005/mri
- cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.20260/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.20260/ones.mgz
- sysname Linux
- hostname snake4
- machine x86_64
- user fkaule
- input ./tmp.mri_nu_correct.mni.20260/nu2.mnc
- frame 0
- nErode3d 0
- nErode2d 0
- output ./tmp.mri_nu_correct.mni.20260/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.20260/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.20260/sum.junk --avgwf ./tmp.mri_nu_correct.mni.20260/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.20260/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.20260/sum.junk --avgwf ./tmp.mri_nu_correct.mni.20260/input.mean.dat
- sysname Linux
- hostname snake4
- machine x86_64
- user fkaule
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.20260/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.20260/input.mean.dat
- mri_segstats done
- mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.20260/ones.mgz --i ./tmp.mri_nu_correct.mni.20260/nu2.mnc --sum ./tmp.mri_nu_correct.mni.20260/sum.junk --avgwf ./tmp.mri_nu_correct.mni.20260/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.20260/ones.mgz --i ./tmp.mri_nu_correct.mni.20260/nu2.mnc --sum ./tmp.mri_nu_correct.mni.20260/sum.junk --avgwf ./tmp.mri_nu_correct.mni.20260/output.mean.dat
- sysname Linux
- hostname snake4
- machine x86_64
- user fkaule
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.20260/ones.mgz
- Loading ./tmp.mri_nu_correct.mni.20260/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.20260/output.mean.dat
- mri_segstats done
- mris_calc -o ./tmp.mri_nu_correct.mni.20260/nu2.mnc ./tmp.mri_nu_correct.mni.20260/nu2.mnc mul .93128273976889651174
- Saving result to './tmp.mri_nu_correct.mni.20260/nu2.mnc' (type = MINC ) [ ok ]
- mri_convert ./tmp.mri_nu_correct.mni.20260/nu2.mnc nu.mgz --like orig.mgz
- mri_convert ./tmp.mri_nu_correct.mni.20260/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.20260/nu2.mnc...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, 4.19095e-09, 3.72529e-09)
- j_ras = (7.45058e-09, 1.49012e-08, -1)
- k_ras = (-6.0536e-09, 1, -1.49012e-08)
- INFO: transform src into the like-volume: orig.mgz
- writing to nu.mgz...
- mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz
- type change took 0 minutes and 7 seconds.
- mapping (14, 160) to ( 3, 110)
-
-
- Thu Aug 8 11:00:56 CEST 2013
- mri_nu_correct.mni done
- mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/talairach.xfm nu.mgz nu.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Intensity Normalization Thu Aug 8 11:00:58 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri
- mri_normalize -g 1 nu.mgz T1.mgz
- using max gradient = 1.000
- reading from nu.mgz...
- normalizing image...
- talairach transform
- 1.191 0.081 0.051 3.985;
- -0.133 1.061 0.435 -29.785;
- 0.011 -0.481 1.181 -2.834;
- 0.000 0.000 0.000 1.000;
- processing without aseg, no1d=0
- MRInormInit():
- INFO: Modifying talairach volume c_(r,a,s) based on average_305
- MRInormalize():
- MRIsplineNormalize(): npeaks = 17
- Starting OpenSpline(): npoints = 17
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Iterating 2 times
- ---------------------------------
- 3d normalization pass 1 of 2
- white matter peak found at 111
- white matter peak found at 108
- gm peak at 56 (56), valley at 42 (42)
- csf peak at 28, setting threshold to 46
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- ---------------------------------
- 3d normalization pass 2 of 2
- white matter peak found at 111
- white matter peak found at 110
- gm peak at 56 (56), valley at 41 (41)
- csf peak at 28, setting threshold to 46
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Done iterating ---------------------------------
- writing output to T1.mgz
- 3D bias adjustment took 2 minutes and 48 seconds.
- #--------------------------------------------
- #@# Skull Stripping Thu Aug 8 11:03:46 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri
- mri_em_register -skull nu.mgz /opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta
- ======= NUMBER OF OPENMP THREADS = 1 =======
- aligning to atlas containing skull, setting unknown_nbr_spacing = 5
- reading 1 input volumes...
- logging results to talairach_with_skull.log
- reading '/opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca'...
- average std = 23.1 using min determinant for regularization = 53.4
- 0 singular and 5702 ill-conditioned covariance matrices regularized
- reading 'nu.mgz'...
- freeing gibbs priors...done.
- bounding unknown intensity as < 20.2 or > 943.7
- total sample mean = 92.0 (1443 zeros)
- ************************************************
- spacing=8, using 3481 sample points, tol=1.00e-05...
- ************************************************
- register_mri: find_optimal_transform
- find_optimal_transform: nsamples 3481, passno 0, spacing 8
- resetting wm mean[0]: 117 --> 126
- resetting gm mean[0]: 74 --> 74
- input volume #1 is the most T1-like
- using real data threshold=8.0
- skull bounding box = (52, 13, 10) --> (201, 255, 209)
- using (102, 94, 110) as brain centroid...
- mean wm in atlas = 126, using box (84,64,85) --> (120, 123,134) to find MRI wm
- before smoothing, mri peak at 108
- after smoothing, mri peak at 108, scaling input intensities by 1.167
- scaling channel 0 by 1.16667
- initial log_p = -4.8
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -4.553914 @ (-9.091, 27.273, -9.091)
- max log p = -4.487499 @ (4.545, -4.545, -4.545)
- max log p = -4.483190 @ (2.273, -6.818, 6.818)
- max log p = -4.472748 @ (1.136, 1.136, -3.409)
- max log p = -4.469653 @ (0.568, -0.568, 0.568)
- max log p = -4.464366 @ (-1.420, 0.284, 2.557)
- Found translation: (-2.0, 16.8, -7.1): log p = -4.464
- ****************************************
- 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)
- 1.140 0.057 -0.139 -9.943;
- 0.000 1.142 0.473 -43.109;
- 0.161 -0.469 1.132 4.165;
- 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)
- 1.226 0.062 -0.149 -20.121;
- 0.000 1.228 0.509 -55.426;
- 0.149 -0.434 1.047 11.805;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 2 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1)
- 1.226 0.062 -0.149 -20.121;
- 0.000 1.228 0.509 -55.426;
- 0.149 -0.434 1.047 11.805;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.2500
- ****************************************
- Nine parameter search. iteration 3 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.1 (thresh=-4.1)
- 1.184 0.047 -0.110 -19.960;
- -0.012 1.242 0.390 -40.153;
- 0.105 -0.320 1.116 0.548;
- 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)
- 1.184 0.047 -0.110 -19.960;
- -0.012 1.242 0.390 -40.153;
- 0.105 -0.320 1.116 0.548;
- 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)
- 1.180 0.063 -0.125 -19.391;
- -0.021 1.243 0.402 -40.394;
- 0.124 -0.329 1.111 -0.027;
- 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)
- 1.180 0.063 -0.125 -19.391;
- -0.021 1.243 0.402 -40.394;
- 0.124 -0.329 1.111 -0.027;
- 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
- 1.18046 0.06254 -0.12483 -19.39090;
- -0.02094 1.24275 0.40179 -40.39419;
- 0.12427 -0.32903 1.11130 -0.02731;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 3481
- Quasinewton: input matrix
- 1.18046 0.06254 -0.12483 -19.39090;
- -0.02094 1.24275 0.40179 -40.39419;
- 0.12427 -0.32903 1.11130 -0.02731;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 1.180 0.063 -0.125 -19.391;
- -0.021 1.243 0.402 -40.394;
- 0.124 -0.329 1.111 -0.027;
- 0.000 0.000 0.000 1.000;
- pass 1, spacing 8: log(p) = -4.0 (old=-4.8)
- transform before final EM align:
- 1.180 0.063 -0.125 -19.391;
- -0.021 1.243 0.402 -40.394;
- 0.124 -0.329 1.111 -0.027;
- 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
- 1.18046 0.06254 -0.12483 -19.39090;
- -0.02094 1.24275 0.40179 -40.39419;
- 0.12427 -0.32903 1.11130 -0.02731;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 382743
- Quasinewton: input matrix
- 1.18046 0.06254 -0.12483 -19.39090;
- -0.02094 1.24275 0.40179 -40.39419;
- 0.12427 -0.32903 1.11130 -0.02731;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = 4.4 tol 0.000000
- final transform:
- 1.180 0.063 -0.125 -19.391;
- -0.021 1.243 0.402 -40.394;
- 0.124 -0.329 1.111 -0.027;
- 0.000 0.000 0.000 1.000;
- writing output transformation to transforms/talairach_with_skull.lta...
- registration took 33 minutes and 41 seconds.
- mri_watershed -T1 -brain_atlas /opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz
- Mode: T1 normalized volume
- Mode: Use the information of atlas (default parms, --help for details)
- *********************************************************
- The input file is T1.mgz
- The output file is brainmask.auto.mgz
- Weighting the input with atlas information before watershed
- *************************WATERSHED**************************
- Sorting...
- first estimation of the COG coord: x=131 y=83 z=112 r=103
- first estimation of the main basin volume: 4591295 voxels
- Looking for seedpoints
- 2 found in the cerebellum
- 14 found in the rest of the brain
- global maximum in x=157, y=91, z=82, Imax=255
- CSF=12, WM_intensity=110, WM_VARIANCE=5
- WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110
- preflooding height equal to 10 percent
- done.
- Analyze...
- main basin size=18116230071 voxels, voxel volume =1.000
- = 18116230071 mmm3 = 18116229.120 cm3
- done.
- PostAnalyze...Basin Prior
- 70 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=129,y=94, z=108, r=10265 iterations
- ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^
- GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 45567
- RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1032253284
- LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = 1083673940
- RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1065167473
- LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1061764480
- OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=18 , nb = 1080145814
-
- CSF_MAX TRANSITION GM_MIN GM
- GLOBAL
- before analyzing : 4, 6, 30, 50
- after analyzing : 4, 22, 30, 29
- RIGHT_CER
- before analyzing : 4, 4, 24, 64
- after analyzing : 4, 18, 25, 29
- LEFT_CER
- before analyzing : 5, 6, 25, 59
- after analyzing : 5, 18, 25, 28
- RIGHT_BRAIN
- before analyzing : 4, 6, 30, 50
- after analyzing : 4, 22, 30, 29
- LEFT_BRAIN
- before analyzing : 4, 6, 29, 50
- after analyzing : 4, 21, 29, 28
- OTHER
- before analyzing : 18, 23, 30, 50
- after analyzing : 18, 27, 30, 32
- mri_strip_skull: done peeling brain
- highly tesselated surface with 10242 vertices
- matching...66 iterations
- *********************VALIDATION*********************
- curvature mean = -0.013, std = 0.012
- curvature mean = 69.916, std = 7.602
- No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
- before rotation: sse = 3.44, sigma = 7.07
- after rotation: sse = 3.44, sigma = 7.07
- Localization of inacurate regions: Erosion-Dilation steps
- the sse mean is 4.27, its var is 10.70
- before Erosion-Dilatation 2.14% of inacurate vertices
- after Erosion-Dilatation 2.08% 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...31 iterations
- mri_strip_skull: done peeling brain
- Brain Size = 1621646 voxels, voxel volume = 1.000 mm3
- = 1621646 mmm3 = 1621.646 cm3
- ******************************
- Saving brainmask.auto.mgz
- done
- cp brainmask.auto.mgz brainmask.mgz
- #-------------------------------------
- #@# EM Registration Thu Aug 8 11:37:54 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 = (65, 37, 29) --> (193, 173, 196)
- using (108, 82, 113) as brain centroid...
- mean wm in atlas = 107, using box (92,65,92) --> (123, 98,133) to find MRI wm
- before smoothing, mri peak at 107
- after smoothing, mri peak at 106, scaling input intensities by 1.009
- scaling channel 0 by 1.00943
- initial log_p = -4.5
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -4.085262 @ (-9.091, 27.273, -9.091)
- max log p = -4.023158 @ (4.545, -4.545, -4.545)
- max log p = -4.007773 @ (2.273, -2.273, 2.273)
- max log p = -3.975749 @ (-1.136, 1.136, -1.136)
- max log p = -3.940902 @ (-0.568, 0.568, 1.705)
- max log p = -3.933861 @ (-0.284, 2.557, 0.852)
- Found translation: (-4.3, 24.7, -9.9): log p = -3.934
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.6, old_max_log_p =-3.9 (thresh=-3.9)
- 1.150 0.000 0.000 -23.922;
- 0.000 1.111 0.298 -20.026;
- 0.000 -0.236 0.883 25.853;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.6, old_max_log_p =-3.6 (thresh=-3.6)
- 1.150 0.000 0.000 -23.922;
- 0.000 1.111 0.298 -20.026;
- 0.000 -0.236 0.883 25.853;
- 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=-3.5, old_max_log_p =-3.6 (thresh=-3.6)
- 1.101 0.054 -0.075 -14.044;
- -0.045 1.144 0.243 -11.221;
- 0.111 -0.172 0.947 -0.263;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 3 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.5, old_max_log_p =-3.5 (thresh=-3.5)
- 1.104 0.046 -0.045 -17.138;
- -0.038 1.152 0.310 -18.537;
- 0.079 -0.253 0.949 13.278;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 4 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.5, old_max_log_p =-3.5 (thresh=-3.5)
- 1.101 0.055 -0.075 -14.198;
- -0.036 1.143 0.341 -21.475;
- 0.116 -0.289 0.936 13.160;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 5 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.5, old_max_log_p =-3.5 (thresh=-3.5)
- 1.101 0.055 -0.075 -14.198;
- -0.036 1.143 0.341 -21.475;
- 0.116 -0.289 0.936 13.160;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.0625
- ****************************************
- Nine parameter search. iteration 6 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.4, old_max_log_p =-3.5 (thresh=-3.5)
- 1.102 0.041 -0.062 -15.344;
- -0.028 1.147 0.324 -20.465;
- 0.098 -0.272 0.946 13.810;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 7 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4)
- 1.098 0.041 -0.062 -14.845;
- -0.028 1.149 0.325 -20.792;
- 0.098 -0.272 0.946 13.810;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 8 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4)
- 1.098 0.041 -0.062 -14.845;
- -0.028 1.149 0.325 -20.792;
- 0.098 -0.272 0.946 13.810;
- 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
- 1.09796 0.04098 -0.06217 -14.84461;
- -0.02848 1.14937 0.32503 -20.79175;
- 0.09809 -0.27194 0.94600 13.81043;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 2772
- Quasinewton: input matrix
- 1.09796 0.04098 -0.06217 -14.84461;
- -0.02848 1.14937 0.32503 -20.79175;
- 0.09809 -0.27194 0.94600 13.81043;
- 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: 011: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 1.098 0.041 -0.062 -14.845;
- -0.028 1.149 0.325 -20.792;
- 0.098 -0.272 0.946 13.810;
- 0.000 0.000 0.000 1.000;
- pass 1, spacing 8: log(p) = -3.4 (old=-4.5)
- transform before final EM align:
- 1.098 0.041 -0.062 -14.845;
- -0.028 1.149 0.325 -20.792;
- 0.098 -0.272 0.946 13.810;
- 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
- 1.09796 0.04098 -0.06217 -14.84461;
- -0.02848 1.14937 0.32503 -20.79175;
- 0.09809 -0.27194 0.94600 13.81043;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 312841
- Quasinewton: input matrix
- 1.09796 0.04098 -0.06217 -14.84461;
- -0.02848 1.14937 0.32503 -20.79175;
- 0.09809 -0.27194 0.94600 13.81043;
- 0.00000 0.00000 0.00000 1.00000;
- dfp_em_step_func: 012: -log(p) = 4.0
- after pass:transform: ( 1.10, 0.04, -0.06, -14.84)
- ( -0.03, 1.15, 0.33, -20.79)
- ( 0.10, -0.27, 0.95, 13.81)
- dfp_em_step_func: 013: -log(p) = 3.9
- after pass:transform: ( 1.10, 0.04, -0.06, -14.84)
- ( -0.03, 1.15, 0.33, -20.79)
- ( 0.10, -0.27, 0.95, 13.81)
- dfp_em_step_func: 014: -log(p) = 3.9
- after pass:transform: ( 1.10, 0.04, -0.06, -14.84)
- ( -0.03, 1.15, 0.33, -20.79)
- ( 0.10, -0.27, 0.95, 13.81)
- dfp_em_step_func: 015: -log(p) = 3.9
- after pass:transform: ( 1.10, 0.04, -0.06, -14.84)
- ( -0.03, 1.15, 0.33, -20.79)
- ( 0.10, -0.27, 0.95, 13.81)
- dfp_em_step_func: 016: -log(p) = 3.9
- after pass:transform: ( 1.10, 0.04, -0.06, -14.84)
- ( -0.03, 1.15, 0.33, -20.79)
- ( 0.10, -0.27, 0.95, 13.81)
- dfp_em_step_func: 017: -log(p) = 3.9
- after pass:transform: ( 1.10, 0.04, -0.06, -14.84)
- ( -0.03, 1.15, 0.33, -20.79)
- ( 0.10, -0.27, 0.95, 13.81)
- dfp_em_step_func: 018: -log(p) = 3.9
- after pass:transform: ( 1.10, 0.04, -0.06, -14.84)
- ( -0.03, 1.15, 0.33, -20.79)
- ( 0.10, -0.27, 0.95, 13.81)
- dfp_em_step_func: 019: -log(p) = 3.9
- after pass:transform: ( 1.10, 0.04, -0.06, -14.84)
- ( -0.03, 1.15, 0.33, -20.79)
- ( 0.10, -0.27, 0.95, 13.81)
- dfp_em_step_func: 020: -log(p) = 3.9
- after pass:transform: ( 1.10, 0.04, -0.06, -14.84)
- ( -0.03, 1.15, 0.33, -20.79)
- ( 0.10, -0.27, 0.95, 13.81)
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization...
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 022: -log(p) = 3.9 tol 0.000000
- final transform:
- 1.099 0.042 -0.061 -14.845;
- -0.028 1.149 0.325 -20.792;
- 0.099 -0.272 0.946 13.810;
- 0.000 0.000 0.000 1.000;
- writing output transformation to transforms/talairach.lta...
- registration took 34 minutes and 1 seconds.
- #--------------------------------------
- #@# CA Normalize Thu Aug 8 12:11:54 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 = (65, 37, 29) --> (193, 173, 197)
- using (108, 82, 113) as brain centroid...
- mean wm in atlas = 107, using box (92,65,92) --> (123, 98,133) to find MRI wm
- before smoothing, mri peak at 107
- after smoothing, mri peak at 106, scaling input intensities by 1.009
- scaling channel 0 by 1.00943
- using 244171 sample points...
- INFO: compute sample coordinates transform
- 1.099 0.042 -0.061 -14.845;
- -0.028 1.149 0.325 -20.792;
- 0.099 -0.272 0.946 13.810;
- 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 (124, 38, 34) --> (189, 140, 197)
- Left_Cerebral_White_Matter: limiting intensities to 104.0 --> 153.0
- 0 of 10 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 40735 control points for structure...
- bounding box (71, 36, 35) --> (134, 131, 200)
- Right_Cerebral_White_Matter: limiting intensities to 103.0 --> 153.0
- 0 of 14 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3012 control points for structure...
- bounding box (129, 114, 62) --> (173, 154, 115)
- Left_Cerebellum_White_Matter: limiting intensities to 89.0 --> 153.0
- 0 of 9 (0.0%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2764 control points for structure...
- bounding box (86, 114, 62) --> (129, 151, 119)
- Right_Cerebellum_White_Matter: limiting intensities to 90.0 --> 153.0
- 0 of 14 (0.0%) samples deleted
- finding control points in Brain_Stem....
- found 3520 control points for structure...
- bounding box (115, 103, 97) --> (145, 163, 128)
- Brain_Stem: limiting intensities to 83.0 --> 153.0
- 3 of 8 (37.5%) samples deleted
- using 55 total control points for intensity normalization...
- bias field = 0.932 +- 0.060
- 0 of 52 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 41584 control points for structure...
- bounding box (124, 38, 34) --> (189, 140, 197)
- Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 144.0
- 0 of 89 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 40735 control points for structure...
- bounding box (71, 36, 35) --> (134, 131, 200)
- Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 144.0
- 2 of 88 (2.3%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3012 control points for structure...
- bounding box (129, 114, 62) --> (173, 154, 115)
- Left_Cerebellum_White_Matter: limiting intensities to 80.0 --> 144.0
- 0 of 9 (0.0%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2764 control points for structure...
- bounding box (86, 114, 62) --> (129, 151, 119)
- Right_Cerebellum_White_Matter: limiting intensities to 84.0 --> 144.0
- 0 of 9 (0.0%) samples deleted
- finding control points in Brain_Stem....
- found 3520 control points for structure...
- bounding box (115, 103, 97) --> (145, 163, 128)
- Brain_Stem: limiting intensities to 88.0 --> 144.0
- 43 of 50 (86.0%) samples deleted
- using 245 total control points for intensity normalization...
- bias field = 0.982 +- 0.048
- 0 of 200 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 41584 control points for structure...
- bounding box (124, 38, 34) --> (189, 140, 197)
- Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 135.0
- 0 of 213 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 40735 control points for structure...
- bounding box (71, 36, 35) --> (134, 131, 200)
- Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 135.0
- 0 of 160 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3012 control points for structure...
- bounding box (129, 114, 62) --> (173, 154, 115)
- Left_Cerebellum_White_Matter: limiting intensities to 95.0 --> 135.0
- 13 of 16 (81.2%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2764 control points for structure...
- bounding box (86, 114, 62) --> (129, 151, 119)
- Right_Cerebellum_White_Matter: limiting intensities to 78.0 --> 135.0
- 0 of 8 (0.0%) samples deleted
- finding control points in Brain_Stem....
- found 3520 control points for structure...
- bounding box (115, 103, 97) --> (145, 163, 128)
- Brain_Stem: limiting intensities to 61.0 --> 135.0
- 1 of 71 (1.4%) samples deleted
- using 468 total control points for intensity normalization...
- bias field = 1.028 +- 0.070
- 1 of 454 control points discarded
- writing normalized volume to norm.mgz...
- writing control points to ctrl_pts.mgz
- freeing GCA...done.
- normalization took 2 minutes and 3 seconds.
- #--------------------------------------
- #@# CA Reg Thu Aug 8 12:13:57 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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) = 1.30 (predicted orig area = 6.1)
- label assignment complete, 0 changed (0.00%)
- freeing gibbs priors...done.
- average std[0] = 5.0
- **************** pass 1 of 1 ************************
- setting smoothness coefficient to 0.039
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.901, neg=0, invalid=96777
- 0001: dt=129.472000, rms=0.801 (11.014%), neg=0, invalid=96777
- 0002: dt=129.472000, rms=0.774 (3.392%), neg=0, invalid=96777
- 0003: dt=129.472000, rms=0.764 (1.329%), neg=0, invalid=96777
- 0004: dt=129.472000, rms=0.757 (0.886%), neg=0, invalid=96777
- 0005: dt=129.472000, rms=0.752 (0.654%), neg=0, invalid=96777
- 0006: dt=129.472000, rms=0.748 (0.571%), neg=0, invalid=96777
- 0007: dt=129.472000, rms=0.745 (0.443%), neg=0, invalid=96777
- 0008: dt=129.472000, rms=0.741 (0.425%), neg=0, invalid=96777
- 0009: dt=129.472000, rms=0.739 (0.356%), neg=0, invalid=96777
- 0010: dt=129.472000, rms=0.736 (0.332%), neg=0, invalid=96777
- 0011: dt=129.472000, rms=0.734 (0.284%), neg=0, invalid=96777
- 0012: dt=129.472000, rms=0.732 (0.247%), neg=0, invalid=96777
- 0013: dt=129.472000, rms=0.731 (0.237%), neg=0, invalid=96777
- 0014: dt=129.472000, rms=0.728 (0.420%), neg=0, invalid=96777
- 0015: dt=129.472000, rms=0.724 (0.497%), neg=0, invalid=96777
- 0016: dt=129.472000, rms=0.720 (0.592%), neg=0, invalid=96777
- 0017: dt=129.472000, rms=0.716 (0.505%), neg=0, invalid=96777
- 0018: dt=129.472000, rms=0.714 (0.345%), neg=0, invalid=96777
- 0019: dt=129.472000, rms=0.712 (0.241%), neg=0, invalid=96777
- 0020: dt=129.472000, rms=0.710 (0.294%), neg=0, invalid=96777
- 0021: dt=129.472000, rms=0.708 (0.310%), neg=0, invalid=96777
- 0022: dt=129.472000, rms=0.705 (0.419%), neg=0, invalid=96777
- 0023: dt=129.472000, rms=0.702 (0.323%), neg=0, invalid=96777
- 0024: dt=129.472000, rms=0.700 (0.276%), neg=0, invalid=96777
- 0025: dt=129.472000, rms=0.699 (0.241%), neg=0, invalid=96777
- 0026: dt=129.472000, rms=0.697 (0.265%), neg=0, invalid=96777
- 0027: dt=129.472000, rms=0.695 (0.203%), neg=0, invalid=96777
- 0028: dt=129.472000, rms=0.694 (0.180%), neg=0, invalid=96777
- 0029: dt=129.472000, rms=0.693 (0.191%), neg=0, invalid=96777
- 0030: dt=129.472000, rms=0.691 (0.191%), neg=0, invalid=96777
- 0031: dt=129.472000, rms=0.690 (0.181%), neg=0, invalid=96777
- 0032: dt=129.472000, rms=0.689 (0.164%), neg=0, invalid=96777
- 0033: dt=129.472000, rms=0.688 (0.157%), neg=0, invalid=96777
- 0034: dt=129.472000, rms=0.687 (0.170%), neg=0, invalid=96777
- 0035: dt=129.472000, rms=0.686 (0.180%), neg=0, invalid=96777
- 0036: dt=129.472000, rms=0.684 (0.173%), neg=0, invalid=96777
- 0037: dt=129.472000, rms=0.683 (0.166%), neg=0, invalid=96777
- 0038: dt=129.472000, rms=0.682 (0.140%), neg=0, invalid=96777
- 0039: dt=129.472000, rms=0.682 (0.117%), neg=0, invalid=96777
- 0040: dt=129.472000, rms=0.681 (0.106%), neg=0, invalid=96777
- 0041: dt=129.472000, rms=0.681 (0.033%), neg=0, invalid=96777
- 0042: dt=129.472000, rms=0.681 (-0.002%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.681, neg=0, invalid=96777
- 0043: dt=92.480000, rms=0.680 (0.038%), neg=0, invalid=96777
- 0044: dt=369.920000, rms=0.679 (0.171%), neg=0, invalid=96777
- 0045: dt=32.368000, rms=0.679 (0.020%), neg=0, invalid=96777
- 0046: dt=32.368000, rms=0.679 (0.014%), neg=0, invalid=96777
- 0047: dt=32.368000, rms=0.679 (0.016%), neg=0, invalid=96777
- 0048: dt=32.368000, rms=0.679 (0.018%), neg=0, invalid=96777
- 0049: dt=32.368000, rms=0.679 (0.031%), neg=0, invalid=96777
- 0050: dt=32.368000, rms=0.678 (0.042%), neg=0, invalid=96777
- 0051: dt=32.368000, rms=0.678 (0.046%), neg=0, invalid=96777
- 0052: dt=32.368000, rms=0.678 (0.038%), neg=0, invalid=96777
- 0053: dt=32.368000, rms=0.677 (0.028%), neg=0, invalid=96777
- setting smoothness coefficient to 0.154
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.685, neg=0, invalid=96777
- 0054: dt=145.152000, rms=0.676 (1.407%), neg=0, invalid=96777
- 0055: dt=103.680000, rms=0.670 (0.904%), neg=0, invalid=96777
- 0056: dt=36.288000, rms=0.665 (0.762%), neg=0, invalid=96777
- 0057: dt=36.288000, rms=0.664 (0.117%), neg=0, invalid=96777
- 0058: dt=36.288000, rms=0.661 (0.392%), neg=0, invalid=96777
- 0059: dt=36.288000, rms=0.658 (0.488%), neg=0, invalid=96777
- 0060: dt=36.288000, rms=0.654 (0.561%), neg=0, invalid=96777
- 0061: dt=36.288000, rms=0.650 (0.689%), neg=0, invalid=96777
- 0062: dt=36.288000, rms=0.644 (0.841%), neg=0, invalid=96777
- 0063: dt=36.288000, rms=0.640 (0.720%), neg=0, invalid=96777
- 0064: dt=36.288000, rms=0.636 (0.553%), neg=0, invalid=96777
- 0065: dt=36.288000, rms=0.633 (0.455%), neg=0, invalid=96777
- 0066: dt=36.288000, rms=0.630 (0.529%), neg=0, invalid=96777
- 0067: dt=36.288000, rms=0.627 (0.404%), neg=0, invalid=96777
- 0068: dt=36.288000, rms=0.625 (0.338%), neg=0, invalid=96777
- 0069: dt=36.288000, rms=0.624 (0.253%), neg=0, invalid=96777
- 0070: dt=36.288000, rms=0.622 (0.307%), neg=0, invalid=96777
- 0071: dt=36.288000, rms=0.620 (0.251%), neg=0, invalid=96777
- 0072: dt=36.288000, rms=0.619 (0.212%), neg=0, invalid=96777
- 0073: dt=36.288000, rms=0.618 (0.166%), neg=0, invalid=96777
- 0074: dt=36.288000, rms=0.617 (0.128%), neg=0, invalid=96777
- 0075: dt=36.288000, rms=0.616 (0.156%), neg=0, invalid=96777
- 0076: dt=36.288000, rms=0.615 (0.103%), neg=0, invalid=96777
- 0077: dt=36.288000, rms=0.615 (0.087%), neg=0, invalid=96777
- 0078: dt=145.152000, rms=0.614 (0.126%), neg=0, invalid=96777
- 0079: dt=9.072000, rms=0.614 (0.003%), neg=0, invalid=96777
- 0080: dt=9.072000, rms=0.614 (0.006%), neg=0, invalid=96777
- 0081: dt=9.072000, rms=0.614 (-0.002%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.614, neg=0, invalid=96777
- 0082: dt=20.736000, rms=0.614 (0.015%), neg=0, invalid=96777
- 0083: dt=36.288000, rms=0.614 (0.028%), neg=0, invalid=96777
- 0084: dt=15.552000, rms=0.614 (0.002%), neg=0, invalid=96777
- 0085: dt=15.552000, rms=0.614 (0.005%), neg=0, invalid=96777
- 0086: dt=15.552000, rms=0.614 (0.001%), neg=0, invalid=96777
- 0087: dt=15.552000, rms=0.614 (-0.010%), neg=0, invalid=96777
- setting smoothness coefficient to 0.588
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.643, neg=0, invalid=96777
- 0088: dt=5.423729, rms=0.643 (0.056%), neg=0, invalid=96777
- 0089: dt=1.600000, rms=0.643 (0.006%), neg=0, invalid=96777
- 0090: dt=1.600000, rms=0.643 (-0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.643, neg=0, invalid=96777
- 0091: dt=0.000000, rms=0.643 (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=0.723, neg=0, invalid=96777
- 0092: dt=5.319372, rms=0.702 (2.891%), neg=0, invalid=96777
- 0093: dt=3.194030, rms=0.700 (0.187%), neg=0, invalid=96777
- 0094: dt=3.194030, rms=0.700 (-0.021%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.700, neg=0, invalid=96777
- 0095: dt=0.000000, rms=0.700 (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=0.779, neg=0, invalid=96777
- 0096: dt=1.111639, rms=0.775 (0.523%), neg=0, invalid=96777
- 0097: dt=2.377246, rms=0.767 (0.938%), neg=0, invalid=96777
- 0098: dt=0.448000, rms=0.767 (0.069%), neg=0, invalid=96777
- 0099: dt=0.448000, rms=0.767 (0.029%), neg=0, invalid=96777
- 0100: dt=0.448000, rms=0.766 (0.037%), neg=0, invalid=96777
- 0101: dt=0.448000, rms=0.766 (0.032%), neg=0, invalid=96777
- 0102: dt=0.448000, rms=0.766 (0.010%), neg=0, invalid=96777
- 0103: dt=2.227273, rms=0.765 (0.133%), neg=0, invalid=96777
- 0104: dt=0.000000, rms=0.765 (0.004%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.765, neg=0, invalid=96777
- 0105: dt=0.544118, rms=0.764 (0.081%), neg=0, invalid=96777
- 0106: dt=0.080000, rms=0.764 (-0.002%), neg=0, invalid=96777
- resetting metric properties...
- setting smoothness coefficient to 10.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.716, neg=0, invalid=96777
- 0107: dt=0.154661, rms=0.708 (1.114%), neg=0, invalid=96777
- 0108: dt=0.000000, rms=0.708 (0.002%), neg=0, invalid=96777
- 0109: dt=0.050000, rms=0.708 (-0.013%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.708, neg=0, invalid=96777
- 0110: dt=0.347584, rms=0.704 (0.542%), neg=0, invalid=96777
- 0111: dt=0.064000, rms=0.703 (0.118%), neg=0, invalid=96777
- 0112: dt=0.064000, rms=0.703 (-0.007%), neg=0, invalid=96777
- renormalizing by structure alignment....
- renormalizing input #0
- gca peak = 0.11725 (24)
- mri peak = 0.14301 (55)
- Left_Lateral_Ventricle (4): linear fit = 2.20 x + 0.0 (1178 voxels, overlap=0.005)
- Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (1178 voxels, peak = 53), gca=36.0
- gca peak = 0.14022 (22)
- mri peak = 0.10960 ( 7)
- Right_Lateral_Ventricle (43): linear fit = 0.22 x + 0.0 (604 voxels, overlap=0.005)
- Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (604 voxels, peak = 5), gca=8.8
- gca peak = 0.24234 (100)
- mri peak = 0.12385 (75)
- Right_Pallidum (52): linear fit = 0.80 x + 0.0 (357 voxels, overlap=0.032)
- Right_Pallidum (52): linear fit = 0.80 x + 0.0 (357 voxels, peak = 80), gca=79.5
- gca peak = 0.19192 (97)
- mri peak = 0.18787 (75)
- Left_Pallidum (13): linear fit = 0.77 x + 0.0 (315 voxels, overlap=0.484)
- Left_Pallidum (13): linear fit = 0.77 x + 0.0 (315 voxels, peak = 75), gca=75.2
- gca peak = 0.24007 (63)
- mri peak = 0.08999 (56)
- Right_Hippocampus (53): linear fit = 0.85 x + 0.0 (418 voxels, overlap=0.201)
- Right_Hippocampus (53): linear fit = 0.85 x + 0.0 (418 voxels, peak = 53), gca=53.2
- gca peak = 0.29892 (64)
- mri peak = 0.09388 (58)
- Left_Hippocampus (17): linear fit = 0.85 x + 0.0 (485 voxels, overlap=0.142)
- Left_Hippocampus (17): linear fit = 0.85 x + 0.0 (485 voxels, peak = 54), gca=54.1
- gca peak = 0.12541 (104)
- mri peak = 0.06489 (107)
- Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (56578 voxels, overlap=0.897)
- Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (56578 voxels, peak = 107), gca=106.6
- gca peak = 0.13686 (104)
- mri peak = 0.07498 (107)
- Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (57418 voxels, overlap=0.772)
- Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (57418 voxels, peak = 108), gca=107.6
- gca peak = 0.11691 (63)
- mri peak = 0.05213 (50)
- Left_Cerebral_Cortex (3): linear fit = 0.80 x + 0.0 (14833 voxels, overlap=0.119)
- Left_Cerebral_Cortex (3): linear fit = 0.80 x + 0.0 (14833 voxels, peak = 50), gca=50.1
- gca peak = 0.13270 (63)
- mri peak = 0.06223 (51)
- Right_Cerebral_Cortex (42): linear fit = 0.80 x + 0.0 (15455 voxels, overlap=0.110)
- Right_Cerebral_Cortex (42): linear fit = 0.80 x + 0.0 (15455 voxels, peak = 50), gca=50.1
- gca peak = 0.15182 (70)
- mri peak = 0.10308 (56)
- Right_Caudate (50): linear fit = 0.79 x + 0.0 (462 voxels, overlap=0.011)
- Right_Caudate (50): linear fit = 0.79 x + 0.0 (462 voxels, peak = 55), gca=55.0
- gca peak = 0.14251 (76)
- mri peak = 0.11050 (58)
- Left_Caudate (11): linear fit = 0.75 x + 0.0 (568 voxels, overlap=0.021)
- Left_Caudate (11): linear fit = 0.75 x + 0.0 (568 voxels, peak = 57), gca=57.4
- gca peak = 0.12116 (60)
- mri peak = 0.05451 (59)
- Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (9961 voxels, overlap=0.989)
- Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (9961 voxels, peak = 58), gca=57.9
- gca peak = 0.12723 (61)
- mri peak = 0.05544 (58)
- Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (11865 voxels, overlap=0.991)
- Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (11865 voxels, peak = 60), gca=60.1
- gca peak = 0.22684 (88)
- mri peak = 0.05818 (90)
- Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (5713 voxels, overlap=0.949)
- Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (5713 voxels, peak = 89), gca=89.3
- gca peak = 0.21067 (87)
- mri peak = 0.05650 (87)
- Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5353 voxels, overlap=0.982)
- Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5353 voxels, peak = 87), gca=86.6
- gca peak = 0.25455 (62)
- mri peak = 0.08370 (58)
- Left_Amygdala (18): linear fit = 0.88 x + 0.0 (258 voxels, overlap=0.694)
- Left_Amygdala (18): linear fit = 0.88 x + 0.0 (258 voxels, peak = 54), gca=54.2
- gca peak = 0.39668 (62)
- mri peak = 0.12756 (53)
- Right_Amygdala (54): linear fit = 0.85 x + 0.0 (308 voxels, overlap=0.055)
- Right_Amygdala (54): linear fit = 0.85 x + 0.0 (308 voxels, peak = 52), gca=52.4
- gca peak = 0.10129 (93)
- mri peak = 0.04906 (85)
- Left_Thalamus_Proper (10): linear fit = 0.92 x + 0.0 (4675 voxels, overlap=0.919)
- Left_Thalamus_Proper (10): linear fit = 0.92 x + 0.0 (4675 voxels, peak = 85), gca=85.1
- gca peak = 0.12071 (89)
- mri peak = 0.10826 (77)
- Right_Thalamus_Proper (49): linear fit = 0.94 x + 0.0 (3726 voxels, overlap=0.445)
- Right_Thalamus_Proper (49): linear fit = 0.94 x + 0.0 (3726 voxels, peak = 83), gca=83.2
- gca peak = 0.13716 (82)
- mri peak = 0.05377 (75)
- Left_Putamen (12): linear fit = 0.88 x + 0.0 (1483 voxels, overlap=0.416)
- Left_Putamen (12): linear fit = 0.88 x + 0.0 (1483 voxels, peak = 73), gca=72.6
- gca peak = 0.15214 (84)
- mri peak = 0.07704 (65)
- Right_Putamen (51): linear fit = 0.81 x + 0.0 (1907 voxels, overlap=0.013)
- Right_Putamen (51): linear fit = 0.81 x + 0.0 (1907 voxels, peak = 68), gca=67.6
- gca peak = 0.08983 (85)
- mri peak = 0.10973 (80)
- Brain_Stem (16): linear fit = 0.99 x + 0.0 (8634 voxels, overlap=0.767)
- Brain_Stem (16): linear fit = 0.99 x + 0.0 (8634 voxels, peak = 84), gca=83.7
- gca peak = 0.11809 (92)
- mri peak = 0.13966 (83)
- Right_VentralDC (60): linear fit = 0.90 x + 0.0 (805 voxels, overlap=0.345)
- Right_VentralDC (60): linear fit = 0.90 x + 0.0 (805 voxels, peak = 83), gca=83.3
- gca peak = 0.12914 (94)
- mri peak = 0.10058 (83)
- Left_VentralDC (28): linear fit = 0.89 x + 0.0 (928 voxels, overlap=0.419)
- Left_VentralDC (28): linear fit = 0.89 x + 0.0 (928 voxels, peak = 84), gca=84.1
- gca peak = 0.21100 (36)
- mri peak = 0.12694 (54)
- Third_Ventricle (14): linear fit = 1.46 x + 0.0 (71 voxels, overlap=0.081)
- Third_Ventricle (14): linear fit = 1.46 x + 0.0 (71 voxels, peak = 52), gca=52.4
- gca peak = 0.13542 (27)
- mri peak = 0.18125 ( 8)
- Fourth_Ventricle (15): linear fit = 0.22 x + 0.0 (210 voxels, overlap=0.020)
- Fourth_Ventricle (15): linear fit = 0.22 x + 0.0 (210 voxels, peak = 6), gca=6.1
- gca peak Unknown = 0.94427 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.21802 (40)
- 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 1.03 x + 0.0
- estimating mean csf scale to be 1.12 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=0.737, neg=0, invalid=96777
- 0113: dt=129.472000, rms=0.727 (1.399%), neg=0, invalid=96777
- 0114: dt=110.976000, rms=0.723 (0.515%), neg=0, invalid=96777
- 0115: dt=129.472000, rms=0.720 (0.375%), neg=0, invalid=96777
- 0116: dt=73.984000, rms=0.719 (0.263%), neg=0, invalid=96777
- 0117: dt=295.936000, rms=0.716 (0.292%), neg=0, invalid=96777
- 0118: dt=55.488000, rms=0.715 (0.255%), neg=0, invalid=96777
- 0119: dt=1479.680000, rms=0.709 (0.823%), neg=0, invalid=96777
- 0120: dt=295.936000, rms=0.707 (0.202%), neg=0, invalid=96777
- 0121: dt=32.368000, rms=0.707 (0.049%), neg=0, invalid=96777
- 0122: dt=32.368000, rms=0.707 (0.019%), neg=0, invalid=96777
- 0123: dt=32.368000, rms=0.707 (0.020%), neg=0, invalid=96777
- 0124: dt=32.368000, rms=0.707 (0.022%), neg=0, invalid=96777
- 0125: dt=32.368000, rms=0.706 (0.041%), neg=0, invalid=96777
- 0126: dt=32.368000, rms=0.706 (0.067%), neg=0, invalid=96777
- 0127: dt=32.368000, rms=0.705 (0.083%), neg=0, invalid=96777
- 0128: dt=32.368000, rms=0.705 (0.082%), neg=0, invalid=96777
- 0129: dt=32.368000, rms=0.704 (0.073%), neg=0, invalid=96777
- 0130: dt=32.368000, rms=0.704 (0.070%), neg=0, invalid=96777
- 0131: dt=32.368000, rms=0.703 (0.066%), neg=0, invalid=96777
- 0132: dt=32.368000, rms=0.703 (0.063%), neg=0, invalid=96777
- 0133: dt=32.368000, rms=0.702 (0.063%), neg=0, invalid=96777
- 0134: dt=32.368000, rms=0.702 (0.072%), neg=0, invalid=96777
- 0135: dt=32.368000, rms=0.701 (0.072%), neg=0, invalid=96777
- 0136: dt=32.368000, rms=0.701 (0.071%), neg=0, invalid=96777
- 0137: dt=32.368000, rms=0.700 (0.064%), neg=0, invalid=96777
- 0138: dt=32.368000, rms=0.700 (0.056%), neg=0, invalid=96777
- 0139: dt=32.368000, rms=0.700 (0.046%), neg=0, invalid=96777
- 0140: dt=32.368000, rms=0.699 (0.046%), neg=0, invalid=96777
- 0141: dt=32.368000, rms=0.699 (0.045%), neg=0, invalid=96777
- 0142: dt=32.368000, rms=0.699 (0.048%), neg=0, invalid=96777
- 0143: dt=32.368000, rms=0.698 (0.043%), neg=0, invalid=96777
- 0144: dt=32.368000, rms=0.698 (0.040%), neg=0, invalid=96777
- 0145: dt=32.368000, rms=0.698 (0.039%), neg=0, invalid=96777
- 0146: dt=32.368000, rms=0.698 (0.033%), neg=0, invalid=96777
- 0147: dt=32.368000, rms=0.697 (0.030%), neg=0, invalid=96777
- 0148: dt=32.368000, rms=0.697 (0.031%), neg=0, invalid=96777
- 0149: dt=32.368000, rms=0.697 (0.033%), neg=0, invalid=96777
- 0150: dt=32.368000, rms=0.697 (0.035%), neg=0, invalid=96777
- 0151: dt=32.368000, rms=0.696 (0.037%), neg=0, invalid=96777
- 0152: dt=32.368000, rms=0.696 (0.035%), neg=0, invalid=96777
- 0153: dt=32.368000, rms=0.696 (0.033%), neg=0, invalid=96777
- 0154: dt=32.368000, rms=0.696 (0.033%), neg=0, invalid=96777
- 0155: dt=32.368000, rms=0.695 (0.035%), neg=0, invalid=96777
- 0156: dt=32.368000, rms=0.695 (0.034%), neg=0, invalid=96777
- 0157: dt=32.368000, rms=0.695 (0.034%), neg=0, invalid=96777
- 0158: dt=32.368000, rms=0.695 (0.033%), neg=0, invalid=96777
- 0159: dt=32.368000, rms=0.695 (0.030%), neg=0, invalid=96777
- 0160: dt=32.368000, rms=0.694 (0.026%), neg=0, invalid=96777
- 0161: dt=32.368000, rms=0.694 (0.025%), neg=0, invalid=96777
- 0162: dt=32.368000, rms=0.694 (0.025%), neg=0, invalid=96777
- 0163: dt=32.368000, rms=0.694 (0.027%), neg=0, invalid=96777
- 0164: dt=32.368000, rms=0.694 (0.028%), neg=0, invalid=96777
- 0165: dt=32.368000, rms=0.693 (0.030%), neg=0, invalid=96777
- 0166: dt=32.368000, rms=0.693 (0.030%), neg=0, invalid=96777
- 0167: dt=32.368000, rms=0.693 (0.030%), neg=0, invalid=96777
- 0168: dt=32.368000, rms=0.693 (0.022%), neg=0, invalid=96777
- 0169: dt=32.368000, rms=0.693 (0.021%), neg=0, invalid=96777
- 0170: dt=32.368000, rms=0.693 (0.001%), neg=0, invalid=96777
- 0171: dt=32.368000, rms=0.693 (0.001%), neg=0, invalid=96777
- 0172: dt=32.368000, rms=0.693 (0.003%), neg=0, invalid=96777
- 0173: dt=32.368000, rms=0.693 (0.003%), neg=0, invalid=96777
- 0174: dt=32.368000, rms=0.693 (0.008%), neg=0, invalid=96777
- 0175: dt=32.368000, rms=0.693 (0.009%), neg=0, invalid=96777
- 0176: dt=32.368000, rms=0.692 (0.011%), neg=0, invalid=96777
- 0177: dt=32.368000, rms=0.692 (0.014%), neg=0, invalid=96777
- 0178: dt=32.368000, rms=0.692 (0.015%), neg=0, invalid=96777
- 0179: dt=32.368000, rms=0.692 (0.015%), neg=0, invalid=96777
- 0180: dt=32.368000, rms=0.692 (0.015%), neg=0, invalid=96777
- 0181: dt=32.368000, rms=0.692 (0.015%), neg=0, invalid=96777
- 0182: dt=32.368000, rms=0.692 (0.014%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.692, neg=0, invalid=96777
- 0183: dt=295.936000, rms=0.690 (0.328%), neg=0, invalid=96777
- 0184: dt=73.984000, rms=0.689 (0.043%), neg=0, invalid=96777
- 0185: dt=73.984000, rms=0.689 (0.021%), neg=0, invalid=96777
- 0186: dt=73.984000, rms=0.689 (0.040%), neg=0, invalid=96777
- 0187: dt=73.984000, rms=0.689 (0.051%), neg=0, invalid=96777
- 0188: dt=73.984000, rms=0.688 (0.061%), neg=0, invalid=96777
- 0189: dt=73.984000, rms=0.688 (0.071%), neg=0, invalid=96777
- 0190: dt=73.984000, rms=0.687 (0.071%), neg=0, invalid=96777
- 0191: dt=73.984000, rms=0.687 (0.061%), neg=0, invalid=96777
- 0192: dt=73.984000, rms=0.686 (0.050%), neg=0, invalid=96777
- 0193: dt=73.984000, rms=0.686 (0.045%), neg=0, invalid=96777
- 0194: dt=73.984000, rms=0.686 (0.039%), neg=0, invalid=96777
- 0195: dt=73.984000, rms=0.686 (0.039%), neg=0, invalid=96777
- 0196: dt=73.984000, rms=0.685 (0.042%), neg=0, invalid=96777
- 0197: dt=73.984000, rms=0.685 (0.046%), neg=0, invalid=96777
- 0198: dt=73.984000, rms=0.685 (0.049%), neg=0, invalid=96777
- 0199: dt=73.984000, rms=0.684 (0.053%), neg=0, invalid=96777
- 0200: dt=73.984000, rms=0.684 (0.050%), neg=0, invalid=96777
- 0201: dt=73.984000, rms=0.684 (0.045%), neg=0, invalid=96777
- 0202: dt=73.984000, rms=0.683 (0.041%), neg=0, invalid=96777
- 0203: dt=73.984000, rms=0.683 (0.035%), neg=0, invalid=96777
- 0204: dt=73.984000, rms=0.683 (0.036%), neg=0, invalid=96777
- 0205: dt=73.984000, rms=0.683 (0.036%), neg=0, invalid=96777
- 0206: dt=73.984000, rms=0.682 (0.040%), neg=0, invalid=96777
- 0207: dt=73.984000, rms=0.682 (0.038%), neg=0, invalid=96777
- 0208: dt=73.984000, rms=0.682 (0.035%), neg=0, invalid=96777
- 0209: dt=73.984000, rms=0.682 (0.032%), neg=0, invalid=96777
- 0210: dt=73.984000, rms=0.681 (0.027%), neg=0, invalid=96777
- 0211: dt=73.984000, rms=0.681 (0.025%), neg=0, invalid=96777
- 0212: dt=73.984000, rms=0.681 (0.023%), neg=0, invalid=96777
- 0213: dt=1479.680000, rms=0.681 (0.059%), neg=0, invalid=96777
- 0214: dt=73.984000, rms=0.681 (0.027%), neg=0, invalid=96777
- 0215: dt=73.984000, rms=0.680 (-0.004%), neg=0, invalid=96777
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.681, neg=0, invalid=96777
- 0216: dt=124.416000, rms=0.675 (0.873%), neg=0, invalid=96777
- 0217: dt=82.944000, rms=0.670 (0.693%), neg=0, invalid=96777
- 0218: dt=36.288000, rms=0.667 (0.581%), neg=0, invalid=96777
- 0219: dt=25.920000, rms=0.665 (0.205%), neg=0, invalid=96777
- 0220: dt=145.152000, rms=0.660 (0.744%), neg=0, invalid=96777
- 0221: dt=20.736000, rms=0.658 (0.388%), neg=0, invalid=96777
- 0222: dt=580.608000, rms=0.647 (1.701%), neg=0, invalid=96777
- 0223: dt=20.025157, rms=0.642 (0.715%), neg=0, invalid=96777
- 0224: dt=145.152000, rms=0.640 (0.361%), neg=0, invalid=96777
- 0225: dt=36.288000, rms=0.638 (0.169%), neg=0, invalid=96777
- 0226: dt=145.152000, rms=0.637 (0.280%), neg=0, invalid=96777
- 0227: dt=31.104000, rms=0.636 (0.163%), neg=0, invalid=96777
- 0228: dt=36.288000, rms=0.635 (0.037%), neg=0, invalid=96777
- 0229: dt=36.288000, rms=0.635 (0.096%), neg=0, invalid=96777
- 0230: dt=36.288000, rms=0.634 (0.129%), neg=0, invalid=96777
- 0231: dt=36.288000, rms=0.633 (0.159%), neg=0, invalid=96777
- 0232: dt=36.288000, rms=0.632 (0.214%), neg=0, invalid=96777
- 0233: dt=36.288000, rms=0.630 (0.265%), neg=0, invalid=96777
- 0234: dt=36.288000, rms=0.628 (0.266%), neg=0, invalid=96777
- 0235: dt=36.288000, rms=0.627 (0.269%), neg=0, invalid=96777
- 0236: dt=36.288000, rms=0.625 (0.272%), neg=0, invalid=96777
- 0237: dt=36.288000, rms=0.623 (0.294%), neg=0, invalid=96777
- 0238: dt=36.288000, rms=0.621 (0.268%), neg=0, invalid=96777
- 0239: dt=36.288000, rms=0.620 (0.246%), neg=0, invalid=96777
- 0240: dt=36.288000, rms=0.618 (0.223%), neg=0, invalid=96777
- 0241: dt=36.288000, rms=0.617 (0.229%), neg=0, invalid=96777
- 0242: dt=36.288000, rms=0.616 (0.206%), neg=0, invalid=96777
- 0243: dt=36.288000, rms=0.615 (0.191%), neg=0, invalid=96777
- 0244: dt=36.288000, rms=0.613 (0.188%), neg=0, invalid=96777
- 0245: dt=36.288000, rms=0.612 (0.180%), neg=0, invalid=96777
- 0246: dt=36.288000, rms=0.611 (0.180%), neg=0, invalid=96777
- 0247: dt=36.288000, rms=0.610 (0.164%), neg=0, invalid=96777
- 0248: dt=36.288000, rms=0.609 (0.166%), neg=0, invalid=96777
- 0249: dt=36.288000, rms=0.608 (0.152%), neg=0, invalid=96777
- 0250: dt=36.288000, rms=0.607 (0.154%), neg=0, invalid=96777
- 0251: dt=36.288000, rms=0.607 (0.137%), neg=0, invalid=96777
- 0252: dt=36.288000, rms=0.606 (0.142%), neg=0, invalid=96777
- 0253: dt=36.288000, rms=0.605 (0.127%), neg=0, invalid=96777
- 0254: dt=36.288000, rms=0.604 (0.113%), neg=0, invalid=96777
- 0255: dt=36.288000, rms=0.604 (0.089%), neg=0, invalid=96777
- 0256: dt=36.288000, rms=0.603 (0.097%), neg=0, invalid=96777
- 0257: dt=36.288000, rms=0.602 (0.102%), neg=0, invalid=96777
- 0258: dt=36.288000, rms=0.602 (0.095%), neg=0, invalid=96777
- 0259: dt=36.288000, rms=0.601 (0.078%), neg=0, invalid=96777
- 0260: dt=36.288000, rms=0.601 (0.069%), neg=0, invalid=96777
- 0261: dt=36.288000, rms=0.601 (0.072%), neg=0, invalid=96777
- 0262: dt=36.288000, rms=0.600 (0.076%), neg=0, invalid=96777
- 0263: dt=36.288000, rms=0.600 (0.074%), neg=0, invalid=96777
- 0264: dt=36.288000, rms=0.599 (0.063%), neg=0, invalid=96777
- 0265: dt=36.288000, rms=0.599 (0.060%), neg=0, invalid=96777
- 0266: dt=36.288000, rms=0.599 (0.049%), neg=0, invalid=96777
- 0267: dt=36.288000, rms=0.598 (0.063%), neg=0, invalid=96777
- 0268: dt=36.288000, rms=0.598 (0.064%), neg=0, invalid=96777
- 0269: dt=36.288000, rms=0.598 (0.064%), neg=0, invalid=96777
- 0270: dt=36.288000, rms=0.597 (0.057%), neg=0, invalid=96777
- 0271: dt=36.288000, rms=0.597 (0.048%), neg=0, invalid=96777
- 0272: dt=36.288000, rms=0.597 (0.041%), neg=0, invalid=96777
- 0273: dt=36.288000, rms=0.596 (0.050%), neg=0, invalid=96777
- 0274: dt=36.288000, rms=0.596 (0.054%), neg=0, invalid=96777
- 0275: dt=36.288000, rms=0.596 (0.048%), neg=0, invalid=96777
- 0276: dt=36.288000, rms=0.595 (0.043%), neg=0, invalid=96777
- 0277: dt=36.288000, rms=0.595 (0.039%), neg=0, invalid=96777
- 0278: dt=36.288000, rms=0.595 (0.044%), neg=0, invalid=96777
- 0279: dt=36.288000, rms=0.595 (0.054%), neg=0, invalid=96777
- 0280: dt=36.288000, rms=0.594 (0.047%), neg=0, invalid=96777
- 0281: dt=36.288000, rms=0.594 (0.037%), neg=0, invalid=96777
- 0282: dt=36.288000, rms=0.594 (0.029%), neg=0, invalid=96777
- 0283: dt=36.288000, rms=0.594 (0.035%), neg=0, invalid=96777
- 0284: dt=36.288000, rms=0.594 (0.036%), neg=0, invalid=96777
- 0285: dt=36.288000, rms=0.593 (0.045%), neg=0, invalid=96777
- 0286: dt=36.288000, rms=0.593 (0.040%), neg=0, invalid=96777
- 0287: dt=36.288000, rms=0.593 (0.040%), neg=0, invalid=96777
- 0288: dt=36.288000, rms=0.593 (0.032%), neg=0, invalid=96777
- 0289: dt=36.288000, rms=0.592 (0.029%), neg=0, invalid=96777
- 0290: dt=36.288000, rms=0.592 (0.024%), neg=0, invalid=96777
- 0291: dt=36.288000, rms=0.592 (0.029%), neg=0, invalid=96777
- 0292: dt=36.288000, rms=0.592 (0.030%), neg=0, invalid=96777
- 0293: dt=36.288000, rms=0.592 (0.032%), neg=0, invalid=96777
- 0294: dt=36.288000, rms=0.592 (0.027%), neg=0, invalid=96777
- 0295: dt=36.288000, rms=0.591 (0.027%), neg=0, invalid=96777
- 0296: dt=36.288000, rms=0.591 (0.037%), neg=0, invalid=96777
- 0297: dt=36.288000, rms=0.591 (0.027%), neg=0, invalid=96777
- 0298: dt=36.288000, rms=0.591 (0.036%), neg=0, invalid=96777
- 0299: dt=36.288000, rms=0.591 (0.024%), neg=0, invalid=96777
- 0300: dt=36.288000, rms=0.591 (0.026%), neg=0, invalid=96777
- 0301: dt=36.288000, rms=0.590 (0.026%), neg=0, invalid=96777
- 0302: dt=36.288000, rms=0.590 (0.037%), neg=0, invalid=96777
- 0303: dt=36.288000, rms=0.590 (0.035%), neg=0, invalid=96777
- 0304: dt=36.288000, rms=0.590 (0.031%), neg=0, invalid=96777
- 0305: dt=36.288000, rms=0.590 (0.026%), neg=0, invalid=96777
- 0306: dt=36.288000, rms=0.590 (0.019%), neg=0, invalid=96777
- 0307: dt=36.288000, rms=0.589 (0.020%), neg=0, invalid=96777
- 0308: dt=36.288000, rms=0.589 (0.031%), neg=0, invalid=96777
- 0309: dt=36.288000, rms=0.589 (0.031%), neg=0, invalid=96777
- 0310: dt=36.288000, rms=0.589 (0.032%), neg=0, invalid=96777
- 0311: dt=36.288000, rms=0.589 (0.020%), neg=0, invalid=96777
- 0312: dt=36.288000, rms=0.589 (0.013%), neg=0, invalid=96777
- 0313: dt=145.152000, rms=0.588 (0.031%), neg=0, invalid=96777
- 0314: dt=2.268000, rms=0.588 (0.000%), neg=0, invalid=96777
- 0315: dt=2.268000, rms=0.588 (0.000%), neg=0, invalid=96777
- 0316: dt=2.268000, rms=0.589 (-0.002%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.589, neg=0, invalid=96777
- 0317: dt=103.680000, rms=0.587 (0.247%), neg=0, invalid=96777
- 0318: dt=31.104000, rms=0.586 (0.133%), neg=0, invalid=96777
- 0319: dt=31.104000, rms=0.586 (0.049%), neg=0, invalid=96777
- 0320: dt=31.104000, rms=0.586 (0.057%), neg=0, invalid=96777
- 0321: dt=31.104000, rms=0.585 (0.070%), neg=0, invalid=96777
- 0322: dt=31.104000, rms=0.585 (0.090%), neg=0, invalid=96777
- 0323: dt=31.104000, rms=0.584 (0.069%), neg=0, invalid=96777
- 0324: dt=31.104000, rms=0.584 (0.087%), neg=0, invalid=96777
- 0325: dt=31.104000, rms=0.583 (0.081%), neg=0, invalid=96777
- 0326: dt=31.104000, rms=0.583 (0.079%), neg=0, invalid=96777
- 0327: dt=31.104000, rms=0.582 (0.063%), neg=0, invalid=96777
- 0328: dt=31.104000, rms=0.582 (0.056%), neg=0, invalid=96777
- 0329: dt=31.104000, rms=0.582 (0.069%), neg=0, invalid=96777
- 0330: dt=31.104000, rms=0.581 (0.059%), neg=0, invalid=96777
- 0331: dt=31.104000, rms=0.581 (0.057%), neg=0, invalid=96777
- 0332: dt=31.104000, rms=0.581 (0.042%), neg=0, invalid=96777
- 0333: dt=31.104000, rms=0.581 (0.055%), neg=0, invalid=96777
- 0334: dt=31.104000, rms=0.580 (0.049%), neg=0, invalid=96777
- 0335: dt=31.104000, rms=0.580 (0.047%), neg=0, invalid=96777
- 0336: dt=31.104000, rms=0.580 (0.033%), neg=0, invalid=96777
- 0337: dt=31.104000, rms=0.580 (0.035%), neg=0, invalid=96777
- 0338: dt=31.104000, rms=0.579 (0.048%), neg=0, invalid=96777
- 0339: dt=31.104000, rms=0.579 (0.042%), neg=0, invalid=96777
- 0340: dt=31.104000, rms=0.579 (0.049%), neg=0, invalid=96777
- 0341: dt=31.104000, rms=0.579 (0.028%), neg=0, invalid=96777
- 0342: dt=31.104000, rms=0.578 (0.047%), neg=0, invalid=96777
- 0343: dt=31.104000, rms=0.578 (0.037%), neg=0, invalid=96777
- 0344: dt=31.104000, rms=0.578 (0.034%), neg=0, invalid=96777
- 0345: dt=31.104000, rms=0.578 (0.042%), neg=0, invalid=96777
- 0346: dt=31.104000, rms=0.577 (0.033%), neg=0, invalid=96777
- 0347: dt=31.104000, rms=0.577 (0.036%), neg=0, invalid=96777
- 0348: dt=31.104000, rms=0.577 (0.031%), neg=0, invalid=96777
- 0349: dt=31.104000, rms=0.577 (0.031%), neg=0, invalid=96777
- 0350: dt=31.104000, rms=0.577 (0.031%), neg=0, invalid=96777
- 0351: dt=31.104000, rms=0.577 (0.019%), neg=0, invalid=96777
- 0352: dt=31.104000, rms=0.576 (0.032%), neg=0, invalid=96777
- 0353: dt=31.104000, rms=0.576 (0.027%), neg=0, invalid=96777
- 0354: dt=31.104000, rms=0.576 (0.026%), neg=0, invalid=96777
- 0355: dt=31.104000, rms=0.576 (0.028%), neg=0, invalid=96777
- 0356: dt=31.104000, rms=0.576 (0.029%), neg=0, invalid=96777
- 0357: dt=31.104000, rms=0.576 (0.031%), neg=0, invalid=96777
- 0358: dt=31.104000, rms=0.575 (0.024%), neg=0, invalid=96777
- 0359: dt=31.104000, rms=0.575 (0.020%), neg=0, invalid=96777
- 0360: dt=82.944000, rms=0.575 (0.011%), neg=0, invalid=96777
- 0361: dt=82.944000, rms=0.575 (-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=0.585, neg=0, invalid=96777
- 0362: dt=25.600000, rms=0.583 (0.206%), neg=0, invalid=96777
- 0363: dt=25.600000, rms=0.582 (0.207%), neg=0, invalid=96777
- 0364: dt=8.622222, rms=0.581 (0.138%), neg=0, invalid=96777
- 0365: dt=32.000000, rms=0.580 (0.214%), neg=0, invalid=96777
- 0366: dt=8.000000, rms=0.579 (0.173%), neg=0, invalid=96777
- 0367: dt=38.400000, rms=0.578 (0.202%), neg=0, invalid=96777
- 0368: dt=7.439252, rms=0.577 (0.233%), neg=0, invalid=96777
- 0369: dt=128.000000, rms=0.574 (0.510%), neg=0, invalid=96777
- 0370: dt=9.182266, rms=0.572 (0.315%), neg=0, invalid=96777
- 0371: dt=11.200000, rms=0.571 (0.166%), neg=0, invalid=96777
- 0372: dt=19.200000, rms=0.570 (0.168%), neg=0, invalid=96777
- 0373: dt=10.295652, rms=0.569 (0.201%), neg=0, invalid=96777
- 0374: dt=11.200000, rms=0.568 (0.170%), neg=0, invalid=96777
- 0375: dt=11.200000, rms=0.567 (0.094%), neg=0, invalid=96777
- 0376: dt=11.200000, rms=0.567 (0.100%), neg=0, invalid=96777
- 0377: dt=25.600000, rms=0.566 (0.090%), neg=0, invalid=96777
- 0378: dt=9.600000, rms=0.566 (0.130%), neg=0, invalid=96777
- 0379: dt=11.200000, rms=0.565 (0.069%), neg=0, invalid=96777
- 0380: dt=19.200000, rms=0.565 (0.102%), neg=0, invalid=96777
- 0381: dt=8.000000, rms=0.564 (0.076%), neg=0, invalid=96777
- 0382: dt=44.800000, rms=0.563 (0.142%), neg=0, invalid=96777
- 0383: dt=6.925373, rms=0.563 (0.137%), neg=0, invalid=96777
- 0384: dt=153.600000, rms=0.561 (0.251%), neg=0, invalid=96777
- 0385: dt=8.075829, rms=0.559 (0.406%), neg=0, invalid=96777
- 0386: dt=9.600000, rms=0.558 (0.162%), neg=0, invalid=96777
- 0387: dt=11.200000, rms=0.558 (0.063%), neg=0, invalid=96777
- 0388: dt=32.000000, rms=0.557 (0.070%), neg=0, invalid=96777
- 0389: dt=8.000000, rms=0.557 (0.070%), neg=0, invalid=96777
- 0390: dt=19.200000, rms=0.557 (0.048%), neg=0, invalid=96777
- 0391: dt=19.200000, rms=0.557 (0.004%), neg=0, invalid=96777
- 0392: dt=19.200000, rms=0.556 (0.132%), neg=0, invalid=96777
- 0393: dt=19.200000, rms=0.555 (0.224%), neg=0, invalid=96777
- 0394: dt=19.200000, rms=0.553 (0.195%), neg=0, invalid=96777
- 0395: dt=19.200000, rms=0.552 (0.210%), neg=0, invalid=96777
- 0396: dt=19.200000, rms=0.551 (0.259%), neg=0, invalid=96777
- 0397: dt=19.200000, rms=0.549 (0.320%), neg=0, invalid=96777
- 0398: dt=19.200000, rms=0.548 (0.234%), neg=0, invalid=96777
- 0399: dt=19.200000, rms=0.547 (0.227%), neg=0, invalid=96777
- 0400: dt=19.200000, rms=0.545 (0.294%), neg=0, invalid=96777
- 0401: dt=19.200000, rms=0.544 (0.233%), neg=0, invalid=96777
- 0402: dt=19.200000, rms=0.542 (0.237%), neg=0, invalid=96777
- 0403: dt=19.200000, rms=0.541 (0.204%), neg=0, invalid=96777
- 0404: dt=19.200000, rms=0.540 (0.171%), neg=0, invalid=96777
- 0405: dt=19.200000, rms=0.539 (0.210%), neg=0, invalid=96777
- 0406: dt=19.200000, rms=0.539 (0.125%), neg=0, invalid=96777
- 0407: dt=19.200000, rms=0.538 (0.154%), neg=0, invalid=96777
- 0408: dt=19.200000, rms=0.537 (0.173%), neg=0, invalid=96777
- 0409: dt=19.200000, rms=0.536 (0.109%), neg=0, invalid=96777
- 0410: dt=19.200000, rms=0.536 (0.116%), neg=0, invalid=96777
- 0411: dt=19.200000, rms=0.535 (0.116%), neg=0, invalid=96777
- 0412: dt=19.200000, rms=0.534 (0.118%), neg=0, invalid=96777
- 0413: dt=19.200000, rms=0.534 (0.107%), neg=0, invalid=96777
- 0414: dt=19.200000, rms=0.534 (0.028%), neg=0, invalid=96777
- 0415: dt=19.200000, rms=0.533 (0.109%), neg=0, invalid=96777
- 0416: dt=19.200000, rms=0.533 (0.086%), neg=0, invalid=96777
- 0417: dt=19.200000, rms=0.533 (-0.004%), neg=0, invalid=96777
- 0418: dt=2.800000, rms=0.533 (0.004%), neg=0, invalid=96777
- 0419: dt=2.800000, rms=0.533 (0.002%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.533, neg=0, invalid=96777
- 0420: dt=32.000000, rms=0.531 (0.271%), neg=0, invalid=96777
- 0421: dt=19.200000, rms=0.530 (0.159%), neg=0, invalid=96777
- 0422: dt=6.400000, rms=0.530 (0.033%), neg=0, invalid=96777
- 0423: dt=6.400000, rms=0.530 (0.030%), neg=0, invalid=96777
- 0424: dt=6.400000, rms=0.530 (0.035%), neg=0, invalid=96777
- 0425: dt=6.400000, rms=0.530 (0.041%), neg=0, invalid=96777
- 0426: dt=6.400000, rms=0.529 (0.050%), neg=0, invalid=96777
- 0427: dt=6.400000, rms=0.529 (0.057%), neg=0, invalid=96777
- 0428: dt=6.400000, rms=0.529 (0.046%), neg=0, invalid=96777
- 0429: dt=6.400000, rms=0.529 (0.039%), neg=0, invalid=96777
- 0430: dt=6.400000, rms=0.528 (0.035%), neg=0, invalid=96777
- 0431: dt=6.400000, rms=0.528 (0.017%), neg=0, invalid=96777
- 0432: dt=6.400000, rms=0.528 (0.017%), neg=0, invalid=96777
- 0433: dt=6.400000, rms=0.528 (0.023%), neg=0, invalid=96777
- 0434: dt=6.400000, rms=0.528 (0.023%), neg=0, invalid=96777
- 0435: dt=6.400000, rms=0.528 (0.018%), neg=0, invalid=96777
- 0436: dt=44.800000, rms=0.528 (0.056%), neg=0, invalid=96777
- 0437: dt=11.200000, rms=0.527 (0.034%), neg=0, invalid=96777
- 0438: dt=11.200000, rms=0.527 (0.008%), neg=0, invalid=96777
- 0439: dt=11.200000, rms=0.527 (0.021%), neg=0, invalid=96777
- 0440: dt=11.200000, rms=0.527 (0.036%), neg=0, invalid=96777
- 0441: dt=11.200000, rms=0.527 (0.040%), neg=0, invalid=96777
- 0442: dt=11.200000, rms=0.527 (0.036%), neg=0, invalid=96777
- 0443: dt=11.200000, rms=0.526 (0.043%), neg=0, invalid=96777
- 0444: dt=11.200000, rms=0.526 (0.044%), neg=0, invalid=96777
- 0445: dt=11.200000, rms=0.526 (0.038%), neg=0, invalid=96777
- 0446: dt=11.200000, rms=0.526 (0.041%), neg=0, invalid=96777
- 0447: dt=11.200000, rms=0.526 (0.037%), neg=0, invalid=96777
- 0448: dt=11.200000, rms=0.525 (0.041%), neg=0, invalid=96777
- 0449: dt=11.200000, rms=0.525 (0.040%), neg=0, invalid=96777
- 0450: dt=11.200000, rms=0.525 (0.037%), neg=0, invalid=96777
- 0451: dt=11.200000, rms=0.525 (0.034%), neg=0, invalid=96777
- 0452: dt=11.200000, rms=0.525 (0.028%), neg=0, invalid=96777
- 0453: dt=11.200000, rms=0.524 (0.035%), neg=0, invalid=96777
- 0454: dt=11.200000, rms=0.524 (0.020%), neg=0, invalid=96777
- 0455: dt=11.200000, rms=0.524 (0.022%), neg=0, invalid=96777
- 0456: dt=11.200000, rms=0.524 (0.019%), neg=0, invalid=96777
- 0457: dt=44.800000, rms=0.524 (0.030%), neg=0, invalid=96777
- 0458: dt=0.000488, rms=0.524 (-0.006%), neg=0, invalid=96777
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.545, neg=0, invalid=96777
- 0459: dt=0.000000, rms=0.545 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.545, neg=0, invalid=96777
- 0460: dt=0.000000, rms=0.545 (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=0.586, neg=0, invalid=96777
- 0461: dt=0.448000, rms=0.584 (0.294%), neg=0, invalid=96777
- 0462: dt=0.520833, rms=0.583 (0.137%), neg=0, invalid=96777
- 0463: dt=0.080827, rms=0.583 (0.003%), neg=0, invalid=96777
- 0464: dt=0.080827, rms=0.583 (0.003%), neg=0, invalid=96777
- 0465: dt=0.080827, rms=0.583 (-0.006%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.583, neg=0, invalid=96777
- 0466: dt=0.458333, rms=0.583 (0.071%), neg=0, invalid=96777
- 0467: dt=0.112000, rms=0.583 (0.002%), neg=0, invalid=96777
- 0468: dt=0.112000, rms=0.583 (0.002%), neg=0, invalid=96777
- 0469: dt=0.112000, rms=0.583 (-0.011%), 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=0.533, neg=0, invalid=96777
- 0470: dt=0.112000, rms=0.528 (0.914%), neg=0, invalid=96777
- 0471: dt=0.112000, rms=0.524 (0.720%), neg=0, invalid=96777
- 0472: dt=0.007000, rms=0.524 (0.036%), neg=0, invalid=96777
- 0473: dt=0.007000, rms=0.524 (0.035%), neg=0, invalid=96777
- 0474: dt=0.007000, rms=0.524 (0.067%), neg=0, invalid=96777
- 0475: dt=0.007000, rms=0.523 (0.095%), neg=0, invalid=96777
- 0476: dt=0.007000, rms=0.522 (0.117%), neg=0, invalid=96777
- 0477: dt=0.007000, rms=0.522 (0.135%), neg=0, invalid=96777
- 0478: dt=0.007000, rms=0.521 (0.151%), neg=0, invalid=96777
- 0479: dt=0.007000, rms=0.520 (0.165%), neg=0, invalid=96777
- 0480: dt=0.007000, rms=0.519 (0.172%), neg=0, invalid=96777
- 0481: dt=0.007000, rms=0.518 (0.180%), neg=0, invalid=96777
- 0482: dt=0.007000, rms=0.517 (0.182%), neg=0, invalid=96777
- 0483: dt=0.007000, rms=0.516 (0.184%), neg=0, invalid=96777
- 0484: dt=0.007000, rms=0.515 (0.180%), neg=0, invalid=96777
- 0485: dt=0.007000, rms=0.515 (0.179%), neg=0, invalid=96777
- 0486: dt=0.007000, rms=0.514 (0.174%), neg=0, invalid=96777
- 0487: dt=0.007000, rms=0.513 (0.165%), neg=0, invalid=96777
- 0488: dt=0.007000, rms=0.512 (0.159%), neg=0, invalid=96777
- 0489: dt=0.007000, rms=0.511 (0.146%), neg=0, invalid=96777
- 0490: dt=0.007000, rms=0.510 (0.140%), neg=0, invalid=96777
- 0491: dt=0.007000, rms=0.510 (0.130%), neg=0, invalid=96777
- 0492: dt=0.007000, rms=0.509 (0.119%), neg=0, invalid=96777
- 0493: dt=0.007000, rms=0.509 (0.108%), neg=0, invalid=96777
- 0494: dt=0.007000, rms=0.508 (0.099%), neg=0, invalid=96777
- 0495: dt=0.007000, rms=0.508 (0.089%), neg=0, invalid=96777
- 0496: dt=0.007000, rms=0.507 (0.079%), neg=0, invalid=96777
- 0497: dt=0.007000, rms=0.507 (0.069%), neg=0, invalid=96777
- 0498: dt=0.007000, rms=0.507 (0.057%), neg=0, invalid=96777
- 0499: dt=0.007000, rms=0.506 (0.050%), neg=0, invalid=96777
- 0500: dt=0.007000, rms=0.506 (0.043%), neg=0, invalid=96777
- 0501: dt=0.007000, rms=0.506 (0.039%), neg=0, invalid=96777
- 0502: dt=0.007000, rms=0.506 (0.029%), neg=0, invalid=96777
- 0503: dt=0.007000, rms=0.506 (0.024%), neg=0, invalid=96777
- 0504: dt=0.007000, rms=0.506 (0.019%), neg=0, invalid=96777
- 0505: dt=0.000000, rms=0.506 (-0.002%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.506, neg=0, invalid=96777
- 0506: dt=0.112000, rms=0.504 (0.287%), neg=0, invalid=96777
- 0507: dt=0.112000, rms=0.503 (0.219%), neg=0, invalid=96777
- 0508: dt=0.028000, rms=0.503 (0.040%), neg=0, invalid=96777
- 0509: dt=0.028000, rms=0.503 (0.042%), neg=0, invalid=96777
- 0510: dt=0.028000, rms=0.502 (0.071%), neg=0, invalid=96777
- 0511: dt=0.028000, rms=0.502 (0.101%), neg=0, invalid=96777
- 0512: dt=0.028000, rms=0.501 (0.116%), neg=0, invalid=96777
- 0513: dt=0.028000, rms=0.501 (0.021%), neg=0, invalid=96777
- 0514: dt=0.028000, rms=0.501 (0.040%), neg=0, invalid=96777
- 0515: dt=0.028000, rms=0.501 (0.054%), neg=0, invalid=96777
- 0516: dt=0.028000, rms=0.500 (0.064%), neg=0, invalid=96777
- 0517: dt=0.028000, rms=0.500 (0.070%), neg=0, invalid=96777
- 0518: dt=0.028000, rms=0.500 (0.074%), neg=0, invalid=96777
- 0519: dt=0.028000, rms=0.499 (0.071%), neg=0, invalid=96777
- 0520: dt=0.028000, rms=0.499 (0.069%), neg=0, invalid=96777
- 0521: dt=0.028000, rms=0.499 (0.058%), neg=0, invalid=96777
- 0522: dt=0.028000, rms=0.498 (0.053%), neg=0, invalid=96777
- 0523: dt=0.028000, rms=0.498 (0.041%), neg=0, invalid=96777
- 0524: dt=0.028000, rms=0.498 (0.032%), neg=0, invalid=96777
- 0525: dt=0.028000, rms=0.498 (0.026%), neg=0, invalid=96777
- 0526: dt=0.028000, rms=0.498 (0.016%), neg=0, invalid=96777
- 0527: dt=0.028000, rms=0.498 (0.005%), neg=0, invalid=96777
- 0528: dt=0.000000, rms=0.498 (0.002%), neg=0, invalid=96777
- 0529: dt=0.050000, rms=0.498 (-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=0.496, neg=0, invalid=96777
- 0530: dt=0.000000, rms=0.496 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.496, neg=0, invalid=96777
- 0531: dt=129.472000, rms=0.496 (0.034%), neg=0, invalid=96777
- 0532: dt=129.472000, rms=0.496 (0.018%), neg=0, invalid=96777
- 0533: dt=129.472000, rms=0.495 (0.015%), neg=0, invalid=96777
- 0534: dt=129.472000, rms=0.495 (0.014%), neg=0, invalid=96777
- 0535: dt=129.472000, rms=0.495 (0.032%), neg=0, invalid=96777
- 0536: dt=129.472000, rms=0.495 (0.032%), neg=0, invalid=96777
- 0537: dt=129.472000, rms=0.495 (-0.003%), neg=0, invalid=96777
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.495, neg=0, invalid=96777
- 0538: dt=25.920000, rms=0.495 (0.045%), neg=0, invalid=96777
- 0539: dt=7.776000, rms=0.495 (-0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.495, neg=0, invalid=96777
- 0540: dt=103.680000, rms=0.494 (0.232%), neg=0, invalid=96777
- 0541: dt=36.288000, rms=0.493 (0.157%), neg=0, invalid=96777
- 0542: dt=36.288000, rms=0.493 (0.022%), neg=0, invalid=96777
- 0543: dt=36.288000, rms=0.492 (0.112%), neg=0, invalid=96777
- 0544: dt=36.288000, rms=0.492 (0.128%), neg=0, invalid=96777
- 0545: dt=36.288000, rms=0.491 (0.114%), neg=0, invalid=96777
- 0546: dt=36.288000, rms=0.491 (0.037%), neg=0, invalid=96777
- 0547: dt=31.104000, rms=0.491 (0.076%), neg=0, invalid=96777
- 0548: dt=9.072000, rms=0.491 (0.002%), neg=0, invalid=96777
- 0549: dt=9.072000, rms=0.491 (0.003%), neg=0, invalid=96777
- 0550: dt=9.072000, rms=0.491 (0.002%), neg=0, invalid=96777
- 0551: dt=9.072000, rms=0.490 (0.013%), neg=0, invalid=96777
- 0552: dt=9.072000, rms=0.490 (0.017%), neg=0, invalid=96777
- 0553: dt=9.072000, rms=0.490 (0.017%), neg=0, invalid=96777
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.490, neg=0, invalid=96777
- iter 0, gcam->neg = 3
- after 6 iterations, nbhd size=1, neg = 0
- 0554: dt=32.000000, rms=0.488 (0.495%), neg=0, invalid=96777
- iter 0, gcam->neg = 51
- after 31 iterations, nbhd size=3, neg = 0
- 0555: dt=32.000000, rms=0.487 (0.282%), neg=0, invalid=96777
- 0556: dt=8.000000, rms=0.486 (0.111%), neg=0, invalid=96777
- 0557: dt=8.000000, rms=0.486 (0.081%), neg=0, invalid=96777
- iter 0, gcam->neg = 3
- after 13 iterations, nbhd size=2, neg = 0
- 0558: dt=8.000000, rms=0.485 (0.109%), neg=0, invalid=96777
- 0559: dt=8.000000, rms=0.484 (0.150%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 5 iterations, nbhd size=1, neg = 0
- 0560: dt=8.000000, rms=0.484 (0.134%), neg=0, invalid=96777
- iter 0, gcam->neg = 2
- after 1 iterations, nbhd size=0, neg = 0
- 0561: dt=8.000000, rms=0.483 (0.130%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 5 iterations, nbhd size=1, neg = 0
- 0562: dt=8.000000, rms=0.483 (0.114%), neg=0, invalid=96777
- 0563: dt=8.000000, rms=0.482 (0.099%), neg=0, invalid=96777
- 0564: dt=11.200000, rms=0.482 (0.053%), neg=0, invalid=96777
- 0565: dt=11.200000, rms=0.482 (0.041%), neg=0, invalid=96777
- 0566: dt=11.200000, rms=0.481 (0.090%), neg=0, invalid=96777
- 0567: dt=11.200000, rms=0.481 (0.100%), neg=0, invalid=96777
- 0568: dt=11.200000, rms=0.480 (0.105%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0569: dt=11.200000, rms=0.480 (0.111%), neg=0, invalid=96777
- 0570: dt=11.200000, rms=0.479 (0.082%), neg=0, invalid=96777
- iter 0, gcam->neg = 7
- after 19 iterations, nbhd size=3, neg = 0
- 0571: dt=11.200000, rms=0.479 (0.081%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.479, neg=0, invalid=96777
- iter 0, gcam->neg = 7
- after 21 iterations, nbhd size=2, neg = 0
- 0572: dt=38.400000, rms=0.475 (0.740%), neg=0, invalid=96777
- 0573: dt=8.000000, rms=0.474 (0.222%), neg=0, invalid=96777
- 0574: dt=8.000000, rms=0.474 (0.136%), neg=0, invalid=96777
- iter 0, gcam->neg = 3
- after 5 iterations, nbhd size=1, neg = 0
- 0575: dt=8.000000, rms=0.473 (0.140%), neg=0, invalid=96777
- 0576: dt=8.000000, rms=0.472 (0.228%), neg=0, invalid=96777
- 0577: dt=8.000000, rms=0.471 (0.177%), neg=0, invalid=96777
- iter 0, gcam->neg = 3
- after 6 iterations, nbhd size=1, neg = 0
- 0578: dt=8.000000, rms=0.470 (0.181%), neg=0, invalid=96777
- 0579: dt=8.000000, rms=0.470 (0.155%), neg=0, invalid=96777
- 0580: dt=8.000000, rms=0.469 (0.120%), neg=0, invalid=96777
- 0581: dt=8.000000, rms=0.468 (0.122%), neg=0, invalid=96777
- 0582: dt=8.000000, rms=0.468 (0.089%), neg=0, invalid=96777
- 0583: dt=9.600000, rms=0.468 (0.024%), neg=0, invalid=96777
- 0584: dt=9.600000, rms=0.468 (0.054%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 5 iterations, nbhd size=1, neg = 0
- 0585: dt=9.600000, rms=0.467 (0.041%), neg=0, invalid=96777
- 0586: dt=9.600000, rms=0.467 (0.038%), neg=0, invalid=96777
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.471, neg=0, invalid=96777
- iter 0, gcam->neg = 18
- after 17 iterations, nbhd size=1, neg = 0
- 0587: dt=2.333333, rms=0.471 (0.046%), neg=0, invalid=96777
- 0588: dt=1.008000, rms=0.471 (0.011%), neg=0, invalid=96777
- 0589: dt=1.008000, rms=0.471 (0.024%), neg=0, invalid=96777
- 0590: dt=1.008000, rms=0.470 (0.035%), neg=0, invalid=96777
- iter 0, gcam->neg = 8
- after 9 iterations, nbhd size=1, neg = 0
- 0591: dt=1.008000, rms=0.470 (0.022%), neg=0, invalid=96777
- iter 0, gcam->neg = 7
- after 7 iterations, nbhd size=1, neg = 0
- 0592: dt=1.008000, rms=0.470 (-0.018%), 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 = 19
- after 11 iterations, nbhd size=1, neg = 0
- 0593: dt=4.258065, rms=0.470 (0.149%), neg=0, invalid=96777
- iter 0, gcam->neg = 44
- after 16 iterations, nbhd size=1, neg = 0
- 0594: dt=7.111111, rms=0.468 (0.246%), neg=0, invalid=96777
- 0595: dt=0.015750, rms=0.468 (0.003%), neg=0, invalid=96777
- 0596: dt=0.015750, rms=0.468 (0.000%), neg=0, invalid=96777
- 0597: dt=0.015750, rms=0.468 (0.000%), neg=0, invalid=96777
- 0598: dt=0.015750, rms=0.468 (0.000%), neg=0, invalid=96777
- 0599: dt=0.015750, rms=0.468 (0.001%), neg=0, invalid=96777
- 0600: dt=0.015750, rms=0.468 (0.001%), neg=0, invalid=96777
- 0601: dt=0.015750, rms=0.468 (0.001%), neg=0, invalid=96777
- setting smoothness coefficient to 1.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.474, neg=0, invalid=96777
- 0602: dt=0.000000, rms=0.474 (-0.002%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.474, neg=0, invalid=96777
- 0603: dt=0.000000, rms=0.474 (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=0.465, neg=0, invalid=96777
- iter 0, gcam->neg = 802
- after 29 iterations, nbhd size=2, neg = 0
- 0604: dt=1.832792, rms=0.423 (8.972%), neg=0, invalid=96777
- 0605: dt=0.000109, rms=0.423 (-0.003%), neg=0, invalid=96777
- 0606: dt=0.000109, rms=0.423 (0.001%), neg=0, invalid=96777
- 0607: dt=0.000109, rms=0.423 (-0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.423, neg=0, invalid=96777
- 0608: dt=0.000313, rms=0.423 (0.000%), neg=0, invalid=96777
- 0609: dt=0.000000, rms=0.423 (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=0.408, neg=0, invalid=96777
- 0610: dt=0.000000, rms=0.409 (-0.320%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.409, neg=0, invalid=96777
- 0611: dt=8.092000, rms=0.409 (0.001%), neg=0, invalid=96777
- 0612: dt=8.092000, rms=0.409 (0.000%), neg=0, invalid=96777
- 0613: dt=8.092000, rms=0.409 (-0.000%), neg=0, invalid=96777
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.409, neg=0, invalid=96777
- 0614: dt=0.000000, rms=0.409 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.409, neg=0, invalid=96777
- 0615: dt=15.552000, rms=0.409 (0.012%), neg=0, invalid=96777
- 0616: dt=9.072000, rms=0.409 (0.002%), neg=0, invalid=96777
- 0617: dt=9.072000, rms=0.409 (0.000%), neg=0, invalid=96777
- 0618: dt=9.072000, rms=0.409 (-0.003%), neg=0, invalid=96777
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.410, neg=0, invalid=96777
- 0619: dt=2.800000, rms=0.410 (0.010%), neg=0, invalid=96777
- 0620: dt=1.600000, rms=0.410 (0.001%), neg=0, invalid=96777
- 0621: dt=1.600000, rms=0.410 (0.002%), neg=0, invalid=96777
- 0622: dt=1.600000, rms=0.410 (-0.004%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.410, neg=0, invalid=96777
- iter 0, gcam->neg = 2
- after 7 iterations, nbhd size=1, neg = 0
- 0623: dt=32.000000, rms=0.409 (0.182%), neg=0, invalid=96777
- iter 0, gcam->neg = 16
- after 16 iterations, nbhd size=2, neg = 0
- 0624: dt=25.600000, rms=0.409 (0.131%), neg=0, invalid=96777
- iter 0, gcam->neg = 17
- after 45 iterations, nbhd size=1, neg = 0
- 0625: dt=25.600000, rms=0.409 (-0.628%), neg=0, invalid=96777
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.411, neg=0, invalid=96777
- 0626: dt=0.009000, rms=0.411 (0.000%), neg=0, invalid=96777
- iter 0, gcam->neg = 8
- after 29 iterations, nbhd size=3, neg = 0
- 0627: dt=1.142857, rms=0.411 (0.016%), neg=0, invalid=96777
- 0628: dt=0.063000, rms=0.411 (0.001%), neg=0, invalid=96777
- 0629: dt=0.063000, rms=0.411 (0.003%), neg=0, invalid=96777
- 0630: dt=0.063000, rms=0.411 (0.007%), neg=0, invalid=96777
- 0631: dt=0.063000, rms=0.411 (0.010%), neg=0, invalid=96777
- 0632: dt=0.063000, rms=0.411 (0.013%), neg=0, invalid=96777
- iter 0, gcam->neg = 2
- after 0 iterations, nbhd size=0, neg = 0
- 0633: dt=0.063000, rms=0.411 (0.015%), neg=0, invalid=96777
- 0634: dt=0.063000, rms=0.411 (0.013%), neg=0, invalid=96777
- 0635: dt=0.063000, rms=0.410 (0.014%), neg=0, invalid=96777
- 0636: dt=0.063000, rms=0.410 (0.016%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0637: dt=0.063000, rms=0.410 (0.017%), neg=0, invalid=96777
- 0638: dt=0.063000, rms=0.410 (0.018%), neg=0, invalid=96777
- 0639: dt=0.063000, rms=0.410 (0.019%), neg=0, invalid=96777
- 0640: dt=0.063000, rms=0.410 (0.019%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 5 iterations, nbhd size=1, neg = 0
- 0641: dt=0.063000, rms=0.410 (0.026%), neg=0, invalid=96777
- 0642: dt=0.063000, rms=0.410 (0.019%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.410, neg=0, invalid=96777
- iter 0, gcam->neg = 43
- after 51 iterations, nbhd size=4, neg = 0
- 0643: dt=7.161905, rms=0.408 (0.428%), neg=0, invalid=96777
- 0644: dt=0.003938, rms=0.408 (0.000%), neg=0, invalid=96777
- 0645: dt=0.003938, rms=0.408 (0.000%), neg=0, invalid=96777
- 0646: dt=0.003938, rms=0.408 (0.000%), neg=0, invalid=96777
- 0647: dt=0.003938, rms=0.408 (0.000%), neg=0, invalid=96777
- 0648: dt=0.003938, rms=0.408 (0.001%), neg=0, invalid=96777
- 0649: dt=0.003938, rms=0.408 (0.001%), neg=0, invalid=96777
- 0650: dt=0.003938, rms=0.408 (0.001%), neg=0, invalid=96777
- 0651: dt=0.003938, rms=0.408 (0.001%), neg=0, invalid=96777
- 0652: dt=0.003938, rms=0.408 (0.001%), neg=0, invalid=96777
- 0653: dt=0.003938, rms=0.408 (0.001%), neg=0, invalid=96777
- 0654: dt=0.003938, rms=0.408 (0.001%), neg=0, invalid=96777
- 0655: dt=0.003938, rms=0.408 (0.001%), neg=0, invalid=96777
- 0656: dt=0.003938, rms=0.408 (0.001%), neg=0, invalid=96777
- 0657: dt=0.003938, rms=0.408 (0.001%), neg=0, invalid=96777
- 0658: dt=0.003938, rms=0.408 (0.001%), neg=0, invalid=96777
- 0659: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
- 0660: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
- 0661: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
- 0662: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
- 0663: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
- 0664: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
- 0665: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
- 0666: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
- 0667: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
- 0668: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
- 0669: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
- 0670: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
- 0671: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
- 0672: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
- 0673: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
- 0674: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
- 0675: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
- 0676: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
- 0677: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
- 0678: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
- 0679: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
- 0680: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
- 0681: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
- 0682: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
- 0683: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
- 0684: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
- 0685: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
- iter 0, gcam->neg = 132
- after 56 iterations, nbhd size=4, neg = 0
- 0686: dt=13.824000, rms=0.406 (0.376%), neg=0, invalid=96777
- 0687: dt=0.000984, rms=0.406 (0.000%), neg=0, invalid=96777
- 0688: dt=0.000984, rms=0.406 (0.000%), neg=0, invalid=96777
- 0689: dt=0.000984, rms=0.406 (-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=0.412, neg=0, invalid=96777
- 0690: dt=0.000160, rms=0.412 (0.000%), neg=0, invalid=96777
- 0691: dt=0.000000, rms=0.412 (-0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.412, neg=0, invalid=96777
- 0692: dt=0.000078, rms=0.412 (0.000%), neg=0, invalid=96777
- 0693: dt=0.000078, rms=0.412 (-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=0.403, neg=0, invalid=96777
- iter 0, gcam->neg = 224
- after 35 iterations, nbhd size=3, neg = 0
- 0694: dt=0.448000, rms=0.394 (2.045%), neg=0, invalid=96777
- 0695: dt=0.000015, rms=0.394 (0.001%), neg=0, invalid=96777
- 0696: dt=0.000015, rms=0.394 (0.000%), neg=0, invalid=96777
- 0697: dt=0.000015, rms=0.394 (0.000%), neg=0, invalid=96777
- 0698: dt=0.000015, rms=0.394 (0.000%), neg=0, invalid=96777
- 0699: dt=0.000015, rms=0.394 (0.000%), neg=0, invalid=96777
- 0700: dt=0.000750, rms=0.394 (0.000%), neg=0, invalid=96777
- iter 0, gcam->neg = 6
- after 6 iterations, nbhd size=1, neg = 0
- 0701: dt=0.024000, rms=0.394 (0.010%), neg=0, invalid=96777
- 0702: dt=0.000004, rms=0.394 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.394, neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 5 iterations, nbhd size=1, neg = 0
- 0703: dt=0.000250, rms=0.394 (0.001%), neg=0, invalid=96777
- 0704: dt=0.000027, rms=0.394 (0.000%), neg=0, invalid=96777
- 0705: dt=0.000027, rms=0.394 (0.000%), neg=0, invalid=96777
- 0706: dt=0.000027, rms=0.394 (0.000%), neg=0, invalid=96777
- 0707: dt=0.000027, rms=0.394 (0.000%), neg=0, invalid=96777
- 0708: dt=0.000027, rms=0.394 (0.000%), neg=0, invalid=96777
- 0709: dt=0.000027, rms=0.394 (0.000%), neg=0, invalid=96777
- 0710: dt=0.000027, rms=0.394 (0.000%), neg=0, invalid=96777
- 0711: dt=0.000027, rms=0.394 (0.000%), neg=0, invalid=96777
- 0712: dt=0.000027, rms=0.394 (0.000%), neg=0, invalid=96777
- 0713: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
- 0714: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
- 0715: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
- 0716: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
- 0717: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
- 0718: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
- 0719: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
- 0720: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
- 0721: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
- 0722: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
- 0723: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
- 0724: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
- 0725: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
- 0726: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
- 0727: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
- 0728: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
- 0729: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
- 0730: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
- 0731: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
- 0732: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
- 0733: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
- 0734: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
- 0735: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
- 0736: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
- 0737: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
- 0738: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
- 0739: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
- 0740: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
- 0741: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
- 0742: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
- 0743: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
- 0744: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
- 0745: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
- 0746: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
- 0747: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
- writing output transformation to transforms/talairach.m3z...
- GCAMwrite
- registration took 4 hours, 18 minutes and 0 seconds.
- #--------------------------------------
- #@# CA Reg Inv Thu Aug 8 16:31:57 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 16:33:31 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...
- 11389683 nonbrain voxels erased
- writing output to nu_noneck.mgz...
- nonbrain removal took 1 minutes and 34 seconds.
- #--------------------------------------
- #@# SkullLTA Thu Aug 8 16:35:04 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=9.0
- skull bounding box = (54, 13, 0) --> (212, 197, 196)
- using (107, 74, 98) as brain centroid...
- mean wm in atlas = 126, using box (88,51,74) --> (126, 96,122) to find MRI wm
- before smoothing, mri peak at 108
- after smoothing, mri peak at 107, scaling input intensities by 1.178
- scaling channel 0 by 1.17757
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.2 (thresh=-4.2)
- 1.264 0.048 -0.071 -35.935;
- -0.018 1.270 0.513 -54.525;
- 0.125 -0.518 1.107 15.895;
- 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)
- 1.264 0.048 -0.071 -35.935;
- -0.018 1.270 0.513 -54.525;
- 0.125 -0.518 1.107 15.895;
- 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)
- 1.239 0.047 -0.069 -30.915;
- -0.022 1.310 0.483 -52.599;
- 0.125 -0.478 1.123 12.280;
- 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)
- 1.239 0.047 -0.069 -30.915;
- -0.022 1.285 0.474 -49.342;
- 0.122 -0.469 1.102 14.038;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.0625
- ****************************************
- Nine parameter search. iteration 4 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.236 0.047 -0.069 -30.548;
- -0.021 1.283 0.484 -50.756;
- 0.123 -0.480 1.098 14.970;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 5 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.236 0.047 -0.069 -30.548;
- -0.021 1.283 0.484 -50.756;
- 0.123 -0.480 1.098 14.970;
- 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
- 1.23617 0.04681 -0.06911 -30.54774;
- -0.02084 1.28282 0.48392 -50.75591;
- 0.12254 -0.47982 1.09813 14.96986;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 3481
- Quasinewton: input matrix
- 1.23617 0.04681 -0.06911 -30.54774;
- -0.02084 1.28282 0.48392 -50.75591;
- 0.12254 -0.47982 1.09813 14.96986;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 4 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 007: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 1.236 0.047 -0.069 -30.548;
- -0.021 1.283 0.484 -50.756;
- 0.123 -0.480 1.098 14.970;
- 0.000 0.000 0.000 1.000;
- pass 1, spacing 8: log(p) = -4.0 (old=-4.2)
- transform before final EM align:
- 1.236 0.047 -0.069 -30.548;
- -0.021 1.283 0.484 -50.756;
- 0.123 -0.480 1.098 14.970;
- 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
- 1.23617 0.04681 -0.06911 -30.54774;
- -0.02084 1.28282 0.48392 -50.75591;
- 0.12254 -0.47982 1.09813 14.96986;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 382743
- Quasinewton: input matrix
- 1.23617 0.04681 -0.06911 -30.54774;
- -0.02084 1.28282 0.48392 -50.75591;
- 0.12254 -0.47982 1.09813 14.96986;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = 4.4 tol 0.000000
- final transform:
- 1.236 0.047 -0.069 -30.548;
- -0.021 1.283 0.484 -50.756;
- 0.123 -0.480 1.098 14.970;
- 0.000 0.000 0.000 1.000;
- writing output transformation to transforms/talairach_with_skull_2.lta...
- registration took 31 minutes and 47 seconds.
- #--------------------------------------
- #@# SubCort Seg Thu Aug 8 17:06:52 CEST 2013
- mri_ca_label -align norm.mgz transforms/talairach.m3z /opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz
- sysname Linux
- hostname snake4
- machine x86_64
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 = 0.10814 ( 4)
- Left_Lateral_Ventricle (4): linear fit = 0.12 x + 0.0 (311 voxels, overlap=0.085)
- Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (311 voxels, peak = 3), gca=10.8
- gca peak = 0.14982 (20)
- mri peak = 0.14647 ( 5)
- Right_Lateral_Ventricle (43): linear fit = 0.19 x + 0.0 (179 voxels, overlap=0.007)
- Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (179 voxels, peak = 4), gca=8.0
- gca peak = 0.28003 (97)
- mri peak = 0.12552 (83)
- Right_Pallidum (52): linear fit = 0.82 x + 0.0 (321 voxels, overlap=0.039)
- Right_Pallidum (52): linear fit = 0.82 x + 0.0 (321 voxels, peak = 80), gca=80.0
- gca peak = 0.18160 (96)
- mri peak = 0.12184 (78)
- Left_Pallidum (13): linear fit = 0.79 x + 0.0 (271 voxels, overlap=0.047)
- Left_Pallidum (13): linear fit = 0.79 x + 0.0 (271 voxels, peak = 75), gca=75.4
- gca peak = 0.27536 (62)
- mri peak = 0.10294 (53)
- Right_Hippocampus (53): linear fit = 0.83 x + 0.0 (530 voxels, overlap=0.031)
- Right_Hippocampus (53): linear fit = 0.83 x + 0.0 (530 voxels, peak = 52), gca=51.8
- gca peak = 0.32745 (63)
- mri peak = 0.09040 (58)
- Left_Hippocampus (17): linear fit = 0.85 x + 0.0 (600 voxels, overlap=0.060)
- Left_Hippocampus (17): linear fit = 0.85 x + 0.0 (600 voxels, peak = 53), gca=53.2
- gca peak = 0.08597 (105)
- mri peak = 0.06879 (108)
- Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (31675 voxels, overlap=0.786)
- Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (31675 voxels, peak = 107), gca=106.6
- gca peak = 0.09209 (106)
- mri peak = 0.07904 (108)
- Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (30610 voxels, overlap=0.709)
- Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (30610 voxels, peak = 109), gca=108.6
- gca peak = 0.07826 (63)
- mri peak = 0.05015 (50)
- Left_Cerebral_Cortex (3): linear fit = 0.80 x + 0.0 (15235 voxels, overlap=0.375)
- Left_Cerebral_Cortex (3): linear fit = 0.80 x + 0.0 (15235 voxels, peak = 50), gca=50.1
- gca peak = 0.08598 (64)
- mri peak = 0.05696 (51)
- Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (14577 voxels, overlap=0.266)
- Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (14577 voxels, peak = 53), gca=52.8
- gca peak = 0.24164 (71)
- mri peak = 0.12107 (58)
- Right_Caudate (50): linear fit = 0.79 x + 0.0 (638 voxels, overlap=0.024)
- Right_Caudate (50): linear fit = 0.79 x + 0.0 (638 voxels, peak = 56), gca=55.7
- gca peak = 0.18227 (75)
- mri peak = 0.10473 (58)
- Left_Caudate (11): linear fit = 0.77 x + 0.0 (590 voxels, overlap=0.026)
- Left_Caudate (11): linear fit = 0.77 x + 0.0 (590 voxels, peak = 58), gca=58.1
- gca peak = 0.10629 (62)
- mri peak = 0.06110 (59)
- Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (10502 voxels, overlap=0.995)
- Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (10502 voxels, peak = 61), gca=61.1
- gca peak = 0.11668 (59)
- mri peak = 0.05820 (61)
- Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (9892 voxels, overlap=0.999)
- Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (9892 voxels, peak = 60), gca=60.5
- gca peak = 0.17849 (88)
- mri peak = 0.08017 (90)
- Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (3946 voxels, overlap=0.991)
- Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (3946 voxels, peak = 88), gca=87.6
- gca peak = 0.16819 (86)
- mri peak = 0.06108 (89)
- Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (3732 voxels, overlap=0.997)
- Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (3732 voxels, peak = 87), gca=87.3
- gca peak = 0.41688 (64)
- mri peak = 0.10381 (55)
- Left_Amygdala (18): linear fit = 0.85 x + 0.0 (337 voxels, overlap=0.763)
- Left_Amygdala (18): linear fit = 0.85 x + 0.0 (337 voxels, peak = 54), gca=54.1
- gca peak = 0.42394 (62)
- mri peak = 0.15749 (54)
- Right_Amygdala (54): linear fit = 0.86 x + 0.0 (156 voxels, overlap=0.052)
- Right_Amygdala (54): linear fit = 0.86 x + 0.0 (156 voxels, peak = 53), gca=53.0
- gca peak = 0.10041 (96)
- mri peak = 0.07050 (80)
- Left_Thalamus_Proper (10): linear fit = 0.88 x + 0.0 (2851 voxels, overlap=0.291)
- Left_Thalamus_Proper (10): linear fit = 0.88 x + 0.0 (2851 voxels, peak = 84), gca=84.0
- gca peak = 0.13978 (88)
- mri peak = 0.10651 (77)
- Right_Thalamus_Proper (49): linear fit = 0.89 x + 0.0 (3096 voxels, overlap=0.419)
- Right_Thalamus_Proper (49): linear fit = 0.89 x + 0.0 (3096 voxels, peak = 79), gca=78.8
- gca peak = 0.08514 (81)
- mri peak = 0.07602 (68)
- Left_Putamen (12): linear fit = 0.81 x + 0.0 (1997 voxels, overlap=0.127)
- Left_Putamen (12): linear fit = 0.81 x + 0.0 (1997 voxels, peak = 65), gca=65.2
- gca peak = 0.09624 (82)
- mri peak = 0.09486 (66)
- Right_Putamen (51): linear fit = 0.79 x + 0.0 (1835 voxels, overlap=0.013)
- Right_Putamen (51): linear fit = 0.79 x + 0.0 (1835 voxels, peak = 64), gca=64.4
- gca peak = 0.07543 (88)
- mri peak = 0.10827 (83)
- Brain_Stem (16): linear fit = 0.96 x + 0.0 (7866 voxels, overlap=0.698)
- Brain_Stem (16): linear fit = 0.96 x + 0.0 (7866 voxels, peak = 85), gca=84.9
- gca peak = 0.12757 (95)
- mri peak = 0.12170 (85)
- Right_VentralDC (60): linear fit = 0.90 x + 0.0 (818 voxels, overlap=0.213)
- Right_VentralDC (60): linear fit = 0.90 x + 0.0 (818 voxels, peak = 86), gca=86.0
- gca peak = 0.17004 (92)
- mri peak = 0.10560 (83)
- Left_VentralDC (28): linear fit = 0.89 x + 0.0 (884 voxels, overlap=0.452)
- Left_VentralDC (28): linear fit = 0.89 x + 0.0 (884 voxels, peak = 82), gca=82.3
- gca peak = 0.21361 (36)
- mri peak = 0.15680 (54)
- gca peak = 0.26069 (23)
- mri peak = 0.17261 ( 8)
- Fourth_Ventricle (15): linear fit = 0.26 x + 0.0 (233 voxels, overlap=0.024)
- Fourth_Ventricle (15): linear fit = 0.26 x + 0.0 (233 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 1.02 x + 0.0
- estimating mean csf scale to be 0.40 x + 0.0
- saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
- renormalizing by structure alignment....
- renormalizing input #0
- gca peak = 0.31600 (11)
- mri peak = 0.10814 ( 4)
- Left_Lateral_Ventricle (4): linear fit = 0.28 x + 0.0 (311 voxels, overlap=0.465)
- Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (311 voxels, peak = 3), gca=4.4
- gca peak = 0.29325 ( 9)
- mri peak = 0.14647 ( 5)
- Right_Lateral_Ventricle (43): linear fit = 0.44 x + 0.0 (179 voxels, overlap=0.716)
- Right_Lateral_Ventricle (43): linear fit = 0.44 x + 0.0 (179 voxels, peak = 4), gca=4.0
- gca peak = 0.26612 (81)
- mri peak = 0.12552 (83)
- Right_Pallidum (52): linear fit = 1.00 x + 0.0 (321 voxels, overlap=0.995)
- Right_Pallidum (52): linear fit = 1.00 x + 0.0 (321 voxels, peak = 81), gca=81.0
- gca peak = 0.23030 (75)
- mri peak = 0.12184 (78)
- Left_Pallidum (13): linear fit = 1.00 x + 0.0 (271 voxels, overlap=1.006)
- Left_Pallidum (13): linear fit = 1.00 x + 0.0 (271 voxels, peak = 75), gca=75.0
- gca peak = 0.32075 (52)
- mri peak = 0.10294 (53)
- Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (530 voxels, overlap=1.005)
- Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (530 voxels, peak = 52), gca=52.0
- gca peak = 0.29771 (53)
- mri peak = 0.09040 (58)
- Left_Hippocampus (17): linear fit = 1.01 x + 0.0 (600 voxels, overlap=1.004)
- Left_Hippocampus (17): linear fit = 1.01 x + 0.0 (600 voxels, peak = 54), gca=53.8
- gca peak = 0.08541 (107)
- mri peak = 0.06879 (108)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (31675 voxels, overlap=0.834)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (31675 voxels, peak = 108), gca=107.5
- gca peak = 0.08551 (108)
- mri peak = 0.07904 (108)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (30610 voxels, overlap=0.783)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (30610 voxels, peak = 108), gca=108.0
- gca peak = 0.09720 (50)
- mri peak = 0.05015 (50)
- Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (15235 voxels, overlap=0.993)
- Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (15235 voxels, peak = 50), gca=50.0
- gca peak = 0.10545 (53)
- mri peak = 0.05696 (51)
- Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (14577 voxels, overlap=0.985)
- Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (14577 voxels, peak = 52), gca=52.2
- gca peak = 0.26700 (58)
- mri peak = 0.12107 (58)
- Right_Caudate (50): linear fit = 1.04 x + 0.0 (638 voxels, overlap=0.999)
- Right_Caudate (50): linear fit = 1.04 x + 0.0 (638 voxels, peak = 61), gca=60.6
- gca peak = 0.19395 (58)
- mri peak = 0.10473 (58)
- Left_Caudate (11): linear fit = 1.00 x + 0.0 (590 voxels, overlap=0.986)
- Left_Caudate (11): linear fit = 1.00 x + 0.0 (590 voxels, peak = 58), gca=58.0
- gca peak = 0.11171 (61)
- mri peak = 0.06110 (59)
- Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (10502 voxels, overlap=0.991)
- Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (10502 voxels, peak = 63), gca=62.5
- gca peak = 0.12569 (61)
- mri peak = 0.05820 (61)
- Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (9892 voxels, overlap=0.992)
- Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (9892 voxels, peak = 59), gca=58.9
- gca peak = 0.18438 (87)
- mri peak = 0.08017 (90)
- Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (3946 voxels, overlap=0.987)
- Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (3946 voxels, peak = 88), gca=88.3
- gca peak = 0.16063 (88)
- mri peak = 0.06108 (89)
- Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (3732 voxels, overlap=1.000)
- Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (3732 voxels, peak = 88), gca=87.6
- gca peak = 0.57967 (54)
- mri peak = 0.10381 (55)
- Left_Amygdala (18): linear fit = 1.00 x + 0.0 (337 voxels, overlap=1.023)
- Left_Amygdala (18): linear fit = 1.00 x + 0.0 (337 voxels, peak = 54), gca=54.0
- gca peak = 0.49427 (53)
- mri peak = 0.15749 (54)
- Right_Amygdala (54): linear fit = 1.00 x + 0.0 (156 voxels, overlap=1.014)
- Right_Amygdala (54): linear fit = 1.00 x + 0.0 (156 voxels, peak = 53), gca=53.0
- gca peak = 0.10699 (84)
- mri peak = 0.07050 (80)
- Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (2851 voxels, overlap=0.969)
- Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (2851 voxels, peak = 84), gca=83.6
- gca peak = 0.10983 (79)
- mri peak = 0.10651 (77)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3096 voxels, overlap=0.894)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3096 voxels, peak = 79), gca=78.6
- gca peak = 0.10378 (65)
- mri peak = 0.07602 (68)
- Left_Putamen (12): linear fit = 1.02 x + 0.0 (1997 voxels, overlap=0.991)
- Left_Putamen (12): linear fit = 1.02 x + 0.0 (1997 voxels, peak = 67), gca=66.6
- gca peak = 0.12788 (60)
- mri peak = 0.09486 (66)
- Right_Putamen (51): linear fit = 1.02 x + 0.0 (1835 voxels, overlap=0.990)
- Right_Putamen (51): linear fit = 1.02 x + 0.0 (1835 voxels, peak = 62), gca=61.5
- gca peak = 0.08675 (85)
- mri peak = 0.10827 (83)
- Brain_Stem (16): linear fit = 1.02 x + 0.0 (7866 voxels, overlap=0.662)
- Brain_Stem (16): linear fit = 1.02 x + 0.0 (7866 voxels, peak = 87), gca=87.1
- gca peak = 0.12656 (86)
- mri peak = 0.12170 (85)
- Right_VentralDC (60): linear fit = 1.00 x + 0.0 (818 voxels, overlap=0.780)
- Right_VentralDC (60): linear fit = 1.00 x + 0.0 (818 voxels, peak = 86), gca=86.0
- gca peak = 0.15972 (83)
- mri peak = 0.10560 (83)
- Left_VentralDC (28): linear fit = 1.01 x + 0.0 (884 voxels, overlap=0.856)
- Left_VentralDC (28): linear fit = 1.01 x + 0.0 (884 voxels, peak = 84), gca=84.2
- gca peak = 0.35640 (14)
- mri peak = 0.15680 (54)
- gca peak = 0.33827 ( 9)
- mri peak = 0.17261 ( 8)
- Fourth_Ventricle (15): linear fit = 0.68 x + 0.0 (233 voxels, overlap=0.798)
- Fourth_Ventricle (15): linear fit = 0.68 x + 0.0 (233 voxels, peak = 6), gca=6.1
- 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 = 0.58351 (54)
- gca peak Left_undetermined = 1.00000 (35)
- gca peak Left_vessel = 0.43797 (61)
- gca peak Left_choroid_plexus = 0.09084 (48)
- gca peak Right_Inf_Lat_Vent = 0.30433 (27)
- gca peak Right_Accumbens_area = 0.41720 (58)
- gca peak Right_vessel = 0.57787 (60)
- gca peak Right_choroid_plexus = 0.10381 (48)
- gca peak Fifth_Ventricle = 0.45329 (19)
- gca peak WM_hypointensities = 0.17688 (83)
- gca peak non_WM_hypointensities = 0.11865 (54)
- gca peak Optic_Chiasm = 0.34833 (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 0.51 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
- 11423 gm and wm labels changed (%12 to gray, %88 to white out of all changed labels)
- 289 hippocampal voxels changed.
- 2 amygdala voxels changed.
- pass 1: 88309 changed. image ll: -2.193, PF=1.000
- pass 2: 15767 changed. image ll: -2.190, PF=1.000
- pass 3: 5631 changed.
- pass 4: 2444 changed.
- writing labeled volume to aseg.auto_noCCseg.mgz...
- auto-labeling took 20 minutes and 45 seconds.
- mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/cc_up.lta sub005
- 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/sub005/mri/transforms/cc_up.lta
- reading aseg from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/aseg.auto_noCCseg.mgz
- reading norm from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/norm.mgz
- 37418 voxels in left wm, 96637 in right wm, xrange [119, 135]
- searching rotation angles z=[-11 3], y=[-11 3]
-
searching scale 1 Z rot -10.7
searching scale 1 Z rot -10.4
searching scale 1 Z rot -10.2
searching scale 1 Z rot -9.9
searching scale 1 Z rot -9.7
searching scale 1 Z rot -9.4
searching scale 1 Z rot -9.2
searching scale 1 Z rot -8.9
searching scale 1 Z rot -8.7
searching scale 1 Z rot -8.4
searching scale 1 Z rot -8.2
searching scale 1 Z rot -7.9
searching scale 1 Z rot -7.7
searching scale 1 Z rot -7.4
searching scale 1 Z rot -7.2
searching scale 1 Z rot -6.9
searching scale 1 Z rot -6.7
searching scale 1 Z rot -6.4
searching scale 1 Z rot -6.2
searching scale 1 Z rot -5.9
searching scale 1 Z rot -5.7
searching scale 1 Z rot -5.4
searching scale 1 Z rot -5.2
searching scale 1 Z rot -4.9
searching scale 1 Z rot -4.7
searching scale 1 Z rot -4.4
searching scale 1 Z rot -4.2
searching scale 1 Z rot -3.9
searching scale 1 Z rot -3.7
searching scale 1 Z rot -3.4
searching scale 1 Z rot -3.2
searching scale 1 Z rot -2.9
searching scale 1 Z rot -2.7
searching scale 1 Z rot -2.4
searching scale 1 Z rot -2.2
searching scale 1 Z rot -1.9
searching scale 1 Z rot -1.7
searching scale 1 Z rot -1.4
searching scale 1 Z rot -1.2
searching scale 1 Z rot -0.9
searching scale 1 Z rot -0.7
searching scale 1 Z rot -0.4
searching scale 1 Z rot -0.2
searching scale 1 Z rot 0.1
searching scale 1 Z rot 0.3
searching scale 1 Z rot 0.6
searching scale 1 Z rot 0.8
searching scale 1 Z rot 1.1
searching scale 1 Z rot 1.3
searching scale 1 Z rot 1.6
searching scale 1 Z rot 1.8
searching scale 1 Z rot 2.1
searching scale 1 Z rot 2.3
searching scale 1 Z rot 2.6
searching scale 1 Z rot 2.8
searching scale 1 Z rot 3.1
searching scale 1 Z rot 3.3
searching scale 1 Z rot 3.6
searching scale 1 Z rot 3.8 global minimum found at slice 129.0, rotations (-4.50, -3.17)
- final transformation (x=129.0, yr=-4.495, zr=-3.173):
- 0.995 0.055 -0.078 2.066;
- -0.055 0.998 0.004 50.852;
- 0.078 -0.000 0.997 27.169;
- 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 128 143 135
- eigenvectors:
- -0.001 -0.003 1.000;
- -0.190 -0.982 -0.003;
- 0.982 -0.190 0.001;
- error in mid anterior detected - correcting...
- writing aseg with callosum to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/aseg.auto.mgz...
- corpus callosum matter segmentation took 1.7 minutes
- #--------------------------------------
- #@# Merge ASeg Thu Aug 8 17:29:22 CEST 2013
- cp aseg.auto.mgz aseg.mgz
- #--------------------------------------------
- #@# Intensity Normalization2 Thu Aug 8 17:29:22 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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...
- 2381 control points removed
- Building bias image
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 0...
- Smoothing with sigma 8
- Applying bias correction
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Iterating 2 times
- ---------------------------------
- 3d normalization pass 1 of 2
- white matter peak found at 111
- white matter peak found at 109
- gm peak at 56 (56), valley at 20 (20)
- csf peak at 28, setting threshold to 46
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- ---------------------------------
- 3d normalization pass 2 of 2
- white matter peak found at 111
- white matter peak found at 110
- gm peak at 56 (56), valley at 19 (19)
- 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 18 seconds.
- #--------------------------------------------
- #@# Mask BFS Thu Aug 8 17:33:42 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri
- mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
- threshold mask volume at 5
- DoAbs = 0
- Found 1476227 voxels in mask (pct= 8.80)
- Writing masked volume to brain.finalsurfs.mgz...done.
- #--------------------------------------------
- #@# WM Segmentation Thu Aug 8 17:33:44 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): 107.1 +- 4.9 [80.0 --> 125.0]
- GM (67.0) : 66.0 +- 9.4 [30.0 --> 96.0]
- setting bottom of white matter range to 75.4
- setting top of gray matter range to 84.7
- 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...
- 8711 sparsely connected voxels removed...
- thickening thin strands....
- 20 segments, 6051 filled
- 785 bright non-wm voxels segmented.
- 4744 diagonally connected voxels added...
- white matter segmentation took 1.8 minutes
- writing output to wm.seg.mgz...
- mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz
- preserving editing changes in input volume...
- auto filling took 0.62 minutes
- reading wm segmentation from wm.seg.mgz...
- 92 voxels added to wm to prevent paths from MTL structures to cortex
- 791 additional wm voxels added
- 0 additional wm voxels added
- SEG EDIT: 38026 voxels turned on, 36556 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+): 17 found - 17 modified | TOTAL: 17
- pass 2 (xy+): 0 found - 17 modified | TOTAL: 17
- pass 1 (xy-): 22 found - 22 modified | TOTAL: 39
- pass 2 (xy-): 0 found - 22 modified | TOTAL: 39
- pass 1 (yz+): 34 found - 34 modified | TOTAL: 73
- pass 2 (yz+): 0 found - 34 modified | TOTAL: 73
- pass 1 (yz-): 30 found - 30 modified | TOTAL: 103
- pass 2 (yz-): 0 found - 30 modified | TOTAL: 103
- pass 1 (xz+): 20 found - 20 modified | TOTAL: 123
- pass 2 (xz+): 0 found - 20 modified | TOTAL: 123
- pass 1 (xz-): 23 found - 23 modified | TOTAL: 146
- pass 2 (xz-): 0 found - 23 modified | TOTAL: 146
- Iteration Number : 1
- pass 1 (+++): 10 found - 10 modified | TOTAL: 10
- pass 2 (+++): 0 found - 10 modified | TOTAL: 10
- pass 1 (+++): 12 found - 12 modified | TOTAL: 22
- pass 2 (+++): 0 found - 12 modified | TOTAL: 22
- pass 1 (+++): 12 found - 12 modified | TOTAL: 34
- pass 2 (+++): 0 found - 12 modified | TOTAL: 34
- pass 1 (+++): 11 found - 11 modified | TOTAL: 45
- pass 2 (+++): 0 found - 11 modified | TOTAL: 45
- Iteration Number : 1
- pass 1 (++): 290 found - 290 modified | TOTAL: 290
- pass 2 (++): 0 found - 290 modified | TOTAL: 290
- pass 1 (+-): 235 found - 235 modified | TOTAL: 525
- pass 2 (+-): 1 found - 236 modified | TOTAL: 526
- pass 3 (+-): 0 found - 236 modified | TOTAL: 526
- pass 1 (--): 257 found - 257 modified | TOTAL: 783
- pass 2 (--): 0 found - 257 modified | TOTAL: 783
- pass 1 (-+): 240 found - 240 modified | TOTAL: 1023
- pass 2 (-+): 0 found - 240 modified | TOTAL: 1023
- Iteration Number : 2
- pass 1 (xy+): 5 found - 5 modified | TOTAL: 5
- pass 2 (xy+): 0 found - 5 modified | TOTAL: 5
- pass 1 (xy-): 7 found - 7 modified | TOTAL: 12
- pass 2 (xy-): 0 found - 7 modified | TOTAL: 12
- pass 1 (yz+): 3 found - 3 modified | TOTAL: 15
- pass 2 (yz+): 0 found - 3 modified | TOTAL: 15
- pass 1 (yz-): 4 found - 4 modified | TOTAL: 19
- pass 2 (yz-): 0 found - 4 modified | TOTAL: 19
- pass 1 (xz+): 5 found - 5 modified | TOTAL: 24
- pass 2 (xz+): 0 found - 5 modified | TOTAL: 24
- pass 1 (xz-): 2 found - 2 modified | TOTAL: 26
- pass 2 (xz-): 0 found - 2 modified | TOTAL: 26
- Iteration Number : 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 4 found - 4 modified | TOTAL: 4
- pass 2 (+++): 0 found - 4 modified | TOTAL: 4
- pass 1 (+++): 0 found - 0 modified | TOTAL: 4
- pass 1 (+++): 0 found - 0 modified | TOTAL: 4
- Iteration Number : 2
- pass 1 (++): 1 found - 1 modified | TOTAL: 1
- pass 2 (++): 0 found - 1 modified | TOTAL: 1
- pass 1 (+-): 0 found - 0 modified | TOTAL: 1
- pass 1 (--): 1 found - 1 modified | TOTAL: 2
- pass 2 (--): 0 found - 1 modified | TOTAL: 2
- pass 1 (-+): 1 found - 1 modified | TOTAL: 3
- pass 2 (-+): 0 found - 1 modified | TOTAL: 3
- Iteration Number : 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-): 1 found - 1 modified | TOTAL: 1
- pass 2 (xz-): 0 found - 1 modified | TOTAL: 1
- Iteration Number : 3
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 3
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 4
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 4
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 4
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Total Number of Modified Voxels = 1248 (out of 502039: 0.248586)
- binarizing input wm segmentation...
- Ambiguous edge configurations...
- mri_pretess done
- #--------------------------------------------
- #@# Fill Thu Aug 8 17:36:13 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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
- 1.099 0.042 -0.061 -14.845;
- -0.028 1.149 0.325 -20.792;
- 0.099 -0.272 0.946 13.810;
- 0.000 0.000 0.000 1.000;
- voxel to talairach voxel transform
- 1.099 0.042 -0.061 -14.845;
- -0.028 1.149 0.325 -20.792;
- 0.099 -0.272 0.946 13.810;
- 0.000 0.000 0.000 1.000;
- reading segmented volume aseg.auto_noCCseg.mgz...
- Looking for area (min, max) = (350, 1400)
- area[0] = 2587 (min = 350, max = 1400), aspect = 1.43 (min = 0.10, max = 0.75)
- need search nearby
- using seed (126, 116, 146), TAL = (2.0, 18.0, 12.0)
- talairach voxel to voxel transform
- 0.904 -0.017 0.065 12.161;
- 0.045 0.804 -0.273 21.157;
- -0.081 0.233 0.972 -9.785;
- 0.000 0.000 0.000 1.000;
- segmentation indicates cc at (126, 116, 146) --> (2.0, 18.0, 12.0)
- done.
- writing output to filled.mgz...
- filling took 0.9 minutes
- talairach cc position changed to (2.00, 18.00, 12.00)
- Erasing brainstem...done.
- seed_search_size = 9, min_neighbors = 5
- search rh wm seed point around talairach space:(20.00, 18.00, 12.00) SRC: (117.19, 79.40, 150.28)
- search lh wm seed point around talairach space (-16.00, 18.00, 12.00), SRC: (149.73, 81.03, 147.36)
- 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 17:37:08 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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+): 0 found - 0 modified | TOTAL: 3
- pass 1 (yz-): 1 found - 1 modified | TOTAL: 4
- pass 2 (yz-): 0 found - 1 modified | TOTAL: 4
- pass 1 (xz+): 1 found - 1 modified | TOTAL: 5
- pass 2 (xz+): 0 found - 1 modified | TOTAL: 5
- pass 1 (xz-): 3 found - 3 modified | TOTAL: 8
- pass 2 (xz-): 0 found - 3 modified | TOTAL: 8
- Iteration Number : 1
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 1
- pass 1 (++): 1 found - 1 modified | TOTAL: 1
- pass 2 (++): 0 found - 1 modified | TOTAL: 1
- pass 1 (+-): 1 found - 1 modified | TOTAL: 2
- pass 2 (+-): 0 found - 1 modified | TOTAL: 2
- pass 1 (--): 0 found - 0 modified | TOTAL: 2
- pass 1 (-+): 1 found - 1 modified | TOTAL: 3
- pass 2 (-+): 0 found - 1 modified | TOTAL: 3
- Iteration Number : 2
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Total Number of Modified Voxels = 11 (out of 243070: 0.004525)
- Ambiguous edge configurations...
- mri_pretess done
- mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix
- $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- slice 30: 275 vertices, 334 faces
- slice 40: 5225 vertices, 5463 faces
- slice 50: 14011 vertices, 14356 faces
- slice 60: 25378 vertices, 25806 faces
- slice 70: 37928 vertices, 38377 faces
- slice 80: 49484 vertices, 49874 faces
- slice 90: 60012 vertices, 60374 faces
- slice 100: 71070 vertices, 71447 faces
- slice 110: 81719 vertices, 82133 faces
- slice 120: 92216 vertices, 92635 faces
- slice 130: 102284 vertices, 102683 faces
- slice 140: 112784 vertices, 113151 faces
- slice 150: 121893 vertices, 122235 faces
- slice 160: 129983 vertices, 130269 faces
- slice 170: 135798 vertices, 136026 faces
- slice 180: 140298 vertices, 140506 faces
- slice 190: 143125 vertices, 143245 faces
- slice 200: 143522 vertices, 143568 faces
- slice 210: 143522 vertices, 143568 faces
- slice 220: 143522 vertices, 143568 faces
- slice 230: 143522 vertices, 143568 faces
- slice 240: 143522 vertices, 143568 faces
- slice 250: 143522 vertices, 143568 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...
- 143522 voxel in cpt #1: X=-46 [v=143522,e=430704,f=287136] located at (-27.371929, -26.230808, 38.191643)
- For the whole surface: X=-46 [v=143522,e=430704,f=287136]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Smooth1 lh Thu Aug 8 17:37:15 CEST 2013
- mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 17:37:20 CEST 2013
- mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
- avg radius = 47.8 mm, total surface area = 74380 mm^2
- writing inflated surface to ../surf/lh.inflated.nofix
- inflation took 0.6 minutes
- Not saving sulc
-
step 000: RMS=0.104 (target=0.015)
step 005: RMS=0.076 (target=0.015)
step 010: RMS=0.056 (target=0.015)
step 015: RMS=0.047 (target=0.015)
step 020: RMS=0.040 (target=0.015)
step 025: RMS=0.036 (target=0.015)
step 030: RMS=0.032 (target=0.015)
step 035: RMS=0.029 (target=0.015)
step 040: RMS=0.028 (target=0.015)
step 045: RMS=0.026 (target=0.015)
step 050: RMS=0.025 (target=0.015)
step 055: RMS=0.025 (target=0.015)
step 060: RMS=0.025 (target=0.015)
- inflation complete.
- Not saving sulc
- #--------------------------------------------
- #@# QSphere lh Thu Aug 8 17:37:54 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
- mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix
- doing quick spherical unfolding.
- setting seed for random number genererator to 1234
- $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading original vertex positions...
- unfolding cortex into spherical form...
- surface projected - minimizing metric distortion...
- vertex spacing 0.96 +- 0.59 (0.00-->7.70) (max @ vno 59673 --> 60711)
- face area 0.02 +- 0.03 (-0.22-->0.80)
- scaling brain by 0.302...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=176.621, avgs=0
- 005/300: dt: 0.9000, rms radial error=176.366, avgs=0
- 010/300: dt: 0.9000, rms radial error=175.818, avgs=0
- 015/300: dt: 0.9000, rms radial error=175.096, avgs=0
- 020/300: dt: 0.9000, rms radial error=174.271, avgs=0
- 025/300: dt: 0.9000, rms radial error=173.388, avgs=0
- 030/300: dt: 0.9000, rms radial error=172.468, avgs=0
- 035/300: dt: 0.9000, rms radial error=171.533, avgs=0
- 040/300: dt: 0.9000, rms radial error=170.590, avgs=0
- 045/300: dt: 0.9000, rms radial error=169.645, avgs=0
- 050/300: dt: 0.9000, rms radial error=168.701, avgs=0
- 055/300: dt: 0.9000, rms radial error=167.760, avgs=0
- 060/300: dt: 0.9000, rms radial error=166.822, avgs=0
- 065/300: dt: 0.9000, rms radial error=165.889, avgs=0
- 070/300: dt: 0.9000, rms radial error=164.960, avgs=0
- 075/300: dt: 0.9000, rms radial error=164.035, avgs=0
- 080/300: dt: 0.9000, rms radial error=163.116, avgs=0
- 085/300: dt: 0.9000, rms radial error=162.202, avgs=0
- 090/300: dt: 0.9000, rms radial error=161.292, avgs=0
- 095/300: dt: 0.9000, rms radial error=160.387, avgs=0
- 100/300: dt: 0.9000, rms radial error=159.487, avgs=0
- 105/300: dt: 0.9000, rms radial error=158.592, avgs=0
- 110/300: dt: 0.9000, rms radial error=157.702, avgs=0
- 115/300: dt: 0.9000, rms radial error=156.816, avgs=0
- 120/300: dt: 0.9000, rms radial error=155.935, avgs=0
- 125/300: dt: 0.9000, rms radial error=155.059, avgs=0
- 130/300: dt: 0.9000, rms radial error=154.187, avgs=0
- 135/300: dt: 0.9000, rms radial error=153.320, avgs=0
- 140/300: dt: 0.9000, rms radial error=152.458, avgs=0
- 145/300: dt: 0.9000, rms radial error=151.600, avgs=0
- 150/300: dt: 0.9000, rms radial error=150.747, avgs=0
- 155/300: dt: 0.9000, rms radial error=149.898, avgs=0
- 160/300: dt: 0.9000, rms radial error=149.055, avgs=0
- 165/300: dt: 0.9000, rms radial error=148.216, avgs=0
- 170/300: dt: 0.9000, rms radial error=147.382, avgs=0
- 175/300: dt: 0.9000, rms radial error=146.552, avgs=0
- 180/300: dt: 0.9000, rms radial error=145.727, avgs=0
- 185/300: dt: 0.9000, rms radial error=144.906, avgs=0
- 190/300: dt: 0.9000, rms radial error=144.090, avgs=0
- 195/300: dt: 0.9000, rms radial error=143.279, avgs=0
- 200/300: dt: 0.9000, rms radial error=142.471, avgs=0
- 205/300: dt: 0.9000, rms radial error=141.669, avgs=0
- 210/300: dt: 0.9000, rms radial error=140.870, avgs=0
- 215/300: dt: 0.9000, rms radial error=140.077, avgs=0
- 220/300: dt: 0.9000, rms radial error=139.287, avgs=0
- 225/300: dt: 0.9000, rms radial error=138.502, avgs=0
- 230/300: dt: 0.9000, rms radial error=137.721, avgs=0
- 235/300: dt: 0.9000, rms radial error=136.945, avgs=0
- 240/300: dt: 0.9000, rms radial error=136.172, avgs=0
- 245/300: dt: 0.9000, rms radial error=135.405, avgs=0
- 250/300: dt: 0.9000, rms radial error=134.641, avgs=0
- 255/300: dt: 0.9000, rms radial error=133.882, avgs=0
- 260/300: dt: 0.9000, rms radial error=133.127, avgs=0
- 265/300: dt: 0.9000, rms radial error=132.376, avgs=0
- 270/300: dt: 0.9000, rms radial error=131.629, avgs=0
- 275/300: dt: 0.9000, rms radial error=130.886, avgs=0
- 280/300: dt: 0.9000, rms radial error=130.148, avgs=0
- 285/300: dt: 0.9000, rms radial error=129.414, avgs=0
- 290/300: dt: 0.9000, rms radial error=128.683, avgs=0
- 295/300: dt: 0.9000, rms radial error=127.957, avgs=0
- 300/300: dt: 0.9000, rms radial error=127.235, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 17016.37
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00014
- epoch 2 (K=40.0), pass 1, starting sse = 2959.58
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00002
- epoch 3 (K=160.0), pass 1, starting sse = 342.52
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.06/11 = 0.00504
- epoch 4 (K=640.0), pass 1, starting sse = 26.16
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.12/13 = 0.00932
- 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 17:42:53 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/sub005/scripts
- mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub005 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=-46 (nv=143522, nf=287136, ne=430704, g=24)
- 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 13 iterations
- marking ambiguous vertices...
- 3404 ambiguous faces found in tessellation
- segmenting defects...
- 32 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- -merging segment 5 into 4
- 31 defects to be corrected
- 0 vertices coincident
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -9.8018 (-4.9009)
- -vertex loglikelihood: -6.6801 (-3.3400)
- -normal dot loglikelihood: -3.6316 (-3.6316)
- -quad curv loglikelihood: -6.5082 (-3.2541)
- Total Loglikelihood : -26.6216
- CORRECTING DEFECT 0 (vertices=36, convex hull=80)
- After retessellation of defect 0, euler #=-28 (141428,423391,281935) : difference with theory (-28) = 0
- CORRECTING DEFECT 1 (vertices=33, convex hull=67)
- After retessellation of defect 1, euler #=-27 (141442,423458,281989) : difference with theory (-27) = 0
- CORRECTING DEFECT 2 (vertices=26, convex hull=40)
- After retessellation of defect 2, euler #=-26 (141444,423480,282010) : difference with theory (-26) = 0
- CORRECTING DEFECT 3 (vertices=7, convex hull=30)
- After retessellation of defect 3, euler #=-25 (141447,423499,282027) : difference with theory (-25) = 0
- CORRECTING DEFECT 4 (vertices=213, convex hull=130)
- After retessellation of defect 4, euler #=-23 (141496,423706,282187) : difference with theory (-24) = -1
- CORRECTING DEFECT 5 (vertices=54, convex hull=64)
- After retessellation of defect 5, euler #=-22 (141520,423802,282260) : difference with theory (-23) = -1
- CORRECTING DEFECT 6 (vertices=43, convex hull=89)
- After retessellation of defect 6, euler #=-21 (141536,423888,282331) : difference with theory (-22) = -1
- CORRECTING DEFECT 7 (vertices=44, convex hull=76)
- After retessellation of defect 7, euler #=-20 (141565,424007,282422) : difference with theory (-21) = -1
- CORRECTING DEFECT 8 (vertices=26, convex hull=62)
- After retessellation of defect 8, euler #=-19 (141582,424082,282481) : difference with theory (-20) = -1
- CORRECTING DEFECT 9 (vertices=24, convex hull=68)
- After retessellation of defect 9, euler #=-18 (141596,424151,282537) : difference with theory (-19) = -1
- CORRECTING DEFECT 10 (vertices=358, convex hull=225)
- After retessellation of defect 10, euler #=-17 (141611,424305,282677) : difference with theory (-18) = -1
- CORRECTING DEFECT 11 (vertices=28, convex hull=57)
- After retessellation of defect 11, euler #=-16 (141631,424387,282740) : difference with theory (-17) = -1
- CORRECTING DEFECT 12 (vertices=11, convex hull=25)
- After retessellation of defect 12, euler #=-15 (141634,424403,282754) : difference with theory (-16) = -1
- CORRECTING DEFECT 13 (vertices=11, convex hull=30)
- After retessellation of defect 13, euler #=-14 (141637,424422,282771) : difference with theory (-15) = -1
- CORRECTING DEFECT 14 (vertices=49, convex hull=21)
- After retessellation of defect 14, euler #=-13 (141638,424431,282780) : difference with theory (-14) = -1
- CORRECTING DEFECT 15 (vertices=170, convex hull=93)
- After retessellation of defect 15, euler #=-13 (141666,424567,282888) : difference with theory (-13) = 0
- CORRECTING DEFECT 16 (vertices=23, convex hull=18)
- After retessellation of defect 16, euler #=-12 (141672,424590,282906) : difference with theory (-12) = 0
- CORRECTING DEFECT 17 (vertices=197, convex hull=176)
- After retessellation of defect 17, euler #=-11 (141715,424800,283074) : difference with theory (-11) = 0
- CORRECTING DEFECT 18 (vertices=72, convex hull=82)
- After retessellation of defect 18, euler #=-10 (141744,424925,283171) : difference with theory (-10) = 0
- CORRECTING DEFECT 19 (vertices=5, convex hull=19)
- After retessellation of defect 19, euler #=-9 (141744,424931,283178) : difference with theory (-9) = 0
- CORRECTING DEFECT 20 (vertices=57, convex hull=81)
- After retessellation of defect 20, euler #=-8 (141770,425043,283265) : difference with theory (-8) = 0
- CORRECTING DEFECT 21 (vertices=8, convex hull=9)
- After retessellation of defect 21, euler #=-7 (141770,425045,283268) : difference with theory (-7) = 0
- CORRECTING DEFECT 22 (vertices=25, convex hull=63)
- After retessellation of defect 22, euler #=-6 (141787,425123,283330) : difference with theory (-6) = 0
- CORRECTING DEFECT 23 (vertices=240, convex hull=50)
- After retessellation of defect 23, euler #=-5 (141798,425178,283375) : difference with theory (-5) = 0
- CORRECTING DEFECT 24 (vertices=88, convex hull=55)
- After retessellation of defect 24, euler #=-4 (141813,425246,283429) : difference with theory (-4) = 0
- CORRECTING DEFECT 25 (vertices=83, convex hull=104)
- After retessellation of defect 25, euler #=-3 (141858,425428,283567) : difference with theory (-3) = 0
- CORRECTING DEFECT 26 (vertices=89, convex hull=105)
- After retessellation of defect 26, euler #=-2 (141884,425552,283666) : difference with theory (-2) = 0
- CORRECTING DEFECT 27 (vertices=10, convex hull=34)
- After retessellation of defect 27, euler #=-1 (141886,425569,283682) : difference with theory (-1) = 0
- CORRECTING DEFECT 28 (vertices=32, convex hull=70)
- After retessellation of defect 28, euler #=0 (141900,425638,283738) : difference with theory (0) = 0
- CORRECTING DEFECT 29 (vertices=29, convex hull=68)
- After retessellation of defect 29, euler #=1 (141909,425693,283785) : difference with theory (1) = 0
- CORRECTING DEFECT 30 (vertices=19, convex hull=68)
- After retessellation of defect 30, euler #=2 (141918,425748,283832) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.88 +- 0.23 (0.06-->9.14) (max @ vno 60346 --> 65969)
- face area 0.00 +- 0.00 (0.00-->0.00)
- performing soap bubble on retessellated vertices for 0 iterations...
- vertex spacing 0.88 +- 0.23 (0.06-->9.14) (max @ vno 60346 --> 65969)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 93 mutations (33.5%), 185 crossovers (66.5%), 223 vertices were eliminated
- building final representation...
- 1604 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=141918, nf=283832, ne=425748, g=0)
- writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 26.5 minutes
- 0 defective edges
- removing intersecting faces
- 000: 220 intersecting
- 001: 15 intersecting
- mris_euler_number ../surf/lh.orig
- euler # = v-e+f = 2g-2: 141918 - 425748 + 283832 = 2 --> 0 holes
- F =2V-4: 283832 = 283836-4 (0)
- 2E=3F: 851496 = 851496 (0)
- total defect index = 0
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
- mris_remove_intersection ../surf/lh.orig ../surf/lh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 18 intersecting
- writing corrected surface to ../surf/lh.orig
- rm ../surf/lh.inflated
- #--------------------------------------------
- #@# Make White Surf lh Thu Aug 8 18:09:28 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
- mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub005 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/sub005/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz...
- 16905 bright wm thresholded.
- 908 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.orig...
- computing class statistics...
- border white: 254363 voxels (1.52%)
- border gray 296177 voxels (1.77%)
- WM (91.0): 92.4 +- 10.3 [70.0 --> 110.0]
- GM (74.0) : 72.6 +- 12.7 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 46.3 (was 70)
- setting MAX_BORDER_WHITE to 114.3 (was 105)
- setting MIN_BORDER_WHITE to 59.0 (was 85)
- setting MAX_CSF to 33.6 (was 40)
- setting MAX_GRAY to 93.7 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 52.7 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 20.9 (was 40)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.81 +- 0.22 (0.01-->3.88) (max @ vno 67884 --> 71912)
- face area 0.28 +- 0.12 (0.00-->6.13)
- mean absolute distance = 0.64 +- 0.75
- 4354 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=104, GM=59
- mean inside = 92.3, mean outside = 67.9
- smoothing surface for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- removing 3 vertex label from ripped group
- mean border=72.7, 45 (45) missing vertices, mean dist 0.3 [0.5 (%33.5)->0.7 (%66.5))]
- %74 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 0
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.92 +- 0.27 (0.04-->5.98) (max @ vno 60346 --> 65969)
- face area 0.28 +- 0.13 (0.00-->4.83)
- mean absolute distance = 0.29 +- 0.45
- 2871 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=7465551.0, rms=13.21
- 001: dt: 0.5000, sse=7823105.0, rms=9.481 (0.000%)
- 002: dt: 0.5000, sse=8288571.5, rms=7.465 (0.000%)
- 003: dt: 0.5000, sse=8446310.0, rms=6.251 (0.000%)
- 004: dt: 0.5000, sse=8744839.0, rms=5.521 (0.000%)
- 005: dt: 0.5000, sse=8775113.0, rms=5.122 (0.000%)
- 006: dt: 0.5000, sse=8937678.0, rms=4.871 (0.000%)
- 007: dt: 0.5000, sse=8850499.0, rms=4.747 (0.000%)
- 008: dt: 0.5000, sse=8937956.0, rms=4.631 (0.000%)
- rms = 4.59, time step reduction 1 of 3 to 0.250...
- 009: dt: 0.5000, sse=8824802.0, rms=4.586 (0.000%)
- 010: dt: 0.2500, sse=5836391.5, rms=3.250 (0.000%)
- 011: dt: 0.2500, sse=5373295.5, rms=2.813 (0.000%)
- 012: dt: 0.2500, sse=5091939.5, rms=2.713 (0.000%)
- 013: dt: 0.2500, sse=5008144.0, rms=2.627 (0.000%)
- rms = 2.60, time step reduction 2 of 3 to 0.125...
- 014: dt: 0.2500, sse=4908885.0, rms=2.600 (0.000%)
- 015: dt: 0.1250, sse=4619963.5, rms=2.301 (0.000%)
- rms = 2.26, time step reduction 3 of 3 to 0.062...
- 016: dt: 0.1250, sse=4568109.0, rms=2.259 (0.000%)
- positioning took 2.1 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 1 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 1 vertex label from ripped group
- mean border=76.9, 33 (3) missing vertices, mean dist -0.2 [0.3 (%77.2)->0.2 (%22.8))]
- %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 (0.06-->6.25) (max @ vno 60346 --> 65969)
- face area 0.35 +- 0.17 (0.00-->6.29)
- mean absolute distance = 0.21 +- 0.30
- 3014 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5456520.0, rms=5.76
- 017: dt: 0.5000, sse=5856689.5, rms=4.107 (0.000%)
- rms = 4.62, time step reduction 1 of 3 to 0.250...
- 018: dt: 0.2500, sse=5323868.5, rms=2.954 (0.000%)
- 019: dt: 0.2500, sse=5138993.5, rms=2.467 (0.000%)
- 020: dt: 0.2500, sse=5071286.5, rms=2.113 (0.000%)
- rms = 2.09, time step reduction 2 of 3 to 0.125...
- 021: dt: 0.2500, sse=5062744.5, rms=2.086 (0.000%)
- 022: dt: 0.1250, sse=4871787.0, rms=1.829 (0.000%)
- rms = 1.79, time step reduction 3 of 3 to 0.062...
- 023: dt: 0.1250, sse=4819964.5, rms=1.785 (0.000%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 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 2 vertex label from ripped group
- mean border=80.0, 24 (1) missing vertices, mean dist -0.1 [0.2 (%74.6)->0.2 (%25.4))]
- %89 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.25 (0.12-->6.37) (max @ vno 60346 --> 65969)
- face area 0.34 +- 0.17 (0.00-->6.20)
- mean absolute distance = 0.16 +- 0.25
- 2371 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5157340.0, rms=4.08
- rms = 4.12, time step reduction 1 of 3 to 0.250...
- 024: dt: 0.2500, sse=4968705.0, rms=2.871 (0.000%)
- 025: dt: 0.2500, sse=4855665.0, rms=1.873 (0.000%)
- 026: dt: 0.2500, sse=4894005.0, rms=1.737 (0.000%)
- 027: dt: 0.2500, sse=4925580.5, rms=1.673 (0.000%)
- rms = 1.73, time step reduction 2 of 3 to 0.125...
- 028: dt: 0.1250, sse=4866839.0, rms=1.601 (0.000%)
- 029: dt: 0.1250, sse=4781871.5, rms=1.520 (0.000%)
- rms = 1.52, time step reduction 3 of 3 to 0.062...
- 030: dt: 0.1250, sse=4781871.5, rms=1.520 (0.002%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- removing 1 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 2 vertex label from ripped group
- mean border=81.0, 36 (1) missing vertices, mean dist -0.0 [0.2 (%57.8)->0.2 (%42.2))]
- %91 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- writing white matter surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white...
- writing smoothed curvature to lh.curv
- 000: dt: 0.0000, sse=4805187.0, rms=1.86
- rms = 2.87, time step reduction 1 of 3 to 0.250...
- 031: dt: 0.2500, sse=4889560.5, rms=1.247 (0.000%)
- 032: dt: 0.2500, sse=5074887.5, rms=1.124 (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...
- 033: dt: 0.1250, sse=5078172.0, rms=1.111 (0.000%)
- positioning took 0.6 minutes
- inhibiting deformation at non-cortical midline structures...
- generating cortex label...
- 9 non-cortical segments detected
- only using segment with 1837 vertices
- erasing segment 1 (vno[0] = 86517)
- erasing segment 2 (vno[0] = 93790)
- erasing segment 3 (vno[0] = 100688)
- erasing segment 4 (vno[0] = 102748)
- erasing segment 5 (vno[0] = 107796)
- erasing segment 6 (vno[0] = 107856)
- erasing segment 7 (vno[0] = 108814)
- erasing segment 8 (vno[0] = 109084)
- writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/lh.cortex.label...
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.curv
- writing smoothed area to lh.area
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.area
- vertex spacing 0.90 +- 0.26 (0.06-->6.37) (max @ vno 60346 --> 65969)
- face area 0.34 +- 0.16 (0.00-->6.17)
- refinement took 6.9 minutes
- #--------------------------------------------
- #@# Smooth2 lh Thu Aug 8 18:16:24 CEST 2013
- mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
- smoothing for 3 iterations
- setting seed for random number generator to 1234
- smoothing surface tessellation for 3 iterations...
- smoothing complete - recomputing first and second fundamental forms...
- #--------------------------------------------
- #@# Inflation2 lh Thu Aug 8 18:16:28 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
- mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated
- avg radius = 48.1 mm, total surface area = 86492 mm^2
- writing inflated surface to ../surf/lh.inflated
- writing sulcal depths to ../surf/lh.sulc
-
step 000: RMS=0.121 (target=0.015)
step 005: RMS=0.082 (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=0.028 (target=0.015)
step 035: RMS=0.023 (target=0.015)
step 040: RMS=0.020 (target=0.015)
step 045: RMS=0.018 (target=0.015)
step 050: RMS=0.016 (target=0.015)
step 055: 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
- 156 vertices thresholded to be in k1 ~ [-0.22 1.31], k2 ~ [-0.11 0.05]
- total integrated curvature = 0.539*4pi (6.769) --> 0 handles
- ICI = 1.6, FI = 11.3, variation=188.525
- 116 vertices thresholded to be in [-0.04 0.01]
- writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level
- curvature mean = 0.000, std = 0.001
- 106 vertices thresholded to be in [-0.14 0.28]
- done.
- writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.017, std = 0.023
- done.
- #-----------------------------------------
- #@# Curvature Stats lh Thu Aug 8 18:18:49 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub005 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 [ sub005/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 [ 252 ]
- Gb_filter = 0
- WARN: S lookup min: -0.208057
- WARN: S explicit min: 0.000000 vertex = 345
- #--------------------------------------------
- #@# Sphere lh Thu Aug 8 18:18:54 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 0.279...
- MRISunfold() max_passes = 1 -------
- tol=5.0e-01, sigma=0.0, host=snake, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
- using quadratic fit line minimization
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 1.000000
- desired_rms_height -1.000000
- momentum 0.900000
- nbhd_size 7
- max_nbrs 8
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 1234
- --------------------
- mrisRemoveNegativeArea()
- pass 1: epoch 1 of 3 starting distance error %21.03
- pass 1: epoch 2 of 3 starting distance error %20.99
- unfolding complete - removing small folds...
- starting distance error %20.92
- removing remaining folds...
- final distance error %20.94
- MRISunfold() return, current seed 1234
- writing spherical brain to ../surf/lh.sphere
- spherical transformation took 0.93 hours
- #--------------------------------------------
- #@# Surf Reg lh Thu Aug 8 19:14:36 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 = 0.565
- curvature mean = 0.044, std = 0.936
- curvature mean = 0.024, std = 0.846
- Starting MRISrigidBodyAlignGlobal()
- d=64.00 min @ (0.00, -16.00, 0.00) sse = 346648.8, tmin=1.1476
- d=32.00 min @ (8.00, 0.00, -8.00) sse = 268100.4, tmin=2.2979
- d=16.00 min @ (0.00, 4.00, 0.00) sse = 239922.3, tmin=3.4634
- d=4.00 min @ (-1.00, -1.00, 0.00) sse = 237072.4, tmin=5.8038
- d=2.00 min @ (0.00, 0.50, -0.50) sse = 236492.4, tmin=6.9803
- d=1.00 min @ (0.00, -0.25, 0.00) sse = 236457.6, tmin=8.1529
- d=0.50 min @ (-0.12, 0.00, 0.12) sse = 236426.1, tmin=9.3353
- tol=1.0e+00, sigma=0.5, host=snake, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
- using quadratic fit line minimization
- MRISrigidBodyAlignGlobal() done 9.34 min
- curvature mean = 0.008, std = 0.945
- curvature mean = 0.012, std = 0.931
- curvature mean = 0.005, std = 0.957
- curvature mean = 0.006, std = 0.967
- curvature mean = 0.003, std = 0.958
- curvature mean = 0.002, std = 0.984
- 2 Reading smoothwm
- curvature mean = -0.023, std = 0.319
- curvature mean = 0.003, std = 0.067
- curvature mean = 0.075, std = 0.300
- curvature mean = 0.003, std = 0.079
- curvature mean = 0.035, std = 0.481
- curvature mean = 0.004, std = 0.084
- curvature mean = 0.018, std = 0.625
- curvature mean = 0.004, std = 0.087
- curvature mean = 0.007, std = 0.740
- MRISregister() return, current seed 0
- writing registered surface to ../surf/lh.sphere.reg...
- expanding nbhd size to 1
- #--------------------------------------------
- #@# Jacobian white lh Thu Aug 8 19:42:54 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 19:42:56 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 19:42:58 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub005 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...
- 1217 labels changed using aseg
- relabeling using gibbs priors...
- 000: 3352 changed, 141918 examined...
- 001: 780 changed, 14134 examined...
- 002: 182 changed, 4320 examined...
- 003: 74 changed, 1125 examined...
- 004: 25 changed, 423 examined...
- 005: 12 changed, 157 examined...
- 006: 2 changed, 74 examined...
- 007: 3 changed, 14 examined...
- 008: 3 changed, 14 examined...
- 009: 0 changed, 17 examined...
- 217 labels changed using aseg
- 000: 129 total segments, 79 labels (294 vertices) changed
- 001: 51 total segments, 3 labels (8 vertices) changed
- 002: 48 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 53 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 1496 vertices marked for relabeling...
- 1496 labels changed in reclassification.
- writing output to ../label/lh.aparc.annot...
- classification took 1 minutes and 3 seconds.
- #--------------------------------------------
- #@# Make Pial Surf lh Thu Aug 8 19:44:01 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
- mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub005 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/sub005/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz...
- 16905 bright wm thresholded.
- 908 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.orig...
- computing class statistics...
- border white: 254363 voxels (1.52%)
- border gray 296177 voxels (1.77%)
- WM (91.0): 92.4 +- 10.3 [70.0 --> 110.0]
- GM (74.0) : 72.6 +- 12.7 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 46.3 (was 70)
- setting MAX_BORDER_WHITE to 114.3 (was 105)
- setting MIN_BORDER_WHITE to 59.0 (was 85)
- setting MAX_CSF to 33.6 (was 40)
- setting MAX_GRAY to 93.7 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 52.7 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 20.9 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=104, GM=59
- mean inside = 92.3, mean outside = 67.9
- smoothing surface for 5 iterations...
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.81 +- 0.22 (0.01-->3.88) (max @ vno 67884 --> 71912)
- face area 0.28 +- 0.12 (0.00-->6.13)
- mean absolute distance = 0.64 +- 0.75
- 4354 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 5 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 1 with 3 points - only 0.00% unknown
- deleting segment 4 with 7 points - only 0.00% unknown
- deleting segment 5 with 10 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 6 with 3 points - only 0.00% unknown
- deleting segment 7 with 12 points - only 0.00% unknown
- deleting segment 8 with 11 points - only 0.00% unknown
- mean border=72.7, 45 (45) missing vertices, mean dist 0.3 [0.5 (%33.5)->0.7 (%66.5))]
- %74 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 0
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.92 +- 0.27 (0.04-->5.98) (max @ vno 60346 --> 65969)
- face area 0.28 +- 0.13 (0.00-->4.83)
- mean absolute distance = 0.29 +- 0.45
- 2898 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=7467556.5, rms=13.21
- 001: dt: 0.5000, sse=7823144.0, rms=9.481 (0.000%)
- 002: dt: 0.5000, sse=8288121.5, rms=7.465 (0.000%)
- 003: dt: 0.5000, sse=8444273.0, rms=6.250 (0.000%)
- 004: dt: 0.5000, sse=8744771.0, rms=5.521 (0.000%)
- 005: dt: 0.5000, sse=8774059.0, rms=5.121 (0.000%)
- 006: dt: 0.5000, sse=8938711.0, rms=4.871 (0.000%)
- 007: dt: 0.5000, sse=8848783.0, rms=4.747 (0.000%)
- 008: dt: 0.5000, sse=8938806.0, rms=4.631 (0.000%)
- rms = 4.59, time step reduction 1 of 3 to 0.250...
- 009: dt: 0.5000, sse=8824362.0, rms=4.586 (0.000%)
- 010: dt: 0.2500, sse=5834917.0, rms=3.249 (0.000%)
- 011: dt: 0.2500, sse=5370926.5, rms=2.813 (0.000%)
- 012: dt: 0.2500, sse=5090155.0, rms=2.713 (0.000%)
- 013: dt: 0.2500, sse=5006923.0, rms=2.627 (0.000%)
- rms = 2.60, time step reduction 2 of 3 to 0.125...
- 014: dt: 0.2500, sse=4908233.0, rms=2.600 (0.000%)
- 015: dt: 0.1250, sse=4618744.5, rms=2.301 (0.000%)
- rms = 2.26, time step reduction 3 of 3 to 0.062...
- 016: dt: 0.1250, sse=4566825.0, rms=2.259 (0.000%)
- positioning took 2.0 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 5 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 1 with 2 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- removing 3 vertex label from ripped group
- deleting segment 3 with 3 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- removing 1 vertex label from ripped group
- deleting segment 6 with 1 points - only 0.00% unknown
- deleting segment 8 with 7 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 9 with 2 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- removing 4 vertex label from ripped group
- deleting segment 12 with 5 points - only 0.00% unknown
- deleting segment 16 with 10 points - only 0.00% unknown
- deleting segment 17 with 26 points - only 0.00% unknown
- deleting segment 18 with 13 points - only 0.00% unknown
- mean border=76.9, 33 (3) missing vertices, mean dist -0.2 [0.3 (%77.2)->0.2 (%22.8))]
- %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 (0.06-->6.25) (max @ vno 60346 --> 65969)
- face area 0.35 +- 0.17 (0.00-->6.29)
- mean absolute distance = 0.21 +- 0.31
- 3043 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5461817.5, rms=5.76
- 017: dt: 0.5000, sse=5862041.5, rms=4.109 (0.000%)
- rms = 4.62, time step reduction 1 of 3 to 0.250...
- 018: dt: 0.2500, sse=5328916.0, rms=2.957 (0.000%)
- 019: dt: 0.2500, sse=5143362.5, rms=2.471 (0.000%)
- 020: dt: 0.2500, sse=5076333.5, rms=2.117 (0.000%)
- rms = 2.09, time step reduction 2 of 3 to 0.125...
- 021: dt: 0.2500, sse=5067423.0, rms=2.090 (0.000%)
- 022: dt: 0.1250, sse=4876173.5, rms=1.833 (0.000%)
- rms = 1.79, time step reduction 3 of 3 to 0.062...
- 023: dt: 0.1250, sse=4825049.0, rms=1.789 (0.000%)
- positioning took 0.9 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 5 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 1 with 2 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 3 with 3 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- removing 3 vertex label from ripped group
- deleting segment 5 with 3 points - only 0.00% unknown
- deleting segment 6 with 12 points - only 0.00% unknown
- deleting segment 7 with 6 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 9 with 9 points - only 0.00% unknown
- deleting segment 11 with 10 points - only 0.00% unknown
- deleting segment 12 with 10 points - only 0.00% unknown
- deleting segment 13 with 23 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 14 with 2 points - only 0.00% unknown
- deleting segment 15 with 13 points - only 0.00% unknown
- mean border=80.0, 26 (1) missing vertices, mean dist -0.1 [0.2 (%74.6)->0.2 (%25.4))]
- %89 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.25 (0.12-->6.37) (max @ vno 60346 --> 65969)
- face area 0.34 +- 0.17 (0.00-->6.20)
- mean absolute distance = 0.16 +- 0.25
- 2374 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5162456.5, rms=4.07
- rms = 4.12, time step reduction 1 of 3 to 0.250...
- 024: dt: 0.2500, sse=4973562.0, rms=2.871 (0.000%)
- 025: dt: 0.2500, sse=4860126.5, rms=1.874 (0.000%)
- 026: dt: 0.2500, sse=4898094.5, rms=1.739 (0.000%)
- 027: dt: 0.2500, sse=4930149.0, rms=1.674 (0.000%)
- rms = 1.74, time step reduction 2 of 3 to 0.125...
- 028: dt: 0.1250, sse=4871542.5, rms=1.603 (0.000%)
- 029: dt: 0.1250, sse=4786188.0, rms=1.522 (0.000%)
- rms = 1.52, time step reduction 3 of 3 to 0.062...
- 030: dt: 0.1250, sse=4786188.0, rms=1.522 (0.002%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 7 points - only 0.00% unknown
- deleting segment 1 with 5 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 2 with 3 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 3 with 1 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 4 with 3 points - only 0.00% unknown
- deleting segment 5 with 12 points - only 0.00% unknown
- deleting segment 6 with 8 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 8 with 9 points - only 0.00% unknown
- deleting segment 9 with 10 points - only 0.00% unknown
- deleting segment 10 with 26 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 13 points - only 0.00% unknown
- mean border=81.0, 37 (1) missing vertices, mean dist -0.0 [0.2 (%57.8)->0.2 (%42.2))]
- %91 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- repositioning cortical surface to gray/csf boundary.
- smoothing T1 volume with sigma = 2.000
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4809803.0, rms=1.86
- rms = 2.87, time step reduction 1 of 3 to 0.250...
- 031: dt: 0.2500, sse=4895558.5, rms=1.248 (0.000%)
- 032: dt: 0.2500, sse=5083564.5, rms=1.125 (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...
- 033: dt: 0.1250, sse=5086603.5, rms=1.112 (0.000%)
- positioning took 0.5 minutes
- inhibiting deformation at non-cortical midline structures...
- smoothing surface for 5 iterations...
- mean border=48.8, 50 (50) missing vertices, mean dist 1.7 [0.1 (%0.0)->2.4 (%100.0))]
- %14 local maxima, %53 large gradients and %29 min vals, 2134 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=30289990.0, rms=31.59
- 001: dt: 0.5000, sse=21800954.0, rms=26.170 (0.000%)
- 002: dt: 0.5000, sse=15971152.0, rms=21.701 (0.000%)
- 003: dt: 0.5000, sse=12148614.0, rms=18.115 (0.000%)
- 004: dt: 0.5000, sse=9780426.0, rms=15.278 (0.000%)
- 005: dt: 0.5000, sse=8437585.0, rms=13.078 (0.000%)
- 006: dt: 0.5000, sse=7662182.0, rms=11.387 (0.000%)
- 007: dt: 0.5000, sse=7225883.0, rms=9.970 (0.000%)
- 008: dt: 0.5000, sse=6913676.0, rms=8.697 (0.000%)
- 009: dt: 0.5000, sse=6786730.5, rms=7.576 (0.000%)
- 010: dt: 0.5000, sse=6749302.0, rms=6.605 (0.000%)
- 011: dt: 0.5000, sse=6830642.0, rms=5.824 (0.000%)
- 012: dt: 0.5000, sse=6971648.0, rms=5.217 (0.000%)
- 013: dt: 0.5000, sse=7091683.0, rms=4.818 (0.000%)
- 014: dt: 0.5000, sse=7275634.5, rms=4.533 (0.000%)
- 015: dt: 0.5000, sse=7341044.0, rms=4.376 (0.000%)
- 016: dt: 0.5000, sse=7434937.0, rms=4.253 (0.000%)
- 017: dt: 0.5000, sse=7446205.5, rms=4.195 (0.000%)
- 018: dt: 0.5000, sse=7537203.0, rms=4.118 (0.000%)
- rms = 4.08, time step reduction 1 of 3 to 0.250...
- 019: dt: 0.5000, sse=7507748.0, rms=4.084 (0.000%)
- 020: dt: 0.2500, sse=5595185.5, rms=3.491 (0.000%)
- 021: dt: 0.2500, sse=5435547.5, rms=3.331 (0.000%)
- rms = 3.31, time step reduction 2 of 3 to 0.125...
- 022: dt: 0.2500, sse=5313698.0, rms=3.315 (0.000%)
- 023: dt: 0.1250, sse=5111725.5, rms=3.205 (0.000%)
- rms = 3.19, time step reduction 3 of 3 to 0.062...
- 024: dt: 0.1250, sse=5080553.5, rms=3.191 (0.000%)
- positioning took 3.0 minutes
- mean border=46.7, 968 (6) missing vertices, mean dist 0.2 [0.2 (%49.6)->0.7 (%50.4))]
- %31 local maxima, %41 large gradients and %24 min vals, 755 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=5729900.0, rms=4.94
- 025: dt: 0.5000, sse=6068042.5, rms=4.384 (0.000%)
- 026: dt: 0.5000, sse=7701572.0, rms=4.262 (0.000%)
- rms = 4.25, time step reduction 1 of 3 to 0.250...
- 027: dt: 0.5000, sse=7383714.0, rms=4.246 (0.000%)
- 028: dt: 0.2500, sse=6186324.5, rms=3.485 (0.000%)
- 029: dt: 0.2500, sse=6044504.0, rms=3.247 (0.000%)
- rms = 3.22, time step reduction 2 of 3 to 0.125...
- 030: dt: 0.2500, sse=5939641.0, rms=3.225 (0.000%)
- 031: dt: 0.1250, sse=5726174.5, rms=3.064 (0.000%)
- rms = 3.04, time step reduction 3 of 3 to 0.062...
- 032: dt: 0.1250, sse=5701814.5, rms=3.035 (0.000%)
- positioning took 1.0 minutes
- mean border=44.5, 1143 (6) missing vertices, mean dist 0.1 [0.2 (%38.5)->0.4 (%61.5))]
- %50 local maxima, %21 large gradients and %24 min vals, 972 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=5982376.5, rms=4.27
- 033: dt: 0.5000, sse=6237107.0, rms=4.116 (0.000%)
- rms = 4.08, time step reduction 1 of 3 to 0.250...
- 034: dt: 0.5000, sse=8157539.0, rms=4.081 (0.000%)
- 035: dt: 0.2500, sse=6246182.0, rms=3.293 (0.000%)
- 036: dt: 0.2500, sse=6389504.5, rms=3.050 (0.000%)
- rms = 3.06, time step reduction 2 of 3 to 0.125...
- 037: dt: 0.1250, sse=6265465.5, rms=2.968 (0.000%)
- 038: dt: 0.1250, sse=6056920.0, rms=2.853 (0.000%)
- rms = 2.83, time step reduction 3 of 3 to 0.062...
- 039: dt: 0.1250, sse=6003770.5, rms=2.835 (0.000%)
- positioning took 1.0 minutes
- mean border=43.4, 2406 (4) missing vertices, mean dist 0.1 [0.2 (%44.6)->0.3 (%55.4))]
- %54 local maxima, %17 large gradients and %24 min vals, 744 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/sub005/surf/lh.pial...
- writing smoothed curvature to lh.curv.pial
- 000: dt: 0.0000, sse=6071459.0, rms=3.22
- rms = 3.84, time step reduction 1 of 3 to 0.250...
- 040: dt: 0.2500, sse=5918450.0, rms=2.969 (0.000%)
- 041: dt: 0.2500, sse=6100094.5, rms=2.889 (0.000%)
- rms = 2.87, time step reduction 2 of 3 to 0.125...
- 042: dt: 0.2500, sse=6193060.5, rms=2.868 (0.000%)
- 043: dt: 0.1250, sse=6082456.0, rms=2.754 (0.000%)
- rms = 2.73, time step reduction 3 of 3 to 0.062...
- 044: dt: 0.1250, sse=6088207.0, rms=2.734 (0.000%)
- positioning took 0.7 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.curv.pial
- writing smoothed area to lh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.area.pial
- vertex spacing 1.03 +- 0.44 (0.06-->9.25) (max @ vno 100866 --> 99891)
- face area 0.42 +- 0.32 (0.00-->11.30)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 141918 vertices processed
- 25000 of 141918 vertices processed
- 50000 of 141918 vertices processed
- 75000 of 141918 vertices processed
- 100000 of 141918 vertices processed
- 125000 of 141918 vertices processed
- 0 of 141918 vertices processed
- 25000 of 141918 vertices processed
- 50000 of 141918 vertices processed
- 75000 of 141918 vertices processed
- 100000 of 141918 vertices processed
- 125000 of 141918 vertices processed
- thickness calculation complete, 398:1170 truncations.
- 26237 vertices at 0 distance
- 88713 vertices at 1 distance
- 94532 vertices at 2 distance
- 43911 vertices at 3 distance
- 13606 vertices at 4 distance
- 3907 vertices at 5 distance
- 1120 vertices at 6 distance
- 387 vertices at 7 distance
- 191 vertices at 8 distance
- 98 vertices at 9 distance
- 53 vertices at 10 distance
- 43 vertices at 11 distance
- 26 vertices at 12 distance
- 28 vertices at 13 distance
- 16 vertices at 14 distance
- 19 vertices at 15 distance
- 27 vertices at 16 distance
- 17 vertices at 17 distance
- 6 vertices at 18 distance
- 9 vertices at 19 distance
- 14 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.thickness
- positioning took 13.8 minutes
- #--------------------------------------------
- #@# Surf Volume lh Thu Aug 8 19:57:51 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 19:57:51 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
- pctsurfcon --s sub005 --lh-only
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts/pctsurfcon.log
- Thu Aug 8 19:57:51 CEST 2013
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
- /opt/freesurfer/5.3.0/bin/pctsurfcon
- $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $
- Linux snake4 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
- FREESURFER_HOME /opt/freesurfer/5.3.0
- mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/tmp.pctsurfcon.32269/lh.wm.mgh --regheader sub005 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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/sub005/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/lh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 = 109466
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/lh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/tmp.pctsurfcon.32269/lh.wm.mgh
- Dim: 141918 1 1
- mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/tmp.pctsurfcon.32269/lh.gm.mgh --projfrac 0.3 --regheader sub005 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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/sub005/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/lh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white
- Done reading source surface
- Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 = 126137
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/lh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/tmp.pctsurfcon.32269/lh.gm.mgh
- Dim: 141918 1 1
- mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/tmp.pctsurfcon.32269/lh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/tmp.pctsurfcon.32269/lh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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/sub005/surf/lh.w-g.pct.mgh
- mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.w-g.pct.mgh --annot sub005 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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/sub005/surf/lh.w-g.pct.mgh --annot sub005 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/stats/lh.w-g.pct.stats --snr
- sysname Linux
- hostname snake4
- machine x86_64
- user fkaule
- UseRobust 0
- Constructing seg from annotation
- Reading annotation
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
- Seg base 1000
- Loading /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.w-g.pct.mgh
- Vertex Area is 0.670531 mm^3
- Generating list of segmentation ids
- Found 36 segmentations
- Computing statistics for each segmentation
- 0 1000 unknown 0 0.000
- 1 1001 bankssts 1722 1207.068
- 2 1002 caudalanteriorcingulate 877 616.236
- 3 1003 caudalmiddlefrontal 3619 2446.539
- 4 1004 corpuscallosum 0 0.000
- 5 1005 cuneus 2565 1689.801
- 6 1006 entorhinal 606 428.386
- 7 1007 fusiform 4512 3134.628
- 8 1008 inferiorparietal 6034 3977.454
- 9 1009 inferiortemporal 5113 3484.146
- 10 1010 isthmuscingulate 1632 1065.528
- 11 1011 lateraloccipital 9016 5810.531
- 12 1012 lateralorbitofrontal 4111 2725.845
- 13 1013 lingual 5608 3867.486
- 14 1014 medialorbitofrontal 2772 1890.563
- 15 1015 middletemporal 4814 3256.627
- 16 1016 parahippocampal 926 622.722
- 17 1017 paracentral 1973 1270.574
- 18 1018 parsopercularis 2922 1995.094
- 19 1019 parsorbitalis 1048 686.831
- 20 1020 parstriangularis 2076 1369.012
- 21 1021 pericalcarine 2558 1771.464
- 22 1022 postcentral 7081 4667.076
- 23 1023 posteriorcingulate 1867 1243.578
- 24 1024 precentral 6904 4575.087
- 25 1025 precuneus 5653 3799.979
- 26 1026 rostralanteriorcingulate 1532 1033.005
- 27 1027 rostralmiddlefrontal 8995 6119.219
- 28 1028 superiorfrontal 11617 7997.352
- 29 1029 superiorparietal 8754 5766.701
- 30 1030 superiortemporal 6406 4413.473
- 31 1031 supramarginal 5764 3893.233
- 32 1032 frontalpole 418 251.037
- 33 1033 temporalpole 837 553.961
- 34 1034 transversetemporal 822 507.131
- 35 1035 insula 3345 2193.028
- Reporting on 34 segmentations
- mri_segstats done
- Cleaning up
- #-----------------------------------------
- #@# Parcellation Stats lh Thu Aug 8 19:58:04 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 sub005 lh white
- computing statistics for each annotation in ../label/lh.aparc.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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
- 1722 1207 2999 2.567 0.457 0.135 0.038 20 2.6 bankssts
- 877 616 1558 2.320 0.599 0.145 0.045 16 1.5 caudalanteriorcingulate
- 3619 2447 6845 2.489 0.417 0.140 0.042 51 6.3 caudalmiddlefrontal
- 2565 1690 4212 2.219 0.475 0.166 0.064 57 7.2 cuneus
- 606 428 2268 3.682 0.648 0.171 0.072 11 1.9 entorhinal
- 4512 3135 9751 2.761 0.589 0.161 0.060 88 10.9 fusiform
- 6034 3977 11629 2.586 0.463 0.147 0.059 122 12.9 inferiorparietal
- 5113 3484 11423 2.753 0.658 0.160 0.089 143 15.3 inferiortemporal
- 1632 1066 3029 2.570 0.730 0.165 0.074 38 4.5 isthmuscingulate
- 9016 5811 14639 2.251 0.483 0.160 0.071 215 24.2 lateraloccipital
- 4111 2726 8158 2.581 0.671 0.158 0.070 97 10.8 lateralorbitofrontal
- 5608 3867 9904 2.311 0.556 0.175 0.077 134 17.1 lingual
- 2772 1891 5268 2.243 0.856 0.190 0.115 142 10.7 medialorbitofrontal
- 4814 3257 11042 2.672 0.611 0.156 0.070 117 12.8 middletemporal
- 926 623 2362 3.298 0.667 0.155 0.062 20 2.2 parahippocampal
- 1973 1271 3634 2.482 0.539 0.128 0.041 26 3.2 paracentral
- 2922 1995 6104 2.625 0.434 0.151 0.056 54 6.6 parsopercularis
- 1048 687 2215 2.421 0.659 0.171 0.076 29 2.8 parsorbitalis
- 2076 1369 3814 2.470 0.558 0.148 0.056 38 4.5 parstriangularis
- 2558 1771 3523 2.023 0.528 0.164 0.076 45 7.3 pericalcarine
- 7081 4667 12024 2.211 0.588 0.146 0.053 132 14.9 postcentral
- 1867 1244 3475 2.633 0.551 0.169 0.124 149 5.1 posteriorcingulate
- 6904 4575 13529 2.642 0.519 0.128 0.056 105 16.4 precentral
- 5653 3800 10487 2.603 0.500 0.153 0.062 113 13.2 precuneus
- 1532 1033 3300 2.736 0.720 0.153 0.061 33 3.9 rostralanteriorcingulate
- 8995 6119 16203 2.242 0.560 0.179 0.095 275 32.4 rostralmiddlefrontal
- 11617 7997 23675 2.528 0.561 0.148 0.053 215 24.3 superiorfrontal
- 8754 5767 14762 2.282 0.417 0.139 0.064 296 28.4 superiorparietal
- 6406 4413 14656 2.846 0.591 0.150 0.051 126 13.8 superiortemporal
- 5764 3893 11519 2.656 0.490 0.152 0.064 113 14.9 supramarginal
- 418 251 782 2.194 0.751 0.219 0.132 26 2.2 frontalpole
- 837 554 2851 3.583 0.651 0.154 0.072 15 2.6 temporalpole
- 822 507 1644 2.808 0.362 0.145 0.049 13 1.6 transversetemporal
- 3345 2193 7111 3.161 0.837 0.124 0.068 55 7.9 insula
- #-----------------------------------------
- #@# Cortical Parc 2 lh Thu Aug 8 19:58:23 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub005 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...
- 52 labels changed using aseg
- relabeling using gibbs priors...
- 000: 9826 changed, 141918 examined...
- 001: 2460 changed, 37405 examined...
- 002: 781 changed, 12468 examined...
- 003: 300 changed, 4185 examined...
- 004: 116 changed, 1682 examined...
- 005: 71 changed, 654 examined...
- 006: 42 changed, 404 examined...
- 007: 21 changed, 221 examined...
- 008: 19 changed, 124 examined...
- 009: 14 changed, 92 examined...
- 010: 5 changed, 61 examined...
- 011: 0 changed, 25 examined...
- 14 labels changed using aseg
- 000: 310 total segments, 227 labels (2923 vertices) changed
- 001: 105 total segments, 22 labels (72 vertices) changed
- 002: 83 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 154 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 849 vertices marked for relabeling...
- 849 labels changed in reclassification.
- writing output to ../label/lh.aparc.a2009s.annot...
- classification took 1 minutes and 12 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 2 lh Thu Aug 8 19:59:34 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 sub005 lh white
- computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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
- 1378 920 2400 2.108 0.663 0.191 0.113 51 5.6 G_and_S_frontomargin
- 2137 1388 4192 2.534 0.497 0.172 0.075 48 5.4 G_and_S_occipital_inf
- 1433 892 2756 2.463 0.533 0.143 0.113 38 6.4 G_and_S_paracentral
- 1687 1137 3728 2.800 0.498 0.158 0.057 34 4.1 G_and_S_subcentral
- 855 564 1523 2.088 0.539 0.203 0.151 37 4.2 G_and_S_transv_frontopol
- 2884 1986 5490 2.523 0.718 0.150 0.053 53 6.2 G_and_S_cingul-Ant
- 1436 1023 2855 2.592 0.537 0.137 0.060 35 3.0 G_and_S_cingul-Mid-Ant
- 1437 979 2702 2.627 0.433 0.134 0.045 20 2.4 G_and_S_cingul-Mid-Post
- 555 371 1371 2.977 0.492 0.198 0.098 20 2.4 G_cingul-Post-dorsal
- 419 269 860 2.553 0.872 0.173 0.087 12 1.2 G_cingul-Post-ventral
- 2319 1544 3782 2.101 0.476 0.179 0.077 60 7.8 G_cuneus
- 1839 1236 4307 2.751 0.443 0.163 0.065 43 4.6 G_front_inf-Opercular
- 308 188 818 2.873 0.439 0.169 0.063 8 0.8 G_front_inf-Orbital
- 1298 865 3033 2.748 0.476 0.179 0.087 38 4.4 G_front_inf-Triangul
- 4376 2983 9909 2.551 0.482 0.185 0.093 148 16.4 G_front_middle
- 7586 5135 17357 2.653 0.542 0.158 0.062 165 18.4 G_front_sup
- 411 247 1034 3.697 0.833 0.128 0.069 7 1.1 G_Ins_lg_and_S_cent_ins
- 828 506 2535 3.749 0.786 0.155 0.139 31 3.8 G_insular_short
- 2469 1549 5012 2.536 0.418 0.169 0.073 82 7.4 G_occipital_middle
- 2099 1345 3730 2.273 0.505 0.156 0.146 193 17.5 G_occipital_sup
- 1349 941 3454 2.830 0.453 0.187 0.076 39 4.3 G_oc-temp_lat-fusifor
- 3839 2584 7020 2.335 0.577 0.194 0.094 113 14.3 G_oc-temp_med-Lingual
- 1312 897 3979 3.324 0.692 0.165 0.067 27 3.5 G_oc-temp_med-Parahip
- 2634 1745 6352 2.661 0.726 0.185 0.099 93 9.7 G_orbital
- 2305 1493 5492 2.809 0.400 0.165 0.077 71 6.6 G_pariet_inf-Angular
- 2786 1914 6816 2.834 0.494 0.168 0.076 73 8.7 G_pariet_inf-Supramar
- 2945 1960 5603 2.359 0.396 0.152 0.054 64 6.3 G_parietal_sup
- 2788 1803 5312 2.286 0.517 0.158 0.062 70 6.5 G_postcentral
- 2489 1608 6267 2.854 0.473 0.136 0.055 45 5.8 G_precentral
- 2128 1440 5062 2.863 0.443 0.178 0.079 62 5.9 G_precuneus
- 971 642 2029 2.161 0.743 0.225 0.136 84 4.3 G_rectus
- 386 280 996 3.136 0.819 0.243 0.230 31 2.8 G_subcallosal
- 735 447 1700 2.922 0.329 0.159 0.055 14 1.6 G_temp_sup-G_T_transv
- 2548 1741 7321 3.120 0.549 0.182 0.076 81 7.6 G_temp_sup-Lateral
- 809 613 2338 3.316 0.753 0.145 0.048 11 1.7 G_temp_sup-Plan_polar
- 1099 752 2287 2.648 0.476 0.123 0.046 15 1.8 G_temp_sup-Plan_tempo
- 2622 1759 6914 2.844 0.720 0.181 0.122 105 10.3 G_temporal_inf
- 3152 2141 8157 2.712 0.602 0.168 0.078 90 8.9 G_temporal_middle
- 334 216 424 2.220 0.372 0.102 0.028 2 0.3 Lat_Fis-ant-Horizont
- 313 216 569 2.707 0.398 0.136 0.039 3 0.6 Lat_Fis-ant-Vertical
- 1254 838 1702 2.478 0.385 0.130 0.039 13 2.1 Lat_Fis-post
- 2689 1680 3876 2.019 0.502 0.168 0.094 82 9.5 Pole_occipital
- 2203 1485 7022 3.451 0.652 0.174 0.087 58 7.3 Pole_temporal
- 3185 2225 4539 2.107 0.553 0.147 0.063 49 7.5 S_calcarine
- 3244 2207 4057 1.992 0.570 0.120 0.032 25 4.5 S_central
- 1047 695 1580 2.329 0.491 0.158 0.064 22 2.4 S_cingul-Marginalis
- 517 342 915 2.774 0.424 0.099 0.024 2 0.6 S_circular_insula_ant
- 1382 936 2162 2.717 0.609 0.098 0.022 7 1.3 S_circular_insula_inf
- 1891 1288 2962 2.584 0.481 0.113 0.035 14 2.6 S_circular_insula_sup
- 1249 895 2023 2.493 0.408 0.110 0.022 9 1.2 S_collat_transv_ant
- 641 434 732 2.152 0.335 0.154 0.049 9 1.3 S_collat_transv_post
- 2379 1609 3381 2.168 0.452 0.139 0.041 32 4.1 S_front_inf
- 1677 1160 2496 2.029 0.499 0.158 0.078 34 5.0 S_front_middle
- 3655 2520 5939 2.264 0.444 0.140 0.040 55 6.0 S_front_sup
- 283 196 376 2.214 0.280 0.120 0.024 2 0.4 S_interm_prim-Jensen
- 2513 1694 3835 2.315 0.343 0.135 0.040 33 3.9 S_intrapariet_and_P_trans
- 1281 890 1710 2.027 0.401 0.140 0.039 14 2.1 S_oc_middle_and_Lunatus
- 1579 1040 2518 2.320 0.388 0.145 0.048 24 3.1 S_oc_sup_and_transversal
- 1113 759 1706 2.322 0.394 0.128 0.040 12 1.6 S_occipital_ant
- 815 566 1243 2.458 0.445 0.143 0.051 11 1.5 S_oc-temp_lat
- 2022 1442 3743 2.711 0.603 0.141 0.044 29 3.5 S_oc-temp_med_and_Lingual
- 349 244 476 1.709 0.481 0.160 0.054 7 0.7 S_orbital_lateral
- 869 577 1213 2.181 0.985 0.114 0.031 7 1.0 S_orbital_med-olfact
- 1647 1094 2575 2.338 0.505 0.148 0.058 25 3.4 S_orbital-H_Shaped
- 2922 1941 4366 2.454 0.442 0.127 0.036 30 4.4 S_parieto_occipital
- 1242 762 1435 2.260 0.699 0.150 0.130 119 2.8 S_pericallosal
- 3378 2213 4710 2.252 0.418 0.122 0.038 33 5.3 S_postcentral
- 1443 960 2116 2.453 0.379 0.110 0.025 11 1.6 S_precentral-inf-part
- 1417 987 2064 2.378 0.371 0.114 0.033 13 2.1 S_precentral-sup-part
- 727 499 1459 2.366 0.805 0.193 0.111 25 3.0 S_suborbital
- 908 626 1673 2.536 0.422 0.148 0.061 14 2.4 S_subparietal
- 1618 1090 2551 2.494 0.570 0.140 0.044 20 3.1 S_temporal_inf
- 5634 3826 9162 2.498 0.446 0.129 0.046 71 10.2 S_temporal_sup
- 428 292 591 2.311 0.348 0.129 0.038 4 0.7 S_temporal_transverse
- #-----------------------------------------
- #@# Cortical Parc 3 lh Thu Aug 8 19:59:53 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub005 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...
- 885 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2945 changed, 141918 examined...
- 001: 688 changed, 12520 examined...
- 002: 204 changed, 3815 examined...
- 003: 64 changed, 1156 examined...
- 004: 29 changed, 370 examined...
- 005: 19 changed, 181 examined...
- 006: 6 changed, 103 examined...
- 007: 5 changed, 33 examined...
- 008: 6 changed, 29 examined...
- 009: 4 changed, 32 examined...
- 010: 2 changed, 24 examined...
- 011: 2 changed, 13 examined...
- 012: 0 changed, 9 examined...
- 120 labels changed using aseg
- 000: 76 total segments, 43 labels (294 vertices) changed
- 001: 33 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 50 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 548 vertices marked for relabeling...
- 548 labels changed in reclassification.
- writing output to ../label/lh.aparc.DKTatlas40.annot...
- classification took 1 minutes and 3 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 3 lh Thu Aug 8 20:00:57 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 sub005 lh white
- computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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
- 1671 1153 3163 2.490 0.601 0.142 0.052 38 2.9 caudalanteriorcingulate
- 3626 2449 6864 2.490 0.417 0.139 0.042 51 6.3 caudalmiddlefrontal
- 3762 2482 6201 2.243 0.484 0.158 0.060 76 9.5 cuneus
- 573 410 2117 3.651 0.657 0.175 0.072 11 1.7 entorhinal
- 3815 2663 7446 2.660 0.490 0.157 0.055 70 8.5 fusiform
- 5685 3744 10981 2.586 0.459 0.147 0.059 117 12.1 inferiorparietal
- 5444 3708 13060 2.824 0.711 0.162 0.090 152 16.7 inferiortemporal
- 1575 1036 2928 2.568 0.738 0.167 0.075 37 4.5 isthmuscingulate
- 9358 6044 15353 2.247 0.493 0.159 0.071 223 24.8 lateraloccipital
- 4491 2954 8915 2.535 0.742 0.168 0.086 129 13.8 lateralorbitofrontal
- 5567 3840 9821 2.313 0.551 0.175 0.077 132 16.9 lingual
- 2370 1617 4625 2.223 0.858 0.199 0.125 137 10.1 medialorbitofrontal
- 6389 4331 13618 2.615 0.587 0.151 0.062 136 15.6 middletemporal
- 950 640 2411 3.280 0.675 0.156 0.061 21 2.3 parahippocampal
- 2314 1496 4189 2.477 0.514 0.126 0.041 29 3.8 paracentral
- 2616 1773 5364 2.620 0.442 0.151 0.058 51 6.0 parsopercularis
- 1199 780 2457 2.532 0.517 0.141 0.050 21 2.4 parsorbitalis
- 2606 1746 4857 2.452 0.549 0.150 0.055 47 5.9 parstriangularis
- 2555 1773 3550 2.032 0.526 0.161 0.073 44 7.0 pericalcarine
- 7867 5196 13271 2.227 0.579 0.147 0.053 144 16.6 postcentral
- 1950 1311 3572 2.629 0.520 0.165 0.111 139 5.0 posteriorcingulate
- 6928 4596 13547 2.643 0.516 0.127 0.055 104 16.4 precentral
- 5405 3636 10347 2.613 0.499 0.154 0.063 110 13.0 precuneus
- 1926 1309 4152 2.719 0.746 0.156 0.062 42 4.8 rostralanteriorcingulate
- 5870 3989 10343 2.256 0.562 0.176 0.088 170 20.5 rostralmiddlefrontal
- 13343 9154 26756 2.445 0.580 0.157 0.066 300 33.3 superiorfrontal
- 6797 4449 11473 2.299 0.410 0.140 0.069 268 24.9 superiorparietal
- 8836 6083 20519 2.901 0.635 0.150 0.054 166 19.6 superiortemporal
- 5438 3668 10765 2.660 0.490 0.151 0.064 107 14.1 supramarginal
- 775 478 1556 2.808 0.357 0.144 0.049 12 1.4 transversetemporal
- 2798 1822 6173 3.228 0.806 0.120 0.069 46 6.8 insula
- #--------------------------------------------
- #@# Tessellate rh Thu Aug 8 20:01:16 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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+): 0 found - 0 modified | TOTAL: 4
- pass 1 (yz-): 6 found - 6 modified | TOTAL: 10
- pass 2 (yz-): 0 found - 6 modified | TOTAL: 10
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 10
- pass 1 (xz-): 1 found - 1 modified | TOTAL: 11
- pass 2 (xz-): 0 found - 1 modified | TOTAL: 11
- 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 (--): 3 found - 3 modified | TOTAL: 3
- pass 2 (--): 0 found - 3 modified | TOTAL: 3
- pass 1 (-+): 1 found - 1 modified | TOTAL: 4
- pass 2 (-+): 0 found - 1 modified | TOTAL: 4
- Iteration Number : 2
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Total Number of Modified Voxels = 15 (out of 240260: 0.006243)
- Ambiguous edge configurations...
- mri_pretess done
- mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix
- $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- slice 40: 1452 vertices, 1594 faces
- slice 50: 7719 vertices, 8000 faces
- slice 60: 16737 vertices, 17128 faces
- slice 70: 28710 vertices, 29125 faces
- slice 80: 40003 vertices, 40388 faces
- slice 90: 51408 vertices, 51787 faces
- slice 100: 62316 vertices, 62685 faces
- slice 110: 72926 vertices, 73310 faces
- slice 120: 83757 vertices, 84160 faces
- slice 130: 94781 vertices, 95175 faces
- slice 140: 106061 vertices, 106508 faces
- slice 150: 117008 vertices, 117377 faces
- slice 160: 126598 vertices, 126940 faces
- slice 170: 133174 vertices, 133404 faces
- slice 180: 138488 vertices, 138680 faces
- slice 190: 142387 vertices, 142536 faces
- slice 200: 143688 vertices, 143714 faces
- slice 210: 143688 vertices, 143714 faces
- slice 220: 143688 vertices, 143714 faces
- slice 230: 143688 vertices, 143714 faces
- slice 240: 143688 vertices, 143714 faces
- slice 250: 143688 vertices, 143714 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...
- 143688 voxel in cpt #1: X=-26 [v=143688,e=431142,f=287428] located at (24.793489, -19.142183, 42.190880)
- For the whole surface: X=-26 [v=143688,e=431142,f=287428]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Smooth1 rh Thu Aug 8 20:01:23 CEST 2013
- mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
- setting seed for random number generator to 1234
- smoothing surface tessellation for 10 iterations...
- smoothing complete - recomputing first and second fundamental forms...
- #--------------------------------------------
- #@# Inflation1 rh Thu Aug 8 20:01:28 CEST 2013
- mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
- avg radius = 46.7 mm, total surface area = 74244 mm^2
- writing inflated surface to ../surf/rh.inflated.nofix
- inflation took 0.7 minutes
- Not saving sulc
-
step 000: RMS=0.103 (target=0.015)
step 005: RMS=0.075 (target=0.015)
step 010: RMS=0.054 (target=0.015)
step 015: RMS=0.045 (target=0.015)
step 020: RMS=0.039 (target=0.015)
step 025: RMS=0.034 (target=0.015)
step 030: RMS=0.030 (target=0.015)
step 035: RMS=0.028 (target=0.015)
step 040: RMS=0.026 (target=0.015)
step 045: RMS=0.024 (target=0.015)
step 050: RMS=0.023 (target=0.015)
step 055: RMS=0.022 (target=0.015)
step 060: RMS=0.022 (target=0.015)
- inflation complete.
- Not saving sulc
- #--------------------------------------------
- #@# QSphere rh Thu Aug 8 20:02:08 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
- mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix
- doing quick spherical unfolding.
- setting seed for random number genererator to 1234
- $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading original vertex positions...
- unfolding cortex into spherical form...
- surface projected - minimizing metric distortion...
- vertex spacing 0.97 +- 0.58 (0.00-->6.28) (max @ vno 59778 --> 60967)
- face area 0.02 +- 0.03 (-0.07-->0.60)
- scaling brain by 0.306...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=176.619, avgs=0
- 005/300: dt: 0.9000, rms radial error=176.360, avgs=0
- 010/300: dt: 0.9000, rms radial error=175.805, avgs=0
- 015/300: dt: 0.9000, rms radial error=175.076, avgs=0
- 020/300: dt: 0.9000, rms radial error=174.245, avgs=0
- 025/300: dt: 0.9000, rms radial error=173.354, avgs=0
- 030/300: dt: 0.9000, rms radial error=172.432, avgs=0
- 035/300: dt: 0.9000, rms radial error=171.492, avgs=0
- 040/300: dt: 0.9000, rms radial error=170.546, avgs=0
- 045/300: dt: 0.9000, rms radial error=169.603, avgs=0
- 050/300: dt: 0.9000, rms radial error=168.661, avgs=0
- 055/300: dt: 0.9000, rms radial error=167.721, avgs=0
- 060/300: dt: 0.9000, rms radial error=166.784, avgs=0
- 065/300: dt: 0.9000, rms radial error=165.852, avgs=0
- 070/300: dt: 0.9000, rms radial error=164.924, avgs=0
- 075/300: dt: 0.9000, rms radial error=164.000, avgs=0
- 080/300: dt: 0.9000, rms radial error=163.082, avgs=0
- 085/300: dt: 0.9000, rms radial error=162.168, avgs=0
- 090/300: dt: 0.9000, rms radial error=161.259, avgs=0
- 095/300: dt: 0.9000, rms radial error=160.355, avgs=0
- 100/300: dt: 0.9000, rms radial error=159.456, avgs=0
- 105/300: dt: 0.9000, rms radial error=158.562, avgs=0
- 110/300: dt: 0.9000, rms radial error=157.673, avgs=0
- 115/300: dt: 0.9000, rms radial error=156.788, avgs=0
- 120/300: dt: 0.9000, rms radial error=155.909, avgs=0
- 125/300: dt: 0.9000, rms radial error=155.034, avgs=0
- 130/300: dt: 0.9000, rms radial error=154.163, avgs=0
- 135/300: dt: 0.9000, rms radial error=153.298, avgs=0
- 140/300: dt: 0.9000, rms radial error=152.437, avgs=0
- 145/300: dt: 0.9000, rms radial error=151.581, avgs=0
- 150/300: dt: 0.9000, rms radial error=150.730, avgs=0
- 155/300: dt: 0.9000, rms radial error=149.883, avgs=0
- 160/300: dt: 0.9000, rms radial error=149.040, avgs=0
- 165/300: dt: 0.9000, rms radial error=148.203, avgs=0
- 170/300: dt: 0.9000, rms radial error=147.370, avgs=0
- 175/300: dt: 0.9000, rms radial error=146.541, avgs=0
- 180/300: dt: 0.9000, rms radial error=145.717, avgs=0
- 185/300: dt: 0.9000, rms radial error=144.898, avgs=0
- 190/300: dt: 0.9000, rms radial error=144.083, avgs=0
- 195/300: dt: 0.9000, rms radial error=143.273, avgs=0
- 200/300: dt: 0.9000, rms radial error=142.467, avgs=0
- 205/300: dt: 0.9000, rms radial error=141.665, avgs=0
- 210/300: dt: 0.9000, rms radial error=140.868, avgs=0
- 215/300: dt: 0.9000, rms radial error=140.075, avgs=0
- 220/300: dt: 0.9000, rms radial error=139.286, avgs=0
- 225/300: dt: 0.9000, rms radial error=138.502, avgs=0
- 230/300: dt: 0.9000, rms radial error=137.722, avgs=0
- 235/300: dt: 0.9000, rms radial error=136.947, avgs=0
- 240/300: dt: 0.9000, rms radial error=136.175, avgs=0
- 245/300: dt: 0.9000, rms radial error=135.409, avgs=0
- 250/300: dt: 0.9000, rms radial error=134.646, avgs=0
- 255/300: dt: 0.9000, rms radial error=133.888, avgs=0
- 260/300: dt: 0.9000, rms radial error=133.133, avgs=0
- 265/300: dt: 0.9000, rms radial error=132.384, avgs=0
- 270/300: dt: 0.9000, rms radial error=131.638, avgs=0
- 275/300: dt: 0.9000, rms radial error=130.897, avgs=0
- 280/300: dt: 0.9000, rms radial error=130.159, avgs=0
- 285/300: dt: 0.9000, rms radial error=129.426, avgs=0
- 290/300: dt: 0.9000, rms radial error=128.697, avgs=0
- 295/300: dt: 0.9000, rms radial error=127.972, avgs=0
- 300/300: dt: 0.9000, rms radial error=127.251, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 16961.32
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00011
- epoch 2 (K=40.0), pass 1, starting sse = 2903.24
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00010
- epoch 3 (K=160.0), pass 1, starting sse = 313.09
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.09/11 = 0.00783
- epoch 4 (K=640.0), pass 1, starting sse = 17.73
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.11/13 = 0.00827
- final writing spherical brain to ../surf/rh.qsphere.nofix
- spherical transformation took 0.08 hours
- distance error %100000.00
- #--------------------------------------------
- #@# Fix Topology rh Thu Aug 8 20:06:51 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/sub005/scripts
- mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub005 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=-26 (nv=143688, nf=287428, ne=431142, g=14)
- 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 12 iterations
- marking ambiguous vertices...
- 2055 ambiguous faces found in tessellation
- segmenting defects...
- 27 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- 27 defects to be corrected
- 0 vertices coincident
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -9.8290 (-4.9145)
- -vertex loglikelihood: -6.6454 (-3.3227)
- -normal dot loglikelihood: -3.5952 (-3.5952)
- -quad curv loglikelihood: -6.5467 (-3.2734)
- Total Loglikelihood : -26.6163
- CORRECTING DEFECT 0 (vertices=19, convex hull=60)
- After retessellation of defect 0, euler #=-24 (142408,426667,284235) : difference with theory (-24) = 0
- CORRECTING DEFECT 1 (vertices=33, convex hull=49)
- After retessellation of defect 1, euler #=-23 (142413,426700,284264) : difference with theory (-23) = 0
- CORRECTING DEFECT 2 (vertices=85, convex hull=62)
- After retessellation of defect 2, euler #=-22 (142430,426773,284321) : difference with theory (-22) = 0
- CORRECTING DEFECT 3 (vertices=91, convex hull=93)
- After retessellation of defect 3, euler #=-21 (142440,426843,284382) : difference with theory (-21) = 0
- CORRECTING DEFECT 4 (vertices=25, convex hull=67)
- After retessellation of defect 4, euler #=-20 (142450,426900,284430) : difference with theory (-20) = 0
- CORRECTING DEFECT 5 (vertices=18, convex hull=25)
- After retessellation of defect 5, euler #=-19 (142453,426917,284445) : difference with theory (-19) = 0
- CORRECTING DEFECT 6 (vertices=35, convex hull=59)
- After retessellation of defect 6, euler #=-18 (142462,426970,284490) : difference with theory (-18) = 0
- CORRECTING DEFECT 7 (vertices=48, convex hull=67)
- After retessellation of defect 7, euler #=-17 (142491,427087,284579) : difference with theory (-17) = 0
- CORRECTING DEFECT 8 (vertices=15, convex hull=32)
- After retessellation of defect 8, euler #=-16 (142496,427112,284600) : difference with theory (-16) = 0
- CORRECTING DEFECT 9 (vertices=136, convex hull=30)
- After retessellation of defect 9, euler #=-15 (142504,427145,284626) : difference with theory (-15) = 0
- CORRECTING DEFECT 10 (vertices=6, convex hull=13)
- After retessellation of defect 10, euler #=-14 (142504,427148,284630) : difference with theory (-14) = 0
- CORRECTING DEFECT 11 (vertices=88, convex hull=27)
- After retessellation of defect 11, euler #=-13 (142512,427179,284654) : difference with theory (-13) = 0
- CORRECTING DEFECT 12 (vertices=18, convex hull=23)
- After retessellation of defect 12, euler #=-12 (142515,427195,284668) : difference with theory (-12) = 0
- CORRECTING DEFECT 13 (vertices=39, convex hull=56)
- After retessellation of defect 13, euler #=-11 (142535,427275,284729) : difference with theory (-11) = 0
- CORRECTING DEFECT 14 (vertices=56, convex hull=53)
- After retessellation of defect 14, euler #=-10 (142553,427353,284790) : difference with theory (-10) = 0
- CORRECTING DEFECT 15 (vertices=10, convex hull=14)
- After retessellation of defect 15, euler #=-9 (142555,427364,284800) : difference with theory (-9) = 0
- CORRECTING DEFECT 16 (vertices=84, convex hull=79)
- After retessellation of defect 16, euler #=-8 (142574,427456,284874) : difference with theory (-8) = 0
- CORRECTING DEFECT 17 (vertices=32, convex hull=61)
- After retessellation of defect 17, euler #=-7 (142594,427544,284943) : difference with theory (-7) = 0
- CORRECTING DEFECT 18 (vertices=20, convex hull=50)
- After retessellation of defect 18, euler #=-6 (142606,427599,284987) : difference with theory (-6) = 0
- CORRECTING DEFECT 19 (vertices=128, convex hull=53)
- After retessellation of defect 19, euler #=-5 (142614,427645,285026) : difference with theory (-5) = 0
- CORRECTING DEFECT 20 (vertices=45, convex hull=90)
- After retessellation of defect 20, euler #=-4 (142639,427755,285112) : difference with theory (-4) = 0
- CORRECTING DEFECT 21 (vertices=69, convex hull=84)
- After retessellation of defect 21, euler #=-3 (142657,427841,285181) : difference with theory (-3) = 0
- CORRECTING DEFECT 22 (vertices=47, convex hull=66)
- After retessellation of defect 22, euler #=-2 (142685,427954,285267) : difference with theory (-2) = 0
- CORRECTING DEFECT 23 (vertices=86, convex hull=95)
- After retessellation of defect 23, euler #=-1 (142711,428075,285363) : difference with theory (-1) = 0
- CORRECTING DEFECT 24 (vertices=11, convex hull=19)
- After retessellation of defect 24, euler #=0 (142712,428082,285370) : difference with theory (0) = 0
- CORRECTING DEFECT 25 (vertices=24, convex hull=53)
- After retessellation of defect 25, euler #=1 (142722,428134,285413) : difference with theory (1) = 0
- CORRECTING DEFECT 26 (vertices=23, convex hull=66)
- After retessellation of defect 26, euler #=2 (142731,428187,285458) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.88 +- 0.22 (0.08-->9.58) (max @ vno 16176 --> 26838)
- 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 (0.08-->9.58) (max @ vno 16176 --> 26838)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 103 mutations (36.1%), 182 crossovers (63.9%), 53 vertices were eliminated
- building final representation...
- 957 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=142731, nf=285458, ne=428187, g=0)
- writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 16.0 minutes
- 0 defective edges
- removing intersecting faces
- 000: 77 intersecting
- mris_euler_number ../surf/rh.orig
- euler # = v-e+f = 2g-2: 142731 - 428187 + 285458 = 2 --> 0 holes
- F =2V-4: 285458 = 285462-4 (0)
- 2E=3F: 856374 = 856374 (0)
- total defect index = 0
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
- mris_remove_intersection ../surf/rh.orig ../surf/rh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 16 intersecting
- 001: 6 intersecting
- writing corrected surface to ../surf/rh.orig
- rm ../surf/rh.inflated
- #--------------------------------------------
- #@# Make White Surf rh Thu Aug 8 20:22:58 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
- mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub005 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/sub005/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz...
- 17487 bright wm thresholded.
- 908 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.orig...
- computing class statistics...
- border white: 254363 voxels (1.52%)
- border gray 296177 voxels (1.77%)
- WM (91.0): 92.5 +- 10.3 [70.0 --> 110.0]
- GM (74.0) : 72.5 +- 12.8 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 44.2 (was 70)
- setting MAX_BORDER_WHITE to 115.3 (was 105)
- setting MIN_BORDER_WHITE to 57.0 (was 85)
- setting MAX_CSF to 31.3 (was 40)
- setting MAX_GRAY to 94.7 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 50.6 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 18.5 (was 40)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.81 +- 0.22 (0.01-->3.89) (max @ vno 16176 --> 26838)
- face area 0.27 +- 0.12 (0.00-->1.52)
- mean absolute distance = 0.64 +- 0.71
- 5092 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 = 92.4, mean outside = 67.6
- smoothing surface for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 1 vertex label from ripped group
- removing 3 vertex label from ripped group
- mean border=71.6, 17 (17) missing vertices, mean dist 0.4 [0.4 (%30.8)->0.7 (%69.2))]
- %78 local maxima, %18 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 (0.08-->3.85) (max @ vno 100129 --> 101238)
- face area 0.27 +- 0.13 (0.00-->1.99)
- mean absolute distance = 0.29 +- 0.43
- 3359 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=7953829.5, rms=13.82
- 001: dt: 0.5000, sse=8023892.0, rms=9.975 (0.000%)
- 002: dt: 0.5000, sse=8355369.0, rms=7.823 (0.000%)
- 003: dt: 0.5000, sse=8480620.0, rms=6.470 (0.000%)
- 004: dt: 0.5000, sse=8764958.0, rms=5.656 (0.000%)
- 005: dt: 0.5000, sse=8813126.0, rms=5.178 (0.000%)
- 006: dt: 0.5000, sse=8973657.0, rms=4.904 (0.000%)
- 007: dt: 0.5000, sse=8960889.0, rms=4.754 (0.000%)
- 008: dt: 0.5000, sse=9043888.0, rms=4.639 (0.000%)
- 009: dt: 0.5000, sse=8924771.0, rms=4.582 (0.000%)
- 010: dt: 0.5000, sse=8987706.0, rms=4.514 (0.000%)
- rms = 4.49, time step reduction 1 of 3 to 0.250...
- 011: dt: 0.5000, sse=8876608.0, rms=4.495 (0.000%)
- 012: dt: 0.2500, sse=5798995.0, rms=3.158 (0.000%)
- 013: dt: 0.2500, sse=5317273.0, rms=2.702 (0.000%)
- 014: dt: 0.2500, sse=5017348.5, rms=2.594 (0.000%)
- 015: dt: 0.2500, sse=4933934.5, rms=2.504 (0.000%)
- rms = 2.47, time step reduction 2 of 3 to 0.125...
- 016: dt: 0.2500, sse=4830886.0, rms=2.471 (0.000%)
- 017: dt: 0.1250, sse=4575423.5, rms=2.219 (0.000%)
- rms = 2.18, time step reduction 3 of 3 to 0.062...
- 018: dt: 0.1250, sse=4526973.0, rms=2.184 (0.000%)
- positioning took 2.3 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- mean border=76.1, 30 (0) missing vertices, mean dist -0.2 [0.3 (%78.7)->0.2 (%21.3))]
- %86 local maxima, % 9 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 (0.03-->3.41) (max @ vno 16176 --> 26838)
- face area 0.35 +- 0.17 (0.00-->2.12)
- mean absolute distance = 0.21 +- 0.29
- 2676 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5551025.0, rms=6.07
- 019: dt: 0.5000, sse=5772346.5, rms=4.079 (0.000%)
- rms = 4.63, time step reduction 1 of 3 to 0.250...
- 020: dt: 0.2500, sse=5267387.5, rms=2.914 (0.000%)
- 021: dt: 0.2500, sse=5100009.5, rms=2.430 (0.000%)
- 022: dt: 0.2500, sse=5021002.0, rms=2.053 (0.000%)
- rms = 2.02, time step reduction 2 of 3 to 0.125...
- 023: dt: 0.2500, sse=5002119.0, rms=2.023 (0.000%)
- 024: dt: 0.1250, sse=4814917.5, rms=1.773 (0.000%)
- rms = 1.74, time step reduction 3 of 3 to 0.062...
- 025: dt: 0.1250, sse=4759359.5, rms=1.740 (0.000%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 1 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- mean border=79.4, 26 (0) missing vertices, mean dist -0.1 [0.2 (%76.4)->0.2 (%23.6))]
- %92 local maxima, % 3 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 (0.05-->3.40) (max @ vno 16176 --> 26838)
- face area 0.34 +- 0.16 (0.00-->1.90)
- mean absolute distance = 0.16 +- 0.23
- 2959 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5157159.5, rms=4.29
- 026: dt: 0.5000, sse=5526874.5, rms=4.197 (0.000%)
- rms = 4.46, time step reduction 1 of 3 to 0.250...
- 027: dt: 0.2500, sse=5029497.0, rms=2.643 (0.000%)
- 028: dt: 0.2500, sse=4918106.5, rms=2.197 (0.000%)
- 029: dt: 0.2500, sse=4975793.0, rms=1.864 (0.000%)
- rms = 1.92, time step reduction 2 of 3 to 0.125...
- 030: dt: 0.1250, sse=4901236.0, rms=1.721 (0.000%)
- 031: dt: 0.1250, sse=4798075.0, rms=1.525 (0.000%)
- rms = 1.51, time step reduction 3 of 3 to 0.062...
- 032: dt: 0.1250, sse=4759845.5, rms=1.507 (0.000%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 3 vertex label from ripped group
- mean border=80.5, 27 (0) missing vertices, mean dist -0.0 [0.2 (%58.4)->0.2 (%41.6))]
- %93 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/sub005/surf/rh.white...
- writing smoothed curvature to rh.curv
- 000: dt: 0.0000, sse=4783962.0, rms=1.86
- rms = 2.90, time step reduction 1 of 3 to 0.250...
- 033: dt: 0.2500, sse=4886889.0, rms=1.227 (0.000%)
- 034: dt: 0.2500, sse=5051746.0, rms=1.116 (0.000%)
- rms = 1.11, time step reduction 2 of 3 to 0.125...
- 035: dt: 0.2500, sse=5147129.5, rms=1.115 (0.000%)
- rms = 1.09, time step reduction 3 of 3 to 0.062...
- 036: dt: 0.1250, sse=5181376.0, rms=1.094 (0.000%)
- positioning took 0.6 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- generating cortex label...
- 10 non-cortical segments detected
- only using segment with 1811 vertices
- erasing segment 1 (vno[0] = 64919)
- erasing segment 2 (vno[0] = 65987)
- erasing segment 3 (vno[0] = 87960)
- erasing segment 4 (vno[0] = 90268)
- erasing segment 5 (vno[0] = 95842)
- erasing segment 6 (vno[0] = 101342)
- erasing segment 7 (vno[0] = 101668)
- erasing segment 8 (vno[0] = 107056)
- erasing segment 9 (vno[0] = 113300)
- writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/rh.cortex.label...
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.curv
- writing smoothed area to rh.area
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.area
- vertex spacing 0.90 +- 0.25 (0.04-->3.45) (max @ vno 16176 --> 26838)
- face area 0.34 +- 0.16 (0.00-->1.92)
- refinement took 7.0 minutes
- #--------------------------------------------
- #@# Smooth2 rh Thu Aug 8 20:30:00 CEST 2013
- mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
- smoothing for 3 iterations
- setting seed for random number generator to 1234
- smoothing surface tessellation for 3 iterations...
- smoothing complete - recomputing first and second fundamental forms...
- #--------------------------------------------
- #@# Inflation2 rh Thu Aug 8 20:30:05 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
- mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated
- avg radius = 46.9 mm, total surface area = 86834 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=0.058 (target=0.015)
step 015: RMS=0.048 (target=0.015)
step 020: RMS=0.039 (target=0.015)
step 025: RMS=0.033 (target=0.015)
step 030: RMS=0.027 (target=0.015)
step 035: RMS=0.022 (target=0.015)
step 040: RMS=0.019 (target=0.015)
step 045: RMS=0.018 (target=0.015)
step 050: RMS=0.016 (target=0.015)
step 055: RMS=0.015 (target=0.015)
- inflation complete.
- inflation took 0.6 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
- 151 vertices thresholded to be in k1 ~ [-0.20 1.09], k2 ~ [-0.08 0.07]
- total integrated curvature = 0.660*4pi (8.297) --> 0 handles
- ICI = 1.7, FI = 10.8, variation=182.011
- 123 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
- 118 vertices thresholded to be in [-0.11 0.24]
- done.
- writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.016, std = 0.023
- done.
- #-----------------------------------------
- #@# Curvature Stats rh Thu Aug 8 20:32:31 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub005 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 [ sub005/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 [ 270 ]
- Gb_filter = 0
- WARN: S lookup min: -0.130205
- WARN: S explicit min: 0.000000 vertex = 162
- #--------------------------------------------
- #@# Sphere rh Thu Aug 8 20:32:36 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 0.282...
- MRISunfold() max_passes = 1 -------
- tol=5.0e-01, sigma=0.0, host=snake, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
- using quadratic fit line minimization
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 1.000000
- desired_rms_height -1.000000
- momentum 0.900000
- nbhd_size 7
- max_nbrs 8
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 1234
- --------------------
- mrisRemoveNegativeArea()
- pass 1: epoch 1 of 3 starting distance error %21.20
- pass 1: epoch 2 of 3 starting distance error %21.15
- unfolding complete - removing small folds...
- starting distance error %21.07
- removing remaining folds...
- final distance error %21.09
- MRISunfold() return, current seed 1234
- writing spherical brain to ../surf/rh.sphere
- spherical transformation took 1.12 hours
- #--------------------------------------------
- #@# Surf Reg rh Thu Aug 8 21:40:02 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 = 0.576
- curvature mean = 0.032, std = 0.936
- curvature mean = 0.024, std = 0.848
- Starting MRISrigidBodyAlignGlobal()
- d=64.00 min @ (16.00, 0.00, 0.00) sse = 379358.7, tmin=1.1240
- d=32.00 min @ (0.00, -8.00, 0.00) sse = 276429.3, tmin=2.2516
- d=16.00 min @ (-4.00, 0.00, 0.00) sse = 261174.7, tmin=3.3972
- d=8.00 min @ (2.00, 0.00, 0.00) sse = 259918.8, tmin=4.5631
- d=4.00 min @ (-1.00, 0.00, 0.00) sse = 258530.6, tmin=5.7408
- d=2.00 min @ (0.00, -0.50, -0.50) sse = 257876.9, tmin=6.9290
- d=1.00 min @ (0.00, 0.00, 0.25) sse = 257809.8, tmin=8.1105
- d=0.50 min @ (0.00, 0.00, -0.12) sse = 257800.2, tmin=9.2995
- tol=1.0e+00, sigma=0.5, host=snake, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
- using quadratic fit line minimization
- MRISrigidBodyAlignGlobal() done 9.30 min
- curvature mean = 0.003, std = 0.940
- curvature mean = 0.012, std = 0.934
- curvature mean = -0.003, std = 0.946
- curvature mean = 0.006, std = 0.969
- curvature mean = -0.004, std = 0.946
- curvature mean = 0.001, std = 0.987
- 2 Reading smoothwm
- curvature mean = -0.026, std = 0.339
- curvature mean = 0.005, std = 0.070
- curvature mean = 0.066, std = 0.291
- curvature mean = 0.006, std = 0.083
- curvature mean = 0.033, std = 0.463
- curvature mean = 0.006, std = 0.089
- curvature mean = 0.018, std = 0.596
- curvature mean = 0.007, std = 0.090
- curvature mean = 0.006, std = 0.707
- MRISregister() return, current seed 0
- writing registered surface to ../surf/rh.sphere.reg...
- expanding nbhd size to 1
- #--------------------------------------------
- #@# Jacobian white rh Thu Aug 8 22:09:57 CEST 2013
- mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white
- reading surface from ../surf/rh.white...
- writing curvature file ../surf/rh.jacobian_white
- #--------------------------------------------
- #@# AvgCurv rh Thu Aug 8 22:09:59 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
- mrisp_paint -a 5 /opt/freesurfer/5.3.0/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv
- averaging curvature patterns 5 times...
- reading surface from ../surf/rh.sphere.reg...
- reading template parameterization from /opt/freesurfer/5.3.0/average/rh.average.curvature.filled.buckner40.tif...
- writing curvature file to ../surf/rh.avg_curv...
- #-----------------------------------------
- #@# Cortical Parc rh Thu Aug 8 22:10:01 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub005 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...
- 1263 labels changed using aseg
- relabeling using gibbs priors...
- 000: 3060 changed, 142731 examined...
- 001: 693 changed, 13043 examined...
- 002: 182 changed, 3884 examined...
- 003: 63 changed, 1039 examined...
- 004: 33 changed, 395 examined...
- 005: 15 changed, 211 examined...
- 006: 7 changed, 82 examined...
- 007: 3 changed, 46 examined...
- 008: 3 changed, 17 examined...
- 009: 2 changed, 16 examined...
- 010: 1 changed, 12 examined...
- 011: 0 changed, 10 examined...
- 179 labels changed using aseg
- 000: 106 total segments, 69 labels (430 vertices) changed
- 001: 41 total segments, 4 labels (9 vertices) changed
- 002: 37 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 34 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 1537 vertices marked for relabeling...
- 1537 labels changed in reclassification.
- writing output to ../label/rh.aparc.annot...
- classification took 1 minutes and 4 seconds.
- #--------------------------------------------
- #@# Make Pial Surf rh Thu Aug 8 22:11:05 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
- mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub005 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/sub005/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz...
- 17487 bright wm thresholded.
- 908 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.orig...
- computing class statistics...
- border white: 254363 voxels (1.52%)
- border gray 296177 voxels (1.77%)
- WM (91.0): 92.5 +- 10.3 [70.0 --> 110.0]
- GM (74.0) : 72.5 +- 12.8 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 44.2 (was 70)
- setting MAX_BORDER_WHITE to 115.3 (was 105)
- setting MIN_BORDER_WHITE to 57.0 (was 85)
- setting MAX_CSF to 31.3 (was 40)
- setting MAX_GRAY to 94.7 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 50.6 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 18.5 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=105, GM=57
- mean inside = 92.4, mean outside = 67.6
- 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/sub005/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.81 +- 0.22 (0.01-->3.89) (max @ vno 16176 --> 26838)
- face area 0.27 +- 0.12 (0.00-->1.52)
- mean absolute distance = 0.64 +- 0.71
- 4497 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 21 points - only 0.00% unknown
- deleting segment 3 with 407 points - only 0.00% unknown
- deleting segment 4 with 6 points - only 0.00% unknown
- deleting segment 5 with 15 points - only 0.00% unknown
- deleting segment 6 with 35 points - only 0.00% unknown
- deleting segment 8 with 131 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- removing 1 vertex label from ripped group
- deleting segment 10 with 1 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 11 with 3 points - only 0.00% unknown
- mean border=71.5, 17 (17) missing vertices, mean dist 0.4 [0.4 (%30.8)->0.7 (%69.2))]
- %78 local maxima, %18 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 (0.08-->3.85) (max @ vno 100129 --> 101238)
- face area 0.27 +- 0.13 (0.00-->1.99)
- mean absolute distance = 0.29 +- 0.43
- 2898 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=7974956.0, rms=13.81
- 001: dt: 0.5000, sse=8051567.5, rms=9.964 (0.000%)
- 002: dt: 0.5000, sse=8390382.0, rms=7.816 (0.000%)
- 003: dt: 0.5000, sse=8513470.0, rms=6.464 (0.000%)
- 004: dt: 0.5000, sse=8805081.0, rms=5.650 (0.000%)
- 005: dt: 0.5000, sse=8847354.0, rms=5.173 (0.000%)
- 006: dt: 0.5000, sse=9017397.0, rms=4.899 (0.000%)
- 007: dt: 0.5000, sse=8997915.0, rms=4.750 (0.000%)
- 008: dt: 0.5000, sse=9087754.0, rms=4.635 (0.000%)
- 009: dt: 0.5000, sse=8963565.0, rms=4.578 (0.000%)
- 010: dt: 0.5000, sse=9031501.0, rms=4.510 (0.000%)
- rms = 4.49, time step reduction 1 of 3 to 0.250...
- 011: dt: 0.5000, sse=8915012.0, rms=4.491 (0.000%)
- 012: dt: 0.2500, sse=5827361.5, rms=3.157 (0.000%)
- 013: dt: 0.2500, sse=5342220.0, rms=2.702 (0.000%)
- 014: dt: 0.2500, sse=5041012.5, rms=2.594 (0.000%)
- 015: dt: 0.2500, sse=4959373.0, rms=2.504 (0.000%)
- rms = 2.47, time step reduction 2 of 3 to 0.125...
- 016: dt: 0.2500, sse=4856800.0, rms=2.472 (0.000%)
- 017: dt: 0.1250, sse=4602698.0, rms=2.221 (0.000%)
- rms = 2.19, time step reduction 3 of 3 to 0.062...
- 018: dt: 0.1250, sse=4552583.0, rms=2.186 (0.000%)
- positioning took 2.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 24 points - only 0.00% unknown
- deleting segment 2 with 337 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 4 with 14 points - only 0.00% unknown
- deleting segment 5 with 21 points - only 0.00% unknown
- deleting segment 6 with 82 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- removing 1 vertex label from ripped group
- deleting segment 10 with 1 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 11 with 2 points - only 0.00% unknown
- mean border=76.1, 36 (0) missing vertices, mean dist -0.2 [0.3 (%78.7)->0.2 (%21.3))]
- %87 local maxima, % 9 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 (0.03-->3.41) (max @ vno 16176 --> 26838)
- face area 0.35 +- 0.16 (0.00-->2.12)
- mean absolute distance = 0.21 +- 0.29
- 2731 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5578387.0, rms=6.06
- 019: dt: 0.5000, sse=5803824.0, rms=4.075 (0.000%)
- rms = 4.63, time step reduction 1 of 3 to 0.250...
- 020: dt: 0.2500, sse=5297082.0, rms=2.913 (0.000%)
- 021: dt: 0.2500, sse=5130555.0, rms=2.431 (0.000%)
- 022: dt: 0.2500, sse=5050317.0, rms=2.056 (0.000%)
- rms = 2.03, time step reduction 2 of 3 to 0.125...
- 023: dt: 0.2500, sse=5033606.5, rms=2.025 (0.000%)
- 024: dt: 0.1250, sse=4846455.0, rms=1.777 (0.000%)
- rms = 1.74, time step reduction 3 of 3 to 0.062...
- 025: dt: 0.1250, sse=4789915.5, rms=1.745 (0.000%)
- positioning took 0.9 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 26 points - only 0.00% unknown
- deleting segment 1 with 347 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 3 with 14 points - only 0.00% unknown
- deleting segment 4 with 35 points - only 0.00% unknown
- deleting segment 5 with 96 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- deleting segment 7 with 2 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 8 with 2 points - only 0.00% unknown
- mean border=79.4, 36 (0) missing vertices, mean dist -0.1 [0.2 (%76.3)->0.2 (%23.7))]
- %92 local maxima, % 3 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 (0.05-->3.40) (max @ vno 16176 --> 26838)
- face area 0.34 +- 0.16 (0.00-->1.90)
- mean absolute distance = 0.16 +- 0.24
- 3015 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5188923.0, rms=4.29
- 026: dt: 0.5000, sse=5556812.0, rms=4.194 (0.000%)
- rms = 4.45, time step reduction 1 of 3 to 0.250...
- 027: dt: 0.2500, sse=5059351.0, rms=2.643 (0.000%)
- 028: dt: 0.2500, sse=4949751.0, rms=2.198 (0.000%)
- 029: dt: 0.2500, sse=5007317.0, rms=1.866 (0.000%)
- rms = 1.93, time step reduction 2 of 3 to 0.125...
- 030: dt: 0.1250, sse=4932588.0, rms=1.724 (0.000%)
- 031: dt: 0.1250, sse=4830113.5, rms=1.528 (0.000%)
- rms = 1.51, time step reduction 3 of 3 to 0.062...
- 032: dt: 0.1250, sse=4792010.5, rms=1.511 (0.000%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 27 points - only 0.00% unknown
- deleting segment 1 with 357 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 3 with 14 points - only 0.00% unknown
- deleting segment 4 with 38 points - only 0.00% unknown
- deleting segment 5 with 97 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- deleting segment 7 with 2 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 8 with 3 points - only 0.00% unknown
- mean border=80.4, 44 (0) missing vertices, mean dist -0.0 [0.2 (%58.3)->0.2 (%41.7))]
- %94 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=4816013.0, rms=1.86
- rms = 2.89, time step reduction 1 of 3 to 0.250...
- 033: dt: 0.2500, sse=4921099.0, rms=1.229 (0.000%)
- 034: dt: 0.2500, sse=5086477.0, rms=1.120 (0.000%)
- rms = 1.12, time step reduction 2 of 3 to 0.125...
- 035: dt: 0.2500, sse=5182359.5, rms=1.118 (0.000%)
- rms = 1.10, time step reduction 3 of 3 to 0.062...
- 036: dt: 0.1250, sse=5216694.0, rms=1.098 (0.000%)
- positioning took 0.6 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- smoothing surface for 5 iterations...
- mean border=47.0, 17 (17) missing vertices, mean dist 1.6 [0.1 (%0.0)->2.5 (%100.0))]
- %13 local maxima, %49 large gradients and %34 min vals, 1981 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=32687258.0, rms=32.87
- 001: dt: 0.5000, sse=23541896.0, rms=27.294 (0.000%)
- 002: dt: 0.5000, sse=17181850.0, rms=22.662 (0.000%)
- 003: dt: 0.5000, sse=12882107.0, rms=18.921 (0.000%)
- 004: dt: 0.5000, sse=10166871.0, rms=15.962 (0.000%)
- 005: dt: 0.5000, sse=8560958.0, rms=13.686 (0.000%)
- 006: dt: 0.5000, sse=7721739.0, rms=11.966 (0.000%)
- 007: dt: 0.5000, sse=7264538.5, rms=10.538 (0.000%)
- 008: dt: 0.5000, sse=6987229.0, rms=9.271 (0.000%)
- 009: dt: 0.5000, sse=6821755.0, rms=8.116 (0.000%)
- 010: dt: 0.5000, sse=6813513.0, rms=7.128 (0.000%)
- 011: dt: 0.5000, sse=6887935.5, rms=6.267 (0.000%)
- 012: dt: 0.5000, sse=7026273.0, rms=5.592 (0.000%)
- 013: dt: 0.5000, sse=7175993.5, rms=5.107 (0.000%)
- 014: dt: 0.5000, sse=7383276.0, rms=4.783 (0.000%)
- 015: dt: 0.5000, sse=7477753.5, rms=4.552 (0.000%)
- 016: dt: 0.5000, sse=7615588.5, rms=4.414 (0.000%)
- 017: dt: 0.5000, sse=7696858.0, rms=4.308 (0.000%)
- 018: dt: 0.5000, sse=7721887.0, rms=4.250 (0.000%)
- 019: dt: 0.5000, sse=7753909.5, rms=4.193 (0.000%)
- rms = 4.16, time step reduction 1 of 3 to 0.250...
- 020: dt: 0.5000, sse=7737565.0, rms=4.163 (0.000%)
- 021: dt: 0.2500, sse=5664220.0, rms=3.557 (0.000%)
- 022: dt: 0.2500, sse=5510557.0, rms=3.383 (0.000%)
- rms = 3.37, time step reduction 2 of 3 to 0.125...
- 023: dt: 0.2500, sse=5390627.0, rms=3.371 (0.000%)
- 024: dt: 0.1250, sse=5130935.0, rms=3.255 (0.000%)
- rms = 3.24, time step reduction 3 of 3 to 0.062...
- 025: dt: 0.1250, sse=5100158.5, rms=3.240 (0.000%)
- positioning took 3.2 minutes
- mean border=45.2, 1262 (1) missing vertices, mean dist 0.1 [0.2 (%51.6)->0.6 (%48.4))]
- %27 local maxima, %40 large gradients and %29 min vals, 627 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=5669908.5, rms=4.67
- 026: dt: 0.5000, sse=6032153.5, rms=4.185 (0.000%)
- rms = 4.18, time step reduction 1 of 3 to 0.250...
- 027: dt: 0.5000, sse=7871497.5, rms=4.175 (0.000%)
- 028: dt: 0.2500, sse=5947648.0, rms=3.437 (0.000%)
- 029: dt: 0.2500, sse=6007609.0, rms=3.230 (0.000%)
- rms = 3.21, time step reduction 2 of 3 to 0.125...
- 030: dt: 0.2500, sse=5869163.0, rms=3.211 (0.000%)
- 031: dt: 0.1250, sse=5675499.5, rms=3.045 (0.000%)
- rms = 3.02, time step reduction 3 of 3 to 0.062...
- 032: dt: 0.1250, sse=5653774.5, rms=3.019 (0.000%)
- positioning took 0.9 minutes
- mean border=43.2, 1446 (0) missing vertices, mean dist 0.1 [0.2 (%40.2)->0.4 (%59.8))]
- %46 local maxima, %20 large gradients and %29 min vals, 845 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=5880118.5, rms=4.05
- rms = 4.11, time step reduction 1 of 3 to 0.250...
- 033: dt: 0.2500, sse=5654855.5, rms=3.538 (0.000%)
- 034: dt: 0.2500, sse=5666655.5, rms=3.227 (0.000%)
- 035: dt: 0.2500, sse=5916288.0, rms=3.131 (0.000%)
- rms = 3.11, time step reduction 2 of 3 to 0.125...
- 036: dt: 0.2500, sse=6017766.0, rms=3.107 (0.000%)
- 037: dt: 0.1250, sse=5807498.5, rms=2.969 (0.000%)
- rms = 2.94, time step reduction 3 of 3 to 0.062...
- 038: dt: 0.1250, sse=5821897.5, rms=2.941 (0.000%)
- positioning took 0.9 minutes
- mean border=42.2, 3039 (0) missing vertices, mean dist 0.0 [0.2 (%46.3)->0.3 (%53.7))]
- %49 local maxima, %17 large gradients and %28 min vals, 714 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/sub005/surf/rh.pial...
- writing smoothed curvature to rh.curv.pial
- 000: dt: 0.0000, sse=5880054.5, rms=3.27
- rms = 3.94, time step reduction 1 of 3 to 0.250...
- 039: dt: 0.2500, sse=5762743.0, rms=3.028 (0.000%)
- 040: dt: 0.2500, sse=6033981.0, rms=2.963 (0.000%)
- rms = 2.94, time step reduction 2 of 3 to 0.125...
- 041: dt: 0.2500, sse=6114455.5, rms=2.939 (0.000%)
- 042: dt: 0.1250, sse=5996697.0, rms=2.822 (0.000%)
- rms = 2.80, time step reduction 3 of 3 to 0.062...
- 043: dt: 0.1250, sse=6027581.5, rms=2.799 (0.000%)
- positioning took 0.8 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.curv.pial
- writing smoothed area to rh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.area.pial
- vertex spacing 1.02 +- 0.44 (0.08-->10.36) (max @ vno 100313 --> 100290)
- face area 0.41 +- 0.31 (0.00-->8.44)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 142731 vertices processed
- 25000 of 142731 vertices processed
- 50000 of 142731 vertices processed
- 75000 of 142731 vertices processed
- 100000 of 142731 vertices processed
- 125000 of 142731 vertices processed
- 0 of 142731 vertices processed
- 25000 of 142731 vertices processed
- 50000 of 142731 vertices processed
- 75000 of 142731 vertices processed
- 100000 of 142731 vertices processed
- 125000 of 142731 vertices processed
- thickness calculation complete, 509:894 truncations.
- 26532 vertices at 0 distance
- 86068 vertices at 1 distance
- 94051 vertices at 2 distance
- 45703 vertices at 3 distance
- 15020 vertices at 4 distance
- 4402 vertices at 5 distance
- 1461 vertices at 6 distance
- 497 vertices at 7 distance
- 208 vertices at 8 distance
- 99 vertices at 9 distance
- 69 vertices at 10 distance
- 54 vertices at 11 distance
- 42 vertices at 12 distance
- 31 vertices at 13 distance
- 41 vertices at 14 distance
- 27 vertices at 15 distance
- 22 vertices at 16 distance
- 30 vertices at 17 distance
- 15 vertices at 18 distance
- 26 vertices at 19 distance
- 30 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.thickness
- positioning took 14.0 minutes
- #--------------------------------------------
- #@# Surf Volume rh Thu Aug 8 22:25:08 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf
- mris_calc -o rh.area.mid rh.area add rh.area.pial
- Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o rh.area.mid rh.area.mid div 2
- Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o rh.volume rh.area.mid mul rh.thickness
- Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ]
- #-----------------------------------------
- #@# WM/GM Contrast rh Thu Aug 8 22:25:08 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
- pctsurfcon --s sub005 --rh-only
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts/pctsurfcon.log
- Thu Aug 8 22:25:08 CEST 2013
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
- /opt/freesurfer/5.3.0/bin/pctsurfcon
- $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $
- Linux snake4 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
- FREESURFER_HOME /opt/freesurfer/5.3.0
- mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/tmp.pctsurfcon.3128/rh.wm.mgh --regheader sub005 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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/sub005/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/rh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 = 109659
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/rh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/tmp.pctsurfcon.3128/rh.wm.mgh
- Dim: 142731 1 1
- mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/tmp.pctsurfcon.3128/rh.gm.mgh --projfrac 0.3 --regheader sub005 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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/sub005/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/rh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white
- Done reading source surface
- Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 = 126459
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/rh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/tmp.pctsurfcon.3128/rh.gm.mgh
- Dim: 142731 1 1
- mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/tmp.pctsurfcon.3128/rh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/tmp.pctsurfcon.3128/rh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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/sub005/surf/rh.w-g.pct.mgh
- mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.w-g.pct.mgh --annot sub005 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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/sub005/surf/rh.w-g.pct.mgh --annot sub005 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/stats/rh.w-g.pct.stats --snr
- sysname Linux
- hostname snake4
- machine x86_64
- user fkaule
- UseRobust 0
- Constructing seg from annotation
- Reading annotation
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
- Seg base 2000
- Loading /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.w-g.pct.mgh
- Vertex Area is 0.668906 mm^3
- Generating list of segmentation ids
- Found 36 segmentations
- Computing statistics for each segmentation
- 0 2000 unknown 0 0.000
- 1 2001 bankssts 1466 1011.292
- 2 2002 caudalanteriorcingulate 1392 963.256
- 3 2003 caudalmiddlefrontal 2933 1968.508
- 4 2004 corpuscallosum 0 0.000
- 5 2005 cuneus 2742 1828.445
- 6 2006 entorhinal 409 296.847
- 7 2007 fusiform 4234 2918.080
- 8 2008 inferiorparietal 7531 5073.565
- 9 2009 inferiortemporal 4962 3371.515
- 10 2010 isthmuscingulate 1391 913.005
- 11 2011 lateraloccipital 8721 5637.396
- 12 2012 lateralorbitofrontal 3882 2586.580
- 13 2013 lingual 5061 3518.732
- 14 2014 medialorbitofrontal 2758 1879.153
- 15 2015 middletemporal 5832 3893.341
- 16 2016 parahippocampal 1017 695.444
- 17 2017 paracentral 2053 1357.055
- 18 2018 parsopercularis 2225 1508.707
- 19 2019 parsorbitalis 1283 864.903
- 20 2020 parstriangularis 2251 1520.839
- 21 2021 pericalcarine 2693 1885.410
- 22 2022 postcentral 7051 4680.771
- 23 2023 posteriorcingulate 2072 1355.862
- 24 2024 precentral 7509 4989.827
- 25 2025 precuneus 6367 4323.134
- 26 2026 rostralanteriorcingulate 1172 801.977
- 27 2027 rostralmiddlefrontal 9311 6297.768
- 28 2028 superiorfrontal 11943 8113.219
- 29 2029 superiorparietal 8560 5645.194
- 30 2030 superiortemporal 6303 4164.996
- 31 2031 supramarginal 5440 3636.528
- 32 2032 frontalpole 440 298.384
- 33 2033 temporalpole 609 439.274
- 34 2034 transversetemporal 586 359.799
- 35 2035 insula 3048 1982.912
- Reporting on 34 segmentations
- mri_segstats done
- Cleaning up
- #-----------------------------------------
- #@# Parcellation Stats rh Thu Aug 8 22:25:22 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 sub005 rh white
- computing statistics for each annotation in ../label/rh.aparc.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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
- 1466 1011 2843 2.862 0.444 0.123 0.031 12 2.0 bankssts
- 1392 963 2920 2.794 0.861 0.162 0.047 32 2.6 caudalanteriorcingulate
- 2933 1969 5442 2.524 0.420 0.135 0.045 41 4.9 caudalmiddlefrontal
- 2742 1828 4417 2.135 0.463 0.186 0.068 63 8.2 cuneus
- 409 297 1418 3.459 0.640 0.181 0.065 8 1.1 entorhinal
- 4234 2918 8870 2.747 0.626 0.162 0.066 93 10.4 fusiform
- 7531 5074 14195 2.456 0.488 0.152 0.059 161 17.2 inferiorparietal
- 4962 3372 10567 2.743 0.649 0.166 0.081 127 15.5 inferiortemporal
- 1391 913 2984 2.722 0.737 0.168 0.073 33 3.7 isthmuscingulate
- 8721 5637 14933 2.342 0.487 0.159 0.063 184 21.4 lateraloccipital
- 3882 2587 7910 2.706 0.679 0.153 0.072 75 11.5 lateralorbitofrontal
- 5061 3519 8685 2.272 0.570 0.179 0.076 121 15.5 lingual
- 2758 1879 5533 2.555 0.737 0.170 0.094 87 10.8 medialorbitofrontal
- 5832 3893 14311 3.017 0.593 0.155 0.061 126 14.2 middletemporal
- 1017 695 2693 3.388 0.725 0.164 0.082 19 2.7 parahippocampal
- 2053 1357 3598 2.404 0.521 0.128 0.040 25 3.7 paracentral
- 2225 1509 4406 2.626 0.412 0.151 0.054 41 5.0 parsopercularis
- 1283 865 2929 2.632 0.624 0.169 0.074 35 3.7 parsorbitalis
- 2251 1521 4403 2.572 0.544 0.151 0.076 48 5.0 parstriangularis
- 2693 1885 3347 1.868 0.385 0.154 0.060 41 6.6 pericalcarine
- 7051 4681 12337 2.291 0.666 0.146 0.052 123 15.2 postcentral
- 2072 1356 3583 2.553 0.782 0.152 0.053 37 4.3 posteriorcingulate
- 7509 4990 14781 2.617 0.529 0.131 0.040 100 12.6 precentral
- 6367 4323 11532 2.516 0.534 0.160 0.104 181 16.1 precuneus
- 1172 802 2983 3.140 0.563 0.186 0.074 36 3.3 rostralanteriorcingulate
- 9311 6298 18017 2.411 0.516 0.174 0.083 262 27.8 rostralmiddlefrontal
- 11943 8113 24982 2.643 0.527 0.148 0.049 204 24.7 superiorfrontal
- 8560 5645 13489 2.166 0.385 0.134 0.046 150 15.9 superiorparietal
- 6303 4165 14776 3.025 0.565 0.131 0.044 83 10.8 superiortemporal
- 5440 3637 10297 2.539 0.506 0.147 0.050 101 11.1 supramarginal
- 440 298 1089 2.682 0.473 0.235 0.149 24 2.0 frontalpole
- 609 439 2191 3.708 0.776 0.194 0.112 18 2.7 temporalpole
- 586 360 1196 2.869 0.399 0.140 0.043 8 1.1 transversetemporal
- 3048 1983 6248 3.030 0.721 0.146 0.132 122 9.1 insula
- #-----------------------------------------
- #@# Cortical Parc 2 rh Thu Aug 8 22:25:40 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub005 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...
- 1 labels changed using aseg
- relabeling using gibbs priors...
- 000: 10303 changed, 142731 examined...
- 001: 2418 changed, 39284 examined...
- 002: 725 changed, 12393 examined...
- 003: 309 changed, 4022 examined...
- 004: 137 changed, 1713 examined...
- 005: 71 changed, 771 examined...
- 006: 32 changed, 398 examined...
- 007: 14 changed, 171 examined...
- 008: 6 changed, 73 examined...
- 009: 1 changed, 33 examined...
- 010: 0 changed, 7 examined...
- 1 labels changed using aseg
- 000: 280 total segments, 198 labels (2806 vertices) changed
- 001: 91 total segments, 10 labels (85 vertices) changed
- 002: 81 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 170 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 1015 vertices marked for relabeling...
- 1015 labels changed in reclassification.
- writing output to ../label/rh.aparc.a2009s.annot...
- classification took 1 minutes and 12 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 2 rh Thu Aug 8 22:26:52 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 sub005 rh white
- computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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
- 1108 756 2276 2.516 0.659 0.190 0.096 35 3.8 G_and_S_frontomargin
- 1549 1024 3239 2.627 0.567 0.172 0.063 32 4.0 G_and_S_occipital_inf
- 1222 811 2579 2.497 0.536 0.144 0.052 22 2.7 G_and_S_paracentral
- 1584 1077 3694 2.983 0.569 0.178 0.068 40 4.2 G_and_S_subcentral
- 1041 722 2191 2.400 0.478 0.209 0.114 45 4.3 G_and_S_transv_frontopol
- 3083 2124 6447 2.783 0.627 0.150 0.051 60 6.4 G_and_S_cingul-Ant
- 1743 1230 3628 2.861 0.606 0.143 0.044 28 3.0 G_and_S_cingul-Mid-Ant
- 1618 1066 3101 2.762 0.553 0.140 0.045 23 2.9 G_and_S_cingul-Mid-Post
- 583 391 1516 3.170 0.616 0.182 0.075 13 1.8 G_cingul-Post-dorsal
- 308 216 907 3.088 0.494 0.180 0.083 8 0.9 G_cingul-Post-ventral
- 2424 1653 3889 2.027 0.462 0.186 0.068 58 7.1 G_cuneus
- 1253 880 3286 2.796 0.384 0.175 0.068 37 3.5 G_front_inf-Opercular
- 453 281 1074 2.807 0.388 0.157 0.067 13 1.2 G_front_inf-Orbital
- 1146 767 2911 2.875 0.525 0.182 0.120 40 3.4 G_front_inf-Triangul
- 4282 2878 9989 2.613 0.466 0.186 0.096 135 13.7 G_front_middle
- 7812 5249 17851 2.690 0.535 0.162 0.062 167 19.9 G_front_sup
- 390 231 858 3.242 0.844 0.142 0.131 27 1.8 G_Ins_lg_and_S_cent_ins
- 492 334 1657 3.445 0.769 0.205 0.130 20 2.2 G_insular_short
- 2484 1587 5560 2.651 0.431 0.181 0.079 73 7.6 G_occipital_middle
- 2166 1376 3595 2.218 0.372 0.138 0.048 42 4.2 G_occipital_sup
- 1465 977 3183 2.673 0.588 0.179 0.086 42 4.3 G_oc-temp_lat-fusifor
- 3441 2387 6426 2.338 0.597 0.202 0.096 104 12.9 G_oc-temp_med-Lingual
- 1347 922 3927 3.392 0.615 0.198 0.225 87 5.2 G_oc-temp_med-Parahip
- 2825 1869 6987 2.844 0.761 0.173 0.090 81 9.6 G_orbital
- 2767 1853 6243 2.630 0.483 0.175 0.084 89 8.5 G_pariet_inf-Angular
- 2999 1989 6905 2.695 0.507 0.159 0.058 74 7.4 G_pariet_inf-Supramar
- 2514 1656 4383 2.177 0.417 0.137 0.055 56 5.2 G_parietal_sup
- 2687 1736 5477 2.442 0.541 0.162 0.062 63 7.2 G_postcentral
- 2735 1754 6735 2.862 0.465 0.139 0.046 45 5.4 G_precentral
- 2549 1693 5430 2.552 0.442 0.184 0.185 129 8.6 G_precuneus
- 685 458 1499 2.414 0.604 0.208 0.129 36 3.5 G_rectus
- 374 237 946 3.492 0.658 0.086 0.032 2 0.4 G_subcallosal
- 524 318 1175 3.038 0.408 0.143 0.045 8 1.0 G_temp_sup-G_T_transv
- 2216 1451 6790 3.273 0.525 0.156 0.066 48 5.3 G_temp_sup-Lateral
- 803 540 2236 3.614 0.548 0.148 0.056 11 1.6 G_temp_sup-Plan_polar
- 653 444 1390 2.803 0.463 0.123 0.035 9 0.9 G_temp_sup-Plan_tempo
- 2620 1772 6373 2.819 0.664 0.190 0.112 98 10.8 G_temporal_inf
- 3481 2316 10197 3.233 0.555 0.178 0.077 104 10.9 G_temporal_middle
- 433 291 554 2.153 0.328 0.103 0.024 2 0.5 Lat_Fis-ant-Horizont
- 158 113 278 2.516 0.396 0.111 0.027 1 0.1 Lat_Fis-ant-Vertical
- 1337 878 1965 2.681 0.452 0.139 0.046 14 2.6 Lat_Fis-post
- 3497 2251 5303 2.118 0.487 0.172 0.074 90 10.2 Pole_occipital
- 1904 1290 5707 3.275 0.754 0.177 0.094 48 7.0 Pole_temporal
- 3123 2185 4083 1.994 0.518 0.153 0.060 51 7.8 S_calcarine
- 3113 2117 3790 1.947 0.568 0.117 0.033 25 4.4 S_central
- 1331 897 2062 2.218 0.436 0.130 0.044 17 2.4 S_cingul-Marginalis
- 431 296 765 2.350 0.543 0.102 0.027 2 0.5 S_circular_insula_ant
- 1472 972 2444 2.834 0.576 0.104 0.027 9 1.8 S_circular_insula_inf
- 1536 1030 2456 2.611 0.424 0.110 0.031 11 2.1 S_circular_insula_sup
- 961 688 1533 2.438 0.422 0.120 0.030 9 1.3 S_collat_transv_ant
- 799 548 1074 2.381 0.488 0.160 0.056 12 1.7 S_collat_transv_post
- 2330 1591 3634 2.315 0.407 0.159 0.056 46 5.5 S_front_inf
- 2032 1370 3355 2.210 0.451 0.139 0.054 46 4.2 S_front_middle
- 2901 1990 4381 2.289 0.397 0.122 0.033 27 4.1 S_front_sup
- 422 273 513 2.178 0.362 0.128 0.034 4 0.6 S_interm_prim-Jensen
- 3092 2104 4297 2.096 0.341 0.125 0.035 36 4.8 S_intrapariet_and_P_trans
- 1401 949 1795 2.019 0.388 0.136 0.041 14 2.3 S_oc_middle_and_Lunatus
- 1895 1251 2820 2.315 0.386 0.123 0.032 20 2.5 S_oc_sup_and_transversal
- 885 598 1491 2.553 0.382 0.132 0.038 11 1.4 S_occipital_ant
- 797 561 1483 2.375 0.461 0.145 0.044 13 1.3 S_oc-temp_lat
- 1772 1259 3190 2.769 0.570 0.127 0.034 15 2.6 S_oc-temp_med_and_Lingual
- 450 314 821 2.505 0.712 0.184 0.077 10 1.5 S_orbital_lateral
- 753 542 1293 2.471 0.675 0.113 0.030 6 0.8 S_orbital_med-olfact
- 1514 1011 2576 2.517 0.533 0.159 0.075 27 5.2 S_orbital-H_Shaped
- 3033 2023 4590 2.512 0.573 0.141 0.048 39 5.8 S_parieto_occipital
- 1733 1106 2170 2.203 0.868 0.150 0.051 33 3.1 S_pericallosal
- 2790 1867 3906 2.182 0.423 0.124 0.039 30 4.4 S_postcentral
- 2078 1365 3190 2.500 0.359 0.133 0.044 25 3.6 S_precentral-inf-part
- 1550 1044 2302 2.351 0.395 0.110 0.024 10 1.7 S_precentral-sup-part
- 546 387 1188 2.761 0.685 0.199 0.128 19 3.4 S_suborbital
- 1409 949 2539 2.483 0.419 0.152 0.054 27 3.1 S_subparietal
- 1527 1037 2351 2.573 0.517 0.127 0.032 13 2.2 S_temporal_inf
- 6414 4323 10724 2.609 0.502 0.120 0.032 56 8.4 S_temporal_sup
- 402 288 735 2.728 0.391 0.101 0.017 2 0.3 S_temporal_transverse
- #-----------------------------------------
- #@# Cortical Parc 3 rh Thu Aug 8 22:27:12 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub005 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...
- 868 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2762 changed, 142731 examined...
- 001: 620 changed, 11882 examined...
- 002: 150 changed, 3350 examined...
- 003: 56 changed, 873 examined...
- 004: 29 changed, 336 examined...
- 005: 21 changed, 188 examined...
- 006: 11 changed, 112 examined...
- 007: 6 changed, 56 examined...
- 008: 2 changed, 28 examined...
- 009: 2 changed, 12 examined...
- 010: 3 changed, 14 examined...
- 011: 1 changed, 10 examined...
- 012: 2 changed, 8 examined...
- 013: 4 changed, 9 examined...
- 014: 2 changed, 17 examined...
- 015: 4 changed, 16 examined...
- 016: 5 changed, 22 examined...
- 017: 3 changed, 25 examined...
- 018: 2 changed, 17 examined...
- 019: 2 changed, 10 examined...
- 020: 4 changed, 15 examined...
- 021: 4 changed, 20 examined...
- 022: 6 changed, 19 examined...
- 023: 2 changed, 24 examined...
- 024: 0 changed, 14 examined...
- 123 labels changed using aseg
- 000: 60 total segments, 27 labels (142 vertices) changed
- 001: 33 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 38 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 882 vertices marked for relabeling...
- 882 labels changed in reclassification.
- writing output to ../label/rh.aparc.DKTatlas40.annot...
- classification took 1 minutes and 3 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 3 rh Thu Aug 8 22:28:15 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 sub005 rh white
- computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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
- 1481 1023 3113 2.785 0.879 0.164 0.048 34 2.8 caudalanteriorcingulate
- 3008 2012 5518 2.522 0.418 0.136 0.045 42 5.0 caudalmiddlefrontal
- 3414 2266 5375 2.168 0.474 0.179 0.062 75 9.3 cuneus
- 476 348 1547 3.386 0.667 0.177 0.063 9 1.3 entorhinal
- 3620 2523 7105 2.663 0.563 0.158 0.062 77 8.1 fusiform
- 7071 4757 13141 2.429 0.488 0.150 0.058 149 15.8 inferiorparietal
- 5470 3706 12225 2.807 0.682 0.168 0.083 141 17.7 inferiortemporal
- 1456 951 3021 2.667 0.747 0.159 0.067 30 3.5 isthmuscingulate
- 9060 5834 15587 2.343 0.492 0.160 0.063 195 22.6 lateraloccipital
- 4314 2878 9192 2.727 0.706 0.163 0.079 98 13.4 lateralorbitofrontal
- 5028 3488 8609 2.273 0.571 0.177 0.075 119 15.2 lingual
- 2228 1510 4623 2.599 0.779 0.170 0.093 72 9.0 medialorbitofrontal
- 6930 4654 16399 2.990 0.569 0.151 0.057 137 15.9 middletemporal
- 1013 692 2666 3.367 0.724 0.164 0.082 19 2.7 parahippocampal
- 2206 1456 3926 2.411 0.514 0.128 0.042 28 4.0 paracentral
- 2296 1547 4447 2.602 0.406 0.151 0.056 43 5.2 parsopercularis
- 1376 923 2876 2.597 0.564 0.150 0.059 28 3.2 parsorbitalis
- 2428 1648 4962 2.613 0.550 0.168 0.086 68 6.8 parstriangularis
- 2731 1925 3440 1.870 0.384 0.157 0.064 43 7.1 pericalcarine
- 7512 5021 13182 2.294 0.654 0.146 0.053 138 16.2 postcentral
- 2084 1363 3682 2.633 0.759 0.154 0.054 38 4.4 posteriorcingulate
- 7216 4802 14396 2.640 0.530 0.132 0.040 97 12.1 precentral
- 6437 4368 11732 2.493 0.534 0.158 0.103 185 16.3 precuneus
- 1289 882 3250 3.113 0.561 0.183 0.071 37 3.5 rostralanteriorcingulate
- 6222 4217 11979 2.401 0.498 0.171 0.082 169 18.0 rostralmiddlefrontal
- 15115 10273 30789 2.575 0.537 0.153 0.058 297 35.1 superiorfrontal
- 7177 4734 11399 2.172 0.390 0.134 0.045 120 13.3 superiorparietal
- 8069 5373 19040 3.048 0.613 0.139 0.071 164 16.1 superiortemporal
- 5127 3422 9698 2.542 0.504 0.148 0.050 95 10.4 supramarginal
- 567 346 1170 2.872 0.397 0.139 0.043 8 1.1 transversetemporal
- 2826 1840 5815 2.961 0.706 0.134 0.068 64 7.2 insula
- #--------------------------------------------
- #@# Refine Pial Surfs w/ T2/FLAIR Thu Aug 8 22:28:33 CEST 2013
- bbregister --s sub005 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.lta --init-fsl --T2
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.dat.log
- Thu Aug 8 22:28:33 CEST 2013
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
- /opt/freesurfer/5.3.0/bin/bbregister --s sub005 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.lta --init-fsl --T2
- $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $
- Linux snake4 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
- FREESURFER_HOME /opt/freesurfer/5.3.0
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/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/sub005/mri/orig/T2raw.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.998148, -0.0400878, -0.0457496)
- j_ras = (-0.0459461, 0.989757, 0.135168)
- k_ras = (-0.0398624, -0.13702, 0.989766)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii...
- fslregister --s sub005 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister --dof 6 --fsvol brainmask.mgz
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/reg.init.dat.fslregister.log
- Thu Aug 8 22:28:38 CEST 2013
- --s sub005 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister --dof 6 --fsvol brainmask.mgz
- $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $
- snake4
- Linux snake4 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
- nIters 1
- --------------------------------------
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister/refvol.fslregister.nii
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/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/sub005/mri/brainmask.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, 4.19095e-09, 3.72529e-09)
- j_ras = (7.45058e-09, 1.49012e-08, -1)
- k_ras = (-6.0536e-09, 1, -1.49012e-08)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister/refvol.fslregister.nii...
- --------------------------------------
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister/movvol.fslregister.nii --frame 0
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/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/sub005/mri/transforms/tmp.bbregister.3373/template.nii...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.998148, -0.0400878, -0.0457496)
- j_ras = (-0.0459461, 0.989757, 0.135168)
- k_ras = (-0.0398624, -0.13702, 0.989766)
- keeping frame 0
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister/movvol.fslregister.nii...
- Mov determinant is -0.311072
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
- tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister/movvol.fslregister.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister/reg0.3412.dat --regheader --fslregout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/reg.init.dat.fsl.mat0 --s sub005 --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/sub005/mri/transforms/tmp.bbregister.3373/fslregister/movvol.fslregister.nii
- reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister/reg0.3412.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/sub005/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/sub005/mri/transforms/tmp.bbregister.3373/fslregister/movvol.fslregister.nii
- Tmov: --------------------
- -0.700 0.000 0.000 95.888;
- 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 0.040 0.046 0.000;
- -0.040 -0.137 0.990 0.000;
- 0.046 -0.990 -0.135 -0.000;
- 0.000 0.000 0.000 1.000;
- ---------------------------------------
- ---- Input registration matrix --------
- 0.998 0.040 0.046 0.000;
- -0.040 -0.137 0.990 0.000;
- 0.046 -0.990 -0.135 -0.000;
- 0.000 0.000 0.000 1.000;
- Determinant 1
- subject = sub005
- RegMat ---------------------------
- 0.998 0.040 0.046 0.000;
- -0.040 -0.137 0.990 0.000;
- 0.046 -0.990 -0.135 -0.000;
- 0.000 0.000 0.000 1.000;
- FSLOUTPUTTYPE NIFTI
- tkreg2FSL: mov det = -0.311072, ref det = -1
- Thu Aug 8 22:28:45 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
- flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/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/sub005/mri/transforms/tmp.bbregister.3373/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/reg.init.dat.fsl.mat0
- Thu Aug 8 22:33:07 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
- flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/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/sub005/mri/transforms/tmp.bbregister.3373/reg.init.dat.fsl.mat -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister/fslmat0.trans.mat -schedule /opt/freesurfer/5.3.0/bin/flirt.newdefault.20080811.sch
- tkregister2_cmdl --s sub005 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/reg.init.dat --fslreg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/reg.init.dat.fsl.mat --noedit
- tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl
- ---- FSL registration matrix --------
- 0.998 0.047 0.039 21.016;
- 0.045 -0.142 -0.989 269.550;
- -0.041 0.989 -0.144 23.522;
- 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/sub005/mri/transforms/tmp.bbregister.3373/template.nii
- reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/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/sub005/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/sub005/mri/transforms/tmp.bbregister.3373/template.nii
- Tmov: --------------------
- -0.700 0.000 0.000 95.888;
- 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 = -0.311072, ref det = -1
- ---- Input registration matrix (computed) --------
- 0.998 0.041 0.045 -0.245;
- -0.039 -0.144 0.989 1.084;
- 0.047 -0.989 -0.142 -0.427;
- 0.000 0.000 0.000 1.000;
- ---------------------------------------
- ---- Input registration matrix --------
- 0.998 0.041 0.045 -0.245;
- -0.039 -0.144 0.989 1.084;
- 0.047 -0.989 -0.142 -0.427;
- 0.000 0.000 0.000 1.000;
- Determinant 1
- subject = sub005
- RegMat ---------------------------
- 0.998 0.041 0.045 -0.245;
- -0.039 -0.144 0.989 1.084;
- 0.047 -0.989 -0.142 -0.427;
- 0.000 0.000 0.000 1.000;
-
- Started at Thu Aug 8 22:28:38 CEST 2013
- Ended at Thu Aug 8 22:39:14 CEST 2013
-
- fslregister Done
-
- To check results, run:
- tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/reg.init.dat --surf orig
-
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/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/sub005/scripts
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5
- sysname Linux
- hostname snake4
- machine x86_64
- user fkaule
- movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii
- regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/reg.init.dat
- subject sub005
- dof 6
- outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/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 1376880629
- TransRandMax 0.000000
- RotRandMax 0.000000
- Translations 0.000000 0.000000 0.000000
- Rotations 0.000000 0.000000 0.000000
- Input reg
- 0.998 0.041 0.045 -0.245;
- -0.039 -0.144 0.989 1.084;
- 0.047 -0.989 -0.142 -0.427;
- 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 1.023099
- 1 -25.0 -25.0 25.0 0.979907
- 2 -25.0 25.0 -25.0 1.030559
- 3 -25.0 25.0 25.0 0.988352
- 4 25.0 -25.0 -25.0 1.019131
- 5 25.0 -25.0 25.0 1.007005
- 6 25.0 25.0 -25.0 0.997025
- 7 25.0 25.0 25.0 0.996223
- REL: 8 0.289642 8.041302 1.005163 rel = 0.288155
- Initial costs ----------------
- Number of surface hits 2708
- WM Intensity 62.0586 +/- 9.7971
- Ctx Intensity 75.0981 +/- 11.8063
- Pct Contrast 18.8287 +/- 18.3670
- Cost 0.2896
- RelCost 0.2882
- ------------------------------------
- Brute force preopt -4 4 4, n = 729
- 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9907 0.9907 0.0
- 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.9867 0.9867 0.0
- 6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.9472 0.9472 0.0
- 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.8797 0.8797 0.0
- 21 -4.0000 -4.0000 -4.0000 4.0000 0.0000 -4.0000 0.8635 0.8635 0.0
- 39 -4.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.8061 0.8061 0.0
- 102 -4.0000 0.0000 -4.0000 4.0000 0.0000 -4.0000 0.7972 0.7972 0.0
- 120 -4.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.6820 0.6820 0.0
- 346 0.0000 0.0000 -4.0000 4.0000 0.0000 0.0000 0.6487 0.6487 0.0
- 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.2896 0.2896 0.0
- Brute Force --------------------------
- Min cost was 0.289642
- Number of iterations 729
- Search time 2.071000 sec
- Parameters at best (transmm, rotdeg)
- 0.000 0.000 0.000 0.000 0.000 0.000
- --------------------------------------------
- Starting Powell Minimization
- Init Powel Params dof = 6
- 0 0
- 1 0
- 2 0
- 3 0
- 4 0
- 5 0
- 6 0.382 0.000 0.000 0.000 0.000 0.000 0.2875510287
- 7 0.222 0.000 0.000 0.000 0.000 0.000 0.2849389020
- 9 0.242 0.000 0.000 0.000 0.000 0.000 0.2847667733
- 10 0.295 0.000 0.000 0.000 0.000 0.000 0.2843241020
- 13 0.302 0.000 0.000 0.000 0.000 0.000 0.2842948424
- 15 0.304 0.000 0.000 0.000 0.000 0.000 0.2842915679
- 16 0.305 0.000 0.000 0.000 0.000 0.000 0.2842905660
- 20 0.305 -1.618 0.000 0.000 0.000 0.000 0.2495972257
- 21 0.305 -0.949 0.000 0.000 0.000 0.000 0.2002943882
- 26 0.305 -0.927 0.000 0.000 0.000 0.000 0.2002444441
- 27 0.305 -0.926 0.000 0.000 0.000 0.000 0.2002406533
- 28 0.305 -0.907 0.000 0.000 0.000 0.000 0.2001984559
- 30 0.305 -0.911 0.000 0.000 0.000 0.000 0.2001899098
- 32 0.305 -0.912 0.000 0.000 0.000 0.000 0.2001892511
- 33 0.305 -0.913 0.000 0.000 0.000 0.000 0.2001891441
- 36 0.305 -0.913 1.000 0.000 0.000 0.000 0.1381889852
- 40 0.305 -0.913 0.618 0.000 0.000 0.000 0.1324581935
- 41 0.305 -0.913 0.723 0.000 0.000 0.000 0.1297224871
- 52 0.305 -0.913 0.723 0.186 0.000 0.000 0.1236983204
- 55 0.305 -0.913 0.723 0.205 0.000 0.000 0.1236259223
- 56 0.305 -0.913 0.723 0.201 0.000 0.000 0.1236165933
- 58 0.305 -0.913 0.723 0.202 0.000 0.000 0.1236164808
- 66 0.305 -0.913 0.723 0.202 -0.055 0.000 0.1236023184
- 67 0.305 -0.913 0.723 0.202 -0.028 0.000 0.1233162785
- 69 0.305 -0.913 0.723 0.202 -0.031 0.000 0.1233137649
- 71 0.305 -0.913 0.723 0.202 -0.030 0.000 0.1233131600
- 78 0.305 -0.913 0.723 0.202 -0.030 0.014 0.1232478044
- 80 0.305 -0.913 0.723 0.202 -0.030 0.013 0.1232431079
- 82 0.305 -0.913 0.723 0.202 -0.030 0.011 0.1232418379
- 91 0.131 -0.913 0.723 0.202 -0.030 0.011 0.1215356273
- 92 0.169 -0.913 0.723 0.202 -0.030 0.011 0.1212382536
- 93 0.180 -0.913 0.723 0.202 -0.030 0.011 0.1209722775
- 95 0.201 -0.913 0.723 0.202 -0.030 0.011 0.1207660962
- 96 0.202 -0.913 0.723 0.202 -0.030 0.011 0.1207640196
- 98 0.203 -0.913 0.723 0.202 -0.030 0.011 0.1207634108
- 104 0.203 -0.531 0.723 0.202 -0.030 0.011 0.1199165303
- 105 0.203 -0.712 0.723 0.202 -0.030 0.011 0.1172291128
- 106 0.203 -0.709 0.723 0.202 -0.030 0.011 0.1171359149
- 107 0.203 -0.648 0.723 0.202 -0.030 0.011 0.1149859175
- 109 0.203 -0.646 0.723 0.202 -0.030 0.011 0.1149601028
- 110 0.203 -0.638 0.723 0.202 -0.030 0.011 0.1149341249
- 112 0.203 -0.641 0.723 0.202 -0.030 0.011 0.1149093135
- 114 0.203 -0.640 0.723 0.202 -0.030 0.011 0.1149081895
- 122 0.203 -0.640 0.618 0.202 -0.030 0.011 0.1137925047
- 123 0.203 -0.640 0.637 0.202 -0.030 0.011 0.1133155955
- 124 0.203 -0.640 0.658 0.202 -0.030 0.011 0.1131624220
- 126 0.203 -0.640 0.659 0.202 -0.030 0.011 0.1131607241
- 138 0.203 -0.640 0.659 0.239 -0.030 0.011 0.1117690752
- 139 0.203 -0.640 0.659 0.249 -0.030 0.011 0.1116990746
- 148 0.203 -0.640 0.659 0.249 0.002 0.011 0.1110058374
- 150 0.203 -0.640 0.659 0.249 0.009 0.011 0.1109928885
- 152 0.203 -0.640 0.659 0.249 0.012 0.011 0.1109923277
- 155 0.203 -0.640 0.659 0.249 0.011 0.011 0.1109918560
- 165 0.203 -0.640 0.659 0.249 0.011 0.023 0.1108774772
- 166 0.203 -0.640 0.659 0.249 0.011 0.025 0.1108740055
- 176 0.185 -0.640 0.659 0.249 0.011 0.025 0.1104775027
- 178 0.148 -0.640 0.659 0.249 0.011 0.025 0.1101365746
- 179 0.147 -0.640 0.659 0.249 0.011 0.025 0.1101230889
- 181 0.141 -0.640 0.659 0.249 0.011 0.025 0.1101047797
- 182 0.142 -0.640 0.659 0.249 0.011 0.025 0.1101038582
- 193 0.142 -0.637 0.659 0.249 0.011 0.025 0.1100936795
- 194 0.142 -0.636 0.659 0.249 0.011 0.025 0.1100920155
- 203 0.142 -0.636 0.624 0.249 0.011 0.025 0.1099191270
- 204 0.142 -0.636 0.626 0.249 0.011 0.025 0.1099004090
- 205 0.142 -0.636 0.635 0.249 0.011 0.025 0.1098696713
- 206 0.142 -0.636 0.634 0.249 0.011 0.025 0.1098682124
- 207 0.142 -0.636 0.633 0.249 0.011 0.025 0.1098679143
- 218 0.142 -0.636 0.633 0.275 0.011 0.025 0.1095496118
- 219 0.142 -0.636 0.633 0.272 0.011 0.025 0.1095292521
- 220 0.142 -0.636 0.633 0.269 0.011 0.025 0.1095254362
- 222 0.142 -0.636 0.633 0.268 0.011 0.025 0.1095240561
- 225 0.142 -0.636 0.633 0.267 0.011 0.025 0.1095237670
- 236 0.142 -0.636 0.633 0.267 0.008 0.025 0.1095152913
- 246 0.142 -0.636 0.633 0.267 0.008 0.016 0.1094430861
- 248 0.142 -0.636 0.633 0.267 0.008 0.013 0.1094347720
- 251 0.081 -0.631 0.608 0.285 0.005 0.001 0.1092368770
- 258 0.070 -0.630 0.604 0.289 0.004 -0.001 0.1091834610
- 259 0.064 -0.630 0.601 0.290 0.004 -0.002 0.1091705622
- 261 0.063 -0.630 0.601 0.291 0.004 -0.002 0.1091695847
- 262 0.063 -0.630 0.601 0.291 0.004 -0.002 0.1091694202
- 276 0.063 -0.630 0.601 0.291 0.004 -0.018 0.1090683424
- 278 0.063 -0.630 0.601 0.291 0.004 -0.016 0.1090664895
- 287 0.063 -0.697 0.601 0.291 0.004 -0.016 0.1088188134
- 288 0.063 -0.675 0.601 0.291 0.004 -0.016 0.1087908274
- 289 0.063 -0.680 0.601 0.291 0.004 -0.016 0.1087791364
- 290 0.063 -0.683 0.601 0.291 0.004 -0.016 0.1087740261
- 292 0.063 -0.685 0.601 0.291 0.004 -0.016 0.1087714766
- 300 0.063 -0.685 0.527 0.291 0.004 -0.016 0.1086968602
- 301 0.063 -0.685 0.561 0.291 0.004 -0.016 0.1084013625
- 304 0.063 -0.685 0.559 0.291 0.004 -0.016 0.1083982760
- 312 0.063 -0.685 0.559 0.374 0.004 -0.016 0.1074879688
- 313 0.063 -0.685 0.559 0.359 0.004 -0.016 0.1073068643
- 314 0.063 -0.685 0.559 0.348 0.004 -0.016 0.1072600868
- 316 0.063 -0.685 0.559 0.350 0.004 -0.016 0.1072584777
- 319 0.063 -0.685 0.559 0.349 0.004 -0.016 0.1072583324
- 329 0.063 -0.685 0.559 0.349 -0.007 -0.016 0.1072306562
- 330 0.063 -0.685 0.559 0.349 -0.005 -0.016 0.1072226564
- 331 0.063 -0.685 0.559 0.349 -0.003 -0.016 0.1072206461
- 338 0.040 -0.683 0.549 0.356 -0.004 -0.020 0.1069850578
- 340 0.037 -0.683 0.548 0.357 -0.005 -0.021 0.1069819009
- 344 0.037 -0.683 0.548 0.357 -0.005 -0.021 0.1069818886
- 345 0.037 -0.683 0.548 0.357 -0.005 -0.021 0.1069818819
- 346 0.037 -0.683 0.548 0.357 -0.005 -0.021 0.1069814242
- 357 0.037 -0.683 0.548 0.357 -0.005 -0.033 0.1069710359
- 358 0.037 -0.683 0.548 0.357 -0.005 -0.029 0.1069617699
- 359 0.037 -0.683 0.548 0.357 -0.005 -0.028 0.1069584656
- 360 0.037 -0.683 0.548 0.357 -0.005 -0.025 0.1069570477
- 362 0.037 -0.683 0.548 0.357 -0.005 -0.026 0.1069561095
- 369 0.037 -0.684 0.548 0.357 -0.005 -0.026 0.1069349676
- 372 0.037 -0.704 0.548 0.357 -0.005 -0.026 0.1066906814
- 374 0.037 -0.706 0.548 0.357 -0.005 -0.026 0.1066889689
- 383 0.037 -0.706 0.521 0.357 -0.005 -0.026 0.1063755448
- 385 0.037 -0.706 0.520 0.357 -0.005 -0.026 0.1063749633
- 395 0.037 -0.706 0.520 0.366 -0.005 -0.026 0.1063218328
- 396 0.037 -0.706 0.520 0.365 -0.005 -0.026 0.1063215903
- 407 0.037 -0.706 0.520 0.365 0.001 -0.026 0.1062978189
- 408 0.037 -0.706 0.520 0.365 0.003 -0.026 0.1062949581
- 435 0.037 -0.706 0.520 0.365 0.003 -0.030 0.1062665141
- 436 0.037 -0.706 0.520 0.365 0.003 -0.037 0.1062642181
- 438 0.037 -0.706 0.520 0.365 0.003 -0.034 0.1062610066
- 449 0.037 -0.702 0.520 0.365 0.003 -0.034 0.1062574819
- 450 0.037 -0.703 0.520 0.365 0.003 -0.034 0.1062574307
- 451 0.037 -0.704 0.520 0.365 0.003 -0.034 0.1062573129
- 459 0.037 -0.704 0.514 0.365 0.003 -0.034 0.1062290992
- 461 0.037 -0.704 0.512 0.365 0.003 -0.034 0.1062276281
- 463 0.037 -0.704 0.513 0.365 0.003 -0.034 0.1062273500
- 472 0.037 -0.704 0.513 0.368 0.003 -0.034 0.1062175192
- 484 0.037 -0.704 0.513 0.368 0.004 -0.034 0.1062170679
- 492 0.036 -0.704 0.513 0.368 0.004 -0.034 0.1062162706
- 493 0.035 -0.704 0.512 0.368 0.004 -0.034 0.1062161029
- 494 0.036 -0.704 0.512 0.368 0.004 -0.034 0.1062159616
- 495 0.036 -0.704 0.513 0.368 0.004 -0.034 0.1062158085
- 497 0.036 -0.704 0.513 0.368 0.004 -0.034 0.1062158018
- 509 0.036 -0.704 0.513 0.368 0.004 -0.033 0.1062156146
- 519 0.036 -0.699 0.513 0.368 0.004 -0.033 0.1062084337
- 520 0.036 -0.700 0.513 0.368 0.004 -0.033 0.1062080971
- 529 0.036 -0.700 0.511 0.368 0.004 -0.033 0.1062052817
- 531 0.036 -0.700 0.510 0.368 0.004 -0.033 0.1062044378
- 541 0.036 -0.700 0.510 0.371 0.004 -0.033 0.1061932443
- 553 0.036 -0.700 0.510 0.371 0.005 -0.033 0.1061928190
- 568 0.036 -0.696 0.507 0.374 0.006 -0.032 0.1061794847
- 571 0.036 -0.691 0.502 0.378 0.008 -0.030 0.1061737460
- 572 0.036 -0.692 0.503 0.378 0.008 -0.031 0.1061729740
- 590 0.036 -0.692 0.503 0.378 0.008 -0.029 0.1061704114
- 601 0.036 -0.694 0.503 0.378 0.008 -0.029 0.1061696215
- 611 0.036 -0.694 0.502 0.378 0.008 -0.029 0.1061683423
- 620 0.037 -0.694 0.502 0.377 0.008 -0.029 0.1061682512
- 621 0.036 -0.694 0.502 0.377 0.008 -0.029 0.1061681329
- 634 0.036 -0.694 0.502 0.377 0.006 -0.029 0.1061662794
- 637 0.036 -0.690 0.499 0.380 0.008 -0.028 0.1061635550
- 642 0.036 -0.689 0.499 0.381 0.008 -0.028 0.1061633157
- 643 0.036 -0.689 0.498 0.381 0.008 -0.028 0.1061632022
- 649 0.036 -0.689 0.498 0.381 0.008 -0.028 0.1061630480
- 651 0.036 -0.689 0.498 0.381 0.008 -0.028 0.1061627578
- Powell done niters = 7
- Computing relative cost
- 0 -25.0 -25.0 -25.0 1.019498
- 1 -25.0 -25.0 25.0 0.985191
- 2 -25.0 25.0 -25.0 1.045901
- 3 -25.0 25.0 25.0 0.969446
- 4 25.0 -25.0 -25.0 1.019311
- 5 25.0 -25.0 25.0 1.015777
- 6 25.0 25.0 -25.0 1.017980
- 7 25.0 25.0 25.0 0.995817
- REL: 8 0.106163 8.068922 1.008615 rel = 0.105256
- Number of iterations 7
- Min cost was 0.106163
- Number of FunctionCalls 653
- TolPowell 0.000100
- nMaxItersPowell 36
- OptimizationTime 1.758000 sec
- Parameters at optimum (transmm) 0.03647 -0.68907 0.49831
- Parameters at optimum (rotdeg) 0.38096 0.00784 -0.02772
- Final costs ----------------
- Number of surface hits 2708
- WM Intensity 61.6351 +/- 8.8930
- Ctx Intensity 74.6180 +/- 8.4127
- Pct Contrast 19.3022 +/- 12.5299
- Cost 0.1062
- RelCost 0.2882
- Reg at min cost was
- 0.998 0.040 0.046 -0.208;
- -0.040 -0.138 0.990 0.397;
- 0.046 -0.990 -0.136 0.078;
- 0.000 0.000 0.000 1.000;
- Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/bbr.pass1.dat, type = 14
- Original Reg
- 0.998 0.041 0.045 -0.245;
- -0.039 -0.144 0.989 1.084;
- 0.047 -0.989 -0.142 -0.427;
- 0.000 0.000 0.000 1.000;
- Original Reg - Optimal Reg
- 0.000 0.000 -0.000 -0.037;
- 0.001 -0.007 -0.001 0.686;
- 0.000 0.001 -0.007 -0.506;
- 0.000 0.000 0.000 0.000;
- Computing change in lh position
- LH rmsDiffMean 1.154599
- Computing change in rh position
- Surface RMS Diff (mm) 1.150041 1.538647
- mri_segreg done
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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/sub005/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/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/sub005/scripts
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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/sub005/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5
- sysname Linux
- hostname snake4
- machine x86_64
- user fkaule
- movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii
- regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/bbr.pass1.dat
- subject sub005
- dof 6
- outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 1375996544
- TransRandMax 0.000000
- RotRandMax 0.000000
- Translations 0.000000 0.000000 0.000000
- Rotations 0.000000 0.000000 0.000000
- Input reg
- 0.998 0.040 0.046 -0.208;
- -0.040 -0.138 0.990 0.397;
- 0.046 -0.990 -0.136 0.078;
- 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 1.005462
- 1 -25.0 -25.0 25.0 0.992291
- 2 -25.0 25.0 -25.0 0.996881
- 3 -25.0 25.0 25.0 1.003206
- 4 25.0 -25.0 -25.0 1.011859
- 5 25.0 -25.0 25.0 1.013799
- 6 25.0 25.0 -25.0 1.010146
- 7 25.0 25.0 25.0 1.017436
- REL: 8 0.128535 8.051080 1.006385 rel = 0.127719
- Initial costs ----------------
- Number of surface hits 269746
- WM Intensity 61.6292 +/- 8.6363
- Ctx Intensity 74.3609 +/- 8.5585
- Pct Contrast 18.9094 +/- 12.8492
- Cost 0.1285
- RelCost 0.1277
- ------------------------------------
- Brute force preopt -0.1 0.1 0.1, n = 729
- 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1173 0.1173 0.0
- 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.1115 0.1115 0.0
- 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.1090 0.1090 0.0
- 30 -0.1000 -0.1000 0.0000 -0.1000 0.0000 -0.1000 0.1083 0.1083 0.0
- 39 -0.1000 -0.1000 0.0000 0.0000 0.0000 -0.1000 0.1074 0.1074 0.0
- 174 -0.1000 0.1000 -0.1000 0.0000 0.0000 -0.1000 0.1074 0.1074 0.0
- 177 -0.1000 0.1000 -0.1000 0.0000 0.1000 -0.1000 0.1069 0.1069 0.0
- 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1062 0.1062 0.0
- Brute Force --------------------------
- Min cost was 0.106163
- Number of iterations 729
- Search time 1.975000 sec
- Parameters at best (transmm, rotdeg)
- 0.000 0.000 0.000 0.000 0.000 0.000
- --------------------------------------------
- Starting Powell Minimization
- Init Powel Params dof = 6
- 0 0
- 1 0
- 2 0
- 3 0
- 4 0
- 5 0
- 7 0.095 0.000 0.000 0.000 0.000 0.000 0.1276986789
- 8 0.086 0.000 0.000 0.000 0.000 0.000 0.1276851776
- 17 0.086 -0.033 0.000 0.000 0.000 0.000 0.1276021483
- 18 0.086 -0.026 0.000 0.000 0.000 0.000 0.1275904397
- 19 0.086 -0.024 0.000 0.000 0.000 0.000 0.1275888059
- 20 0.086 -0.023 0.000 0.000 0.000 0.000 0.1275887083
- 29 0.086 -0.023 -0.025 0.000 0.000 0.000 0.1275488480
- 31 0.086 -0.023 -0.018 0.000 0.000 0.000 0.1275401496
- 40 0.086 -0.023 -0.018 0.057 0.000 0.000 0.1273557294
- 41 0.086 -0.023 -0.018 0.037 0.000 0.000 0.1272652095
- 42 0.086 -0.023 -0.018 0.036 0.000 0.000 0.1272638958
- 43 0.086 -0.023 -0.018 0.032 0.000 0.000 0.1272637054
- 45 0.086 -0.023 -0.018 0.034 0.000 0.000 0.1272628172
- 53 0.086 -0.023 -0.018 0.034 0.073 0.000 0.1262796992
- 54 0.086 -0.023 -0.018 0.034 0.082 0.000 0.1262495215
- 55 0.086 -0.023 -0.018 0.034 0.091 0.000 0.1262414946
- 56 0.086 -0.023 -0.018 0.034 0.090 0.000 0.1262411198
- 64 0.086 -0.023 -0.018 0.034 0.090 -0.061 0.1259444663
- 65 0.086 -0.023 -0.018 0.034 0.090 -0.047 0.1259245357
- 66 0.086 -0.023 -0.018 0.034 0.090 -0.049 0.1259242525
- 75 0.028 -0.023 -0.018 0.034 0.090 -0.049 0.1253291140
- 76 0.011 -0.023 -0.018 0.034 0.090 -0.049 0.1253221404
- 77 0.018 -0.023 -0.018 0.034 0.090 -0.049 0.1253176300
- 86 0.018 -0.020 -0.018 0.034 0.090 -0.049 0.1253106241
- 87 0.018 -0.012 -0.018 0.034 0.090 -0.049 0.1253004838
- 89 0.018 -0.013 -0.018 0.034 0.090 -0.049 0.1253004170
- 98 0.018 -0.013 -0.029 0.034 0.090 -0.049 0.1252166108
- 99 0.018 -0.013 -0.060 0.034 0.090 -0.049 0.1251544413
- 101 0.018 -0.013 -0.052 0.034 0.090 -0.049 0.1251455374
- 111 0.018 -0.013 -0.052 0.055 0.090 -0.049 0.1250470272
- 113 0.018 -0.013 -0.052 0.054 0.090 -0.049 0.1250469694
- 123 0.018 -0.013 -0.052 0.054 0.104 -0.049 0.1250054866
- 134 0.018 -0.013 -0.052 0.054 0.105 -0.101 0.1247433447
- 135 0.018 -0.013 -0.052 0.054 0.105 -0.092 0.1247348076
- 136 0.018 -0.013 -0.052 0.054 0.105 -0.093 0.1247346904
- 138 -0.051 -0.002 -0.085 0.073 0.121 -0.138 0.1241889945
- 145 -0.064 -0.000 -0.092 0.077 0.124 -0.147 0.1241772385
- 146 -0.063 -0.001 -0.091 0.077 0.124 -0.146 0.1241769550
- 147 -0.062 -0.001 -0.091 0.076 0.123 -0.146 0.1241769070
- 148 -0.062 -0.001 -0.091 0.077 0.123 -0.146 0.1241768290
- 150 -0.062 -0.001 -0.091 0.077 0.123 -0.146 0.1241768221
- 159 -0.062 -0.001 -0.091 0.077 0.124 -0.142 0.1241742429
- 161 -0.062 -0.001 -0.091 0.077 0.124 -0.140 0.1241741537
- 163 -0.062 -0.001 -0.091 0.077 0.124 -0.141 0.1241740603
- 170 -0.062 -0.008 -0.091 0.077 0.124 -0.141 0.1241513131
- 171 -0.062 -0.018 -0.091 0.077 0.124 -0.141 0.1241390012
- 172 -0.062 -0.017 -0.091 0.077 0.124 -0.141 0.1241385887
- 181 -0.062 -0.017 -0.100 0.077 0.124 -0.141 0.1241307105
- 191 -0.062 -0.017 -0.100 0.078 0.124 -0.141 0.1241300920
- 192 -0.062 -0.017 -0.100 0.079 0.124 -0.141 0.1241300738
- 202 -0.062 -0.017 -0.100 0.079 0.121 -0.141 0.1241295335
- 229 -0.062 -0.017 -0.100 0.079 0.121 -0.144 0.1241288897
- 240 -0.062 -0.016 -0.100 0.079 0.121 -0.144 0.1241288124
- 249 -0.062 -0.016 -0.101 0.079 0.121 -0.144 0.1241284920
- 268 -0.062 -0.016 -0.101 0.079 0.122 -0.144 0.1241283505
- 283 -0.061 -0.016 -0.101 0.078 0.122 -0.143 0.1241282091
- 284 -0.061 -0.016 -0.101 0.078 0.122 -0.143 0.1241281650
- Powell done niters = 4
- Computing relative cost
- 0 -25.0 -25.0 -25.0 1.005757
- 1 -25.0 -25.0 25.0 0.993111
- 2 -25.0 25.0 -25.0 0.997448
- 3 -25.0 25.0 25.0 1.004378
- 4 25.0 -25.0 -25.0 1.012542
- 5 25.0 -25.0 25.0 1.014481
- 6 25.0 25.0 -25.0 1.010670
- 7 25.0 25.0 25.0 1.015250
- REL: 8 0.124128 8.053638 1.006705 rel = 0.123301
- Number of iterations 4
- Min cost was 0.124128
- Number of FunctionCalls 347
- TolPowell 0.000000
- nMaxItersPowell 36
- OptimizationTime 37.643000 sec
- Parameters at optimum (transmm) -0.06133 -0.01618 -0.10078
- Parameters at optimum (rotdeg) 0.07825 0.12163 -0.14307
- Final costs ----------------
- Number of surface hits 269746
- WM Intensity 61.6231 +/- 8.6135
- Ctx Intensity 74.3282 +/- 8.5477
- Pct Contrast 18.8727 +/- 12.8167
- Cost 0.1241
- RelCost 0.1277
- Reg at min cost was
- 0.998 0.038 0.048 -0.268;
- -0.042 -0.136 0.990 0.382;
- 0.044 -0.990 -0.134 -0.021;
- 0.000 0.000 0.000 1.000;
- Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.dat, type = 14
- Original Reg
- 0.998 0.040 0.046 -0.208;
- -0.040 -0.138 0.990 0.397;
- 0.046 -0.990 -0.136 0.078;
- 0.000 0.000 0.000 1.000;
- Original Reg - Optimal Reg
- 0.000 0.002 -0.002 0.060;
- 0.003 -0.001 -0.000 0.016;
- 0.002 0.000 -0.001 0.100;
- 0.000 0.000 0.000 0.000;
- Computing change in lh position
- LH rmsDiffMean 0.148487
- Computing change in rh position
- Surface RMS Diff (mm) 0.171396 0.321705
- mri_segreg done
- tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.dat --noedit --ltaout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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/sub005/mri/orig/T2raw.mgz
- reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 0.038 0.048 -0.268;
- -0.042 -0.136 0.990 0.382;
- 0.044 -0.990 -0.134 -0.021;
- 0.000 0.000 0.000 1.000;
- float2int = 0
- ---------------------------------------
- INFO: loading target /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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/sub005/mri/orig/T2raw.mgz
- Tmov: --------------------
- -0.700 0.000 0.000 95.888;
- 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 0.038 0.048 -0.268;
- -0.042 -0.136 0.990 0.382;
- 0.044 -0.990 -0.134 -0.021;
- 0.000 0.000 0.000 1.000;
- Determinant 1
- subject = sub005
- RegMat ---------------------------
- 0.998 0.038 0.048 -0.268;
- -0.042 -0.136 0.990 0.382;
- 0.044 -0.990 -0.134 -0.021;
- 0.000 0.000 0.000 1.000;
- transformed matrix:
- 1.000 0.002 -0.002 0.180;
- -0.002 1.000 0.001 0.052;
- 0.002 -0.001 1.000 -0.349;
- 0.000 0.000 0.000 1.000;
- transformed matrix:
- 0.699 0.029 0.028 20.940;
- 0.034 -0.090 -0.660 267.665;
- -0.027 0.660 -0.091 22.410;
- 0.000 0.000 0.000 1.000;
- Cleaning up
-
- Started at Thu Aug 8 22:28:33 CEST 2013
- Ended at Thu Aug 8 22:40:43 CEST 2013
- BBR-Run-Time-Sec 730
-
- bbregister Done
- To check results, run:
- tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.dat --surf
-
- mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/T2.mgz
- mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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/sub005/mri/orig/T2raw.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.998148, -0.0400878, -0.0457496)
- j_ras = (-0.0459461, 0.989757, 0.135168)
- k_ras = (-0.0398624, -0.13702, 0.989766)
- INFO: Reading transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.lta...
- Reading transform with LTAreadEx()
- reading extra input line subject sub005
- reading extra input line fscale 0.150000
- reading template info from volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig.mgz...
- INFO: Applying transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.lta...
- ---------------------------------
- INFO: Transform Matrix (linear_ras_to_ras)
- 1.000 0.002 -0.002 0.180;
- -0.002 1.000 0.001 0.052;
- 0.002 -0.001 1.000 -0.349;
- 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/sub005/mri/T2.mgz...
- mri_normalize -aseg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/aseg.mgz -sigma 4 -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white identity.nofile -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white identity.nofile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/T2.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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/sub005/mri/T2.mgz...
- computing distance transform
- computing distance transform
- computing nonmaximum suppression
- 8547 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/sub005/mri/T2.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
- cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.woT2.pial
- `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.woT2.pial'
- mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub005 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/sub005/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz...
- 16905 bright wm thresholded.
- 908 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.orig...
- computing class statistics...
- border white: 254363 voxels (1.52%)
- border gray 296177 voxels (1.77%)
- WM (91.0): 92.4 +- 10.3 [70.0 --> 110.0]
- GM (74.0) : 72.6 +- 12.7 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 46.3 (was 70)
- setting MAX_BORDER_WHITE to 114.3 (was 105)
- setting MIN_BORDER_WHITE to 59.0 (was 85)
- setting MAX_CSF to 33.6 (was 40)
- setting MAX_GRAY to 93.7 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 52.7 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 20.9 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=104, GM=59
- mean inside = 92.3, mean outside = 67.9
- smoothing surface for 5 iterations...
- reading initial white vertex positions from white...
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.90 +- 0.26 (0.02-->6.37) (max @ vno 60346 --> 65969)
- face area 0.34 +- 0.16 (0.00-->6.14)
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 5 points - only 0.00% unknown
- deleting segment 1 with 5 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 7 points - only 0.00% unknown
- deleting segment 7 with 7 points - only 0.00% unknown
- deleting segment 8 with 10 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 10 with 7 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 11 with 1 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 12 with 1 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 13 with 2 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 14 with 2 points - only 0.00% unknown
- deleting segment 15 with 11 points - only 0.00% unknown
- tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.90 +- 0.25 (0.07-->6.37) (max @ vno 60346 --> 65969)
- face area 0.34 +- 0.16 (0.00-->6.14)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5050607.0, rms=0.00
- rms = 2.57, time step reduction 1 of 3 to 0.250...
- rms = 0.65, time step reduction 2 of 3 to 0.125...
- rms = 0.08, time step reduction 3 of 3 to 0.062...
- 001: dt: 0.1250, sse=5050607.0, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 5 points - only 0.00% unknown
- deleting segment 1 with 5 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 2 with 3 points - only 0.00% unknown
- deleting segment 3 with 7 points - only 0.00% unknown
- deleting segment 4 with 7 points - only 0.00% unknown
- deleting segment 5 with 10 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 7 with 7 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 8 with 1 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 9 with 1 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 10 with 2 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 11 points - only 0.00% unknown
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.90 +- 0.25 (0.07-->6.37) (max @ vno 60346 --> 65969)
- face area 0.34 +- 0.16 (0.00-->6.14)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5050607.0, rms=0.00
- rms = 2.58, time step reduction 1 of 3 to 0.250...
- rms = 0.66, time step reduction 2 of 3 to 0.125...
- rms = 0.08, time step reduction 3 of 3 to 0.062...
- 002: dt: 0.1250, sse=5050607.0, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 5 points - only 0.00% unknown
- deleting segment 1 with 5 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 2 with 3 points - only 0.00% unknown
- deleting segment 3 with 7 points - only 0.00% unknown
- deleting segment 4 with 7 points - only 0.00% unknown
- deleting segment 5 with 10 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 7 with 7 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 8 with 1 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 9 with 1 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 10 with 2 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 11 points - only 0.00% unknown
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.25 (0.07-->6.37) (max @ vno 60346 --> 65969)
- face area 0.34 +- 0.16 (0.00-->6.14)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5050607.0, rms=0.00
- rms = 2.57, time step reduction 1 of 3 to 0.250...
- rms = 0.65, time step reduction 2 of 3 to 0.125...
- rms = 0.08, time step reduction 3 of 3 to 0.062...
- 003: dt: 0.1250, sse=5050607.0, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 5 points - only 0.00% unknown
- deleting segment 1 with 5 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 2 with 3 points - only 0.00% unknown
- deleting segment 3 with 7 points - only 0.00% unknown
- deleting segment 4 with 7 points - only 0.00% unknown
- deleting segment 5 with 10 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 7 with 7 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 8 with 1 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 9 with 1 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 10 with 2 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 11 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=5050607.0, rms=0.00
- rms = 2.58, time step reduction 1 of 3 to 0.250...
- rms = 0.66, time step reduction 2 of 3 to 0.125...
- rms = 0.08, time step reduction 3 of 3 to 0.062...
- 004: dt: 0.1250, sse=5050607.0, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- smoothing surface for 5 iterations...
- reading initial pial vertex positions from woT2.pial...
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [93.00 201.00], gm=147.00+-18.00, and vertices in regions > 138.0
- 39902 surface locations found to contain inconsistent values (4917 in, 34985 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=600642.1, rms=0.23
- 001: dt: 0.5000, sse=558236.2, rms=0.225 (0.000%)
- 002: dt: 0.5000, sse=533914.7, rms=0.213 (0.000%)
- 003: dt: 0.5000, sse=515651.6, rms=0.204 (0.000%)
- 004: dt: 0.5000, sse=502599.2, rms=0.196 (0.000%)
- 005: dt: 0.5000, sse=492409.3, rms=0.188 (0.000%)
- 006: dt: 0.5000, sse=483755.8, rms=0.182 (0.000%)
- 007: dt: 0.5000, sse=476508.9, rms=0.177 (0.000%)
- 008: dt: 0.5000, sse=470561.8, rms=0.173 (0.000%)
- 009: dt: 0.5000, sse=466122.2, rms=0.169 (0.000%)
- 010: dt: 0.5000, sse=461843.5, rms=0.166 (0.000%)
- 011: dt: 0.5000, sse=458462.7, rms=0.163 (0.000%)
- 012: dt: 0.5000, sse=454836.3, rms=0.161 (0.000%)
- 013: dt: 0.5000, sse=451619.2, rms=0.159 (0.000%)
- 014: dt: 0.5000, sse=448957.2, rms=0.157 (0.000%)
- 015: dt: 0.5000, sse=446102.2, rms=0.156 (0.000%)
- 016: dt: 0.5000, sse=443480.9, rms=0.155 (0.000%)
- 017: dt: 0.5000, sse=441197.8, rms=0.154 (0.000%)
- 018: dt: 0.5000, sse=439113.6, rms=0.153 (0.000%)
- 019: dt: 0.5000, sse=437142.9, rms=0.152 (0.000%)
- 020: dt: 0.5000, sse=435140.2, rms=0.152 (0.000%)
- 021: dt: 0.5000, sse=433160.8, rms=0.152 (0.000%)
- 022: dt: 0.5000, sse=431352.5, rms=0.151 (0.000%)
- 023: dt: 0.5000, sse=429420.1, rms=0.151 (0.000%)
- 024: dt: 0.5000, sse=427848.3, rms=0.151 (0.000%)
- 025: dt: 0.5000, sse=426204.8, rms=0.152 (0.000%)
- 026: dt: 0.5000, sse=424777.1, rms=0.152 (0.000%)
- 027: dt: 0.5000, sse=423328.6, rms=0.152 (0.000%)
- 028: dt: 0.5000, sse=421760.3, rms=0.152 (0.000%)
- 029: dt: 0.5000, sse=420302.5, rms=0.153 (0.000%)
- 030: dt: 0.5000, sse=418962.1, rms=0.153 (0.000%)
- positioning took 3.9 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [95.00 203.00], gm=149.00+-18.00, and vertices in regions > 140.0
- 33374 surface locations found to contain inconsistent values (2355 in, 31019 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=43511.0, rms=0.13
- 031: dt: 0.5000, sse=43237.3, rms=0.124 (0.000%)
- 032: dt: 0.5000, sse=44110.6, rms=0.114 (0.000%)
- 033: dt: 0.5000, sse=45179.7, rms=0.106 (0.000%)
- 034: dt: 0.5000, sse=46053.3, rms=0.101 (0.000%)
- 035: dt: 0.5000, sse=46756.7, rms=0.096 (0.000%)
- 036: dt: 0.5000, sse=47483.6, rms=0.091 (0.000%)
- 037: dt: 0.5000, sse=48150.4, rms=0.087 (0.000%)
- 038: dt: 0.5000, sse=48806.6, rms=0.083 (0.000%)
- 039: dt: 0.5000, sse=49470.3, rms=0.079 (0.000%)
- 040: dt: 0.5000, sse=50079.9, rms=0.076 (0.000%)
- 041: dt: 0.5000, sse=50691.2, rms=0.072 (0.000%)
- 042: dt: 0.5000, sse=51227.9, rms=0.070 (0.000%)
- 043: dt: 0.5000, sse=51750.8, rms=0.067 (0.000%)
- 044: dt: 0.5000, sse=52241.1, rms=0.064 (0.000%)
- 045: dt: 0.5000, sse=52685.6, rms=0.062 (0.000%)
- 046: dt: 0.5000, sse=53108.8, rms=0.060 (0.000%)
- 047: dt: 0.5000, sse=53478.3, rms=0.058 (0.000%)
- 048: dt: 0.5000, sse=53860.7, rms=0.056 (0.000%)
- 049: dt: 0.5000, sse=54227.8, rms=0.055 (0.000%)
- 050: dt: 0.5000, sse=54557.1, rms=0.053 (0.000%)
- 051: dt: 0.5000, sse=54863.1, rms=0.051 (0.000%)
- 052: dt: 0.5000, sse=55143.0, rms=0.050 (0.000%)
- 053: dt: 0.5000, sse=55400.5, rms=0.049 (0.000%)
- 054: dt: 0.5000, sse=55647.8, rms=0.048 (0.000%)
- 055: dt: 0.5000, sse=55892.6, rms=0.047 (0.000%)
- 056: dt: 0.5000, sse=56113.1, rms=0.045 (0.000%)
- 057: dt: 0.5000, sse=56309.4, rms=0.044 (0.000%)
- 058: dt: 0.5000, sse=56514.7, rms=0.044 (0.000%)
- 059: dt: 0.5000, sse=56702.4, rms=0.043 (0.000%)
- 060: dt: 0.5000, sse=56866.8, rms=0.042 (0.000%)
- positioning took 3.8 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [86.70 207.30], gm=147.00+-20.10, and vertices in regions > 136.9
- 31361 surface locations found to contain inconsistent values (145 in, 31216 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=6152.8, rms=0.06
- 061: dt: 0.5000, sse=6117.8, rms=0.056 (0.000%)
- 062: dt: 0.5000, sse=6198.5, rms=0.049 (0.000%)
- 063: dt: 0.5000, sse=6289.8, rms=0.045 (0.000%)
- 064: dt: 0.5000, sse=6363.1, rms=0.042 (0.000%)
- 065: dt: 0.5000, sse=6414.4, rms=0.040 (0.000%)
- 066: dt: 0.5000, sse=6444.6, rms=0.038 (0.000%)
- 067: dt: 0.5000, sse=6463.7, rms=0.037 (0.000%)
- 068: dt: 0.5000, sse=6477.9, rms=0.035 (0.000%)
- 069: dt: 0.5000, sse=6494.1, rms=0.034 (0.000%)
- 070: dt: 0.5000, sse=6508.1, rms=0.033 (0.000%)
- 071: dt: 0.5000, sse=6521.8, rms=0.032 (0.000%)
- 072: dt: 0.5000, sse=6535.8, rms=0.031 (0.000%)
- 073: dt: 0.5000, sse=6546.9, rms=0.030 (0.000%)
- 074: dt: 0.5000, sse=6556.2, rms=0.030 (0.000%)
- 075: dt: 0.5000, sse=6563.5, rms=0.029 (0.000%)
- 076: dt: 0.5000, sse=6570.3, rms=0.028 (0.000%)
- 077: dt: 0.5000, sse=6577.6, rms=0.028 (0.000%)
- 078: dt: 0.5000, sse=6583.6, rms=0.027 (0.000%)
- 079: dt: 0.5000, sse=6590.4, rms=0.027 (0.000%)
- 080: dt: 0.5000, sse=6594.0, rms=0.026 (0.000%)
- 081: dt: 0.5000, sse=6597.6, rms=0.026 (0.000%)
- 082: dt: 0.5000, sse=6603.0, rms=0.026 (0.000%)
- 083: dt: 0.5000, sse=6605.6, rms=0.025 (0.000%)
- 084: dt: 0.5000, sse=6609.8, rms=0.025 (0.000%)
- 085: dt: 0.5000, sse=6612.6, rms=0.025 (0.000%)
- 086: dt: 0.5000, sse=6617.1, rms=0.025 (0.000%)
- 087: dt: 0.5000, sse=6619.4, rms=0.025 (0.000%)
- 088: dt: 0.5000, sse=6621.2, rms=0.024 (0.000%)
- 089: dt: 0.5000, sse=6622.7, rms=0.024 (0.000%)
- 090: dt: 0.5000, sse=6622.9, rms=0.024 (0.000%)
- positioning took 3.8 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [94.50 205.50], gm=150.00+-18.50, and vertices in regions > 140.7
- 30232 surface locations found to contain inconsistent values (315 in, 29917 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/sub005/surf/lh.pial...
- writing smoothed curvature to lh.curv.pial
- 000: dt: 0.0000, sse=788.6, rms=0.03
- 091: dt: 0.5000, sse=787.5, rms=0.031 (0.000%)
- 092: dt: 0.5000, sse=777.6, rms=0.030 (0.000%)
- 093: dt: 0.5000, sse=770.0, rms=0.029 (0.000%)
- 094: dt: 0.5000, sse=763.9, rms=0.028 (0.000%)
- 095: dt: 0.5000, sse=758.1, rms=0.027 (0.000%)
- 096: dt: 0.5000, sse=754.1, rms=0.026 (0.000%)
- 097: dt: 0.5000, sse=751.2, rms=0.026 (0.000%)
- 098: dt: 0.5000, sse=748.6, rms=0.026 (0.000%)
- 099: dt: 0.5000, sse=746.1, rms=0.025 (0.000%)
- 100: dt: 0.5000, sse=743.8, rms=0.025 (0.000%)
- 101: dt: 0.5000, sse=741.2, rms=0.025 (0.000%)
- 102: dt: 0.5000, sse=739.0, rms=0.024 (0.000%)
- 103: dt: 0.5000, sse=736.9, rms=0.024 (0.000%)
- 104: dt: 0.5000, sse=735.0, rms=0.023 (0.000%)
- 105: dt: 0.5000, sse=733.7, rms=0.023 (0.000%)
- 106: dt: 0.5000, sse=732.3, rms=0.023 (0.000%)
- 107: dt: 0.5000, sse=730.8, rms=0.023 (0.000%)
- 108: dt: 0.5000, sse=729.8, rms=0.023 (0.000%)
- 109: dt: 0.5000, sse=728.8, rms=0.022 (0.000%)
- 110: dt: 0.5000, sse=727.3, rms=0.022 (0.000%)
- 111: dt: 0.5000, sse=726.6, rms=0.022 (0.000%)
- 112: dt: 0.5000, sse=725.8, rms=0.022 (0.000%)
- 113: dt: 0.5000, sse=725.5, rms=0.022 (0.000%)
- 114: dt: 0.5000, sse=724.7, rms=0.022 (0.000%)
- 115: dt: 0.5000, sse=724.0, rms=0.022 (0.000%)
- 116: dt: 0.5000, sse=723.7, rms=0.021 (0.000%)
- 117: dt: 0.5000, sse=723.5, rms=0.021 (0.000%)
- 118: dt: 0.5000, sse=723.0, rms=0.021 (0.000%)
- 119: dt: 0.5000, sse=722.6, rms=0.021 (0.000%)
- 120: dt: 0.5000, sse=722.6, rms=0.021 (0.000%)
- positioning took 3.8 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.curv.pial
- writing smoothed area to lh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.area.pial
- vertex spacing 1.03 +- 0.45 (0.07-->9.27) (max @ vno 100866 --> 99891)
- face area 0.42 +- 0.33 (0.00-->7.39)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 141918 vertices processed
- 25000 of 141918 vertices processed
- 50000 of 141918 vertices processed
- 75000 of 141918 vertices processed
- 100000 of 141918 vertices processed
- 125000 of 141918 vertices processed
- 0 of 141918 vertices processed
- 25000 of 141918 vertices processed
- 50000 of 141918 vertices processed
- 75000 of 141918 vertices processed
- 100000 of 141918 vertices processed
- 125000 of 141918 vertices processed
- thickness calculation complete, 408:1172 truncations.
- 26003 vertices at 0 distance
- 88664 vertices at 1 distance
- 93876 vertices at 2 distance
- 44360 vertices at 3 distance
- 13906 vertices at 4 distance
- 3987 vertices at 5 distance
- 1213 vertices at 6 distance
- 454 vertices at 7 distance
- 208 vertices at 8 distance
- 105 vertices at 9 distance
- 62 vertices at 10 distance
- 50 vertices at 11 distance
- 21 vertices at 12 distance
- 28 vertices at 13 distance
- 13 vertices at 14 distance
- 16 vertices at 15 distance
- 13 vertices at 16 distance
- 14 vertices at 17 distance
- 8 vertices at 18 distance
- 6 vertices at 19 distance
- 9 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.thickness
- positioning took 18.7 minutes
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
- cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.woT2.pial
- `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.woT2.pial'
- mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub005 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/sub005/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz...
- 17487 bright wm thresholded.
- 908 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.orig...
- computing class statistics...
- border white: 254363 voxels (1.52%)
- border gray 296177 voxels (1.77%)
- WM (91.0): 92.5 +- 10.3 [70.0 --> 110.0]
- GM (74.0) : 72.5 +- 12.8 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 44.2 (was 70)
- setting MAX_BORDER_WHITE to 115.3 (was 105)
- setting MIN_BORDER_WHITE to 57.0 (was 85)
- setting MAX_CSF to 31.3 (was 40)
- setting MAX_GRAY to 94.7 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 50.6 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 18.5 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=105, GM=57
- mean inside = 92.4, mean outside = 67.6
- 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/sub005/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.90 +- 0.25 (0.01-->3.85) (max @ vno 100129 --> 101238)
- face area 0.33 +- 0.16 (0.00-->1.91)
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 23 points - only 0.00% unknown
- deleting segment 3 with 417 points - only 0.00% unknown
- deleting segment 4 with 6 points - only 0.00% unknown
- deleting segment 5 with 15 points - only 0.00% unknown
- deleting segment 6 with 35 points - only 0.00% unknown
- deleting segment 8 with 123 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- deleting segment 10 with 2 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 11 with 3 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 12 with 2 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 13 with 1 points - only 0.00% unknown
- tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.90 +- 0.25 (0.04-->3.45) (max @ vno 16176 --> 26838)
- face area 0.33 +- 0.16 (0.00-->1.91)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5162962.0, rms=0.00
- rms = 1.14, 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=5162962.0, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 23 points - only 0.00% unknown
- deleting segment 1 with 417 points - only 0.00% unknown
- deleting segment 2 with 6 points - only 0.00% unknown
- deleting segment 3 with 15 points - only 0.00% unknown
- deleting segment 4 with 35 points - only 0.00% unknown
- deleting segment 5 with 123 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- deleting segment 7 with 2 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 8 with 3 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 9 with 2 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 10 with 1 points - only 0.00% unknown
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.90 +- 0.25 (0.04-->3.45) (max @ vno 16176 --> 26838)
- face area 0.33 +- 0.16 (0.00-->1.91)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5162962.0, rms=0.00
- rms = 1.14, 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=5162962.0, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 23 points - only 0.00% unknown
- deleting segment 1 with 417 points - only 0.00% unknown
- deleting segment 2 with 6 points - only 0.00% unknown
- deleting segment 3 with 15 points - only 0.00% unknown
- deleting segment 4 with 35 points - only 0.00% unknown
- deleting segment 5 with 123 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- deleting segment 7 with 2 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 8 with 3 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 9 with 2 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 10 with 1 points - only 0.00% unknown
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.25 (0.04-->3.45) (max @ vno 16176 --> 26838)
- face area 0.33 +- 0.16 (0.00-->1.91)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5162962.0, rms=0.00
- rms = 1.14, 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=5162962.0, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 23 points - only 0.00% unknown
- deleting segment 1 with 417 points - only 0.00% unknown
- deleting segment 2 with 6 points - only 0.00% unknown
- deleting segment 3 with 15 points - only 0.00% unknown
- deleting segment 4 with 35 points - only 0.00% unknown
- deleting segment 5 with 123 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- deleting segment 7 with 2 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 8 with 3 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 9 with 2 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 10 with 1 points - only 0.00% unknown
- tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- repositioning cortical surface to gray/csf boundary.
- smoothing T1 volume with sigma = 2.000
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5162962.0, rms=0.00
- rms = 1.14, 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=5162962.0, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- 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 [109.60 186.40], gm=148.00+-12.80, and vertices in regions > 141.6
- 47738 surface locations found to contain inconsistent values (14669 in, 33069 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=595744.5, rms=0.30
- 001: dt: 0.5000, sse=553502.8, rms=0.293 (0.000%)
- 002: dt: 0.5000, sse=526265.1, rms=0.278 (0.000%)
- 003: dt: 0.5000, sse=507833.2, rms=0.267 (0.000%)
- 004: dt: 0.5000, sse=493413.0, rms=0.256 (0.000%)
- 005: dt: 0.5000, sse=482884.1, rms=0.247 (0.000%)
- 006: dt: 0.5000, sse=475175.9, rms=0.238 (0.000%)
- 007: dt: 0.5000, sse=468719.2, rms=0.231 (0.000%)
- 008: dt: 0.5000, sse=464184.7, rms=0.224 (0.000%)
- 009: dt: 0.5000, sse=460380.4, rms=0.218 (0.000%)
- 010: dt: 0.5000, sse=456370.3, rms=0.213 (0.000%)
- 011: dt: 0.5000, sse=452858.3, rms=0.208 (0.000%)
- 012: dt: 0.5000, sse=449262.8, rms=0.204 (0.000%)
- 013: dt: 0.5000, sse=447372.7, rms=0.200 (0.000%)
- 014: dt: 0.5000, sse=445664.4, rms=0.196 (0.000%)
- 015: dt: 0.5000, sse=442769.7, rms=0.193 (0.000%)
- 016: dt: 0.5000, sse=440411.4, rms=0.190 (0.000%)
- 017: dt: 0.5000, sse=438380.6, rms=0.188 (0.000%)
- 018: dt: 0.5000, sse=436463.2, rms=0.186 (0.000%)
- 019: dt: 0.5000, sse=434983.2, rms=0.184 (0.000%)
- 020: dt: 0.5000, sse=433417.6, rms=0.182 (0.000%)
- 021: dt: 0.5000, sse=431715.5, rms=0.181 (0.000%)
- 022: dt: 0.5000, sse=430139.5, rms=0.180 (0.000%)
- 023: dt: 0.5000, sse=428766.2, rms=0.179 (0.000%)
- 024: dt: 0.5000, sse=427525.1, rms=0.178 (0.000%)
- 025: dt: 0.5000, sse=426358.1, rms=0.177 (0.000%)
- 026: dt: 0.5000, sse=425162.5, rms=0.176 (0.000%)
- 027: dt: 0.5000, sse=423851.8, rms=0.175 (0.000%)
- 028: dt: 0.5000, sse=422741.6, rms=0.175 (0.000%)
- 029: dt: 0.5000, sse=421578.2, rms=0.175 (0.000%)
- 030: dt: 0.5000, sse=420429.8, rms=0.174 (0.000%)
- positioning took 4.0 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [92.50 203.50], gm=148.00+-18.50, and vertices in regions > 138.7
- 33313 surface locations found to contain inconsistent values (596 in, 32717 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=44169.9, rms=0.15
- 031: dt: 0.5000, sse=43709.6, rms=0.140 (0.000%)
- 032: dt: 0.5000, sse=43635.3, rms=0.126 (0.000%)
- 033: dt: 0.5000, sse=44064.6, rms=0.116 (0.000%)
- 034: dt: 0.5000, sse=44681.9, rms=0.109 (0.000%)
- 035: dt: 0.5000, sse=45409.6, rms=0.102 (0.000%)
- 036: dt: 0.5000, sse=46091.4, rms=0.096 (0.000%)
- 037: dt: 0.5000, sse=46703.8, rms=0.092 (0.000%)
- 038: dt: 0.5000, sse=47346.7, rms=0.087 (0.000%)
- 039: dt: 0.5000, sse=48021.3, rms=0.083 (0.000%)
- 040: dt: 0.5000, sse=48703.4, rms=0.080 (0.000%)
- 041: dt: 0.5000, sse=49356.8, rms=0.076 (0.000%)
- 042: dt: 0.5000, sse=49973.1, rms=0.073 (0.000%)
- 043: dt: 0.5000, sse=50597.7, rms=0.070 (0.000%)
- 044: dt: 0.5000, sse=51164.7, rms=0.068 (0.000%)
- 045: dt: 0.5000, sse=51701.1, rms=0.065 (0.000%)
- 046: dt: 0.5000, sse=52197.3, rms=0.063 (0.000%)
- 047: dt: 0.5000, sse=52662.8, rms=0.061 (0.000%)
- 048: dt: 0.5000, sse=53139.7, rms=0.059 (0.000%)
- 049: dt: 0.5000, sse=53547.9, rms=0.057 (0.000%)
- 050: dt: 0.5000, sse=53955.6, rms=0.056 (0.000%)
- 051: dt: 0.5000, sse=54322.5, rms=0.054 (0.000%)
- 052: dt: 0.5000, sse=54684.1, rms=0.053 (0.000%)
- 053: dt: 0.5000, sse=55005.9, rms=0.052 (0.000%)
- 054: dt: 0.5000, sse=55301.5, rms=0.050 (0.000%)
- 055: dt: 0.5000, sse=55574.7, rms=0.049 (0.000%)
- 056: dt: 0.5000, sse=55856.3, rms=0.048 (0.000%)
- 057: dt: 0.5000, sse=56084.7, rms=0.047 (0.000%)
- 058: dt: 0.5000, sse=56310.9, rms=0.046 (0.000%)
- 059: dt: 0.5000, sse=56538.4, rms=0.045 (0.000%)
- 060: dt: 0.5000, sse=56739.1, rms=0.045 (0.000%)
- positioning took 3.9 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [91.00 205.00], gm=148.00+-19.00, and vertices in regions > 138.5
- 32297 surface locations found to contain inconsistent values (167 in, 32130 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=6056.2, rms=0.05
- 061: dt: 0.5000, sse=6037.1, rms=0.052 (0.000%)
- 062: dt: 0.5000, sse=6115.4, rms=0.046 (0.000%)
- 063: dt: 0.5000, sse=6191.6, rms=0.042 (0.000%)
- 064: dt: 0.5000, sse=6254.1, rms=0.040 (0.000%)
- 065: dt: 0.5000, sse=6296.4, rms=0.038 (0.000%)
- 066: dt: 0.5000, sse=6318.2, rms=0.037 (0.000%)
- 067: dt: 0.5000, sse=6332.2, rms=0.035 (0.000%)
- 068: dt: 0.5000, sse=6344.6, rms=0.034 (0.000%)
- 069: dt: 0.5000, sse=6354.9, rms=0.033 (0.000%)
- 070: dt: 0.5000, sse=6366.8, rms=0.033 (0.000%)
- 071: dt: 0.5000, sse=6376.0, rms=0.032 (0.000%)
- 072: dt: 0.5000, sse=6388.8, rms=0.031 (0.000%)
- 073: dt: 0.5000, sse=6396.9, rms=0.030 (0.000%)
- 074: dt: 0.5000, sse=6404.4, rms=0.030 (0.000%)
- 075: dt: 0.5000, sse=6411.4, rms=0.029 (0.000%)
- 076: dt: 0.5000, sse=6418.0, rms=0.029 (0.000%)
- 077: dt: 0.5000, sse=6423.0, rms=0.028 (0.000%)
- 078: dt: 0.5000, sse=6428.2, rms=0.028 (0.000%)
- 079: dt: 0.5000, sse=6431.9, rms=0.028 (0.000%)
- 080: dt: 0.5000, sse=6435.7, rms=0.027 (0.000%)
- 081: dt: 0.5000, sse=6438.2, rms=0.027 (0.000%)
- 082: dt: 0.5000, sse=6443.0, rms=0.027 (0.000%)
- 083: dt: 0.5000, sse=6445.1, rms=0.026 (0.000%)
- 084: dt: 0.5000, sse=6448.3, rms=0.026 (0.000%)
- 085: dt: 0.5000, sse=6451.8, rms=0.026 (0.000%)
- 086: dt: 0.5000, sse=6454.8, rms=0.026 (0.000%)
- 087: dt: 0.5000, sse=6456.1, rms=0.026 (0.000%)
- 088: dt: 0.5000, sse=6458.5, rms=0.026 (0.000%)
- 089: dt: 0.5000, sse=6458.8, rms=0.026 (0.000%)
- 090: dt: 0.5000, sse=6460.6, rms=0.025 (0.000%)
- positioning took 3.8 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [90.10 205.90], gm=148.00+-19.30, and vertices in regions > 138.3
- 32407 surface locations found to contain inconsistent values (38 in, 32369 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/sub005/surf/rh.pial...
- writing smoothed curvature to rh.curv.pial
- 000: dt: 0.0000, sse=790.5, rms=0.03
- 091: dt: 0.5000, sse=783.6, rms=0.033 (0.000%)
- 092: dt: 0.5000, sse=761.9, rms=0.029 (0.000%)
- 093: dt: 0.5000, sse=755.3, rms=0.028 (0.000%)
- 094: dt: 0.5000, sse=752.2, rms=0.027 (0.000%)
- 095: dt: 0.5000, sse=749.1, rms=0.026 (0.000%)
- 096: dt: 0.5000, sse=746.9, rms=0.026 (0.000%)
- 097: dt: 0.5000, sse=745.1, rms=0.026 (0.000%)
- 098: dt: 0.5000, sse=743.6, rms=0.026 (0.000%)
- 099: dt: 0.5000, sse=741.8, rms=0.025 (0.000%)
- 100: dt: 0.5000, sse=740.3, rms=0.025 (0.000%)
- 101: dt: 0.5000, sse=739.0, rms=0.025 (0.000%)
- 102: dt: 0.5000, sse=737.9, rms=0.025 (0.000%)
- 103: dt: 0.5000, sse=736.8, rms=0.024 (0.000%)
- 104: dt: 0.5000, sse=735.8, rms=0.024 (0.000%)
- 105: dt: 0.5000, sse=735.2, rms=0.024 (0.000%)
- 106: dt: 0.5000, sse=734.3, rms=0.024 (0.000%)
- 107: dt: 0.5000, sse=733.7, rms=0.024 (0.000%)
- 108: dt: 0.5000, sse=733.1, rms=0.024 (0.000%)
- 109: dt: 0.5000, sse=732.4, rms=0.024 (0.000%)
- 110: dt: 0.5000, sse=732.1, rms=0.024 (0.000%)
- 111: dt: 0.5000, sse=731.6, rms=0.024 (0.000%)
- 112: dt: 0.5000, sse=731.3, rms=0.023 (0.000%)
- 113: dt: 0.5000, sse=731.4, rms=0.023 (0.000%)
- 114: dt: 0.5000, sse=731.1, rms=0.023 (0.000%)
- 115: dt: 0.5000, sse=730.8, rms=0.023 (0.000%)
- 116: dt: 0.5000, sse=730.6, rms=0.023 (0.000%)
- 117: dt: 0.5000, sse=730.5, rms=0.023 (0.000%)
- 118: dt: 0.5000, sse=730.4, rms=0.023 (0.000%)
- 119: dt: 0.5000, sse=730.3, rms=0.023 (0.000%)
- 120: dt: 0.5000, sse=730.0, rms=0.023 (0.000%)
- positioning took 3.8 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.curv.pial
- writing smoothed area to rh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.area.pial
- vertex spacing 1.03 +- 0.45 (0.06-->9.77) (max @ vno 101427 --> 100291)
- face area 0.41 +- 0.32 (0.00-->8.28)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 142731 vertices processed
- 25000 of 142731 vertices processed
- 50000 of 142731 vertices processed
- 75000 of 142731 vertices processed
- 100000 of 142731 vertices processed
- 125000 of 142731 vertices processed
- 0 of 142731 vertices processed
- 25000 of 142731 vertices processed
- 50000 of 142731 vertices processed
- 75000 of 142731 vertices processed
- 100000 of 142731 vertices processed
- 125000 of 142731 vertices processed
- thickness calculation complete, 479:847 truncations.
- 26619 vertices at 0 distance
- 86850 vertices at 1 distance
- 93570 vertices at 2 distance
- 45217 vertices at 3 distance
- 14907 vertices at 4 distance
- 4679 vertices at 5 distance
- 1443 vertices at 6 distance
- 510 vertices at 7 distance
- 201 vertices at 8 distance
- 105 vertices at 9 distance
- 67 vertices at 10 distance
- 46 vertices at 11 distance
- 39 vertices at 12 distance
- 35 vertices at 13 distance
- 32 vertices at 14 distance
- 22 vertices at 15 distance
- 23 vertices at 16 distance
- 28 vertices at 17 distance
- 14 vertices at 18 distance
- 27 vertices at 19 distance
- 32 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.thickness
- positioning took 19.2 minutes
- #--------------------------------------------
- #@# Surf Volume lh Thu Aug 8 23:20:13 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf
- mris_calc -o lh.area.mid lh.area add lh.area.pial
- Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o lh.area.mid lh.area.mid div 2
- Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o lh.volume lh.area.mid mul lh.thickness
- Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ]
- #--------------------------------------------
- #@# Surf Volume rh Thu Aug 8 23:20:13 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf
- mris_calc -o rh.area.mid rh.area add rh.area.pial
- Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o rh.area.mid rh.area.mid div 2
- Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o rh.volume rh.area.mid mul rh.thickness
- Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ]
- #--------------------------------------------
- #@# Cortical ribbon mask Thu Aug 8 23:20:14 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri
- mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon sub005
- 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 = 11
- writing volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/ribbon.mgz
- writing ribbon files
- #--------------------------------------------
- #@# ASeg Stats Thu Aug 8 23:37:33 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005
- 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 sub005
- $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 sub005
- sysname Linux
- hostname snake4
- machine x86_64
- user fkaule
- UseRobust 0
- atlas_icv (eTIV) = 1108117 mm^3 (det: 1.758032 )
- Computing euler number
- orig.nofix lheno = -46, rheno = -26
- orig.nofix lhholes = 24, rhholes = 14
- Loading mri/aseg.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 265530.343 264563.000 diff= 967.3 pctdiff= 0.364
- rhCtxGM: 265717.542 264874.000 diff= 843.5 pctdiff= 0.317
- lhCtxWM: 210790.046 210779.500 diff= 10.5 pctdiff= 0.005
- rhCtxWM: 210686.930 210543.500 diff= 143.4 pctdiff= 0.068
- SubCortGMVol 62575.000
- SupraTentVol 1025743.861 (1023088.000) diff=2655.861 pctdiff=0.259
- SupraTentVolNotVent 1016210.861 (1013555.000) diff=2655.861 pctdiff=0.261
- BrainSegVol 1150498.000 (1149006.000) diff=1492.000 pctdiff=0.130
- BrainSegVolNotVent 1139009.000 (1140759.861) diff=-1750.861 pctdiff=-0.154
- BrainSegVolNotVent 1139009.000
- CerebellumVol 125240.000
- VentChorVol 9533.000
- 3rd4th5thCSF 1956.000
- CSFVol 477.000, OptChiasmVol 201.000
- MaskVol 1526731.000
- 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 3278 3277.959
- 4 5 Left-Inf-Lat-Vent 580 579.936
- 5 7 Left-Cerebellum-White-Matter 12975 12975.378
- 6 8 Left-Cerebellum-Cortex 49757 49756.992
- 7 10 Left-Thalamus-Proper 7832 7832.081
- 8 11 Left-Caudate 3508 3508.107
- 9 12 Left-Putamen 6400 6400.005
- 10 13 Left-Pallidum 1978 1978.220
- 11 14 3rd-Ventricle 341 341.234
- 12 15 4th-Ventricle 1298 1297.907
- 13 16 Brain-Stem 20989 20988.875
- 14 17 Left-Hippocampus 3854 3853.685
- 15 18 Left-Amygdala 1671 1670.966
- 16 24 CSF 491 491.288
- 17 26 Left-Accumbens-area 577 577.471
- 18 28 Left-VentralDC 4012 4012.331
- 19 30 Left-vessel 127 127.376
- 20 31 Left-choroid-plexus 1356 1356.293
- 23 43 Right-Lateral-Ventricle 2569 2569.490
- 24 44 Right-Inf-Lat-Vent 409 409.412
- 25 46 Right-Cerebellum-White-Matter 14142 14142.228
- 26 47 Right-Cerebellum-Cortex 50562 50562.211
- 27 49 Right-Thalamus-Proper 7753 7752.948
- 28 50 Right-Caudate 3833 3832.621
- 29 51 Right-Putamen 6146 6145.553
- 30 52 Right-Pallidum 2178 2178.489
- 31 53 Right-Hippocampus 4059 4058.912
- 32 54 Right-Amygdala 1391 1391.412
- 33 58 Right-Accumbens-area 632 631.959
- 34 60 Right-VentralDC 4180 4180.111
- 35 62 Right-vessel 65 65.004
- 36 63 Right-choroid-plexus 1217 1216.556
- 37 72 5th-Ventricle 0 0.000
- 38 77 WM-hypointensities 1410 1410.145
- 39 78 Left-WM-hypointensities 0 0.000
- 40 79 Right-WM-hypointensities 0 0.000
- 41 80 non-WM-hypointensities 9 9.365
- 42 81 Left-non-WM-hypointensities 0 0.000
- 43 82 Right-non-WM-hypointensities 0 0.000
- 44 85 Optic-Chiasm 220 220.139
- 45 251 CC_Posterior 700 700.031
- 46 252 CC_Mid_Posterior 332 332.204
- 47 253 CC_Central 354 353.958
- 48 254 CC_Mid_Anterior 393 392.745
- 49 255 CC_Anterior 742 742.297
- Reporting on 45 segmentations
- mri_segstats done
- #-----------------------------------------
- #@# AParc-to-ASeg Thu Aug 8 23:40:22 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005
- mri_aparc2aseg --s sub005 --volmask
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- subject sub005
- outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/aparc+aseg.mgz
- useribbon 0
- baseoffset 0
- RipUnknown 0
- Reading lh white surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white
- Reading lh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.pial
- Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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/sub005/surf/rh.white
- Reading rh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.pial
- Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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/sub005/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/sub005/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 = 527907
- Used brute-force search on 0 voxels
- Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/aparc+aseg.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005
- mri_aparc2aseg --s sub005 --volmask --a2009s
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- subject sub005
- outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/aparc.a2009s+aseg.mgz
- useribbon 0
- baseoffset 10100
- RipUnknown 0
- Reading lh white surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white
- Reading lh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.pial
- Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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/sub005/surf/rh.white
- Reading rh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.pial
- Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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/sub005/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/sub005/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 = 527907
- Used brute-force search on 0 voxels
- Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/aparc.a2009s+aseg.mgz
- #-----------------------------------------
- #@# WMParc Thu Aug 8 23:45:15 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005
- mri_aparc2aseg --s sub005 --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 sub005
- 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/sub005/mri/aparc+aseg.mgz
- Reading lh white surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white
- Reading lh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.pial
- Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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/sub005/surf/rh.white
- Reading rh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.pial
- Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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/sub005/mri/ribbon.mgz
- Loading filled from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/filled.mgz
- Ripping vertices labeled as unkown
- Ripped 7419 vertices from left hemi
- Ripped 7484 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/sub005/mri/aseg.mgz
- Loading Ctx Seg File /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 = 948174
- Used brute-force search on 3 voxels
- Fixing Parahip LH WM
- Found 11 clusters
- 0 k 1.000000
- 1 k 1.000000
- 2 k 1.000000
- 3 k 4.000000
- 4 k 6.000000
- 5 k 1.000000
- 6 k 1.000000
- 7 k 3.000000
- 8 k 2.000000
- 9 k 1266.000000
- 10 k 5.000000
- Fixing Parahip RH WM
- Found 1 clusters
- 0 k 1504.000000
- Writing output aseg to mri/wmparc.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005
- 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 sub005 --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 sub005 --surf-wm-vol --ctab /opt/freesurfer/5.3.0/WMParcStatsLUT.txt --etiv
- sysname Linux
- hostname snake4
- machine x86_64
- user fkaule
- UseRobust 0
- atlas_icv (eTIV) = 1108117 mm^3 (det: 1.758032 )
- Loading mri/wmparc.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 265530.343 264563.000 diff= 967.3 pctdiff= 0.364
- rhCtxGM: 265717.542 264874.000 diff= 843.5 pctdiff= 0.317
- lhCtxWM: 210790.046 210779.500 diff= 10.5 pctdiff= 0.005
- rhCtxWM: 210686.930 210543.500 diff= 143.4 pctdiff= 0.068
- SubCortGMVol 62575.000
- SupraTentVol 1025743.861 (1023088.000) diff=2655.861 pctdiff=0.259
- SupraTentVolNotVent 1016210.861 (1013555.000) diff=2655.861 pctdiff=0.261
- BrainSegVol 1150498.000 (1149006.000) diff=1492.000 pctdiff=0.130
- BrainSegVolNotVent 1139009.000 (1140759.861) diff=-1750.861 pctdiff=-0.154
- BrainSegVolNotVent 1139009.000
- CerebellumVol 125240.000
- VentChorVol 9533.000
- 3rd4th5thCSF 1956.000
- CSFVol 477.000, OptChiasmVol 201.000
- MaskVol 1526731.000
- 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 3450 3450.128
- 2 3002 wm-lh-caudalanteriorcingulate 3079 3079.494
- 3 3003 wm-lh-caudalmiddlefrontal 5858 5858.020
- 4 3004 wm-lh-corpuscallosum 0 0.000
- 5 3005 wm-lh-cuneus 2317 2316.710
- 6 3006 wm-lh-entorhinal 737 737.111
- 7 3007 wm-lh-fusiform 6795 6795.264
- 8 3008 wm-lh-inferiorparietal 8042 8041.741
- 9 3009 wm-lh-inferiortemporal 5693 5693.238
- 10 3010 wm-lh-isthmuscingulate 3544 3544.322
- 11 3011 wm-lh-lateraloccipital 9210 9210.244
- 12 3012 wm-lh-lateralorbitofrontal 6234 6234.106
- 13 3013 wm-lh-lingual 5646 5646.042
- 14 3014 wm-lh-medialorbitofrontal 2965 2965.262
- 15 3015 wm-lh-middletemporal 4819 4819.383
- 16 3016 wm-lh-parahippocampal 1324 1324.135
- 17 3017 wm-lh-paracentral 2937 2937.116
- 18 3018 wm-lh-parsopercularis 3904 3903.856
- 19 3019 wm-lh-parsorbitalis 887 887.268
- 20 3020 wm-lh-parstriangularis 3079 3079.248
- 21 3021 wm-lh-pericalcarine 3652 3652.237
- 22 3022 wm-lh-postcentral 7938 7937.846
- 23 3023 wm-lh-posteriorcingulate 4597 4596.842
- 24 3024 wm-lh-precentral 11645 11645.031
- 25 3025 wm-lh-precuneus 8653 8652.616
- 26 3026 wm-lh-rostralanteriorcingulate 3059 3058.752
- 27 3027 wm-lh-rostralmiddlefrontal 12814 12814.424
- 28 3028 wm-lh-superiorfrontal 17570 17569.916
- 29 3029 wm-lh-superiorparietal 9900 9900.281
- 30 3030 wm-lh-superiortemporal 8486 8486.334
- 31 3031 wm-lh-supramarginal 8145 8145.244
- 32 3032 wm-lh-frontalpole 244 244.129
- 33 3033 wm-lh-temporalpole 612 612.238
- 34 3034 wm-lh-transversetemporal 894 894.139
- 35 3035 wm-lh-insula 8582 8582.195
- 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 3220 3219.576
- 120 4002 wm-rh-caudalanteriorcingulate 3311 3310.707
- 121 4003 wm-rh-caudalmiddlefrontal 4912 4912.257
- 122 4004 wm-rh-corpuscallosum 0 0.000
- 123 4005 wm-rh-cuneus 2049 2048.841
- 124 4006 wm-rh-entorhinal 470 469.973
- 125 4007 wm-rh-fusiform 5955 5954.564
- 126 4008 wm-rh-inferiorparietal 9604 9604.001
- 127 4009 wm-rh-inferiortemporal 5882 5882.254
- 128 4010 wm-rh-isthmuscingulate 2583 2582.677
- 129 4011 wm-rh-lateraloccipital 9286 9286.469
- 130 4012 wm-rh-lateralorbitofrontal 6155 6154.931
- 131 4013 wm-rh-lingual 5510 5509.599
- 132 4014 wm-rh-medialorbitofrontal 3455 3455.048
- 133 4015 wm-rh-middletemporal 6159 6158.569
- 134 4016 wm-rh-parahippocampal 1559 1558.510
- 135 4017 wm-rh-paracentral 3884 3884.006
- 136 4018 wm-rh-parsopercularis 3478 3478.004
- 137 4019 wm-rh-parsorbitalis 1207 1207.092
- 138 4020 wm-rh-parstriangularis 3691 3690.768
- 139 4021 wm-rh-pericalcarine 3452 3452.041
- 140 4022 wm-rh-postcentral 7737 7737.457
- 141 4023 wm-rh-posteriorcingulate 5053 5053.350
- 142 4024 wm-rh-precentral 12575 12574.738
- 143 4025 wm-rh-precuneus 9707 9706.634
- 144 4026 wm-rh-rostralanteriorcingulate 2264 2264.011
- 145 4027 wm-rh-rostralmiddlefrontal 12224 12223.950
- 146 4028 wm-rh-superiorfrontal 17833 17832.582
- 147 4029 wm-rh-superiorparietal 9683 9682.954
- 148 4030 wm-rh-superiortemporal 7574 7574.444
- 149 4031 wm-rh-supramarginal 7712 7712.035
- 150 4032 wm-rh-frontalpole 276 275.609
- 151 4033 wm-rh-temporalpole 623 622.763
- 152 4034 wm-rh-transversetemporal 632 632.412
- 153 4035 wm-rh-insula 7648 7648.365
- 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 24132 24131.932
- 237 5002 Right-UnsegmentedWhiteMatter 24033 24033.498
- 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/sub005/label
- #--------------------------------------------
- #@# BA Labels lh Thu Aug 8 23:56:39 CEST 2013
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
- Number of reverse mapping hits = 365
- Checking for and removing duplicates
- Writing label file ./lh.BA1.label 4494
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
- Number of reverse mapping hits = 907
- Checking for and removing duplicates
- Writing label file ./lh.BA2.label 8816
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
- Number of reverse mapping hits = 198
- Checking for and removing duplicates
- Writing label file ./lh.BA3a.label 4275
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
- Number of reverse mapping hits = 428
- Checking for and removing duplicates
- Writing label file ./lh.BA3b.label 6411
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
- Number of reverse mapping hits = 261
- Checking for and removing duplicates
- Writing label file ./lh.BA4a.label 6045
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
- Number of reverse mapping hits = 239
- Checking for and removing duplicates
- Writing label file ./lh.BA4p.label 4309
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
- Number of reverse mapping hits = 1562
- Checking for and removing duplicates
- Writing label file ./lh.BA6.label 15151
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
- Number of reverse mapping hits = 621
- Checking for and removing duplicates
- Writing label file ./lh.BA44.label 4802
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
- Number of reverse mapping hits = 994
- Checking for and removing duplicates
- Writing label file ./lh.BA45.label 4416
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
- Number of reverse mapping hits = 2066
- Checking for and removing duplicates
- Writing label file ./lh.V1.label 6707
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
- Number of reverse mapping hits = 4214
- Checking for and removing duplicates
- Writing label file ./lh.V2.label 12328
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
- Number of reverse mapping hits = 844
- Checking for and removing duplicates
- Writing label file ./lh.MT.label 2862
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.perirhinal.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
- Number of reverse mapping hits = 171
- Checking for and removing duplicates
- Writing label file ./lh.perirhinal.label 1370
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.thresh.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
- Number of reverse mapping hits = 53
- Checking for and removing duplicates
- Writing label file ./lh.BA1.thresh.label 1067
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.thresh.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
- Number of reverse mapping hits = 421
- Checking for and removing duplicates
- Writing label file ./lh.BA2.thresh.label 2513
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.thresh.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
- Number of reverse mapping hits = 35
- Checking for and removing duplicates
- Writing label file ./lh.BA3a.thresh.label 1539
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.thresh.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
- Number of reverse mapping hits = 160
- Checking for and removing duplicates
- Writing label file ./lh.BA3b.thresh.label 2156
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.thresh.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
- Number of reverse mapping hits = 108
- Checking for and removing duplicates
- Writing label file ./lh.BA4a.thresh.label 2427
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.thresh.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
- Number of reverse mapping hits = 119
- Checking for and removing duplicates
- Writing label file ./lh.BA4p.thresh.label 1668
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.thresh.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
- Number of reverse mapping hits = 682
- Checking for and removing duplicates
- Writing label file ./lh.BA6.thresh.label 7717
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.thresh.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
- Number of reverse mapping hits = 285
- Checking for and removing duplicates
- Writing label file ./lh.BA44.thresh.label 2197
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.thresh.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
- Number of reverse mapping hits = 531
- Checking for and removing duplicates
- Writing label file ./lh.BA45.thresh.label 1682
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.thresh.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
- Number of reverse mapping hits = 1544
- Checking for and removing duplicates
- Writing label file ./lh.V1.thresh.label 4949
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.thresh.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
- Number of reverse mapping hits = 1787
- Checking for and removing duplicates
- Writing label file ./lh.V2.thresh.label 5121
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.thresh.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
- Number of reverse mapping hits = 248
- Checking for and removing duplicates
- Writing label file ./lh.MT.thresh.label 761
- mri_label2label: Done
- mris_label2annot --s sub005 --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/sub005/label
- cmdline mris_label2annot --s sub005 --hemi lh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --l lh.perirhinal.label --a BA --maxstatwinner --noverbose
- sysname Linux
- hostname snake4
- machine x86_64
- user fkaule
- subject sub005
- 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/sub005/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 95912 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/lh.BA.annot
- mris_label2annot --s sub005 --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/sub005/label
- cmdline mris_label2annot --s sub005 --hemi lh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l lh.BA1.thresh.label --l lh.BA2.thresh.label --l lh.BA3a.thresh.label --l lh.BA3b.thresh.label --l lh.BA4a.thresh.label --l lh.BA4p.thresh.label --l lh.BA6.thresh.label --l lh.BA44.thresh.label --l lh.BA45.thresh.label --l lh.V1.thresh.label --l lh.V2.thresh.label --l lh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose
- sysname Linux
- hostname snake4
- machine x86_64
- user fkaule
- subject sub005
- 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/sub005/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 115470 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/lh.BA.thresh.annot
- mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab sub005 lh white
- computing statistics for each annotation in ./lh.BA.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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
- 1026 622 2411 2.723 0.400 0.177 0.069 27 2.7 BA1
- 4750 3166 8222 2.418 0.459 0.134 0.044 64 8.5 BA2
- 981 660 1032 2.009 0.416 0.131 0.073 10 1.6 BA3a
- 2545 1704 4262 2.134 0.609 0.142 0.056 55 5.5 BA3b
- 1426 887 3348 2.907 0.563 0.122 0.057 23 3.4 BA4a
- 1346 911 2520 2.663 0.446 0.118 0.074 23 5.7 BA4p
- 10036 6823 23603 2.795 0.545 0.135 0.043 150 18.1 BA6
- 2472 1671 5347 2.737 0.459 0.148 0.050 44 4.8 BA44
- 3412 2305 6933 2.529 0.607 0.155 0.063 69 8.4 BA45
- 4350 3000 6105 1.972 0.520 0.166 0.079 87 12.6 V1
- 9950 6520 15611 2.236 0.515 0.173 0.084 254 31.5 V2
- 2611 1725 4760 2.450 0.433 0.156 0.064 59 6.7 MT
- 1101 746 3309 3.365 0.725 0.175 0.102 29 4.1 perirhinal
- mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab sub005 lh white
- computing statistics for each annotation in ./lh.BA.thresh.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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
- 630 380 1469 2.704 0.443 0.183 0.077 17 1.7 BA1
- 2031 1338 3733 2.372 0.437 0.144 0.055 35 4.4 BA2
- 815 554 815 1.971 0.412 0.139 0.040 7 1.3 BA3a
- 1591 1079 2219 1.844 0.441 0.121 0.033 16 2.3 BA3b
- 1353 861 3359 2.992 0.504 0.119 0.057 21 3.3 BA4a
- 1134 759 1989 2.619 0.429 0.110 0.030 8 1.4 BA4p
- 5447 3689 12997 2.825 0.542 0.137 0.043 78 9.9 BA6
- 1718 1154 3620 2.670 0.455 0.142 0.044 27 3.1 BA44
- 1585 1060 3854 2.844 0.441 0.182 0.085 45 5.4 BA45
- 4634 3169 6415 1.960 0.513 0.166 0.079 92 13.8 V1
- 4772 3149 7474 2.177 0.540 0.187 0.100 143 17.3 V2
- 738 500 1210 2.380 0.431 0.136 0.041 8 1.2 MT
- #--------------------------------------------
- #@# BA Labels rh Fri Aug 9 00:01:11 CEST 2013
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 3962 nlabel points
- Performing mapping from target back to the source label 142731
- Number of reverse mapping hits = 464
- Checking for and removing duplicates
- Writing label file ./rh.BA1.label 4426
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 6687 nlabel points
- Performing mapping from target back to the source label 142731
- Number of reverse mapping hits = 750
- Checking for and removing duplicates
- Writing label file ./rh.BA2.label 7437
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 3980 nlabel points
- Performing mapping from target back to the source label 142731
- Number of reverse mapping hits = 223
- Checking for and removing duplicates
- Writing label file ./rh.BA3a.label 4203
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 4522 nlabel points
- Performing mapping from target back to the source label 142731
- Number of reverse mapping hits = 370
- Checking for and removing duplicates
- Writing label file ./rh.BA3b.label 4892
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 5747 nlabel points
- Performing mapping from target back to the source label 142731
- Number of reverse mapping hits = 244
- Checking for and removing duplicates
- Writing label file ./rh.BA4a.label 5991
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 4473 nlabel points
- Performing mapping from target back to the source label 142731
- Number of reverse mapping hits = 184
- Checking for and removing duplicates
- Writing label file ./rh.BA4p.label 4657
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 12256 nlabel points
- Performing mapping from target back to the source label 142731
- Number of reverse mapping hits = 1182
- Checking for and removing duplicates
- Writing label file ./rh.BA6.label 13438
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 6912 nlabel points
- Performing mapping from target back to the source label 142731
- Number of reverse mapping hits = 1300
- Checking for and removing duplicates
- Writing label file ./rh.BA44.label 8212
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 5355 nlabel points
- Performing mapping from target back to the source label 142731
- Number of reverse mapping hits = 1267
- Checking for and removing duplicates
- Writing label file ./rh.BA45.label 6622
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 4727 nlabel points
- Performing mapping from target back to the source label 142731
- Number of reverse mapping hits = 2180
- Checking for and removing duplicates
- Writing label file ./rh.V1.label 6907
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 8016 nlabel points
- Performing mapping from target back to the source label 142731
- Number of reverse mapping hits = 4090
- Checking for and removing duplicates
- Writing label file ./rh.V2.label 12106
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 1932 nlabel points
- Performing mapping from target back to the source label 142731
- Number of reverse mapping hits = 678
- Checking for and removing duplicates
- Writing label file ./rh.MT.label 2610
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.perirhinal.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 752 nlabel points
- Performing mapping from target back to the source label 142731
- Number of reverse mapping hits = 67
- Checking for and removing duplicates
- Writing label file ./rh.perirhinal.label 819
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.thresh.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 876 nlabel points
- Performing mapping from target back to the source label 142731
- Number of reverse mapping hits = 85
- Checking for and removing duplicates
- Writing label file ./rh.BA1.thresh.label 961
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.thresh.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 2688 nlabel points
- Performing mapping from target back to the source label 142731
- Number of reverse mapping hits = 400
- Checking for and removing duplicates
- Writing label file ./rh.BA2.thresh.label 3088
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.thresh.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 1698 nlabel points
- Performing mapping from target back to the source label 142731
- Number of reverse mapping hits = 51
- Checking for and removing duplicates
- Writing label file ./rh.BA3a.thresh.label 1749
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.thresh.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 2183 nlabel points
- Performing mapping from target back to the source label 142731
- Number of reverse mapping hits = 253
- Checking for and removing duplicates
- Writing label file ./rh.BA3b.thresh.label 2436
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.thresh.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 1388 nlabel points
- Performing mapping from target back to the source label 142731
- Number of reverse mapping hits = 52
- Checking for and removing duplicates
- Writing label file ./rh.BA4a.thresh.label 1440
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.thresh.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 1489 nlabel points
- Performing mapping from target back to the source label 142731
- Number of reverse mapping hits = 84
- Checking for and removing duplicates
- Writing label file ./rh.BA4p.thresh.label 1573
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.thresh.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 6959 nlabel points
- Performing mapping from target back to the source label 142731
- Number of reverse mapping hits = 634
- Checking for and removing duplicates
- Writing label file ./rh.BA6.thresh.label 7593
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.thresh.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 1012 nlabel points
- Performing mapping from target back to the source label 142731
- Number of reverse mapping hits = 294
- Checking for and removing duplicates
- Writing label file ./rh.BA44.thresh.label 1306
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.thresh.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 1178 nlabel points
- Performing mapping from target back to the source label 142731
- Number of reverse mapping hits = 210
- Checking for and removing duplicates
- Writing label file ./rh.BA45.thresh.label 1388
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.thresh.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 3232 nlabel points
- Performing mapping from target back to the source label 142731
- Number of reverse mapping hits = 1478
- Checking for and removing duplicates
- Writing label file ./rh.V1.thresh.label 4710
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.thresh.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 3437 nlabel points
- Performing mapping from target back to the source label 142731
- Number of reverse mapping hits = 1846
- Checking for and removing duplicates
- Writing label file ./rh.V2.thresh.label 5283
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.thresh.label --trgsubject sub005 --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 = sub005
- 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/sub005/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Building target registration hash (res=16).
- Building source registration hash (res=16).
- INFO: found 268 nlabel points
- Performing mapping from target back to the source label 142731
- Number of reverse mapping hits = 104
- Checking for and removing duplicates
- Writing label file ./rh.MT.thresh.label 372
- mri_label2label: Done
- mris_label2annot --s sub005 --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/sub005/label
- cmdline mris_label2annot --s sub005 --hemi rh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --l rh.perirhinal.label --a BA --maxstatwinner --noverbose
- sysname Linux
- hostname snake4
- machine x86_64
- user fkaule
- subject sub005
- 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/sub005/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 97144 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/rh.BA.annot
- mris_label2annot --s sub005 --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/sub005/label
- cmdline mris_label2annot --s sub005 --hemi rh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l rh.BA1.thresh.label --l rh.BA2.thresh.label --l rh.BA3a.thresh.label --l rh.BA3b.thresh.label --l rh.BA4a.thresh.label --l rh.BA4p.thresh.label --l rh.BA6.thresh.label --l rh.BA44.thresh.label --l rh.BA45.thresh.label --l rh.V1.thresh.label --l rh.V2.thresh.label --l rh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose
- sysname Linux
- hostname snake4
- machine x86_64
- user fkaule
- subject sub005
- 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/sub005/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 117875 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/rh.BA.thresh.annot
- mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab sub005 rh white
- computing statistics for each annotation in ./rh.BA.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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
- 975 595 2203 2.639 0.530 0.171 0.065 25 2.4 BA1
- 3840 2574 6869 2.407 0.495 0.136 0.047 59 7.9 BA2
- 1071 723 1151 1.991 0.455 0.139 0.040 11 2.0 BA3a
- 2158 1451 3589 2.086 0.615 0.137 0.043 32 3.8 BA3b
- 1379 886 3306 2.871 0.451 0.115 0.035 12 2.1 BA4a
- 1210 820 2193 2.588 0.464 0.111 0.033 10 1.6 BA4p
- 8459 5637 20058 2.858 0.530 0.138 0.045 124 16.2 BA6
- 4455 3008 8970 2.721 0.412 0.147 0.049 78 9.3 BA44
- 4707 3204 10460 2.699 0.493 0.171 0.081 127 13.1 BA45
- 4620 3252 6567 1.959 0.449 0.171 0.075 105 13.7 V1
- 9723 6398 14910 2.208 0.498 0.173 0.075 268 27.2 V2
- 2416 1636 4124 2.457 0.483 0.137 0.043 34 4.3 MT
- 574 404 1552 3.250 0.612 0.181 0.076 11 1.9 perirhinal
- mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab sub005 rh white
- computing statistics for each annotation in ./rh.BA.thresh.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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
- 657 378 1476 2.700 0.521 0.167 0.062 17 1.6 BA1
- 2341 1576 4341 2.410 0.509 0.137 0.045 36 4.0 BA2
- 896 602 889 1.983 0.436 0.140 0.040 8 1.5 BA3a
- 1801 1240 2555 1.856 0.456 0.123 0.035 19 2.8 BA3b
- 787 493 1834 2.889 0.432 0.120 0.039 9 1.3 BA4a
- 1029 701 1835 2.580 0.468 0.110 0.032 8 1.4 BA4p
- 5314 3504 12341 2.823 0.558 0.133 0.043 74 9.7 BA6
- 1147 777 2509 2.793 0.368 0.152 0.056 23 2.7 BA44
- 1152 784 3010 2.942 0.412 0.186 0.119 42 3.4 BA45
- 4420 3110 6220 1.954 0.446 0.166 0.073 96 12.7 V1
- 4971 3333 7490 2.104 0.529 0.188 0.093 178 15.6 V2
- 341 227 697 2.638 0.407 0.158 0.064 8 0.9 MT
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label
- #--------------------------------------------
- #@# Ex-vivo Entorhinal Cortex Label lh Fri Aug 9 00:05:43 CEST 2013
- mris_spherical_average -erode 1 -orig white -t 0.4 -o sub005 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label
- painting output onto subject sub005.
- processing subject lh.EC_average...
- reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 1036 points to lh.entorhinal_exvivo.label...
- mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label sub005 lh white
- limiting computations to label ./lh.entorhinal_exvivo.label.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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
- 348 238 1115 3.022 0.738 0.148 0.061 6 1.1 ./lh.entorhinal_exvivo.label
- #--------------------------------------------
- #@# Ex-vivo Entorhinal Cortex Label rh Fri Aug 9 00:05:58 CEST 2013
- mris_spherical_average -erode 1 -orig white -t 0.4 -o sub005 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label
- painting output onto subject sub005.
- processing subject rh.EC_average...
- reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 680 points to rh.entorhinal_exvivo.label...
- mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label sub005 rh white
- limiting computations to label ./rh.entorhinal_exvivo.label.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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
- 186 126 548 2.946 0.441 0.175 0.047 4 0.4 ./rh.entorhinal_exvivo.label
- #------------------------------------------
- Started at Thu Aug 8 10:53:42 CEST 2013
- Ended at Fri Aug 9 00:06:13 CEST 2013
- #@#%# recon-all-run-time-hours 13.209
- recon-all -s sub005 finished without error at Fri Aug 9 00:06:14 CEST 2013
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