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- Thu Aug 8 10:53:42 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001
- /opt/freesurfer/5.3.0/bin/recon-all
- -i /home/data/exppsy/forrest_gump/openfmri.org/sub001/anatomy/highres001.nii.gz -cw256 -all -T2 /home/data/exppsy/forrest_gump/openfmri.org/sub001/anatomy/other/t2w001.nii.gz -T2pial -subjid sub001 -sd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- subjid sub001
- 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 snake1 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 96576076 2625616 0 174132 94774232
- -/+ buffers/cache: 1627712 97573980
- Swap: 25165780 928 25164852
- ########################################
- 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: snake1 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: snake1 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: snake1 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: snake1 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: snake1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:43-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: snake1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:43-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: snake1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:43-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: snake1 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: snake1 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: snake1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:44-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: snake1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:44-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: snake1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:44-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: snake1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:44-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: snake1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:44-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: snake1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:44-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: snake1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:44-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: snake1 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: snake1 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: snake1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:45-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: snake1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:45-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: snake1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:45-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: snake1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:45-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: snake1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:45-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: snake1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:45-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: snake1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:45-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: snake1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:45-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: snake1 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: snake1 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: snake1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:46-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: snake1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:46-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: snake1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:46-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: snake1 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: 2013/08/08-08:53:46-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: snake1 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: 2013/08/08-08:53:46-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: snake1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:46-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: snake1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:46-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: snake1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:46-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: snake1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:47-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: snake1 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/sub001
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub001/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/orig/001.mgz
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub001/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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/sub001/anatomy/highres001.nii.gz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.990502, 0.046145, 0.129524)
- j_ras = (0.0675335, 0.98382, 0.165943)
- k_ras = (0.119771, -0.173114, 0.977592)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/orig/001.mgz...
- #--------------------------------------------
- #@# T2/FLAIR Input Thu Aug 8 10:54:02 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub001/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/orig/T2raw.mgz
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub001/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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/sub001/anatomy/other/t2w001.nii.gz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.990502, 0.046145, 0.129524)
- j_ras = (0.0675335, 0.98382, 0.165943)
- k_ras = (0.119771, -0.173114, 0.977592)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/orig/T2raw.mgz...
- #--------------------------------------------
- #@# MotionCor Thu Aug 8 10:54:17 CEST 2013
- Found 1 runs
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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/sub001/mri/orig/001.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/rawavg.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/orig.mgz --conform --cw256
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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/sub001/mri/rawavg.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.990502, 0.046145, 0.129524)
- j_ras = (0.0675335, 0.98382, 0.165943)
- k_ras = (0.119771, -0.173114, 0.977592)
- Original Data has (0.699928, 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/sub001/mri/orig.mgz...
- mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/talairach.xfm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/orig.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Talairach Thu Aug 8 10:54:56 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri
- mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
- talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
- cp transforms/talairach.auto.xfm transforms/talairach.xfm
- #--------------------------------------------
- #@# Talairach Failure Detection Thu Aug 8 10:57:12 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri
- talairach_afd -T 0.005 -xfm transforms/talairach.xfm
- talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.4951, pval=0.1531 >= threshold=0.0050)
- awk -f /opt/freesurfer/5.3.0/bin/extract_talairach_avi_QA.awk /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/talairach_avi.log
- tal_QC_AZS /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/talairach_avi.log
- TalAviQA: 0.96923
- z-score: -2
- #--------------------------------------------
- #@# Nu Intensity Correction Thu Aug 8 10:57:12 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/sub001/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 snake1 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
- Thu Aug 8 10:57:12 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.32484
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.32484/nu0.mnc -odt float
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.32484/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, -3.72529e-09, 0)
- j_ras = (0, -1.49012e-08, -1)
- k_ras = (1.86265e-09, 1, 1.49012e-08)
- changing data type from uchar to float (noscale = 0)...
- writing to ./tmp.mri_nu_correct.mni.32484/nu0.mnc...
-
- --------------------------------------------------------
- Iteration 1 Thu Aug 8 10:57:15 CEST 2013
- nu_correct -clobber ./tmp.mri_nu_correct.mni.32484/nu0.mnc ./tmp.mri_nu_correct.mni.32484/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.32484/0/
- [fkaule@snake1:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/] [2013-08-08 10:57:16] 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.32484/0/ ./tmp.mri_nu_correct.mni.32484/nu0.mnc ./tmp.mri_nu_correct.mni.32484/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
- Number of iterations: 22
- CV of field change: 0.000993395
- [fkaule@snake1:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/] [2013-08-08 10:57:37] running:
- /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.32484/nu0.mnc ./tmp.mri_nu_correct.mni.32484/0//template.mnc
- Transforming slices:......................................................................................Done
- Transforming slices:................................................................................................................................................................................................................................................................Done
-
-
- --------------------------------------------------------
- Iteration 2 Thu Aug 8 10:57:45 CEST 2013
- nu_correct -clobber ./tmp.mri_nu_correct.mni.32484/nu1.mnc ./tmp.mri_nu_correct.mni.32484/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.32484/1/
- [fkaule@snake1:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/] [2013-08-08 10:57:45] 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.32484/1/ ./tmp.mri_nu_correct.mni.32484/nu1.mnc ./tmp.mri_nu_correct.mni.32484/nu2.imp
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Number of iterations: 19
- CV of field change: 0.00099538
- [fkaule@snake1:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/] [2013-08-08 10:58:03] running:
- /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.32484/nu1.mnc ./tmp.mri_nu_correct.mni.32484/1//template.mnc
- Transforming slices:......................................................................................Done
- Transforming slices:................................................................................................................................................................................................................................................................Done
-
-
-
- mri_binarize --i ./tmp.mri_nu_correct.mni.32484/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.32484/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/sub001/mri
- cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.32484/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.32484/ones.mgz
- sysname Linux
- hostname snake1
- machine x86_64
- user fkaule
- input ./tmp.mri_nu_correct.mni.32484/nu2.mnc
- frame 0
- nErode3d 0
- nErode2d 0
- output ./tmp.mri_nu_correct.mni.32484/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.32484/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.32484/sum.junk --avgwf ./tmp.mri_nu_correct.mni.32484/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.32484/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.32484/sum.junk --avgwf ./tmp.mri_nu_correct.mni.32484/input.mean.dat
- sysname Linux
- hostname snake1
- machine x86_64
- user fkaule
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.32484/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.32484/input.mean.dat
- mri_segstats done
- mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.32484/ones.mgz --i ./tmp.mri_nu_correct.mni.32484/nu2.mnc --sum ./tmp.mri_nu_correct.mni.32484/sum.junk --avgwf ./tmp.mri_nu_correct.mni.32484/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.32484/ones.mgz --i ./tmp.mri_nu_correct.mni.32484/nu2.mnc --sum ./tmp.mri_nu_correct.mni.32484/sum.junk --avgwf ./tmp.mri_nu_correct.mni.32484/output.mean.dat
- sysname Linux
- hostname snake1
- machine x86_64
- user fkaule
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.32484/ones.mgz
- Loading ./tmp.mri_nu_correct.mni.32484/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.32484/output.mean.dat
- mri_segstats done
- mris_calc -o ./tmp.mri_nu_correct.mni.32484/nu2.mnc ./tmp.mri_nu_correct.mni.32484/nu2.mnc mul .94115139856038905528
- Saving result to './tmp.mri_nu_correct.mni.32484/nu2.mnc' (type = MINC ) [ ok ]
- mri_convert ./tmp.mri_nu_correct.mni.32484/nu2.mnc nu.mgz --like orig.mgz
- mri_convert ./tmp.mri_nu_correct.mni.32484/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.32484/nu2.mnc...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, -3.72529e-09, 0)
- j_ras = (0, -1.49012e-08, -1)
- k_ras = (1.86264e-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 (10, 146) to ( 3, 110)
-
-
- Thu Aug 8 10:58:48 CEST 2013
- mri_nu_correct.mni done
- mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/talairach.xfm nu.mgz nu.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Intensity Normalization Thu Aug 8 10:58:49 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri
- mri_normalize -g 1 nu.mgz T1.mgz
- using max gradient = 1.000
- reading from nu.mgz...
- normalizing image...
- talairach transform
- 1.147 -0.079 -0.081 -3.596;
- 0.113 1.007 0.442 -32.399;
- 0.058 -0.526 1.069 10.872;
- 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 = 21
- Starting OpenSpline(): npoints = 21
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Iterating 2 times
- ---------------------------------
- 3d normalization pass 1 of 2
- white matter peak found at 111
- white matter peak found at 109
- gm peak at 54 (54), valley at 43 (43)
- csf peak at 10, setting threshold to 39
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- ---------------------------------
- 3d normalization pass 2 of 2
- white matter peak found at 111
- white matter peak found at 110
- gm peak at 51 (51), valley at 34 (34)
- csf peak at 10, setting threshold to 37
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Done iterating ---------------------------------
- writing output to T1.mgz
- 3D bias adjustment took 2 minutes and 47 seconds.
- #--------------------------------------------
- #@# Skull Stripping Thu Aug 8 11:01:37 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 = (56, 19, 14) --> (198, 255, 201)
- using (103, 98, 108) as brain centroid...
- mean wm in atlas = 126, using box (86,69,85) --> (120, 127,131) 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 = -4.7
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -4.582981 @ (-9.091, 9.091, -9.091)
- max log p = -4.451757 @ (13.636, 4.545, 4.545)
- max log p = -4.395702 @ (-2.273, 2.273, -2.273)
- max log p = -4.384327 @ (-1.136, -1.136, -3.409)
- max log p = -4.368116 @ (-0.568, 0.568, -0.568)
- max log p = -4.368116 @ (0.000, 0.000, 0.000)
- Found translation: (0.6, 15.3, -10.8): log p = -4.368
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.4 (thresh=-4.4)
- 1.140 -0.057 0.139 -24.909;
- 0.000 1.062 0.440 -29.768;
- -0.139 -0.404 0.974 60.204;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.140 -0.057 0.139 -24.909;
- 0.000 1.062 0.440 -29.768;
- -0.139 -0.404 0.974 60.204;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.2500
- ****************************************
- Nine parameter search. iteration 2 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-4.0 (thresh=-4.0)
- 1.100 -0.080 0.089 -16.229;
- 0.050 1.073 0.341 -30.105;
- -0.093 -0.285 0.960 40.463;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 3 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 1.121 -0.106 0.046 -9.733;
- 0.083 1.060 0.374 -34.790;
- -0.057 -0.316 0.933 43.930;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 4 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 1.121 -0.106 0.046 -9.733;
- 0.083 1.060 0.374 -34.790;
- -0.057 -0.316 0.933 43.930;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.0625
- ****************************************
- Nine parameter search. iteration 5 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 1.115 -0.137 0.025 -4.468;
- 0.118 1.050 0.399 -41.924;
- -0.050 -0.342 0.920 45.922;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 6 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 1.113 -0.137 0.025 -4.315;
- 0.118 1.048 0.398 -41.542;
- -0.050 -0.342 0.919 45.993;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 7 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 1.113 -0.131 0.036 -5.981;
- 0.109 1.051 0.390 -39.783;
- -0.058 -0.332 0.921 45.801;
- 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
- 1.11253 -0.13081 0.03603 -5.98061;
- 0.10904 1.05066 0.38974 -39.78325;
- -0.05795 -0.33151 0.92115 45.80098;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 3481
- Quasinewton: input matrix
- 1.11253 -0.13081 0.03603 -5.98061;
- 0.10904 1.05066 0.38974 -39.78325;
- -0.05795 -0.33151 0.92115 45.80098;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 1.113 -0.131 0.036 -5.981;
- 0.109 1.051 0.390 -39.783;
- -0.058 -0.332 0.921 45.801;
- 0.000 0.000 0.000 1.000;
- pass 1, spacing 8: log(p) = -3.9 (old=-4.7)
- transform before final EM align:
- 1.113 -0.131 0.036 -5.981;
- 0.109 1.051 0.390 -39.783;
- -0.058 -0.332 0.921 45.801;
- 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
- 1.11253 -0.13081 0.03603 -5.98061;
- 0.10904 1.05066 0.38974 -39.78325;
- -0.05795 -0.33151 0.92115 45.80098;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 382743
- Quasinewton: input matrix
- 1.11253 -0.13081 0.03603 -5.98061;
- 0.10904 1.05066 0.38974 -39.78325;
- -0.05795 -0.33151 0.92115 45.80098;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 012: -log(p) = 4.3 tol 0.000000
- final transform:
- 1.113 -0.131 0.036 -5.981;
- 0.109 1.051 0.390 -39.783;
- -0.058 -0.332 0.921 45.801;
- 0.000 0.000 0.000 1.000;
- writing output transformation to transforms/talairach_with_skull.lta...
- registration took 38 minutes and 33 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=126 y=89 z=111 r=90
- first estimation of the main basin volume: 3088445 voxels
- Looking for seedpoints
- 2 found in the cerebellum
- 18 found in the rest of the brain
- global maximum in x=109, y=85, z=68, Imax=255
- CSF=14, 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=22693482306 voxels, voxel volume =1.000
- = 22693482306 mmm3 = 22693482.496 cm3
- done.
- PostAnalyze...Basin Prior
- 121 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=125,y=100, z=107, r=10259 iterations
- ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^
- GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = 45514
- RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=24 , nb = -1029788761
- LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=16 , nb = 1096754606
- RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1085496510
- LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=7 , nb = 1067666300
- OTHER CSF_MIN=0, CSF_intensity=9, CSF_MAX=19 , nb = 1082694334
-
- CSF_MAX TRANSITION GM_MIN GM
- GLOBAL
- before analyzing : 5, 7, 28, 58
- after analyzing : 5, 21, 28, 30
- RIGHT_CER
- before analyzing : 24, 26, 30, 61
- after analyzing : 24, 28, 30, 36
- LEFT_CER
- before analyzing : 16, 21, 33, 61
- after analyzing : 16, 29, 33, 37
- RIGHT_BRAIN
- before analyzing : 4, 5, 25, 58
- after analyzing : 4, 18, 25, 28
- LEFT_BRAIN
- before analyzing : 7, 10, 30, 58
- after analyzing : 7, 23, 30, 31
- OTHER
- before analyzing : 19, 52, 85, 95
- after analyzing : 19, 74, 85, 79
- mri_strip_skull: done peeling brain
- highly tesselated surface with 10242 vertices
- matching...71 iterations
- *********************VALIDATION*********************
- curvature mean = -0.012, std = 0.012
- curvature mean = 71.267, std = 8.339
- No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
- before rotation: sse = 3.26, sigma = 5.80
- after rotation: sse = 3.26, sigma = 5.80
- Localization of inacurate regions: Erosion-Dilation steps
- the sse mean is 3.87, its var is 7.01
- before Erosion-Dilatation 1.38% of inacurate vertices
- after Erosion-Dilatation 1.74% 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...43 iterations
- mri_strip_skull: done peeling brain
- Brain Size = 1779476 voxels, voxel volume = 1.000 mm3
- = 1779476 mmm3 = 1779.476 cm3
- ******************************
- Saving brainmask.auto.mgz
- done
- cp brainmask.auto.mgz brainmask.mgz
- #-------------------------------------
- #@# EM Registration Thu Aug 8 11:40:38 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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=21.9
- skull bounding box = (61, 33, 32) --> (191, 176, 198)
- using (104, 81, 115) as brain centroid...
- mean wm in atlas = 107, using box (88,63,95) --> (119, 98,135) to find MRI wm
- before smoothing, mri peak at 108
- after smoothing, mri peak at 108, scaling input intensities by 0.991
- scaling channel 0 by 0.990741
- initial log_p = -4.3
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -4.166615 @ (-9.091, 9.091, -9.091)
- max log p = -3.907213 @ (13.636, 13.636, 4.545)
- max log p = -3.844955 @ (-6.818, -6.818, -6.818)
- max log p = -3.827213 @ (1.136, -1.136, 1.136)
- max log p = -3.802566 @ (1.705, 2.841, 3.977)
- max log p = -3.802566 @ (0.000, 0.000, 0.000)
- Found translation: (0.6, 17.6, -6.3): log p = -3.803
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.4, old_max_log_p =-3.8 (thresh=-3.8)
- 1.066 -0.056 0.129 -16.418;
- 0.000 1.068 0.421 -36.217;
- -0.121 -0.368 0.843 63.841;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4)
- 1.066 -0.056 0.129 -16.418;
- 0.000 1.068 0.421 -36.217;
- -0.121 -0.368 0.843 63.841;
- 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=-3.2, old_max_log_p =-3.4 (thresh=-3.4)
- 1.089 -0.083 0.088 -14.151;
- 0.038 1.096 0.403 -38.459;
- -0.092 -0.354 0.909 53.457;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 3 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.1, old_max_log_p =-3.2 (thresh=-3.2)
- 1.089 -0.083 0.088 -12.276;
- 0.039 1.047 0.351 -27.913;
- -0.092 -0.326 0.937 47.687;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 4 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.1, old_max_log_p =-3.1 (thresh=-3.1)
- 1.089 -0.083 0.088 -12.276;
- 0.039 1.027 0.344 -25.161;
- -0.092 -0.326 0.937 47.687;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 5 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.1, old_max_log_p =-3.1 (thresh=-3.1)
- 1.089 -0.083 0.088 -12.276;
- 0.039 1.027 0.344 -25.161;
- -0.092 -0.326 0.937 47.687;
- 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=-3.1, old_max_log_p =-3.1 (thresh=-3.1)
- 1.093 -0.075 0.091 -14.405;
- 0.030 1.031 0.344 -24.059;
- -0.093 -0.327 0.939 48.036;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 7 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.1, old_max_log_p =-3.1 (thresh=-3.1)
- 1.095 -0.075 0.091 -14.736;
- 0.030 1.035 0.346 -24.562;
- -0.093 -0.328 0.942 47.835;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 8 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.1, old_max_log_p =-3.1 (thresh=-3.1)
- 1.095 -0.075 0.091 -14.736;
- 0.030 1.035 0.346 -24.562;
- -0.093 -0.329 0.945 47.700;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 9 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.1, old_max_log_p =-3.1 (thresh=-3.1)
- 1.095 -0.075 0.091 -14.736;
- 0.030 1.035 0.346 -24.562;
- -0.093 -0.329 0.945 47.700;
- 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
- 1.09533 -0.07518 0.09136 -14.73587;
- 0.02983 1.03504 0.34570 -24.56173;
- -0.09313 -0.32883 0.94460 47.70000;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 2772
- Quasinewton: input matrix
- 1.09533 -0.07518 0.09136 -14.73587;
- 0.02983 1.03504 0.34570 -24.56173;
- -0.09313 -0.32883 0.94460 47.70000;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 012: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 1.095 -0.075 0.091 -14.736;
- 0.030 1.035 0.346 -24.562;
- -0.093 -0.329 0.945 47.700;
- 0.000 0.000 0.000 1.000;
- pass 1, spacing 8: log(p) = -3.1 (old=-4.3)
- transform before final EM align:
- 1.095 -0.075 0.091 -14.736;
- 0.030 1.035 0.346 -24.562;
- -0.093 -0.329 0.945 47.700;
- 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
- 1.09533 -0.07518 0.09136 -14.73587;
- 0.02983 1.03504 0.34570 -24.56173;
- -0.09313 -0.32883 0.94460 47.70000;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 312841
- Quasinewton: input matrix
- 1.09533 -0.07518 0.09136 -14.73587;
- 0.02983 1.03504 0.34570 -24.56173;
- -0.09313 -0.32883 0.94460 47.70000;
- 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: 014: -log(p) = 3.7 tol 0.000000
- final transform:
- 1.095 -0.075 0.091 -14.736;
- 0.030 1.035 0.346 -24.562;
- -0.093 -0.329 0.945 47.700;
- 0.000 0.000 0.000 1.000;
- writing output transformation to transforms/talairach.lta...
- registration took 36 minutes and 40 seconds.
- #--------------------------------------
- #@# CA Normalize Thu Aug 8 12:17:18 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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=21.9
- skull bounding box = (61, 33, 32) --> (191, 176, 198)
- using (104, 81, 115) as brain centroid...
- mean wm in atlas = 107, using box (88,63,95) --> (119, 98,135) to find MRI wm
- before smoothing, mri peak at 108
- after smoothing, mri peak at 108, scaling input intensities by 0.991
- scaling channel 0 by 0.990741
- using 244171 sample points...
- INFO: compute sample coordinates transform
- 1.095 -0.075 0.091 -14.736;
- 0.030 1.035 0.346 -24.562;
- -0.093 -0.329 0.945 47.700;
- 0.000 0.000 0.000 1.000;
- INFO: transform used
- finding control points in Left_Cerebral_White_Matter....
- found 41584 control points for structure...
- bounding box (122, 37, 35) --> (188, 148, 196)
- Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 192.0
- 0 of 54 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 40735 control points for structure...
- bounding box (66, 38, 33) --> (129, 142, 195)
- Right_Cerebral_White_Matter: limiting intensities to 98.0 --> 192.0
- 0 of 39 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3012 control points for structure...
- bounding box (131, 122, 68) --> (176, 162, 119)
- Left_Cerebellum_White_Matter: limiting intensities to 93.0 --> 192.0
- 0 of 12 (0.0%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2764 control points for structure...
- bounding box (89, 122, 62) --> (132, 164, 118)
- Right_Cerebellum_White_Matter: limiting intensities to 93.0 --> 192.0
- 0 of 12 (0.0%) samples deleted
- finding control points in Brain_Stem....
- found 3520 control points for structure...
- bounding box (113, 109, 97) --> (143, 173, 128)
- Brain_Stem: limiting intensities to 83.0 --> 192.0
- 0 of 14 (0.0%) samples deleted
- using 131 total control points for intensity normalization...
- bias field = 0.973 +- 0.075
- 0 of 131 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 41584 control points for structure...
- bounding box (122, 37, 35) --> (188, 148, 196)
- Left_Cerebral_White_Matter: limiting intensities to 87.0 --> 176.0
- 1 of 117 (0.9%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 40735 control points for structure...
- bounding box (66, 38, 33) --> (129, 142, 195)
- Right_Cerebral_White_Matter: limiting intensities to 94.0 --> 176.0
- 0 of 120 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3012 control points for structure...
- bounding box (131, 122, 68) --> (176, 162, 119)
- Left_Cerebellum_White_Matter: limiting intensities to 83.0 --> 176.0
- 0 of 45 (0.0%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2764 control points for structure...
- bounding box (89, 122, 62) --> (132, 164, 118)
- Right_Cerebellum_White_Matter: limiting intensities to 82.0 --> 176.0
- 0 of 52 (0.0%) samples deleted
- finding control points in Brain_Stem....
- found 3520 control points for structure...
- bounding box (113, 109, 97) --> (143, 173, 128)
- Brain_Stem: limiting intensities to 93.0 --> 176.0
- 40 of 59 (67.8%) samples deleted
- using 393 total control points for intensity normalization...
- bias field = 0.998 +- 0.058
- 0 of 352 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 41584 control points for structure...
- bounding box (122, 37, 35) --> (188, 148, 196)
- Left_Cerebral_White_Matter: limiting intensities to 94.0 --> 174.0
- 0 of 204 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 40735 control points for structure...
- bounding box (66, 38, 33) --> (129, 142, 195)
- Right_Cerebral_White_Matter: limiting intensities to 93.0 --> 174.0
- 0 of 207 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3012 control points for structure...
- bounding box (131, 122, 68) --> (176, 162, 119)
- Left_Cerebellum_White_Matter: limiting intensities to 79.0 --> 174.0
- 0 of 59 (0.0%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2764 control points for structure...
- bounding box (89, 122, 62) --> (132, 164, 118)
- Right_Cerebellum_White_Matter: limiting intensities to 79.0 --> 174.0
- 0 of 58 (0.0%) samples deleted
- finding control points in Brain_Stem....
- found 3520 control points for structure...
- bounding box (113, 109, 97) --> (143, 173, 128)
- Brain_Stem: limiting intensities to 73.0 --> 174.0
- 0 of 81 (0.0%) samples deleted
- using 609 total control points for intensity normalization...
- bias field = 1.002 +- 0.042
- 1 of 609 control points discarded
- writing normalized volume to norm.mgz...
- writing control points to ctrl_pts.mgz
- freeing GCA...done.
- normalization took 2 minutes and 1 seconds.
- #--------------------------------------
- #@# CA Reg Thu Aug 8 12:19:20 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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) = 1.21 (predicted orig area = 6.6)
- label assignment complete, 0 changed (0.00%)
- freeing gibbs priors...done.
- average std[0] = 5.0
- **************** pass 1 of 1 ************************
- setting smoothness coefficient to 0.039
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.799, neg=0, invalid=96777
- 0001: dt=129.472000, rms=0.741 (7.298%), neg=0, invalid=96777
- 0002: dt=129.472000, rms=0.730 (1.441%), neg=0, invalid=96777
- 0003: dt=129.472000, rms=0.721 (1.244%), neg=0, invalid=96777
- 0004: dt=129.472000, rms=0.716 (0.619%), neg=0, invalid=96777
- 0005: dt=129.472000, rms=0.712 (0.657%), neg=0, invalid=96777
- 0006: dt=110.976000, rms=0.709 (0.363%), neg=0, invalid=96777
- 0007: dt=129.472000, rms=0.706 (0.443%), neg=0, invalid=96777
- 0008: dt=129.472000, rms=0.704 (0.283%), neg=0, invalid=96777
- 0009: dt=129.472000, rms=0.702 (0.331%), neg=0, invalid=96777
- 0010: dt=129.472000, rms=0.700 (0.224%), neg=0, invalid=96777
- 0011: dt=129.472000, rms=0.698 (0.257%), neg=0, invalid=96777
- 0012: dt=129.472000, rms=0.696 (0.384%), neg=0, invalid=96777
- 0013: dt=129.472000, rms=0.693 (0.377%), neg=0, invalid=96777
- 0014: dt=129.472000, rms=0.689 (0.503%), neg=0, invalid=96777
- 0015: dt=129.472000, rms=0.686 (0.433%), neg=0, invalid=96777
- 0016: dt=129.472000, rms=0.683 (0.463%), neg=0, invalid=96777
- 0017: dt=129.472000, rms=0.681 (0.384%), neg=0, invalid=96777
- 0018: dt=129.472000, rms=0.678 (0.372%), neg=0, invalid=96777
- 0019: dt=129.472000, rms=0.676 (0.251%), neg=0, invalid=96777
- 0020: dt=129.472000, rms=0.674 (0.302%), neg=0, invalid=96777
- 0021: dt=129.472000, rms=0.673 (0.280%), neg=0, invalid=96777
- 0022: dt=129.472000, rms=0.671 (0.235%), neg=0, invalid=96777
- 0023: dt=129.472000, rms=0.670 (0.181%), neg=0, invalid=96777
- 0024: dt=129.472000, rms=0.668 (0.212%), neg=0, invalid=96777
- 0025: dt=129.472000, rms=0.667 (0.173%), neg=0, invalid=96777
- 0026: dt=129.472000, rms=0.666 (0.182%), neg=0, invalid=96777
- 0027: dt=129.472000, rms=0.665 (0.188%), neg=0, invalid=96777
- 0028: dt=129.472000, rms=0.664 (0.173%), neg=0, invalid=96777
- 0029: dt=129.472000, rms=0.663 (0.150%), neg=0, invalid=96777
- 0030: dt=129.472000, rms=0.661 (0.191%), neg=0, invalid=96777
- 0031: dt=129.472000, rms=0.660 (0.160%), neg=0, invalid=96777
- 0032: dt=129.472000, rms=0.659 (0.141%), neg=0, invalid=96777
- 0033: dt=129.472000, rms=0.659 (0.116%), neg=0, invalid=96777
- 0034: dt=129.472000, rms=0.658 (0.143%), neg=0, invalid=96777
- 0035: dt=129.472000, rms=0.657 (0.117%), neg=0, invalid=96777
- 0036: dt=129.472000, rms=0.656 (0.107%), neg=0, invalid=96777
- 0037: dt=295.936000, rms=0.656 (0.025%), neg=0, invalid=96777
- 0038: dt=295.936000, rms=0.656 (-0.017%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.656, neg=0, invalid=96777
- 0039: dt=129.472000, rms=0.655 (0.153%), neg=0, invalid=96777
- 0040: dt=295.936000, rms=0.654 (0.078%), neg=0, invalid=96777
- 0041: dt=295.936000, rms=0.654 (0.030%), neg=0, invalid=96777
- 0042: dt=295.936000, rms=0.654 (0.046%), neg=0, invalid=96777
- 0043: dt=295.936000, rms=0.653 (0.198%), neg=0, invalid=96777
- 0044: dt=295.936000, rms=0.653 (-0.598%), neg=0, invalid=96777
- 0045: dt=32.368000, rms=0.653 (0.022%), neg=0, invalid=96777
- 0046: dt=8.092000, rms=0.652 (0.005%), neg=0, invalid=96777
- setting smoothness coefficient to 0.154
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.658, neg=0, invalid=96777
- 0047: dt=124.416000, rms=0.653 (0.761%), neg=0, invalid=96777
- 0048: dt=36.288000, rms=0.648 (0.717%), neg=0, invalid=96777
- 0049: dt=36.288000, rms=0.647 (0.164%), neg=0, invalid=96777
- 0050: dt=36.288000, rms=0.644 (0.468%), neg=0, invalid=96777
- 0051: dt=36.288000, rms=0.641 (0.505%), neg=0, invalid=96777
- 0052: dt=36.288000, rms=0.638 (0.496%), neg=0, invalid=96777
- 0053: dt=36.288000, rms=0.633 (0.700%), neg=0, invalid=96777
- 0054: dt=36.288000, rms=0.628 (0.866%), neg=0, invalid=96777
- 0055: dt=36.288000, rms=0.624 (0.683%), neg=0, invalid=96777
- 0056: dt=36.288000, rms=0.620 (0.566%), neg=0, invalid=96777
- 0057: dt=36.288000, rms=0.617 (0.528%), neg=0, invalid=96777
- 0058: dt=36.288000, rms=0.613 (0.633%), neg=0, invalid=96777
- 0059: dt=36.288000, rms=0.610 (0.484%), neg=0, invalid=96777
- 0060: dt=36.288000, rms=0.607 (0.406%), neg=0, invalid=96777
- 0061: dt=36.288000, rms=0.605 (0.318%), neg=0, invalid=96777
- 0062: dt=36.288000, rms=0.603 (0.417%), neg=0, invalid=96777
- 0063: dt=36.288000, rms=0.601 (0.308%), neg=0, invalid=96777
- 0064: dt=36.288000, rms=0.600 (0.215%), neg=0, invalid=96777
- 0065: dt=36.288000, rms=0.599 (0.094%), neg=0, invalid=96777
- 0066: dt=36.288000, rms=0.598 (0.180%), neg=0, invalid=96777
- 0067: dt=36.288000, rms=0.597 (0.162%), neg=0, invalid=96777
- 0068: dt=36.288000, rms=0.597 (0.098%), neg=0, invalid=96777
- 0069: dt=36.288000, rms=0.596 (0.073%), neg=0, invalid=96777
- 0070: dt=36.288000, rms=0.596 (0.112%), neg=0, invalid=96777
- 0071: dt=9.072000, rms=0.595 (0.003%), neg=0, invalid=96777
- 0072: dt=9.072000, rms=0.595 (0.004%), neg=0, invalid=96777
- 0073: dt=9.072000, rms=0.595 (0.007%), neg=0, invalid=96777
- 0074: dt=9.072000, rms=0.595 (0.011%), neg=0, invalid=96777
- 0075: dt=9.072000, rms=0.595 (0.023%), neg=0, invalid=96777
- 0076: dt=9.072000, rms=0.595 (0.029%), neg=0, invalid=96777
- 0077: dt=9.072000, rms=0.595 (0.033%), neg=0, invalid=96777
- 0078: dt=9.072000, rms=0.595 (0.033%), neg=0, invalid=96777
- 0079: dt=9.072000, rms=0.594 (0.030%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.594, neg=0, invalid=96777
- 0080: dt=36.288000, rms=0.594 (0.082%), neg=0, invalid=96777
- 0081: dt=82.944000, rms=0.594 (0.077%), neg=0, invalid=96777
- 0082: dt=82.944000, rms=0.594 (-0.249%), neg=0, invalid=96777
- setting smoothness coefficient to 0.588
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.616, neg=0, invalid=96777
- 0083: dt=2.800000, rms=0.616 (0.027%), neg=0, invalid=96777
- 0084: dt=2.400000, rms=0.616 (0.010%), neg=0, invalid=96777
- 0085: dt=2.400000, rms=0.616 (0.004%), neg=0, invalid=96777
- 0086: dt=2.400000, rms=0.616 (-0.036%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.616, neg=0, invalid=96777
- 0087: dt=0.000000, rms=0.616 (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=0.677, neg=0, invalid=96777
- 0088: dt=5.126844, rms=0.660 (2.523%), neg=0, invalid=96777
- 0089: dt=2.452830, rms=0.660 (0.107%), neg=0, invalid=96777
- 0090: dt=2.452830, rms=0.660 (-0.025%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.660, neg=0, invalid=96777
- 0091: dt=0.000000, rms=0.660 (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=0.720, neg=0, invalid=96777
- 0092: dt=1.151961, rms=0.716 (0.579%), neg=0, invalid=96777
- 0093: dt=2.250000, rms=0.710 (0.842%), neg=0, invalid=96777
- 0094: dt=0.448000, rms=0.710 (0.037%), neg=0, invalid=96777
- 0095: dt=0.448000, rms=0.709 (0.030%), neg=0, invalid=96777
- 0096: dt=0.448000, rms=0.709 (0.038%), neg=0, invalid=96777
- 0097: dt=0.448000, rms=0.709 (0.033%), neg=0, invalid=96777
- 0098: dt=0.448000, rms=0.709 (0.011%), neg=0, invalid=96777
- 0099: dt=2.160000, rms=0.708 (0.153%), neg=0, invalid=96777
- 0100: dt=0.000000, rms=0.708 (0.001%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.708, neg=0, invalid=96777
- 0101: dt=0.453125, rms=0.707 (0.049%), neg=0, invalid=96777
- 0102: dt=0.448000, rms=0.707 (0.005%), neg=0, invalid=96777
- 0103: dt=0.448000, rms=0.707 (-0.000%), neg=0, invalid=96777
- resetting metric properties...
- setting smoothness coefficient to 10.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.675, neg=0, invalid=96777
- 0104: dt=0.448000, rms=0.657 (2.711%), neg=0, invalid=96777
- 0105: dt=0.000000, rms=0.657 (0.004%), neg=0, invalid=96777
- 0106: dt=0.050000, rms=0.657 (-0.469%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.657, neg=0, invalid=96777
- 0107: dt=0.000000, rms=0.657 (0.000%), neg=0, invalid=96777
- renormalizing by structure alignment....
- renormalizing input #0
- gca peak = 0.11725 (24)
- mri peak = 0.12190 ( 7)
- Left_Lateral_Ventricle (4): linear fit = 0.25 x + 0.0 (1194 voxels, overlap=0.005)
- Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (1194 voxels, peak = 6), gca=9.6
- gca peak = 0.14022 (22)
- mri peak = 0.17481 ( 7)
- Right_Lateral_Ventricle (43): linear fit = 0.25 x + 0.0 (967 voxels, overlap=0.007)
- Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (967 voxels, peak = 6), gca=8.8
- gca peak = 0.24234 (100)
- mri peak = 0.08399 (83)
- Right_Pallidum (52): linear fit = 0.83 x + 0.0 (389 voxels, overlap=0.043)
- Right_Pallidum (52): linear fit = 0.83 x + 0.0 (389 voxels, peak = 84), gca=83.5
- gca peak = 0.19192 (97)
- mri peak = 0.07586 (84)
- Left_Pallidum (13): linear fit = 0.82 x + 0.0 (232 voxels, overlap=0.049)
- Left_Pallidum (13): linear fit = 0.82 x + 0.0 (232 voxels, peak = 80), gca=80.0
- gca peak = 0.24007 (63)
- mri peak = 0.07148 (56)
- Right_Hippocampus (53): linear fit = 0.90 x + 0.0 (500 voxels, overlap=0.374)
- Right_Hippocampus (53): linear fit = 0.90 x + 0.0 (500 voxels, peak = 57), gca=57.0
- gca peak = 0.29892 (64)
- mri peak = 0.07617 (61)
- Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (490 voxels, overlap=0.929)
- Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (490 voxels, peak = 59), gca=59.2
- gca peak = 0.12541 (104)
- mri peak = 0.08628 (107)
- Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (68451 voxels, overlap=0.760)
- Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (68451 voxels, peak = 107), gca=106.6
- gca peak = 0.13686 (104)
- mri peak = 0.08602 (104)
- Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (71191 voxels, overlap=0.772)
- Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (71191 voxels, peak = 106), gca=105.6
- gca peak = 0.11691 (63)
- mri peak = 0.04607 (56)
- Left_Cerebral_Cortex (3): linear fit = 0.85 x + 0.0 (17191 voxels, overlap=0.496)
- Left_Cerebral_Cortex (3): linear fit = 0.85 x + 0.0 (17191 voxels, peak = 53), gca=53.2
- gca peak = 0.13270 (63)
- mri peak = 0.04391 (52)
- Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (17892 voxels, overlap=0.382)
- Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (17892 voxels, peak = 52), gca=52.0
- gca peak = 0.15182 (70)
- mri peak = 0.08303 (62)
- Right_Caudate (50): linear fit = 0.89 x + 0.0 (594 voxels, overlap=0.608)
- Right_Caudate (50): linear fit = 0.89 x + 0.0 (594 voxels, peak = 63), gca=62.6
- gca peak = 0.14251 (76)
- mri peak = 0.04742 (62)
- Left_Caudate (11): linear fit = 0.81 x + 0.0 (561 voxels, overlap=0.263)
- Left_Caudate (11): linear fit = 0.81 x + 0.0 (561 voxels, peak = 61), gca=61.2
- gca peak = 0.12116 (60)
- mri peak = 0.04383 (56)
- Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (9285 voxels, overlap=0.843)
- Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (9285 voxels, peak = 56), gca=56.1
- gca peak = 0.12723 (61)
- mri peak = 0.04490 (57)
- Right_Cerebellum_Cortex (47): linear fit = 0.92 x + 0.0 (10465 voxels, overlap=0.927)
- Right_Cerebellum_Cortex (47): linear fit = 0.92 x + 0.0 (10465 voxels, peak = 56), gca=55.8
- gca peak = 0.22684 (88)
- mri peak = 0.08905 (93)
- Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (7569 voxels, overlap=0.843)
- Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (7569 voxels, peak = 93), gca=92.8
- gca peak = 0.21067 (87)
- mri peak = 0.07890 (93)
- Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (6814 voxels, overlap=0.923)
- Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (6814 voxels, peak = 92), gca=91.8
- gca peak = 0.25455 (62)
- mri peak = 0.09524 (58)
- Left_Amygdala (18): linear fit = 0.93 x + 0.0 (266 voxels, overlap=0.853)
- Left_Amygdala (18): linear fit = 0.93 x + 0.0 (266 voxels, peak = 57), gca=57.4
- gca peak = 0.39668 (62)
- mri peak = 0.09319 (55)
- Right_Amygdala (54): linear fit = 0.88 x + 0.0 (309 voxels, overlap=0.992)
- Right_Amygdala (54): linear fit = 0.88 x + 0.0 (309 voxels, peak = 54), gca=54.2
- gca peak = 0.10129 (93)
- mri peak = 0.05570 (98)
- Left_Thalamus_Proper (10): linear fit = 1.03 x + 0.0 (5272 voxels, overlap=0.896)
- Left_Thalamus_Proper (10): linear fit = 1.03 x + 0.0 (5272 voxels, peak = 96), gca=96.3
- gca peak = 0.12071 (89)
- mri peak = 0.05396 (92)
- Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (3958 voxels, overlap=0.943)
- Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (3958 voxels, peak = 91), gca=91.2
- gca peak = 0.13716 (82)
- mri peak = 0.06073 (77)
- Left_Putamen (12): linear fit = 0.93 x + 0.0 (1771 voxels, overlap=0.628)
- Left_Putamen (12): linear fit = 0.93 x + 0.0 (1771 voxels, peak = 76), gca=75.8
- gca peak = 0.15214 (84)
- mri peak = 0.05482 (72)
- Right_Putamen (51): linear fit = 0.88 x + 0.0 (1979 voxels, overlap=0.217)
- Right_Putamen (51): linear fit = 0.88 x + 0.0 (1979 voxels, peak = 74), gca=74.3
- gca peak = 0.08983 (85)
- mri peak = 0.07168 (87)
- Brain_Stem (16): linear fit = 1.04 x + 0.0 (11574 voxels, overlap=0.778)
- Brain_Stem (16): linear fit = 1.04 x + 0.0 (11574 voxels, peak = 89), gca=88.8
- gca peak = 0.11809 (92)
- mri peak = 0.08095 (91)
- Right_VentralDC (60): linear fit = 1.04 x + 0.0 (744 voxels, overlap=0.806)
- Right_VentralDC (60): linear fit = 1.04 x + 0.0 (744 voxels, peak = 96), gca=96.1
- gca peak = 0.12914 (94)
- mri peak = 0.06386 (99)
- Left_VentralDC (28): linear fit = 1.01 x + 0.0 (942 voxels, overlap=0.918)
- Left_VentralDC (28): linear fit = 1.01 x + 0.0 (942 voxels, peak = 95), gca=95.4
- gca peak = 0.21100 (36)
- mri peak = 1.00000 (55)
- gca peak = 0.13542 (27)
- mri peak = 0.14585 ( 8)
- Fourth_Ventricle (15): linear fit = 0.22 x + 0.0 (224 voxels, overlap=0.027)
- Fourth_Ventricle (15): linear fit = 0.22 x + 0.0 (224 voxels, peak = 6), gca=6.1
- gca peak Unknown = 0.94427 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.21802 (40)
- gca peak Third_Ventricle = 0.21100 (36)
- gca peak Fourth_Ventricle = 0.13542 (27)
- gca peak CSF = 0.17123 (45)
- gca peak Left_Accumbens_area = 0.25875 (69)
- gca peak Left_undetermined = 0.96240 (36)
- gca peak Left_vessel = 0.33262 (65)
- gca peak Left_choroid_plexus = 0.09846 (46)
- gca peak Right_Inf_Lat_Vent = 0.28113 (34)
- gca peak Right_Accumbens_area = 0.27120 (72)
- gca peak Right_vessel = 0.61915 (60)
- gca peak Right_choroid_plexus = 0.12775 (51)
- gca peak Fifth_Ventricle = 0.45329 (44)
- gca peak WM_hypointensities = 0.11729 (81)
- gca peak non_WM_hypointensities = 0.10912 (56)
- gca peak Optic_Chiasm = 0.33287 (75)
- label assignment complete, 0 changed (0.00%)
- not using caudate to estimate GM means
- estimating mean gm scale to be 0.88 x + 0.0
- estimating mean wm scale to be 1.02 x + 0.0
- estimating mean csf scale to be 0.40 x + 0.0
- saving intensity scales to talairach.label_intensities.txt
- **************** pass 1 of 1 ************************
- setting smoothness coefficient to 0.008
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.688, neg=0, invalid=96777
- 0108: dt=110.976000, rms=0.683 (0.764%), neg=0, invalid=96777
- 0109: dt=295.936000, rms=0.679 (0.630%), neg=0, invalid=96777
- 0110: dt=73.984000, rms=0.677 (0.243%), neg=0, invalid=96777
- 0111: dt=369.920000, rms=0.675 (0.293%), neg=0, invalid=96777
- 0112: dt=32.368000, rms=0.674 (0.131%), neg=0, invalid=96777
- 0113: dt=73.984000, rms=0.674 (0.053%), neg=0, invalid=96777
- 0114: dt=295.936000, rms=0.673 (0.129%), neg=0, invalid=96777
- 0115: dt=55.488000, rms=0.672 (0.080%), neg=0, invalid=96777
- 0116: dt=1183.744000, rms=0.670 (0.314%), neg=0, invalid=96777
- 0117: dt=110.976000, rms=0.669 (0.142%), neg=0, invalid=96777
- 0118: dt=73.984000, rms=0.669 (0.066%), neg=0, invalid=96777
- 0119: dt=129.472000, rms=0.669 (0.017%), neg=0, invalid=96777
- 0120: dt=129.472000, rms=0.668 (0.048%), neg=0, invalid=96777
- 0121: dt=129.472000, rms=0.668 (0.059%), neg=0, invalid=96777
- 0122: dt=129.472000, rms=0.668 (0.067%), neg=0, invalid=96777
- 0123: dt=129.472000, rms=0.667 (0.100%), neg=0, invalid=96777
- 0124: dt=129.472000, rms=0.666 (0.100%), neg=0, invalid=96777
- 0125: dt=129.472000, rms=0.666 (0.094%), neg=0, invalid=96777
- 0126: dt=129.472000, rms=0.665 (0.079%), neg=0, invalid=96777
- 0127: dt=129.472000, rms=0.665 (0.079%), neg=0, invalid=96777
- 0128: dt=129.472000, rms=0.664 (0.085%), neg=0, invalid=96777
- 0129: dt=129.472000, rms=0.663 (0.074%), neg=0, invalid=96777
- 0130: dt=129.472000, rms=0.663 (0.069%), neg=0, invalid=96777
- 0131: dt=129.472000, rms=0.663 (0.075%), neg=0, invalid=96777
- 0132: dt=129.472000, rms=0.662 (0.074%), neg=0, invalid=96777
- 0133: dt=129.472000, rms=0.662 (0.072%), neg=0, invalid=96777
- 0134: dt=129.472000, rms=0.661 (0.075%), neg=0, invalid=96777
- 0135: dt=129.472000, rms=0.661 (0.074%), neg=0, invalid=96777
- 0136: dt=129.472000, rms=0.660 (0.073%), neg=0, invalid=96777
- 0137: dt=129.472000, rms=0.660 (0.074%), neg=0, invalid=96777
- 0138: dt=129.472000, rms=0.659 (0.071%), neg=0, invalid=96777
- 0139: dt=129.472000, rms=0.659 (0.066%), neg=0, invalid=96777
- 0140: dt=129.472000, rms=0.658 (0.065%), neg=0, invalid=96777
- 0141: dt=129.472000, rms=0.658 (0.065%), neg=0, invalid=96777
- 0142: dt=129.472000, rms=0.657 (0.063%), neg=0, invalid=96777
- 0143: dt=129.472000, rms=0.657 (0.058%), neg=0, invalid=96777
- 0144: dt=129.472000, rms=0.657 (0.050%), neg=0, invalid=96777
- 0145: dt=129.472000, rms=0.656 (0.052%), neg=0, invalid=96777
- 0146: dt=129.472000, rms=0.656 (0.049%), neg=0, invalid=96777
- 0147: dt=129.472000, rms=0.656 (0.033%), neg=0, invalid=96777
- 0148: dt=129.472000, rms=0.656 (0.054%), neg=0, invalid=96777
- 0149: dt=129.472000, rms=0.655 (0.049%), neg=0, invalid=96777
- 0150: dt=129.472000, rms=0.655 (0.040%), neg=0, invalid=96777
- 0151: dt=129.472000, rms=0.655 (0.033%), neg=0, invalid=96777
- 0152: dt=129.472000, rms=0.654 (0.033%), neg=0, invalid=96777
- 0153: dt=129.472000, rms=0.654 (0.040%), neg=0, invalid=96777
- 0154: dt=129.472000, rms=0.654 (0.049%), neg=0, invalid=96777
- 0155: dt=129.472000, rms=0.654 (0.032%), neg=0, invalid=96777
- 0156: dt=129.472000, rms=0.654 (0.022%), neg=0, invalid=96777
- 0157: dt=129.472000, rms=0.653 (0.028%), neg=0, invalid=96777
- 0158: dt=129.472000, rms=0.653 (0.040%), neg=0, invalid=96777
- 0159: dt=129.472000, rms=0.653 (0.030%), neg=0, invalid=96777
- 0160: dt=129.472000, rms=0.653 (0.021%), neg=0, invalid=96777
- 0161: dt=129.472000, rms=0.653 (0.026%), neg=0, invalid=96777
- 0162: dt=129.472000, rms=0.652 (0.032%), neg=0, invalid=96777
- 0163: dt=129.472000, rms=0.652 (0.029%), neg=0, invalid=96777
- 0164: dt=129.472000, rms=0.652 (0.027%), neg=0, invalid=96777
- 0165: dt=129.472000, rms=0.652 (0.027%), neg=0, invalid=96777
- 0166: dt=129.472000, rms=0.652 (0.027%), neg=0, invalid=96777
- 0167: dt=129.472000, rms=0.652 (0.025%), neg=0, invalid=96777
- 0168: dt=129.472000, rms=0.651 (0.022%), neg=0, invalid=96777
- 0169: dt=129.472000, rms=0.651 (0.019%), neg=0, invalid=96777
- 0170: dt=295.936000, rms=0.651 (0.001%), neg=0, invalid=96777
- 0171: dt=295.936000, rms=0.651 (-0.005%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.651, neg=0, invalid=96777
- 0172: dt=295.936000, rms=0.650 (0.176%), neg=0, invalid=96777
- 0173: dt=92.480000, rms=0.650 (0.013%), neg=0, invalid=96777
- 0174: dt=92.480000, rms=0.650 (0.021%), neg=0, invalid=96777
- 0175: dt=92.480000, rms=0.650 (0.028%), neg=0, invalid=96777
- 0176: dt=92.480000, rms=0.649 (0.037%), neg=0, invalid=96777
- 0177: dt=92.480000, rms=0.649 (0.044%), neg=0, invalid=96777
- 0178: dt=92.480000, rms=0.649 (0.045%), neg=0, invalid=96777
- 0179: dt=92.480000, rms=0.649 (0.044%), neg=0, invalid=96777
- 0180: dt=92.480000, rms=0.648 (0.035%), neg=0, invalid=96777
- 0181: dt=92.480000, rms=0.648 (0.027%), neg=0, invalid=96777
- 0182: dt=92.480000, rms=0.648 (0.029%), neg=0, invalid=96777
- 0183: dt=92.480000, rms=0.648 (0.025%), neg=0, invalid=96777
- 0184: dt=92.480000, rms=0.648 (0.027%), neg=0, invalid=96777
- 0185: dt=92.480000, rms=0.647 (0.023%), neg=0, invalid=96777
- 0186: dt=92.480000, rms=0.647 (0.019%), neg=0, invalid=96777
- 0187: dt=129.472000, rms=0.647 (-0.001%), neg=0, invalid=96777
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.648, neg=0, invalid=96777
- 0188: dt=145.152000, rms=0.644 (0.674%), neg=0, invalid=96777
- 0189: dt=145.152000, rms=0.638 (0.949%), neg=0, invalid=96777
- 0190: dt=36.288000, rms=0.635 (0.460%), neg=0, invalid=96777
- 0191: dt=124.416000, rms=0.633 (0.317%), neg=0, invalid=96777
- 0192: dt=31.104000, rms=0.631 (0.332%), neg=0, invalid=96777
- 0193: dt=31.104000, rms=0.630 (0.134%), neg=0, invalid=96777
- 0194: dt=36.288000, rms=0.629 (0.209%), neg=0, invalid=96777
- 0195: dt=62.208000, rms=0.628 (0.148%), neg=0, invalid=96777
- 0196: dt=36.288000, rms=0.626 (0.236%), neg=0, invalid=96777
- 0197: dt=20.736000, rms=0.626 (0.073%), neg=0, invalid=96777
- 0198: dt=580.608000, rms=0.619 (1.088%), neg=0, invalid=96777
- 0199: dt=31.104000, rms=0.615 (0.569%), neg=0, invalid=96777
- 0200: dt=25.920000, rms=0.614 (0.219%), neg=0, invalid=96777
- 0201: dt=36.288000, rms=0.613 (0.146%), neg=0, invalid=96777
- 0202: dt=36.288000, rms=0.613 (0.061%), neg=0, invalid=96777
- 0203: dt=36.288000, rms=0.612 (0.123%), neg=0, invalid=96777
- 0204: dt=36.288000, rms=0.612 (0.038%), neg=0, invalid=96777
- 0205: dt=36.288000, rms=0.611 (0.119%), neg=0, invalid=96777
- 0206: dt=36.288000, rms=0.610 (0.131%), neg=0, invalid=96777
- 0207: dt=36.288000, rms=0.609 (0.162%), neg=0, invalid=96777
- 0208: dt=36.288000, rms=0.608 (0.215%), neg=0, invalid=96777
- 0209: dt=36.288000, rms=0.606 (0.298%), neg=0, invalid=96777
- 0210: dt=36.288000, rms=0.605 (0.277%), neg=0, invalid=96777
- 0211: dt=36.288000, rms=0.603 (0.261%), neg=0, invalid=96777
- 0212: dt=36.288000, rms=0.601 (0.283%), neg=0, invalid=96777
- 0213: dt=36.288000, rms=0.599 (0.314%), neg=0, invalid=96777
- 0214: dt=36.288000, rms=0.598 (0.293%), neg=0, invalid=96777
- 0215: dt=36.288000, rms=0.596 (0.269%), neg=0, invalid=96777
- 0216: dt=36.288000, rms=0.594 (0.272%), neg=0, invalid=96777
- 0217: dt=36.288000, rms=0.593 (0.288%), neg=0, invalid=96777
- 0218: dt=36.288000, rms=0.591 (0.264%), neg=0, invalid=96777
- 0219: dt=36.288000, rms=0.590 (0.220%), neg=0, invalid=96777
- 0220: dt=36.288000, rms=0.588 (0.230%), neg=0, invalid=96777
- 0221: dt=36.288000, rms=0.587 (0.226%), neg=0, invalid=96777
- 0222: dt=36.288000, rms=0.586 (0.224%), neg=0, invalid=96777
- 0223: dt=36.288000, rms=0.585 (0.187%), neg=0, invalid=96777
- 0224: dt=36.288000, rms=0.584 (0.188%), neg=0, invalid=96777
- 0225: dt=36.288000, rms=0.582 (0.190%), neg=0, invalid=96777
- 0226: dt=36.288000, rms=0.581 (0.186%), neg=0, invalid=96777
- 0227: dt=36.288000, rms=0.580 (0.156%), neg=0, invalid=96777
- 0228: dt=36.288000, rms=0.580 (0.141%), neg=0, invalid=96777
- 0229: dt=36.288000, rms=0.579 (0.138%), neg=0, invalid=96777
- 0230: dt=36.288000, rms=0.578 (0.132%), neg=0, invalid=96777
- 0231: dt=36.288000, rms=0.577 (0.133%), neg=0, invalid=96777
- 0232: dt=36.288000, rms=0.577 (0.119%), neg=0, invalid=96777
- 0233: dt=36.288000, rms=0.576 (0.131%), neg=0, invalid=96777
- 0234: dt=36.288000, rms=0.575 (0.116%), neg=0, invalid=96777
- 0235: dt=36.288000, rms=0.575 (0.104%), neg=0, invalid=96777
- 0236: dt=36.288000, rms=0.574 (0.091%), neg=0, invalid=96777
- 0237: dt=36.288000, rms=0.573 (0.109%), neg=0, invalid=96777
- 0238: dt=36.288000, rms=0.573 (0.093%), neg=0, invalid=96777
- 0239: dt=36.288000, rms=0.573 (-0.005%), neg=0, invalid=96777
- 0240: dt=9.072000, rms=0.573 (0.001%), neg=0, invalid=96777
- 0241: dt=31.104000, rms=0.573 (0.001%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.573, neg=0, invalid=96777
- 0242: dt=145.152000, rms=0.571 (0.387%), neg=0, invalid=96777
- 0243: dt=36.288000, rms=0.570 (0.082%), neg=0, invalid=96777
- 0244: dt=36.288000, rms=0.570 (0.055%), neg=0, invalid=96777
- 0245: dt=36.288000, rms=0.570 (0.035%), neg=0, invalid=96777
- 0246: dt=36.288000, rms=0.569 (0.042%), neg=0, invalid=96777
- 0247: dt=36.288000, rms=0.569 (0.060%), neg=0, invalid=96777
- 0248: dt=36.288000, rms=0.569 (0.068%), neg=0, invalid=96777
- 0249: dt=36.288000, rms=0.568 (0.094%), neg=0, invalid=96777
- 0250: dt=36.288000, rms=0.568 (0.094%), neg=0, invalid=96777
- 0251: dt=36.288000, rms=0.567 (0.089%), neg=0, invalid=96777
- 0252: dt=36.288000, rms=0.567 (0.081%), neg=0, invalid=96777
- 0253: dt=36.288000, rms=0.566 (0.075%), neg=0, invalid=96777
- 0254: dt=36.288000, rms=0.566 (0.075%), neg=0, invalid=96777
- 0255: dt=36.288000, rms=0.565 (0.070%), neg=0, invalid=96777
- 0256: dt=36.288000, rms=0.565 (0.061%), neg=0, invalid=96777
- 0257: dt=36.288000, rms=0.565 (0.057%), neg=0, invalid=96777
- 0258: dt=36.288000, rms=0.565 (0.054%), neg=0, invalid=96777
- 0259: dt=36.288000, rms=0.564 (0.075%), neg=0, invalid=96777
- 0260: dt=36.288000, rms=0.564 (0.052%), neg=0, invalid=96777
- 0261: dt=36.288000, rms=0.564 (0.050%), neg=0, invalid=96777
- 0262: dt=36.288000, rms=0.563 (0.056%), neg=0, invalid=96777
- 0263: dt=36.288000, rms=0.563 (0.064%), neg=0, invalid=96777
- 0264: dt=36.288000, rms=0.563 (0.058%), neg=0, invalid=96777
- 0265: dt=36.288000, rms=0.562 (0.064%), neg=0, invalid=96777
- 0266: dt=36.288000, rms=0.562 (0.050%), neg=0, invalid=96777
- 0267: dt=36.288000, rms=0.562 (0.060%), neg=0, invalid=96777
- 0268: dt=36.288000, rms=0.561 (0.052%), neg=0, invalid=96777
- 0269: dt=36.288000, rms=0.561 (0.044%), neg=0, invalid=96777
- 0270: dt=36.288000, rms=0.561 (0.047%), neg=0, invalid=96777
- 0271: dt=36.288000, rms=0.560 (0.046%), neg=0, invalid=96777
- 0272: dt=36.288000, rms=0.560 (0.053%), neg=0, invalid=96777
- 0273: dt=36.288000, rms=0.560 (0.040%), neg=0, invalid=96777
- 0274: dt=36.288000, rms=0.560 (0.045%), neg=0, invalid=96777
- 0275: dt=36.288000, rms=0.559 (0.047%), neg=0, invalid=96777
- 0276: dt=36.288000, rms=0.559 (0.045%), neg=0, invalid=96777
- 0277: dt=36.288000, rms=0.559 (0.051%), neg=0, invalid=96777
- 0278: dt=36.288000, rms=0.559 (0.054%), neg=0, invalid=96777
- 0279: dt=36.288000, rms=0.558 (0.048%), neg=0, invalid=96777
- 0280: dt=36.288000, rms=0.558 (0.038%), neg=0, invalid=96777
- 0281: dt=36.288000, rms=0.558 (0.043%), neg=0, invalid=96777
- 0282: dt=36.288000, rms=0.558 (0.046%), neg=0, invalid=96777
- 0283: dt=36.288000, rms=0.557 (0.039%), neg=0, invalid=96777
- 0284: dt=36.288000, rms=0.557 (0.040%), neg=0, invalid=96777
- 0285: dt=36.288000, rms=0.557 (0.040%), neg=0, invalid=96777
- 0286: dt=36.288000, rms=0.557 (0.031%), neg=0, invalid=96777
- 0287: dt=36.288000, rms=0.557 (0.039%), neg=0, invalid=96777
- 0288: dt=36.288000, rms=0.556 (0.031%), neg=0, invalid=96777
- 0289: dt=36.288000, rms=0.556 (0.042%), neg=0, invalid=96777
- 0290: dt=36.288000, rms=0.556 (0.038%), neg=0, invalid=96777
- 0291: dt=36.288000, rms=0.556 (0.031%), neg=0, invalid=96777
- 0292: dt=36.288000, rms=0.556 (0.027%), neg=0, invalid=96777
- 0293: dt=36.288000, rms=0.555 (0.031%), neg=0, invalid=96777
- 0294: dt=36.288000, rms=0.555 (0.026%), neg=0, invalid=96777
- 0295: dt=36.288000, rms=0.555 (0.029%), neg=0, invalid=96777
- 0296: dt=36.288000, rms=0.555 (0.041%), neg=0, invalid=96777
- 0297: dt=36.288000, rms=0.555 (0.035%), neg=0, invalid=96777
- 0298: dt=36.288000, rms=0.555 (0.027%), neg=0, invalid=96777
- 0299: dt=36.288000, rms=0.554 (0.035%), neg=0, invalid=96777
- 0300: dt=36.288000, rms=0.554 (0.034%), neg=0, invalid=96777
- 0301: dt=36.288000, rms=0.554 (0.034%), neg=0, invalid=96777
- 0302: dt=36.288000, rms=0.554 (0.032%), neg=0, invalid=96777
- 0303: dt=36.288000, rms=0.554 (0.025%), neg=0, invalid=96777
- 0304: dt=36.288000, rms=0.554 (0.027%), neg=0, invalid=96777
- 0305: dt=36.288000, rms=0.553 (0.018%), neg=0, invalid=96777
- 0306: dt=36.288000, rms=0.553 (0.030%), neg=0, invalid=96777
- 0307: dt=36.288000, rms=0.553 (0.032%), neg=0, invalid=96777
- 0308: dt=36.288000, rms=0.553 (0.035%), neg=0, invalid=96777
- 0309: dt=36.288000, rms=0.553 (0.023%), neg=0, invalid=96777
- 0310: dt=36.288000, rms=0.553 (0.028%), neg=0, invalid=96777
- 0311: dt=36.288000, rms=0.552 (0.025%), neg=0, invalid=96777
- 0312: dt=36.288000, rms=0.552 (0.026%), neg=0, invalid=96777
- 0313: dt=36.288000, rms=0.552 (0.032%), neg=0, invalid=96777
- 0314: dt=36.288000, rms=0.552 (0.025%), neg=0, invalid=96777
- 0315: dt=36.288000, rms=0.552 (0.022%), neg=0, invalid=96777
- 0316: dt=31.104000, rms=0.552 (0.001%), neg=0, invalid=96777
- 0317: dt=31.104000, rms=0.552 (0.008%), neg=0, invalid=96777
- 0318: dt=31.104000, rms=0.552 (-0.001%), neg=0, invalid=96777
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.560, neg=0, invalid=96777
- 0319: dt=25.600000, rms=0.558 (0.253%), neg=0, invalid=96777
- 0320: dt=44.800000, rms=0.556 (0.362%), neg=0, invalid=96777
- 0321: dt=6.759358, rms=0.555 (0.180%), neg=0, invalid=96777
- 0322: dt=38.400000, rms=0.553 (0.351%), neg=0, invalid=96777
- 0323: dt=7.720930, rms=0.552 (0.180%), neg=0, invalid=96777
- 0324: dt=11.200000, rms=0.552 (0.171%), neg=0, invalid=96777
- 0325: dt=128.000000, rms=0.548 (0.690%), neg=0, invalid=96777
- 0326: dt=12.913386, rms=0.546 (0.368%), neg=0, invalid=96777
- 0327: dt=19.200000, rms=0.544 (0.255%), neg=0, invalid=96777
- 0328: dt=8.000000, rms=0.544 (0.124%), neg=0, invalid=96777
- 0329: dt=32.000000, rms=0.543 (0.172%), neg=0, invalid=96777
- 0330: dt=11.200000, rms=0.542 (0.141%), neg=0, invalid=96777
- 0331: dt=11.200000, rms=0.541 (0.104%), neg=0, invalid=96777
- 0332: dt=11.200000, rms=0.541 (0.050%), neg=0, invalid=96777
- 0333: dt=11.200000, rms=0.541 (0.096%), neg=0, invalid=96777
- 0334: dt=11.200000, rms=0.540 (0.047%), neg=0, invalid=96777
- 0335: dt=11.200000, rms=0.540 (0.085%), neg=0, invalid=96777
- 0336: dt=11.200000, rms=0.539 (0.118%), neg=0, invalid=96777
- 0337: dt=11.200000, rms=0.538 (0.146%), neg=0, invalid=96777
- 0338: dt=11.200000, rms=0.537 (0.214%), neg=0, invalid=96777
- 0339: dt=11.200000, rms=0.536 (0.249%), neg=0, invalid=96777
- 0340: dt=11.200000, rms=0.535 (0.246%), neg=0, invalid=96777
- 0341: dt=11.200000, rms=0.533 (0.256%), neg=0, invalid=96777
- 0342: dt=11.200000, rms=0.532 (0.285%), neg=0, invalid=96777
- 0343: dt=11.200000, rms=0.530 (0.272%), neg=0, invalid=96777
- 0344: dt=11.200000, rms=0.529 (0.254%), neg=0, invalid=96777
- 0345: dt=11.200000, rms=0.528 (0.231%), neg=0, invalid=96777
- 0346: dt=11.200000, rms=0.527 (0.232%), neg=0, invalid=96777
- 0347: dt=11.200000, rms=0.525 (0.225%), neg=0, invalid=96777
- 0348: dt=11.200000, rms=0.524 (0.207%), neg=0, invalid=96777
- 0349: dt=11.200000, rms=0.523 (0.199%), neg=0, invalid=96777
- 0350: dt=11.200000, rms=0.522 (0.192%), neg=0, invalid=96777
- 0351: dt=11.200000, rms=0.521 (0.182%), neg=0, invalid=96777
- 0352: dt=11.200000, rms=0.520 (0.162%), neg=0, invalid=96777
- 0353: dt=11.200000, rms=0.520 (0.145%), neg=0, invalid=96777
- 0354: dt=11.200000, rms=0.519 (0.139%), neg=0, invalid=96777
- 0355: dt=11.200000, rms=0.518 (0.135%), neg=0, invalid=96777
- 0356: dt=11.200000, rms=0.518 (0.113%), neg=0, invalid=96777
- 0357: dt=11.200000, rms=0.517 (0.111%), neg=0, invalid=96777
- 0358: dt=11.200000, rms=0.517 (0.104%), neg=0, invalid=96777
- 0359: dt=11.200000, rms=0.516 (0.104%), neg=0, invalid=96777
- 0360: dt=11.200000, rms=0.515 (0.096%), neg=0, invalid=96777
- 0361: dt=11.200000, rms=0.515 (0.076%), neg=0, invalid=96777
- 0362: dt=11.200000, rms=0.515 (0.064%), neg=0, invalid=96777
- 0363: dt=11.200000, rms=0.514 (0.058%), neg=0, invalid=96777
- 0364: dt=11.200000, rms=0.514 (0.077%), neg=0, invalid=96777
- 0365: dt=11.200000, rms=0.514 (0.061%), neg=0, invalid=96777
- 0366: dt=11.200000, rms=0.513 (0.060%), neg=0, invalid=96777
- 0367: dt=11.200000, rms=0.513 (0.052%), neg=0, invalid=96777
- 0368: dt=11.200000, rms=0.513 (0.041%), neg=0, invalid=96777
- 0369: dt=11.200000, rms=0.513 (0.049%), neg=0, invalid=96777
- 0370: dt=11.200000, rms=0.512 (0.053%), neg=0, invalid=96777
- 0371: dt=11.200000, rms=0.512 (0.036%), neg=0, invalid=96777
- 0372: dt=11.200000, rms=0.512 (0.047%), neg=0, invalid=96777
- 0373: dt=11.200000, rms=0.512 (0.055%), neg=0, invalid=96777
- 0374: dt=11.200000, rms=0.511 (0.065%), neg=0, invalid=96777
- 0375: dt=11.200000, rms=0.511 (0.046%), neg=0, invalid=96777
- 0376: dt=11.200000, rms=0.511 (0.045%), neg=0, invalid=96777
- 0377: dt=11.200000, rms=0.511 (0.042%), neg=0, invalid=96777
- 0378: dt=11.200000, rms=0.511 (0.032%), neg=0, invalid=96777
- 0379: dt=11.200000, rms=0.510 (0.033%), neg=0, invalid=96777
- 0380: dt=11.200000, rms=0.510 (0.039%), neg=0, invalid=96777
- 0381: dt=11.200000, rms=0.510 (0.039%), neg=0, invalid=96777
- 0382: dt=11.200000, rms=0.510 (0.044%), neg=0, invalid=96777
- 0383: dt=11.200000, rms=0.510 (0.041%), neg=0, invalid=96777
- 0384: dt=11.200000, rms=0.509 (0.036%), neg=0, invalid=96777
- 0385: dt=11.200000, rms=0.509 (0.030%), neg=0, invalid=96777
- 0386: dt=11.200000, rms=0.509 (0.015%), neg=0, invalid=96777
- 0387: dt=11.200000, rms=0.509 (0.029%), neg=0, invalid=96777
- 0388: dt=11.200000, rms=0.509 (0.040%), neg=0, invalid=96777
- 0389: dt=11.200000, rms=0.509 (0.032%), neg=0, invalid=96777
- 0390: dt=11.200000, rms=0.509 (0.027%), neg=0, invalid=96777
- 0391: dt=11.200000, rms=0.508 (0.028%), neg=0, invalid=96777
- 0392: dt=11.200000, rms=0.508 (0.037%), neg=0, invalid=96777
- 0393: dt=11.200000, rms=0.508 (0.028%), neg=0, invalid=96777
- 0394: dt=11.200000, rms=0.508 (0.025%), neg=0, invalid=96777
- 0395: dt=11.200000, rms=0.508 (0.020%), neg=0, invalid=96777
- 0396: dt=11.200000, rms=0.508 (0.006%), neg=0, invalid=96777
- 0397: dt=11.200000, rms=0.508 (-0.005%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.508, neg=0, invalid=96777
- 0398: dt=44.800000, rms=0.506 (0.341%), neg=0, invalid=96777
- 0399: dt=11.200000, rms=0.506 (0.080%), neg=0, invalid=96777
- 0400: dt=4.800000, rms=0.506 (0.014%), neg=0, invalid=96777
- 0401: dt=4.800000, rms=0.505 (0.015%), neg=0, invalid=96777
- 0402: dt=4.800000, rms=0.505 (0.017%), neg=0, invalid=96777
- 0403: dt=4.800000, rms=0.505 (0.022%), neg=0, invalid=96777
- 0404: dt=4.800000, rms=0.505 (0.022%), neg=0, invalid=96777
- 0405: dt=4.800000, rms=0.505 (0.019%), neg=0, invalid=96777
- 0406: dt=4.800000, rms=0.505 (0.020%), neg=0, invalid=96777
- 0407: dt=4.800000, rms=0.505 (0.013%), neg=0, invalid=96777
- 0408: dt=44.800000, rms=0.505 (0.023%), neg=0, invalid=96777
- 0409: dt=9.600000, rms=0.505 (0.008%), neg=0, invalid=96777
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.528, neg=0, invalid=96777
- 0410: dt=0.000000, rms=0.528 (0.004%), neg=0, invalid=96777
- 0411: dt=0.000000, rms=0.528 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.528, neg=0, invalid=96777
- 0412: dt=0.000000, rms=0.528 (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=0.574, neg=0, invalid=96777
- 0413: dt=1.193122, rms=0.569 (0.749%), neg=0, invalid=96777
- 0414: dt=0.256000, rms=0.569 (0.015%), neg=0, invalid=96777
- 0415: dt=0.256000, rms=0.569 (-0.010%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.569, neg=0, invalid=96777
- 0416: dt=0.448000, rms=0.569 (0.080%), neg=0, invalid=96777
- 0417: dt=0.288462, rms=0.569 (0.013%), neg=0, invalid=96777
- 0418: dt=0.288462, rms=0.569 (-0.008%), 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=0.519, neg=0, invalid=96777
- 0419: dt=0.320000, rms=0.506 (2.482%), neg=0, invalid=96777
- 0420: dt=0.115302, rms=0.505 (0.365%), neg=0, invalid=96777
- 0421: dt=0.448000, rms=0.499 (1.148%), neg=0, invalid=96777
- 0422: dt=0.448000, rms=0.497 (0.410%), neg=0, invalid=96777
- 0423: dt=0.028000, rms=0.497 (0.014%), neg=0, invalid=96777
- 0424: dt=0.028000, rms=0.497 (0.018%), neg=0, invalid=96777
- 0425: dt=0.028000, rms=0.496 (0.033%), neg=0, invalid=96777
- 0426: dt=0.028000, rms=0.496 (0.043%), neg=0, invalid=96777
- 0427: dt=0.028000, rms=0.496 (0.054%), neg=0, invalid=96777
- 0428: dt=0.028000, rms=0.496 (0.063%), neg=0, invalid=96777
- 0429: dt=0.028000, rms=0.495 (0.068%), neg=0, invalid=96777
- 0430: dt=0.028000, rms=0.495 (0.013%), neg=0, invalid=96777
- 0431: dt=0.028000, rms=0.495 (0.020%), neg=0, invalid=96777
- 0432: dt=0.028000, rms=0.495 (0.029%), neg=0, invalid=96777
- 0433: dt=0.028000, rms=0.495 (0.038%), neg=0, invalid=96777
- 0434: dt=0.028000, rms=0.495 (0.044%), neg=0, invalid=96777
- 0435: dt=0.028000, rms=0.494 (0.048%), neg=0, invalid=96777
- 0436: dt=0.028000, rms=0.494 (0.051%), neg=0, invalid=96777
- 0437: dt=0.028000, rms=0.494 (0.056%), neg=0, invalid=96777
- 0438: dt=0.028000, rms=0.494 (0.054%), neg=0, invalid=96777
- 0439: dt=0.028000, rms=0.493 (0.051%), neg=0, invalid=96777
- 0440: dt=0.028000, rms=0.493 (0.056%), neg=0, invalid=96777
- 0441: dt=0.028000, rms=0.493 (0.050%), neg=0, invalid=96777
- 0442: dt=0.028000, rms=0.493 (0.055%), neg=0, invalid=96777
- 0443: dt=0.028000, rms=0.492 (0.049%), neg=0, invalid=96777
- 0444: dt=0.028000, rms=0.492 (0.045%), neg=0, invalid=96777
- 0445: dt=0.028000, rms=0.492 (0.038%), neg=0, invalid=96777
- 0446: dt=0.028000, rms=0.492 (0.043%), neg=0, invalid=96777
- 0447: dt=0.028000, rms=0.491 (0.039%), neg=0, invalid=96777
- 0448: dt=0.028000, rms=0.491 (0.036%), neg=0, invalid=96777
- 0449: dt=0.028000, rms=0.491 (0.029%), neg=0, invalid=96777
- 0450: dt=0.028000, rms=0.491 (0.029%), neg=0, invalid=96777
- 0451: dt=0.028000, rms=0.491 (0.023%), neg=0, invalid=96777
- 0452: dt=0.028000, rms=0.491 (0.014%), neg=0, invalid=96777
- 0453: dt=0.000000, rms=0.491 (0.001%), neg=0, invalid=96777
- 0454: dt=0.050000, rms=0.491 (-0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.491, neg=0, invalid=96777
- 0455: dt=0.448000, rms=0.485 (1.081%), neg=0, invalid=96777
- 0456: dt=0.024000, rms=0.485 (0.007%), neg=0, invalid=96777
- 0457: dt=0.024000, rms=0.485 (0.003%), neg=0, invalid=96777
- 0458: dt=0.024000, rms=0.485 (-0.003%), neg=0, invalid=96777
- label assignment complete, 0 changed (0.00%)
- *********************************************************************************************
- *********************************************************************************************
- *********************************************************************************************
- ********************* ALLOWING NEGATIVE NODES IN DEFORMATION ********************************
- *********************************************************************************************
- *********************************************************************************************
- *********************************************************************************************
- **************** pass 1 of 1 ************************
- setting smoothness coefficient to 0.008
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.483, neg=0, invalid=96777
- 0459: dt=0.000000, rms=0.483 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.483, neg=0, invalid=96777
- 0460: dt=129.472000, rms=0.483 (0.026%), neg=0, invalid=96777
- 0461: dt=129.472000, rms=0.483 (0.023%), neg=0, invalid=96777
- 0462: dt=129.472000, rms=0.483 (-0.001%), neg=0, invalid=96777
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.483, neg=0, invalid=96777
- 0463: dt=36.288000, rms=0.483 (0.091%), neg=0, invalid=96777
- 0464: dt=36.288000, rms=0.482 (0.050%), neg=0, invalid=96777
- 0465: dt=36.288000, rms=0.482 (0.049%), neg=0, invalid=96777
- 0466: dt=36.288000, rms=0.482 (0.041%), neg=0, invalid=96777
- 0467: dt=36.288000, rms=0.482 (-0.039%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.482, neg=0, invalid=96777
- 0468: dt=103.680000, rms=0.480 (0.347%), neg=0, invalid=96777
- 0469: dt=36.288000, rms=0.480 (0.120%), neg=0, invalid=96777
- 0470: dt=36.288000, rms=0.480 (0.008%), neg=0, invalid=96777
- 0471: dt=36.288000, rms=0.479 (0.147%), neg=0, invalid=96777
- 0472: dt=36.288000, rms=0.479 (0.086%), neg=0, invalid=96777
- 0473: dt=36.288000, rms=0.478 (0.187%), neg=0, invalid=96777
- 0474: dt=36.288000, rms=0.477 (0.059%), neg=0, invalid=96777
- 0475: dt=36.288000, rms=0.477 (0.176%), neg=0, invalid=96777
- 0476: dt=36.288000, rms=0.476 (0.092%), neg=0, invalid=96777
- 0477: dt=36.288000, rms=0.476 (0.113%), neg=0, invalid=96777
- 0478: dt=36.288000, rms=0.475 (0.055%), neg=0, invalid=96777
- 0479: dt=20.736000, rms=0.475 (0.035%), neg=0, invalid=96777
- 0480: dt=20.736000, rms=0.475 (0.006%), neg=0, invalid=96777
- 0481: dt=20.736000, rms=0.475 (0.008%), neg=0, invalid=96777
- 0482: dt=20.736000, rms=0.475 (0.014%), neg=0, invalid=96777
- 0483: dt=20.736000, rms=0.475 (0.027%), neg=0, invalid=96777
- 0484: dt=20.736000, rms=0.475 (0.026%), neg=0, invalid=96777
- 0485: dt=20.736000, rms=0.475 (0.018%), neg=0, invalid=96777
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.475, neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0486: dt=44.800000, rms=0.472 (0.540%), neg=0, invalid=96777
- 0487: dt=25.600000, rms=0.471 (0.257%), neg=0, invalid=96777
- 0488: dt=8.793893, rms=0.470 (0.243%), neg=0, invalid=96777
- 0489: dt=8.793893, rms=0.470 (0.098%), neg=0, invalid=96777
- 0490: dt=8.793893, rms=0.469 (0.142%), neg=0, invalid=96777
- 0491: dt=8.793893, rms=0.468 (0.207%), neg=0, invalid=96777
- 0492: dt=8.793893, rms=0.467 (0.213%), neg=0, invalid=96777
- 0493: dt=8.793893, rms=0.466 (0.206%), neg=0, invalid=96777
- 0494: dt=8.793893, rms=0.465 (0.183%), neg=0, invalid=96777
- 0495: dt=8.793893, rms=0.464 (0.202%), neg=0, invalid=96777
- 0496: dt=8.793893, rms=0.463 (0.151%), neg=0, invalid=96777
- 0497: dt=8.793893, rms=0.463 (0.144%), neg=0, invalid=96777
- 0498: dt=8.793893, rms=0.462 (0.129%), neg=0, invalid=96777
- 0499: dt=8.793893, rms=0.462 (0.140%), neg=0, invalid=96777
- 0500: dt=8.793893, rms=0.461 (0.151%), neg=0, invalid=96777
- 0501: dt=8.793893, rms=0.460 (0.130%), neg=0, invalid=96777
- 0502: dt=8.793893, rms=0.460 (0.135%), neg=0, invalid=96777
- 0503: dt=8.793893, rms=0.459 (0.110%), neg=0, invalid=96777
- 0504: dt=8.793893, rms=0.459 (0.118%), neg=0, invalid=96777
- 0505: dt=8.793893, rms=0.458 (0.105%), neg=0, invalid=96777
- 0506: dt=8.000000, rms=0.458 (0.008%), neg=0, invalid=96777
- 0507: dt=8.000000, rms=0.458 (0.017%), neg=0, invalid=96777
- 0508: dt=8.000000, rms=0.458 (0.018%), neg=0, invalid=96777
- 0509: dt=8.000000, rms=0.458 (0.019%), neg=0, invalid=96777
- 0510: dt=8.000000, rms=0.458 (0.027%), neg=0, invalid=96777
- 0511: dt=8.000000, rms=0.458 (0.033%), neg=0, invalid=96777
- 0512: dt=8.000000, rms=0.457 (0.027%), neg=0, invalid=96777
- 0513: dt=8.000000, rms=0.457 (0.023%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.457, neg=0, invalid=96777
- 0514: dt=44.800000, rms=0.454 (0.665%), neg=0, invalid=96777
- 0515: dt=11.200000, rms=0.454 (0.119%), neg=0, invalid=96777
- 0516: dt=11.200000, rms=0.453 (0.105%), neg=0, invalid=96777
- 0517: dt=11.200000, rms=0.453 (0.118%), neg=0, invalid=96777
- 0518: dt=11.200000, rms=0.452 (0.118%), neg=0, invalid=96777
- 0519: dt=11.200000, rms=0.452 (0.145%), neg=0, invalid=96777
- 0520: dt=11.200000, rms=0.451 (0.123%), neg=0, invalid=96777
- 0521: dt=11.200000, rms=0.451 (0.095%), neg=0, invalid=96777
- 0522: dt=9.600000, rms=0.450 (0.022%), neg=0, invalid=96777
- 0523: dt=9.600000, rms=0.450 (0.016%), neg=0, invalid=96777
- 0524: dt=9.600000, rms=0.450 (0.015%), neg=0, invalid=96777
- 0525: dt=9.600000, rms=0.450 (0.027%), neg=0, invalid=96777
- 0526: dt=9.600000, rms=0.450 (0.028%), neg=0, invalid=96777
- 0527: dt=9.600000, rms=0.450 (0.033%), neg=0, invalid=96777
- 0528: dt=9.600000, rms=0.450 (0.030%), neg=0, invalid=96777
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.454, neg=0, invalid=96777
- 0529: dt=1.008000, rms=0.454 (0.003%), neg=0, invalid=96777
- 0530: dt=0.720000, rms=0.454 (-0.001%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.454, neg=0, invalid=96777
- 0531: dt=4.032000, rms=0.454 (0.046%), neg=0, invalid=96777
- 0532: dt=3.456000, rms=0.454 (0.025%), neg=0, invalid=96777
- 0533: dt=3.456000, rms=0.454 (0.010%), neg=0, invalid=96777
- 0534: dt=3.456000, rms=0.454 (-0.011%), neg=0, invalid=96777
- setting smoothness coefficient to 1.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.460, neg=0, invalid=96777
- 0535: dt=0.000000, rms=0.460 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.460, neg=0, invalid=96777
- 0536: dt=0.448000, rms=0.460 (0.022%), neg=0, invalid=96777
- 0537: dt=0.320000, rms=0.460 (0.007%), neg=0, invalid=96777
- 0538: dt=0.320000, rms=0.460 (-0.003%), 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=0.451, neg=0, invalid=96777
- iter 0, gcam->neg = 728
- after 15 iterations, nbhd size=1, neg = 0
- 0539: dt=2.028120, rms=0.409 (9.191%), neg=0, invalid=96777
- 0540: dt=0.000313, rms=0.409 (-0.003%), neg=0, invalid=96777
- 0541: dt=0.000313, rms=0.409 (0.001%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0542: dt=0.000313, rms=0.409 (-0.001%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.409, neg=0, invalid=96777
- 0543: dt=0.000438, rms=0.409 (0.000%), neg=0, invalid=96777
- 0544: dt=0.000000, rms=0.409 (0.000%), neg=0, invalid=96777
- iter 0, gcam->neg = 36
- after 8 iterations, nbhd size=1, neg = 0
- 0545: dt=0.050000, rms=0.409 (-0.215%), 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=0.391, neg=0, invalid=96777
- 0546: dt=0.000000, rms=0.392 (-0.282%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.392, neg=0, invalid=96777
- 0547: dt=8.092000, rms=0.392 (0.000%), neg=0, invalid=96777
- 0548: dt=0.014450, rms=0.392 (0.000%), neg=0, invalid=96777
- 0549: dt=0.014450, rms=0.392 (-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=0.393, neg=0, invalid=96777
- 0550: dt=0.000000, rms=0.393 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.393, neg=0, invalid=96777
- 0551: dt=15.552000, rms=0.393 (0.008%), neg=0, invalid=96777
- 0552: dt=7.776000, rms=0.393 (0.001%), neg=0, invalid=96777
- 0553: dt=7.776000, rms=0.393 (-0.000%), neg=0, invalid=96777
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.393, neg=0, invalid=96777
- 0554: dt=11.200000, rms=0.393 (0.044%), neg=0, invalid=96777
- 0555: dt=4.800000, rms=0.393 (0.005%), neg=0, invalid=96777
- 0556: dt=4.800000, rms=0.393 (0.001%), neg=0, invalid=96777
- 0557: dt=4.800000, rms=0.393 (-0.016%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.393, neg=0, invalid=96777
- 0558: dt=44.800000, rms=0.392 (0.280%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 5 iterations, nbhd size=1, neg = 0
- 0559: dt=38.400000, rms=0.391 (0.175%), neg=0, invalid=96777
- iter 0, gcam->neg = 7
- after 7 iterations, nbhd size=1, neg = 0
- 0560: dt=38.400000, rms=0.391 (-0.436%), neg=0, invalid=96777
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.394, neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0561: dt=0.252000, rms=0.394 (0.003%), neg=0, invalid=96777
- iter 0, gcam->neg = 37
- after 19 iterations, nbhd size=2, neg = 0
- 0562: dt=8.668810, rms=0.393 (0.238%), neg=0, invalid=96777
- 0563: dt=0.013500, rms=0.393 (0.000%), neg=0, invalid=96777
- 0564: dt=0.013500, rms=0.393 (0.000%), neg=0, invalid=96777
- 0565: dt=0.013500, rms=0.393 (0.000%), neg=0, invalid=96777
- 0566: dt=0.013500, rms=0.393 (0.000%), neg=0, invalid=96777
- 0567: dt=0.013500, rms=0.393 (0.001%), neg=0, invalid=96777
- 0568: dt=0.013500, rms=0.393 (0.001%), neg=0, invalid=96777
- 0569: dt=0.013500, rms=0.393 (0.001%), neg=0, invalid=96777
- 0570: dt=0.013500, rms=0.393 (0.001%), neg=0, invalid=96777
- 0571: dt=0.013500, rms=0.393 (0.002%), neg=0, invalid=96777
- 0572: dt=0.013500, rms=0.393 (0.002%), neg=0, invalid=96777
- 0573: dt=0.013500, rms=0.393 (0.002%), neg=0, invalid=96777
- 0574: dt=0.013500, rms=0.393 (0.002%), neg=0, invalid=96777
- 0575: dt=0.013500, rms=0.393 (0.002%), neg=0, invalid=96777
- 0576: dt=0.013500, rms=0.393 (0.002%), neg=0, invalid=96777
- 0577: dt=0.013500, rms=0.393 (0.002%), neg=0, invalid=96777
- 0578: dt=0.013500, rms=0.393 (0.003%), neg=0, invalid=96777
- 0579: dt=0.013500, rms=0.393 (0.003%), neg=0, invalid=96777
- 0580: dt=0.013500, rms=0.393 (0.003%), neg=0, invalid=96777
- 0581: dt=0.013500, rms=0.393 (0.003%), neg=0, invalid=96777
- 0582: dt=0.013500, rms=0.393 (0.003%), neg=0, invalid=96777
- 0583: dt=0.013500, rms=0.393 (0.003%), neg=0, invalid=96777
- 0584: dt=0.013500, rms=0.393 (0.003%), neg=0, invalid=96777
- 0585: dt=0.013500, rms=0.393 (0.003%), neg=0, invalid=96777
- 0586: dt=0.013500, rms=0.393 (0.003%), neg=0, invalid=96777
- 0587: dt=0.013500, rms=0.393 (0.003%), neg=0, invalid=96777
- 0588: dt=0.013500, rms=0.393 (0.003%), neg=0, invalid=96777
- 0589: dt=0.013500, rms=0.393 (0.003%), neg=0, invalid=96777
- 0590: dt=0.013500, rms=0.393 (0.003%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.393, neg=0, invalid=96777
- iter 0, gcam->neg = 77
- after 11 iterations, nbhd size=1, neg = 0
- 0591: dt=16.128000, rms=0.390 (0.679%), neg=0, invalid=96777
- 0592: dt=0.011250, rms=0.390 (0.000%), neg=0, invalid=96777
- 0593: dt=0.011250, rms=0.390 (0.000%), neg=0, invalid=96777
- 0594: dt=0.011250, rms=0.390 (-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=0.397, neg=0, invalid=96777
- 0595: dt=0.000000, rms=0.397 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.397, neg=0, invalid=96777
- 0596: dt=0.000000, rms=0.397 (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=0.386, neg=0, invalid=96777
- iter 0, gcam->neg = 407
- after 23 iterations, nbhd size=2, neg = 0
- 0597: dt=0.689744, rms=0.375 (2.827%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0598: dt=0.000023, rms=0.375 (0.001%), neg=0, invalid=96777
- 0599: dt=0.000023, rms=0.375 (0.001%), neg=0, invalid=96777
- 0600: dt=0.000023, rms=0.375 (0.000%), neg=0, invalid=96777
- 0601: dt=0.000023, rms=0.375 (0.000%), neg=0, invalid=96777
- 0602: dt=0.000094, rms=0.375 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.375, neg=0, invalid=96777
- 0603: dt=0.001000, rms=0.375 (0.001%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0604: dt=0.028000, rms=0.375 (0.016%), neg=0, invalid=96777
- 0605: dt=0.000109, rms=0.375 (0.000%), neg=0, invalid=96777
- 0606: dt=0.000109, rms=0.375 (0.000%), neg=0, invalid=96777
- 0607: dt=0.000109, rms=0.375 (0.000%), neg=0, invalid=96777
- 0608: dt=0.000109, rms=0.375 (0.000%), neg=0, invalid=96777
- 0609: dt=0.000109, rms=0.375 (0.000%), neg=0, invalid=96777
- 0610: dt=0.000109, rms=0.375 (0.000%), neg=0, invalid=96777
- 0611: dt=0.000109, rms=0.375 (0.000%), neg=0, invalid=96777
- 0612: dt=0.000109, rms=0.375 (0.000%), neg=0, invalid=96777
- 0613: dt=0.000109, rms=0.375 (0.001%), neg=0, invalid=96777
- 0614: dt=0.000109, rms=0.375 (0.001%), neg=0, invalid=96777
- 0615: dt=0.000109, rms=0.375 (0.001%), neg=0, invalid=96777
- 0616: dt=0.000109, rms=0.375 (0.001%), neg=0, invalid=96777
- 0617: dt=0.000109, rms=0.375 (0.001%), neg=0, invalid=96777
- 0618: dt=0.000109, rms=0.375 (0.001%), neg=0, invalid=96777
- 0619: dt=0.000109, rms=0.375 (0.001%), neg=0, invalid=96777
- 0620: dt=0.000109, rms=0.375 (0.001%), neg=0, invalid=96777
- 0621: dt=0.000109, rms=0.375 (0.001%), neg=0, invalid=96777
- 0622: dt=0.000109, rms=0.375 (0.001%), neg=0, invalid=96777
- 0623: dt=0.000109, rms=0.375 (0.001%), neg=0, invalid=96777
- 0624: dt=0.000109, rms=0.375 (0.001%), neg=0, invalid=96777
- 0625: dt=0.000109, rms=0.375 (0.001%), neg=0, invalid=96777
- 0626: dt=0.000109, rms=0.375 (0.001%), neg=0, invalid=96777
- 0627: dt=0.000109, rms=0.375 (0.001%), neg=0, invalid=96777
- 0628: dt=0.000109, rms=0.375 (0.001%), neg=0, invalid=96777
- 0629: dt=0.000109, rms=0.375 (0.001%), neg=0, invalid=96777
- 0630: dt=0.000109, rms=0.375 (0.001%), neg=0, invalid=96777
- 0631: dt=0.000109, rms=0.375 (0.001%), neg=0, invalid=96777
- 0632: dt=0.000109, rms=0.375 (0.001%), neg=0, invalid=96777
- 0633: dt=0.000109, rms=0.375 (0.001%), neg=0, invalid=96777
- 0634: dt=0.000109, rms=0.375 (0.001%), neg=0, invalid=96777
- writing output transformation to transforms/talairach.m3z...
- GCAMwrite
- registration took 3 hours, 14 minutes and 27 seconds.
- #--------------------------------------
- #@# CA Reg Inv Thu Aug 8 15:33:47 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri
- mri_ca_register -invert-and-save transforms/talairach.m3z
- Loading, Inverting, Saving, Exiting ...
- Reading transforms/talairach.m3z
- Inverting GCAM
- Saving inverse
- #--------------------------------------
- #@# Remove Neck Thu Aug 8 15:35:05 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...
- 11084364 nonbrain voxels erased
- writing output to nu_noneck.mgz...
- nonbrain removal took 1 minutes and 19 seconds.
- #--------------------------------------
- #@# SkullLTA Thu Aug 8 15:36:24 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=8.0
- skull bounding box = (48, 19, 16) --> (200, 205, 202)
- using (99, 81, 109) as brain centroid...
- mean wm in atlas = 126, using box (80,58,86) --> (117, 103,131) 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
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.9, old_max_log_p =-4.0 (thresh=-4.0)
- 1.095 -0.075 0.091 -14.736;
- 0.030 1.035 0.346 -24.562;
- -0.093 -0.329 0.945 47.700;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 1.095 -0.075 0.091 -14.736;
- 0.030 1.035 0.346 -24.562;
- -0.093 -0.329 0.945 47.700;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.2500
- ****************************************
- Nine parameter search. iteration 2 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 1.075 -0.099 0.047 -6.822;
- 0.066 1.071 0.360 -34.306;
- -0.056 -0.325 0.929 44.358;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 3 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 1.092 -0.136 0.034 -2.057;
- 0.099 1.063 0.430 -45.323;
- -0.059 -0.387 0.886 55.618;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.0625
- ****************************************
- Nine parameter search. iteration 4 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 1.095 -0.122 0.049 -6.272;
- 0.080 1.066 0.438 -43.751;
- -0.069 -0.395 0.883 59.003;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 5 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 1.095 -0.122 0.049 -6.272;
- 0.081 1.067 0.438 -43.944;
- -0.069 -0.394 0.882 59.058;
- 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
- 1.09453 -0.12176 0.04872 -6.27205;
- 0.08059 1.06731 0.43837 -43.94444;
- -0.06922 -0.39445 0.88219 59.05766;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 3481
- Quasinewton: input matrix
- 1.09453 -0.12176 0.04872 -6.27205;
- 0.08059 1.06731 0.43837 -43.94444;
- -0.06922 -0.39445 0.88219 59.05766;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 007: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 1.095 -0.122 0.049 -6.272;
- 0.081 1.067 0.438 -43.944;
- -0.069 -0.394 0.882 59.058;
- 0.000 0.000 0.000 1.000;
- pass 1, spacing 8: log(p) = -3.9 (old=-4.0)
- transform before final EM align:
- 1.095 -0.122 0.049 -6.272;
- 0.081 1.067 0.438 -43.944;
- -0.069 -0.394 0.882 59.058;
- 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
- 1.09453 -0.12176 0.04872 -6.27205;
- 0.08059 1.06731 0.43837 -43.94444;
- -0.06922 -0.39445 0.88219 59.05766;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 382743
- Quasinewton: input matrix
- 1.09453 -0.12176 0.04872 -6.27205;
- 0.08059 1.06731 0.43837 -43.94444;
- -0.06922 -0.39445 0.88219 59.05766;
- 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) = 4.3 tol 0.000000
- final transform:
- 1.095 -0.122 0.049 -6.272;
- 0.081 1.067 0.438 -43.944;
- -0.069 -0.394 0.882 59.058;
- 0.000 0.000 0.000 1.000;
- writing output transformation to transforms/talairach_with_skull_2.lta...
- registration took 28 minutes and 56 seconds.
- #--------------------------------------
- #@# SubCort Seg Thu Aug 8 16:05:21 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 snake1
- machine x86_64
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 = 0.13909 ( 7)
- Left_Lateral_Ventricle (4): linear fit = 0.25 x + 0.0 (789 voxels, overlap=0.007)
- Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (789 voxels, peak = 7), gca=10.8
- gca peak = 0.14982 (20)
- mri peak = 0.14868 ( 7)
- Right_Lateral_Ventricle (43): linear fit = 0.28 x + 0.0 (1355 voxels, overlap=0.009)
- Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (1355 voxels, peak = 6), gca=8.0
- gca peak = 0.28003 (97)
- mri peak = 0.10638 (90)
- Right_Pallidum (52): linear fit = 0.92 x + 0.0 (470 voxels, overlap=0.049)
- Right_Pallidum (52): linear fit = 0.92 x + 0.0 (470 voxels, peak = 89), gca=88.8
- gca peak = 0.18160 (96)
- mri peak = 0.09209 (89)
- Left_Pallidum (13): linear fit = 0.88 x + 0.0 (347 voxels, overlap=0.078)
- Left_Pallidum (13): linear fit = 0.88 x + 0.0 (347 voxels, peak = 85), gca=85.0
- gca peak = 0.27536 (62)
- mri peak = 0.08958 (56)
- Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (538 voxels, overlap=0.631)
- Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (538 voxels, peak = 55), gca=54.9
- gca peak = 0.32745 (63)
- mri peak = 0.08707 (60)
- Left_Hippocampus (17): linear fit = 0.90 x + 0.0 (517 voxels, overlap=0.783)
- Left_Hippocampus (17): linear fit = 0.90 x + 0.0 (517 voxels, peak = 57), gca=57.0
- gca peak = 0.08597 (105)
- mri peak = 0.08623 (107)
- Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (47998 voxels, overlap=0.701)
- Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (47998 voxels, peak = 108), gca=107.6
- gca peak = 0.09209 (106)
- mri peak = 0.08121 (106)
- Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (50158 voxels, overlap=0.709)
- Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (50158 voxels, peak = 109), gca=108.6
- gca peak = 0.07826 (63)
- mri peak = 0.05160 (57)
- Left_Cerebral_Cortex (3): linear fit = 0.86 x + 0.0 (13277 voxels, overlap=0.445)
- Left_Cerebral_Cortex (3): linear fit = 0.86 x + 0.0 (13277 voxels, peak = 54), gca=53.9
- gca peak = 0.08598 (64)
- mri peak = 0.04557 (56)
- Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (11967 voxels, overlap=0.266)
- Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (11967 voxels, peak = 53), gca=52.8
- gca peak = 0.24164 (71)
- mri peak = 0.08978 (68)
- Right_Caudate (50): linear fit = 0.92 x + 0.0 (721 voxels, overlap=0.858)
- Right_Caudate (50): linear fit = 0.92 x + 0.0 (721 voxels, peak = 65), gca=65.0
- gca peak = 0.18227 (75)
- mri peak = 0.08903 (66)
- Left_Caudate (11): linear fit = 0.87 x + 0.0 (1066 voxels, overlap=0.333)
- Left_Caudate (11): linear fit = 0.87 x + 0.0 (1066 voxels, peak = 65), gca=64.9
- gca peak = 0.10629 (62)
- mri peak = 0.05051 (57)
- Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (7911 voxels, overlap=0.927)
- Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (7911 voxels, peak = 58), gca=58.0
- gca peak = 0.11668 (59)
- mri peak = 0.05062 (55)
- Right_Cerebellum_Cortex (47): linear fit = 0.92 x + 0.0 (8157 voxels, overlap=0.830)
- Right_Cerebellum_Cortex (47): linear fit = 0.92 x + 0.0 (8157 voxels, peak = 54), gca=54.0
- gca peak = 0.17849 (88)
- mri peak = 0.09641 (93)
- Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (6277 voxels, overlap=0.921)
- Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (6277 voxels, peak = 92), gca=92.0
- gca peak = 0.16819 (86)
- mri peak = 0.08981 (93)
- Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (5943 voxels, overlap=0.944)
- Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (5943 voxels, peak = 89), gca=89.0
- gca peak = 0.41688 (64)
- mri peak = 0.08099 (61)
- Left_Amygdala (18): linear fit = 0.98 x + 0.0 (284 voxels, overlap=1.041)
- Left_Amygdala (18): linear fit = 0.98 x + 0.0 (284 voxels, peak = 62), gca=62.4
- gca peak = 0.42394 (62)
- mri peak = 0.09272 (59)
- Right_Amygdala (54): linear fit = 0.94 x + 0.0 (312 voxels, overlap=1.036)
- Right_Amygdala (54): linear fit = 0.94 x + 0.0 (312 voxels, peak = 59), gca=58.6
- gca peak = 0.10041 (96)
- mri peak = 0.06401 (92)
- Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (3835 voxels, overlap=0.992)
- Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (3835 voxels, peak = 95), gca=94.6
- gca peak = 0.13978 (88)
- mri peak = 0.06302 (91)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3420 voxels, overlap=1.000)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3420 voxels, peak = 88), gca=87.6
- gca peak = 0.08514 (81)
- mri peak = 0.05769 (75)
- Left_Putamen (12): linear fit = 0.87 x + 0.0 (2148 voxels, overlap=0.612)
- Left_Putamen (12): linear fit = 0.87 x + 0.0 (2148 voxels, peak = 70), gca=70.1
- gca peak = 0.09624 (82)
- mri peak = 0.06418 (73)
- Right_Putamen (51): linear fit = 0.88 x + 0.0 (1919 voxels, overlap=0.477)
- Right_Putamen (51): linear fit = 0.88 x + 0.0 (1919 voxels, peak = 73), gca=72.6
- gca peak = 0.07543 (88)
- mri peak = 0.07397 (87)
- Brain_Stem (16): linear fit = 1.03 x + 0.0 (10638 voxels, overlap=0.765)
- Brain_Stem (16): linear fit = 1.03 x + 0.0 (10638 voxels, peak = 91), gca=91.1
- gca peak = 0.12757 (95)
- mri peak = 0.06772 (97)
- Right_VentralDC (60): linear fit = 1.02 x + 0.0 (1137 voxels, overlap=0.834)
- Right_VentralDC (60): linear fit = 1.02 x + 0.0 (1137 voxels, peak = 97), gca=97.4
- gca peak = 0.17004 (92)
- mri peak = 0.07330 (99)
- Left_VentralDC (28): linear fit = 1.03 x + 0.0 (1173 voxels, overlap=0.884)
- Left_VentralDC (28): linear fit = 1.03 x + 0.0 (1173 voxels, peak = 95), gca=95.2
- gca peak = 0.21361 (36)
- mri peak = 1.00000 (53)
- gca peak = 0.26069 (23)
- mri peak = 0.18182 ( 8)
- Fourth_Ventricle (15): linear fit = 0.31 x + 0.0 (117 voxels, overlap=0.027)
- Fourth_Ventricle (15): linear fit = 0.31 x + 0.0 (117 voxels, peak = 7), gca=7.0
- 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 0.90 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 = 0.13909 ( 7)
- Left_Lateral_Ventricle (4): linear fit = 0.62 x + 0.0 (789 voxels, overlap=0.874)
- Left_Lateral_Ventricle (4): linear fit = 0.62 x + 0.0 (789 voxels, peak = 7), gca=6.9
- gca peak = 0.29325 ( 9)
- mri peak = 0.14868 ( 7)
- Right_Lateral_Ventricle (43): linear fit = 0.79 x + 0.0 (1355 voxels, overlap=0.970)
- Right_Lateral_Ventricle (43): linear fit = 0.79 x + 0.0 (1355 voxels, peak = 7), gca=7.1
- gca peak = 0.32165 (89)
- mri peak = 0.10638 (90)
- Right_Pallidum (52): linear fit = 1.00 x + 0.0 (470 voxels, overlap=1.021)
- Right_Pallidum (52): linear fit = 1.00 x + 0.0 (470 voxels, peak = 89), gca=88.6
- gca peak = 0.20111 (85)
- mri peak = 0.09209 (89)
- Left_Pallidum (13): linear fit = 1.03 x + 0.0 (347 voxels, overlap=1.008)
- Left_Pallidum (13): linear fit = 1.03 x + 0.0 (347 voxels, peak = 88), gca=88.0
- gca peak = 0.31426 (55)
- mri peak = 0.08958 (56)
- Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (538 voxels, overlap=1.008)
- Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (538 voxels, peak = 55), gca=55.0
- gca peak = 0.31920 (57)
- mri peak = 0.08707 (60)
- Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (517 voxels, overlap=1.007)
- Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (517 voxels, peak = 57), gca=57.0
- gca peak = 0.08345 (108)
- mri peak = 0.08623 (107)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (47998 voxels, overlap=0.777)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (47998 voxels, peak = 108), gca=108.0
- gca peak = 0.08551 (108)
- mri peak = 0.08121 (106)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (50158 voxels, overlap=0.783)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (50158 voxels, peak = 108), gca=108.0
- gca peak = 0.09237 (54)
- mri peak = 0.05160 (57)
- Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (13277 voxels, overlap=0.981)
- Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (13277 voxels, peak = 54), gca=54.0
- gca peak = 0.10548 (53)
- mri peak = 0.04557 (56)
- Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (11967 voxels, overlap=0.993)
- Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (11967 voxels, peak = 52), gca=52.2
- gca peak = 0.25856 (67)
- mri peak = 0.08978 (68)
- Right_Caudate (50): linear fit = 1.00 x + 0.0 (721 voxels, overlap=1.002)
- Right_Caudate (50): linear fit = 1.00 x + 0.0 (721 voxels, peak = 67), gca=67.0
- gca peak = 0.18203 (65)
- mri peak = 0.08903 (66)
- Left_Caudate (11): linear fit = 1.00 x + 0.0 (1066 voxels, overlap=1.000)
- Left_Caudate (11): linear fit = 1.00 x + 0.0 (1066 voxels, peak = 65), gca=65.0
- gca peak = 0.11249 (57)
- mri peak = 0.05051 (57)
- Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (7911 voxels, overlap=0.998)
- Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (7911 voxels, peak = 58), gca=58.4
- gca peak = 0.13073 (55)
- mri peak = 0.05062 (55)
- Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (8157 voxels, overlap=1.000)
- Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (8157 voxels, peak = 55), gca=55.0
- gca peak = 0.17369 (92)
- mri peak = 0.09641 (93)
- Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6277 voxels, overlap=0.994)
- Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6277 voxels, peak = 92), gca=91.5
- gca peak = 0.16430 (89)
- mri peak = 0.08981 (93)
- Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5943 voxels, overlap=0.995)
- Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5943 voxels, peak = 89), gca=88.6
- gca peak = 0.33142 (62)
- mri peak = 0.08099 (61)
- Left_Amygdala (18): linear fit = 1.01 x + 0.0 (284 voxels, overlap=1.027)
- Left_Amygdala (18): linear fit = 1.01 x + 0.0 (284 voxels, peak = 63), gca=62.9
- gca peak = 0.36545 (59)
- mri peak = 0.09272 (59)
- Right_Amygdala (54): linear fit = 1.02 x + 0.0 (312 voxels, overlap=1.027)
- Right_Amygdala (54): linear fit = 1.02 x + 0.0 (312 voxels, peak = 60), gca=60.5
- gca peak = 0.10399 (93)
- mri peak = 0.06401 (92)
- Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3835 voxels, overlap=0.978)
- Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3835 voxels, peak = 93), gca=92.5
- gca peak = 0.10243 (87)
- mri peak = 0.06302 (91)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3420 voxels, overlap=1.001)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3420 voxels, peak = 87), gca=86.6
- gca peak = 0.09485 (74)
- mri peak = 0.05769 (75)
- Left_Putamen (12): linear fit = 1.03 x + 0.0 (2148 voxels, overlap=1.001)
- Left_Putamen (12): linear fit = 1.03 x + 0.0 (2148 voxels, peak = 77), gca=76.6
- gca peak = 0.12029 (67)
- mri peak = 0.06418 (73)
- Right_Putamen (51): linear fit = 0.99 x + 0.0 (1919 voxels, overlap=0.999)
- Right_Putamen (51): linear fit = 0.99 x + 0.0 (1919 voxels, peak = 66), gca=66.0
- gca peak = 0.07011 (88)
- mri peak = 0.07397 (87)
- Brain_Stem (16): linear fit = 1.00 x + 0.0 (10638 voxels, overlap=0.836)
- Brain_Stem (16): linear fit = 1.00 x + 0.0 (10638 voxels, peak = 88), gca=87.6
- gca peak = 0.14163 (97)
- mri peak = 0.06772 (97)
- Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1137 voxels, overlap=0.858)
- Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1137 voxels, peak = 97), gca=97.5
- gca peak = 0.14333 (95)
- mri peak = 0.07330 (99)
- Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1173 voxels, overlap=0.912)
- Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1173 voxels, peak = 95), gca=95.5
- gca peak = 0.35640 (14)
- mri peak = 1.00000 (53)
- gca peak = 0.33827 ( 9)
- mri peak = 0.18182 ( 8)
- Fourth_Ventricle (15): linear fit = 0.75 x + 0.0 (117 voxels, overlap=0.868)
- Fourth_Ventricle (15): linear fit = 0.75 x + 0.0 (117 voxels, peak = 7), gca=6.7
- gca peak Unknown = 0.94427 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.27695 (32)
- gca peak Third_Ventricle = 0.35640 (14)
- gca peak CSF = 0.30128 (18)
- gca peak Left_Accumbens_area = 0.44858 (60)
- gca peak Left_undetermined = 1.00000 (35)
- gca peak Left_vessel = 0.38932 (62)
- gca peak Left_choroid_plexus = 0.09084 (48)
- gca peak Right_Inf_Lat_Vent = 0.33369 (28)
- gca peak Right_Accumbens_area = 0.30176 (66)
- gca peak Right_vessel = 0.60254 (60)
- gca peak Right_choroid_plexus = 0.10278 (48)
- gca peak Fifth_Ventricle = 0.45329 (19)
- gca peak WM_hypointensities = 0.14093 (84)
- gca peak non_WM_hypointensities = 0.12378 (54)
- gca peak Optic_Chiasm = 0.34849 (76)
- not using caudate to estimate GM means
- estimating mean gm scale to be 1.00 x + 0.0
- estimating mean wm scale to be 1.00 x + 0.0
- estimating mean csf scale to be 0.72 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
- 12807 gm and wm labels changed (%13 to gray, %87 to white out of all changed labels)
- 303 hippocampal voxels changed.
- 9 amygdala voxels changed.
- pass 1: 89187 changed. image ll: -2.201, PF=1.000
- pass 2: 16022 changed. image ll: -2.198, PF=1.000
- pass 3: 5981 changed.
- pass 4: 2652 changed.
- writing labeled volume to aseg.auto_noCCseg.mgz...
- auto-labeling took 18 minutes and 14 seconds.
- mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/cc_up.lta sub001
- 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/sub001/mri/transforms/cc_up.lta
- reading aseg from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/aseg.auto_noCCseg.mgz
- reading norm from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/norm.mgz
- 85844 voxels in left wm, 67962 in right wm, xrange [118, 135]
- searching rotation angles z=[-3 11], y=[-3 11]
-
searching scale 1 Z rot -2.9
searching scale 1 Z rot -2.6
searching scale 1 Z rot -2.4
searching scale 1 Z rot -2.1
searching scale 1 Z rot -1.9
searching scale 1 Z rot -1.6
searching scale 1 Z rot -1.4
searching scale 1 Z rot -1.1
searching scale 1 Z rot -0.9
searching scale 1 Z rot -0.6
searching scale 1 Z rot -0.4
searching scale 1 Z rot -0.1
searching scale 1 Z rot 0.1
searching scale 1 Z rot 0.4
searching scale 1 Z rot 0.6
searching scale 1 Z rot 0.9
searching scale 1 Z rot 1.1
searching scale 1 Z rot 1.4
searching scale 1 Z rot 1.6
searching scale 1 Z rot 1.9
searching scale 1 Z rot 2.1
searching scale 1 Z rot 2.4
searching scale 1 Z rot 2.6
searching scale 1 Z rot 2.9
searching scale 1 Z rot 3.1
searching scale 1 Z rot 3.4
searching scale 1 Z rot 3.6
searching scale 1 Z rot 3.9
searching scale 1 Z rot 4.1
searching scale 1 Z rot 4.4
searching scale 1 Z rot 4.6
searching scale 1 Z rot 4.9
searching scale 1 Z rot 5.1
searching scale 1 Z rot 5.4
searching scale 1 Z rot 5.6
searching scale 1 Z rot 5.9
searching scale 1 Z rot 6.1
searching scale 1 Z rot 6.4
searching scale 1 Z rot 6.6
searching scale 1 Z rot 6.9
searching scale 1 Z rot 7.1
searching scale 1 Z rot 7.4
searching scale 1 Z rot 7.6
searching scale 1 Z rot 7.9
searching scale 1 Z rot 8.1
searching scale 1 Z rot 8.4
searching scale 1 Z rot 8.6
searching scale 1 Z rot 8.9
searching scale 1 Z rot 9.1
searching scale 1 Z rot 9.4
searching scale 1 Z rot 9.6
searching scale 1 Z rot 9.9
searching scale 1 Z rot 10.1
searching scale 1 Z rot 10.4
searching scale 1 Z rot 10.6
searching scale 1 Z rot 10.9 global minimum found at slice 125.5, rotations (4.21, 4.10)
- final transformation (x=125.5, yr=4.210, zr=4.101):
- 0.995 -0.072 0.073 1.721;
- 0.071 0.997 0.005 39.744;
- -0.073 -0.000 0.997 40.475;
- 0.000 0.000 0.000 1.000;
- updating x range to be [122, 131] in xformed coordinates
- best xformed slice 128
- cc center is found at 128 157 117
- eigenvectors:
- 0.000 0.002 1.000;
- -0.239 -0.971 0.002;
- 0.971 -0.239 0.000;
- error in mid anterior detected - correcting...
- writing aseg with callosum to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/aseg.auto.mgz...
- corpus callosum matter segmentation took 1.9 minutes
- #--------------------------------------
- #@# Merge ASeg Thu Aug 8 16:25:30 CEST 2013
- cp aseg.auto.mgz aseg.mgz
- #--------------------------------------------
- #@# Intensity Normalization2 Thu Aug 8 16:25:30 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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...
- 2103 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 110
- gm peak at 57 (57), valley at 30 (30)
- csf peak at 28, setting threshold to 47
- 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 60 (60), valley at 31 (31)
- csf peak at 30, setting threshold to 50
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Done iterating ---------------------------------
- writing output to brain.mgz
- 3D bias adjustment took 4 minutes and 13 seconds.
- #--------------------------------------------
- #@# Mask BFS Thu Aug 8 16:29:45 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri
- mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
- threshold mask volume at 5
- DoAbs = 0
- Found 1637125 voxels in mask (pct= 9.76)
- Writing masked volume to brain.finalsurfs.mgz...done.
- #--------------------------------------------
- #@# WM Segmentation Thu Aug 8 16:29:47 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): 107.5 +- 4.6 [80.0 --> 125.0]
- GM (68.0) : 67.8 +- 9.1 [30.0 --> 96.0]
- setting bottom of white matter range to 76.9
- setting top of gray matter range to 86.0
- doing initial intensity segmentation...
- using local statistics to label ambiguous voxels...
- using local geometry to label remaining ambiguous voxels...
- reclassifying voxels using Gaussian border classifier...
- removing voxels with positive offset direction...
- smoothing T1 volume with sigma = 0.250
- removing 1-dimensional structures...
- 7106 sparsely connected voxels removed...
- thickening thin strands....
- 20 segments, 5850 filled
- 218 bright non-wm voxels segmented.
- 3904 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 0.61 minutes
- reading wm segmentation from wm.seg.mgz...
- 64 voxels added to wm to prevent paths from MTL structures to cortex
- 1213 additional wm voxels added
- 0 additional wm voxels added
- SEG EDIT: 51151 voxels turned on, 48012 voxels turned off.
- propagating editing to output volume from wm.seg.mgz
- 115,126,128 old 0 new 0
- 115,126,128 old 0 new 0
- writing edited volume to wm.asegedit.mgz....
- mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz
- Iteration Number : 1
- pass 1 (xy+): 19 found - 19 modified | TOTAL: 19
- pass 2 (xy+): 0 found - 19 modified | TOTAL: 19
- pass 1 (xy-): 20 found - 20 modified | TOTAL: 39
- pass 2 (xy-): 0 found - 20 modified | TOTAL: 39
- pass 1 (yz+): 37 found - 37 modified | TOTAL: 76
- pass 2 (yz+): 0 found - 37 modified | TOTAL: 76
- pass 1 (yz-): 21 found - 21 modified | TOTAL: 97
- pass 2 (yz-): 0 found - 21 modified | TOTAL: 97
- pass 1 (xz+): 15 found - 15 modified | TOTAL: 112
- pass 2 (xz+): 0 found - 15 modified | TOTAL: 112
- pass 1 (xz-): 26 found - 26 modified | TOTAL: 138
- pass 2 (xz-): 0 found - 26 modified | TOTAL: 138
- Iteration Number : 1
- pass 1 (+++): 7 found - 7 modified | TOTAL: 7
- pass 2 (+++): 0 found - 7 modified | TOTAL: 7
- pass 1 (+++): 16 found - 16 modified | TOTAL: 23
- pass 2 (+++): 0 found - 16 modified | TOTAL: 23
- pass 1 (+++): 14 found - 14 modified | TOTAL: 37
- pass 2 (+++): 0 found - 14 modified | TOTAL: 37
- pass 1 (+++): 14 found - 14 modified | TOTAL: 51
- pass 2 (+++): 0 found - 14 modified | TOTAL: 51
- Iteration Number : 1
- pass 1 (++): 134 found - 134 modified | TOTAL: 134
- pass 2 (++): 0 found - 134 modified | TOTAL: 134
- pass 1 (+-): 95 found - 95 modified | TOTAL: 229
- pass 2 (+-): 0 found - 95 modified | TOTAL: 229
- pass 1 (--): 129 found - 129 modified | TOTAL: 358
- pass 2 (--): 0 found - 129 modified | TOTAL: 358
- pass 1 (-+): 107 found - 107 modified | TOTAL: 465
- pass 2 (-+): 0 found - 107 modified | TOTAL: 465
- Iteration Number : 2
- pass 1 (xy+): 4 found - 4 modified | TOTAL: 4
- pass 2 (xy+): 0 found - 4 modified | TOTAL: 4
- pass 1 (xy-): 3 found - 3 modified | TOTAL: 7
- pass 2 (xy-): 0 found - 3 modified | TOTAL: 7
- pass 1 (yz+): 4 found - 4 modified | TOTAL: 11
- pass 2 (yz+): 0 found - 4 modified | TOTAL: 11
- pass 1 (yz-): 5 found - 5 modified | TOTAL: 16
- pass 2 (yz-): 0 found - 5 modified | TOTAL: 16
- pass 1 (xz+): 3 found - 3 modified | TOTAL: 19
- pass 2 (xz+): 0 found - 3 modified | TOTAL: 19
- pass 1 (xz-): 7 found - 7 modified | TOTAL: 26
- pass 2 (xz-): 0 found - 7 modified | TOTAL: 26
- Iteration Number : 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 2 found - 2 modified | TOTAL: 2
- pass 2 (+++): 0 found - 2 modified | TOTAL: 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 2
- Iteration Number : 2
- pass 1 (++): 5 found - 5 modified | TOTAL: 5
- pass 2 (++): 0 found - 5 modified | TOTAL: 5
- pass 1 (+-): 4 found - 4 modified | TOTAL: 9
- pass 2 (+-): 0 found - 4 modified | TOTAL: 9
- pass 1 (--): 0 found - 0 modified | TOTAL: 9
- pass 1 (-+): 4 found - 4 modified | TOTAL: 13
- pass 2 (-+): 0 found - 4 modified | TOTAL: 13
- Iteration Number : 3
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 1 found - 1 modified | TOTAL: 1
- pass 2 (yz+): 0 found - 1 modified | TOTAL: 1
- pass 1 (yz-): 1 found - 1 modified | TOTAL: 2
- pass 2 (yz-): 0 found - 1 modified | TOTAL: 2
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 2
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 2
- 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 = 697 (out of 626925: 0.111178)
- binarizing input wm segmentation...
- Ambiguous edge configurations...
- mri_pretess done
- #--------------------------------------------
- #@# Fill Thu Aug 8 16:32:19 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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
- 1.095 -0.075 0.091 -14.736;
- 0.030 1.035 0.346 -24.562;
- -0.093 -0.329 0.945 47.700;
- 0.000 0.000 0.000 1.000;
- voxel to talairach voxel transform
- 1.095 -0.075 0.091 -14.736;
- 0.030 1.035 0.346 -24.562;
- -0.093 -0.329 0.945 47.700;
- 0.000 0.000 0.000 1.000;
- reading segmented volume aseg.auto_noCCseg.mgz...
- Looking for area (min, max) = (350, 1400)
- area[0] = 1920 (min = 350, max = 1400), aspect = 0.68 (min = 0.10, max = 0.75)
- need search nearby
- using seed (126, 120, 153), TAL = (2.0, 25.0, 8.0)
- talairach voxel to voxel transform
- 0.904 0.034 -0.100 18.908;
- -0.050 0.864 -0.311 35.322;
- 0.072 0.304 0.940 -36.337;
- 0.000 0.000 0.000 1.000;
- segmentation indicates cc at (126, 120, 153) --> (2.0, 25.0, 8.0)
- done.
- writing output to filled.mgz...
- filling took 0.9 minutes
- talairach cc position changed to (2.00, 25.00, 8.00)
- Erasing brainstem...done.
- seed_search_size = 9, min_neighbors = 5
- search rh wm seed point around talairach space:(20.00, 25.00, 8.00) SRC: (105.29, 85.94, 151.77)
- search lh wm seed point around talairach space (-16.00, 25.00, 8.00), SRC: (137.82, 84.14, 154.36)
- 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 16:33:12 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/scripts
- mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz
- Iteration Number : 1
- pass 1 (xy+): 5 found - 5 modified | TOTAL: 5
- pass 2 (xy+): 0 found - 5 modified | TOTAL: 5
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 5
- pass 1 (yz+): 4 found - 4 modified | TOTAL: 9
- pass 2 (yz+): 0 found - 4 modified | TOTAL: 9
- pass 1 (yz-): 2 found - 2 modified | TOTAL: 11
- pass 2 (yz-): 0 found - 2 modified | TOTAL: 11
- pass 1 (xz+): 4 found - 4 modified | TOTAL: 15
- pass 2 (xz+): 0 found - 4 modified | TOTAL: 15
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 15
- Iteration Number : 1
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 1
- pass 1 (++): 1 found - 1 modified | TOTAL: 1
- pass 2 (++): 0 found - 1 modified | TOTAL: 1
- pass 1 (+-): 0 found - 0 modified | TOTAL: 1
- pass 1 (--): 3 found - 3 modified | TOTAL: 4
- pass 2 (--): 0 found - 3 modified | TOTAL: 4
- pass 1 (-+): 0 found - 0 modified | TOTAL: 4
- Iteration Number : 2
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Total Number of Modified Voxels = 19 (out of 299752: 0.006339)
- Ambiguous edge configurations...
- mri_pretess done
- mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix
- $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- slice 40: 2116 vertices, 2294 faces
- slice 50: 9788 vertices, 10138 faces
- slice 60: 20454 vertices, 20862 faces
- slice 70: 32418 vertices, 32799 faces
- slice 80: 45156 vertices, 45565 faces
- slice 90: 57599 vertices, 57978 faces
- slice 100: 69741 vertices, 70145 faces
- slice 110: 81890 vertices, 82309 faces
- slice 120: 93169 vertices, 93581 faces
- slice 130: 104379 vertices, 104820 faces
- slice 140: 115351 vertices, 115741 faces
- slice 150: 124866 vertices, 125204 faces
- slice 160: 133160 vertices, 133458 faces
- slice 170: 140209 vertices, 140458 faces
- slice 180: 146054 vertices, 146287 faces
- slice 190: 150789 vertices, 150952 faces
- slice 200: 152644 vertices, 152678 faces
- slice 210: 152644 vertices, 152678 faces
- slice 220: 152644 vertices, 152678 faces
- slice 230: 152644 vertices, 152678 faces
- slice 240: 152644 vertices, 152678 faces
- slice 250: 152644 vertices, 152678 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...
- 152644 voxel in cpt #1: X=-34 [v=152644,e=458034,f=305356] located at (-24.746771, -20.925776, 37.239571)
- For the whole surface: X=-34 [v=152644,e=458034,f=305356]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Smooth1 lh Thu Aug 8 16:33:20 CEST 2013
- mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 16:33:25 CEST 2013
- mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/scripts
- avg radius = 48.9 mm, total surface area = 80451 mm^2
- writing inflated surface to ../surf/lh.inflated.nofix
- inflation took 0.6 minutes
- Not saving sulc
-
step 000: RMS=0.099 (target=0.015)
step 005: RMS=0.071 (target=0.015)
step 010: RMS=0.052 (target=0.015)
step 015: RMS=0.043 (target=0.015)
step 020: RMS=0.037 (target=0.015)
step 025: RMS=0.032 (target=0.015)
step 030: RMS=0.028 (target=0.015)
step 035: RMS=0.026 (target=0.015)
step 040: RMS=0.024 (target=0.015)
step 045: RMS=0.023 (target=0.015)
step 050: RMS=0.022 (target=0.015)
step 055: RMS=0.022 (target=0.015)
step 060: RMS=0.021 (target=0.015)
- inflation complete.
- Not saving sulc
- #--------------------------------------------
- #@# QSphere lh Thu Aug 8 16:34:00 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/scripts
- mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix
- doing quick spherical unfolding.
- setting seed for random number genererator to 1234
- $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading original vertex positions...
- unfolding cortex into spherical form...
- surface projected - minimizing metric distortion...
- vertex spacing 0.94 +- 0.55 (0.00-->6.95) (max @ vno 70593 --> 70606)
- face area 0.02 +- 0.03 (-0.22-->0.61)
- scaling brain by 0.302...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=176.107, avgs=0
- 005/300: dt: 0.9000, rms radial error=175.850, avgs=0
- 010/300: dt: 0.9000, rms radial error=175.296, avgs=0
- 015/300: dt: 0.9000, rms radial error=174.567, avgs=0
- 020/300: dt: 0.9000, rms radial error=173.737, avgs=0
- 025/300: dt: 0.9000, rms radial error=172.849, avgs=0
- 030/300: dt: 0.9000, rms radial error=171.927, avgs=0
- 035/300: dt: 0.9000, rms radial error=170.987, avgs=0
- 040/300: dt: 0.9000, rms radial error=170.039, avgs=0
- 045/300: dt: 0.9000, rms radial error=169.088, avgs=0
- 050/300: dt: 0.9000, rms radial error=168.136, avgs=0
- 055/300: dt: 0.9000, rms radial error=167.187, avgs=0
- 060/300: dt: 0.9000, rms radial error=166.243, avgs=0
- 065/300: dt: 0.9000, rms radial error=165.308, avgs=0
- 070/300: dt: 0.9000, rms radial error=164.378, avgs=0
- 075/300: dt: 0.9000, rms radial error=163.453, avgs=0
- 080/300: dt: 0.9000, rms radial error=162.533, avgs=0
- 085/300: dt: 0.9000, rms radial error=161.617, avgs=0
- 090/300: dt: 0.9000, rms radial error=160.707, avgs=0
- 095/300: dt: 0.9000, rms radial error=159.802, avgs=0
- 100/300: dt: 0.9000, rms radial error=158.902, avgs=0
- 105/300: dt: 0.9000, rms radial error=158.007, avgs=0
- 110/300: dt: 0.9000, rms radial error=157.117, avgs=0
- 115/300: dt: 0.9000, rms radial error=156.231, avgs=0
- 120/300: dt: 0.9000, rms radial error=155.351, avgs=0
- 125/300: dt: 0.9000, rms radial error=154.477, avgs=0
- 130/300: dt: 0.9000, rms radial error=153.610, avgs=0
- 135/300: dt: 0.9000, rms radial error=152.747, avgs=0
- 140/300: dt: 0.9000, rms radial error=151.889, avgs=0
- 145/300: dt: 0.9000, rms radial error=151.036, avgs=0
- 150/300: dt: 0.9000, rms radial error=150.188, avgs=0
- 155/300: dt: 0.9000, rms radial error=149.345, avgs=0
- 160/300: dt: 0.9000, rms radial error=148.506, avgs=0
- 165/300: dt: 0.9000, rms radial error=147.672, avgs=0
- 170/300: dt: 0.9000, rms radial error=146.842, avgs=0
- 175/300: dt: 0.9000, rms radial error=146.017, avgs=0
- 180/300: dt: 0.9000, rms radial error=145.196, avgs=0
- 185/300: dt: 0.9000, rms radial error=144.380, avgs=0
- 190/300: dt: 0.9000, rms radial error=143.569, avgs=0
- 195/300: dt: 0.9000, rms radial error=142.762, avgs=0
- 200/300: dt: 0.9000, rms radial error=141.959, avgs=0
- 205/300: dt: 0.9000, rms radial error=141.160, avgs=0
- 210/300: dt: 0.9000, rms radial error=140.367, avgs=0
- 215/300: dt: 0.9000, rms radial error=139.578, avgs=0
- 220/300: dt: 0.9000, rms radial error=138.793, avgs=0
- 225/300: dt: 0.9000, rms radial error=138.012, avgs=0
- 230/300: dt: 0.9000, rms radial error=137.236, avgs=0
- 235/300: dt: 0.9000, rms radial error=136.464, avgs=0
- 240/300: dt: 0.9000, rms radial error=135.696, avgs=0
- 245/300: dt: 0.9000, rms radial error=134.933, avgs=0
- 250/300: dt: 0.9000, rms radial error=134.174, avgs=0
- 255/300: dt: 0.9000, rms radial error=133.419, avgs=0
- 260/300: dt: 0.9000, rms radial error=132.668, avgs=0
- 265/300: dt: 0.9000, rms radial error=131.921, avgs=0
- 270/300: dt: 0.9000, rms radial error=131.179, avgs=0
- 275/300: dt: 0.9000, rms radial error=130.441, avgs=0
- 280/300: dt: 0.9000, rms radial error=129.707, avgs=0
- 285/300: dt: 0.9000, rms radial error=128.977, avgs=0
- 290/300: dt: 0.9000, rms radial error=128.251, avgs=0
- 295/300: dt: 0.9000, rms radial error=127.529, avgs=0
- 300/300: dt: 0.9000, rms radial error=126.811, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 18028.29
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00016
- epoch 2 (K=40.0), pass 1, starting sse = 3070.94
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00005
- epoch 3 (K=160.0), pass 1, starting sse = 321.72
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.08/11 = 0.00689
- epoch 4 (K=640.0), pass 1, starting sse = 18.25
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.16/15 = 0.01094
- final writing spherical brain to ../surf/lh.qsphere.nofix
- spherical transformation took 0.09 hours
- distance error %100000.00
- #--------------------------------------------
- #@# Fix Topology lh Thu Aug 8 16:39:31 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/sub001/scripts
- mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub001 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=-34 (nv=152644, nf=305356, ne=458034, g=18)
- using quasi-homeomorphic spherical map to tessellate cortical surface...
- Correction of the Topology
- Finding true center and radius of Spherical Surface...done
- Surface centered at (0,0,0) with radius 100.0 in 11 iterations
- marking ambiguous vertices...
- 2813 ambiguous faces found in tessellation
- segmenting defects...
- 26 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- -merging segment 9 into 5
- -merging segment 11 into 16
- 24 defects to be corrected
- 0 vertices coincident
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/lh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -9.6647 (-4.8324)
- -vertex loglikelihood: -6.5607 (-3.2803)
- -normal dot loglikelihood: -3.5770 (-3.5770)
- -quad curv loglikelihood: -6.3164 (-3.1582)
- Total Loglikelihood : -26.1189
- CORRECTING DEFECT 0 (vertices=18, convex hull=24)
- After retessellation of defect 0, euler #=-22 (150904,452023,301097) : difference with theory (-21) = 1
- CORRECTING DEFECT 1 (vertices=187, convex hull=205)
- normal vector of length zero at vertex 150981 with 3 faces
- normal vector of length zero at vertex 150981 with 3 faces
- normal vector of length zero at vertex 150981 with 3 faces
- normal vector of length zero at vertex 150981 with 3 faces
- normal vector of length zero at vertex 150981 with 3 faces
- normal vector of length zero at vertex 150981 with 3 faces
- normal vector of length zero at vertex 150981 with 3 faces
- normal vector of length zero at vertex 150981 with 3 faces
- normal vector of length zero at vertex 150981 with 3 faces
- normal vector of length zero at vertex 150981 with 3 faces
- normal vector of length zero at vertex 150981 with 3 faces
- normal vector of length zero at vertex 150981 with 3 faces
- normal vector of length zero at vertex 150981 with 3 faces
- normal vector of length zero at vertex 150981 with 3 faces
- normal vector of length zero at vertex 150981 with 3 faces
- normal vector of length zero at vertex 150981 with 3 faces
- normal vector of length zero at vertex 150981 with 3 faces
- After retessellation of defect 1, euler #=-21 (150919,452170,301230) : difference with theory (-20) = 1
- CORRECTING DEFECT 2 (vertices=25, convex hull=50)
- After retessellation of defect 2, euler #=-20 (150925,452206,301261) : difference with theory (-19) = 1
- CORRECTING DEFECT 3 (vertices=19, convex hull=30)
- After retessellation of defect 3, euler #=-19 (150932,452238,301287) : difference with theory (-18) = 1
- CORRECTING DEFECT 4 (vertices=9, convex hull=26)
- After retessellation of defect 4, euler #=-18 (150935,452254,301301) : difference with theory (-17) = 1
- CORRECTING DEFECT 5 (vertices=300, convex hull=146)
- After retessellation of defect 5, euler #=-16 (150969,452435,301450) : difference with theory (-16) = 0
- CORRECTING DEFECT 6 (vertices=165, convex hull=176)
- After retessellation of defect 6, euler #=-15 (151045,452745,301685) : difference with theory (-15) = 0
- CORRECTING DEFECT 7 (vertices=60, convex hull=96)
- After retessellation of defect 7, euler #=-14 (151084,452904,301806) : difference with theory (-14) = 0
- CORRECTING DEFECT 8 (vertices=38, convex hull=72)
- After retessellation of defect 8, euler #=-13 (151105,452994,301876) : difference with theory (-13) = 0
- CORRECTING DEFECT 9 (vertices=51, convex hull=65)
- After retessellation of defect 9, euler #=-12 (151128,453089,301949) : difference with theory (-12) = 0
- CORRECTING DEFECT 10 (vertices=102, convex hull=54)
- After retessellation of defect 10, euler #=-11 (151140,453147,301996) : difference with theory (-11) = 0
- CORRECTING DEFECT 11 (vertices=321, convex hull=98)
- After retessellation of defect 11, euler #=-10 (151177,453302,302115) : difference with theory (-10) = 0
- CORRECTING DEFECT 12 (vertices=39, convex hull=28)
- After retessellation of defect 12, euler #=-9 (151182,453323,302132) : difference with theory (-9) = 0
- CORRECTING DEFECT 13 (vertices=12, convex hull=18)
- After retessellation of defect 13, euler #=-8 (151185,453337,302144) : difference with theory (-8) = 0
- CORRECTING DEFECT 14 (vertices=152, convex hull=131)
- After retessellation of defect 14, euler #=-7 (151211,453482,302264) : difference with theory (-7) = 0
- CORRECTING DEFECT 15 (vertices=19, convex hull=23)
- After retessellation of defect 15, euler #=-6 (151214,453498,302278) : difference with theory (-6) = 0
- CORRECTING DEFECT 16 (vertices=74, convex hull=61)
- After retessellation of defect 16, euler #=-5 (151227,453560,302328) : difference with theory (-5) = 0
- CORRECTING DEFECT 17 (vertices=19, convex hull=24)
- After retessellation of defect 17, euler #=-4 (151236,453592,302352) : difference with theory (-4) = 0
- CORRECTING DEFECT 18 (vertices=19, convex hull=48)
- After retessellation of defect 18, euler #=-3 (151245,453636,302388) : difference with theory (-3) = 0
- CORRECTING DEFECT 19 (vertices=30, convex hull=50)
- After retessellation of defect 19, euler #=-2 (151262,453707,302443) : difference with theory (-2) = 0
- CORRECTING DEFECT 20 (vertices=25, convex hull=60)
- After retessellation of defect 20, euler #=-1 (151274,453768,302493) : difference with theory (-1) = 0
- CORRECTING DEFECT 21 (vertices=6, convex hull=16)
- After retessellation of defect 21, euler #=0 (151275,453776,302501) : difference with theory (0) = 0
- CORRECTING DEFECT 22 (vertices=26, convex hull=57)
- After retessellation of defect 22, euler #=1 (151284,453824,302541) : difference with theory (1) = 0
- CORRECTING DEFECT 23 (vertices=27, convex hull=53)
- After retessellation of defect 23, euler #=2 (151296,453882,302588) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.88 +- 0.22 (0.04-->7.55) (max @ vno 110452 --> 111594)
- 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 (0.04-->7.55) (max @ vno 110452 --> 111594)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 91 mutations (37.3%), 153 crossovers (62.7%), 224 vertices were eliminated
- building final representation...
- 1348 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=151296, nf=302588, ne=453882, g=0)
- writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/lh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 21.6 minutes
- 0 defective edges
- removing intersecting faces
- 000: 194 intersecting
- 001: 2 intersecting
- mris_euler_number ../surf/lh.orig
- euler # = v-e+f = 2g-2: 151296 - 453882 + 302588 = 2 --> 0 holes
- F =2V-4: 302588 = 302592-4 (0)
- 2E=3F: 907764 = 907764 (0)
- total defect index = 0
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/scripts
- mris_remove_intersection ../surf/lh.orig ../surf/lh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 37 intersecting
- writing corrected surface to ../surf/lh.orig
- rm ../surf/lh.inflated
- #--------------------------------------------
- #@# Make White Surf lh Thu Aug 8 17:01:13 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/scripts
- mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub001 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/sub001/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/wm.mgz...
- 22126 bright wm thresholded.
- 274 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/lh.orig...
- computing class statistics...
- border white: 284449 voxels (1.70%)
- border gray 312227 voxels (1.86%)
- WM (94.0): 94.7 +- 9.7 [70.0 --> 110.0]
- GM (77.0) : 75.7 +- 12.7 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 50.3 (was 70)
- setting MAX_BORDER_WHITE to 115.7 (was 105)
- setting MIN_BORDER_WHITE to 63.0 (was 85)
- setting MAX_CSF to 37.5 (was 40)
- setting MAX_GRAY to 96.3 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 56.6 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 24.8 (was 40)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.82 +- 0.21 (0.04-->3.50) (max @ vno 102287 --> 103434)
- face area 0.28 +- 0.12 (0.00-->3.12)
- mean absolute distance = 0.65 +- 0.82
- 2904 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=106, GM=63
- mean inside = 94.5, mean outside = 70.9
- smoothing surface for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- mean border=76.4, 63 (63) missing vertices, mean dist 0.3 [0.5 (%35.4)->0.7 (%64.6))]
- %71 local maxima, %23 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 0.91 +- 0.25 (0.10-->4.09) (max @ vno 102287 --> 103434)
- face area 0.28 +- 0.13 (0.00-->3.01)
- mean absolute distance = 0.32 +- 0.52
- 3599 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=7479267.0, rms=12.95
- 001: dt: 0.5000, sse=7568679.0, rms=9.034 (0.000%)
- 002: dt: 0.5000, sse=7950398.0, rms=6.765 (0.000%)
- 003: dt: 0.5000, sse=8210213.5, rms=5.451 (0.000%)
- 004: dt: 0.5000, sse=8579517.0, rms=4.752 (0.000%)
- 005: dt: 0.5000, sse=8641970.0, rms=4.454 (0.000%)
- 006: dt: 0.5000, sse=8797336.0, rms=4.291 (0.000%)
- rms = 4.25, time step reduction 1 of 3 to 0.250...
- 007: dt: 0.5000, sse=8709132.0, rms=4.250 (0.000%)
- 008: dt: 0.2500, sse=5408502.5, rms=2.882 (0.000%)
- 009: dt: 0.2500, sse=4896344.0, rms=2.416 (0.000%)
- 010: dt: 0.2500, sse=4601770.0, rms=2.289 (0.000%)
- 011: dt: 0.2500, sse=4511942.5, rms=2.199 (0.000%)
- rms = 2.15, time step reduction 2 of 3 to 0.125...
- 012: dt: 0.2500, sse=4406335.5, rms=2.154 (0.000%)
- 013: dt: 0.1250, sse=4179499.5, rms=1.930 (0.000%)
- rms = 1.90, time step reduction 3 of 3 to 0.062...
- 014: dt: 0.1250, sse=4131300.0, rms=1.902 (0.000%)
- positioning took 1.8 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 1 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 3 vertex label from ripped group
- mean border=80.5, 42 (6) missing vertices, mean dist -0.2 [0.3 (%76.9)->0.2 (%23.1))]
- %81 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.90 +- 0.24 (0.05-->4.20) (max @ vno 102287 --> 103434)
- face area 0.34 +- 0.16 (0.00-->4.33)
- mean absolute distance = 0.21 +- 0.32
- 2726 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5120937.5, rms=5.82
- 015: dt: 0.5000, sse=5371199.5, rms=4.052 (0.000%)
- rms = 4.37, time step reduction 1 of 3 to 0.250...
- 016: dt: 0.2500, sse=4864177.5, rms=2.970 (0.000%)
- 017: dt: 0.2500, sse=4690957.0, rms=2.341 (0.000%)
- 018: dt: 0.2500, sse=4612590.0, rms=1.936 (0.000%)
- 019: dt: 0.2500, sse=4590838.0, rms=1.838 (0.000%)
- 020: dt: 0.2500, sse=4514417.0, rms=1.734 (0.000%)
- rms = 1.71, time step reduction 2 of 3 to 0.125...
- 021: dt: 0.2500, sse=4520996.0, rms=1.706 (0.000%)
- 022: dt: 0.1250, sse=4385355.0, rms=1.556 (0.000%)
- rms = 1.54, time step reduction 3 of 3 to 0.062...
- 023: dt: 0.1250, sse=4341749.5, rms=1.540 (0.000%)
- positioning took 1.2 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 4 vertex label from ripped group
- mean border=83.7, 40 (4) missing vertices, mean dist -0.1 [0.2 (%77.4)->0.2 (%22.6))]
- %88 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.89 +- 0.24 (0.07-->4.24) (max @ vno 102287 --> 103434)
- face area 0.33 +- 0.16 (0.00-->4.47)
- mean absolute distance = 0.16 +- 0.27
- 2817 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4715030.5, rms=4.03
- 024: dt: 0.5000, sse=5133040.0, rms=3.934 (0.000%)
- rms = 4.16, time step reduction 1 of 3 to 0.250...
- 025: dt: 0.2500, sse=4635884.5, rms=2.469 (0.000%)
- 026: dt: 0.2500, sse=4504973.0, rms=1.926 (0.000%)
- 027: dt: 0.2500, sse=4584896.0, rms=1.618 (0.000%)
- rms = 1.64, time step reduction 2 of 3 to 0.125...
- 028: dt: 0.1250, sse=4519868.5, rms=1.512 (0.000%)
- 029: dt: 0.1250, sse=4427206.0, rms=1.366 (0.000%)
- rms = 1.36, time step reduction 3 of 3 to 0.062...
- 030: dt: 0.1250, sse=4385522.0, rms=1.358 (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 4 vertex label from ripped group
- mean border=84.7, 29 (2) missing vertices, mean dist -0.0 [0.2 (%58.8)->0.2 (%41.2))]
- %90 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- writing white matter surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/lh.white...
- writing smoothed curvature to lh.curv
- 000: dt: 0.0000, sse=4400438.0, rms=1.74
- rms = 2.56, time step reduction 1 of 3 to 0.250...
- 031: dt: 0.2500, sse=4487576.5, rms=1.146 (0.000%)
- 032: dt: 0.2500, sse=4624040.5, rms=1.014 (0.000%)
- rms = 1.02, time step reduction 2 of 3 to 0.125...
- rms = 1.01, time step reduction 3 of 3 to 0.062...
- 033: dt: 0.1250, sse=4624353.5, rms=1.006 (0.000%)
- positioning took 0.5 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- generating cortex label...
- 15 non-cortical segments detected
- only using segment with 2181 vertices
- erasing segment 1 (vno[0] = 92429)
- erasing segment 2 (vno[0] = 93438)
- erasing segment 3 (vno[0] = 105225)
- erasing segment 4 (vno[0] = 107299)
- erasing segment 5 (vno[0] = 110452)
- erasing segment 6 (vno[0] = 111595)
- erasing segment 7 (vno[0] = 113689)
- erasing segment 8 (vno[0] = 113710)
- erasing segment 9 (vno[0] = 113712)
- erasing segment 10 (vno[0] = 116561)
- erasing segment 11 (vno[0] = 116629)
- erasing segment 12 (vno[0] = 116662)
- erasing segment 13 (vno[0] = 119392)
- erasing segment 14 (vno[0] = 120282)
- writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/label/lh.cortex.label...
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/lh.curv
- writing smoothed area to lh.area
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/lh.area
- vertex spacing 0.89 +- 0.25 (0.05-->4.37) (max @ vno 102287 --> 103434)
- face area 0.33 +- 0.15 (0.00-->4.50)
- refinement took 6.9 minutes
- #--------------------------------------------
- #@# Smooth2 lh Thu Aug 8 17:08:08 CEST 2013
- mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/scripts
- smoothing for 3 iterations
- setting seed for random number generator to 1234
- smoothing surface tessellation for 3 iterations...
- smoothing complete - recomputing first and second fundamental forms...
- #--------------------------------------------
- #@# Inflation2 lh Thu Aug 8 17:08:12 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/scripts
- mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated
- avg radius = 49.1 mm, total surface area = 91219 mm^2
- writing inflated surface to ../surf/lh.inflated
- writing sulcal depths to ../surf/lh.sulc
-
step 000: RMS=0.114 (target=0.015)
step 005: RMS=0.078 (target=0.015)
step 010: RMS=0.056 (target=0.015)
step 015: RMS=0.045 (target=0.015)
step 020: RMS=0.037 (target=0.015)
step 025: RMS=0.031 (target=0.015)
step 030: RMS=0.026 (target=0.015)
step 035: RMS=0.021 (target=0.015)
step 040: RMS=0.018 (target=0.015)
step 045: RMS=0.016 (target=0.015)
- inflation complete.
- inflation took 0.5 minutes
- mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated
- normalizing curvature values.
- averaging curvature patterns 5 times.
- sampling 10 neighbors out to a distance of 10 mm
- 246 vertices thresholded to be in k1 ~ [-0.24 0.33], k2 ~ [-0.10 0.06]
- total integrated curvature = 0.583*4pi (7.330) --> 0 handles
- ICI = 1.9, FI = 14.3, variation=233.198
- 139 vertices thresholded to be in [-0.01 0.02]
- writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level
- curvature mean = 0.000, std = 0.001
- 156 vertices thresholded to be in [-0.14 0.17]
- done.
- writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.016, std = 0.026
- done.
- #-----------------------------------------
- #@# Curvature Stats lh Thu Aug 8 17:10:36 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub001 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 [ sub001/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 [ 267 ]
- Gb_filter = 0
- WARN: S lookup min: -0.597248
- WARN: S explicit min: 0.000000 vertex = 2835
- #--------------------------------------------
- #@# Sphere lh Thu Aug 8 17:10:41 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 0.285...
- MRISunfold() max_passes = 1 -------
- tol=5.0e-01, sigma=0.0, host=snake, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
- using quadratic fit line minimization
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 1.000000
- desired_rms_height -1.000000
- momentum 0.900000
- nbhd_size 7
- max_nbrs 8
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 1234
- --------------------
- mrisRemoveNegativeArea()
- pass 1: epoch 1 of 3 starting distance error %19.83
- pass 1: epoch 2 of 3 starting distance error %19.84
- unfolding complete - removing small folds...
- starting distance error %19.83
- removing remaining folds...
- final distance error %19.83
- MRISunfold() return, current seed 1234
- writing spherical brain to ../surf/lh.sphere
- spherical transformation took 0.84 hours
- #--------------------------------------------
- #@# Surf Reg lh Thu Aug 8 18:01:10 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 = 0.568
- curvature mean = 0.025, std = 0.938
- curvature mean = 0.028, std = 0.834
- Starting MRISrigidBodyAlignGlobal()
- d=32.00 min @ (0.00, -8.00, -8.00) sse = 273307.7, tmin=2.3560
- d=8.00 min @ (-2.00, 0.00, 0.00) sse = 270165.3, tmin=4.7350
- d=4.00 min @ (1.00, 0.00, 1.00) sse = 269466.2, tmin=5.9317
- d=2.00 min @ (-0.50, -0.50, -0.50) sse = 268750.1, tmin=7.1416
- d=1.00 min @ (0.00, 0.25, 0.00) sse = 268635.9, tmin=8.3679
- 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 9.61 min
- curvature mean = 0.002, std = 0.934
- curvature mean = 0.014, std = 0.928
- curvature mean = 0.000, std = 0.941
- curvature mean = 0.007, std = 0.968
- curvature mean = -0.001, std = 0.940
- curvature mean = 0.002, std = 0.986
- 2 Reading smoothwm
- curvature mean = -0.021, std = 0.281
- curvature mean = 0.003, std = 0.066
- curvature mean = 0.071, std = 0.334
- curvature mean = 0.003, std = 0.077
- curvature mean = 0.028, std = 0.539
- curvature mean = 0.003, std = 0.083
- curvature mean = 0.014, std = 0.689
- curvature mean = 0.004, std = 0.085
- curvature mean = 0.005, std = 0.801
- MRISregister() return, current seed 0
- writing registered surface to ../surf/lh.sphere.reg...
- #--------------------------------------------
- #@# Jacobian white lh Thu Aug 8 18:29:26 CEST 2013
- mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white
- reading surface from ../surf/lh.white...
- writing curvature file ../surf/lh.jacobian_white
- #--------------------------------------------
- #@# AvgCurv lh Thu Aug 8 18:29:28 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/scripts
- mrisp_paint -a 5 /opt/freesurfer/5.3.0/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv
- averaging curvature patterns 5 times...
- reading surface from ../surf/lh.sphere.reg...
- reading template parameterization from /opt/freesurfer/5.3.0/average/lh.average.curvature.filled.buckner40.tif...
- writing curvature file to ../surf/lh.avg_curv...
- #-----------------------------------------
- #@# Cortical Parc lh Thu Aug 8 18:29:30 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub001 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...
- 1482 labels changed using aseg
- relabeling using gibbs priors...
- 000: 3428 changed, 151296 examined...
- 001: 811 changed, 14681 examined...
- 002: 204 changed, 4560 examined...
- 003: 69 changed, 1177 examined...
- 004: 30 changed, 428 examined...
- 005: 10 changed, 189 examined...
- 006: 3 changed, 63 examined...
- 007: 1 changed, 21 examined...
- 008: 0 changed, 8 examined...
- 248 labels changed using aseg
- 000: 133 total segments, 89 labels (500 vertices) changed
- 001: 45 total segments, 5 labels (10 vertices) changed
- 002: 40 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...
- 935 vertices marked for relabeling...
- 935 labels changed in reclassification.
- writing output to ../label/lh.aparc.annot...
- classification took 1 minutes and 7 seconds.
- #--------------------------------------------
- #@# Make Pial Surf lh Thu Aug 8 18:30:37 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/scripts
- mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub001 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/sub001/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/wm.mgz...
- 22126 bright wm thresholded.
- 274 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/lh.orig...
- computing class statistics...
- border white: 284449 voxels (1.70%)
- border gray 312227 voxels (1.86%)
- WM (94.0): 94.7 +- 9.7 [70.0 --> 110.0]
- GM (77.0) : 75.7 +- 12.7 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 50.3 (was 70)
- setting MAX_BORDER_WHITE to 115.7 (was 105)
- setting MIN_BORDER_WHITE to 63.0 (was 85)
- setting MAX_CSF to 37.5 (was 40)
- setting MAX_GRAY to 96.3 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 56.6 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 24.8 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=106, GM=63
- mean inside = 94.5, mean outside = 70.9
- 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/sub001/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.82 +- 0.21 (0.04-->3.50) (max @ vno 102287 --> 103434)
- face area 0.28 +- 0.12 (0.00-->3.12)
- mean absolute distance = 0.65 +- 0.82
- 2928 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 31 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 1 with 2 points - only 0.00% unknown
- deleting segment 4 with 865 points - only 0.00% unknown
- deleting segment 6 with 10 points - only 0.00% unknown
- deleting segment 7 with 8 points - only 0.00% unknown
- deleting segment 9 with 6 points - only 0.00% unknown
- deleting segment 10 with 6 points - only 0.00% unknown
- deleting segment 11 with 5 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 12 with 2 points - only 0.00% unknown
- mean border=76.3, 63 (63) missing vertices, mean dist 0.3 [0.5 (%35.4)->0.7 (%64.6))]
- %72 local maxima, %24 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 0.91 +- 0.25 (0.10-->4.09) (max @ vno 102287 --> 103434)
- face area 0.28 +- 0.13 (0.00-->3.00)
- mean absolute distance = 0.32 +- 0.52
- 3604 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=7501677.5, rms=12.92
- 001: dt: 0.5000, sse=7606438.5, rms=9.015 (0.000%)
- 002: dt: 0.5000, sse=7992211.5, rms=6.751 (0.000%)
- 003: dt: 0.5000, sse=8254959.0, rms=5.440 (0.000%)
- 004: dt: 0.5000, sse=8625985.0, rms=4.744 (0.000%)
- 005: dt: 0.5000, sse=8692486.0, rms=4.447 (0.000%)
- 006: dt: 0.5000, sse=8847022.0, rms=4.286 (0.000%)
- rms = 4.24, time step reduction 1 of 3 to 0.250...
- 007: dt: 0.5000, sse=8760105.0, rms=4.244 (0.000%)
- 008: dt: 0.2500, sse=5433708.0, rms=2.878 (0.000%)
- 009: dt: 0.2500, sse=4918901.0, rms=2.412 (0.000%)
- 010: dt: 0.2500, sse=4622632.5, rms=2.286 (0.000%)
- 011: dt: 0.2500, sse=4532754.0, rms=2.196 (0.000%)
- rms = 2.15, time step reduction 2 of 3 to 0.125...
- 012: dt: 0.2500, sse=4427595.0, rms=2.151 (0.000%)
- 013: dt: 0.1250, sse=4200319.5, rms=1.928 (0.000%)
- rms = 1.90, time step reduction 3 of 3 to 0.062...
- 014: dt: 0.1250, sse=4151781.0, rms=1.900 (0.000%)
- positioning took 1.9 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 37 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 1 with 2 points - only 0.00% unknown
- deleting segment 3 with 645 points - only 0.00% unknown
- deleting segment 4 with 8 points - only 0.00% unknown
- deleting segment 5 with 11 points - only 0.00% unknown
- deleting segment 9 with 5 points - only 0.00% unknown
- deleting segment 10 with 8 points - only 0.00% unknown
- deleting segment 11 with 8 points - only 0.00% unknown
- deleting segment 12 with 8 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 13 with 3 points - only 0.00% unknown
- mean border=80.5, 42 (6) missing vertices, mean dist -0.2 [0.3 (%76.8)->0.2 (%23.2))]
- %82 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.90 +- 0.24 (0.05-->4.20) (max @ vno 102287 --> 103434)
- face area 0.34 +- 0.16 (0.00-->4.33)
- mean absolute distance = 0.21 +- 0.32
- 2766 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5144833.0, rms=5.81
- 015: dt: 0.5000, sse=5397598.0, rms=4.044 (0.000%)
- rms = 4.37, time step reduction 1 of 3 to 0.250...
- 016: dt: 0.2500, sse=4887706.5, rms=2.964 (0.000%)
- 017: dt: 0.2500, sse=4714847.5, rms=2.336 (0.000%)
- 018: dt: 0.2500, sse=4636121.0, rms=1.933 (0.000%)
- 019: dt: 0.2500, sse=4613878.0, rms=1.835 (0.000%)
- 020: dt: 0.2500, sse=4538353.0, rms=1.732 (0.000%)
- rms = 1.70, time step reduction 2 of 3 to 0.125...
- 021: dt: 0.2500, sse=4545766.5, rms=1.705 (0.000%)
- 022: dt: 0.1250, sse=4410098.0, rms=1.555 (0.000%)
- rms = 1.54, time step reduction 3 of 3 to 0.062...
- 023: dt: 0.1250, sse=4366226.0, rms=1.539 (0.000%)
- positioning took 1.2 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 35 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 1 with 2 points - only 0.00% unknown
- deleting segment 2 with 753 points - only 0.00% unknown
- deleting segment 3 with 8 points - only 0.00% unknown
- deleting segment 5 with 10 points - only 0.00% unknown
- deleting segment 7 with 10 points - only 0.00% unknown
- deleting segment 8 with 17 points - only 0.00% unknown
- deleting segment 9 with 8 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 10 with 4 points - only 0.00% unknown
- mean border=83.7, 39 (4) missing vertices, mean dist -0.1 [0.2 (%77.3)->0.2 (%22.7))]
- %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 0.89 +- 0.24 (0.07-->4.24) (max @ vno 102287 --> 103434)
- face area 0.33 +- 0.15 (0.00-->4.47)
- mean absolute distance = 0.16 +- 0.27
- 2867 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4740342.0, rms=4.02
- 024: dt: 0.5000, sse=5162782.5, rms=3.927 (0.000%)
- rms = 4.15, time step reduction 1 of 3 to 0.250...
- 025: dt: 0.2500, sse=4662537.5, rms=2.466 (0.000%)
- 026: dt: 0.2500, sse=4531298.0, rms=1.923 (0.000%)
- 027: dt: 0.2500, sse=4610655.0, rms=1.617 (0.000%)
- rms = 1.64, time step reduction 2 of 3 to 0.125...
- 028: dt: 0.1250, sse=4545187.0, rms=1.511 (0.000%)
- 029: dt: 0.1250, sse=4452559.5, rms=1.366 (0.000%)
- rms = 1.36, time step reduction 3 of 3 to 0.062...
- 030: dt: 0.1250, sse=4410965.0, rms=1.358 (0.000%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 38 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 1 with 4 points - only 0.00% unknown
- deleting segment 2 with 727 points - only 0.00% unknown
- deleting segment 3 with 9 points - only 0.00% unknown
- deleting segment 4 with 10 points - only 0.00% unknown
- deleting segment 6 with 10 points - only 0.00% unknown
- deleting segment 7 with 15 points - only 0.00% unknown
- deleting segment 8 with 8 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 9 with 1 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 10 with 4 points - only 0.00% unknown
- mean border=84.6, 29 (2) missing vertices, mean dist -0.0 [0.2 (%58.7)->0.2 (%41.3))]
- %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=4425986.5, rms=1.74
- rms = 2.55, time step reduction 1 of 3 to 0.250...
- 031: dt: 0.2500, sse=4515405.0, rms=1.146 (0.000%)
- 032: dt: 0.2500, sse=4653913.0, rms=1.014 (0.000%)
- rms = 1.02, time step reduction 2 of 3 to 0.125...
- rms = 1.01, time step reduction 3 of 3 to 0.062...
- 033: dt: 0.1250, sse=4654615.0, rms=1.006 (0.000%)
- positioning took 0.5 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- smoothing surface for 5 iterations...
- mean border=52.9, 29 (29) missing vertices, mean dist 1.6 [0.4 (%0.0)->2.2 (%100.0))]
- %16 local maxima, %54 large gradients and %26 min vals, 1667 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=31541776.0, rms=31.48
- 001: dt: 0.5000, sse=22633614.0, rms=26.110 (0.000%)
- 002: dt: 0.5000, sse=16364890.0, rms=21.576 (0.000%)
- 003: dt: 0.5000, sse=12225721.0, rms=17.852 (0.000%)
- 004: dt: 0.5000, sse=9715540.0, rms=14.881 (0.000%)
- 005: dt: 0.5000, sse=8314529.5, rms=12.582 (0.000%)
- 006: dt: 0.5000, sse=7522506.5, rms=10.782 (0.000%)
- 007: dt: 0.5000, sse=7046120.0, rms=9.186 (0.000%)
- 008: dt: 0.5000, sse=6763321.5, rms=7.712 (0.000%)
- 009: dt: 0.5000, sse=6630784.5, rms=6.384 (0.000%)
- 010: dt: 0.5000, sse=6758218.5, rms=5.333 (0.000%)
- 011: dt: 0.5000, sse=6982404.0, rms=4.654 (0.000%)
- 012: dt: 0.5000, sse=7204873.0, rms=4.261 (0.000%)
- 013: dt: 0.5000, sse=7374593.5, rms=4.072 (0.000%)
- 014: dt: 0.5000, sse=7476237.5, rms=3.983 (0.000%)
- 015: dt: 0.5000, sse=7552397.0, rms=3.919 (0.000%)
- rms = 3.87, time step reduction 1 of 3 to 0.250...
- 016: dt: 0.5000, sse=7575074.5, rms=3.872 (0.000%)
- 017: dt: 0.2500, sse=5271608.5, rms=3.168 (0.000%)
- 018: dt: 0.2500, sse=5075954.0, rms=2.973 (0.000%)
- rms = 2.94, time step reduction 2 of 3 to 0.125...
- 019: dt: 0.2500, sse=4925140.0, rms=2.942 (0.000%)
- 020: dt: 0.1250, sse=4710801.5, rms=2.821 (0.000%)
- rms = 2.80, time step reduction 3 of 3 to 0.062...
- 021: dt: 0.1250, sse=4687392.0, rms=2.802 (0.000%)
- positioning took 2.7 minutes
- mean border=50.5, 996 (4) missing vertices, mean dist 0.2 [0.2 (%49.3)->0.6 (%50.7))]
- %32 local maxima, %41 large gradients and %22 min vals, 549 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=5442640.0, rms=5.10
- 022: dt: 0.5000, sse=5707268.0, rms=4.146 (0.000%)
- 023: dt: 0.5000, sse=7407391.5, rms=3.990 (0.000%)
- rms = 3.98, time step reduction 1 of 3 to 0.250...
- 024: dt: 0.5000, sse=7271568.5, rms=3.979 (0.000%)
- 025: dt: 0.2500, sse=5781878.5, rms=3.074 (0.000%)
- 026: dt: 0.2500, sse=5627059.5, rms=2.807 (0.000%)
- rms = 2.79, time step reduction 2 of 3 to 0.125...
- 027: dt: 0.2500, sse=5487438.5, rms=2.789 (0.000%)
- 028: dt: 0.1250, sse=5273686.5, rms=2.623 (0.000%)
- rms = 2.60, time step reduction 3 of 3 to 0.062...
- 029: dt: 0.1250, sse=5245089.0, rms=2.600 (0.000%)
- positioning took 1.0 minutes
- mean border=48.0, 1287 (3) missing vertices, mean dist 0.1 [0.2 (%36.7)->0.4 (%63.3))]
- %53 local maxima, %21 large gradients and %22 min vals, 747 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=5598627.5, rms=4.23
- 030: dt: 0.5000, sse=5789430.5, rms=3.928 (0.000%)
- rms = 3.89, time step reduction 1 of 3 to 0.250...
- 031: dt: 0.5000, sse=7785924.5, rms=3.888 (0.000%)
- 032: dt: 0.2500, sse=5733902.5, rms=2.974 (0.000%)
- 033: dt: 0.2500, sse=5908978.0, rms=2.688 (0.000%)
- rms = 2.71, time step reduction 2 of 3 to 0.125...
- 034: dt: 0.1250, sse=5773519.5, rms=2.601 (0.000%)
- 035: dt: 0.1250, sse=5540110.5, rms=2.482 (0.000%)
- rms = 2.47, time step reduction 3 of 3 to 0.062...
- 036: dt: 0.1250, sse=5481629.0, rms=2.468 (0.000%)
- positioning took 1.0 minutes
- mean border=46.7, 2370 (3) missing vertices, mean dist 0.1 [0.2 (%43.1)->0.3 (%56.9))]
- %57 local maxima, %16 large gradients and %21 min vals, 569 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/sub001/surf/lh.pial...
- writing smoothed curvature to lh.curv.pial
- 000: dt: 0.0000, sse=5554100.5, rms=2.93
- rms = 3.64, time step reduction 1 of 3 to 0.250...
- 037: dt: 0.2500, sse=5368755.5, rms=2.622 (0.000%)
- 038: dt: 0.2500, sse=5524598.0, rms=2.530 (0.000%)
- rms = 2.52, time step reduction 2 of 3 to 0.125...
- 039: dt: 0.2500, sse=5609665.0, rms=2.519 (0.000%)
- 040: dt: 0.1250, sse=5488124.0, rms=2.400 (0.000%)
- rms = 2.39, time step reduction 3 of 3 to 0.062...
- 041: dt: 0.1250, sse=5499762.5, rms=2.389 (0.000%)
- positioning took 0.8 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/lh.curv.pial
- writing smoothed area to lh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/lh.area.pial
- vertex spacing 1.00 +- 0.40 (0.04-->6.44) (max @ vno 107312 --> 107311)
- face area 0.40 +- 0.28 (0.00-->7.60)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 151296 vertices processed
- 25000 of 151296 vertices processed
- 50000 of 151296 vertices processed
- 75000 of 151296 vertices processed
- 100000 of 151296 vertices processed
- 125000 of 151296 vertices processed
- 150000 of 151296 vertices processed
- 0 of 151296 vertices processed
- 25000 of 151296 vertices processed
- 50000 of 151296 vertices processed
- 75000 of 151296 vertices processed
- 100000 of 151296 vertices processed
- 125000 of 151296 vertices processed
- 150000 of 151296 vertices processed
- thickness calculation complete, 212:472 truncations.
- 35961 vertices at 0 distance
- 111376 vertices at 1 distance
- 96006 vertices at 2 distance
- 33972 vertices at 3 distance
- 8714 vertices at 4 distance
- 2272 vertices at 5 distance
- 682 vertices at 6 distance
- 205 vertices at 7 distance
- 75 vertices at 8 distance
- 24 vertices at 9 distance
- 16 vertices at 10 distance
- 18 vertices at 11 distance
- 11 vertices at 12 distance
- 12 vertices at 13 distance
- 7 vertices at 14 distance
- 3 vertices at 15 distance
- 4 vertices at 16 distance
- 2 vertices at 17 distance
- 1 vertices at 18 distance
- 4 vertices at 19 distance
- 5 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/lh.thickness
- positioning took 13.9 minutes
- #--------------------------------------------
- #@# Surf Volume lh Thu Aug 8 18:44:30 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 18:44:30 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/scripts
- pctsurfcon --s sub001 --lh-only
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/scripts/pctsurfcon.log
- Thu Aug 8 18:44:30 CEST 2013
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/scripts
- /opt/freesurfer/5.3.0/bin/pctsurfcon
- $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $
- Linux snake1 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/sub001/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/tmp.pctsurfcon.5199/lh.wm.mgh --regheader sub001 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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/sub001/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/label/lh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 = 117054
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/label/lh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/tmp.pctsurfcon.5199/lh.wm.mgh
- Dim: 151296 1 1
- mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/tmp.pctsurfcon.5199/lh.gm.mgh --projfrac 0.3 --regheader sub001 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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/sub001/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/label/lh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/lh.white
- Done reading source surface
- Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 = 134694
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/label/lh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/tmp.pctsurfcon.5199/lh.gm.mgh
- Dim: 151296 1 1
- mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/tmp.pctsurfcon.5199/lh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/tmp.pctsurfcon.5199/lh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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/sub001/surf/lh.w-g.pct.mgh
- mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/lh.w-g.pct.mgh --annot sub001 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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/sub001/surf/lh.w-g.pct.mgh --annot sub001 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/stats/lh.w-g.pct.stats --snr
- sysname Linux
- hostname snake1
- 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/sub001/surf/lh.w-g.pct.mgh
- Vertex Area is 0.658076 mm^3
- Generating list of segmentation ids
- Found 36 segmentations
- Computing statistics for each segmentation
- 0 1000 unknown 0 0.000
- 1 1001 bankssts 1991 1340.166
- 2 1002 caudalanteriorcingulate 1304 884.984
- 3 1003 caudalmiddlefrontal 4027 2693.795
- 4 1004 corpuscallosum 0 0.000
- 5 1005 cuneus 2225 1424.734
- 6 1006 entorhinal 741 514.341
- 7 1007 fusiform 6392 4318.380
- 8 1008 inferiorparietal 9043 5970.152
- 9 1009 inferiortemporal 5407 3608.547
- 10 1010 isthmuscingulate 1773 1162.061
- 11 1011 lateraloccipital 7691 4929.976
- 12 1012 lateralorbitofrontal 3857 2535.380
- 13 1013 lingual 4597 3027.000
- 14 1014 medialorbitofrontal 2240 1482.326
- 15 1015 middletemporal 4932 3340.288
- 16 1016 parahippocampal 1128 773.673
- 17 1017 paracentral 2375 1478.550
- 18 1018 parsopercularis 2379 1607.085
- 19 1019 parsorbitalis 1109 706.300
- 20 1020 parstriangularis 2132 1436.581
- 21 1021 pericalcarine 2085 1385.042
- 22 1022 postcentral 7247 4680.602
- 23 1023 posteriorcingulate 2148 1403.580
- 24 1024 precentral 8326 5193.957
- 25 1025 precuneus 7078 4653.826
- 26 1026 rostralanteriorcingulate 1791 1152.834
- 27 1027 rostralmiddlefrontal 9962 6640.618
- 28 1028 superiorfrontal 12210 8174.208
- 29 1029 superiorparietal 8503 5444.482
- 30 1030 superiortemporal 5845 3935.643
- 31 1031 supramarginal 6371 4198.933
- 32 1032 frontalpole 269 183.004
- 33 1033 temporalpole 778 554.522
- 34 1034 transversetemporal 821 498.250
- 35 1035 insula 3269 2148.338
- Reporting on 34 segmentations
- mri_segstats done
- Cleaning up
- #-----------------------------------------
- #@# Parcellation Stats lh Thu Aug 8 18:44:43 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 sub001 lh white
- computing statistics for each annotation in ../label/lh.aparc.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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
- 1991 1340 3380 2.570 0.460 0.128 0.034 20 2.8 bankssts
- 1304 885 2137 2.212 0.540 0.154 0.049 26 2.2 caudalanteriorcingulate
- 4027 2694 7212 2.481 0.387 0.136 0.039 49 6.5 caudalmiddlefrontal
- 2225 1425 3196 2.034 0.352 0.171 0.071 49 6.8 cuneus
- 741 514 2099 2.983 0.847 0.147 0.065 11 1.8 entorhinal
- 6392 4318 13408 2.669 0.528 0.141 0.047 109 13.0 fusiform
- 9043 5970 15318 2.375 0.419 0.144 0.048 141 17.9 inferiorparietal
- 5407 3609 10369 2.550 0.565 0.155 0.055 108 12.4 inferiortemporal
- 1773 1162 2893 2.320 0.705 0.157 0.075 38 4.6 isthmuscingulate
- 7691 4930 11558 2.089 0.409 0.154 0.071 240 22.9 lateraloccipital
- 3857 2535 6668 2.278 0.616 0.166 0.080 93 12.2 lateralorbitofrontal
- 4597 3027 6602 2.057 0.552 0.161 0.067 101 13.9 lingual
- 2240 1482 3364 1.945 0.681 0.174 0.128 119 8.9 medialorbitofrontal
- 4932 3340 10564 2.611 0.540 0.150 0.064 99 10.0 middletemporal
- 1128 774 2185 2.515 0.480 0.123 0.040 17 1.8 parahippocampal
- 2375 1479 4084 2.414 0.502 0.135 0.066 42 7.8 paracentral
- 2379 1607 4347 2.411 0.372 0.126 0.037 29 3.5 parsopercularis
- 1109 706 2257 2.511 0.526 0.159 0.055 23 2.4 parsorbitalis
- 2132 1437 3682 2.306 0.469 0.143 0.046 34 3.9 parstriangularis
- 2085 1385 2230 1.756 0.392 0.156 0.060 32 5.0 pericalcarine
- 7247 4681 11194 2.120 0.561 0.129 0.041 95 12.9 postcentral
- 2148 1404 3623 2.357 0.646 0.153 0.047 36 4.2 posteriorcingulate
- 8326 5194 14991 2.614 0.500 0.124 0.061 293 16.3 precentral
- 7078 4654 12067 2.412 0.440 0.142 0.049 112 13.9 precuneus
- 1791 1153 2959 2.125 0.598 0.161 0.075 44 5.0 rostralanteriorcingulate
- 9962 6641 16495 2.172 0.472 0.160 0.060 210 24.0 rostralmiddlefrontal
- 12210 8174 24173 2.547 0.550 0.137 0.042 160 20.7 superiorfrontal
- 8503 5444 13634 2.273 0.372 0.132 0.042 114 14.3 superiorparietal
- 5845 3936 11726 2.635 0.603 0.130 0.041 76 9.8 superiortemporal
- 6371 4199 11408 2.476 0.431 0.139 0.048 92 11.2 supramarginal
- 269 183 630 2.505 0.351 0.214 0.086 9 1.0 frontalpole
- 778 555 2571 3.445 0.848 0.168 0.077 20 2.2 temporalpole
- 821 498 1360 2.520 0.361 0.141 0.046 11 1.5 transversetemporal
- 3269 2148 6638 2.890 0.764 0.127 0.057 57 7.3 insula
- #-----------------------------------------
- #@# Cortical Parc 2 lh Thu Aug 8 18:45:03 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub001 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...
- 71 labels changed using aseg
- relabeling using gibbs priors...
- 000: 10178 changed, 151296 examined...
- 001: 2553 changed, 39415 examined...
- 002: 823 changed, 12862 examined...
- 003: 360 changed, 4497 examined...
- 004: 195 changed, 2012 examined...
- 005: 113 changed, 1114 examined...
- 006: 49 changed, 625 examined...
- 007: 29 changed, 265 examined...
- 008: 19 changed, 172 examined...
- 009: 20 changed, 103 examined...
- 010: 8 changed, 94 examined...
- 011: 6 changed, 43 examined...
- 012: 5 changed, 35 examined...
- 013: 1 changed, 27 examined...
- 014: 2 changed, 10 examined...
- 015: 1 changed, 6 examined...
- 016: 1 changed, 11 examined...
- 017: 1 changed, 5 examined...
- 018: 1 changed, 5 examined...
- 019: 2 changed, 10 examined...
- 020: 1 changed, 9 examined...
- 021: 0 changed, 5 examined...
- 11 labels changed using aseg
- 000: 306 total segments, 221 labels (3147 vertices) changed
- 001: 102 total segments, 19 labels (204 vertices) changed
- 002: 84 total segments, 1 labels (1 vertices) changed
- 003: 83 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 115 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 445 vertices marked for relabeling...
- 445 labels changed in reclassification.
- writing output to ../label/lh.aparc.a2009s.annot...
- classification took 1 minutes and 17 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 2 lh Thu Aug 8 18:46:21 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 sub001 lh white
- computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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
- 1250 855 2021 2.055 0.453 0.157 0.064 25 2.8 G_and_S_frontomargin
- 1767 1172 3069 2.220 0.434 0.148 0.047 28 3.3 G_and_S_occipital_inf
- 1879 1122 3092 2.300 0.478 0.136 0.049 28 3.9 G_and_S_paracentral
- 1607 1061 3253 2.662 0.449 0.142 0.046 25 3.0 G_and_S_subcentral
- 645 456 1304 2.252 0.377 0.220 0.101 23 2.6 G_and_S_transv_frontopol
- 2920 1972 4804 2.113 0.602 0.147 0.058 52 6.2 G_and_S_cingul-Ant
- 1725 1173 2945 2.342 0.444 0.140 0.045 25 2.7 G_and_S_cingul-Mid-Ant
- 1598 1090 2847 2.581 0.414 0.153 0.048 24 3.2 G_and_S_cingul-Mid-Post
- 638 417 1535 2.783 0.440 0.164 0.082 17 1.4 G_cingul-Post-dorsal
- 336 213 528 2.247 0.723 0.200 0.101 11 1.4 G_cingul-Post-ventral
- 2120 1310 3107 2.018 0.387 0.175 0.080 54 6.9 G_cuneus
- 1414 943 3206 2.595 0.334 0.141 0.048 24 2.8 G_front_inf-Opercular
- 325 212 820 2.708 0.496 0.169 0.069 7 0.8 G_front_inf-Orbital
- 1189 792 2454 2.430 0.420 0.158 0.055 26 2.5 G_front_inf-Triangul
- 5910 3951 12018 2.396 0.484 0.164 0.063 141 15.1 G_front_middle
- 8097 5312 18096 2.692 0.564 0.140 0.050 127 17.8 G_front_sup
- 590 384 1393 3.219 0.526 0.135 0.076 19 1.1 G_Ins_lg_and_S_cent_ins
- 809 523 2406 3.510 0.803 0.147 0.091 25 3.2 G_insular_short
- 2640 1686 4566 2.220 0.384 0.151 0.052 53 5.2 G_occipital_middle
- 1566 990 2591 2.305 0.380 0.148 0.048 23 2.9 G_occipital_sup
- 2820 1851 6401 2.783 0.529 0.150 0.055 62 6.7 G_oc-temp_lat-fusifor
- 2958 1902 4557 2.039 0.624 0.180 0.086 87 11.3 G_oc-temp_med-Lingual
- 1197 806 3002 2.763 0.682 0.133 0.051 18 2.5 G_oc-temp_med-Parahip
- 2753 1739 5515 2.419 0.641 0.175 0.092 86 10.0 G_orbital
- 3335 2184 6812 2.512 0.435 0.152 0.055 65 7.5 G_pariet_inf-Angular
- 3411 2223 6971 2.540 0.396 0.145 0.055 58 6.5 G_pariet_inf-Supramar
- 3227 2038 6136 2.434 0.388 0.144 0.051 56 6.4 G_parietal_sup
- 2902 1770 5293 2.323 0.497 0.135 0.052 50 6.5 G_postcentral
- 3411 1947 7286 2.842 0.438 0.123 0.053 75 8.4 G_precentral
- 3772 2415 7350 2.458 0.433 0.152 0.055 75 8.5 G_precuneus
- 840 511 1405 2.104 0.546 0.231 0.232 78 5.0 G_rectus
- 270 170 518 2.876 0.817 0.119 0.108 12 1.3 G_subcallosal
- 589 349 1088 2.535 0.315 0.142 0.048 8 1.2 G_temp_sup-G_T_transv
- 2188 1435 5570 2.825 0.480 0.153 0.052 41 4.6 G_temp_sup-Lateral
- 730 505 1814 3.335 0.916 0.141 0.066 10 1.9 G_temp_sup-Plan_polar
- 997 679 1925 2.429 0.456 0.110 0.026 9 1.2 G_temp_sup-Plan_tempo
- 3025 2000 6836 2.592 0.610 0.174 0.071 85 8.9 G_temporal_inf
- 3129 2099 7625 2.745 0.509 0.161 0.060 66 7.1 G_temporal_middle
- 385 254 560 2.436 0.510 0.133 0.042 5 0.6 Lat_Fis-ant-Horizont
- 353 255 490 2.191 0.329 0.103 0.023 2 0.3 Lat_Fis-ant-Vertical
- 1129 755 1421 2.435 0.406 0.129 0.038 9 1.8 Lat_Fis-post
- 2203 1380 2930 1.901 0.395 0.170 0.126 148 12.4 Pole_occipital
- 2117 1481 6012 3.010 0.754 0.162 0.064 48 5.3 Pole_temporal
- 2935 1970 3484 1.964 0.513 0.146 0.050 42 6.2 S_calcarine
- 3584 2413 4218 1.943 0.549 0.124 0.075 200 5.7 S_central
- 1211 817 1790 2.257 0.384 0.119 0.034 11 1.5 S_cingul-Marginalis
- 461 314 806 2.695 0.563 0.119 0.033 3 0.7 S_circular_insula_ant
- 1438 965 2175 2.555 0.638 0.101 0.025 7 1.6 S_circular_insula_inf
- 1726 1152 2281 2.261 0.384 0.114 0.033 13 2.3 S_circular_insula_sup
- 1065 742 1985 2.741 0.470 0.134 0.041 13 1.9 S_collat_transv_ant
- 596 406 716 2.038 0.388 0.135 0.039 6 1.0 S_collat_transv_post
- 2573 1721 3561 2.176 0.381 0.134 0.036 28 4.1 S_front_inf
- 2130 1434 2840 2.058 0.392 0.145 0.043 28 3.9 S_front_middle
- 3123 2108 4762 2.366 0.336 0.124 0.034 32 4.4 S_front_sup
- 543 355 855 2.574 0.502 0.147 0.046 6 1.1 S_interm_prim-Jensen
- 3389 2247 4579 2.184 0.292 0.120 0.036 32 4.8 S_intrapariet_and_P_trans
- 1367 902 1653 1.916 0.321 0.139 0.043 17 2.3 S_oc_middle_and_Lunatus
- 1055 704 1416 2.161 0.269 0.120 0.032 9 1.4 S_oc_sup_and_transversal
- 437 294 642 2.123 0.356 0.145 0.041 5 0.8 S_occipital_ant
- 1382 913 2093 2.471 0.377 0.126 0.035 15 2.2 S_oc-temp_lat
- 2436 1718 3728 2.374 0.374 0.127 0.034 23 3.5 S_oc-temp_med_and_Lingual
- 527 342 640 1.781 0.405 0.140 0.054 8 0.9 S_orbital_lateral
- 406 303 569 1.672 0.531 0.153 0.048 4 0.9 S_orbital_med-olfact
- 1575 1047 2256 2.088 0.561 0.156 0.057 26 3.7 S_orbital-H_Shaped
- 2111 1415 2930 2.328 0.476 0.137 0.047 25 4.2 S_parieto_occipital
- 1417 865 1268 1.705 0.572 0.155 0.058 29 3.1 S_pericallosal
- 3182 2099 4164 2.115 0.387 0.117 0.030 29 4.1 S_postcentral
- 1734 1162 2703 2.488 0.415 0.117 0.032 15 2.2 S_precentral-inf-part
- 1182 811 1710 2.431 0.328 0.127 0.034 9 1.7 S_precentral-sup-part
- 854 567 1101 1.732 0.543 0.158 0.066 30 2.4 S_suborbital
- 1537 1041 2293 2.308 0.436 0.126 0.036 13 2.4 S_subparietal
- 1504 1010 2050 2.310 0.496 0.120 0.067 18 2.1 S_temporal_inf
- 7363 4974 11567 2.445 0.428 0.133 0.042 94 12.4 S_temporal_sup
- 437 287 616 2.356 0.427 0.143 0.033 7 0.6 S_temporal_transverse
- #-----------------------------------------
- #@# Cortical Parc 3 lh Thu Aug 8 18:46:41 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub001 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...
- 1344 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2885 changed, 151296 examined...
- 001: 686 changed, 12204 examined...
- 002: 174 changed, 3714 examined...
- 003: 64 changed, 1004 examined...
- 004: 31 changed, 373 examined...
- 005: 10 changed, 180 examined...
- 006: 2 changed, 60 examined...
- 007: 2 changed, 13 examined...
- 008: 3 changed, 10 examined...
- 009: 1 changed, 13 examined...
- 010: 0 changed, 9 examined...
- 143 labels changed using aseg
- 000: 63 total segments, 30 labels (377 vertices) changed
- 001: 33 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 42 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 412 vertices marked for relabeling...
- 412 labels changed in reclassification.
- writing output to ../label/lh.aparc.DKTatlas40.annot...
- classification took 1 minutes and 7 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 3 lh Thu Aug 8 18:47:48 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 sub001 lh white
- computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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
- 2140 1428 3603 2.302 0.514 0.144 0.043 35 3.4 caudalanteriorcingulate
- 4133 2755 7501 2.495 0.387 0.135 0.039 50 6.6 caudalmiddlefrontal
- 3078 1992 4401 2.077 0.377 0.160 0.062 58 8.2 cuneus
- 685 477 1963 2.994 0.875 0.141 0.057 9 1.5 entorhinal
- 5932 4014 11979 2.629 0.495 0.138 0.045 97 11.5 fusiform
- 8376 5528 14219 2.370 0.420 0.145 0.048 131 16.2 inferiorparietal
- 5564 3719 11243 2.602 0.603 0.157 0.058 115 13.4 inferiortemporal
- 1765 1158 2896 2.331 0.700 0.158 0.076 38 4.6 isthmuscingulate
- 8022 5124 12026 2.096 0.412 0.154 0.070 244 23.5 lateraloccipital
- 3965 2599 7040 2.243 0.621 0.170 0.087 106 13.4 lateralorbitofrontal
- 4526 2990 6540 2.061 0.553 0.161 0.068 100 13.6 lingual
- 1975 1289 3006 1.969 0.710 0.180 0.139 110 8.6 medialorbitofrontal
- 6601 4456 13392 2.573 0.526 0.147 0.058 121 13.3 middletemporal
- 1128 772 2180 2.512 0.482 0.122 0.040 17 1.8 parahippocampal
- 2751 1725 4839 2.463 0.517 0.134 0.061 45 8.3 paracentral
- 2167 1462 3897 2.411 0.363 0.124 0.037 26 3.2 parsopercularis
- 1182 768 2344 2.582 0.507 0.146 0.050 19 2.3 parsorbitalis
- 2592 1757 4406 2.249 0.454 0.143 0.045 40 4.8 parstriangularis
- 2112 1409 2267 1.758 0.396 0.156 0.060 32 5.0 pericalcarine
- 8056 5207 12397 2.128 0.551 0.130 0.042 106 14.5 postcentral
- 2257 1488 3791 2.348 0.641 0.154 0.047 38 4.5 posteriorcingulate
- 8165 5097 14612 2.608 0.505 0.124 0.061 291 16.1 precentral
- 6842 4481 11857 2.414 0.438 0.143 0.049 111 13.7 precuneus
- 2102 1377 3420 2.087 0.586 0.159 0.072 54 5.5 rostralanteriorcingulate
- 7007 4656 11742 2.191 0.501 0.160 0.057 145 16.3 rostralmiddlefrontal
- 13649 9148 26418 2.484 0.548 0.143 0.047 207 25.5 superiorfrontal
- 6816 4365 11030 2.299 0.360 0.129 0.041 89 11.1 superiorparietal
- 8375 5655 17384 2.719 0.659 0.136 0.045 118 15.3 superiortemporal
- 6328 4172 11225 2.456 0.415 0.139 0.048 91 11.2 supramarginal
- 813 493 1348 2.518 0.363 0.141 0.046 11 1.5 transversetemporal
- 2942 1919 6054 2.916 0.748 0.124 0.056 53 6.4 insula
- #--------------------------------------------
- #@# Tessellate rh Thu Aug 8 18:48:08 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/scripts
- mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.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-): 2 found - 2 modified | TOTAL: 4
- pass 2 (xy-): 0 found - 2 modified | TOTAL: 4
- pass 1 (yz+): 4 found - 4 modified | TOTAL: 8
- pass 2 (yz+): 0 found - 4 modified | TOTAL: 8
- pass 1 (yz-): 1 found - 1 modified | TOTAL: 9
- pass 2 (yz-): 0 found - 1 modified | TOTAL: 9
- pass 1 (xz+): 2 found - 2 modified | TOTAL: 11
- pass 2 (xz+): 0 found - 2 modified | TOTAL: 11
- pass 1 (xz-): 2 found - 2 modified | TOTAL: 13
- pass 2 (xz-): 0 found - 2 modified | TOTAL: 13
- Iteration Number : 1
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 2 found - 2 modified | TOTAL: 2
- pass 2 (+++): 0 found - 2 modified | TOTAL: 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 2
- Iteration Number : 1
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 2 found - 2 modified | TOTAL: 2
- pass 2 (+-): 0 found - 2 modified | TOTAL: 2
- pass 1 (--): 2 found - 2 modified | TOTAL: 4
- pass 2 (--): 0 found - 2 modified | TOTAL: 4
- pass 1 (-+): 1 found - 1 modified | TOTAL: 5
- pass 2 (-+): 0 found - 1 modified | TOTAL: 5
- Iteration Number : 2
- pass 1 (xy+): 1 found - 1 modified | TOTAL: 1
- pass 2 (xy+): 0 found - 1 modified | TOTAL: 1
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 1
- pass 1 (yz+): 1 found - 1 modified | TOTAL: 2
- pass 2 (yz+): 0 found - 1 modified | TOTAL: 2
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 2
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 2
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 2
- Iteration Number : 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 1 found - 1 modified | TOTAL: 1
- pass 2 (-+): 0 found - 1 modified | TOTAL: 1
- Iteration Number : 3
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 3
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 3
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Total Number of Modified Voxels = 23 (out of 303595: 0.007576)
- 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: 3111 vertices, 3340 faces
- slice 50: 12626 vertices, 13008 faces
- slice 60: 24710 vertices, 25144 faces
- slice 70: 38150 vertices, 38577 faces
- slice 80: 51425 vertices, 51877 faces
- slice 90: 63954 vertices, 64360 faces
- slice 100: 75960 vertices, 76353 faces
- slice 110: 86963 vertices, 87377 faces
- slice 120: 97973 vertices, 98385 faces
- slice 130: 109040 vertices, 109454 faces
- slice 140: 119270 vertices, 119643 faces
- slice 150: 128267 vertices, 128592 faces
- slice 160: 135777 vertices, 136037 faces
- slice 170: 142541 vertices, 142785 faces
- slice 180: 148092 vertices, 148283 faces
- slice 190: 151715 vertices, 151837 faces
- slice 200: 152626 vertices, 152654 faces
- slice 210: 152626 vertices, 152654 faces
- slice 220: 152626 vertices, 152654 faces
- slice 230: 152626 vertices, 152654 faces
- slice 240: 152626 vertices, 152654 faces
- slice 250: 152626 vertices, 152654 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...
- 152626 voxel in cpt #1: X=-28 [v=152626,e=457962,f=305308] located at (29.374733, -25.030355, 33.376987)
- For the whole surface: X=-28 [v=152626,e=457962,f=305308]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Smooth1 rh Thu Aug 8 18:48:16 CEST 2013
- mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 18:48:21 CEST 2013
- mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/scripts
- avg radius = 49.5 mm, total surface area = 80588 mm^2
- writing inflated surface to ../surf/rh.inflated.nofix
- inflation took 0.6 minutes
- Not saving sulc
-
step 000: RMS=0.098 (target=0.015)
step 005: RMS=0.072 (target=0.015)
step 010: RMS=0.052 (target=0.015)
step 015: RMS=0.043 (target=0.015)
step 020: RMS=0.037 (target=0.015)
step 025: RMS=0.032 (target=0.015)
step 030: RMS=0.029 (target=0.015)
step 035: RMS=0.026 (target=0.015)
step 040: RMS=0.024 (target=0.015)
step 045: RMS=0.022 (target=0.015)
step 050: RMS=0.021 (target=0.015)
step 055: RMS=0.021 (target=0.015)
step 060: RMS=0.021 (target=0.015)
- inflation complete.
- Not saving sulc
- #--------------------------------------------
- #@# QSphere rh Thu Aug 8 18:48:56 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 0.93 +- 0.55 (0.00-->6.70) (max @ vno 117001 --> 117019)
- face area 0.02 +- 0.03 (-0.23-->0.82)
- scaling brain by 0.306...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=175.531, avgs=0
- 005/300: dt: 0.9000, rms radial error=175.277, avgs=0
- 010/300: dt: 0.9000, rms radial error=174.733, avgs=0
- 015/300: dt: 0.9000, rms radial error=174.001, avgs=0
- 020/300: dt: 0.9000, rms radial error=173.166, avgs=0
- 025/300: dt: 0.9000, rms radial error=172.273, avgs=0
- 030/300: dt: 0.9000, rms radial error=171.346, avgs=0
- 035/300: dt: 0.9000, rms radial error=170.403, avgs=0
- 040/300: dt: 0.9000, rms radial error=169.458, avgs=0
- 045/300: dt: 0.9000, rms radial error=168.516, avgs=0
- 050/300: dt: 0.9000, rms radial error=167.575, avgs=0
- 055/300: dt: 0.9000, rms radial error=166.636, avgs=0
- 060/300: dt: 0.9000, rms radial error=165.702, avgs=0
- 065/300: dt: 0.9000, rms radial error=164.773, avgs=0
- 070/300: dt: 0.9000, rms radial error=163.849, avgs=0
- 075/300: dt: 0.9000, rms radial error=162.931, avgs=0
- 080/300: dt: 0.9000, rms radial error=162.017, avgs=0
- 085/300: dt: 0.9000, rms radial error=161.108, avgs=0
- 090/300: dt: 0.9000, rms radial error=160.203, avgs=0
- 095/300: dt: 0.9000, rms radial error=159.304, avgs=0
- 100/300: dt: 0.9000, rms radial error=158.410, avgs=0
- 105/300: dt: 0.9000, rms radial error=157.520, avgs=0
- 110/300: dt: 0.9000, rms radial error=156.635, avgs=0
- 115/300: dt: 0.9000, rms radial error=155.755, avgs=0
- 120/300: dt: 0.9000, rms radial error=154.879, avgs=0
- 125/300: dt: 0.9000, rms radial error=154.008, avgs=0
- 130/300: dt: 0.9000, rms radial error=153.143, avgs=0
- 135/300: dt: 0.9000, rms radial error=152.282, avgs=0
- 140/300: dt: 0.9000, rms radial error=151.425, avgs=0
- 145/300: dt: 0.9000, rms radial error=150.574, avgs=0
- 150/300: dt: 0.9000, rms radial error=149.727, avgs=0
- 155/300: dt: 0.9000, rms radial error=148.885, avgs=0
- 160/300: dt: 0.9000, rms radial error=148.047, avgs=0
- 165/300: dt: 0.9000, rms radial error=147.214, avgs=0
- 170/300: dt: 0.9000, rms radial error=146.385, avgs=0
- 175/300: dt: 0.9000, rms radial error=145.561, avgs=0
- 180/300: dt: 0.9000, rms radial error=144.741, avgs=0
- 185/300: dt: 0.9000, rms radial error=143.926, avgs=0
- 190/300: dt: 0.9000, rms radial error=143.115, avgs=0
- 195/300: dt: 0.9000, rms radial error=142.309, avgs=0
- 200/300: dt: 0.9000, rms radial error=141.508, avgs=0
- 205/300: dt: 0.9000, rms radial error=140.711, avgs=0
- 210/300: dt: 0.9000, rms radial error=139.919, avgs=0
- 215/300: dt: 0.9000, rms radial error=139.132, avgs=0
- 220/300: dt: 0.9000, rms radial error=138.348, avgs=0
- 225/300: dt: 0.9000, rms radial error=137.569, avgs=0
- 230/300: dt: 0.9000, rms radial error=136.795, avgs=0
- 235/300: dt: 0.9000, rms radial error=136.025, avgs=0
- 240/300: dt: 0.9000, rms radial error=135.258, avgs=0
- 245/300: dt: 0.9000, rms radial error=134.497, avgs=0
- 250/300: dt: 0.9000, rms radial error=133.739, avgs=0
- 255/300: dt: 0.9000, rms radial error=132.986, avgs=0
- 260/300: dt: 0.9000, rms radial error=132.237, avgs=0
- 265/300: dt: 0.9000, rms radial error=131.492, avgs=0
- 270/300: dt: 0.9000, rms radial error=130.752, avgs=0
- 275/300: dt: 0.9000, rms radial error=130.015, avgs=0
- 280/300: dt: 0.9000, rms radial error=129.283, avgs=0
- 285/300: dt: 0.9000, rms radial error=128.555, avgs=0
- 290/300: dt: 0.9000, rms radial error=127.830, avgs=0
- 295/300: dt: 0.9000, rms radial error=127.110, avgs=0
- 300/300: dt: 0.9000, rms radial error=126.394, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 17966.28
- 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 = 3053.28
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00007
- epoch 3 (K=160.0), pass 1, starting sse = 314.01
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.07/11 = 0.00655
- epoch 4 (K=640.0), pass 1, starting sse = 17.15
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.11/12 = 0.00946
- 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 18:53:45 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/sub001/scripts
- mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub001 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=-28 (nv=152626, nf=305308, ne=457962, g=15)
- using quasi-homeomorphic spherical map to tessellate cortical surface...
- Correction of the Topology
- Finding true center and radius of Spherical Surface...done
- Surface centered at (0,0,0) with radius 100.0 in 11 iterations
- marking ambiguous vertices...
- 2052 ambiguous faces found in tessellation
- segmenting defects...
- 20 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- 20 defects to be corrected
- 0 vertices coincident
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/rh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -9.7366 (-4.8683)
- -vertex loglikelihood: -6.5865 (-3.2932)
- -normal dot loglikelihood: -3.6402 (-3.6402)
- -quad curv loglikelihood: -6.4425 (-3.2212)
- Total Loglikelihood : -26.4057
- CORRECTING DEFECT 0 (vertices=34, convex hull=70)
- After retessellation of defect 0, euler #=-17 (151371,453650,302262) : difference with theory (-17) = 0
- CORRECTING DEFECT 1 (vertices=17, convex hull=25)
- After retessellation of defect 1, euler #=-16 (151375,453668,302277) : difference with theory (-16) = 0
- CORRECTING DEFECT 2 (vertices=33, convex hull=60)
- After retessellation of defect 2, euler #=-15 (151387,453731,302329) : difference with theory (-15) = 0
- CORRECTING DEFECT 3 (vertices=21, convex hull=33)
- After retessellation of defect 3, euler #=-14 (151394,453762,302354) : difference with theory (-14) = 0
- CORRECTING DEFECT 4 (vertices=18, convex hull=45)
- After retessellation of defect 4, euler #=-13 (151403,453807,302391) : difference with theory (-13) = 0
- CORRECTING DEFECT 5 (vertices=649, convex hull=348)
- After retessellation of defect 5, euler #=-12 (151556,454438,302870) : difference with theory (-12) = 0
- CORRECTING DEFECT 6 (vertices=15, convex hull=14)
- After retessellation of defect 6, euler #=-11 (151558,454447,302878) : difference with theory (-11) = 0
- CORRECTING DEFECT 7 (vertices=43, convex hull=67)
- After retessellation of defect 7, euler #=-10 (151584,454556,302962) : difference with theory (-10) = 0
- CORRECTING DEFECT 8 (vertices=17, convex hull=41)
- After retessellation of defect 8, euler #=-9 (151593,454595,302993) : difference with theory (-9) = 0
- CORRECTING DEFECT 9 (vertices=16, convex hull=30)
- After retessellation of defect 9, euler #=-8 (151596,454613,303009) : difference with theory (-8) = 0
- CORRECTING DEFECT 10 (vertices=31, convex hull=60)
- After retessellation of defect 10, euler #=-7 (151605,454663,303051) : difference with theory (-7) = 0
- CORRECTING DEFECT 11 (vertices=91, convex hull=53)
- After retessellation of defect 11, euler #=-6 (151617,454718,303095) : difference with theory (-6) = 0
- CORRECTING DEFECT 12 (vertices=8, convex hull=22)
- After retessellation of defect 12, euler #=-5 (151618,454726,303103) : difference with theory (-5) = 0
- CORRECTING DEFECT 13 (vertices=35, convex hull=27)
- After retessellation of defect 13, euler #=-4 (151622,454743,303117) : difference with theory (-4) = 0
- CORRECTING DEFECT 14 (vertices=6, convex hull=14)
- After retessellation of defect 14, euler #=-3 (151623,454748,303122) : difference with theory (-3) = 0
- CORRECTING DEFECT 15 (vertices=143, convex hull=87)
- After retessellation of defect 15, euler #=-2 (151659,454897,303236) : difference with theory (-2) = 0
- CORRECTING DEFECT 16 (vertices=19, convex hull=43)
- After retessellation of defect 16, euler #=-1 (151674,454957,303282) : difference with theory (-1) = 0
- CORRECTING DEFECT 17 (vertices=9, convex hull=31)
- After retessellation of defect 17, euler #=0 (151675,454970,303295) : difference with theory (0) = 0
- CORRECTING DEFECT 18 (vertices=22, convex hull=53)
- After retessellation of defect 18, euler #=1 (151684,455020,303337) : difference with theory (1) = 0
- CORRECTING DEFECT 19 (vertices=36, convex hull=69)
- After retessellation of defect 19, euler #=2 (151707,455115,303410) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.88 +- 0.21 (0.12-->8.06) (max @ vno 87601 --> 93039)
- face area 0.00 +- 0.00 (0.00-->0.00)
- performing soap bubble on retessellated vertices for 0 iterations...
- vertex spacing 0.88 +- 0.21 (0.12-->8.06) (max @ vno 87601 --> 93039)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 85 mutations (38.3%), 137 crossovers (61.7%), 125 vertices were eliminated
- building final representation...
- 919 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=151707, nf=303410, ne=455115, g=0)
- writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/rh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 11.7 minutes
- 0 defective edges
- removing intersecting faces
- 000: 118 intersecting
- 001: 4 intersecting
- mris_euler_number ../surf/rh.orig
- euler # = v-e+f = 2g-2: 151707 - 455115 + 303410 = 2 --> 0 holes
- F =2V-4: 303410 = 303414-4 (0)
- 2E=3F: 910230 = 910230 (0)
- total defect index = 0
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/scripts
- mris_remove_intersection ../surf/rh.orig ../surf/rh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 26 intersecting
- 001: 2 intersecting
- writing corrected surface to ../surf/rh.orig
- rm ../surf/rh.inflated
- #--------------------------------------------
- #@# Make White Surf rh Thu Aug 8 19:05:32 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/scripts
- mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub001 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/sub001/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/wm.mgz...
- 20765 bright wm thresholded.
- 275 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/rh.orig...
- computing class statistics...
- border white: 284449 voxels (1.70%)
- border gray 312227 voxels (1.86%)
- WM (94.0): 94.8 +- 9.6 [70.0 --> 110.0]
- GM (78.0) : 75.6 +- 13.1 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 48.9 (was 70)
- setting MAX_BORDER_WHITE to 115.6 (was 105)
- setting MIN_BORDER_WHITE to 62.0 (was 85)
- setting MAX_CSF to 35.9 (was 40)
- setting MAX_GRAY to 96.4 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 55.5 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 22.8 (was 40)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.82 +- 0.21 (0.02-->5.05) (max @ vno 151436 --> 151518)
- face area 0.28 +- 0.12 (0.00-->3.54)
- mean absolute distance = 0.64 +- 0.78
- 3564 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=106, GM=62
- mean inside = 94.4, mean outside = 70.5
- smoothing surface for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 3 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
- removing 3 vertex label from ripped group
- mean border=75.4, 72 (72) missing vertices, mean dist 0.3 [0.5 (%33.9)->0.7 (%66.1))]
- %72 local maxima, %23 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 +- 0.25 (0.11-->3.52) (max @ vno 108765 --> 107753)
- face area 0.28 +- 0.13 (0.00-->2.84)
- mean absolute distance = 0.30 +- 0.48
- 3032 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=7699247.0, rms=13.16
- 001: dt: 0.5000, sse=7792343.0, rms=9.368 (0.000%)
- 002: dt: 0.5000, sse=8179734.0, rms=7.166 (0.000%)
- 003: dt: 0.5000, sse=8307444.0, rms=5.765 (0.000%)
- 004: dt: 0.5000, sse=8624884.0, rms=4.990 (0.000%)
- 005: dt: 0.5000, sse=8726048.0, rms=4.592 (0.000%)
- 006: dt: 0.5000, sse=8835808.0, rms=4.408 (0.000%)
- 007: dt: 0.5000, sse=8808559.0, rms=4.322 (0.000%)
- 008: dt: 0.5000, sse=8848440.0, rms=4.264 (0.000%)
- rms = 4.23, time step reduction 1 of 3 to 0.250...
- 009: dt: 0.5000, sse=8768628.0, rms=4.234 (0.000%)
- 010: dt: 0.2500, sse=5438033.0, rms=2.858 (0.000%)
- 011: dt: 0.2500, sse=4908675.0, rms=2.368 (0.000%)
- 012: dt: 0.2500, sse=4596644.0, rms=2.246 (0.000%)
- 013: dt: 0.2500, sse=4500217.5, rms=2.151 (0.000%)
- rms = 2.11, time step reduction 2 of 3 to 0.125...
- 014: dt: 0.2500, sse=4397736.0, rms=2.115 (0.000%)
- 015: dt: 0.1250, sse=4176407.0, rms=1.894 (0.000%)
- rms = 1.87, time step reduction 3 of 3 to 0.062...
- 016: dt: 0.1250, sse=4131433.0, rms=1.871 (0.000%)
- positioning took 2.1 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- removing 1 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 4 vertex label from ripped group
- mean border=79.5, 37 (11) missing vertices, mean dist -0.2 [0.3 (%77.2)->0.2 (%22.8))]
- %82 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.90 +- 0.24 (0.10-->3.80) (max @ vno 123333 --> 122465)
- face area 0.35 +- 0.16 (0.00-->3.66)
- mean absolute distance = 0.21 +- 0.31
- 3610 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5127655.0, rms=5.75
- 017: dt: 0.5000, sse=5381743.5, rms=4.049 (0.000%)
- rms = 4.39, time step reduction 1 of 3 to 0.250...
- 018: dt: 0.2500, sse=4867655.0, rms=2.936 (0.000%)
- 019: dt: 0.2500, sse=4674792.0, rms=2.324 (0.000%)
- 020: dt: 0.2500, sse=4606009.5, rms=1.927 (0.000%)
- 021: dt: 0.2500, sse=4569353.5, rms=1.842 (0.000%)
- 022: dt: 0.2500, sse=4509551.0, rms=1.741 (0.000%)
- rms = 1.72, time step reduction 2 of 3 to 0.125...
- 023: dt: 0.2500, sse=4515275.5, rms=1.722 (0.000%)
- 024: dt: 0.1250, sse=4382488.0, rms=1.562 (0.000%)
- rms = 1.55, time step reduction 3 of 3 to 0.062...
- 025: dt: 0.1250, sse=4342589.5, rms=1.551 (0.000%)
- positioning took 1.2 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- removing 1 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 2 vertex label from ripped group
- mean border=82.9, 19 (6) missing vertices, mean dist -0.1 [0.2 (%78.4)->0.2 (%21.6))]
- %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 0.89 +- 0.24 (0.08-->3.97) (max @ vno 123333 --> 122465)
- face area 0.34 +- 0.16 (0.00-->3.80)
- mean absolute distance = 0.16 +- 0.24
- 3369 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4753884.5, rms=4.21
- 026: dt: 0.5000, sse=5106813.5, rms=4.047 (0.000%)
- rms = 4.22, time step reduction 1 of 3 to 0.250...
- 027: dt: 0.2500, sse=4616055.5, rms=2.555 (0.000%)
- 028: dt: 0.2500, sse=4503279.5, rms=2.012 (0.000%)
- 029: dt: 0.2500, sse=4560204.5, rms=1.645 (0.000%)
- rms = 1.67, time step reduction 2 of 3 to 0.125...
- 030: dt: 0.1250, sse=4496153.5, rms=1.532 (0.000%)
- 031: dt: 0.1250, sse=4408230.5, rms=1.375 (0.000%)
- rms = 1.36, time step reduction 3 of 3 to 0.062...
- 032: dt: 0.1250, sse=4368325.0, rms=1.362 (0.000%)
- 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 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 2 vertex label from ripped group
- mean border=84.0, 16 (1) missing vertices, mean dist -0.0 [0.2 (%59.2)->0.2 (%40.8))]
- %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/sub001/surf/rh.white...
- writing smoothed curvature to rh.curv
- 000: dt: 0.0000, sse=4395684.0, rms=1.81
- rms = 2.61, time step reduction 1 of 3 to 0.250...
- 033: dt: 0.2500, sse=4480139.0, rms=1.192 (0.000%)
- 034: dt: 0.2500, sse=4616130.0, rms=1.033 (0.000%)
- rms = 1.03, time step reduction 2 of 3 to 0.125...
- 035: dt: 0.2500, sse=4669789.0, rms=1.030 (0.000%)
- rms = 1.02, time step reduction 3 of 3 to 0.062...
- 036: dt: 0.1250, sse=4700977.5, rms=1.018 (0.000%)
- positioning took 0.6 minutes
- inhibiting deformation at non-cortical midline structures...
- generating cortex label...
- 11 non-cortical segments detected
- only using segment with 2085 vertices
- erasing segment 1 (vno[0] = 74292)
- erasing segment 2 (vno[0] = 90820)
- erasing segment 3 (vno[0] = 94940)
- erasing segment 4 (vno[0] = 103515)
- erasing segment 5 (vno[0] = 111783)
- erasing segment 6 (vno[0] = 111841)
- erasing segment 7 (vno[0] = 113774)
- erasing segment 8 (vno[0] = 114804)
- erasing segment 9 (vno[0] = 116792)
- erasing segment 10 (vno[0] = 125972)
- writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/label/rh.cortex.label...
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/rh.curv
- writing smoothed area to rh.area
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/rh.area
- vertex spacing 0.89 +- 0.24 (0.06-->3.93) (max @ vno 107753 --> 108765)
- face area 0.33 +- 0.15 (0.00-->3.85)
- refinement took 7.3 minutes
- #--------------------------------------------
- #@# Smooth2 rh Thu Aug 8 19:12:47 CEST 2013
- mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/scripts
- smoothing for 3 iterations
- setting seed for random number generator to 1234
- smoothing surface tessellation for 3 iterations...
- smoothing complete - recomputing first and second fundamental forms...
- #--------------------------------------------
- #@# Inflation2 rh Thu Aug 8 19:12:52 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/scripts
- mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated
- avg radius = 49.7 mm, total surface area = 91927 mm^2
- writing inflated surface to ../surf/rh.inflated
- writing sulcal depths to ../surf/rh.sulc
-
step 000: RMS=0.113 (target=0.015)
step 005: RMS=0.078 (target=0.015)
step 010: RMS=0.055 (target=0.015)
step 015: RMS=0.045 (target=0.015)
step 020: RMS=0.038 (target=0.015)
step 025: RMS=0.031 (target=0.015)
step 030: RMS=0.026 (target=0.015)
step 035: RMS=0.022 (target=0.015)
step 040: RMS=0.019 (target=0.015)
step 045: RMS=0.017 (target=0.015)
step 050: RMS=0.015 (target=0.015)
- inflation complete.
- inflation took 0.5 minutes
- mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated
- normalizing curvature values.
- averaging curvature patterns 5 times.
- sampling 10 neighbors out to a distance of 10 mm
- 184 vertices thresholded to be in k1 ~ [-0.37 0.42], k2 ~ [-0.24 0.09]
- total integrated curvature = 0.582*4pi (7.308) --> 0 handles
- ICI = 1.7, FI = 12.0, variation=199.297
- 174 vertices thresholded to be in [-0.03 0.02]
- writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level
- curvature mean = 0.000, std = 0.001
- 128 vertices thresholded to be in [-0.15 0.17]
- done.
- writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.015, std = 0.024
- done.
- #-----------------------------------------
- #@# Curvature Stats rh Thu Aug 8 19:15:17 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub001 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 [ sub001/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 [ 247 ]
- Gb_filter = 0
- WARN: S lookup min: -0.250582
- WARN: S explicit min: 0.000000 vertex = 807
- #--------------------------------------------
- #@# Sphere rh Thu Aug 8 19:15:22 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 0.286...
- MRISunfold() max_passes = 1 -------
- tol=5.0e-01, sigma=0.0, host=snake, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
- using quadratic fit line minimization
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 1.000000
- desired_rms_height -1.000000
- momentum 0.900000
- nbhd_size 7
- max_nbrs 8
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 1234
- --------------------
- mrisRemoveNegativeArea()
- pass 1: epoch 1 of 3 starting distance error %20.31
- pass 1: epoch 2 of 3 starting distance error %20.16
- unfolding complete - removing small folds...
- starting distance error %20.05
- removing remaining folds...
- final distance error %20.06
- MRISunfold() return, current seed 1234
- writing spherical brain to ../surf/rh.sphere
- spherical transformation took 0.99 hours
- #--------------------------------------------
- #@# Surf Reg rh Thu Aug 8 20:14:39 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 = 0.580
- curvature mean = 0.014, std = 0.943
- curvature mean = 0.023, std = 0.839
- Starting MRISrigidBodyAlignGlobal()
- d=16.00 min @ (0.00, -4.00, -4.00) sse = 273426.5, tmin=4.0381
- d=4.00 min @ (1.00, 1.00, 1.00) sse = 269350.8, tmin=6.8696
- d=2.00 min @ (-0.50, 0.00, 0.00) sse = 268570.5, tmin=8.2943
- d=0.50 min @ (0.00, -0.12, 0.00) sse = 268524.1, tmin=11.0953
- tol=1.0e+00, sigma=0.5, host=snake, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
- using quadratic fit line minimization
- MRISrigidBodyAlignGlobal() done 11.10 min
- curvature mean = -0.003, std = 0.938
- curvature mean = 0.011, std = 0.933
- curvature mean = -0.006, std = 0.944
- curvature mean = 0.005, std = 0.970
- curvature mean = -0.008, std = 0.941
- curvature mean = 0.001, std = 0.987
- 2 Reading smoothwm
- curvature mean = -0.024, std = 0.298
- curvature mean = 0.005, std = 0.069
- curvature mean = 0.063, std = 0.327
- curvature mean = 0.005, std = 0.082
- curvature mean = 0.029, std = 0.518
- curvature mean = 0.006, std = 0.088
- curvature mean = 0.017, std = 0.653
- curvature mean = 0.006, std = 0.090
- curvature mean = 0.005, std = 0.761
- MRISregister() return, current seed 0
- writing registered surface to ../surf/rh.sphere.reg...
- expanding nbhd size to 1
- #--------------------------------------------
- #@# Jacobian white rh Thu Aug 8 20:48:31 CEST 2013
- mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white
- reading surface from ../surf/rh.white...
- writing curvature file ../surf/rh.jacobian_white
- #--------------------------------------------
- #@# AvgCurv rh Thu Aug 8 20:48:34 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/scripts
- mrisp_paint -a 5 /opt/freesurfer/5.3.0/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv
- averaging curvature patterns 5 times...
- reading surface from ../surf/rh.sphere.reg...
- reading template parameterization from /opt/freesurfer/5.3.0/average/rh.average.curvature.filled.buckner40.tif...
- writing curvature file to ../surf/rh.avg_curv...
- #-----------------------------------------
- #@# Cortical Parc rh Thu Aug 8 20:48:36 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub001 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...
- 1066 labels changed using aseg
- relabeling using gibbs priors...
- 000: 3147 changed, 151707 examined...
- 001: 754 changed, 13668 examined...
- 002: 184 changed, 4061 examined...
- 003: 50 changed, 1051 examined...
- 004: 21 changed, 305 examined...
- 005: 9 changed, 135 examined...
- 006: 2 changed, 61 examined...
- 007: 0 changed, 13 examined...
- 189 labels changed using aseg
- 000: 105 total segments, 62 labels (355 vertices) changed
- 001: 46 total segments, 3 labels (4 vertices) changed
- 002: 43 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 58 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 1448 vertices marked for relabeling...
- 1448 labels changed in reclassification.
- writing output to ../label/rh.aparc.annot...
- classification took 1 minutes and 7 seconds.
- #--------------------------------------------
- #@# Make Pial Surf rh Thu Aug 8 20:49:42 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/scripts
- mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub001 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/sub001/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/wm.mgz...
- 20765 bright wm thresholded.
- 275 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/rh.orig...
- computing class statistics...
- border white: 284449 voxels (1.70%)
- border gray 312227 voxels (1.86%)
- WM (94.0): 94.8 +- 9.6 [70.0 --> 110.0]
- GM (78.0) : 75.6 +- 13.1 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 48.9 (was 70)
- setting MAX_BORDER_WHITE to 115.6 (was 105)
- setting MIN_BORDER_WHITE to 62.0 (was 85)
- setting MAX_CSF to 35.9 (was 40)
- setting MAX_GRAY to 96.4 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 55.5 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 22.8 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=106, GM=62
- mean inside = 94.4, mean outside = 70.5
- smoothing surface for 5 iterations...
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.82 +- 0.21 (0.02-->5.05) (max @ vno 151436 --> 151518)
- face area 0.28 +- 0.12 (0.00-->3.54)
- mean absolute distance = 0.64 +- 0.79
- 3609 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- deleting segment 0 with 3 points - only 0.00% unknown
- deleting segment 1 with 12 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 2 with 2 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 3 with 2 points - only 0.00% unknown
- deleting segment 5 with 47 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 7 with 20 points - only 0.00% unknown
- deleting segment 8 with 301 points - only 0.00% unknown
- deleting segment 9 with 14 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 11 with 3 points - only 0.00% unknown
- deleting segment 12 with 35 points - only 0.00% unknown
- deleting segment 14 with 6 points - only 0.00% unknown
- mean border=75.4, 72 (72) missing vertices, mean dist 0.3 [0.5 (%33.9)->0.7 (%66.1))]
- %72 local maxima, %23 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 +- 0.25 (0.11-->3.42) (max @ vno 69504 --> 70697)
- face area 0.28 +- 0.13 (0.00-->2.84)
- mean absolute distance = 0.30 +- 0.48
- 3516 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=7715141.0, rms=13.15
- 001: dt: 0.5000, sse=7811774.0, rms=9.363 (0.000%)
- 002: dt: 0.5000, sse=8198131.5, rms=7.162 (0.000%)
- 003: dt: 0.5000, sse=8328426.5, rms=5.763 (0.000%)
- 004: dt: 0.5000, sse=8648014.0, rms=4.989 (0.000%)
- 005: dt: 0.5000, sse=8752980.0, rms=4.591 (0.000%)
- 006: dt: 0.5000, sse=8861303.0, rms=4.407 (0.000%)
- 007: dt: 0.5000, sse=8835566.0, rms=4.320 (0.000%)
- 008: dt: 0.5000, sse=8876456.0, rms=4.263 (0.000%)
- rms = 4.23, time step reduction 1 of 3 to 0.250...
- 009: dt: 0.5000, sse=8795966.0, rms=4.232 (0.000%)
- 010: dt: 0.2500, sse=5452780.0, rms=2.857 (0.000%)
- 011: dt: 0.2500, sse=4919706.0, rms=2.367 (0.000%)
- 012: dt: 0.2500, sse=4607159.5, rms=2.245 (0.000%)
- 013: dt: 0.2500, sse=4510595.5, rms=2.150 (0.000%)
- rms = 2.11, time step reduction 2 of 3 to 0.125...
- 014: dt: 0.2500, sse=4408705.5, rms=2.114 (0.000%)
- 015: dt: 0.1250, sse=4187051.2, rms=1.894 (0.000%)
- rms = 1.87, time step reduction 3 of 3 to 0.062...
- 016: dt: 0.1250, sse=4142170.2, rms=1.870 (0.000%)
- positioning took 2.1 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- deleting segment 0 with 3 points - only 0.00% unknown
- deleting segment 1 with 18 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 2 with 1 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 3 with 2 points - only 0.00% unknown
- deleting segment 4 with 24 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 5 with 2 points - only 0.00% unknown
- deleting segment 7 with 6 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 8 with 2 points - only 0.00% unknown
- deleting segment 9 with 244 points - only 0.00% unknown
- deleting segment 10 with 18 points - only 0.00% unknown
- deleting segment 12 with 26 points - only 0.00% unknown
- deleting segment 14 with 8 points - only 0.00% unknown
- mean border=79.5, 37 (11) missing vertices, mean dist -0.2 [0.3 (%77.2)->0.2 (%22.8))]
- %82 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.90 +- 0.24 (0.10-->3.80) (max @ vno 123333 --> 122465)
- face area 0.35 +- 0.16 (0.00-->3.66)
- mean absolute distance = 0.21 +- 0.31
- 3642 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5140258.5, rms=5.74
- 017: dt: 0.5000, sse=5394040.5, rms=4.046 (0.000%)
- rms = 4.39, time step reduction 1 of 3 to 0.250...
- 018: dt: 0.2500, sse=4879282.5, rms=2.934 (0.000%)
- 019: dt: 0.2500, sse=4687885.5, rms=2.323 (0.000%)
- 020: dt: 0.2500, sse=4618615.0, rms=1.926 (0.000%)
- 021: dt: 0.2500, sse=4582087.5, rms=1.841 (0.000%)
- 022: dt: 0.2500, sse=4522037.0, rms=1.740 (0.000%)
- rms = 1.72, time step reduction 2 of 3 to 0.125...
- 023: dt: 0.2500, sse=4527828.5, rms=1.721 (0.000%)
- 024: dt: 0.1250, sse=4395236.5, rms=1.562 (0.000%)
- rms = 1.55, time step reduction 3 of 3 to 0.062...
- 025: dt: 0.1250, sse=4355554.5, rms=1.550 (0.000%)
- positioning took 1.2 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- deleting segment 0 with 3 points - only 0.00% unknown
- deleting segment 1 with 19 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 2 with 1 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 3 with 2 points - only 0.00% unknown
- deleting segment 4 with 15 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 5 with 2 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 6 with 2 points - only 0.00% unknown
- deleting segment 8 with 12 points - only 0.00% unknown
- deleting segment 9 with 267 points - only 0.00% unknown
- deleting segment 10 with 21 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 11 with 4 points - only 0.00% unknown
- deleting segment 12 with 28 points - only 0.00% unknown
- deleting segment 14 with 20 points - only 55.00% unknown
- removing 3 vertex label from ripped group
- removing 2 vertex label from ripped group
- deleting segment 17 with 2 points - only 0.00% unknown
- deleting segment 18 with 8 points - only 0.00% unknown
- mean border=82.9, 19 (6) missing vertices, mean dist -0.1 [0.2 (%78.3)->0.2 (%21.7))]
- %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 0.89 +- 0.24 (0.08-->3.97) (max @ vno 123333 --> 122465)
- face area 0.34 +- 0.15 (0.00-->3.80)
- mean absolute distance = 0.16 +- 0.25
- 2513 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4768939.5, rms=4.20
- 026: dt: 0.5000, sse=5119207.0, rms=4.041 (0.000%)
- rms = 4.21, time step reduction 1 of 3 to 0.250...
- 027: dt: 0.2500, sse=4627778.5, rms=2.550 (0.000%)
- 028: dt: 0.2500, sse=4519923.5, rms=2.008 (0.000%)
- 029: dt: 0.2500, sse=4575827.5, rms=1.643 (0.000%)
- rms = 1.67, time step reduction 2 of 3 to 0.125...
- 030: dt: 0.1250, sse=4511923.0, rms=1.530 (0.000%)
- 031: dt: 0.1250, sse=4424687.0, rms=1.375 (0.000%)
- rms = 1.36, time step reduction 3 of 3 to 0.062...
- 032: dt: 0.1250, sse=4385598.0, rms=1.362 (0.000%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- deleting segment 0 with 3 points - only 0.00% unknown
- deleting segment 1 with 18 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 2 with 1 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 3 with 2 points - only 0.00% unknown
- deleting segment 4 with 10 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 5 with 2 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 6 with 2 points - only 0.00% unknown
- deleting segment 7 with 13 points - only 0.00% unknown
- deleting segment 8 with 265 points - only 0.00% unknown
- deleting segment 9 with 20 points - only 0.00% unknown
- deleting segment 10 with 5 points - only 0.00% unknown
- deleting segment 11 with 32 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 8 points - only 0.00% unknown
- mean border=83.9, 16 (1) missing vertices, mean dist -0.0 [0.2 (%59.2)->0.2 (%40.8))]
- %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=4412813.0, rms=1.81
- rms = 2.61, time step reduction 1 of 3 to 0.250...
- 033: dt: 0.2500, sse=4497327.5, rms=1.190 (0.000%)
- 034: dt: 0.2500, sse=4634119.0, rms=1.033 (0.000%)
- rms = 1.03, time step reduction 2 of 3 to 0.125...
- 035: dt: 0.2500, sse=4689149.5, rms=1.031 (0.000%)
- rms = 1.02, time step reduction 3 of 3 to 0.062...
- 036: dt: 0.1250, sse=4721911.0, rms=1.018 (0.000%)
- positioning took 0.6 minutes
- inhibiting deformation at non-cortical midline structures...
- smoothing surface for 5 iterations...
- mean border=51.7, 55 (55) missing vertices, mean dist 1.6 [0.3 (%0.0)->2.2 (%100.0))]
- %14 local maxima, %55 large gradients and %26 min vals, 1840 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=32522764.0, rms=31.95
- 001: dt: 0.5000, sse=23284750.0, rms=26.483 (0.000%)
- 002: dt: 0.5000, sse=16806702.0, rms=21.886 (0.000%)
- 003: dt: 0.5000, sse=12514036.0, rms=18.127 (0.000%)
- 004: dt: 0.5000, sse=9934478.0, rms=15.107 (0.000%)
- 005: dt: 0.5000, sse=8475635.0, rms=12.748 (0.000%)
- 006: dt: 0.5000, sse=7688068.0, rms=10.890 (0.000%)
- 007: dt: 0.5000, sse=7197713.5, rms=9.281 (0.000%)
- 008: dt: 0.5000, sse=6893226.5, rms=7.810 (0.000%)
- 009: dt: 0.5000, sse=6785695.0, rms=6.494 (0.000%)
- 010: dt: 0.5000, sse=6864943.0, rms=5.425 (0.000%)
- 011: dt: 0.5000, sse=7029911.5, rms=4.723 (0.000%)
- 012: dt: 0.5000, sse=7252196.5, rms=4.303 (0.000%)
- 013: dt: 0.5000, sse=7408405.5, rms=4.109 (0.000%)
- 014: dt: 0.5000, sse=7532442.5, rms=3.994 (0.000%)
- 015: dt: 0.5000, sse=7589320.5, rms=3.940 (0.000%)
- 016: dt: 0.5000, sse=7629084.0, rms=3.872 (0.000%)
- rms = 3.86, time step reduction 1 of 3 to 0.250...
- 017: dt: 0.5000, sse=7653772.0, rms=3.864 (0.000%)
- 018: dt: 0.2500, sse=5321834.0, rms=3.131 (0.000%)
- 019: dt: 0.2500, sse=5122165.5, rms=2.935 (0.000%)
- rms = 2.93, time step reduction 2 of 3 to 0.125...
- 020: dt: 0.2500, sse=4991345.5, rms=2.931 (0.000%)
- 021: dt: 0.1250, sse=4753387.5, rms=2.796 (0.000%)
- rms = 2.78, time step reduction 3 of 3 to 0.062...
- 022: dt: 0.1250, sse=4722816.5, rms=2.782 (0.000%)
- positioning took 2.8 minutes
- mean border=49.5, 1096 (11) missing vertices, mean dist 0.2 [0.2 (%50.3)->0.6 (%49.7))]
- %31 local maxima, %42 large gradients and %22 min vals, 520 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=5405515.5, rms=4.83
- 023: dt: 0.5000, sse=5724932.5, rms=4.038 (0.000%)
- 024: dt: 0.5000, sse=7475842.5, rms=3.988 (0.000%)
- rms = 3.97, time step reduction 1 of 3 to 0.250...
- 025: dt: 0.5000, sse=7184008.5, rms=3.969 (0.000%)
- 026: dt: 0.2500, sse=5799842.0, rms=3.082 (0.000%)
- 027: dt: 0.2500, sse=5653798.0, rms=2.821 (0.000%)
- rms = 2.81, time step reduction 2 of 3 to 0.125...
- 028: dt: 0.2500, sse=5519139.5, rms=2.807 (0.000%)
- 029: dt: 0.1250, sse=5294735.0, rms=2.618 (0.000%)
- rms = 2.59, time step reduction 3 of 3 to 0.062...
- 030: dt: 0.1250, sse=5267366.0, rms=2.591 (0.000%)
- positioning took 1.0 minutes
- mean border=47.0, 1240 (8) missing vertices, mean dist 0.1 [0.2 (%37.5)->0.4 (%62.5))]
- %52 local maxima, %21 large gradients and %22 min vals, 726 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=5612344.5, rms=4.20
- 031: dt: 0.5000, sse=5775778.0, rms=3.888 (0.000%)
- rms = 3.95, time step reduction 1 of 3 to 0.250...
- 032: dt: 0.2500, sse=5420059.0, rms=3.111 (0.000%)
- 033: dt: 0.2500, sse=5668107.0, rms=2.794 (0.000%)
- 034: dt: 0.2500, sse=5577470.0, rms=2.741 (0.000%)
- rms = 2.71, time step reduction 2 of 3 to 0.125...
- 035: dt: 0.2500, sse=5669607.0, rms=2.714 (0.000%)
- 036: dt: 0.1250, sse=5438445.5, rms=2.544 (0.000%)
- rms = 2.52, time step reduction 3 of 3 to 0.062...
- 037: dt: 0.1250, sse=5434236.0, rms=2.519 (0.000%)
- positioning took 1.0 minutes
- mean border=45.8, 2515 (6) missing vertices, mean dist 0.1 [0.2 (%43.7)->0.3 (%56.3))]
- %57 local maxima, %16 large gradients and %21 min vals, 534 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/sub001/surf/rh.pial...
- writing smoothed curvature to rh.curv.pial
- 000: dt: 0.0000, sse=5503334.5, rms=2.95
- rms = 3.63, time step reduction 1 of 3 to 0.250...
- 038: dt: 0.2500, sse=5337283.5, rms=2.660 (0.000%)
- 039: dt: 0.2500, sse=5520699.0, rms=2.570 (0.000%)
- rms = 2.54, time step reduction 2 of 3 to 0.125...
- 040: dt: 0.2500, sse=5620499.5, rms=2.544 (0.000%)
- 041: dt: 0.1250, sse=5504868.0, rms=2.429 (0.000%)
- rms = 2.41, time step reduction 3 of 3 to 0.062...
- 042: dt: 0.1250, sse=5516436.0, rms=2.413 (0.000%)
- positioning took 0.8 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/rh.curv.pial
- writing smoothed area to rh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/rh.area.pial
- vertex spacing 1.00 +- 0.40 (0.05-->6.41) (max @ vno 107784 --> 108801)
- face area 0.40 +- 0.28 (0.00-->5.92)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 151707 vertices processed
- 25000 of 151707 vertices processed
- 50000 of 151707 vertices processed
- 75000 of 151707 vertices processed
- 100000 of 151707 vertices processed
- 125000 of 151707 vertices processed
- 150000 of 151707 vertices processed
- 0 of 151707 vertices processed
- 25000 of 151707 vertices processed
- 50000 of 151707 vertices processed
- 75000 of 151707 vertices processed
- 100000 of 151707 vertices processed
- 125000 of 151707 vertices processed
- 150000 of 151707 vertices processed
- thickness calculation complete, 119:351 truncations.
- 38093 vertices at 0 distance
- 112460 vertices at 1 distance
- 95452 vertices at 2 distance
- 32810 vertices at 3 distance
- 8112 vertices at 4 distance
- 2222 vertices at 5 distance
- 598 vertices at 6 distance
- 186 vertices at 7 distance
- 78 vertices at 8 distance
- 32 vertices at 9 distance
- 22 vertices at 10 distance
- 26 vertices at 11 distance
- 13 vertices at 12 distance
- 10 vertices at 13 distance
- 10 vertices at 14 distance
- 6 vertices at 15 distance
- 4 vertices at 16 distance
- 7 vertices at 17 distance
- 5 vertices at 18 distance
- 1 vertices at 19 distance
- 1 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/rh.thickness
- positioning took 14.3 minutes
- #--------------------------------------------
- #@# Surf Volume rh Thu Aug 8 21:04:00 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf
- mris_calc -o rh.area.mid rh.area add rh.area.pial
- Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o rh.area.mid rh.area.mid div 2
- Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o rh.volume rh.area.mid mul rh.thickness
- Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ]
- #-----------------------------------------
- #@# WM/GM Contrast rh Thu Aug 8 21:04:01 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/scripts
- pctsurfcon --s sub001 --rh-only
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/scripts/pctsurfcon.log
- Thu Aug 8 21:04:01 CEST 2013
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/scripts
- /opt/freesurfer/5.3.0/bin/pctsurfcon
- $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $
- Linux snake1 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/sub001/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/tmp.pctsurfcon.5827/rh.wm.mgh --regheader sub001 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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/sub001/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/label/rh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 = 117451
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/label/rh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/tmp.pctsurfcon.5827/rh.wm.mgh
- Dim: 151707 1 1
- mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/tmp.pctsurfcon.5827/rh.gm.mgh --projfrac 0.3 --regheader sub001 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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/sub001/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/label/rh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/rh.white
- Done reading source surface
- Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 = 135218
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/label/rh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/tmp.pctsurfcon.5827/rh.gm.mgh
- Dim: 151707 1 1
- mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/tmp.pctsurfcon.5827/rh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/tmp.pctsurfcon.5827/rh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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/sub001/surf/rh.w-g.pct.mgh
- mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/rh.w-g.pct.mgh --annot sub001 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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/sub001/surf/rh.w-g.pct.mgh --annot sub001 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/stats/rh.w-g.pct.stats --snr
- sysname Linux
- hostname snake1
- 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/sub001/surf/rh.w-g.pct.mgh
- Vertex Area is 0.660259 mm^3
- Generating list of segmentation ids
- Found 36 segmentations
- Computing statistics for each segmentation
- 0 2000 unknown 0 0.000
- 1 2001 bankssts 1760 1226.870
- 2 2002 caudalanteriorcingulate 1149 852.994
- 3 2003 caudalmiddlefrontal 3951 2656.651
- 4 2004 corpuscallosum 0 0.000
- 5 2005 cuneus 2393 1537.667
- 6 2006 entorhinal 299 207.731
- 7 2007 fusiform 5532 3711.660
- 8 2008 inferiorparietal 9784 6496.064
- 9 2009 inferiortemporal 5507 3670.542
- 10 2010 isthmuscingulate 1536 991.523
- 11 2011 lateraloccipital 7116 4631.318
- 12 2012 lateralorbitofrontal 4251 2746.691
- 13 2013 lingual 5391 3490.283
- 14 2014 medialorbitofrontal 2850 1856.300
- 15 2015 middletemporal 6009 4101.812
- 16 2016 parahippocampal 1138 775.247
- 17 2017 paracentral 3026 1947.429
- 18 2018 parsopercularis 2153 1455.716
- 19 2019 parsorbitalis 1307 885.959
- 20 2020 parstriangularis 2721 1782.424
- 21 2021 pericalcarine 2271 1546.041
- 22 2022 postcentral 6457 4213.947
- 23 2023 posteriorcingulate 1420 989.918
- 24 2024 precentral 8347 5320.286
- 25 2025 precuneus 7618 4947.523
- 26 2026 rostralanteriorcingulate 1132 791.807
- 27 2027 rostralmiddlefrontal 10222 6882.639
- 28 2028 superiorfrontal 11659 7732.630
- 29 2029 superiorparietal 8970 5825.078
- 30 2030 superiortemporal 5876 3863.140
- 31 2031 supramarginal 5875 3879.149
- 32 2032 frontalpole 445 308.135
- 33 2033 temporalpole 458 318.335
- 34 2034 transversetemporal 596 369.521
- 35 2035 insula 3540 2373.174
- Reporting on 34 segmentations
- mri_segstats done
- Cleaning up
- #-----------------------------------------
- #@# Parcellation Stats rh Thu Aug 8 21:04:14 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 sub001 rh white
- computing statistics for each annotation in ../label/rh.aparc.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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
- 1760 1227 3301 2.565 0.352 0.137 0.033 23 2.5 bankssts
- 1149 853 2216 2.274 0.584 0.170 0.059 33 2.6 caudalanteriorcingulate
- 3951 2657 7064 2.423 0.464 0.126 0.035 43 6.0 caudalmiddlefrontal
- 2393 1538 3244 1.941 0.363 0.167 0.067 46 6.5 cuneus
- 299 208 1034 3.159 0.814 0.154 0.052 5 0.7 entorhinal
- 5532 3712 9966 2.390 0.530 0.140 0.053 101 12.5 fusiform
- 9784 6496 16972 2.334 0.414 0.139 0.051 149 17.1 inferiorparietal
- 5507 3671 9915 2.318 0.662 0.161 0.074 161 17.5 inferiortemporal
- 1536 992 2714 2.548 0.596 0.156 0.061 28 3.6 isthmuscingulate
- 7116 4631 10753 2.074 0.393 0.152 0.051 117 15.0 lateraloccipital
- 4251 2747 7508 2.501 0.642 0.150 0.059 69 9.9 lateralorbitofrontal
- 5391 3490 8315 2.172 0.583 0.156 0.071 117 16.2 lingual
- 2850 1856 4530 2.106 0.615 0.168 0.092 99 9.8 medialorbitofrontal
- 6009 4102 12839 2.509 0.576 0.152 0.052 107 12.5 middletemporal
- 1138 775 2170 2.486 0.664 0.127 0.052 20 2.2 parahippocampal
- 3026 1947 5480 2.595 0.402 0.129 0.049 37 7.1 paracentral
- 2153 1456 3934 2.416 0.403 0.134 0.039 27 3.5 parsopercularis
- 1307 886 2770 2.403 0.608 0.149 0.042 20 2.3 parsorbitalis
- 2721 1782 4690 2.291 0.437 0.133 0.040 36 4.6 parstriangularis
- 2271 1546 2445 1.697 0.402 0.162 0.074 39 7.4 pericalcarine
- 6457 4214 9444 1.971 0.557 0.127 0.039 80 10.4 postcentral
- 1420 990 2663 2.562 0.431 0.164 0.060 35 3.4 posteriorcingulate
- 8347 5320 14559 2.485 0.514 0.119 0.051 102 16.2 precentral
- 7618 4948 12881 2.451 0.409 0.138 0.046 109 14.2 precuneus
- 1132 792 2404 2.585 0.560 0.163 0.061 25 2.8 rostralanteriorcingulate
- 10222 6883 17952 2.280 0.474 0.154 0.051 191 20.8 rostralmiddlefrontal
- 11659 7733 22132 2.538 0.491 0.139 0.043 163 20.0 superiorfrontal
- 8970 5825 14837 2.274 0.433 0.139 0.044 117 16.3 superiorparietal
- 5876 3863 11673 2.671 0.617 0.122 0.035 66 9.0 superiortemporal
- 5875 3879 10332 2.449 0.519 0.142 0.046 88 10.5 supramarginal
- 445 308 917 2.243 0.417 0.222 0.123 20 2.0 frontalpole
- 458 318 1469 3.306 0.649 0.177 0.085 11 1.6 temporalpole
- 596 370 928 2.222 0.370 0.145 0.048 9 1.2 transversetemporal
- 3540 2373 6817 2.668 0.748 0.132 0.069 60 8.5 insula
- #-----------------------------------------
- #@# Cortical Parc 2 rh Thu Aug 8 21:04:34 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub001 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...
- 29 labels changed using aseg
- relabeling using gibbs priors...
- 000: 10307 changed, 151707 examined...
- 001: 2373 changed, 39909 examined...
- 002: 701 changed, 12511 examined...
- 003: 300 changed, 3954 examined...
- 004: 158 changed, 1703 examined...
- 005: 84 changed, 849 examined...
- 006: 39 changed, 465 examined...
- 007: 24 changed, 209 examined...
- 008: 7 changed, 137 examined...
- 009: 2 changed, 39 examined...
- 010: 1 changed, 12 examined...
- 011: 1 changed, 8 examined...
- 012: 2 changed, 7 examined...
- 013: 2 changed, 11 examined...
- 014: 2 changed, 12 examined...
- 015: 1 changed, 11 examined...
- 016: 0 changed, 5 examined...
- 12 labels changed using aseg
- 000: 314 total segments, 229 labels (2732 vertices) changed
- 001: 104 total segments, 20 labels (101 vertices) changed
- 002: 84 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 140 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 990 vertices marked for relabeling...
- 990 labels changed in reclassification.
- writing output to ../label/rh.aparc.a2009s.annot...
- classification took 1 minutes and 16 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 2 rh Thu Aug 8 21:05:50 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 sub001 rh white
- computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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
- 1146 769 1892 2.171 0.429 0.181 0.080 33 3.2 G_and_S_frontomargin
- 1252 866 2295 2.279 0.435 0.155 0.047 21 2.4 G_and_S_occipital_inf
- 2024 1217 3512 2.434 0.445 0.125 0.050 27 5.0 G_and_S_paracentral
- 1463 972 2720 2.468 0.613 0.143 0.041 21 2.5 G_and_S_subcentral
- 1332 921 2444 2.259 0.382 0.182 0.078 39 4.1 G_and_S_transv_frontopol
- 2963 2040 5381 2.401 0.477 0.149 0.057 54 6.4 G_and_S_cingul-Ant
- 1549 1104 3028 2.569 0.401 0.142 0.042 27 2.9 G_and_S_cingul-Mid-Ant
- 1442 1027 2739 2.555 0.412 0.149 0.047 26 2.8 G_and_S_cingul-Mid-Post
- 438 311 1129 2.745 0.361 0.180 0.081 12 1.4 G_cingul-Post-dorsal
- 310 192 723 2.951 0.624 0.180 0.086 8 1.0 G_cingul-Post-ventral
- 2274 1446 3129 1.908 0.413 0.168 0.072 45 6.6 G_cuneus
- 1246 834 2870 2.642 0.423 0.141 0.046 21 2.3 G_front_inf-Opercular
- 320 216 740 2.552 0.380 0.139 0.045 5 0.6 G_front_inf-Orbital
- 1294 829 2812 2.491 0.400 0.157 0.050 26 2.8 G_front_inf-Triangul
- 5634 3753 12007 2.507 0.444 0.159 0.055 120 12.4 G_front_middle
- 7780 5077 16963 2.658 0.527 0.151 0.051 135 16.2 G_front_sup
- 599 400 1297 2.763 0.527 0.147 0.071 14 1.9 G_Ins_lg_and_S_cent_ins
- 738 485 2135 3.204 0.671 0.160 0.072 17 2.1 G_insular_short
- 2612 1691 5027 2.280 0.353 0.166 0.061 60 6.2 G_occipital_middle
- 1572 986 2954 2.386 0.387 0.144 0.042 22 2.7 G_occipital_sup
- 2052 1364 4605 2.591 0.563 0.150 0.060 53 4.8 G_oc-temp_lat-fusifor
- 3418 2159 5609 2.220 0.679 0.172 0.092 103 12.9 G_oc-temp_med-Lingual
- 1091 724 2443 2.628 0.860 0.133 0.092 16 2.6 G_oc-temp_med-Parahip
- 3096 2007 6751 2.547 0.668 0.161 0.065 63 8.0 G_orbital
- 3401 2234 7232 2.498 0.394 0.155 0.075 72 7.5 G_pariet_inf-Angular
- 3132 2072 6538 2.591 0.489 0.155 0.053 60 6.2 G_pariet_inf-Supramar
- 3031 1937 5816 2.418 0.401 0.141 0.048 45 6.0 G_parietal_sup
- 2429 1526 4156 2.140 0.513 0.133 0.046 36 4.6 G_postcentral
- 3172 1871 6747 2.754 0.421 0.119 0.077 54 8.3 G_precentral
- 3854 2448 7667 2.526 0.370 0.151 0.052 70 8.4 G_precuneus
- 761 477 1370 2.205 0.615 0.214 0.139 50 3.7 G_rectus
- 535 345 890 2.315 0.782 0.115 0.115 19 2.2 G_subcallosal
- 474 282 806 2.265 0.311 0.133 0.046 7 0.9 G_temp_sup-G_T_transv
- 2173 1396 5469 2.893 0.617 0.152 0.048 40 4.6 G_temp_sup-Lateral
- 717 475 1692 3.056 0.673 0.107 0.053 13 1.6 G_temp_sup-Plan_polar
- 794 555 1557 2.606 0.351 0.112 0.025 6 0.8 G_temp_sup-Plan_tempo
- 3007 1977 6426 2.502 0.710 0.185 0.101 130 13.3 G_temporal_inf
- 3758 2560 9584 2.732 0.519 0.167 0.058 82 8.9 G_temporal_middle
- 554 357 778 2.255 0.392 0.101 0.025 3 0.6 Lat_Fis-ant-Horizont
- 291 205 379 2.005 0.457 0.106 0.022 2 0.2 Lat_Fis-ant-Vertical
- 1438 936 1885 2.418 0.453 0.125 0.039 12 2.3 Lat_Fis-post
- 3150 1975 4316 1.938 0.403 0.163 0.068 63 9.7 Pole_occipital
- 1762 1203 3981 2.458 0.746 0.179 0.092 54 6.9 Pole_temporal
- 2790 1903 3306 1.972 0.518 0.153 0.055 43 6.3 S_calcarine
- 3268 2201 3736 1.850 0.601 0.109 0.033 27 4.8 S_central
- 1427 966 2098 2.418 0.340 0.126 0.036 14 2.2 S_cingul-Marginalis
- 583 392 1027 2.836 0.681 0.124 0.042 6 1.1 S_circular_insula_ant
- 1172 769 1549 2.217 0.397 0.088 0.021 5 1.0 S_circular_insula_inf
- 1496 1020 2117 2.298 0.362 0.113 0.029 9 1.9 S_circular_insula_sup
- 1180 808 1941 2.376 0.570 0.127 0.046 13 2.5 S_collat_transv_ant
- 536 368 771 2.123 0.366 0.144 0.050 8 1.0 S_collat_transv_post
- 2421 1655 3190 2.033 0.395 0.135 0.039 25 3.8 S_front_inf
- 2549 1704 3503 2.134 0.437 0.122 0.031 24 3.3 S_front_middle
- 2833 1948 4306 2.312 0.374 0.115 0.029 23 3.4 S_front_sup
- 655 425 752 2.209 0.366 0.147 0.050 9 1.3 S_interm_prim-Jensen
- 3881 2604 5151 2.153 0.419 0.130 0.036 39 5.8 S_intrapariet_and_P_trans
- 1127 762 1365 1.840 0.374 0.137 0.041 12 1.8 S_oc_middle_and_Lunatus
- 1588 1076 2219 2.153 0.305 0.125 0.030 14 2.0 S_oc_sup_and_transversal
- 627 427 915 2.198 0.354 0.119 0.034 5 0.8 S_occipital_ant
- 1429 967 1893 2.148 0.441 0.125 0.036 13 2.1 S_oc-temp_lat
- 2799 1927 4234 2.277 0.461 0.125 0.035 27 4.2 S_oc-temp_med_and_Lingual
- 581 388 858 2.112 0.471 0.150 0.041 7 1.0 S_orbital_lateral
- 808 555 1062 2.059 0.825 0.124 0.032 6 1.1 S_orbital_med-olfact
- 1726 1130 2628 2.442 0.521 0.148 0.052 23 3.7 S_orbital-H_Shaped
- 2373 1586 3243 2.310 0.436 0.125 0.037 23 3.6 S_parieto_occipital
- 1625 1022 1811 2.192 0.652 0.159 0.055 34 3.4 S_pericallosal
- 2545 1690 3239 1.977 0.371 0.120 0.035 26 3.7 S_postcentral
- 1885 1286 2994 2.420 0.421 0.125 0.033 18 2.6 S_precentral-inf-part
- 1391 944 1902 2.236 0.422 0.122 0.032 11 1.9 S_precentral-sup-part
- 286 187 302 1.657 0.459 0.137 0.033 3 0.4 S_suborbital
- 1587 1052 2535 2.419 0.406 0.124 0.034 15 2.3 S_subparietal
- 1875 1260 2306 2.013 0.410 0.128 0.039 18 2.8 S_temporal_inf
- 7310 4915 10992 2.326 0.477 0.120 0.031 66 9.4 S_temporal_sup
- 328 233 431 2.337 0.521 0.135 0.031 3 0.5 S_temporal_transverse
- #-----------------------------------------
- #@# Cortical Parc 3 rh Thu Aug 8 21:06:11 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub001 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...
- 1340 labels changed using aseg
- relabeling using gibbs priors...
- 000: 3002 changed, 151707 examined...
- 001: 714 changed, 12554 examined...
- 002: 171 changed, 3954 examined...
- 003: 60 changed, 1012 examined...
- 004: 27 changed, 372 examined...
- 005: 13 changed, 153 examined...
- 006: 5 changed, 85 examined...
- 007: 2 changed, 34 examined...
- 008: 0 changed, 10 examined...
- 197 labels changed using aseg
- 000: 70 total segments, 37 labels (376 vertices) changed
- 001: 33 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 55 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 520 vertices marked for relabeling...
- 520 labels changed in reclassification.
- writing output to ../label/rh.aparc.DKTatlas40.annot...
- classification took 1 minutes and 7 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 3 rh Thu Aug 8 21:07:18 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 sub001 rh white
- computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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
- 1182 878 2267 2.271 0.576 0.169 0.058 33 2.6 caudalanteriorcingulate
- 4143 2780 7343 2.426 0.463 0.127 0.036 45 6.5 caudalmiddlefrontal
- 2948 1909 4061 2.008 0.391 0.159 0.061 51 7.3 cuneus
- 302 207 1008 3.081 0.815 0.158 0.053 5 0.7 entorhinal
- 4990 3367 9128 2.413 0.527 0.139 0.048 85 10.2 fusiform
- 9099 6009 15736 2.337 0.409 0.140 0.053 142 16.3 inferiorparietal
- 6063 4033 10844 2.311 0.650 0.161 0.076 179 19.9 inferiortemporal
- 1522 985 2685 2.538 0.593 0.155 0.061 28 3.6 isthmuscingulate
- 7405 4822 11216 2.075 0.397 0.151 0.050 119 15.3 lateraloccipital
- 4808 3148 8495 2.432 0.647 0.155 0.069 88 11.7 lateralorbitofrontal
- 5374 3478 8297 2.173 0.585 0.156 0.070 116 16.0 lingual
- 2286 1484 3723 2.080 0.666 0.166 0.096 87 8.0 medialorbitofrontal
- 7450 5098 15411 2.495 0.555 0.147 0.048 124 14.2 middletemporal
- 1095 749 2083 2.485 0.663 0.125 0.051 19 2.0 parahippocampal
- 3143 2019 5680 2.582 0.409 0.129 0.050 39 7.3 paracentral
- 2146 1449 3844 2.405 0.396 0.135 0.041 28 3.6 parsopercularis
- 1389 927 2826 2.461 0.569 0.136 0.040 19 2.3 parsorbitalis
- 2904 1900 5135 2.314 0.431 0.138 0.043 41 5.1 parstriangularis
- 2313 1567 2511 1.704 0.401 0.165 0.078 42 7.8 pericalcarine
- 6828 4453 9985 1.973 0.554 0.127 0.038 84 10.8 postcentral
- 1589 1100 2966 2.560 0.441 0.165 0.060 38 3.9 posteriorcingulate
- 7943 5084 14087 2.497 0.512 0.119 0.051 98 15.5 precentral
- 7689 4981 13175 2.455 0.405 0.140 0.047 114 14.7 precuneus
- 1232 850 2487 2.539 0.574 0.162 0.061 26 3.0 rostralanteriorcingulate
- 6591 4426 11508 2.262 0.505 0.154 0.050 124 13.2 rostralmiddlefrontal
- 15551 10367 28903 2.468 0.492 0.143 0.047 242 29.1 superiorfrontal
- 7840 5091 12984 2.282 0.440 0.138 0.043 100 14.0 superiorparietal
- 7479 4977 15326 2.711 0.626 0.128 0.040 99 12.9 superiortemporal
- 5740 3785 10023 2.455 0.511 0.142 0.047 86 10.3 supramarginal
- 570 354 887 2.209 0.361 0.143 0.047 9 1.1 transversetemporal
- 3145 2109 6246 2.728 0.670 0.132 0.053 46 7.0 insula
- #--------------------------------------------
- #@# Refine Pial Surfs w/ T2/FLAIR Thu Aug 8 21:07:38 CEST 2013
- bbregister --s sub001 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/T2raw.lta --init-fsl --T2
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/T2raw.dat.log
- Thu Aug 8 21:07:38 CEST 2013
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/scripts
- /opt/freesurfer/5.3.0/bin/bbregister --s sub001 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/T2raw.lta --init-fsl --T2
- $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $
- Linux snake1 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/sub001/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/template.nii
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/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/sub001/mri/orig/T2raw.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.990502, 0.046145, 0.129524)
- j_ras = (0.0675335, 0.98382, 0.165943)
- k_ras = (0.119771, -0.173114, 0.977592)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/template.nii...
- fslregister --s sub001 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/fslregister --dof 6 --fsvol brainmask.mgz
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/reg.init.dat.fslregister.log
- Thu Aug 8 21:07:42 CEST 2013
- --s sub001 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/fslregister --dof 6 --fsvol brainmask.mgz
- $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $
- snake1
- Linux snake1 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/sub001/scripts
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/fslregister/refvol.fslregister.nii
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/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/sub001/mri/brainmask.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, -3.72529e-09, 0)
- j_ras = (0, -1.49012e-08, -1)
- k_ras = (1.86265e-09, 1, 1.49012e-08)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/fslregister/refvol.fslregister.nii...
- --------------------------------------
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/scripts
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/fslregister/movvol.fslregister.nii --frame 0
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/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/sub001/mri/transforms/tmp.bbregister.5983/template.nii...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.990502, 0.046145, 0.129524)
- j_ras = (0.0675335, 0.98382, 0.165943)
- k_ras = (0.119771, -0.173114, 0.977592)
- keeping frame 0
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/fslregister/movvol.fslregister.nii...
- Mov determinant is -0.311079
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/scripts
- tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/fslregister/movvol.fslregister.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/fslregister/reg0.6022.dat --regheader --fslregout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/reg.init.dat.fsl.mat0 --s sub001 --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/sub001/mri/transforms/tmp.bbregister.5983/fslregister/movvol.fslregister.nii
- reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/fslregister/reg0.6022.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/sub001/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/sub001/mri/transforms/tmp.bbregister.5983/fslregister/movvol.fslregister.nii
- Tmov: --------------------
- -0.700 0.000 0.000 95.890;
- 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) --------
- 0.991 -0.046 -0.130 0.000;
- 0.120 -0.173 0.978 0.000;
- -0.068 -0.984 -0.166 0.000;
- 0.000 0.000 0.000 1.000;
- ---------------------------------------
- ---- Input registration matrix --------
- 0.991 -0.046 -0.130 0.000;
- 0.120 -0.173 0.978 0.000;
- -0.068 -0.984 -0.166 0.000;
- 0.000 0.000 0.000 1.000;
- Determinant 1
- subject = sub001
- RegMat ---------------------------
- 0.991 -0.046 -0.130 0.000;
- 0.120 -0.173 0.978 0.000;
- -0.068 -0.984 -0.166 0.000;
- 0.000 0.000 0.000 1.000;
- FSLOUTPUTTYPE NIFTI
- tkreg2FSL: mov det = -0.311079, ref det = -1
- Thu Aug 8 21:07:49 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/scripts
- flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/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/sub001/mri/transforms/tmp.bbregister.5983/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/reg.init.dat.fsl.mat0
- Thu Aug 8 21:12:19 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/scripts
- flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/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/sub001/mri/transforms/tmp.bbregister.5983/reg.init.dat.fsl.mat -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/fslregister/fslmat0.trans.mat -schedule /opt/freesurfer/5.3.0/bin/flirt.newdefault.20080811.sch
- tkregister2_cmdl --s sub001 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/reg.init.dat --fslreg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/reg.init.dat.fsl.mat --noedit
- tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl
- ---- FSL registration matrix --------
- 0.990 -0.064 -0.125 57.714;
- -0.135 -0.174 -0.976 287.933;
- 0.041 0.983 -0.181 20.903;
- 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/sub001/mri/transforms/tmp.bbregister.5983/template.nii
- reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/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/sub001/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/sub001/mri/transforms/tmp.bbregister.5983/template.nii
- Tmov: --------------------
- -0.700 0.000 0.000 95.890;
- 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 = -0.311079, ref det = -1
- ---- Input registration matrix (computed) --------
- 0.990 -0.041 -0.135 0.350;
- 0.125 -0.181 0.976 -0.122;
- -0.064 -0.983 -0.174 -0.483;
- 0.000 0.000 0.000 1.000;
- ---------------------------------------
- ---- Input registration matrix --------
- 0.990 -0.041 -0.135 0.350;
- 0.125 -0.181 0.976 -0.122;
- -0.064 -0.983 -0.174 -0.483;
- 0.000 0.000 0.000 1.000;
- Determinant 1
- subject = sub001
- RegMat ---------------------------
- 0.990 -0.041 -0.135 0.350;
- 0.125 -0.181 0.976 -0.122;
- -0.064 -0.983 -0.174 -0.483;
- 0.000 0.000 0.000 1.000;
-
- Started at Thu Aug 8 21:07:42 CEST 2013
- Ended at Thu Aug 8 21:18:17 CEST 2013
-
- fslregister Done
-
- To check results, run:
- tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/reg.init.dat --surf orig
-
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/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/sub001/scripts
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/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 snake1
- machine x86_64
- user fkaule
- movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/template.nii
- regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/reg.init.dat
- subject sub001
- dof 6
- outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/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 1376486364
- TransRandMax 0.000000
- RotRandMax 0.000000
- Translations 0.000000 0.000000 0.000000
- Rotations 0.000000 0.000000 0.000000
- Input reg
- 0.990 -0.041 -0.135 0.350;
- 0.125 -0.181 0.976 -0.122;
- -0.064 -0.983 -0.174 -0.483;
- 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 1.018153
- 1 -25.0 -25.0 25.0 1.021125
- 2 -25.0 25.0 -25.0 1.007897
- 3 -25.0 25.0 25.0 1.077671
- 4 25.0 -25.0 -25.0 1.077687
- 5 25.0 -25.0 25.0 1.011004
- 6 25.0 25.0 -25.0 1.017099
- 7 25.0 25.0 25.0 1.020310
- REL: 8 0.227834 8.250945 1.031368 rel = 0.220905
- Initial costs ----------------
- Number of surface hits 2861
- WM Intensity 54.0541 +/- 7.4768
- Ctx Intensity 66.0848 +/- 9.7208
- Pct Contrast 19.7653 +/- 16.6727
- Cost 0.2278
- RelCost 0.2209
- ------------------------------------
- Brute force preopt -4 4 4, n = 729
- 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9541 0.9541 0.0
- 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.8732 0.8732 0.0
- 57 -4.0000 -4.0000 4.0000 -4.0000 0.0000 -4.0000 0.8611 0.8611 0.0
- 102 -4.0000 0.0000 -4.0000 4.0000 0.0000 -4.0000 0.8087 0.8087 0.0
- 120 -4.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.7490 0.7490 0.0
- 346 0.0000 0.0000 -4.0000 4.0000 0.0000 0.0000 0.6984 0.6984 0.0
- 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.2278 0.2278 0.0
- Brute Force --------------------------
- Min cost was 0.227834
- Number of iterations 729
- Search time 2.134000 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 -0.042 0.000 0.000 0.000 0.000 0.000 0.2258010178
- 10 -0.073 0.000 0.000 0.000 0.000 0.000 0.2253062128
- 12 -0.070 0.000 0.000 0.000 0.000 0.000 0.2252978562
- 25 -0.070 -0.024 0.000 0.000 0.000 0.000 0.2249992201
- 26 -0.070 -0.023 0.000 0.000 0.000 0.000 0.2249969765
- 27 -0.070 -0.022 0.000 0.000 0.000 0.000 0.2249954097
- 29 -0.070 -0.021 0.000 0.000 0.000 0.000 0.2249953160
- 32 -0.070 -0.021 1.000 0.000 0.000 0.000 0.1202108137
- 37 -0.070 -0.021 1.075 0.000 0.000 0.000 0.1201111246
- 38 -0.070 -0.021 1.043 0.000 0.000 0.000 0.1195592517
- 40 -0.070 -0.021 1.048 0.000 0.000 0.000 0.1195374499
- 41 -0.070 -0.021 1.049 0.000 0.000 0.000 0.1195367893
- 48 -0.070 -0.021 1.049 0.382 0.000 0.000 0.1123138517
- 49 -0.070 -0.021 1.049 0.249 0.000 0.000 0.1087803640
- 50 -0.070 -0.021 1.049 0.243 0.000 0.000 0.1087531648
- 51 -0.070 -0.021 1.049 0.232 0.000 0.000 0.1086272689
- 52 -0.070 -0.021 1.049 0.143 0.000 0.000 0.1083670288
- 56 -0.070 -0.021 1.049 0.147 0.000 0.000 0.1083644245
- 69 -0.070 -0.021 1.049 0.147 -0.006 0.000 0.1083345772
- 71 -0.070 -0.021 1.049 0.147 -0.013 0.000 0.1083341684
- 72 -0.070 -0.021 1.049 0.147 -0.010 0.000 0.1083299177
- 73 -0.070 -0.021 1.049 0.147 -0.009 0.000 0.1083290940
- 81 -0.070 -0.021 1.049 0.147 -0.009 -0.017 0.1080332080
- 84 -0.070 -0.021 1.049 0.147 -0.009 -0.023 0.1080299022
- 85 -0.070 -0.021 1.049 0.147 -0.009 -0.020 0.1080215098
- 95 -0.053 -0.021 1.049 0.147 -0.009 -0.020 0.1076705218
- 97 -0.032 -0.021 1.049 0.147 -0.009 -0.020 0.1075139019
- 98 -0.033 -0.021 1.049 0.147 -0.009 -0.020 0.1075117172
- 99 -0.035 -0.021 1.049 0.147 -0.009 -0.020 0.1075101548
- 108 -0.036 0.361 1.049 0.147 -0.009 -0.020 0.1053708937
- 109 -0.036 0.193 1.049 0.147 -0.009 -0.020 0.0986115209
- 110 -0.036 0.183 1.049 0.147 -0.009 -0.020 0.0983937331
- 112 -0.036 0.164 1.049 0.147 -0.009 -0.020 0.0982287378
- 122 -0.036 0.164 1.004 0.147 -0.009 -0.020 0.0978489499
- 123 -0.036 0.164 1.005 0.147 -0.009 -0.020 0.0978448437
- 124 -0.036 0.164 1.011 0.147 -0.009 -0.020 0.0978365927
- 126 -0.036 0.164 1.010 0.147 -0.009 -0.020 0.0978356939
- 134 -0.036 0.164 1.010 0.277 -0.009 -0.020 0.0929503714
- 136 -0.036 0.164 1.010 0.249 -0.009 -0.020 0.0927839941
- 138 -0.036 0.164 1.010 0.258 -0.009 -0.020 0.0927327334
- 139 -0.036 0.164 1.010 0.257 -0.009 -0.020 0.0927319104
- 140 -0.036 0.164 1.010 0.256 -0.009 -0.020 0.0927312481
- 150 -0.036 0.164 1.010 0.256 -0.015 -0.020 0.0926757384
- 151 -0.036 0.164 1.010 0.256 -0.029 -0.020 0.0926632007
- 153 -0.036 0.164 1.010 0.256 -0.023 -0.020 0.0926509030
- 155 -0.036 0.164 1.010 0.256 -0.022 -0.020 0.0926504878
- 164 -0.036 0.164 1.010 0.256 -0.022 -0.012 0.0925917978
- 166 -0.036 0.164 1.010 0.256 -0.022 -0.006 0.0925726703
- 167 -0.036 0.164 1.010 0.256 -0.022 -0.007 0.0925726435
- 169 -0.002 0.350 0.971 0.366 -0.035 0.007 0.0901983903
- 175 -0.015 0.279 0.985 0.324 -0.030 0.001 0.0895477683
- 176 -0.014 0.284 0.984 0.327 -0.031 0.002 0.0895183172
- 177 -0.012 0.294 0.982 0.333 -0.031 0.003 0.0894861295
- 180 -0.012 0.295 0.982 0.333 -0.032 0.003 0.0894856505
- 183 -0.012 0.295 0.982 0.333 -0.032 0.003 0.0894856134
- 192 0.008 0.295 0.982 0.333 -0.032 0.003 0.0892456368
- 193 0.014 0.295 0.982 0.333 -0.032 0.003 0.0892386643
- 194 0.012 0.295 0.982 0.333 -0.032 0.003 0.0892349427
- 202 0.012 0.295 0.982 0.333 -0.032 0.018 0.0889367060
- 204 0.012 0.295 0.982 0.333 -0.032 0.033 0.0887800589
- 205 0.012 0.295 0.982 0.333 -0.032 0.034 0.0887745667
- 207 0.012 0.295 0.982 0.333 -0.032 0.036 0.0887697827
- 217 0.012 0.295 0.909 0.333 -0.032 0.036 0.0884372024
- 218 0.012 0.295 0.911 0.333 -0.032 0.036 0.0884222165
- 219 0.012 0.295 0.930 0.333 -0.032 0.036 0.0883555897
- 221 0.012 0.295 0.933 0.333 -0.032 0.036 0.0883502887
- 222 0.012 0.295 0.935 0.333 -0.032 0.036 0.0883491451
- 230 0.012 0.295 0.935 0.377 -0.032 0.036 0.0882274917
- 231 0.012 0.295 0.935 0.363 -0.032 0.036 0.0880883378
- 243 0.012 0.295 0.935 0.363 -0.025 0.036 0.0880035003
- 244 0.012 0.295 0.935 0.363 -0.019 0.036 0.0879818089
- 253 0.008 0.272 0.940 0.349 -0.018 0.035 0.0878406533
- 256 0.008 0.272 0.940 0.350 -0.018 0.035 0.0878405216
- 257 0.008 0.272 0.940 0.350 -0.018 0.035 0.0878401449
- 268 0.007 0.272 0.940 0.350 -0.018 0.035 0.0878400370
- 278 0.007 0.272 0.940 0.350 -0.018 0.036 0.0878377232
- 279 0.007 0.272 0.940 0.350 -0.018 0.037 0.0878371737
- 289 0.007 0.272 0.887 0.350 -0.018 0.037 0.0872950113
- 290 0.007 0.272 0.879 0.350 -0.018 0.037 0.0872834129
- 301 0.007 0.272 0.879 0.374 -0.018 0.037 0.0869214129
- 313 0.007 0.272 0.879 0.374 -0.015 0.037 0.0869139899
- 322 0.002 0.245 0.884 0.357 -0.013 0.035 0.0868266496
- 323 0.003 0.251 0.883 0.361 -0.014 0.036 0.0867897003
- 325 0.004 0.253 0.883 0.362 -0.014 0.036 0.0867875990
- 345 0.004 0.253 0.883 0.362 -0.014 0.037 0.0867870989
- 354 0.004 0.253 0.858 0.362 -0.014 0.037 0.0867672643
- 355 0.004 0.253 0.868 0.362 -0.014 0.037 0.0867018364
- 356 0.004 0.253 0.870 0.362 -0.014 0.037 0.0866998813
- 366 0.004 0.253 0.870 0.364 -0.014 0.037 0.0866902370
- 368 0.004 0.253 0.870 0.366 -0.014 0.037 0.0866842160
- 369 0.004 0.253 0.870 0.367 -0.014 0.037 0.0866835818
- 388 0.003 0.250 0.870 0.365 -0.014 0.037 0.0866810985
- 389 0.003 0.250 0.870 0.365 -0.014 0.037 0.0866807680
- 400 0.003 0.249 0.865 0.366 -0.014 0.037 0.0866768250
- 401 0.003 0.249 0.867 0.366 -0.014 0.037 0.0866766333
- 405 0.003 0.249 0.867 0.366 -0.014 0.037 0.0866765763
- 418 0.000 0.249 0.867 0.366 -0.014 0.037 0.0866729252
- 429 0.000 0.249 0.867 0.366 -0.014 0.036 0.0866719921
- 442 0.000 0.249 0.867 0.366 -0.014 0.036 0.0866719031
- 465 0.000 0.249 0.867 0.366 -0.013 0.036 0.0866703080
- 466 0.000 0.249 0.867 0.366 -0.012 0.036 0.0866700366
- 473 0.000 0.249 0.867 0.366 -0.012 0.036 0.0866697309
- 475 0.000 0.249 0.866 0.366 -0.012 0.036 0.0866696832
- Powell done niters = 5
- Computing relative cost
- 0 -25.0 -25.0 -25.0 1.019865
- 1 -25.0 -25.0 25.0 1.032724
- 2 -25.0 25.0 -25.0 1.036737
- 3 -25.0 25.0 25.0 1.055741
- 4 25.0 -25.0 -25.0 1.067120
- 5 25.0 -25.0 25.0 1.005347
- 6 25.0 25.0 -25.0 1.015522
- 7 25.0 25.0 25.0 1.034836
- REL: 8 0.086670 8.267892 1.033486 rel = 0.0838615
- Number of iterations 5
- Min cost was 0.086670
- Number of FunctionCalls 483
- TolPowell 0.000100
- nMaxItersPowell 36
- OptimizationTime 1.510000 sec
- Parameters at optimum (transmm) 0.00027 0.24917 0.86627
- Parameters at optimum (rotdeg) 0.36613 -0.01169 0.03592
- Final costs ----------------
- Number of surface hits 2861
- WM Intensity 53.4908 +/- 6.9763
- Ctx Intensity 65.6951 +/- 7.5516
- Pct Contrast 20.5386 +/- 12.1783
- Cost 0.0867
- RelCost 0.2209
- Reg at min cost was
- 0.990 -0.041 -0.135 0.350;
- 0.126 -0.174 0.977 0.130;
- -0.063 -0.984 -0.167 0.383;
- 0.000 0.000 0.000 1.000;
- Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/bbr.pass1.dat, type = 14
- Original Reg
- 0.990 -0.041 -0.135 0.350;
- 0.125 -0.181 0.976 -0.122;
- -0.064 -0.983 -0.174 -0.483;
- 0.000 0.000 0.000 1.000;
- Original Reg - Optimal Reg
- 0.000 -0.000 0.001 -0.000;
- -0.001 -0.006 -0.001 -0.252;
- -0.001 0.001 -0.006 -0.866;
- 0.000 0.000 0.000 0.000;
- Computing change in lh position
- LH rmsDiffMean 1.136479
- Computing change in rh position
- Surface RMS Diff (mm) 1.154897 1.493696
- mri_segreg done
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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/sub001/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/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/sub001/scripts
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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/sub001/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5
- sysname Linux
- hostname snake1
- machine x86_64
- user fkaule
- movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/template.nii
- regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/tmp.bbregister.5983/bbr.pass1.dat
- subject sub001
- dof 6
- outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 1376546860
- TransRandMax 0.000000
- RotRandMax 0.000000
- Translations 0.000000 0.000000 0.000000
- Rotations 0.000000 0.000000 0.000000
- Input reg
- 0.990 -0.041 -0.135 0.350;
- 0.126 -0.174 0.977 0.130;
- -0.063 -0.984 -0.167 0.383;
- 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 1.010248
- 1 -25.0 -25.0 25.0 1.012062
- 2 -25.0 25.0 -25.0 1.018488
- 3 -25.0 25.0 25.0 1.036102
- 4 25.0 -25.0 -25.0 1.032405
- 5 25.0 -25.0 25.0 1.012938
- 6 25.0 25.0 -25.0 1.016887
- 7 25.0 25.0 25.0 1.019866
- REL: 8 0.093805 8.158997 1.019875 rel = 0.0919773
- Initial costs ----------------
- Number of surface hits 284805
- WM Intensity 53.5348 +/- 6.9723
- Ctx Intensity 65.7593 +/- 7.5746
- Pct Contrast 20.5461 +/- 12.2404
- Cost 0.0938
- RelCost 0.0920
- ------------------------------------
- Brute force preopt -0.1 0.1 0.1, n = 729
- 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0959 0.0959 0.0
- 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.0949 0.0949 0.0
- 9 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 -0.1000 0.0938 0.0938 0.0
- 10 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.0000 0.0934 0.0934 0.0
- 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.0919 0.0919 0.0
- 13 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.0918 0.0918 0.0
- 21 -0.1000 -0.1000 -0.1000 0.1000 0.0000 -0.1000 0.0913 0.0913 0.0
- 39 -0.1000 -0.1000 0.0000 0.0000 0.0000 -0.1000 0.0911 0.0911 0.0
- 93 -0.1000 0.0000 -0.1000 0.0000 0.0000 -0.1000 0.0902 0.0902 0.0
- 120 -0.1000 0.0000 0.0000 0.0000 0.0000 -0.1000 0.0896 0.0896 0.0
- 124 -0.1000 0.0000 0.0000 0.0000 0.1000 0.0000 0.0892 0.0892 0.0
- 337 0.0000 0.0000 -0.1000 0.0000 0.0000 0.0000 0.0882 0.0882 0.0
- 346 0.0000 0.0000 -0.1000 0.1000 0.0000 0.0000 0.0878 0.0878 0.0
- 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0867 0.0867 0.0
- Brute Force --------------------------
- Min cost was 0.086670
- Number of iterations 729
- Search time 2.747000 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 0.034 0.000 0.000 0.000 0.000 0.000 0.0934754491
- 8 0.060 0.000 0.000 0.000 0.000 0.000 0.0934220525
- 9 0.055 0.000 0.000 0.000 0.000 0.000 0.0934198571
- 10 0.056 0.000 0.000 0.000 0.000 0.000 0.0934197391
- 19 0.056 0.005 0.000 0.000 0.000 0.000 0.0934137272
- 28 0.056 0.005 -0.124 0.000 0.000 0.000 0.0920528545
- 29 0.056 0.005 -0.119 0.000 0.000 0.000 0.0920398555
- 30 0.056 0.005 -0.111 0.000 0.000 0.000 0.0920327684
- 32 0.056 0.005 -0.110 0.000 0.000 0.000 0.0920327326
- 41 0.056 0.005 -0.110 0.093 0.000 0.000 0.0906947202
- 42 0.056 0.005 -0.110 0.090 0.000 0.000 0.0906876781
- 43 0.056 0.005 -0.110 0.085 0.000 0.000 0.0906790967
- 46 0.056 0.005 -0.110 0.083 0.000 0.000 0.0906782143
- 54 0.056 0.005 -0.110 0.083 -0.092 0.000 0.0901886224
- 55 0.056 0.005 -0.110 0.083 -0.067 0.000 0.0901330222
- 58 0.056 0.005 -0.110 0.083 -0.068 0.000 0.0901330203
- 65 0.056 0.005 -0.110 0.083 -0.068 0.082 0.0894686206
- 67 0.056 0.005 -0.110 0.083 -0.068 0.086 0.0894667451
- 71 0.111 0.011 -0.220 0.166 -0.136 0.172 0.0888622945
- 99 0.113 0.034 -0.188 0.083 -0.068 0.086 0.0885291370
- 100 0.113 0.034 -0.180 0.083 -0.068 0.086 0.0885258594
- 101 0.113 0.034 -0.182 0.083 -0.068 0.086 0.0885254619
- 109 0.113 0.034 -0.182 0.135 -0.068 0.086 0.0882288197
- 110 0.113 0.034 -0.182 0.127 -0.068 0.086 0.0882175730
- 111 0.113 0.034 -0.182 0.126 -0.068 0.086 0.0882173188
- 112 0.113 0.034 -0.182 0.125 -0.068 0.086 0.0882172810
- 121 0.113 0.034 -0.182 0.125 -0.097 0.086 0.0881661084
- 122 0.113 0.034 -0.182 0.125 -0.090 0.086 0.0881638632
- 131 0.113 0.034 -0.182 0.125 -0.090 0.112 0.0880756205
- 132 0.113 0.034 -0.182 0.125 -0.090 0.115 0.0880723273
- 133 0.113 0.034 -0.182 0.125 -0.090 0.121 0.0880692945
- 136 0.171 0.062 -0.254 0.167 -0.112 0.155 0.0876980211
- 201 0.156 0.069 -0.262 0.167 -0.101 0.151 0.0876648721
- 207 0.148 0.062 -0.247 0.159 -0.099 0.145 0.0876599769
- 208 0.152 0.065 -0.253 0.162 -0.100 0.147 0.0876560269
- 209 0.151 0.065 -0.253 0.162 -0.100 0.147 0.0876559854
- 212 0.151 0.065 -0.253 0.162 -0.100 0.147 0.0876559824
- 231 0.151 0.067 -0.253 0.162 -0.100 0.147 0.0876554788
- 241 0.151 0.067 -0.253 0.162 -0.100 0.143 0.0876552337
- 242 0.151 0.067 -0.253 0.162 -0.100 0.145 0.0876549670
- 251 0.151 0.067 -0.253 0.159 -0.100 0.145 0.0876549005
- 253 0.151 0.067 -0.253 0.160 -0.100 0.145 0.0876548320
- 261 0.151 0.067 -0.253 0.160 -0.101 0.145 0.0876546458
- 270 0.151 0.066 -0.252 0.160 -0.101 0.144 0.0876545133
- 271 0.151 0.066 -0.252 0.160 -0.101 0.145 0.0876545111
- 274 0.151 0.066 -0.252 0.160 -0.101 0.145 0.0876544875
- 283 0.149 0.066 -0.252 0.160 -0.101 0.145 0.0876544450
- 292 0.149 0.065 -0.252 0.160 -0.101 0.145 0.0876543653
- 302 0.149 0.065 -0.252 0.160 -0.101 0.144 0.0876543080
- 326 0.150 0.066 -0.253 0.160 -0.101 0.144 0.0876542333
- 327 0.150 0.066 -0.253 0.160 -0.101 0.144 0.0876541875
- 367 0.150 0.066 -0.253 0.159 -0.101 0.144 0.0876541594
- 383 0.150 0.066 -0.253 0.159 -0.101 0.144 0.0876541045
- 385 0.150 0.066 -0.253 0.159 -0.101 0.144 0.0876540541
- 386 0.150 0.066 -0.253 0.159 -0.101 0.144 0.0876540503
- 387 0.150 0.066 -0.254 0.160 -0.101 0.144 0.0876540275
- 389 0.150 0.066 -0.254 0.160 -0.101 0.144 0.0876540056
- 409 0.150 0.065 -0.254 0.160 -0.101 0.144 0.0876539594
- Powell done niters = 7
- Computing relative cost
- 0 -25.0 -25.0 -25.0 1.009216
- 1 -25.0 -25.0 25.0 1.012267
- 2 -25.0 25.0 -25.0 1.018605
- 3 -25.0 25.0 25.0 1.035298
- 4 25.0 -25.0 -25.0 1.032381
- 5 25.0 -25.0 25.0 1.013880
- 6 25.0 25.0 -25.0 1.017775
- 7 25.0 25.0 25.0 1.020313
- REL: 8 0.087654 8.159736 1.019967 rel = 0.085938
- Number of iterations 7
- Min cost was 0.087654
- Number of FunctionCalls 506
- TolPowell 0.000000
- nMaxItersPowell 36
- OptimizationTime 58.655000 sec
- Parameters at optimum (transmm) 0.15018 0.06522 -0.25364
- Parameters at optimum (rotdeg) 0.15960 -0.10095 0.14426
- Final costs ----------------
- Number of surface hits 284805
- WM Intensity 53.5314 +/- 6.9908
- Ctx Intensity 65.7644 +/- 7.5616
- Pct Contrast 20.5637 +/- 12.1450
- Cost 0.0877
- RelCost 0.0920
- Reg at min cost was
- 0.990 -0.039 -0.137 0.499;
- 0.129 -0.172 0.977 0.195;
- -0.061 -0.984 -0.165 0.130;
- 0.000 0.000 0.000 1.000;
- Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/T2raw.dat, type = 14
- Original Reg
- 0.990 -0.041 -0.135 0.350;
- 0.126 -0.174 0.977 0.130;
- -0.063 -0.984 -0.167 0.383;
- 0.000 0.000 0.000 1.000;
- Original Reg - Optimal Reg
- 0.000 -0.002 0.002 -0.149;
- -0.003 -0.003 -0.000 -0.065;
- -0.002 0.001 -0.002 0.253;
- 0.000 0.000 0.000 0.000;
- Computing change in lh position
- LH rmsDiffMean 0.257677
- Computing change in rh position
- Surface RMS Diff (mm) 0.226087 0.417724
- mri_segreg done
- tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/T2raw.dat --noedit --ltaout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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/sub001/mri/orig/T2raw.mgz
- reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 --------
- 0.990 -0.039 -0.137 0.499;
- 0.129 -0.172 0.977 0.195;
- -0.061 -0.984 -0.165 0.130;
- 0.000 0.000 0.000 1.000;
- float2int = 0
- ---------------------------------------
- INFO: loading target /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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/sub001/mri/orig/T2raw.mgz
- Tmov: --------------------
- -0.700 0.000 0.000 95.890;
- 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 --------
- 0.990 -0.039 -0.137 0.499;
- 0.129 -0.172 0.977 0.195;
- -0.061 -0.984 -0.165 0.130;
- 0.000 0.000 0.000 1.000;
- Determinant 1
- subject = sub001
- RegMat ---------------------------
- 0.990 -0.039 -0.137 0.499;
- 0.129 -0.172 0.977 0.195;
- -0.061 -0.984 -0.165 0.130;
- 0.000 0.000 0.000 1.000;
- transformed matrix:
- 1.000 -0.008 0.008 -0.044;
- 0.008 1.000 0.001 0.182;
- -0.008 -0.000 1.000 -0.072;
- 0.000 0.000 0.000 1.000;
- transformed matrix:
- 0.693 -0.041 -0.086 57.967;
- -0.096 -0.110 -0.651 287.411;
- 0.027 0.656 -0.114 20.447;
- 0.000 0.000 0.000 1.000;
- Cleaning up
-
- Started at Thu Aug 8 21:07:38 CEST 2013
- Ended at Thu Aug 8 21:20:07 CEST 2013
- BBR-Run-Time-Sec 749
-
- bbregister Done
- To check results, run:
- tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/T2raw.dat --surf
-
- mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/T2.mgz
- mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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/sub001/mri/orig/T2raw.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.990502, 0.046145, 0.129524)
- j_ras = (0.0675335, 0.98382, 0.165943)
- k_ras = (0.119771, -0.173114, 0.977592)
- INFO: Reading transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/T2raw.lta...
- Reading transform with LTAreadEx()
- reading extra input line subject sub001
- reading extra input line fscale 0.150000
- reading template info from volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/orig.mgz...
- INFO: Applying transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/transforms/T2raw.lta...
- ---------------------------------
- INFO: Transform Matrix (linear_ras_to_ras)
- 1.000 -0.008 0.008 -0.044;
- 0.008 1.000 0.001 0.182;
- -0.008 -0.000 1.000 -0.071;
- 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/sub001/mri/T2.mgz...
- mri_normalize -aseg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/aseg.mgz -sigma 4 -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/rh.white identity.nofile -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/lh.white identity.nofile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/T2.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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/sub001/mri/T2.mgz...
- computing distance transform
- computing distance transform
- computing nonmaximum suppression
- 14614 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/sub001/mri/T2.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/scripts
- cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/lh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/lh.woT2.pial
- `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/lh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/lh.woT2.pial'
- mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub001 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/sub001/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/wm.mgz...
- 22126 bright wm thresholded.
- 274 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/lh.orig...
- computing class statistics...
- border white: 284449 voxels (1.70%)
- border gray 312227 voxels (1.86%)
- WM (94.0): 94.7 +- 9.7 [70.0 --> 110.0]
- GM (77.0) : 75.7 +- 12.7 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 50.3 (was 70)
- setting MAX_BORDER_WHITE to 115.7 (was 105)
- setting MIN_BORDER_WHITE to 63.0 (was 85)
- setting MAX_CSF to 37.5 (was 40)
- setting MAX_GRAY to 96.3 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 56.6 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 24.8 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=106, GM=63
- mean inside = 94.5, mean outside = 70.9
- 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/sub001/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.89 +- 0.25 (0.04-->4.37) (max @ vno 102287 --> 103434)
- face area 0.33 +- 0.15 (0.00-->4.48)
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 32 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 1 with 2 points - only 0.00% unknown
- deleting segment 4 with 835 points - only 0.00% unknown
- deleting segment 6 with 10 points - only 0.00% unknown
- deleting segment 7 with 8 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 9 with 2 points - only 0.00% unknown
- deleting segment 10 with 6 points - only 0.00% unknown
- deleting segment 11 with 6 points - only 0.00% unknown
- deleting segment 12 with 5 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 13 with 4 points - only 0.00% unknown
- tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.89 +- 0.25 (0.08-->4.37) (max @ vno 102287 --> 103434)
- face area 0.33 +- 0.15 (0.00-->4.48)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4623167.5, rms=0.00
- rms = 1.11, time step reduction 1 of 3 to 0.250...
- rms = 0.28, time step reduction 2 of 3 to 0.125...
- rms = 0.03, time step reduction 3 of 3 to 0.062...
- 001: dt: 0.1250, sse=4623167.5, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 32 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 1 with 2 points - only 0.00% unknown
- deleting segment 2 with 835 points - only 0.00% unknown
- deleting segment 3 with 10 points - only 0.00% unknown
- deleting segment 4 with 8 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 5 with 2 points - only 0.00% unknown
- deleting segment 6 with 6 points - only 0.00% unknown
- deleting segment 7 with 6 points - only 0.00% unknown
- deleting segment 8 with 5 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 9 with 4 points - only 0.00% unknown
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.89 +- 0.25 (0.08-->4.37) (max @ vno 102287 --> 103434)
- face area 0.33 +- 0.15 (0.00-->4.48)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4623167.5, rms=0.00
- rms = 1.11, time step reduction 1 of 3 to 0.250...
- rms = 0.28, time step reduction 2 of 3 to 0.125...
- rms = 0.03, time step reduction 3 of 3 to 0.062...
- 002: dt: 0.1250, sse=4623167.5, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 32 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 1 with 2 points - only 0.00% unknown
- deleting segment 2 with 835 points - only 0.00% unknown
- deleting segment 3 with 10 points - only 0.00% unknown
- deleting segment 4 with 8 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 5 with 2 points - only 0.00% unknown
- deleting segment 6 with 6 points - only 0.00% unknown
- deleting segment 7 with 6 points - only 0.00% unknown
- deleting segment 8 with 5 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 9 with 4 points - only 0.00% unknown
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.89 +- 0.25 (0.08-->4.37) (max @ vno 102287 --> 103434)
- face area 0.33 +- 0.15 (0.00-->4.48)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4623167.5, rms=0.00
- rms = 1.11, time step reduction 1 of 3 to 0.250...
- rms = 0.28, time step reduction 2 of 3 to 0.125...
- rms = 0.03, time step reduction 3 of 3 to 0.062...
- 003: dt: 0.1250, sse=4623167.5, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 32 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 1 with 2 points - only 0.00% unknown
- deleting segment 2 with 835 points - only 0.00% unknown
- deleting segment 3 with 10 points - only 0.00% unknown
- deleting segment 4 with 8 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 5 with 2 points - only 0.00% unknown
- deleting segment 6 with 6 points - only 0.00% unknown
- deleting segment 7 with 6 points - only 0.00% unknown
- deleting segment 8 with 5 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 9 with 4 points - only 0.00% unknown
- 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=4623167.5, rms=0.00
- rms = 1.11, time step reduction 1 of 3 to 0.250...
- rms = 0.28, time step reduction 2 of 3 to 0.125...
- rms = 0.03, time step reduction 3 of 3 to 0.062...
- 004: dt: 0.1250, sse=4623167.5, 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 [89.60 208.40], gm=149.00+-19.80, and vertices in regions > 139.1
- 36408 surface locations found to contain inconsistent values (3507 in, 32901 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=541285.1, rms=0.20
- 001: dt: 0.5000, sse=505975.2, rms=0.196 (0.000%)
- 002: dt: 0.5000, sse=484868.1, rms=0.185 (0.000%)
- 003: dt: 0.5000, sse=471426.6, rms=0.176 (0.000%)
- 004: dt: 0.5000, sse=461083.4, rms=0.168 (0.000%)
- 005: dt: 0.5000, sse=453571.5, rms=0.162 (0.000%)
- 006: dt: 0.5000, sse=448075.9, rms=0.156 (0.000%)
- 007: dt: 0.5000, sse=443408.4, rms=0.151 (0.000%)
- 008: dt: 0.5000, sse=439713.7, rms=0.147 (0.000%)
- 009: dt: 0.5000, sse=436601.8, rms=0.144 (0.000%)
- 010: dt: 0.5000, sse=434165.6, rms=0.142 (0.000%)
- 011: dt: 0.5000, sse=431763.1, rms=0.139 (0.000%)
- 012: dt: 0.5000, sse=429779.5, rms=0.137 (0.000%)
- 013: dt: 0.5000, sse=427923.0, rms=0.136 (0.000%)
- 014: dt: 0.5000, sse=425951.6, rms=0.135 (0.000%)
- 015: dt: 0.5000, sse=424134.0, rms=0.134 (0.000%)
- 016: dt: 0.5000, sse=422731.8, rms=0.133 (0.000%)
- 017: dt: 0.5000, sse=421065.8, rms=0.132 (0.000%)
- 018: dt: 0.5000, sse=419339.0, rms=0.132 (0.000%)
- 019: dt: 0.5000, sse=417992.2, rms=0.132 (0.000%)
- 020: dt: 0.5000, sse=416598.9, rms=0.131 (0.000%)
- 021: dt: 0.5000, sse=415453.1, rms=0.131 (0.000%)
- 022: dt: 0.5000, sse=414034.3, rms=0.131 (0.000%)
- 023: dt: 0.5000, sse=413053.5, rms=0.131 (0.000%)
- 024: dt: 0.5000, sse=411796.2, rms=0.131 (0.000%)
- 025: dt: 0.5000, sse=410574.3, rms=0.131 (0.000%)
- 026: dt: 0.5000, sse=409370.5, rms=0.131 (0.000%)
- 027: dt: 0.5000, sse=408397.6, rms=0.132 (0.000%)
- 028: dt: 0.5000, sse=407430.4, rms=0.132 (0.000%)
- 029: dt: 0.5000, sse=406414.2, rms=0.133 (0.000%)
- 030: dt: 0.5000, sse=405287.4, rms=0.133 (0.000%)
- positioning took 4.0 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [97.00 205.00], gm=151.00+-18.00, and vertices in regions > 142.0
- 29115 surface locations found to contain inconsistent values (3996 in, 25119 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=41931.3, rms=0.11
- 031: dt: 0.5000, sse=41710.2, rms=0.111 (0.000%)
- 032: dt: 0.5000, sse=42388.1, rms=0.101 (0.000%)
- 033: dt: 0.5000, sse=43267.5, rms=0.094 (0.000%)
- 034: dt: 0.5000, sse=44049.8, rms=0.089 (0.000%)
- 035: dt: 0.5000, sse=44711.1, rms=0.085 (0.000%)
- 036: dt: 0.5000, sse=45359.8, rms=0.080 (0.000%)
- 037: dt: 0.5000, sse=45992.2, rms=0.076 (0.000%)
- 038: dt: 0.5000, sse=46605.6, rms=0.073 (0.000%)
- 039: dt: 0.5000, sse=47210.0, rms=0.069 (0.000%)
- 040: dt: 0.5000, sse=47799.4, rms=0.066 (0.000%)
- 041: dt: 0.5000, sse=48398.2, rms=0.063 (0.000%)
- 042: dt: 0.5000, sse=48939.4, rms=0.061 (0.000%)
- 043: dt: 0.5000, sse=49471.1, rms=0.058 (0.000%)
- 044: dt: 0.5000, sse=49960.6, rms=0.056 (0.000%)
- 045: dt: 0.5000, sse=50443.2, rms=0.054 (0.000%)
- 046: dt: 0.5000, sse=50882.2, rms=0.052 (0.000%)
- 047: dt: 0.5000, sse=51295.8, rms=0.050 (0.000%)
- 048: dt: 0.5000, sse=51679.1, rms=0.049 (0.000%)
- 049: dt: 0.5000, sse=52028.8, rms=0.047 (0.000%)
- 050: dt: 0.5000, sse=52372.4, rms=0.046 (0.000%)
- 051: dt: 0.5000, sse=52681.1, rms=0.044 (0.000%)
- 052: dt: 0.5000, sse=52984.0, rms=0.043 (0.000%)
- 053: dt: 0.5000, sse=53225.8, rms=0.042 (0.000%)
- 054: dt: 0.5000, sse=53486.1, rms=0.041 (0.000%)
- 055: dt: 0.5000, sse=53717.1, rms=0.040 (0.000%)
- 056: dt: 0.5000, sse=53922.3, rms=0.039 (0.000%)
- 057: dt: 0.5000, sse=54115.7, rms=0.038 (0.000%)
- 058: dt: 0.5000, sse=54284.8, rms=0.038 (0.000%)
- 059: dt: 0.5000, sse=54455.2, rms=0.037 (0.000%)
- 060: dt: 0.5000, sse=54578.9, rms=0.036 (0.000%)
- positioning took 4.0 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [95.50 206.50], gm=151.00+-18.50, and vertices in regions > 141.7
- 27156 surface locations found to contain inconsistent values (335 in, 26821 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=5794.1, rms=0.05
- 061: dt: 0.5000, sse=5785.9, rms=0.048 (0.000%)
- 062: dt: 0.5000, sse=5863.8, rms=0.043 (0.000%)
- 063: dt: 0.5000, sse=5926.2, rms=0.040 (0.000%)
- 064: dt: 0.5000, sse=5972.3, rms=0.038 (0.000%)
- 065: dt: 0.5000, sse=6001.2, rms=0.036 (0.000%)
- 066: dt: 0.5000, sse=6015.5, rms=0.035 (0.000%)
- 067: dt: 0.5000, sse=6021.8, rms=0.034 (0.000%)
- 068: dt: 0.5000, sse=6027.2, rms=0.033 (0.000%)
- 069: dt: 0.5000, sse=6031.6, rms=0.031 (0.000%)
- 070: dt: 0.5000, sse=6035.7, rms=0.030 (0.000%)
- 071: dt: 0.5000, sse=6041.1, rms=0.030 (0.000%)
- 072: dt: 0.5000, sse=6046.4, rms=0.029 (0.000%)
- 073: dt: 0.5000, sse=6050.8, rms=0.028 (0.000%)
- 074: dt: 0.5000, sse=6055.5, rms=0.027 (0.000%)
- 075: dt: 0.5000, sse=6062.3, rms=0.027 (0.000%)
- 076: dt: 0.5000, sse=6067.3, rms=0.026 (0.000%)
- 077: dt: 0.5000, sse=6071.7, rms=0.025 (0.000%)
- 078: dt: 0.5000, sse=6076.8, rms=0.025 (0.000%)
- 079: dt: 0.5000, sse=6079.5, rms=0.024 (0.000%)
- 080: dt: 0.5000, sse=6084.0, rms=0.024 (0.000%)
- 081: dt: 0.5000, sse=6088.6, rms=0.024 (0.000%)
- 082: dt: 0.5000, sse=6092.2, rms=0.023 (0.000%)
- 083: dt: 0.5000, sse=6095.0, rms=0.023 (0.000%)
- 084: dt: 0.5000, sse=6098.5, rms=0.023 (0.000%)
- 085: dt: 0.5000, sse=6101.7, rms=0.023 (0.000%)
- 086: dt: 0.5000, sse=6106.6, rms=0.022 (0.000%)
- 087: dt: 0.5000, sse=6110.4, rms=0.022 (0.000%)
- 088: dt: 0.5000, sse=6112.9, rms=0.022 (0.000%)
- 089: dt: 0.5000, sse=6114.1, rms=0.022 (0.000%)
- 090: dt: 0.5000, sse=6115.2, rms=0.022 (0.000%)
- positioning took 4.0 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
- 21416 surface locations found to contain inconsistent values (160 in, 21256 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/sub001/surf/lh.pial...
- writing smoothed curvature to lh.curv.pial
- 000: dt: 0.0000, sse=790.3, rms=0.04
- 091: dt: 0.5000, sse=787.5, rms=0.035 (0.000%)
- 092: dt: 0.5000, sse=770.9, rms=0.034 (0.000%)
- 093: dt: 0.5000, sse=757.7, rms=0.032 (0.000%)
- 094: dt: 0.5000, sse=745.2, rms=0.031 (0.000%)
- 095: dt: 0.5000, sse=734.6, rms=0.030 (0.000%)
- 096: dt: 0.5000, sse=728.0, rms=0.029 (0.000%)
- 097: dt: 0.5000, sse=721.5, rms=0.028 (0.000%)
- 098: dt: 0.5000, sse=716.7, rms=0.027 (0.000%)
- 099: dt: 0.5000, sse=711.9, rms=0.027 (0.000%)
- 100: dt: 0.5000, sse=707.6, rms=0.026 (0.000%)
- 101: dt: 0.5000, sse=702.6, rms=0.026 (0.000%)
- 102: dt: 0.5000, sse=698.8, rms=0.025 (0.000%)
- 103: dt: 0.5000, sse=695.9, rms=0.025 (0.000%)
- 104: dt: 0.5000, sse=692.2, rms=0.024 (0.000%)
- 105: dt: 0.5000, sse=688.8, rms=0.024 (0.000%)
- 106: dt: 0.5000, sse=686.2, rms=0.023 (0.000%)
- 107: dt: 0.5000, sse=683.9, rms=0.023 (0.000%)
- 108: dt: 0.5000, sse=681.8, rms=0.022 (0.000%)
- 109: dt: 0.5000, sse=679.7, rms=0.022 (0.000%)
- 110: dt: 0.5000, sse=678.6, rms=0.022 (0.000%)
- 111: dt: 0.5000, sse=677.0, rms=0.022 (0.000%)
- 112: dt: 0.5000, sse=676.8, rms=0.022 (0.000%)
- 113: dt: 0.5000, sse=675.3, rms=0.021 (0.000%)
- 114: dt: 0.5000, sse=673.8, rms=0.021 (0.000%)
- 115: dt: 0.5000, sse=672.6, rms=0.021 (0.000%)
- 116: dt: 0.5000, sse=672.1, rms=0.021 (0.000%)
- 117: dt: 0.5000, sse=670.9, rms=0.020 (0.000%)
- 118: dt: 0.5000, sse=669.9, rms=0.020 (0.000%)
- 119: dt: 0.5000, sse=669.3, rms=0.020 (0.000%)
- 120: dt: 0.5000, sse=668.7, rms=0.020 (0.000%)
- positioning took 4.0 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/lh.curv.pial
- writing smoothed area to lh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/lh.area.pial
- vertex spacing 1.00 +- 0.41 (0.07-->6.44) (max @ vno 107312 --> 107311)
- face area 0.40 +- 0.29 (0.00-->7.46)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 151296 vertices processed
- 25000 of 151296 vertices processed
- 50000 of 151296 vertices processed
- 75000 of 151296 vertices processed
- 100000 of 151296 vertices processed
- 125000 of 151296 vertices processed
- 150000 of 151296 vertices processed
- 0 of 151296 vertices processed
- 25000 of 151296 vertices processed
- 50000 of 151296 vertices processed
- 75000 of 151296 vertices processed
- 100000 of 151296 vertices processed
- 125000 of 151296 vertices processed
- 150000 of 151296 vertices processed
- thickness calculation complete, 224:466 truncations.
- 35870 vertices at 0 distance
- 111187 vertices at 1 distance
- 95714 vertices at 2 distance
- 34311 vertices at 3 distance
- 9031 vertices at 4 distance
- 2366 vertices at 5 distance
- 689 vertices at 6 distance
- 230 vertices at 7 distance
- 73 vertices at 8 distance
- 29 vertices at 9 distance
- 16 vertices at 10 distance
- 16 vertices at 11 distance
- 10 vertices at 12 distance
- 14 vertices at 13 distance
- 13 vertices at 14 distance
- 3 vertices at 15 distance
- 4 vertices at 16 distance
- 1 vertices at 17 distance
- 0 vertices at 18 distance
- 3 vertices at 19 distance
- 8 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/lh.thickness
- positioning took 19.6 minutes
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/scripts
- cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/rh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/rh.woT2.pial
- `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/rh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/rh.woT2.pial'
- mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub001 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/sub001/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/wm.mgz...
- 20765 bright wm thresholded.
- 275 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/rh.orig...
- computing class statistics...
- border white: 284449 voxels (1.70%)
- border gray 312227 voxels (1.86%)
- WM (94.0): 94.8 +- 9.6 [70.0 --> 110.0]
- GM (78.0) : 75.6 +- 13.1 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 48.9 (was 70)
- setting MAX_BORDER_WHITE to 115.6 (was 105)
- setting MIN_BORDER_WHITE to 62.0 (was 85)
- setting MAX_CSF to 35.9 (was 40)
- setting MAX_GRAY to 96.4 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 55.5 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 22.8 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=106, GM=62
- mean inside = 94.4, mean outside = 70.5
- smoothing surface for 5 iterations...
- reading initial white vertex positions from white...
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.89 +- 0.25 (0.03-->5.05) (max @ vno 151436 --> 151518)
- face area 0.33 +- 0.15 (0.00-->3.83)
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- deleting segment 0 with 3 points - only 0.00% unknown
- deleting segment 1 with 10 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 2 with 2 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 3 with 2 points - only 0.00% unknown
- deleting segment 5 with 51 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 6 with 2 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 7 with 3 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 8 with 3 points - only 0.00% unknown
- deleting segment 9 with 20 points - only 0.00% unknown
- deleting segment 10 with 292 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 11 with 1 points - only 0.00% unknown
- deleting segment 12 with 14 points - only 0.00% unknown
- deleting segment 14 with 5 points - only 0.00% unknown
- deleting segment 15 with 37 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- removing 1 vertex label from ripped group
- deleting segment 19 with 1 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 20 with 3 points - only 0.00% unknown
- deleting segment 21 with 6 points - only 0.00% unknown
- tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.89 +- 0.24 (0.06-->3.93) (max @ vno 107753 --> 108765)
- face area 0.33 +- 0.15 (0.00-->3.83)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4684834.0, rms=0.00
- rms = 1.59, time step reduction 1 of 3 to 0.250...
- rms = 0.40, time step reduction 2 of 3 to 0.125...
- rms = 0.05, time step reduction 3 of 3 to 0.062...
- 001: dt: 0.1250, sse=4684834.0, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- deleting segment 0 with 3 points - only 0.00% unknown
- deleting segment 1 with 10 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 2 with 2 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 3 with 2 points - only 0.00% unknown
- deleting segment 4 with 51 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 5 with 2 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 6 with 3 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 7 with 3 points - only 0.00% unknown
- deleting segment 8 with 20 points - only 0.00% unknown
- deleting segment 9 with 292 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 10 with 1 points - only 0.00% unknown
- deleting segment 11 with 14 points - only 0.00% unknown
- deleting segment 12 with 5 points - only 0.00% unknown
- deleting segment 13 with 37 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- removing 1 vertex label from ripped group
- deleting segment 15 with 1 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 16 with 3 points - only 0.00% unknown
- deleting segment 17 with 6 points - only 0.00% unknown
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.89 +- 0.24 (0.06-->3.93) (max @ vno 107753 --> 108765)
- face area 0.33 +- 0.15 (0.00-->3.83)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4684834.0, rms=0.00
- rms = 1.59, time step reduction 1 of 3 to 0.250...
- rms = 0.40, time step reduction 2 of 3 to 0.125...
- rms = 0.05, time step reduction 3 of 3 to 0.062...
- 002: dt: 0.1250, sse=4684834.0, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- deleting segment 0 with 3 points - only 0.00% unknown
- deleting segment 1 with 10 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 2 with 2 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 3 with 2 points - only 0.00% unknown
- deleting segment 4 with 51 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 5 with 2 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 6 with 3 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 7 with 3 points - only 0.00% unknown
- deleting segment 8 with 20 points - only 0.00% unknown
- deleting segment 9 with 292 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 10 with 1 points - only 0.00% unknown
- deleting segment 11 with 14 points - only 0.00% unknown
- deleting segment 12 with 5 points - only 0.00% unknown
- deleting segment 13 with 37 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- removing 1 vertex label from ripped group
- deleting segment 15 with 1 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 16 with 3 points - only 0.00% unknown
- deleting segment 17 with 6 points - only 0.00% unknown
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.89 +- 0.24 (0.06-->3.93) (max @ vno 107753 --> 108765)
- face area 0.33 +- 0.15 (0.00-->3.83)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4684834.0, rms=0.00
- rms = 1.59, time step reduction 1 of 3 to 0.250...
- rms = 0.40, time step reduction 2 of 3 to 0.125...
- rms = 0.05, time step reduction 3 of 3 to 0.062...
- 003: dt: 0.1250, sse=4684834.0, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- deleting segment 0 with 3 points - only 0.00% unknown
- deleting segment 1 with 10 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 2 with 2 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 3 with 2 points - only 0.00% unknown
- deleting segment 4 with 51 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 5 with 2 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 6 with 3 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 7 with 3 points - only 0.00% unknown
- deleting segment 8 with 20 points - only 0.00% unknown
- deleting segment 9 with 292 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 10 with 1 points - only 0.00% unknown
- deleting segment 11 with 14 points - only 0.00% unknown
- deleting segment 12 with 5 points - only 0.00% unknown
- deleting segment 13 with 37 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- removing 1 vertex label from ripped group
- deleting segment 15 with 1 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 16 with 3 points - only 0.00% unknown
- deleting segment 17 with 6 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=4684834.0, rms=0.00
- rms = 1.59, time step reduction 1 of 3 to 0.250...
- rms = 0.40, time step reduction 2 of 3 to 0.125...
- rms = 0.05, time step reduction 3 of 3 to 0.062...
- 004: dt: 0.1250, sse=4684834.0, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- 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 [93.80 204.20], gm=149.00+-18.40, and vertices in regions > 139.8
- 38771 surface locations found to contain inconsistent values (5698 in, 33073 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=548357.3, rms=0.20
- 001: dt: 0.5000, sse=513003.6, rms=0.197 (0.000%)
- 002: dt: 0.5000, sse=490252.4, rms=0.185 (0.000%)
- 003: dt: 0.5000, sse=475013.5, rms=0.175 (0.000%)
- 004: dt: 0.5000, sse=463665.2, rms=0.167 (0.000%)
- 005: dt: 0.5000, sse=455649.7, rms=0.161 (0.000%)
- 006: dt: 0.5000, sse=449396.4, rms=0.155 (0.000%)
- 007: dt: 0.5000, sse=444312.6, rms=0.150 (0.000%)
- 008: dt: 0.5000, sse=440257.7, rms=0.146 (0.000%)
- 009: dt: 0.5000, sse=437161.8, rms=0.143 (0.000%)
- 010: dt: 0.5000, sse=434563.6, rms=0.140 (0.000%)
- 011: dt: 0.5000, sse=432249.4, rms=0.137 (0.000%)
- 012: dt: 0.5000, sse=429998.3, rms=0.136 (0.000%)
- 013: dt: 0.5000, sse=428151.4, rms=0.134 (0.000%)
- 014: dt: 0.5000, sse=426178.2, rms=0.133 (0.000%)
- 015: dt: 0.5000, sse=424367.5, rms=0.132 (0.000%)
- 016: dt: 0.5000, sse=422617.6, rms=0.131 (0.000%)
- 017: dt: 0.5000, sse=421061.5, rms=0.131 (0.000%)
- 018: dt: 0.5000, sse=419447.2, rms=0.130 (0.000%)
- 019: dt: 0.5000, sse=417936.1, rms=0.130 (0.000%)
- 020: dt: 0.5000, sse=416401.3, rms=0.130 (0.000%)
- 021: dt: 0.5000, sse=414970.6, rms=0.130 (0.000%)
- 022: dt: 0.5000, sse=413991.7, rms=0.130 (0.000%)
- 023: dt: 0.5000, sse=412963.9, rms=0.130 (0.000%)
- 024: dt: 0.5000, sse=411243.4, rms=0.130 (0.000%)
- 025: dt: 0.5000, sse=410094.7, rms=0.130 (0.000%)
- 026: dt: 0.5000, sse=408768.5, rms=0.131 (0.000%)
- 027: dt: 0.5000, sse=407918.0, rms=0.131 (0.000%)
- 028: dt: 0.5000, sse=406828.3, rms=0.131 (0.000%)
- 029: dt: 0.5000, sse=405801.1, rms=0.131 (0.000%)
- 030: dt: 0.5000, sse=404359.2, rms=0.132 (0.000%)
- positioning took 4.1 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [92.00 206.00], gm=149.00+-19.00, and vertices in regions > 139.5
- 30556 surface locations found to contain inconsistent values (1471 in, 29085 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=41561.7, rms=0.10
- 031: dt: 0.5000, sse=41314.4, rms=0.103 (0.000%)
- 032: dt: 0.5000, sse=42265.9, rms=0.093 (0.000%)
- 033: dt: 0.5000, sse=43354.6, rms=0.086 (0.000%)
- 034: dt: 0.5000, sse=44273.2, rms=0.082 (0.000%)
- 035: dt: 0.5000, sse=45025.3, rms=0.077 (0.000%)
- 036: dt: 0.5000, sse=45731.3, rms=0.073 (0.000%)
- 037: dt: 0.5000, sse=46402.3, rms=0.069 (0.000%)
- 038: dt: 0.5000, sse=47031.6, rms=0.066 (0.000%)
- 039: dt: 0.5000, sse=47670.7, rms=0.063 (0.000%)
- 040: dt: 0.5000, sse=48262.2, rms=0.060 (0.000%)
- 041: dt: 0.5000, sse=48842.7, rms=0.057 (0.000%)
- 042: dt: 0.5000, sse=49378.8, rms=0.055 (0.000%)
- 043: dt: 0.5000, sse=49885.0, rms=0.052 (0.000%)
- 044: dt: 0.5000, sse=50360.8, rms=0.050 (0.000%)
- 045: dt: 0.5000, sse=50795.7, rms=0.048 (0.000%)
- 046: dt: 0.5000, sse=51220.7, rms=0.047 (0.000%)
- 047: dt: 0.5000, sse=51601.1, rms=0.045 (0.000%)
- 048: dt: 0.5000, sse=51949.8, rms=0.044 (0.000%)
- 049: dt: 0.5000, sse=52271.5, rms=0.042 (0.000%)
- 050: dt: 0.5000, sse=52590.2, rms=0.041 (0.000%)
- 051: dt: 0.5000, sse=52848.4, rms=0.040 (0.000%)
- 052: dt: 0.5000, sse=53109.6, rms=0.039 (0.000%)
- 053: dt: 0.5000, sse=53322.6, rms=0.038 (0.000%)
- 054: dt: 0.5000, sse=53544.5, rms=0.037 (0.000%)
- 055: dt: 0.5000, sse=53744.3, rms=0.036 (0.000%)
- 056: dt: 0.5000, sse=53928.3, rms=0.036 (0.000%)
- 057: dt: 0.5000, sse=54100.4, rms=0.035 (0.000%)
- 058: dt: 0.5000, sse=54256.3, rms=0.034 (0.000%)
- 059: dt: 0.5000, sse=54403.1, rms=0.034 (0.000%)
- 060: dt: 0.5000, sse=54544.0, rms=0.033 (0.000%)
- positioning took 4.0 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [92.00 206.00], gm=149.00+-19.00, and vertices in regions > 139.5
- 28773 surface locations found to contain inconsistent values (394 in, 28379 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=5693.0, rms=0.04
- 061: dt: 0.5000, sse=5687.8, rms=0.040 (0.000%)
- 062: dt: 0.5000, sse=5730.2, rms=0.037 (0.000%)
- 063: dt: 0.5000, sse=5762.4, rms=0.034 (0.000%)
- 064: dt: 0.5000, sse=5787.6, rms=0.032 (0.000%)
- 065: dt: 0.5000, sse=5805.1, rms=0.031 (0.000%)
- 066: dt: 0.5000, sse=5814.5, rms=0.030 (0.000%)
- 067: dt: 0.5000, sse=5821.2, rms=0.029 (0.000%)
- 068: dt: 0.5000, sse=5824.8, rms=0.028 (0.000%)
- 069: dt: 0.5000, sse=5828.6, rms=0.027 (0.000%)
- 070: dt: 0.5000, sse=5834.0, rms=0.026 (0.000%)
- 071: dt: 0.5000, sse=5838.9, rms=0.026 (0.000%)
- 072: dt: 0.5000, sse=5844.3, rms=0.025 (0.000%)
- 073: dt: 0.5000, sse=5848.4, rms=0.024 (0.000%)
- 074: dt: 0.5000, sse=5852.7, rms=0.024 (0.000%)
- 075: dt: 0.5000, sse=5857.2, rms=0.023 (0.000%)
- 076: dt: 0.5000, sse=5862.1, rms=0.023 (0.000%)
- 077: dt: 0.5000, sse=5866.3, rms=0.022 (0.000%)
- 078: dt: 0.5000, sse=5870.4, rms=0.022 (0.000%)
- 079: dt: 0.5000, sse=5874.2, rms=0.022 (0.000%)
- 080: dt: 0.5000, sse=5877.2, rms=0.021 (0.000%)
- 081: dt: 0.5000, sse=5880.2, rms=0.021 (0.000%)
- 082: dt: 0.5000, sse=5883.1, rms=0.021 (0.000%)
- 083: dt: 0.5000, sse=5886.6, rms=0.021 (0.000%)
- 084: dt: 0.5000, sse=5888.4, rms=0.020 (0.000%)
- 085: dt: 0.5000, sse=5890.5, rms=0.020 (0.000%)
- 086: dt: 0.5000, sse=5893.1, rms=0.020 (0.000%)
- 087: dt: 0.5000, sse=5895.1, rms=0.020 (0.000%)
- 088: dt: 0.5000, sse=5897.2, rms=0.020 (0.000%)
- 089: dt: 0.5000, sse=5898.6, rms=0.020 (0.000%)
- 090: dt: 0.5000, sse=5900.0, rms=0.020 (0.000%)
- positioning took 3.9 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [101.60 196.40], gm=149.00+-15.80, and vertices in regions > 141.1
- 15349 surface locations found to contain inconsistent values (8195 in, 7154 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/sub001/surf/rh.pial...
- writing smoothed curvature to rh.curv.pial
- 000: dt: 0.0000, sse=2338.1, rms=0.11
- 091: dt: 0.5000, sse=2229.1, rms=0.106 (0.000%)
- 092: dt: 0.5000, sse=1981.6, rms=0.098 (0.000%)
- 093: dt: 0.5000, sse=1791.5, rms=0.091 (0.000%)
- 094: dt: 0.5000, sse=1639.1, rms=0.085 (0.000%)
- 095: dt: 0.5000, sse=1517.5, rms=0.079 (0.000%)
- 096: dt: 0.5000, sse=1425.4, rms=0.075 (0.000%)
- 097: dt: 0.5000, sse=1352.8, rms=0.072 (0.000%)
- 098: dt: 0.5000, sse=1290.2, rms=0.068 (0.000%)
- 099: dt: 0.5000, sse=1233.3, rms=0.065 (0.000%)
- 100: dt: 0.5000, sse=1177.0, rms=0.062 (0.000%)
- 101: dt: 0.5000, sse=1126.4, rms=0.059 (0.000%)
- 102: dt: 0.5000, sse=1081.9, rms=0.056 (0.000%)
- 103: dt: 0.5000, sse=1042.5, rms=0.053 (0.000%)
- 104: dt: 0.5000, sse=1007.9, rms=0.051 (0.000%)
- 105: dt: 0.5000, sse=977.8, rms=0.048 (0.000%)
- 106: dt: 0.5000, sse=951.9, rms=0.046 (0.000%)
- 107: dt: 0.5000, sse=928.2, rms=0.044 (0.000%)
- 108: dt: 0.5000, sse=907.8, rms=0.042 (0.000%)
- 109: dt: 0.5000, sse=888.8, rms=0.040 (0.000%)
- 110: dt: 0.5000, sse=872.7, rms=0.039 (0.000%)
- 111: dt: 0.5000, sse=858.2, rms=0.037 (0.000%)
- 112: dt: 0.5000, sse=845.8, rms=0.036 (0.000%)
- 113: dt: 0.5000, sse=834.9, rms=0.034 (0.000%)
- 114: dt: 0.5000, sse=825.6, rms=0.033 (0.000%)
- 115: dt: 0.5000, sse=817.8, rms=0.032 (0.000%)
- 116: dt: 0.5000, sse=810.7, rms=0.031 (0.000%)
- 117: dt: 0.5000, sse=804.4, rms=0.030 (0.000%)
- 118: dt: 0.5000, sse=798.9, rms=0.029 (0.000%)
- 119: dt: 0.5000, sse=794.5, rms=0.029 (0.000%)
- 120: dt: 0.5000, sse=790.2, rms=0.028 (0.000%)
- positioning took 3.9 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/rh.curv.pial
- writing smoothed area to rh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/rh.area.pial
- vertex spacing 1.01 +- 0.41 (0.02-->5.93) (max @ vno 109885 --> 110923)
- face area 0.40 +- 0.29 (0.00-->5.83)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 151707 vertices processed
- 25000 of 151707 vertices processed
- 50000 of 151707 vertices processed
- 75000 of 151707 vertices processed
- 100000 of 151707 vertices processed
- 125000 of 151707 vertices processed
- 150000 of 151707 vertices processed
- 0 of 151707 vertices processed
- 25000 of 151707 vertices processed
- 50000 of 151707 vertices processed
- 75000 of 151707 vertices processed
- 100000 of 151707 vertices processed
- 125000 of 151707 vertices processed
- 150000 of 151707 vertices processed
- thickness calculation complete, 95:348 truncations.
- 37653 vertices at 0 distance
- 112668 vertices at 1 distance
- 95238 vertices at 2 distance
- 33088 vertices at 3 distance
- 8278 vertices at 4 distance
- 2292 vertices at 5 distance
- 638 vertices at 6 distance
- 215 vertices at 7 distance
- 77 vertices at 8 distance
- 26 vertices at 9 distance
- 13 vertices at 10 distance
- 22 vertices at 11 distance
- 13 vertices at 12 distance
- 7 vertices at 13 distance
- 7 vertices at 14 distance
- 4 vertices at 15 distance
- 4 vertices at 16 distance
- 5 vertices at 17 distance
- 9 vertices at 18 distance
- 4 vertices at 19 distance
- 3 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/rh.thickness
- positioning took 19.6 minutes
- #--------------------------------------------
- #@# Surf Volume lh Thu Aug 8 22:00:52 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf
- mris_calc -o lh.area.mid lh.area add lh.area.pial
- Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o lh.area.mid lh.area.mid div 2
- Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o lh.volume lh.area.mid mul lh.thickness
- Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ]
- #--------------------------------------------
- #@# Surf Volume rh Thu Aug 8 22:00:53 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf
- mris_calc -o rh.area.mid rh.area add rh.area.pial
- Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o rh.area.mid rh.area.mid div 2
- Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o rh.volume rh.area.mid mul rh.thickness
- Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ]
- #--------------------------------------------
- #@# Cortical ribbon mask Thu Aug 8 22:00:55 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri
- mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon sub001
- 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 = 44
- writing volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/ribbon.mgz
- writing ribbon files
- #--------------------------------------------
- #@# ASeg Stats Thu Aug 8 22:22:58 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001
- 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 sub001
- $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 sub001
- sysname Linux
- hostname snake1
- machine x86_64
- user fkaule
- UseRobust 0
- atlas_icv (eTIV) = 1282781 mm^3 (det: 1.518657 )
- Computing euler number
- orig.nofix lheno = -34, rheno = -28
- orig.nofix lhholes = 18, rhholes = 15
- Loading mri/aseg.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 256356.965 255377.000 diff= 980.0 pctdiff= 0.382
- rhCtxGM: 254460.406 253477.000 diff= 983.4 pctdiff= 0.386
- lhCtxWM: 254108.460 254249.000 diff= -140.5 pctdiff=-0.055
- rhCtxWM: 258558.317 258713.000 diff= -154.7 pctdiff=-0.060
- SubCortGMVol 72018.000
- SupraTentVol 1114201.148 (1111321.000) diff=2880.148 pctdiff=0.258
- SupraTentVolNotVent 1097078.148 (1094198.000) diff=2880.148 pctdiff=0.263
- BrainSegVol 1254375.000 (1252443.000) diff=1932.000 pctdiff=0.154
- BrainSegVolNotVent 1234286.000 (1235684.148) diff=-1398.148 pctdiff=-0.113
- BrainSegVolNotVent 1234286.000
- CerebellumVol 139818.000
- VentChorVol 17123.000
- 3rd4th5thCSF 2966.000
- CSFVol 1058.000, OptChiasmVol 246.000
- MaskVol 1716018.000
- 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 5987 5986.869
- 4 5 Left-Inf-Lat-Vent 65 65.030
- 5 7 Left-Cerebellum-White-Matter 18571 18571.271
- 6 8 Left-Cerebellum-Cortex 51548 51548.266
- 7 10 Left-Thalamus-Proper 9010 9010.481
- 8 11 Left-Caudate 4465 4464.711
- 9 12 Left-Putamen 7412 7411.996
- 10 13 Left-Pallidum 2349 2348.708
- 11 14 3rd-Ventricle 754 753.609
- 12 15 4th-Ventricle 1448 1448.056
- 13 16 Brain-Stem 24755 24755.311
- 14 17 Left-Hippocampus 4113 4113.229
- 15 18 Left-Amygdala 1871 1870.590
- 16 24 CSF 1063 1062.614
- 17 26 Left-Accumbens-area 1018 1017.827
- 18 28 Left-VentralDC 4843 4842.857
- 19 30 Left-vessel 131 130.594
- 20 31 Left-choroid-plexus 1309 1309.073
- 23 43 Right-Lateral-Ventricle 8240 8239.863
- 24 44 Right-Inf-Lat-Vent 121 121.010
- 25 46 Right-Cerebellum-White-Matter 19436 19436.025
- 26 47 Right-Cerebellum-Cortex 52909 52908.625
- 27 49 Right-Thalamus-Proper 7774 7773.903
- 28 50 Right-Caudate 4730 4730.403
- 29 51 Right-Putamen 6973 6973.300
- 30 52 Right-Pallidum 2922 2921.689
- 31 53 Right-Hippocampus 4330 4330.281
- 32 54 Right-Amygdala 2155 2155.312
- 33 58 Right-Accumbens-area 944 944.361
- 34 60 Right-VentralDC 4863 4863.024
- 35 62 Right-vessel 198 198.479
- 36 63 Right-choroid-plexus 1531 1531.125
- 37 72 5th-Ventricle 0 0.000
- 38 77 WM-hypointensities 1050 1049.629
- 39 78 Left-WM-hypointensities 0 0.000
- 40 79 Right-WM-hypointensities 0 0.000
- 41 80 non-WM-hypointensities 19 19.358
- 42 81 Left-non-WM-hypointensities 0 0.000
- 43 82 Right-non-WM-hypointensities 0 0.000
- 44 85 Optic-Chiasm 254 253.911
- 45 251 CC_Posterior 1078 1078.117
- 46 252 CC_Mid_Posterior 537 536.800
- 47 253 CC_Central 493 492.766
- 48 254 CC_Mid_Anterior 519 518.634
- 49 255 CC_Anterior 1059 1059.183
- Reporting on 45 segmentations
- mri_segstats done
- #-----------------------------------------
- #@# AParc-to-ASeg Thu Aug 8 22:26:01 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001
- mri_aparc2aseg --s sub001 --volmask
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- subject sub001
- outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/aparc+aseg.mgz
- useribbon 0
- baseoffset 0
- RipUnknown 0
- Reading lh white surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/lh.white
- Reading lh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/lh.pial
- Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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/sub001/surf/rh.white
- Reading rh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/rh.pial
- Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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/sub001/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/sub001/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 = 506402
- Used brute-force search on 0 voxels
- Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/aparc+aseg.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001
- mri_aparc2aseg --s sub001 --volmask --a2009s
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- subject sub001
- outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/aparc.a2009s+aseg.mgz
- useribbon 0
- baseoffset 10100
- RipUnknown 0
- Reading lh white surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/lh.white
- Reading lh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/lh.pial
- Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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/sub001/surf/rh.white
- Reading rh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/rh.pial
- Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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/sub001/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/sub001/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 = 506402
- Used brute-force search on 0 voxels
- Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/aparc.a2009s+aseg.mgz
- #-----------------------------------------
- #@# WMParc Thu Aug 8 22:31:26 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001
- mri_aparc2aseg --s sub001 --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 sub001
- 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/sub001/mri/aparc+aseg.mgz
- Reading lh white surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/lh.white
- Reading lh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/lh.pial
- Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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/sub001/surf/rh.white
- Reading rh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/rh.pial
- Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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/sub001/mri/ribbon.mgz
- Loading filled from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/filled.mgz
- Ripping vertices labeled as unkown
- Ripped 9250 vertices from left hemi
- Ripped 8948 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/sub001/mri/aseg.mgz
- Loading Ctx Seg File /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 = 1018022
- Used brute-force search on 576 voxels
- Fixing Parahip LH WM
- Found 8 clusters
- 0 k 1.000000
- 1 k 6.000000
- 2 k 1.000000
- 3 k 1766.000000
- 4 k 2.000000
- 5 k 15.000000
- 6 k 51.000000
- 7 k 6.000000
- Fixing Parahip RH WM
- Found 9 clusters
- 0 k 1.000000
- 1 k 1.000000
- 2 k 2.000000
- 3 k 1.000000
- 4 k 1906.000000
- 5 k 2.000000
- 6 k 1.000000
- 7 k 1.000000
- 8 k 1.000000
- Writing output aseg to mri/wmparc.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001
- 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 sub001 --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 sub001 --surf-wm-vol --ctab /opt/freesurfer/5.3.0/WMParcStatsLUT.txt --etiv
- sysname Linux
- hostname snake1
- machine x86_64
- user fkaule
- UseRobust 0
- atlas_icv (eTIV) = 1282781 mm^3 (det: 1.518657 )
- Loading mri/wmparc.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 256356.965 255377.000 diff= 980.0 pctdiff= 0.382
- rhCtxGM: 254460.406 253477.000 diff= 983.4 pctdiff= 0.386
- lhCtxWM: 254108.460 254249.000 diff= -140.5 pctdiff=-0.055
- rhCtxWM: 258558.317 258713.000 diff= -154.7 pctdiff=-0.060
- SubCortGMVol 72018.000
- SupraTentVol 1114201.148 (1111321.000) diff=2880.148 pctdiff=0.258
- SupraTentVolNotVent 1097078.148 (1094198.000) diff=2880.148 pctdiff=0.263
- BrainSegVol 1254375.000 (1252443.000) diff=1932.000 pctdiff=0.154
- BrainSegVolNotVent 1234286.000 (1235684.148) diff=-1398.148 pctdiff=-0.113
- BrainSegVolNotVent 1234286.000
- CerebellumVol 139818.000
- VentChorVol 17123.000
- 3rd4th5thCSF 2966.000
- CSFVol 1058.000, OptChiasmVol 246.000
- MaskVol 1716018.000
- 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 4125 4124.514
- 2 3002 wm-lh-caudalanteriorcingulate 4127 4126.857
- 3 3003 wm-lh-caudalmiddlefrontal 8822 8822.277
- 4 3004 wm-lh-corpuscallosum 0 0.000
- 5 3005 wm-lh-cuneus 2132 2131.703
- 6 3006 wm-lh-entorhinal 1279 1279.292
- 7 3007 wm-lh-fusiform 7992 7992.074
- 8 3008 wm-lh-inferiorparietal 14086 14086.069
- 9 3009 wm-lh-inferiortemporal 7747 7747.353
- 10 3010 wm-lh-isthmuscingulate 4144 4143.687
- 11 3011 wm-lh-lateraloccipital 8613 8612.626
- 12 3012 wm-lh-lateralorbitofrontal 6658 6657.572
- 13 3013 wm-lh-lingual 5569 5568.565
- 14 3014 wm-lh-medialorbitofrontal 2918 2917.942
- 15 3015 wm-lh-middletemporal 5631 5631.117
- 16 3016 wm-lh-parahippocampal 1796 1796.368
- 17 3017 wm-lh-paracentral 3834 3833.567
- 18 3018 wm-lh-parsopercularis 3588 3588.389
- 19 3019 wm-lh-parsorbitalis 1064 1063.724
- 20 3020 wm-lh-parstriangularis 3429 3429.421
- 21 3021 wm-lh-pericalcarine 3249 3248.807
- 22 3022 wm-lh-postcentral 8612 8612.201
- 23 3023 wm-lh-posteriorcingulate 5021 5021.263
- 24 3024 wm-lh-precentral 15077 15076.840
- 25 3025 wm-lh-precuneus 11412 11411.511
- 26 3026 wm-lh-rostralanteriorcingulate 3551 3551.454
- 27 3027 wm-lh-rostralmiddlefrontal 14455 14454.585
- 28 3028 wm-lh-superiorfrontal 20696 20696.264
- 29 3029 wm-lh-superiorparietal 12366 12365.697
- 30 3030 wm-lh-superiortemporal 7771 7770.802
- 31 3031 wm-lh-supramarginal 9423 9423.104
- 32 3032 wm-lh-frontalpole 151 150.624
- 33 3033 wm-lh-temporalpole 825 824.594
- 34 3034 wm-lh-transversetemporal 894 893.866
- 35 3035 wm-lh-insula 8709 8708.542
- 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 3918 3918.115
- 120 4002 wm-rh-caudalanteriorcingulate 3076 3075.843
- 121 4003 wm-rh-caudalmiddlefrontal 7833 7833.343
- 122 4004 wm-rh-corpuscallosum 0 0.000
- 123 4005 wm-rh-cuneus 2159 2159.260
- 124 4006 wm-rh-entorhinal 345 345.067
- 125 4007 wm-rh-fusiform 8309 8309.326
- 126 4008 wm-rh-inferiorparietal 14511 14510.939
- 127 4009 wm-rh-inferiortemporal 6886 6886.277
- 128 4010 wm-rh-isthmuscingulate 3906 3906.298
- 129 4011 wm-rh-lateraloccipital 8777 8776.586
- 130 4012 wm-rh-lateralorbitofrontal 7001 7000.897
- 131 4013 wm-rh-lingual 6042 6042.358
- 132 4014 wm-rh-medialorbitofrontal 4320 4319.557
- 133 4015 wm-rh-middletemporal 7154 7153.642
- 134 4016 wm-rh-parahippocampal 1931 1931.063
- 135 4017 wm-rh-paracentral 6012 6011.856
- 136 4018 wm-rh-parsopercularis 3572 3572.076
- 137 4019 wm-rh-parsorbitalis 1459 1458.895
- 138 4020 wm-rh-parstriangularis 4435 4434.688
- 139 4021 wm-rh-pericalcarine 2879 2879.316
- 140 4022 wm-rh-postcentral 8300 8299.562
- 141 4023 wm-rh-posteriorcingulate 3943 3943.160
- 142 4024 wm-rh-precentral 15467 15466.545
- 143 4025 wm-rh-precuneus 12361 12361.032
- 144 4026 wm-rh-rostralanteriorcingulate 2111 2111.143
- 145 4027 wm-rh-rostralmiddlefrontal 14868 14867.677
- 146 4028 wm-rh-superiorfrontal 21443 21443.166
- 147 4029 wm-rh-superiorparietal 13344 13344.303
- 148 4030 wm-rh-superiortemporal 7316 7315.699
- 149 4031 wm-rh-supramarginal 8483 8482.586
- 150 4032 wm-rh-frontalpole 326 326.381
- 151 4033 wm-rh-temporalpole 484 484.008
- 152 4034 wm-rh-transversetemporal 534 534.246
- 153 4035 wm-rh-insula 8867 8866.657
- 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 33764 33763.656
- 237 5002 Right-UnsegmentedWhiteMatter 38165 38164.652
- 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/sub001/label
- #--------------------------------------------
- #@# BA Labels lh Thu Aug 8 22:44:20 CEST 2013
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151296
- Number of reverse mapping hits = 389
- Checking for and removing duplicates
- Writing label file ./lh.BA1.label 4518
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151296
- Number of reverse mapping hits = 850
- Checking for and removing duplicates
- Writing label file ./lh.BA2.label 8759
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151296
- Number of reverse mapping hits = 285
- Checking for and removing duplicates
- Writing label file ./lh.BA3a.label 4362
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151296
- Number of reverse mapping hits = 470
- Checking for and removing duplicates
- Writing label file ./lh.BA3b.label 6453
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151296
- Number of reverse mapping hits = 701
- Checking for and removing duplicates
- Writing label file ./lh.BA4a.label 6485
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151296
- Number of reverse mapping hits = 507
- Checking for and removing duplicates
- Writing label file ./lh.BA4p.label 4577
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151296
- Number of reverse mapping hits = 2215
- Checking for and removing duplicates
- Writing label file ./lh.BA6.label 15804
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151296
- Number of reverse mapping hits = 505
- Checking for and removing duplicates
- Writing label file ./lh.BA44.label 4686
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151296
- Number of reverse mapping hits = 943
- Checking for and removing duplicates
- Writing label file ./lh.BA45.label 4365
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151296
- Number of reverse mapping hits = 1412
- Checking for and removing duplicates
- Writing label file ./lh.V1.label 6053
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151296
- Number of reverse mapping hits = 3048
- Checking for and removing duplicates
- Writing label file ./lh.V2.label 11162
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151296
- Number of reverse mapping hits = 423
- Checking for and removing duplicates
- Writing label file ./lh.MT.label 2441
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.perirhinal.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151296
- Number of reverse mapping hits = 175
- Checking for and removing duplicates
- Writing label file ./lh.perirhinal.label 1374
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.thresh.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151296
- Number of reverse mapping hits = 69
- Checking for and removing duplicates
- Writing label file ./lh.BA1.thresh.label 1083
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.thresh.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151296
- Number of reverse mapping hits = 319
- Checking for and removing duplicates
- Writing label file ./lh.BA2.thresh.label 2411
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.thresh.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151296
- Number of reverse mapping hits = 47
- Checking for and removing duplicates
- Writing label file ./lh.BA3a.thresh.label 1551
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.thresh.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151296
- Number of reverse mapping hits = 273
- Checking for and removing duplicates
- Writing label file ./lh.BA3b.thresh.label 2269
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.thresh.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151296
- Number of reverse mapping hits = 319
- Checking for and removing duplicates
- Writing label file ./lh.BA4a.thresh.label 2638
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.thresh.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151296
- Number of reverse mapping hits = 152
- Checking for and removing duplicates
- Writing label file ./lh.BA4p.thresh.label 1701
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.thresh.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151296
- Number of reverse mapping hits = 893
- Checking for and removing duplicates
- Writing label file ./lh.BA6.thresh.label 7928
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.thresh.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151296
- Number of reverse mapping hits = 232
- Checking for and removing duplicates
- Writing label file ./lh.BA44.thresh.label 2144
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.thresh.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151296
- Number of reverse mapping hits = 356
- Checking for and removing duplicates
- Writing label file ./lh.BA45.thresh.label 1507
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.thresh.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151296
- Number of reverse mapping hits = 1001
- Checking for and removing duplicates
- Writing label file ./lh.V1.thresh.label 4406
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.thresh.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151296
- Number of reverse mapping hits = 1321
- Checking for and removing duplicates
- Writing label file ./lh.V2.thresh.label 4655
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.thresh.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151296
- Number of reverse mapping hits = 56
- Checking for and removing duplicates
- Writing label file ./lh.MT.thresh.label 569
- mri_label2label: Done
- mris_label2annot --s sub001 --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/sub001/label
- cmdline mris_label2annot --s sub001 --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 snake1
- machine x86_64
- user fkaule
- subject sub001
- 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/sub001/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 105929 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/label/lh.BA.annot
- mris_label2annot --s sub001 --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/sub001/label
- cmdline mris_label2annot --s sub001 --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 snake1
- machine x86_64
- user fkaule
- subject sub001
- 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/sub001/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 125516 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/label/lh.BA.thresh.annot
- mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab sub001 lh white
- computing statistics for each annotation in ./lh.BA.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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
- 1219 691 2368 2.445 0.466 0.139 0.065 24 3.7 BA1
- 4555 2968 7548 2.344 0.435 0.123 0.034 53 6.7 BA2
- 1049 724 1041 1.899 0.384 0.135 0.040 8 1.7 BA3a
- 2751 1819 4251 2.070 0.546 0.134 0.041 36 4.6 BA3b
- 1870 1011 3482 2.800 0.512 0.120 0.141 151 6.7 BA4a
- 1471 967 2523 2.678 0.496 0.120 0.048 70 2.9 BA4p
- 11003 7087 24183 2.790 0.529 0.128 0.040 150 19.1 BA6
- 2728 1823 5413 2.618 0.405 0.126 0.037 33 4.2 BA44
- 3415 2308 6336 2.350 0.438 0.149 0.048 57 6.7 BA45
- 3670 2363 4411 1.842 0.438 0.163 0.107 179 17.0 V1
- 8674 5624 12384 2.079 0.461 0.164 0.061 163 21.7 V2
- 1843 1220 3055 2.264 0.411 0.152 0.048 31 3.5 MT
- 1119 787 2877 2.838 0.715 0.140 0.054 15 2.5 perirhinal
- mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab sub001 lh white
- computing statistics for each annotation in ./lh.BA.thresh.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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
- 691 367 1396 2.581 0.367 0.155 0.077 17 2.6 BA1
- 1941 1246 3275 2.346 0.452 0.107 0.028 18 2.2 BA2
- 858 598 805 1.852 0.347 0.143 0.045 8 1.6 BA3a
- 1812 1197 2407 1.842 0.428 0.125 0.037 21 2.7 BA3b
- 1917 1048 3527 2.826 0.505 0.119 0.143 207 7.1 BA4a
- 1157 779 1860 2.543 0.476 0.120 0.040 9 1.9 BA4p
- 5856 3690 13088 2.835 0.542 0.128 0.044 94 11.8 BA6
- 1675 1130 3461 2.620 0.401 0.134 0.043 24 3.0 BA44
- 1343 904 2839 2.459 0.443 0.156 0.047 24 2.7 BA45
- 3847 2496 4746 1.842 0.441 0.161 0.103 180 17.2 V1
- 4273 2748 5519 1.976 0.429 0.179 0.071 94 12.3 V2
- 410 284 706 2.314 0.413 0.138 0.039 6 0.6 MT
- #--------------------------------------------
- #@# BA Labels rh Thu Aug 8 22:52:51 CEST 2013
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151707
- Number of reverse mapping hits = 355
- Checking for and removing duplicates
- Writing label file ./rh.BA1.label 4317
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151707
- Number of reverse mapping hits = 491
- Checking for and removing duplicates
- Writing label file ./rh.BA2.label 7178
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151707
- Number of reverse mapping hits = 266
- Checking for and removing duplicates
- Writing label file ./rh.BA3a.label 4246
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151707
- Number of reverse mapping hits = 422
- Checking for and removing duplicates
- Writing label file ./rh.BA3b.label 4944
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151707
- Number of reverse mapping hits = 816
- Checking for and removing duplicates
- Writing label file ./rh.BA4a.label 6563
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151707
- Number of reverse mapping hits = 467
- Checking for and removing duplicates
- Writing label file ./rh.BA4p.label 4940
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151707
- Number of reverse mapping hits = 1523
- Checking for and removing duplicates
- Writing label file ./rh.BA6.label 13779
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151707
- Number of reverse mapping hits = 1090
- Checking for and removing duplicates
- Writing label file ./rh.BA44.label 8002
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151707
- Number of reverse mapping hits = 1449
- Checking for and removing duplicates
- Writing label file ./rh.BA45.label 6804
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151707
- Number of reverse mapping hits = 1736
- Checking for and removing duplicates
- Writing label file ./rh.V1.label 6463
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151707
- Number of reverse mapping hits = 3313
- Checking for and removing duplicates
- Writing label file ./rh.V2.label 11329
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151707
- Number of reverse mapping hits = 538
- Checking for and removing duplicates
- Writing label file ./rh.MT.label 2470
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.perirhinal.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151707
- Number of reverse mapping hits = 38
- Checking for and removing duplicates
- Writing label file ./rh.perirhinal.label 790
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.thresh.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151707
- Number of reverse mapping hits = 88
- Checking for and removing duplicates
- Writing label file ./rh.BA1.thresh.label 964
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.thresh.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151707
- Number of reverse mapping hits = 168
- Checking for and removing duplicates
- Writing label file ./rh.BA2.thresh.label 2856
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.thresh.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151707
- Number of reverse mapping hits = 85
- Checking for and removing duplicates
- Writing label file ./rh.BA3a.thresh.label 1783
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.thresh.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151707
- Number of reverse mapping hits = 277
- Checking for and removing duplicates
- Writing label file ./rh.BA3b.thresh.label 2460
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.thresh.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151707
- Number of reverse mapping hits = 311
- Checking for and removing duplicates
- Writing label file ./rh.BA4a.thresh.label 1699
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.thresh.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151707
- Number of reverse mapping hits = 143
- Checking for and removing duplicates
- Writing label file ./rh.BA4p.thresh.label 1632
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.thresh.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151707
- Number of reverse mapping hits = 684
- Checking for and removing duplicates
- Writing label file ./rh.BA6.thresh.label 7643
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.thresh.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151707
- Number of reverse mapping hits = 154
- Checking for and removing duplicates
- Writing label file ./rh.BA44.thresh.label 1166
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.thresh.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151707
- Number of reverse mapping hits = 273
- Checking for and removing duplicates
- Writing label file ./rh.BA45.thresh.label 1451
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.thresh.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151707
- Number of reverse mapping hits = 1116
- Checking for and removing duplicates
- Writing label file ./rh.V1.thresh.label 4348
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.thresh.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151707
- Number of reverse mapping hits = 1562
- Checking for and removing duplicates
- Writing label file ./rh.V2.thresh.label 4999
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.thresh.label --trgsubject sub001 --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 = sub001
- 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/sub001/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 151707
- Number of reverse mapping hits = 66
- Checking for and removing duplicates
- Writing label file ./rh.MT.thresh.label 334
- mri_label2label: Done
- mris_label2annot --s sub001 --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/sub001/label
- cmdline mris_label2annot --s sub001 --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 snake1
- machine x86_64
- user fkaule
- subject sub001
- 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/sub001/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 106613 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/label/rh.BA.annot
- mris_label2annot --s sub001 --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/sub001/label
- cmdline mris_label2annot --s sub001 --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 snake1
- machine x86_64
- user fkaule
- subject sub001
- 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/sub001/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 127079 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/label/rh.BA.thresh.annot
- mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab sub001 rh white
- computing statistics for each annotation in ./rh.BA.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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
- 974 559 2009 2.559 0.328 0.147 0.057 21 2.1 BA1
- 3255 2183 5028 2.154 0.402 0.118 0.032 31 4.5 BA2
- 1163 754 1129 1.825 0.459 0.127 0.037 9 1.8 BA3a
- 2261 1474 3077 1.796 0.454 0.118 0.035 24 3.5 BA3b
- 2102 1248 4036 2.849 0.384 0.109 0.104 38 8.0 BA4a
- 1345 884 2368 2.657 0.429 0.116 0.048 17 3.1 BA4p
- 9028 5863 19420 2.742 0.531 0.129 0.038 105 14.1 BA6
- 4085 2771 7552 2.521 0.439 0.128 0.036 45 6.1 BA44
- 5094 3367 9758 2.391 0.469 0.146 0.045 80 9.6 BA45
- 4125 2735 5163 1.803 0.413 0.165 0.086 92 15.5 V1
- 8925 5670 12983 2.129 0.492 0.158 0.059 165 21.6 V2
- 2227 1508 3640 2.217 0.398 0.139 0.048 30 4.1 MT
- 510 342 1495 2.875 0.790 0.156 0.073 12 1.9 perirhinal
- mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab sub001 rh white
- computing statistics for each annotation in ./rh.BA.thresh.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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
- 660 368 1382 2.536 0.322 0.141 0.060 13 1.6 BA1
- 1847 1233 3003 2.201 0.436 0.119 0.033 20 2.5 BA2
- 1034 662 911 1.784 0.433 0.125 0.037 8 1.6 BA3a
- 1858 1253 2272 1.666 0.362 0.108 0.028 15 2.3 BA3b
- 1374 775 2775 2.916 0.421 0.118 0.146 34 7.2 BA4a
- 1143 772 2034 2.724 0.422 0.113 0.048 14 2.6 BA4p
- 5628 3660 11907 2.691 0.543 0.127 0.036 63 8.5 BA6
- 957 658 1912 2.473 0.425 0.134 0.042 14 1.6 BA44
- 1282 848 2714 2.473 0.420 0.149 0.049 22 2.7 BA45
- 3908 2618 4819 1.793 0.416 0.163 0.085 83 14.7 V1
- 4648 2932 6222 2.024 0.481 0.171 0.066 100 12.9 V2
- 289 208 637 2.431 0.259 0.129 0.034 3 0.5 MT
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/label
- #--------------------------------------------
- #@# Ex-vivo Entorhinal Cortex Label lh Thu Aug 8 22:58:40 CEST 2013
- mris_spherical_average -erode 1 -orig white -t 0.4 -o sub001 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label
- painting output onto subject sub001.
- processing subject lh.EC_average...
- reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 1071 points to lh.entorhinal_exvivo.label...
- mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label sub001 lh white
- limiting computations to label ./lh.entorhinal_exvivo.label.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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
- 366 246 1111 2.865 0.740 0.143 0.068 5 1.2 ./lh.entorhinal_exvivo.label
- #--------------------------------------------
- #@# Ex-vivo Entorhinal Cortex Label rh Thu Aug 8 22:58:57 CEST 2013
- mris_spherical_average -erode 1 -orig white -t 0.4 -o sub001 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label
- painting output onto subject sub001.
- processing subject rh.EC_average...
- reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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 657 points to rh.entorhinal_exvivo.label...
- mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label sub001 rh white
- limiting computations to label ./rh.entorhinal_exvivo.label.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub001/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
- 247 153 736 2.896 0.753 0.173 0.085 7 1.0 ./rh.entorhinal_exvivo.label
- #------------------------------------------
- Started at Thu Aug 8 10:53:42 CEST 2013
- Ended at Thu Aug 8 22:59:17 CEST 2013
- #@#%# recon-all-run-time-hours 12.093
- recon-all -s sub001 finished without error at Thu Aug 8 22:59:17 CEST 2013
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