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- Thu Aug 8 10:54:16 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020
- /opt/freesurfer/5.3.0/bin/recon-all
- -i /home/data/exppsy/forrest_gump/openfmri.org/sub020/anatomy/highres001.nii.gz -cw256 -all -T2 /home/data/exppsy/forrest_gump/openfmri.org/sub020/anatomy/other/t2w001.nii.gz -T2pial -subjid sub020 -sd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- subjid sub020
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Actual FREESURFER_HOME /opt/freesurfer/5.3.0
- build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
- Linux snake6 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
- cputime unlimited
- filesize unlimited
- datasize unlimited
- stacksize unlimited
- coredumpsize 0 kbytes
- memoryuse unlimited
- vmemoryuse unlimited
- descriptors 1024
- memorylocked 64 kbytes
- maxproc unlimited
- maxlocks unlimited
- maxsignal 16382
- maxmessage 819200
- maxnice 0
- maxrtprio 0
- maxrttime unlimited
- total used free shared buffers cached
- Mem: 99201692 96979592 2222100 0 118440 94733892
- -/+ buffers/cache: 2127260 97074432
- Swap: 25165780 2780 25163000
- ########################################
- program versions used
- $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
- $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
- mri_convert -all-info
- ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- FLIRT version 5.5
- $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
- mri_convert --version
- stable5
- ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- Program nu_correct, built from:
- Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
- ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ======= NUMBER OF OPENMP THREADS = 1 =======
- ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $
- ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $
- ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:54:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: fkaule Machine: snake6 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- #######################################
- GCADIR /opt/freesurfer/5.3.0/average
- GCA RB_all_2008-03-26.gca
- GCASkull RB_all_withskull_2008-03-26.gca
- AvgCurvTif average.curvature.filled.buckner40.tif
- GCSDIR /opt/freesurfer/5.3.0/average
- GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
- #######################################
- -cw256 option is now persistent (remove with -clean-cw256)
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub020/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/orig/001.mgz
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub020/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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/sub020/anatomy/highres001.nii.gz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.998287, -0.0504193, 0.0296894)
- j_ras = (-0.0475266, 0.9947, 0.0911741)
- k_ras = (0.034129, -0.0896069, 0.995392)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/orig/001.mgz...
- #--------------------------------------------
- #@# T2/FLAIR Input Thu Aug 8 10:54:36 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub020/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/orig/T2raw.mgz
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub020/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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/sub020/anatomy/other/t2w001.nii.gz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.998287, -0.0504193, 0.0296894)
- j_ras = (-0.0475266, 0.9947, 0.0911741)
- k_ras = (0.034129, -0.0896069, 0.995392)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/orig/T2raw.mgz...
- #--------------------------------------------
- #@# MotionCor Thu Aug 8 10:54:52 CEST 2013
- Found 1 runs
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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/sub020/mri/orig/001.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/rawavg.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/orig.mgz --conform --cw256
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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/sub020/mri/rawavg.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.998287, -0.0504193, 0.0296894)
- j_ras = (-0.0475266, 0.9947, 0.0911741)
- k_ras = (0.034129, -0.0896069, 0.995392)
- 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/sub020/mri/orig.mgz...
- mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/talairach.xfm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/orig.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Talairach Thu Aug 8 10:55:28 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri
- mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
- talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
- cp transforms/talairach.auto.xfm transforms/talairach.xfm
- #--------------------------------------------
- #@# Talairach Failure Detection Thu Aug 8 10:58:19 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri
- talairach_afd -T 0.005 -xfm transforms/talairach.xfm
- talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6716, pval=0.3663 >= threshold=0.0050)
- awk -f /opt/freesurfer/5.3.0/bin/extract_talairach_avi_QA.awk /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/talairach_avi.log
- tal_QC_AZS /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/talairach_avi.log
- TalAviQA: 0.96577
- z-score: -2
- #--------------------------------------------
- #@# Nu Intensity Correction Thu Aug 8 10:58:19 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/sub020/mri
- /opt/freesurfer/5.3.0/bin/mri_nu_correct.mni
- --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
- nIters 2
- $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $
- Linux snake6 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
- Thu Aug 8 10:58:19 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.24677
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.24677/nu0.mnc -odt float
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.24677/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, 6.98492e-09, -3.72529e-09)
- j_ras = (3.72529e-09, 0, -1)
- k_ras = (-1.00117e-08, 1, 7.45058e-09)
- changing data type from uchar to float (noscale = 0)...
- writing to ./tmp.mri_nu_correct.mni.24677/nu0.mnc...
-
- --------------------------------------------------------
- Iteration 1 Thu Aug 8 10:58:23 CEST 2013
- nu_correct -clobber ./tmp.mri_nu_correct.mni.24677/nu0.mnc ./tmp.mri_nu_correct.mni.24677/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.24677/0/
- [fkaule@snake6:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/] [2013-08-08 10:58:23] 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.24677/0/ ./tmp.mri_nu_correct.mni.24677/nu0.mnc ./tmp.mri_nu_correct.mni.24677/nu1.imp
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Number of iterations: 25
- CV of field change: 0.00098862
- [fkaule@snake6:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/] [2013-08-08 10:58:54] running:
- /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.24677/nu0.mnc ./tmp.mri_nu_correct.mni.24677/0//template.mnc
- Transforming slices:......................................................................................Done
- Transforming slices:................................................................................................................................................................................................................................................................Done
-
-
- --------------------------------------------------------
- Iteration 2 Thu Aug 8 10:59:00 CEST 2013
- nu_correct -clobber ./tmp.mri_nu_correct.mni.24677/nu1.mnc ./tmp.mri_nu_correct.mni.24677/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.24677/1/
- [fkaule@snake6:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/] [2013-08-08 10:59:00] running:
- /opt/freesurfer/5.3.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.24677/1/ ./tmp.mri_nu_correct.mni.24677/nu1.mnc ./tmp.mri_nu_correct.mni.24677/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
- Processing:.................................................................Done
- Number of iterations: 20
- CV of field change: 0.00099029
- [fkaule@snake6:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/] [2013-08-08 10:59:27] running:
- /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.24677/nu1.mnc ./tmp.mri_nu_correct.mni.24677/1//template.mnc
- Transforming slices:......................................................................................Done
- Transforming slices:................................................................................................................................................................................................................................................................Done
-
-
-
- mri_binarize --i ./tmp.mri_nu_correct.mni.24677/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.24677/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/sub020/mri
- cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.24677/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.24677/ones.mgz
- sysname Linux
- hostname snake6
- machine x86_64
- user fkaule
- input ./tmp.mri_nu_correct.mni.24677/nu2.mnc
- frame 0
- nErode3d 0
- nErode2d 0
- output ./tmp.mri_nu_correct.mni.24677/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.24677/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.24677/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24677/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.24677/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.24677/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24677/input.mean.dat
- sysname Linux
- hostname snake6
- machine x86_64
- user fkaule
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.24677/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.24677/input.mean.dat
- mri_segstats done
- mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.24677/ones.mgz --i ./tmp.mri_nu_correct.mni.24677/nu2.mnc --sum ./tmp.mri_nu_correct.mni.24677/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24677/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.24677/ones.mgz --i ./tmp.mri_nu_correct.mni.24677/nu2.mnc --sum ./tmp.mri_nu_correct.mni.24677/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24677/output.mean.dat
- sysname Linux
- hostname snake6
- machine x86_64
- user fkaule
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.24677/ones.mgz
- Loading ./tmp.mri_nu_correct.mni.24677/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.24677/output.mean.dat
- mri_segstats done
- mris_calc -o ./tmp.mri_nu_correct.mni.24677/nu2.mnc ./tmp.mri_nu_correct.mni.24677/nu2.mnc mul .96658600609259052332
- Saving result to './tmp.mri_nu_correct.mni.24677/nu2.mnc' (type = MINC ) [ ok ]
- mri_convert ./tmp.mri_nu_correct.mni.24677/nu2.mnc nu.mgz --like orig.mgz
- mri_convert ./tmp.mri_nu_correct.mni.24677/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.24677/nu2.mnc...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, 6.98492e-09, -3.72529e-09)
- j_ras = (3.72529e-09, 0, -1)
- k_ras = (-1.00117e-08, 1, 7.45058e-09)
- INFO: transform src into the like-volume: orig.mgz
- writing to nu.mgz...
- mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz
- type change took 0 minutes and 7 seconds.
- mapping (10, 150) to ( 3, 110)
-
-
- Thu Aug 8 11:00:14 CEST 2013
- mri_nu_correct.mni done
- mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/talairach.xfm nu.mgz nu.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Intensity Normalization Thu Aug 8 11:00:16 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri
- mri_normalize -g 1 nu.mgz T1.mgz
- using max gradient = 1.000
- reading from nu.mgz...
- normalizing image...
- talairach transform
- 1.134 0.063 -0.037 4.292;
- -0.018 1.108 0.381 -37.256;
- 0.055 -0.431 1.152 -0.391;
- 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 108
- gm peak at 55 (55), valley at 36 (36)
- csf peak at 11, setting threshold to 40
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- ---------------------------------
- 3d normalization pass 2 of 2
- white matter peak found at 111
- white matter peak found at 110
- gm peak at 56 (56), valley at 36 (36)
- csf peak at 11, setting threshold to 41
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Done iterating ---------------------------------
- writing output to T1.mgz
- 3D bias adjustment took 2 minutes and 45 seconds.
- #--------------------------------------------
- #@# Skull Stripping Thu Aug 8 11:03:02 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri
- mri_em_register -skull nu.mgz /opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta
- ======= NUMBER OF OPENMP THREADS = 1 =======
- aligning to atlas containing skull, setting unknown_nbr_spacing = 5
- reading 1 input volumes...
- logging results to talairach_with_skull.log
- reading '/opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca'...
- average std = 23.1 using min determinant for regularization = 53.4
- 0 singular and 5702 ill-conditioned covariance matrices regularized
- reading 'nu.mgz'...
- freeing gibbs priors...done.
- bounding unknown intensity as < 20.2 or > 943.7
- total sample mean = 92.0 (1443 zeros)
- ************************************************
- spacing=8, using 3481 sample points, tol=1.00e-05...
- ************************************************
- register_mri: find_optimal_transform
- find_optimal_transform: nsamples 3481, passno 0, spacing 8
- resetting wm mean[0]: 117 --> 126
- resetting gm mean[0]: 74 --> 74
- input volume #1 is the most T1-like
- using real data threshold=7.0
- skull bounding box = (52, 20, 22) --> (200, 255, 200)
- using (101, 98, 111) as brain centroid...
- mean wm in atlas = 126, using box (83,69,89) --> (119, 127,132) to find MRI wm
- before smoothing, mri peak at 108
- after smoothing, mri peak at 108, scaling input intensities by 1.167
- scaling channel 0 by 1.16667
- initial log_p = -4.8
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -4.630169 @ (-9.091, 9.091, -9.091)
- max log p = -4.475038 @ (13.636, 4.545, 4.545)
- max log p = -4.406596 @ (-6.818, 2.273, -6.818)
- max log p = -4.375336 @ (1.136, 1.136, 3.409)
- max log p = -4.375336 @ (0.000, 0.000, 0.000)
- max log p = -4.370543 @ (-0.284, 0.852, -0.284)
- Found translation: (-1.4, 17.9, -8.2): log p = -4.371
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.4 (thresh=-4.4)
- 1.075 0.000 0.000 -10.959;
- 0.000 1.194 0.320 -31.203;
- 0.000 -0.275 1.028 17.035;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1)
- 1.236 0.000 0.000 -31.467;
- 0.000 1.373 0.368 -54.050;
- 0.000 -0.317 1.182 3.685;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.2500
- ****************************************
- Nine parameter search. iteration 2 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.1 (thresh=-4.1)
- 1.168 -0.004 0.004 -20.992;
- 0.002 1.288 0.380 -49.274;
- 0.001 -0.347 1.149 12.141;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 3 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.168 -0.004 0.004 -20.992;
- 0.002 1.264 0.373 -46.080;
- 0.001 -0.347 1.149 12.141;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 4 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.168 -0.004 0.004 -20.992;
- 0.002 1.264 0.373 -46.080;
- 0.001 -0.347 1.149 12.141;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.0625
- ****************************************
- Nine parameter search. iteration 5 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.164 -0.014 0.001 -19.576;
- 0.012 1.258 0.382 -47.176;
- 0.000 -0.359 1.150 13.192;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 6 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.165 -0.004 0.004 -21.113;
- 0.002 1.262 0.373 -45.879;
- 0.001 -0.348 1.152 11.929;
- 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
- 1.16504 -0.00400 0.00449 -21.11334;
- 0.00235 1.26202 0.37262 -45.87941;
- 0.00053 -0.34803 1.15167 11.92887;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 3481
- Quasinewton: input matrix
- 1.16504 -0.00400 0.00449 -21.11334;
- 0.00235 1.26202 0.37262 -45.87941;
- 0.00053 -0.34803 1.15167 11.92887;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 1.165 -0.004 0.004 -21.113;
- 0.002 1.262 0.373 -45.879;
- 0.001 -0.348 1.152 11.929;
- 0.000 0.000 0.000 1.000;
- pass 1, spacing 8: log(p) = -4.0 (old=-4.8)
- transform before final EM align:
- 1.165 -0.004 0.004 -21.113;
- 0.002 1.262 0.373 -45.879;
- 0.001 -0.348 1.152 11.929;
- 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
- 1.16504 -0.00400 0.00449 -21.11334;
- 0.00235 1.26202 0.37262 -45.87941;
- 0.00053 -0.34803 1.15167 11.92887;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 382743
- Quasinewton: input matrix
- 1.16504 -0.00400 0.00449 -21.11334;
- 0.00235 1.26202 0.37262 -45.87941;
- 0.00053 -0.34803 1.15167 11.92887;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = 4.5 tol 0.000000
- final transform:
- 1.165 -0.004 0.004 -21.113;
- 0.002 1.262 0.373 -45.879;
- 0.001 -0.348 1.152 11.929;
- 0.000 0.000 0.000 1.000;
- writing output transformation to transforms/talairach_with_skull.lta...
- registration took 33 minutes and 34 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=91 z=114 r=93
- first estimation of the main basin volume: 3442546 voxels
- Looking for seedpoints
- 2 found in the cerebellum
- 14 found in the rest of the brain
- global maximum in x=153, y=91, z=82, Imax=255
- CSF=13, 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=18284787713 voxels, voxel volume =1.000
- = 18284787713 mmm3 = 18284787.712 cm3
- done.
- PostAnalyze...Basin Prior
- 26 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=97, z=109, r=9853 iterations
- ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^
- GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=7 , nb = 45910
- RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=15 , nb = -1032704820
- LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=18 , nb = 1096518880
- RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=6 , nb = -1071815422
- LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = 1076637710
- OTHER CSF_MIN=0, CSF_intensity=9, CSF_MAX=34 , nb = 1078364416
-
- CSF_MAX TRANSITION GM_MIN GM
- GLOBAL
- before analyzing : 7, 10, 26, 50
- after analyzing : 7, 20, 26, 27
- RIGHT_CER
- before analyzing : 15, 16, 21, 57
- after analyzing : 15, 22, 25, 30
- LEFT_CER
- before analyzing : 18, 19, 23, 56
- after analyzing : 18, 23, 25, 31
- RIGHT_BRAIN
- before analyzing : 6, 8, 26, 50
- after analyzing : 6, 20, 26, 27
- LEFT_BRAIN
- before analyzing : 5, 7, 26, 50
- after analyzing : 5, 19, 26, 26
- OTHER
- before analyzing : 34, 56, 75, 95
- after analyzing : 34, 68, 75, 74
- mri_strip_skull: done peeling brain
- highly tesselated surface with 10242 vertices
- matching...72 iterations
- *********************VALIDATION*********************
- curvature mean = -0.013, std = 0.012
- curvature mean = 69.566, std = 7.656
- No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
- before rotation: sse = 2.46, sigma = 3.98
- after rotation: sse = 2.46, sigma = 3.98
- Localization of inacurate regions: Erosion-Dilation steps
- the sse mean is 2.49, its var is 3.28
- before Erosion-Dilatation 0.21% of inacurate vertices
- after Erosion-Dilatation 0.00% of inacurate vertices
- Validation of the shape of the surface done.
- Scaling of atlas fields onto current surface fields
- ********FINAL ITERATIVE TEMPLATE DEFORMATION********
- Compute Local values csf/gray
- Fine Segmentation...43 iterations
- mri_strip_skull: done peeling brain
- Brain Size = 1662415 voxels, voxel volume = 1.000 mm3
- = 1662415 mmm3 = 1662.415 cm3
- ******************************
- Saving brainmask.auto.mgz
- done
- cp brainmask.auto.mgz brainmask.mgz
- #-------------------------------------
- #@# EM Registration Thu Aug 8 11:37:04 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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=25.0
- skull bounding box = (60, 38, 35) --> (192, 173, 195)
- using (104, 83, 115) as brain centroid...
- mean wm in atlas = 107, using box (88,66,95) --> (120, 99,134) 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 = -4.4
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -4.042720 @ (-9.091, 27.273, -9.091)
- max log p = -3.866872 @ (4.545, -4.545, -4.545)
- max log p = -3.764352 @ (2.273, -6.818, 2.273)
- max log p = -3.757147 @ (3.409, 1.136, -1.136)
- max log p = -3.747304 @ (-1.705, 0.568, 3.977)
- max log p = -3.731718 @ (-0.852, 0.284, 0.284)
- Found translation: (-1.4, 17.9, -8.2): log p = -3.732
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p =-3.7 (thresh=-3.7)
- 1.075 0.000 0.000 -11.038;
- 0.000 1.194 0.320 -38.039;
- 0.000 -0.259 0.966 21.763;
- 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 =-3.5 (thresh=-3.5)
- 1.146 0.036 -0.136 -8.383;
- 0.000 1.105 0.296 -18.771;
- 0.140 -0.257 0.958 4.485;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 2 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4)
- 1.068 0.002 -0.009 -9.349;
- 0.000 1.187 0.318 -36.594;
- -0.010 -0.259 0.967 22.994;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 3 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4)
- 1.068 0.002 -0.009 -9.349;
- 0.000 1.187 0.318 -36.594;
- -0.010 -0.259 0.967 22.994;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.2500
- ****************************************
- Nine parameter search. iteration 4 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.2, old_max_log_p =-3.4 (thresh=-3.4)
- 1.087 -0.036 -0.019 -6.965;
- 0.035 1.142 0.306 -31.391;
- -0.011 -0.269 1.003 21.782;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 5 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2)
- 1.087 -0.036 -0.019 -6.965;
- 0.035 1.142 0.306 -31.391;
- -0.011 -0.269 1.003 21.782;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.0625
- ****************************************
- Nine parameter search. iteration 6 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2)
- 1.083 -0.048 -0.049 -1.454;
- 0.053 1.147 0.289 -32.762;
- 0.017 -0.251 1.007 15.575;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 7 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2)
- 1.084 -0.050 -0.040 -2.782;
- 0.053 1.142 0.305 -34.496;
- 0.007 -0.269 1.001 19.330;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 8 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2)
- 1.084 -0.050 -0.040 -2.782;
- 0.053 1.140 0.305 -34.316;
- 0.007 -0.268 0.999 19.431;
- 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
- 1.08388 -0.05005 -0.04041 -2.78171;
- 0.05280 1.14034 0.30478 -34.31595;
- 0.00693 -0.26849 0.99945 19.43078;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 2772
- Quasinewton: input matrix
- 1.08388 -0.05005 -0.04041 -2.78171;
- 0.05280 1.14034 0.30478 -34.31595;
- 0.00693 -0.26849 0.99945 19.43078;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 1.084 -0.050 -0.040 -2.782;
- 0.053 1.140 0.305 -34.316;
- 0.007 -0.268 0.999 19.431;
- 0.000 0.000 0.000 1.000;
- pass 1, spacing 8: log(p) = -3.2 (old=-4.4)
- transform before final EM align:
- 1.084 -0.050 -0.040 -2.782;
- 0.053 1.140 0.305 -34.316;
- 0.007 -0.268 0.999 19.431;
- 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
- 1.08388 -0.05005 -0.04041 -2.78171;
- 0.05280 1.14034 0.30478 -34.31595;
- 0.00693 -0.26849 0.99945 19.43078;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 312841
- Quasinewton: input matrix
- 1.08388 -0.05005 -0.04041 -2.78171;
- 0.05280 1.14034 0.30478 -34.31595;
- 0.00693 -0.26849 0.99945 19.43078;
- 0.00000 0.00000 0.00000 1.00000;
- dfp_em_step_func: 012: -log(p) = 3.9
- after pass:transform: ( 1.08, -0.05, -0.04, -2.78)
- ( 0.05, 1.14, 0.30, -34.32)
- ( 0.01, -0.27, 1.00, 19.43)
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization...
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 014: -log(p) = 3.9 tol 0.000000
- final transform:
- 1.084 -0.050 -0.040 -2.782;
- 0.053 1.140 0.305 -34.316;
- 0.007 -0.268 0.999 19.431;
- 0.000 0.000 0.000 1.000;
- writing output transformation to transforms/talairach.lta...
- registration took 34 minutes and 18 seconds.
- #--------------------------------------
- #@# CA Normalize Thu Aug 8 12:11:22 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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=25.0
- skull bounding box = (59, 38, 35) --> (192, 173, 195)
- using (103, 83, 115) as brain centroid...
- mean wm in atlas = 107, using box (87,66,95) --> (119, 99,134) 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
- 1.084 -0.050 -0.040 -2.782;
- 0.053 1.140 0.305 -34.316;
- 0.007 -0.268 0.999 19.431;
- 0.000 0.000 0.000 1.000;
- INFO: transform used
- finding control points in Left_Cerebral_White_Matter....
- found 41584 control points for structure...
- bounding box (124, 42, 39) --> (189, 143, 196)
- Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 175.0
- 0 of 39 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 40735 control points for structure...
- bounding box (67, 42, 38) --> (129, 138, 197)
- Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 175.0
- 0 of 13 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3012 control points for structure...
- bounding box (129, 119, 67) --> (175, 157, 117)
- Left_Cerebellum_White_Matter: limiting intensities to 96.0 --> 175.0
- 1 of 11 (9.1%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2764 control points for structure...
- bounding box (87, 119, 65) --> (129, 158, 119)
- Right_Cerebellum_White_Matter: limiting intensities to 93.0 --> 175.0
- 0 of 15 (0.0%) samples deleted
- finding control points in Brain_Stem....
- found 3520 control points for structure...
- bounding box (114, 108, 100) --> (144, 168, 128)
- Brain_Stem: limiting intensities to 87.0 --> 175.0
- 4 of 14 (28.6%) samples deleted
- using 92 total control points for intensity normalization...
- bias field = 0.950 +- 0.083
- 0 of 87 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 41584 control points for structure...
- bounding box (124, 42, 39) --> (189, 143, 196)
- Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 166.0
- 0 of 83 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 40735 control points for structure...
- bounding box (67, 42, 38) --> (129, 138, 197)
- Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 166.0
- 0 of 83 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3012 control points for structure...
- bounding box (129, 119, 67) --> (175, 157, 117)
- Left_Cerebellum_White_Matter: limiting intensities to 80.0 --> 166.0
- 0 of 65 (0.0%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2764 control points for structure...
- bounding box (87, 119, 65) --> (129, 158, 119)
- Right_Cerebellum_White_Matter: limiting intensities to 80.0 --> 166.0
- 0 of 42 (0.0%) samples deleted
- finding control points in Brain_Stem....
- found 3520 control points for structure...
- bounding box (114, 108, 100) --> (144, 168, 128)
- Brain_Stem: limiting intensities to 92.0 --> 166.0
- 39 of 58 (67.2%) samples deleted
- using 331 total control points for intensity normalization...
- bias field = 0.988 +- 0.053
- 2 of 292 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 41584 control points for structure...
- bounding box (124, 42, 39) --> (189, 143, 196)
- Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 163.0
- 0 of 187 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 40735 control points for structure...
- bounding box (67, 42, 38) --> (129, 138, 197)
- Right_Cerebral_White_Matter: limiting intensities to 94.0 --> 163.0
- 0 of 196 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3012 control points for structure...
- bounding box (129, 119, 67) --> (175, 157, 117)
- Left_Cerebellum_White_Matter: limiting intensities to 78.0 --> 163.0
- 0 of 61 (0.0%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2764 control points for structure...
- bounding box (87, 119, 65) --> (129, 158, 119)
- Right_Cerebellum_White_Matter: limiting intensities to 87.0 --> 163.0
- 8 of 35 (22.9%) samples deleted
- finding control points in Brain_Stem....
- found 3520 control points for structure...
- bounding box (114, 108, 100) --> (144, 168, 128)
- Brain_Stem: limiting intensities to 72.0 --> 163.0
- 0 of 100 (0.0%) samples deleted
- using 579 total control points for intensity normalization...
- bias field = 1.000 +- 0.051
- 2 of 571 control points discarded
- writing normalized volume to norm.mgz...
- writing control points to ctrl_pts.mgz
- freeing GCA...done.
- normalization took 2 minutes and 3 seconds.
- #--------------------------------------
- #@# CA Reg Thu Aug 8 12:13:25 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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) = 1.33 (predicted orig area = 6.0)
- label assignment complete, 0 changed (0.00%)
- freeing gibbs priors...done.
- average std[0] = 5.0
- **************** pass 1 of 1 ************************
- setting smoothness coefficient to 0.039
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.878, neg=0, invalid=96777
- 0001: dt=129.472000, rms=0.795 (9.458%), neg=0, invalid=96777
- 0002: dt=221.952000, rms=0.770 (3.090%), neg=0, invalid=96777
- 0003: dt=129.472000, rms=0.761 (1.229%), neg=0, invalid=96777
- 0004: dt=295.936000, rms=0.753 (0.931%), neg=0, invalid=96777
- 0005: dt=129.472000, rms=0.747 (0.915%), neg=0, invalid=96777
- 0006: dt=73.984000, rms=0.745 (0.158%), neg=0, invalid=96777
- 0007: dt=73.984000, rms=0.744 (0.232%), neg=0, invalid=96777
- 0008: dt=73.984000, rms=0.741 (0.363%), neg=0, invalid=96777
- 0009: dt=73.984000, rms=0.738 (0.446%), neg=0, invalid=96777
- 0010: dt=73.984000, rms=0.734 (0.478%), neg=0, invalid=96777
- 0011: dt=73.984000, rms=0.730 (0.508%), neg=0, invalid=96777
- 0012: dt=73.984000, rms=0.727 (0.499%), neg=0, invalid=96777
- 0013: dt=73.984000, rms=0.723 (0.479%), neg=0, invalid=96777
- 0014: dt=73.984000, rms=0.720 (0.438%), neg=0, invalid=96777
- 0015: dt=73.984000, rms=0.717 (0.416%), neg=0, invalid=96777
- 0016: dt=73.984000, rms=0.714 (0.397%), neg=0, invalid=96777
- 0017: dt=73.984000, rms=0.712 (0.384%), neg=0, invalid=96777
- 0018: dt=73.984000, rms=0.709 (0.369%), neg=0, invalid=96777
- 0019: dt=73.984000, rms=0.706 (0.351%), neg=0, invalid=96777
- 0020: dt=73.984000, rms=0.704 (0.306%), neg=0, invalid=96777
- 0021: dt=73.984000, rms=0.702 (0.300%), neg=0, invalid=96777
- 0022: dt=73.984000, rms=0.700 (0.296%), neg=0, invalid=96777
- 0023: dt=73.984000, rms=0.698 (0.277%), neg=0, invalid=96777
- 0024: dt=73.984000, rms=0.696 (0.242%), neg=0, invalid=96777
- 0025: dt=73.984000, rms=0.695 (0.224%), neg=0, invalid=96777
- 0026: dt=73.984000, rms=0.693 (0.213%), neg=0, invalid=96777
- 0027: dt=73.984000, rms=0.692 (0.186%), neg=0, invalid=96777
- 0028: dt=73.984000, rms=0.691 (0.170%), neg=0, invalid=96777
- 0029: dt=73.984000, rms=0.690 (0.178%), neg=0, invalid=96777
- 0030: dt=73.984000, rms=0.688 (0.183%), neg=0, invalid=96777
- 0031: dt=73.984000, rms=0.687 (0.200%), neg=0, invalid=96777
- 0032: dt=73.984000, rms=0.686 (0.198%), neg=0, invalid=96777
- 0033: dt=73.984000, rms=0.685 (0.165%), neg=0, invalid=96777
- 0034: dt=73.984000, rms=0.684 (0.153%), neg=0, invalid=96777
- 0035: dt=73.984000, rms=0.683 (0.142%), neg=0, invalid=96777
- 0036: dt=73.984000, rms=0.682 (0.147%), neg=0, invalid=96777
- 0037: dt=73.984000, rms=0.681 (0.137%), neg=0, invalid=96777
- 0038: dt=73.984000, rms=0.680 (0.118%), neg=0, invalid=96777
- 0039: dt=73.984000, rms=0.679 (0.102%), neg=0, invalid=96777
- 0040: dt=887.808000, rms=0.678 (0.122%), neg=0, invalid=96777
- 0041: dt=8.092000, rms=0.678 (-0.004%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.678, neg=0, invalid=96777
- 0042: dt=23.120000, rms=0.678 (0.007%), neg=0, invalid=96777
- 0043: dt=32.368000, rms=0.678 (0.009%), neg=0, invalid=96777
- 0044: dt=92.480000, rms=0.678 (0.023%), neg=0, invalid=96777
- 0045: dt=369.920000, rms=0.677 (0.110%), neg=0, invalid=96777
- 0046: dt=369.920000, rms=0.677 (0.098%), neg=0, invalid=96777
- 0047: dt=369.920000, rms=0.677 (-0.061%), neg=0, invalid=96777
- setting smoothness coefficient to 0.154
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.683, neg=0, invalid=96777
- 0048: dt=145.152000, rms=0.670 (1.827%), neg=0, invalid=96777
- 0049: dt=82.944000, rms=0.665 (0.781%), neg=0, invalid=96777
- 0050: dt=36.288000, rms=0.660 (0.802%), neg=0, invalid=96777
- 0051: dt=15.552000, rms=0.659 (0.107%), neg=0, invalid=96777
- 0052: dt=15.552000, rms=0.658 (0.117%), neg=0, invalid=96777
- 0053: dt=15.552000, rms=0.657 (0.189%), neg=0, invalid=96777
- 0054: dt=15.552000, rms=0.655 (0.298%), neg=0, invalid=96777
- 0055: dt=15.552000, rms=0.653 (0.396%), neg=0, invalid=96777
- 0056: dt=15.552000, rms=0.650 (0.460%), neg=0, invalid=96777
- 0057: dt=15.552000, rms=0.647 (0.462%), neg=0, invalid=96777
- 0058: dt=15.552000, rms=0.644 (0.447%), neg=0, invalid=96777
- 0059: dt=15.552000, rms=0.641 (0.416%), neg=0, invalid=96777
- 0060: dt=15.552000, rms=0.638 (0.405%), neg=0, invalid=96777
- 0061: dt=15.552000, rms=0.636 (0.399%), neg=0, invalid=96777
- 0062: dt=15.552000, rms=0.633 (0.393%), neg=0, invalid=96777
- 0063: dt=15.552000, rms=0.631 (0.380%), neg=0, invalid=96777
- 0064: dt=15.552000, rms=0.629 (0.342%), neg=0, invalid=96777
- 0065: dt=15.552000, rms=0.627 (0.304%), neg=0, invalid=96777
- 0066: dt=15.552000, rms=0.625 (0.270%), neg=0, invalid=96777
- 0067: dt=15.552000, rms=0.624 (0.253%), neg=0, invalid=96777
- 0068: dt=15.552000, rms=0.622 (0.251%), neg=0, invalid=96777
- 0069: dt=15.552000, rms=0.621 (0.246%), neg=0, invalid=96777
- 0070: dt=15.552000, rms=0.619 (0.222%), neg=0, invalid=96777
- 0071: dt=15.552000, rms=0.618 (0.192%), neg=0, invalid=96777
- 0072: dt=15.552000, rms=0.617 (0.157%), neg=0, invalid=96777
- 0073: dt=15.552000, rms=0.616 (0.146%), neg=0, invalid=96777
- 0074: dt=15.552000, rms=0.615 (0.142%), neg=0, invalid=96777
- 0075: dt=15.552000, rms=0.614 (0.151%), neg=0, invalid=96777
- 0076: dt=15.552000, rms=0.613 (0.141%), neg=0, invalid=96777
- 0077: dt=15.552000, rms=0.613 (0.128%), neg=0, invalid=96777
- 0078: dt=15.552000, rms=0.612 (0.106%), neg=0, invalid=96777
- 0079: dt=15.552000, rms=0.611 (0.094%), neg=0, invalid=96777
- 0080: dt=331.776000, rms=0.611 (0.111%), neg=0, invalid=96777
- 0081: dt=25.920000, rms=0.611 (0.035%), neg=0, invalid=96777
- 0082: dt=25.920000, rms=0.610 (0.041%), neg=0, invalid=96777
- 0083: dt=25.920000, rms=0.610 (0.034%), neg=0, invalid=96777
- 0084: dt=25.920000, rms=0.610 (0.033%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.610, neg=0, invalid=96777
- 0085: dt=36.288000, rms=0.609 (0.108%), neg=0, invalid=96777
- 0086: dt=36.288000, rms=0.609 (0.018%), neg=0, invalid=96777
- 0087: dt=36.288000, rms=0.609 (0.032%), neg=0, invalid=96777
- 0088: dt=36.288000, rms=0.609 (0.003%), neg=0, invalid=96777
- 0089: dt=36.288000, rms=0.609 (-0.066%), neg=0, invalid=96777
- setting smoothness coefficient to 0.588
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.632, neg=0, invalid=96777
- 0090: dt=2.400000, rms=0.632 (0.009%), neg=0, invalid=96777
- 0091: dt=0.700000, rms=0.632 (-0.001%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.632, neg=0, invalid=96777
- 0092: dt=0.000000, rms=0.632 (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=0.701, neg=0, invalid=96777
- 0093: dt=5.036620, rms=0.683 (2.489%), neg=0, invalid=96777
- 0094: dt=1.909091, rms=0.683 (0.064%), neg=0, invalid=96777
- 0095: dt=1.909091, rms=0.683 (-0.017%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.683, neg=0, invalid=96777
- 0096: dt=0.000000, rms=0.683 (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=0.759, neg=0, invalid=96777
- 0097: dt=1.178112, rms=0.754 (0.661%), neg=0, invalid=96777
- 0098: dt=1.989418, rms=0.748 (0.777%), neg=0, invalid=96777
- 0099: dt=0.500000, rms=0.747 (0.098%), neg=0, invalid=96777
- 0100: dt=0.500000, rms=0.747 (0.035%), neg=0, invalid=96777
- 0101: dt=0.500000, rms=0.746 (0.031%), neg=0, invalid=96777
- 0102: dt=0.500000, rms=0.746 (-0.013%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.746, neg=0, invalid=96777
- 0103: dt=1.615385, rms=0.745 (0.249%), neg=0, invalid=96777
- 0104: dt=0.000000, rms=0.745 (0.001%), neg=0, invalid=96777
- 0105: dt=0.100000, rms=0.745 (-0.005%), 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=0.689, neg=0, invalid=96777
- 0106: dt=0.159191, rms=0.681 (1.216%), neg=0, invalid=96777
- 0107: dt=0.000000, rms=0.681 (0.004%), neg=0, invalid=96777
- 0108: dt=0.050000, rms=0.681 (-0.033%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.681, neg=0, invalid=96777
- 0109: dt=0.270428, rms=0.679 (0.315%), neg=0, invalid=96777
- 0110: dt=0.096000, rms=0.678 (0.149%), neg=0, invalid=96777
- 0111: dt=0.096000, rms=0.677 (0.040%), neg=0, invalid=96777
- 0112: dt=0.096000, rms=0.677 (0.073%), neg=0, invalid=96777
- 0113: dt=0.096000, rms=0.676 (0.115%), neg=0, invalid=96777
- 0114: dt=0.096000, rms=0.675 (0.135%), neg=0, invalid=96777
- 0115: dt=0.096000, rms=0.674 (0.129%), neg=0, invalid=96777
- 0116: dt=0.096000, rms=0.674 (0.115%), neg=0, invalid=96777
- 0117: dt=0.096000, rms=0.673 (0.095%), neg=0, invalid=96777
- 0118: dt=0.064000, rms=0.673 (0.001%), neg=0, invalid=96777
- 0119: dt=0.064000, rms=0.673 (-0.002%), neg=0, invalid=96777
- renormalizing by structure alignment....
- renormalizing input #0
- gca peak = 0.11725 (24)
- mri peak = 0.17857 ( 7)
- Left_Lateral_Ventricle (4): linear fit = 0.22 x + 0.0 (1012 voxels, overlap=0.006)
- Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (1012 voxels, peak = 5), gca=9.6
- gca peak = 0.14022 (22)
- mri peak = 0.13500 ( 7)
- Right_Lateral_Ventricle (43): linear fit = 0.25 x + 0.0 (662 voxels, overlap=0.006)
- Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (662 voxels, peak = 6), gca=8.8
- gca peak = 0.24234 (100)
- mri peak = 0.08852 (82)
- Right_Pallidum (52): linear fit = 0.81 x + 0.0 (371 voxels, overlap=0.049)
- Right_Pallidum (52): linear fit = 0.81 x + 0.0 (371 voxels, peak = 80), gca=80.5
- gca peak = 0.19192 (97)
- mri peak = 0.09091 (79)
- Left_Pallidum (13): linear fit = 0.77 x + 0.0 (260 voxels, overlap=0.101)
- Left_Pallidum (13): linear fit = 0.77 x + 0.0 (260 voxels, peak = 75), gca=75.2
- gca peak = 0.24007 (63)
- mri peak = 0.05483 (54)
- Right_Hippocampus (53): linear fit = 0.86 x + 0.0 (335 voxels, overlap=0.565)
- Right_Hippocampus (53): linear fit = 0.86 x + 0.0 (335 voxels, peak = 54), gca=53.9
- gca peak = 0.29892 (64)
- mri peak = 0.07377 (60)
- Left_Hippocampus (17): linear fit = 0.89 x + 0.0 (451 voxels, overlap=0.713)
- Left_Hippocampus (17): linear fit = 0.89 x + 0.0 (451 voxels, peak = 57), gca=57.3
- gca peak = 0.12541 (104)
- mri peak = 0.08711 (105)
- Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (56135 voxels, overlap=0.812)
- Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (56135 voxels, peak = 106), gca=105.6
- gca peak = 0.13686 (104)
- mri peak = 0.08394 (107)
- Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (60816 voxels, overlap=0.713)
- Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (60816 voxels, peak = 108), gca=107.6
- gca peak = 0.11691 (63)
- mri peak = 0.05243 (55)
- Left_Cerebral_Cortex (3): linear fit = 0.82 x + 0.0 (16267 voxels, overlap=0.186)
- Left_Cerebral_Cortex (3): linear fit = 0.82 x + 0.0 (16267 voxels, peak = 52), gca=52.0
- gca peak = 0.13270 (63)
- mri peak = 0.04961 (51)
- Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (17235 voxels, overlap=0.178)
- Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (17235 voxels, peak = 52), gca=52.0
- gca peak = 0.15182 (70)
- mri peak = 0.10708 (60)
- Right_Caudate (50): linear fit = 0.85 x + 0.0 (285 voxels, overlap=0.017)
- Right_Caudate (50): linear fit = 0.85 x + 0.0 (285 voxels, peak = 59), gca=59.2
- gca peak = 0.14251 (76)
- mri peak = 0.09273 (63)
- Left_Caudate (11): linear fit = 0.81 x + 0.0 (666 voxels, overlap=0.092)
- Left_Caudate (11): linear fit = 0.81 x + 0.0 (666 voxels, peak = 62), gca=61.9
- gca peak = 0.12116 (60)
- mri peak = 0.03651 (58)
- Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (7418 voxels, overlap=0.833)
- Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (7418 voxels, peak = 58), gca=57.9
- gca peak = 0.12723 (61)
- mri peak = 0.03361 (58)
- Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (7735 voxels, overlap=0.937)
- Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (7735 voxels, peak = 60), gca=60.1
- gca peak = 0.22684 (88)
- mri peak = 0.08678 (93)
- Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (5936 voxels, overlap=0.770)
- Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (5936 voxels, peak = 93), gca=92.8
- gca peak = 0.21067 (87)
- mri peak = 0.08625 (93)
- Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (4641 voxels, overlap=0.868)
- Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (4641 voxels, peak = 92), gca=91.8
- gca peak = 0.25455 (62)
- mri peak = 0.10692 (61)
- Left_Amygdala (18): linear fit = 0.96 x + 0.0 (323 voxels, overlap=0.994)
- Left_Amygdala (18): linear fit = 0.96 x + 0.0 (323 voxels, peak = 60), gca=59.8
- gca peak = 0.39668 (62)
- mri peak = 0.09488 (56)
- Right_Amygdala (54): linear fit = 0.90 x + 0.0 (275 voxels, overlap=0.552)
- Right_Amygdala (54): linear fit = 0.90 x + 0.0 (275 voxels, peak = 56), gca=56.1
- gca peak = 0.10129 (93)
- mri peak = 0.04968 (90)
- Left_Thalamus_Proper (10): linear fit = 0.96 x + 0.0 (4720 voxels, overlap=0.951)
- Left_Thalamus_Proper (10): linear fit = 0.96 x + 0.0 (4720 voxels, peak = 90), gca=89.7
- gca peak = 0.12071 (89)
- mri peak = 0.06209 (89)
- Right_Thalamus_Proper (49): linear fit = 0.95 x + 0.0 (3262 voxels, overlap=0.887)
- Right_Thalamus_Proper (49): linear fit = 0.95 x + 0.0 (3262 voxels, peak = 85), gca=85.0
- gca peak = 0.13716 (82)
- mri peak = 0.06023 (78)
- Left_Putamen (12): linear fit = 0.92 x + 0.0 (1914 voxels, overlap=0.631)
- Left_Putamen (12): linear fit = 0.92 x + 0.0 (1914 voxels, peak = 75), gca=75.0
- gca peak = 0.15214 (84)
- mri peak = 0.05888 (68)
- Right_Putamen (51): linear fit = 0.83 x + 0.0 (1682 voxels, overlap=0.094)
- Right_Putamen (51): linear fit = 0.83 x + 0.0 (1682 voxels, peak = 70), gca=70.1
- gca peak = 0.08983 (85)
- mri peak = 0.06853 (88)
- Brain_Stem (16): linear fit = 1.07 x + 0.0 (9934 voxels, overlap=0.778)
- Brain_Stem (16): linear fit = 1.07 x + 0.0 (9934 voxels, peak = 91), gca=90.5
- gca peak = 0.11809 (92)
- mri peak = 0.06771 (87)
- Right_VentralDC (60): linear fit = 0.98 x + 0.0 (716 voxels, overlap=0.882)
- Right_VentralDC (60): linear fit = 0.98 x + 0.0 (716 voxels, peak = 90), gca=89.7
- gca peak = 0.12914 (94)
- mri peak = 0.06400 (89)
- Left_VentralDC (28): linear fit = 0.99 x + 0.0 (875 voxels, overlap=0.973)
- Left_VentralDC (28): linear fit = 0.99 x + 0.0 (875 voxels, peak = 93), gca=92.6
- gca peak = 0.21100 (36)
- mri peak = 0.21451 (54)
- gca peak = 0.13542 (27)
- mri peak = 0.15758 ( 9)
- Fourth_Ventricle (15): linear fit = 0.37 x + 0.0 (390 voxels, overlap=0.027)
- Fourth_Ventricle (15): linear fit = 0.37 x + 0.0 (390 voxels, peak = 10), gca=9.9
- 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=0.709, neg=0, invalid=96777
- 0120: dt=129.472000, rms=0.703 (0.827%), neg=0, invalid=96777
- 0121: dt=129.472000, rms=0.700 (0.473%), neg=0, invalid=96777
- 0122: dt=92.480000, rms=0.699 (0.158%), neg=0, invalid=96777
- 0123: dt=129.472000, rms=0.697 (0.273%), neg=0, invalid=96777
- 0124: dt=73.984000, rms=0.696 (0.088%), neg=0, invalid=96777
- 0125: dt=369.920000, rms=0.694 (0.342%), neg=0, invalid=96777
- 0126: dt=32.368000, rms=0.693 (0.160%), neg=0, invalid=96777
- 0127: dt=55.488000, rms=0.693 (0.062%), neg=0, invalid=96777
- 0128: dt=1775.616000, rms=0.686 (0.957%), neg=0, invalid=96777
- 0129: dt=32.368000, rms=0.685 (0.147%), neg=0, invalid=96777
- 0130: dt=32.368000, rms=0.685 (0.039%), neg=0, invalid=96777
- 0131: dt=32.368000, rms=0.684 (0.020%), neg=0, invalid=96777
- 0132: dt=32.368000, rms=0.684 (0.018%), neg=0, invalid=96777
- 0133: dt=32.368000, rms=0.684 (0.031%), neg=0, invalid=96777
- 0134: dt=32.368000, rms=0.684 (0.042%), neg=0, invalid=96777
- 0135: dt=32.368000, rms=0.683 (0.058%), neg=0, invalid=96777
- 0136: dt=32.368000, rms=0.683 (0.056%), neg=0, invalid=96777
- 0137: dt=32.368000, rms=0.683 (0.057%), neg=0, invalid=96777
- 0138: dt=32.368000, rms=0.682 (0.056%), neg=0, invalid=96777
- 0139: dt=32.368000, rms=0.682 (0.055%), neg=0, invalid=96777
- 0140: dt=32.368000, rms=0.682 (0.051%), neg=0, invalid=96777
- 0141: dt=32.368000, rms=0.681 (0.053%), neg=0, invalid=96777
- 0142: dt=32.368000, rms=0.681 (0.057%), neg=0, invalid=96777
- 0143: dt=32.368000, rms=0.680 (0.071%), neg=0, invalid=96777
- 0144: dt=32.368000, rms=0.680 (0.071%), neg=0, invalid=96777
- 0145: dt=32.368000, rms=0.679 (0.066%), neg=0, invalid=96777
- 0146: dt=32.368000, rms=0.679 (0.060%), neg=0, invalid=96777
- 0147: dt=32.368000, rms=0.679 (0.051%), neg=0, invalid=96777
- 0148: dt=32.368000, rms=0.678 (0.044%), neg=0, invalid=96777
- 0149: dt=32.368000, rms=0.678 (0.040%), neg=0, invalid=96777
- 0150: dt=32.368000, rms=0.678 (0.042%), neg=0, invalid=96777
- 0151: dt=32.368000, rms=0.677 (0.047%), neg=0, invalid=96777
- 0152: dt=32.368000, rms=0.677 (0.045%), neg=0, invalid=96777
- 0153: dt=32.368000, rms=0.677 (0.041%), neg=0, invalid=96777
- 0154: dt=32.368000, rms=0.677 (0.041%), neg=0, invalid=96777
- 0155: dt=32.368000, rms=0.676 (0.040%), neg=0, invalid=96777
- 0156: dt=32.368000, rms=0.676 (0.038%), neg=0, invalid=96777
- 0157: dt=32.368000, rms=0.676 (0.039%), neg=0, invalid=96777
- 0158: dt=32.368000, rms=0.676 (0.041%), neg=0, invalid=96777
- 0159: dt=32.368000, rms=0.675 (0.041%), neg=0, invalid=96777
- 0160: dt=32.368000, rms=0.675 (0.039%), neg=0, invalid=96777
- 0161: dt=32.368000, rms=0.675 (0.035%), neg=0, invalid=96777
- 0162: dt=32.368000, rms=0.675 (0.032%), neg=0, invalid=96777
- 0163: dt=32.368000, rms=0.674 (0.031%), neg=0, invalid=96777
- 0164: dt=32.368000, rms=0.674 (0.029%), neg=0, invalid=96777
- 0165: dt=32.368000, rms=0.674 (0.029%), neg=0, invalid=96777
- 0166: dt=32.368000, rms=0.674 (0.032%), neg=0, invalid=96777
- 0167: dt=32.368000, rms=0.674 (0.033%), neg=0, invalid=96777
- 0168: dt=32.368000, rms=0.673 (0.030%), neg=0, invalid=96777
- 0169: dt=32.368000, rms=0.673 (0.029%), neg=0, invalid=96777
- 0170: dt=32.368000, rms=0.673 (0.026%), neg=0, invalid=96777
- 0171: dt=32.368000, rms=0.673 (0.025%), neg=0, invalid=96777
- 0172: dt=32.368000, rms=0.673 (0.027%), neg=0, invalid=96777
- 0173: dt=32.368000, rms=0.672 (0.029%), neg=0, invalid=96777
- 0174: dt=32.368000, rms=0.672 (0.030%), neg=0, invalid=96777
- 0175: dt=32.368000, rms=0.672 (0.027%), neg=0, invalid=96777
- 0176: dt=32.368000, rms=0.672 (0.024%), neg=0, invalid=96777
- 0177: dt=32.368000, rms=0.672 (0.024%), neg=0, invalid=96777
- 0178: dt=1479.680000, rms=0.671 (0.088%), neg=0, invalid=96777
- 0179: dt=32.368000, rms=0.671 (0.040%), neg=0, invalid=96777
- 0180: dt=32.368000, rms=0.671 (0.008%), neg=0, invalid=96777
- 0181: dt=32.368000, rms=0.671 (-0.012%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.671, neg=0, invalid=96777
- 0182: dt=129.472000, rms=0.670 (0.090%), neg=0, invalid=96777
- 0183: dt=221.952000, rms=0.669 (0.107%), neg=0, invalid=96777
- 0184: dt=55.488000, rms=0.669 (0.015%), neg=0, invalid=96777
- 0185: dt=55.488000, rms=0.669 (0.008%), neg=0, invalid=96777
- 0186: dt=55.488000, rms=0.669 (0.014%), neg=0, invalid=96777
- 0187: dt=55.488000, rms=0.669 (0.024%), neg=0, invalid=96777
- 0188: dt=55.488000, rms=0.669 (0.030%), neg=0, invalid=96777
- 0189: dt=55.488000, rms=0.669 (0.027%), neg=0, invalid=96777
- 0190: dt=55.488000, rms=0.668 (0.030%), neg=0, invalid=96777
- 0191: dt=55.488000, rms=0.668 (0.027%), neg=0, invalid=96777
- 0192: dt=55.488000, rms=0.668 (0.030%), neg=0, invalid=96777
- 0193: dt=55.488000, rms=0.668 (0.027%), neg=0, invalid=96777
- 0194: dt=55.488000, rms=0.668 (0.029%), neg=0, invalid=96777
- 0195: dt=55.488000, rms=0.668 (0.025%), neg=0, invalid=96777
- 0196: dt=55.488000, rms=0.667 (0.028%), neg=0, invalid=96777
- 0197: dt=55.488000, rms=0.667 (0.029%), neg=0, invalid=96777
- 0198: dt=55.488000, rms=0.667 (0.026%), neg=0, invalid=96777
- 0199: dt=55.488000, rms=0.667 (0.026%), neg=0, invalid=96777
- 0200: dt=55.488000, rms=0.667 (0.026%), neg=0, invalid=96777
- 0201: dt=55.488000, rms=0.666 (0.027%), neg=0, invalid=96777
- 0202: dt=55.488000, rms=0.666 (0.024%), neg=0, invalid=96777
- 0203: dt=55.488000, rms=0.666 (0.024%), neg=0, invalid=96777
- 0204: dt=55.488000, rms=0.666 (0.024%), neg=0, invalid=96777
- 0205: dt=55.488000, rms=0.666 (0.030%), neg=0, invalid=96777
- 0206: dt=55.488000, rms=0.666 (0.030%), neg=0, invalid=96777
- 0207: dt=55.488000, rms=0.665 (0.026%), neg=0, invalid=96777
- 0208: dt=55.488000, rms=0.665 (0.024%), neg=0, invalid=96777
- 0209: dt=55.488000, rms=0.665 (0.020%), neg=0, invalid=96777
- 0210: dt=295.936000, rms=0.665 (0.008%), neg=0, invalid=96777
- 0211: dt=295.936000, rms=0.665 (-0.025%), neg=0, invalid=96777
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.666, neg=0, invalid=96777
- 0212: dt=145.152000, rms=0.657 (1.274%), neg=0, invalid=96777
- 0213: dt=62.208000, rms=0.653 (0.630%), neg=0, invalid=96777
- 0214: dt=25.920000, rms=0.651 (0.295%), neg=0, invalid=96777
- 0215: dt=103.680000, rms=0.647 (0.540%), neg=0, invalid=96777
- 0216: dt=20.736000, rms=0.645 (0.328%), neg=0, invalid=96777
- 0217: dt=414.720000, rms=0.638 (1.063%), neg=0, invalid=96777
- 0218: dt=20.736000, rms=0.634 (0.773%), neg=0, invalid=96777
- 0219: dt=82.944000, rms=0.631 (0.393%), neg=0, invalid=96777
- 0220: dt=36.288000, rms=0.630 (0.100%), neg=0, invalid=96777
- 0221: dt=145.152000, rms=0.628 (0.379%), neg=0, invalid=96777
- 0222: dt=20.736000, rms=0.627 (0.110%), neg=0, invalid=96777
- 0223: dt=580.608000, rms=0.622 (0.893%), neg=0, invalid=96777
- 0224: dt=31.104000, rms=0.619 (0.416%), neg=0, invalid=96777
- 0225: dt=36.288000, rms=0.619 (0.097%), neg=0, invalid=96777
- 0226: dt=36.288000, rms=0.618 (0.069%), neg=0, invalid=96777
- 0227: dt=82.944000, rms=0.618 (0.072%), neg=0, invalid=96777
- 0228: dt=25.920000, rms=0.617 (0.099%), neg=0, invalid=96777
- 0229: dt=36.288000, rms=0.617 (0.052%), neg=0, invalid=96777
- 0230: dt=62.208000, rms=0.616 (0.086%), neg=0, invalid=96777
- 0231: dt=25.920000, rms=0.616 (0.051%), neg=0, invalid=96777
- 0232: dt=145.152000, rms=0.615 (0.160%), neg=0, invalid=96777
- 0233: dt=25.920000, rms=0.614 (0.096%), neg=0, invalid=96777
- 0234: dt=82.944000, rms=0.614 (0.083%), neg=0, invalid=96777
- 0235: dt=25.920000, rms=0.613 (0.076%), neg=0, invalid=96777
- 0236: dt=124.416000, rms=0.613 (0.097%), neg=0, invalid=96777
- 0237: dt=25.920000, rms=0.612 (0.102%), neg=0, invalid=96777
- 0238: dt=103.680000, rms=0.612 (0.088%), neg=0, invalid=96777
- 0239: dt=25.920000, rms=0.611 (0.078%), neg=0, invalid=96777
- 0240: dt=103.680000, rms=0.611 (0.095%), neg=0, invalid=96777
- 0241: dt=20.736000, rms=0.610 (0.064%), neg=0, invalid=96777
- 0242: dt=1658.880000, rms=0.605 (0.858%), neg=0, invalid=96777
- 0243: dt=20.736000, rms=0.600 (0.783%), neg=0, invalid=96777
- 0244: dt=36.288000, rms=0.599 (0.129%), neg=0, invalid=96777
- 0245: dt=36.288000, rms=0.599 (0.036%), neg=0, invalid=96777
- 0246: dt=36.288000, rms=0.599 (0.032%), neg=0, invalid=96777
- 0247: dt=36.288000, rms=0.599 (0.037%), neg=0, invalid=96777
- 0248: dt=36.288000, rms=0.599 (0.041%), neg=0, invalid=96777
- 0249: dt=36.288000, rms=0.598 (0.065%), neg=0, invalid=96777
- 0250: dt=36.288000, rms=0.598 (0.072%), neg=0, invalid=96777
- 0251: dt=36.288000, rms=0.597 (0.078%), neg=0, invalid=96777
- 0252: dt=36.288000, rms=0.597 (0.088%), neg=0, invalid=96777
- 0253: dt=36.288000, rms=0.596 (0.114%), neg=0, invalid=96777
- 0254: dt=36.288000, rms=0.595 (0.117%), neg=0, invalid=96777
- 0255: dt=36.288000, rms=0.595 (0.117%), neg=0, invalid=96777
- 0256: dt=36.288000, rms=0.594 (0.121%), neg=0, invalid=96777
- 0257: dt=36.288000, rms=0.593 (0.121%), neg=0, invalid=96777
- 0258: dt=36.288000, rms=0.592 (0.126%), neg=0, invalid=96777
- 0259: dt=36.288000, rms=0.592 (0.123%), neg=0, invalid=96777
- 0260: dt=36.288000, rms=0.591 (0.111%), neg=0, invalid=96777
- 0261: dt=36.288000, rms=0.590 (0.110%), neg=0, invalid=96777
- 0262: dt=36.288000, rms=0.590 (0.110%), neg=0, invalid=96777
- 0263: dt=36.288000, rms=0.589 (0.109%), neg=0, invalid=96777
- 0264: dt=36.288000, rms=0.589 (0.092%), neg=0, invalid=96777
- 0265: dt=36.288000, rms=0.588 (0.093%), neg=0, invalid=96777
- 0266: dt=36.288000, rms=0.587 (0.089%), neg=0, invalid=96777
- 0267: dt=36.288000, rms=0.587 (0.088%), neg=0, invalid=96777
- 0268: dt=36.288000, rms=0.586 (0.092%), neg=0, invalid=96777
- 0269: dt=36.288000, rms=0.586 (0.087%), neg=0, invalid=96777
- 0270: dt=36.288000, rms=0.585 (0.079%), neg=0, invalid=96777
- 0271: dt=36.288000, rms=0.585 (0.076%), neg=0, invalid=96777
- 0272: dt=36.288000, rms=0.585 (0.075%), neg=0, invalid=96777
- 0273: dt=36.288000, rms=0.584 (0.065%), neg=0, invalid=96777
- 0274: dt=36.288000, rms=0.584 (0.069%), neg=0, invalid=96777
- 0275: dt=36.288000, rms=0.583 (0.070%), neg=0, invalid=96777
- 0276: dt=36.288000, rms=0.583 (0.067%), neg=0, invalid=96777
- 0277: dt=36.288000, rms=0.583 (0.061%), neg=0, invalid=96777
- 0278: dt=36.288000, rms=0.582 (0.061%), neg=0, invalid=96777
- 0279: dt=36.288000, rms=0.582 (0.062%), neg=0, invalid=96777
- 0280: dt=36.288000, rms=0.582 (0.066%), neg=0, invalid=96777
- 0281: dt=36.288000, rms=0.581 (0.057%), neg=0, invalid=96777
- 0282: dt=36.288000, rms=0.581 (0.054%), neg=0, invalid=96777
- 0283: dt=36.288000, rms=0.581 (0.057%), neg=0, invalid=96777
- 0284: dt=36.288000, rms=0.580 (0.055%), neg=0, invalid=96777
- 0285: dt=36.288000, rms=0.580 (0.047%), neg=0, invalid=96777
- 0286: dt=36.288000, rms=0.580 (0.049%), neg=0, invalid=96777
- 0287: dt=36.288000, rms=0.579 (0.045%), neg=0, invalid=96777
- 0288: dt=36.288000, rms=0.579 (0.047%), neg=0, invalid=96777
- 0289: dt=36.288000, rms=0.579 (0.052%), neg=0, invalid=96777
- 0290: dt=36.288000, rms=0.579 (0.049%), neg=0, invalid=96777
- 0291: dt=36.288000, rms=0.578 (0.044%), neg=0, invalid=96777
- 0292: dt=36.288000, rms=0.578 (0.044%), neg=0, invalid=96777
- 0293: dt=36.288000, rms=0.578 (0.032%), neg=0, invalid=96777
- 0294: dt=36.288000, rms=0.578 (0.037%), neg=0, invalid=96777
- 0295: dt=36.288000, rms=0.577 (0.044%), neg=0, invalid=96777
- 0296: dt=36.288000, rms=0.577 (0.045%), neg=0, invalid=96777
- 0297: dt=36.288000, rms=0.577 (0.041%), neg=0, invalid=96777
- 0298: dt=36.288000, rms=0.577 (0.040%), neg=0, invalid=96777
- 0299: dt=36.288000, rms=0.576 (0.033%), neg=0, invalid=96777
- 0300: dt=36.288000, rms=0.576 (0.035%), neg=0, invalid=96777
- 0301: dt=36.288000, rms=0.576 (0.045%), neg=0, invalid=96777
- 0302: dt=36.288000, rms=0.576 (0.031%), neg=0, invalid=96777
- 0303: dt=36.288000, rms=0.576 (0.038%), neg=0, invalid=96777
- 0304: dt=36.288000, rms=0.575 (0.025%), neg=0, invalid=96777
- 0305: dt=36.288000, rms=0.575 (0.035%), neg=0, invalid=96777
- 0306: dt=36.288000, rms=0.575 (0.031%), neg=0, invalid=96777
- 0307: dt=36.288000, rms=0.575 (0.032%), neg=0, invalid=96777
- 0308: dt=36.288000, rms=0.575 (0.020%), neg=0, invalid=96777
- 0309: dt=36.288000, rms=0.575 (0.027%), neg=0, invalid=96777
- 0310: dt=36.288000, rms=0.574 (0.028%), neg=0, invalid=96777
- 0311: dt=36.288000, rms=0.574 (0.032%), neg=0, invalid=96777
- 0312: dt=36.288000, rms=0.574 (0.030%), neg=0, invalid=96777
- 0313: dt=36.288000, rms=0.574 (0.031%), neg=0, invalid=96777
- 0314: dt=36.288000, rms=0.574 (0.028%), neg=0, invalid=96777
- 0315: dt=36.288000, rms=0.574 (0.029%), neg=0, invalid=96777
- 0316: dt=36.288000, rms=0.574 (0.020%), neg=0, invalid=96777
- 0317: dt=36.288000, rms=0.573 (0.018%), neg=0, invalid=96777
- 0318: dt=124.416000, rms=0.573 (0.016%), neg=0, invalid=96777
- 0319: dt=124.416000, rms=0.573 (-0.161%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.573, neg=0, invalid=96777
- 0320: dt=103.680000, rms=0.572 (0.279%), neg=0, invalid=96777
- 0321: dt=25.920000, rms=0.571 (0.113%), neg=0, invalid=96777
- 0322: dt=36.288000, rms=0.571 (0.072%), neg=0, invalid=96777
- 0323: dt=103.680000, rms=0.570 (0.091%), neg=0, invalid=96777
- 0324: dt=20.736000, rms=0.570 (0.044%), neg=0, invalid=96777
- 0325: dt=20.736000, rms=0.570 (0.022%), neg=0, invalid=96777
- 0326: dt=20.736000, rms=0.570 (0.034%), neg=0, invalid=96777
- 0327: dt=20.736000, rms=0.569 (0.042%), neg=0, invalid=96777
- 0328: dt=20.736000, rms=0.569 (0.050%), neg=0, invalid=96777
- 0329: dt=20.736000, rms=0.569 (0.050%), neg=0, invalid=96777
- 0330: dt=20.736000, rms=0.568 (0.052%), neg=0, invalid=96777
- 0331: dt=20.736000, rms=0.568 (0.050%), neg=0, invalid=96777
- 0332: dt=20.736000, rms=0.568 (0.049%), neg=0, invalid=96777
- 0333: dt=20.736000, rms=0.568 (0.045%), neg=0, invalid=96777
- 0334: dt=20.736000, rms=0.567 (0.043%), neg=0, invalid=96777
- 0335: dt=20.736000, rms=0.567 (0.040%), neg=0, invalid=96777
- 0336: dt=20.736000, rms=0.567 (0.040%), neg=0, invalid=96777
- 0337: dt=20.736000, rms=0.567 (0.035%), neg=0, invalid=96777
- 0338: dt=20.736000, rms=0.567 (0.038%), neg=0, invalid=96777
- 0339: dt=20.736000, rms=0.566 (0.035%), neg=0, invalid=96777
- 0340: dt=20.736000, rms=0.566 (0.038%), neg=0, invalid=96777
- 0341: dt=20.736000, rms=0.566 (0.037%), neg=0, invalid=96777
- 0342: dt=20.736000, rms=0.566 (0.037%), neg=0, invalid=96777
- 0343: dt=20.736000, rms=0.566 (0.034%), neg=0, invalid=96777
- 0344: dt=20.736000, rms=0.565 (0.031%), neg=0, invalid=96777
- 0345: dt=20.736000, rms=0.565 (0.033%), neg=0, invalid=96777
- 0346: dt=20.736000, rms=0.565 (0.032%), neg=0, invalid=96777
- 0347: dt=20.736000, rms=0.565 (0.030%), neg=0, invalid=96777
- 0348: dt=20.736000, rms=0.565 (0.026%), neg=0, invalid=96777
- 0349: dt=20.736000, rms=0.564 (0.026%), neg=0, invalid=96777
- 0350: dt=20.736000, rms=0.564 (0.025%), neg=0, invalid=96777
- 0351: dt=20.736000, rms=0.564 (0.026%), neg=0, invalid=96777
- 0352: dt=20.736000, rms=0.564 (0.026%), neg=0, invalid=96777
- 0353: dt=20.736000, rms=0.564 (0.026%), neg=0, invalid=96777
- 0354: dt=20.736000, rms=0.564 (0.021%), neg=0, invalid=96777
- 0355: dt=20.736000, rms=0.564 (0.022%), neg=0, invalid=96777
- 0356: dt=20.736000, rms=0.564 (0.022%), neg=0, invalid=96777
- 0357: dt=20.736000, rms=0.563 (0.022%), neg=0, invalid=96777
- 0358: dt=20.736000, rms=0.563 (0.025%), neg=0, invalid=96777
- 0359: dt=20.736000, rms=0.563 (0.025%), neg=0, invalid=96777
- 0360: dt=20.736000, rms=0.563 (0.023%), neg=0, invalid=96777
- 0361: dt=20.736000, rms=0.563 (0.020%), neg=0, invalid=96777
- 0362: dt=124.416000, rms=0.563 (0.009%), neg=0, invalid=96777
- 0363: dt=124.416000, rms=0.563 (-0.082%), neg=0, invalid=96777
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.571, neg=0, invalid=96777
- 0364: dt=25.600000, rms=0.569 (0.351%), neg=0, invalid=96777
- 0365: dt=11.200000, rms=0.568 (0.149%), neg=0, invalid=96777
- 0366: dt=32.000000, rms=0.567 (0.257%), neg=0, invalid=96777
- 0367: dt=8.393443, rms=0.565 (0.230%), neg=0, invalid=96777
- 0368: dt=32.000000, rms=0.564 (0.283%), neg=0, invalid=96777
- 0369: dt=7.451264, rms=0.562 (0.252%), neg=0, invalid=96777
- 0370: dt=44.800000, rms=0.561 (0.313%), neg=0, invalid=96777
- 0371: dt=6.953678, rms=0.559 (0.311%), neg=0, invalid=96777
- 0372: dt=44.800000, rms=0.557 (0.374%), neg=0, invalid=96777
- 0373: dt=7.304348, rms=0.556 (0.211%), neg=0, invalid=96777
- 0374: dt=44.800000, rms=0.554 (0.298%), neg=0, invalid=96777
- 0375: dt=7.252336, rms=0.553 (0.211%), neg=0, invalid=96777
- 0376: dt=38.400000, rms=0.552 (0.223%), neg=0, invalid=96777
- 0377: dt=7.854545, rms=0.551 (0.190%), neg=0, invalid=96777
- 0378: dt=25.600000, rms=0.550 (0.143%), neg=0, invalid=96777
- 0379: dt=8.301887, rms=0.549 (0.129%), neg=0, invalid=96777
- 0380: dt=25.600000, rms=0.548 (0.120%), neg=0, invalid=96777
- 0381: dt=8.408163, rms=0.548 (0.128%), neg=0, invalid=96777
- 0382: dt=19.200000, rms=0.547 (0.101%), neg=0, invalid=96777
- 0383: dt=9.600000, rms=0.547 (0.090%), neg=0, invalid=96777
- 0384: dt=11.200000, rms=0.546 (0.086%), neg=0, invalid=96777
- 0385: dt=25.600000, rms=0.546 (0.085%), neg=0, invalid=96777
- 0386: dt=7.200000, rms=0.545 (0.106%), neg=0, invalid=96777
- 0387: dt=44.800000, rms=0.544 (0.155%), neg=0, invalid=96777
- 0388: dt=6.157576, rms=0.544 (0.148%), neg=0, invalid=96777
- 0389: dt=44.800000, rms=0.542 (0.196%), neg=0, invalid=96777
- 0390: dt=9.600000, rms=0.542 (0.082%), neg=0, invalid=96777
- 0391: dt=11.200000, rms=0.542 (0.066%), neg=0, invalid=96777
- 0392: dt=25.600000, rms=0.541 (0.070%), neg=0, invalid=96777
- 0393: dt=9.600000, rms=0.541 (0.079%), neg=0, invalid=96777
- 0394: dt=11.200000, rms=0.541 (0.044%), neg=0, invalid=96777
- 0395: dt=11.200000, rms=0.540 (0.060%), neg=0, invalid=96777
- 0396: dt=11.200000, rms=0.540 (0.096%), neg=0, invalid=96777
- 0397: dt=11.200000, rms=0.539 (0.115%), neg=0, invalid=96777
- 0398: dt=11.200000, rms=0.538 (0.158%), neg=0, invalid=96777
- 0399: dt=11.200000, rms=0.537 (0.183%), neg=0, invalid=96777
- 0400: dt=11.200000, rms=0.536 (0.197%), neg=0, invalid=96777
- 0401: dt=11.200000, rms=0.535 (0.213%), neg=0, invalid=96777
- 0402: dt=11.200000, rms=0.534 (0.220%), neg=0, invalid=96777
- 0403: dt=11.200000, rms=0.533 (0.223%), neg=0, invalid=96777
- 0404: dt=11.200000, rms=0.532 (0.217%), neg=0, invalid=96777
- 0405: dt=11.200000, rms=0.530 (0.209%), neg=0, invalid=96777
- 0406: dt=11.200000, rms=0.529 (0.218%), neg=0, invalid=96777
- 0407: dt=11.200000, rms=0.528 (0.208%), neg=0, invalid=96777
- 0408: dt=11.200000, rms=0.527 (0.199%), neg=0, invalid=96777
- 0409: dt=11.200000, rms=0.526 (0.181%), neg=0, invalid=96777
- 0410: dt=11.200000, rms=0.525 (0.162%), neg=0, invalid=96777
- 0411: dt=11.200000, rms=0.524 (0.167%), neg=0, invalid=96777
- 0412: dt=11.200000, rms=0.524 (0.151%), neg=0, invalid=96777
- 0413: dt=11.200000, rms=0.523 (0.140%), neg=0, invalid=96777
- 0414: dt=11.200000, rms=0.522 (0.121%), neg=0, invalid=96777
- 0415: dt=11.200000, rms=0.522 (0.120%), neg=0, invalid=96777
- 0416: dt=11.200000, rms=0.521 (0.112%), neg=0, invalid=96777
- 0417: dt=11.200000, rms=0.521 (0.092%), neg=0, invalid=96777
- 0418: dt=11.200000, rms=0.520 (0.088%), neg=0, invalid=96777
- 0419: dt=11.200000, rms=0.520 (0.089%), neg=0, invalid=96777
- 0420: dt=11.200000, rms=0.519 (0.081%), neg=0, invalid=96777
- 0421: dt=11.200000, rms=0.519 (0.081%), neg=0, invalid=96777
- 0422: dt=11.200000, rms=0.519 (0.065%), neg=0, invalid=96777
- 0423: dt=11.200000, rms=0.518 (0.068%), neg=0, invalid=96777
- 0424: dt=11.200000, rms=0.518 (0.061%), neg=0, invalid=96777
- 0425: dt=11.200000, rms=0.518 (0.062%), neg=0, invalid=96777
- 0426: dt=11.200000, rms=0.517 (0.042%), neg=0, invalid=96777
- 0427: dt=11.200000, rms=0.517 (0.050%), neg=0, invalid=96777
- 0428: dt=11.200000, rms=0.517 (0.045%), neg=0, invalid=96777
- 0429: dt=11.200000, rms=0.517 (0.050%), neg=0, invalid=96777
- 0430: dt=11.200000, rms=0.516 (0.042%), neg=0, invalid=96777
- 0431: dt=11.200000, rms=0.516 (0.040%), neg=0, invalid=96777
- 0432: dt=11.200000, rms=0.516 (0.045%), neg=0, invalid=96777
- 0433: dt=11.200000, rms=0.516 (0.043%), neg=0, invalid=96777
- 0434: dt=11.200000, rms=0.515 (0.042%), neg=0, invalid=96777
- 0435: dt=11.200000, rms=0.515 (0.044%), neg=0, invalid=96777
- 0436: dt=11.200000, rms=0.515 (0.030%), neg=0, invalid=96777
- 0437: dt=11.200000, rms=0.515 (0.038%), neg=0, invalid=96777
- 0438: dt=11.200000, rms=0.515 (0.037%), neg=0, invalid=96777
- 0439: dt=11.200000, rms=0.515 (0.026%), neg=0, invalid=96777
- 0440: dt=11.200000, rms=0.514 (0.044%), neg=0, invalid=96777
- 0441: dt=11.200000, rms=0.514 (0.049%), neg=0, invalid=96777
- 0442: dt=11.200000, rms=0.514 (0.036%), neg=0, invalid=96777
- 0443: dt=11.200000, rms=0.514 (0.030%), neg=0, invalid=96777
- 0444: dt=11.200000, rms=0.514 (0.030%), neg=0, invalid=96777
- 0445: dt=11.200000, rms=0.514 (0.023%), neg=0, invalid=96777
- 0446: dt=11.200000, rms=0.513 (0.025%), neg=0, invalid=96777
- 0447: dt=11.200000, rms=0.513 (0.033%), neg=0, invalid=96777
- 0448: dt=11.200000, rms=0.513 (0.024%), neg=0, invalid=96777
- 0449: dt=11.200000, rms=0.513 (0.032%), neg=0, invalid=96777
- 0450: dt=11.200000, rms=0.513 (0.025%), neg=0, invalid=96777
- 0451: dt=11.200000, rms=0.513 (0.028%), neg=0, invalid=96777
- 0452: dt=11.200000, rms=0.512 (0.031%), neg=0, invalid=96777
- 0453: dt=11.200000, rms=0.512 (0.027%), neg=0, invalid=96777
- 0454: dt=11.200000, rms=0.512 (0.024%), neg=0, invalid=96777
- 0455: dt=11.200000, rms=0.512 (0.028%), neg=0, invalid=96777
- 0456: dt=11.200000, rms=0.512 (0.018%), neg=0, invalid=96777
- 0457: dt=11.200000, rms=0.512 (0.018%), neg=0, invalid=96777
- 0458: dt=11.200000, rms=0.512 (0.024%), neg=0, invalid=96777
- 0459: dt=11.200000, rms=0.512 (0.013%), neg=0, invalid=96777
- 0460: dt=11.200000, rms=0.512 (0.012%), neg=0, invalid=96777
- 0461: dt=11.200000, rms=0.512 (0.002%), neg=0, invalid=96777
- 0462: dt=11.200000, rms=0.512 (0.007%), neg=0, invalid=96777
- 0463: dt=11.200000, rms=0.512 (-0.001%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.512, neg=0, invalid=96777
- 0464: dt=38.400000, rms=0.510 (0.364%), neg=0, invalid=96777
- 0465: dt=9.600000, rms=0.509 (0.058%), neg=0, invalid=96777
- 0466: dt=11.200000, rms=0.509 (0.058%), neg=0, invalid=96777
- 0467: dt=11.200000, rms=0.509 (0.033%), neg=0, invalid=96777
- 0468: dt=11.200000, rms=0.509 (0.028%), neg=0, invalid=96777
- 0469: dt=11.200000, rms=0.509 (0.037%), neg=0, invalid=96777
- 0470: dt=11.200000, rms=0.508 (0.034%), neg=0, invalid=96777
- 0471: dt=11.200000, rms=0.508 (0.033%), neg=0, invalid=96777
- 0472: dt=11.200000, rms=0.508 (0.034%), neg=0, invalid=96777
- 0473: dt=11.200000, rms=0.508 (0.001%), neg=0, invalid=96777
- 0474: dt=11.200000, rms=0.508 (-0.008%), neg=0, invalid=96777
- 0475: dt=4.800000, rms=0.508 (0.008%), neg=0, invalid=96777
- 0476: dt=32.000000, rms=0.508 (0.016%), neg=0, invalid=96777
- 0477: dt=9.600000, rms=0.508 (0.022%), neg=0, invalid=96777
- 0478: dt=2.800000, rms=0.508 (-0.002%), neg=0, invalid=96777
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.531, neg=0, invalid=96777
- 0479: dt=0.000000, rms=0.531 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.531, neg=0, invalid=96777
- 0480: dt=0.000000, rms=0.531 (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=0.576, neg=0, invalid=96777
- 0481: dt=1.220000, rms=0.572 (0.818%), neg=0, invalid=96777
- 0482: dt=0.250000, rms=0.572 (0.019%), neg=0, invalid=96777
- 0483: dt=0.250000, rms=0.572 (-0.015%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.572, neg=0, invalid=96777
- 0484: dt=0.455882, rms=0.571 (0.075%), neg=0, invalid=96777
- 0485: dt=0.256000, rms=0.571 (0.009%), neg=0, invalid=96777
- 0486: dt=0.256000, rms=0.571 (-0.006%), 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=0.522, neg=0, invalid=96777
- 0487: dt=0.173845, rms=0.515 (1.440%), neg=0, invalid=96777
- 0488: dt=0.112000, rms=0.512 (0.625%), neg=0, invalid=96777
- 0489: dt=0.128708, rms=0.509 (0.575%), neg=0, invalid=96777
- 0490: dt=0.117489, rms=0.507 (0.410%), neg=0, invalid=96777
- 0491: dt=0.112000, rms=0.505 (0.317%), neg=0, invalid=96777
- 0492: dt=0.112000, rms=0.504 (0.261%), neg=0, invalid=96777
- 0493: dt=0.112000, rms=0.503 (0.220%), neg=0, invalid=96777
- 0494: dt=0.112000, rms=0.502 (0.185%), neg=0, invalid=96777
- 0495: dt=0.112000, rms=0.501 (0.161%), neg=0, invalid=96777
- 0496: dt=0.448000, rms=0.498 (0.542%), neg=0, invalid=96777
- 0497: dt=0.112000, rms=0.498 (0.067%), neg=0, invalid=96777
- 0498: dt=0.028000, rms=0.498 (0.017%), neg=0, invalid=96777
- 0499: dt=0.028000, rms=0.498 (0.015%), neg=0, invalid=96777
- 0500: dt=0.028000, rms=0.498 (0.028%), neg=0, invalid=96777
- 0501: dt=0.028000, rms=0.497 (0.040%), neg=0, invalid=96777
- 0502: dt=0.028000, rms=0.497 (0.051%), neg=0, invalid=96777
- 0503: dt=0.028000, rms=0.497 (0.051%), neg=0, invalid=96777
- 0504: dt=0.028000, rms=0.497 (0.065%), neg=0, invalid=96777
- 0505: dt=0.028000, rms=0.496 (0.068%), neg=0, invalid=96777
- 0506: dt=0.028000, rms=0.496 (0.008%), neg=0, invalid=96777
- 0507: dt=0.028000, rms=0.496 (0.020%), neg=0, invalid=96777
- 0508: dt=0.028000, rms=0.496 (0.024%), neg=0, invalid=96777
- 0509: dt=0.028000, rms=0.496 (0.033%), neg=0, invalid=96777
- 0510: dt=0.028000, rms=0.496 (0.037%), neg=0, invalid=96777
- 0511: dt=0.028000, rms=0.495 (0.038%), neg=0, invalid=96777
- 0512: dt=0.028000, rms=0.495 (0.045%), neg=0, invalid=96777
- 0513: dt=0.028000, rms=0.495 (0.044%), neg=0, invalid=96777
- 0514: dt=0.028000, rms=0.495 (0.006%), neg=0, invalid=96777
- 0515: dt=0.028000, rms=0.495 (0.012%), neg=0, invalid=96777
- 0516: dt=0.028000, rms=0.495 (0.014%), neg=0, invalid=96777
- 0517: dt=0.028000, rms=0.495 (0.020%), neg=0, invalid=96777
- 0518: dt=0.028000, rms=0.495 (0.025%), neg=0, invalid=96777
- 0519: dt=0.028000, rms=0.495 (0.005%), neg=0, invalid=96777
- 0520: dt=0.028000, rms=0.495 (0.006%), neg=0, invalid=96777
- 0521: dt=0.028000, rms=0.494 (0.017%), neg=0, invalid=96777
- 0522: dt=0.028000, rms=0.494 (0.019%), neg=0, invalid=96777
- 0523: dt=0.028000, rms=0.494 (0.020%), neg=0, invalid=96777
- 0524: dt=0.028000, rms=0.494 (0.019%), neg=0, invalid=96777
- 0525: dt=0.320000, rms=0.494 (0.047%), neg=0, invalid=96777
- 0526: dt=0.007000, rms=0.494 (0.001%), neg=0, invalid=96777
- 0527: dt=0.007000, rms=0.494 (0.001%), neg=0, invalid=96777
- 0528: dt=0.007000, rms=0.494 (0.002%), neg=0, invalid=96777
- 0529: dt=0.007000, rms=0.494 (0.002%), neg=0, invalid=96777
- 0530: dt=0.007000, rms=0.494 (0.003%), neg=0, invalid=96777
- 0531: dt=0.007000, rms=0.494 (0.004%), neg=0, invalid=96777
- 0532: dt=0.007000, rms=0.494 (0.005%), neg=0, invalid=96777
- 0533: dt=0.007000, rms=0.494 (0.004%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.494, neg=0, invalid=96777
- 0534: dt=0.112000, rms=0.492 (0.295%), neg=0, invalid=96777
- 0535: dt=0.102876, rms=0.491 (0.208%), neg=0, invalid=96777
- 0536: dt=0.028000, rms=0.491 (0.040%), neg=0, invalid=96777
- 0537: dt=0.028000, rms=0.491 (0.041%), neg=0, invalid=96777
- 0538: dt=0.028000, rms=0.491 (0.040%), neg=0, invalid=96777
- 0539: dt=0.028000, rms=0.490 (0.072%), neg=0, invalid=96777
- 0540: dt=0.028000, rms=0.490 (0.094%), neg=0, invalid=96777
- 0541: dt=0.028000, rms=0.489 (0.112%), neg=0, invalid=96777
- 0542: dt=0.028000, rms=0.489 (0.124%), neg=0, invalid=96777
- 0543: dt=0.028000, rms=0.489 (0.013%), neg=0, invalid=96777
- 0544: dt=0.028000, rms=0.489 (0.023%), neg=0, invalid=96777
- 0545: dt=0.028000, rms=0.488 (0.029%), neg=0, invalid=96777
- 0546: dt=0.028000, rms=0.488 (0.040%), neg=0, invalid=96777
- 0547: dt=0.028000, rms=0.488 (0.043%), neg=0, invalid=96777
- 0548: dt=0.028000, rms=0.488 (0.046%), neg=0, invalid=96777
- 0549: dt=0.028000, rms=0.488 (0.041%), neg=0, invalid=96777
- 0550: dt=0.028000, rms=0.487 (0.034%), neg=0, invalid=96777
- 0551: dt=0.028000, rms=0.487 (0.035%), neg=0, invalid=96777
- 0552: dt=0.028000, rms=0.487 (0.028%), neg=0, invalid=96777
- 0553: dt=0.028000, rms=0.487 (0.025%), neg=0, invalid=96777
- 0554: dt=0.028000, rms=0.487 (0.016%), neg=0, invalid=96777
- 0555: dt=0.000000, rms=0.487 (0.000%), neg=0, invalid=96777
- 0556: dt=0.050000, rms=0.487 (-0.008%), 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=0.485, neg=0, invalid=96777
- 0557: dt=0.005645, rms=0.485 (0.000%), neg=0, invalid=96777
- 0558: dt=0.005645, rms=0.485 (-0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.485, neg=0, invalid=96777
- 0559: dt=129.472000, rms=0.485 (0.043%), neg=0, invalid=96777
- 0560: dt=129.472000, rms=0.485 (0.031%), neg=0, invalid=96777
- 0561: dt=129.472000, rms=0.485 (0.005%), neg=0, invalid=96777
- 0562: dt=129.472000, rms=0.484 (0.028%), neg=0, invalid=96777
- 0563: dt=129.472000, rms=0.484 (0.036%), neg=0, invalid=96777
- 0564: dt=129.472000, rms=0.484 (0.024%), neg=0, invalid=96777
- 0565: dt=129.472000, rms=0.484 (0.012%), neg=0, invalid=96777
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.484, neg=0, invalid=96777
- 0566: dt=36.288000, rms=0.484 (0.073%), neg=0, invalid=96777
- 0567: dt=31.104000, rms=0.484 (0.025%), neg=0, invalid=96777
- 0568: dt=31.104000, rms=0.484 (0.009%), neg=0, invalid=96777
- 0569: dt=31.104000, rms=0.484 (-0.020%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.484, neg=0, invalid=96777
- 0570: dt=103.680000, rms=0.482 (0.347%), neg=0, invalid=96777
- 0571: dt=36.288000, rms=0.482 (0.086%), neg=0, invalid=96777
- 0572: dt=36.288000, rms=0.481 (0.075%), neg=0, invalid=96777
- 0573: dt=36.288000, rms=0.481 (0.112%), neg=0, invalid=96777
- 0574: dt=36.288000, rms=0.480 (0.071%), neg=0, invalid=96777
- 0575: dt=36.288000, rms=0.479 (0.180%), neg=0, invalid=96777
- 0576: dt=36.288000, rms=0.479 (0.102%), neg=0, invalid=96777
- 0577: dt=36.288000, rms=0.478 (0.116%), neg=0, invalid=96777
- 0578: dt=36.288000, rms=0.478 (0.094%), neg=0, invalid=96777
- 0579: dt=25.920000, rms=0.478 (0.027%), neg=0, invalid=96777
- 0580: dt=25.920000, rms=0.478 (0.014%), neg=0, invalid=96777
- 0581: dt=25.920000, rms=0.478 (0.017%), neg=0, invalid=96777
- 0582: dt=25.920000, rms=0.477 (0.035%), neg=0, invalid=96777
- 0583: dt=25.920000, rms=0.477 (0.035%), neg=0, invalid=96777
- 0584: dt=25.920000, rms=0.477 (0.033%), neg=0, invalid=96777
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.477, neg=0, invalid=96777
- iter 0, gcam->neg = 2
- after 0 iterations, nbhd size=0, neg = 0
- 0585: dt=38.400000, rms=0.475 (0.579%), neg=0, invalid=96777
- iter 0, gcam->neg = 8
- after 7 iterations, nbhd size=1, neg = 0
- 0586: dt=38.400000, rms=0.473 (0.356%), neg=0, invalid=96777
- 0587: dt=7.262136, rms=0.472 (0.234%), neg=0, invalid=96777
- 0588: dt=7.262136, rms=0.471 (0.097%), neg=0, invalid=96777
- 0589: dt=7.262136, rms=0.471 (0.136%), neg=0, invalid=96777
- iter 0, gcam->neg = 3
- after 8 iterations, nbhd size=1, neg = 0
- 0590: dt=7.262136, rms=0.470 (0.168%), neg=0, invalid=96777
- 0591: dt=7.262136, rms=0.469 (0.173%), neg=0, invalid=96777
- iter 0, gcam->neg = 3
- after 0 iterations, nbhd size=0, neg = 0
- 0592: dt=7.262136, rms=0.468 (0.183%), neg=0, invalid=96777
- 0593: dt=7.262136, rms=0.467 (0.189%), neg=0, invalid=96777
- 0594: dt=7.262136, rms=0.467 (0.163%), neg=0, invalid=96777
- 0595: dt=7.262136, rms=0.466 (0.150%), neg=0, invalid=96777
- 0596: dt=7.262136, rms=0.465 (0.150%), neg=0, invalid=96777
- 0597: dt=7.262136, rms=0.465 (0.152%), neg=0, invalid=96777
- 0598: dt=7.262136, rms=0.464 (0.153%), neg=0, invalid=96777
- 0599: dt=7.262136, rms=0.463 (0.146%), neg=0, invalid=96777
- 0600: dt=7.262136, rms=0.462 (0.137%), neg=0, invalid=96777
- 0601: dt=7.262136, rms=0.462 (0.133%), neg=0, invalid=96777
- 0602: dt=7.262136, rms=0.461 (0.124%), neg=0, invalid=96777
- 0603: dt=7.262136, rms=0.461 (0.113%), neg=0, invalid=96777
- 0604: dt=44.800000, rms=0.460 (0.074%), neg=0, invalid=96777
- 0605: dt=44.800000, rms=0.460 (-0.120%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.460, neg=0, invalid=96777
- 0606: dt=44.800000, rms=0.457 (0.674%), neg=0, invalid=96777
- 0607: dt=7.780220, rms=0.456 (0.255%), neg=0, invalid=96777
- 0608: dt=11.200000, rms=0.456 (0.088%), neg=0, invalid=96777
- 0609: dt=11.200000, rms=0.455 (0.089%), neg=0, invalid=96777
- 0610: dt=11.200000, rms=0.455 (0.112%), neg=0, invalid=96777
- 0611: dt=11.200000, rms=0.454 (0.132%), neg=0, invalid=96777
- 0612: dt=11.200000, rms=0.454 (0.131%), neg=0, invalid=96777
- 0613: dt=11.200000, rms=0.453 (0.125%), neg=0, invalid=96777
- 0614: dt=11.200000, rms=0.453 (0.083%), neg=0, invalid=96777
- 0615: dt=11.200000, rms=0.452 (0.059%), neg=0, invalid=96777
- 0616: dt=11.200000, rms=0.452 (0.038%), neg=0, invalid=96777
- 0617: dt=11.200000, rms=0.452 (0.007%), neg=0, invalid=96777
- 0618: dt=11.200000, rms=0.452 (0.042%), neg=0, invalid=96777
- 0619: dt=11.200000, rms=0.452 (0.037%), neg=0, invalid=96777
- 0620: dt=11.200000, rms=0.452 (0.047%), neg=0, invalid=96777
- 0621: dt=11.200000, rms=0.452 (0.025%), neg=0, invalid=96777
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.456, neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0622: dt=2.333333, rms=0.455 (0.044%), neg=0, invalid=96777
- 0623: dt=1.008000, rms=0.455 (-0.012%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.455, neg=0, invalid=96777
- 0624: dt=4.032000, rms=0.455 (0.051%), neg=0, invalid=96777
- 0625: dt=3.456000, rms=0.455 (0.030%), neg=0, invalid=96777
- 0626: dt=3.456000, rms=0.455 (0.031%), neg=0, invalid=96777
- iter 0, gcam->neg = 13
- after 9 iterations, nbhd size=1, neg = 0
- 0627: dt=3.456000, rms=0.455 (0.019%), neg=0, invalid=96777
- 0628: dt=3.456000, rms=0.455 (-0.043%), 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
- 0629: 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
- 0630: dt=0.000000, rms=0.460 (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=0.452, neg=0, invalid=96777
- iter 0, gcam->neg = 689
- after 26 iterations, nbhd size=2, neg = 0
- 0631: dt=1.792000, rms=0.411 (8.981%), neg=0, invalid=96777
- 0632: dt=0.000109, rms=0.411 (0.007%), neg=0, invalid=96777
- 0633: dt=0.000109, rms=0.411 (-0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.411, neg=0, invalid=96777
- 0634: dt=0.000109, rms=0.411 (0.000%), neg=0, invalid=96777
- 0635: dt=0.000000, rms=0.411 (0.000%), neg=0, invalid=96777
- label assignment complete, 0 changed (0.00%)
- label assignment complete, 0 changed (0.00%)
- ***************** morphing with label term set to 0 *******************************
- **************** pass 1 of 1 ************************
- setting smoothness coefficient to 0.008
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.397, neg=0, invalid=96777
- 0636: dt=0.000000, rms=0.398 (-0.278%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.398, neg=0, invalid=96777
- 0637: dt=8.092000, rms=0.398 (0.001%), neg=0, invalid=96777
- 0638: dt=5.780000, rms=0.398 (0.000%), neg=0, invalid=96777
- 0639: dt=5.780000, rms=0.398 (-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=0.398, neg=0, invalid=96777
- 0640: dt=0.000000, rms=0.398 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.398, neg=0, invalid=96777
- 0641: dt=9.072000, rms=0.398 (0.006%), neg=0, invalid=96777
- 0642: dt=9.072000, rms=0.398 (0.002%), neg=0, invalid=96777
- 0643: dt=9.072000, rms=0.398 (-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=0.399, neg=0, invalid=96777
- iter 0, gcam->neg = 5
- after 34 iterations, nbhd size=4, neg = 0
- 0644: dt=8.000000, rms=0.398 (0.015%), neg=0, invalid=96777
- 0645: dt=0.031478, rms=0.398 (0.000%), neg=0, invalid=96777
- 0646: dt=0.031478, rms=0.398 (0.000%), neg=0, invalid=96777
- 0647: dt=0.031478, rms=0.398 (0.000%), neg=0, invalid=96777
- 0648: dt=0.031478, rms=0.398 (0.000%), neg=0, invalid=96777
- 0649: dt=0.031478, rms=0.398 (0.000%), neg=0, invalid=96777
- 0650: dt=0.031478, rms=0.398 (0.000%), neg=0, invalid=96777
- 0651: dt=0.031478, rms=0.398 (0.001%), neg=0, invalid=96777
- 0652: dt=0.031478, rms=0.398 (0.001%), neg=0, invalid=96777
- 0653: dt=0.031478, rms=0.398 (0.001%), neg=0, invalid=96777
- 0654: dt=0.031478, rms=0.398 (0.001%), neg=0, invalid=96777
- 0655: dt=0.031478, rms=0.398 (0.001%), neg=0, invalid=96777
- 0656: dt=0.031478, rms=0.398 (0.001%), neg=0, invalid=96777
- 0657: dt=0.031478, rms=0.398 (0.001%), neg=0, invalid=96777
- 0658: dt=0.031478, rms=0.398 (0.001%), neg=0, invalid=96777
- 0659: dt=0.031478, rms=0.398 (0.001%), neg=0, invalid=96777
- 0660: dt=0.031478, rms=0.398 (0.001%), neg=0, invalid=96777
- 0661: dt=0.031478, rms=0.398 (0.001%), neg=0, invalid=96777
- 0662: dt=0.031478, rms=0.398 (0.001%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.398, neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 5 iterations, nbhd size=1, neg = 0
- 0663: dt=38.400000, rms=0.397 (0.270%), neg=0, invalid=96777
- 0664: dt=25.600000, rms=0.397 (0.143%), neg=0, invalid=96777
- iter 0, gcam->neg = 3
- after 6 iterations, nbhd size=1, neg = 0
- 0665: dt=25.600000, rms=0.397 (-0.202%), neg=0, invalid=96777
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.399, neg=0, invalid=96777
- 0666: dt=0.252000, rms=0.399 (0.006%), neg=0, invalid=96777
- 0667: dt=0.063000, rms=0.399 (0.000%), neg=0, invalid=96777
- 0668: dt=0.063000, rms=0.399 (0.005%), neg=0, invalid=96777
- 0669: dt=0.063000, rms=0.399 (0.009%), neg=0, invalid=96777
- 0670: dt=0.063000, rms=0.399 (0.013%), neg=0, invalid=96777
- 0671: dt=0.063000, rms=0.399 (0.016%), neg=0, invalid=96777
- 0672: dt=0.063000, rms=0.399 (0.019%), neg=0, invalid=96777
- 0673: dt=0.063000, rms=0.399 (0.021%), neg=0, invalid=96777
- 0674: dt=0.063000, rms=0.399 (0.022%), neg=0, invalid=96777
- 0675: dt=0.063000, rms=0.398 (0.023%), neg=0, invalid=96777
- 0676: dt=0.063000, rms=0.398 (0.024%), neg=0, invalid=96777
- 0677: dt=0.063000, rms=0.398 (0.025%), neg=0, invalid=96777
- 0678: dt=0.063000, rms=0.398 (0.026%), neg=0, invalid=96777
- 0679: dt=0.063000, rms=0.398 (0.026%), neg=0, invalid=96777
- 0680: dt=0.063000, rms=0.398 (0.026%), neg=0, invalid=96777
- 0681: dt=0.063000, rms=0.398 (0.026%), neg=0, invalid=96777
- 0682: dt=0.063000, rms=0.398 (0.026%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.398, neg=0, invalid=96777
- iter 0, gcam->neg = 57
- after 200 iterations, nbhd size=1, neg = 1
- starting rms=0.002, neg=1, removing folds in lattice....
- iter 1, dt=0.000219: new neg 0, old_neg 1, delta 1, rms=0.002 (22.300%)
- 0683: dt=6.912000, rms=0.396 (0.350%), neg=0, invalid=96777
- iter 0, gcam->neg = 53
- after 200 iterations, nbhd size=2, neg = 1
- starting rms=0.002, neg=1, removing folds in lattice....
- iter 1, dt=0.000219: new neg 0, old_neg 1, delta 1, rms=0.002 (18.884%)
- 0684: dt=9.216000, rms=0.395 (0.277%), neg=0, invalid=96777
- iter 0, gcam->neg = 18
- after 200 iterations, nbhd size=2, neg = 1
- starting rms=0.002, neg=1, removing folds in lattice....
- iter 1, dt=0.000219: new neg 0, old_neg 1, delta 1, rms=0.002 (10.718%)
- 0685: dt=3.456000, rms=0.395 (0.096%), neg=0, invalid=96777
- iter 0, gcam->neg = 16
- after 200 iterations, nbhd size=2, neg = 1
- starting rms=0.002, neg=1, removing folds in lattice....
- iter 1, dt=0.000219: new neg 0, old_neg 1, delta 1, rms=0.002 (10.716%)
- 0686: dt=3.456000, rms=0.394 (0.106%), neg=0, invalid=96777
- iter 0, gcam->neg = 18
- after 200 iterations, nbhd size=1, neg = 1
- starting rms=0.002, neg=1, removing folds in lattice....
- iter 1, dt=0.000125: new neg 0, old_neg 1, delta 1, rms=0.002 (13.923%)
- 0687: dt=3.456000, rms=0.394 (0.086%), neg=0, invalid=96777
- iter 0, gcam->neg = 18
- after 200 iterations, nbhd size=2, neg = 1
- starting rms=0.002, neg=1, removing folds in lattice....
- iter 1, dt=0.000219: new neg 0, old_neg 1, delta 1, rms=0.002 (9.444%)
- 0688: dt=3.456000, rms=0.394 (0.064%), neg=0, invalid=96777
- iter 0, gcam->neg = 12
- after 200 iterations, nbhd size=3, neg = 1
- starting rms=0.002, neg=1, removing folds in lattice....
- iter 1, dt=0.000219: new neg 0, old_neg 1, delta 1, rms=0.002 (11.334%)
- 0689: dt=2.304000, rms=0.394 (0.043%), neg=0, invalid=96777
- setting smoothness coefficient to 1.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.399, neg=0, invalid=96777
- 0690: dt=0.000000, rms=0.399 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.399, neg=0, invalid=96777
- 0691: dt=0.000000, rms=0.399 (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=0.390, neg=0, invalid=96777
- iter 0, gcam->neg = 484
- after 20 iterations, nbhd size=2, neg = 0
- 0692: dt=0.815526, rms=0.377 (3.398%), neg=0, invalid=96777
- 0693: dt=0.000078, rms=0.377 (0.003%), neg=0, invalid=96777
- 0694: dt=0.000078, rms=0.377 (0.000%), neg=0, invalid=96777
- 0695: dt=0.000078, rms=0.377 (0.000%), neg=0, invalid=96777
- 0696: dt=0.000078, rms=0.377 (-0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.377, neg=0, invalid=96777
- 0697: dt=0.000438, rms=0.377 (0.000%), neg=0, invalid=96777
- 0698: dt=0.000000, rms=0.377 (0.000%), neg=0, invalid=96777
- writing output transformation to transforms/talairach.m3z...
- GCAMwrite
- registration took 4 hours, 36 minutes and 17 seconds.
- #--------------------------------------
- #@# CA Reg Inv Thu Aug 8 16:49:41 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri
- mri_ca_register -invert-and-save transforms/talairach.m3z
- Loading, Inverting, Saving, Exiting ...
- Reading transforms/talairach.m3z
- Inverting GCAM
- Saving inverse
- #--------------------------------------
- #@# Remove Neck Thu Aug 8 16:51:09 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...
- 11404101 nonbrain voxels erased
- writing output to nu_noneck.mgz...
- nonbrain removal took 1 minutes and 28 seconds.
- #--------------------------------------
- #@# SkullLTA Thu Aug 8 16:52:38 CEST 2013
- mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta
- ======= NUMBER OF OPENMP THREADS = 1 =======
- aligning to atlas containing skull, setting unknown_nbr_spacing = 5
- using previously computed transform transforms/talairach.lta
- reading 1 input volumes...
- logging results to talairach_with_skull_2.log
- reading '/opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca'...
- average std = 23.1 using min determinant for regularization = 53.4
- 0 singular and 5702 ill-conditioned covariance matrices regularized
- reading 'nu_noneck.mgz'...
- freeing gibbs priors...done.
- bounding unknown intensity as < 20.2 or > 943.7
- total sample mean = 92.0 (1443 zeros)
- ************************************************
- spacing=8, using 3481 sample points, tol=1.00e-05...
- ************************************************
- register_mri: find_optimal_transform
- find_optimal_transform: nsamples 3481, passno 0, spacing 8
- resetting wm mean[0]: 117 --> 126
- resetting gm mean[0]: 74 --> 74
- input volume #1 is the most T1-like
- using real data threshold=7.0
- skull bounding box = (45, 20, 19) --> (206, 200, 195)
- using (99, 80, 107) as brain centroid...
- mean wm in atlas = 126, using box (79,58,85) --> (118, 102,128) 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=-4.0, old_max_log_p =-4.1 (thresh=-4.1)
- 1.084 -0.050 -0.040 -2.782;
- 0.053 1.140 0.305 -34.316;
- 0.007 -0.268 0.999 19.431;
- 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)
- 1.084 -0.050 -0.040 -2.782;
- 0.053 1.140 0.305 -34.316;
- 0.007 -0.268 0.999 19.431;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.2500
- ****************************************
- Nine parameter search. iteration 2 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.043 -0.048 -0.039 2.039;
- 0.055 1.173 0.350 -42.998;
- 0.005 -0.323 1.045 21.797;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 3 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.023 -0.037 -0.072 9.003;
- 0.055 1.173 0.350 -42.998;
- 0.040 -0.331 1.063 14.265;
- 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 =-4.0 (thresh=-4.0)
- 1.025 -0.043 -0.055 6.531;
- 0.056 1.159 0.384 -44.584;
- 0.022 -0.369 1.054 21.408;
- 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)
- 1.025 -0.043 -0.055 6.531;
- 0.056 1.155 0.382 -44.002;
- 0.022 -0.369 1.054 21.408;
- 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)
- 1.025 -0.043 -0.055 6.531;
- 0.056 1.151 0.381 -43.422;
- 0.022 -0.369 1.053 21.507;
- 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)
- 1.023 -0.043 -0.054 6.671;
- 0.056 1.148 0.380 -43.036;
- 0.022 -0.369 1.053 21.507;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 8 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 1.023 -0.043 -0.054 6.671;
- 0.056 1.148 0.380 -43.036;
- 0.022 -0.369 1.053 21.507;
- 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
- 1.02343 -0.04290 -0.05449 6.67126;
- 0.05562 1.14836 0.38008 -43.03613;
- 0.02183 -0.36854 1.05324 21.50699;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 3481
- Quasinewton: input matrix
- 1.02343 -0.04290 -0.05449 6.67126;
- 0.05562 1.14836 0.38008 -43.03613;
- 0.02183 -0.36854 1.05324 21.50699;
- 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:
- 1.023 -0.043 -0.054 6.671;
- 0.056 1.148 0.380 -43.036;
- 0.022 -0.369 1.053 21.507;
- 0.000 0.000 0.000 1.000;
- pass 1, spacing 8: log(p) = -3.9 (old=-4.1)
- transform before final EM align:
- 1.023 -0.043 -0.054 6.671;
- 0.056 1.148 0.380 -43.036;
- 0.022 -0.369 1.053 21.507;
- 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
- 1.02343 -0.04290 -0.05449 6.67126;
- 0.05562 1.14836 0.38008 -43.03613;
- 0.02183 -0.36854 1.05324 21.50699;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 382743
- Quasinewton: input matrix
- 1.02343 -0.04290 -0.05449 6.67126;
- 0.05562 1.14836 0.38008 -43.03613;
- 0.02183 -0.36854 1.05324 21.50699;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 012: -log(p) = 4.4 tol 0.000000
- final transform:
- 1.023 -0.043 -0.054 6.671;
- 0.056 1.148 0.380 -43.036;
- 0.022 -0.369 1.053 21.507;
- 0.000 0.000 0.000 1.000;
- writing output transformation to transforms/talairach_with_skull_2.lta...
- registration took 43 minutes and 49 seconds.
- #--------------------------------------
- #@# SubCort Seg Thu Aug 8 17:36:27 CEST 2013
- mri_ca_label -align norm.mgz transforms/talairach.m3z /opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz
- sysname Linux
- hostname snake6
- machine x86_64
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 = 0.10797 ( 7)
- Left_Lateral_Ventricle (4): linear fit = 0.25 x + 0.0 (1906 voxels, overlap=0.008)
- Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (1906 voxels, peak = 7), gca=10.8
- gca peak = 0.14982 (20)
- mri peak = 0.12829 ( 7)
- Right_Lateral_Ventricle (43): linear fit = 0.28 x + 0.0 (424 voxels, overlap=0.008)
- Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (424 voxels, peak = 6), gca=8.0
- gca peak = 0.28003 (97)
- mri peak = 0.10104 (87)
- Right_Pallidum (52): linear fit = 0.88 x + 0.0 (385 voxels, overlap=0.052)
- Right_Pallidum (52): linear fit = 0.88 x + 0.0 (385 voxels, peak = 86), gca=85.8
- gca peak = 0.18160 (96)
- mri peak = 0.08081 (79)
- Left_Pallidum (13): linear fit = 0.82 x + 0.0 (262 voxels, overlap=0.061)
- Left_Pallidum (13): linear fit = 0.82 x + 0.0 (262 voxels, peak = 79), gca=79.2
- gca peak = 0.27536 (62)
- mri peak = 0.07015 (53)
- Right_Hippocampus (53): linear fit = 0.83 x + 0.0 (660 voxels, overlap=0.632)
- Right_Hippocampus (53): linear fit = 0.83 x + 0.0 (660 voxels, peak = 52), gca=51.8
- gca peak = 0.32745 (63)
- mri peak = 0.09060 (61)
- Left_Hippocampus (17): linear fit = 0.90 x + 0.0 (580 voxels, overlap=0.783)
- Left_Hippocampus (17): linear fit = 0.90 x + 0.0 (580 voxels, peak = 57), gca=57.0
- gca peak = 0.08597 (105)
- mri peak = 0.08477 (107)
- Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (43567 voxels, overlap=0.744)
- Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (43567 voxels, peak = 107), gca=106.6
- gca peak = 0.09209 (106)
- mri peak = 0.08672 (107)
- Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (38588 voxels, overlap=0.661)
- Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (38588 voxels, peak = 109), gca=108.6
- gca peak = 0.07826 (63)
- mri peak = 0.05588 (54)
- Left_Cerebral_Cortex (3): linear fit = 0.85 x + 0.0 (11774 voxels, overlap=0.445)
- Left_Cerebral_Cortex (3): linear fit = 0.85 x + 0.0 (11774 voxels, peak = 53), gca=53.2
- gca peak = 0.08598 (64)
- mri peak = 0.05247 (51)
- Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (10855 voxels, overlap=0.343)
- Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (10855 voxels, peak = 53), gca=52.8
- gca peak = 0.24164 (71)
- mri peak = 0.09382 (65)
- Right_Caudate (50): linear fit = 0.88 x + 0.0 (469 voxels, overlap=0.430)
- Right_Caudate (50): linear fit = 0.88 x + 0.0 (469 voxels, peak = 62), gca=62.1
- gca peak = 0.18227 (75)
- mri peak = 0.08433 (67)
- Left_Caudate (11): linear fit = 0.82 x + 0.0 (704 voxels, overlap=0.154)
- Left_Caudate (11): linear fit = 0.82 x + 0.0 (704 voxels, peak = 62), gca=61.9
- gca peak = 0.10629 (62)
- mri peak = 0.05433 (60)
- Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (4510 voxels, overlap=1.000)
- Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (4510 voxels, peak = 60), gca=59.8
- gca peak = 0.11668 (59)
- mri peak = 0.05174 (56)
- Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (4985 voxels, overlap=0.999)
- Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (4985 voxels, peak = 57), gca=56.9
- gca peak = 0.17849 (88)
- mri peak = 0.09635 (93)
- Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (4842 voxels, overlap=0.875)
- Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (4842 voxels, peak = 92), gca=92.0
- gca peak = 0.16819 (86)
- mri peak = 0.10942 (93)
- Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (4467 voxels, overlap=0.944)
- Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (4467 voxels, peak = 92), gca=91.6
- gca peak = 0.41688 (64)
- mri peak = 0.09091 (62)
- Left_Amygdala (18): linear fit = 0.98 x + 0.0 (262 voxels, overlap=1.037)
- Left_Amygdala (18): linear fit = 0.98 x + 0.0 (262 voxels, peak = 62), gca=62.4
- gca peak = 0.42394 (62)
- mri peak = 0.11045 (57)
- Right_Amygdala (54): linear fit = 0.90 x + 0.0 (339 voxels, overlap=1.041)
- Right_Amygdala (54): linear fit = 0.90 x + 0.0 (339 voxels, peak = 56), gca=56.1
- gca peak = 0.10041 (96)
- mri peak = 0.06813 (89)
- Left_Thalamus_Proper (10): linear fit = 0.94 x + 0.0 (3433 voxels, overlap=0.713)
- Left_Thalamus_Proper (10): linear fit = 0.94 x + 0.0 (3433 voxels, peak = 91), gca=90.7
- gca peak = 0.13978 (88)
- mri peak = 0.07226 (83)
- Right_Thalamus_Proper (49): linear fit = 0.95 x + 0.0 (3595 voxels, overlap=0.821)
- Right_Thalamus_Proper (49): linear fit = 0.95 x + 0.0 (3595 voxels, peak = 84), gca=84.0
- gca peak = 0.08514 (81)
- mri peak = 0.05652 (75)
- Left_Putamen (12): linear fit = 0.88 x + 0.0 (1623 voxels, overlap=0.342)
- Left_Putamen (12): linear fit = 0.88 x + 0.0 (1623 voxels, peak = 71), gca=70.9
- gca peak = 0.09624 (82)
- mri peak = 0.06686 (68)
- Right_Putamen (51): linear fit = 0.87 x + 0.0 (1422 voxels, overlap=0.325)
- Right_Putamen (51): linear fit = 0.87 x + 0.0 (1422 voxels, peak = 71), gca=70.9
- gca peak = 0.07543 (88)
- mri peak = 0.06846 (88)
- Brain_Stem (16): linear fit = 1.03 x + 0.0 (10674 voxels, overlap=0.765)
- Brain_Stem (16): linear fit = 1.03 x + 0.0 (10674 voxels, peak = 91), gca=91.1
- gca peak = 0.12757 (95)
- mri peak = 0.07743 (90)
- Right_VentralDC (60): linear fit = 0.94 x + 0.0 (991 voxels, overlap=0.883)
- Right_VentralDC (60): linear fit = 0.94 x + 0.0 (991 voxels, peak = 90), gca=89.8
- gca peak = 0.17004 (92)
- mri peak = 0.06960 (94)
- Left_VentralDC (28): linear fit = 0.96 x + 0.0 (1056 voxels, overlap=0.976)
- Left_VentralDC (28): linear fit = 0.96 x + 0.0 (1056 voxels, peak = 89), gca=88.8
- gca peak = 0.21361 (36)
- mri peak = 0.37569 (13)
- gca peak = 0.26069 (23)
- mri peak = 0.15264 (11)
- Fourth_Ventricle (15): linear fit = 0.35 x + 0.0 (251 voxels, overlap=0.029)
- Fourth_Ventricle (15): linear fit = 0.35 x + 0.0 (251 voxels, peak = 8), gca=8.2
- 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 0.88 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 aseg.auto_noCCseg.label_intensities.txt
- renormalizing by structure alignment....
- renormalizing input #0
- gca peak = 0.31600 (11)
- mri peak = 0.10797 ( 7)
- Left_Lateral_Ventricle (4): linear fit = 0.70 x + 0.0 (1906 voxels, overlap=0.971)
- Left_Lateral_Ventricle (4): linear fit = 0.70 x + 0.0 (1906 voxels, peak = 8), gca=7.8
- gca peak = 0.29325 ( 9)
- mri peak = 0.12829 ( 7)
- Right_Lateral_Ventricle (43): linear fit = 0.76 x + 0.0 (424 voxels, overlap=0.913)
- Right_Lateral_Ventricle (43): linear fit = 0.76 x + 0.0 (424 voxels, peak = 7), gca=6.9
- gca peak = 0.29042 (86)
- mri peak = 0.10104 (87)
- Right_Pallidum (52): linear fit = 1.00 x + 0.0 (385 voxels, overlap=1.019)
- Right_Pallidum (52): linear fit = 1.00 x + 0.0 (385 voxels, peak = 86), gca=85.6
- gca peak = 0.22395 (81)
- mri peak = 0.08081 (79)
- Left_Pallidum (13): linear fit = 1.02 x + 0.0 (262 voxels, overlap=1.006)
- Left_Pallidum (13): linear fit = 1.02 x + 0.0 (262 voxels, peak = 83), gca=83.0
- gca peak = 0.30642 (52)
- mri peak = 0.07015 (53)
- Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (660 voxels, overlap=1.007)
- Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (660 voxels, peak = 54), gca=54.3
- gca peak = 0.31837 (57)
- mri peak = 0.09060 (61)
- Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (580 voxels, overlap=1.007)
- Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (580 voxels, peak = 58), gca=58.4
- gca peak = 0.08540 (107)
- mri peak = 0.08477 (107)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (43567 voxels, overlap=0.799)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (43567 voxels, peak = 107), gca=107.0
- gca peak = 0.08534 (108)
- mri peak = 0.08672 (107)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (38588 voxels, overlap=0.746)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (38588 voxels, peak = 108), gca=108.0
- gca peak = 0.09161 (53)
- mri peak = 0.05588 (54)
- Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (11774 voxels, overlap=0.992)
- Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (11774 voxels, peak = 53), gca=53.0
- gca peak = 0.10560 (53)
- mri peak = 0.05247 (51)
- Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (10855 voxels, overlap=0.994)
- Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (10855 voxels, peak = 52), gca=52.2
- gca peak = 0.24064 (64)
- mri peak = 0.09382 (65)
- Right_Caudate (50): linear fit = 1.00 x + 0.0 (469 voxels, overlap=1.005)
- Right_Caudate (50): linear fit = 1.00 x + 0.0 (469 voxels, peak = 64), gca=64.0
- gca peak = 0.16489 (62)
- mri peak = 0.08433 (67)
- Left_Caudate (11): linear fit = 1.01 x + 0.0 (704 voxels, overlap=1.003)
- Left_Caudate (11): linear fit = 1.01 x + 0.0 (704 voxels, peak = 63), gca=62.9
- gca peak = 0.11102 (59)
- mri peak = 0.05433 (60)
- Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (4510 voxels, overlap=0.997)
- Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (4510 voxels, peak = 60), gca=60.5
- gca peak = 0.12344 (58)
- mri peak = 0.05174 (56)
- Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (4985 voxels, overlap=0.999)
- Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (4985 voxels, peak = 59), gca=59.4
- gca peak = 0.17369 (92)
- mri peak = 0.09635 (93)
- Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4842 voxels, overlap=0.986)
- Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4842 voxels, peak = 92), gca=91.5
- gca peak = 0.16064 (92)
- mri peak = 0.10942 (93)
- Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (4467 voxels, overlap=1.000)
- Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (4467 voxels, peak = 91), gca=90.6
- gca peak = 0.33143 (62)
- mri peak = 0.09091 (62)
- Left_Amygdala (18): linear fit = 0.99 x + 0.0 (262 voxels, overlap=1.027)
- Left_Amygdala (18): linear fit = 0.99 x + 0.0 (262 voxels, peak = 61), gca=61.1
- gca peak = 0.43549 (57)
- mri peak = 0.11045 (57)
- Right_Amygdala (54): linear fit = 1.04 x + 0.0 (339 voxels, overlap=1.018)
- Right_Amygdala (54): linear fit = 1.04 x + 0.0 (339 voxels, peak = 60), gca=59.6
- gca peak = 0.11264 (89)
- mri peak = 0.06813 (89)
- Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3433 voxels, overlap=0.983)
- Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3433 voxels, peak = 89), gca=88.6
- gca peak = 0.14416 (84)
- mri peak = 0.07226 (83)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3595 voxels, overlap=0.992)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3595 voxels, peak = 84), gca=83.6
- gca peak = 0.09324 (72)
- mri peak = 0.05652 (75)
- Left_Putamen (12): linear fit = 1.00 x + 0.0 (1623 voxels, overlap=1.000)
- Left_Putamen (12): linear fit = 1.00 x + 0.0 (1623 voxels, peak = 72), gca=72.0
- gca peak = 0.09625 (71)
- mri peak = 0.06686 (68)
- Right_Putamen (51): linear fit = 1.00 x + 0.0 (1422 voxels, overlap=1.000)
- Right_Putamen (51): linear fit = 1.00 x + 0.0 (1422 voxels, peak = 71), gca=71.0
- gca peak = 0.07164 (88)
- mri peak = 0.06846 (88)
- Brain_Stem (16): linear fit = 1.01 x + 0.0 (10674 voxels, overlap=0.837)
- Brain_Stem (16): linear fit = 1.01 x + 0.0 (10674 voxels, peak = 89), gca=89.3
- gca peak = 0.13285 (86)
- mri peak = 0.07743 (90)
- Right_VentralDC (60): linear fit = 1.00 x + 0.0 (991 voxels, overlap=0.820)
- Right_VentralDC (60): linear fit = 1.00 x + 0.0 (991 voxels, peak = 86), gca=85.6
- gca peak = 0.15883 (89)
- mri peak = 0.06960 (94)
- Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1056 voxels, overlap=0.943)
- Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1056 voxels, peak = 89), gca=88.6
- gca peak = 0.35640 (14)
- mri peak = 0.37569 (13)
- gca peak = 0.33827 ( 9)
- mri peak = 0.15264 (11)
- Fourth_Ventricle (15): linear fit = 0.90 x + 0.0 (251 voxels, overlap=0.963)
- Fourth_Ventricle (15): linear fit = 0.90 x + 0.0 (251 voxels, peak = 8), gca=8.1
- gca peak Unknown = 0.94427 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.27695 (32)
- gca peak Third_Ventricle = 0.35640 (14)
- gca peak CSF = 0.30128 (18)
- gca peak Left_Accumbens_area = 0.51409 (58)
- gca peak Left_undetermined = 1.00000 (35)
- gca peak Left_vessel = 0.38637 (62)
- gca peak Left_choroid_plexus = 0.09087 (48)
- gca peak Right_Inf_Lat_Vent = 0.30433 (27)
- gca peak Right_Accumbens_area = 0.31098 (63)
- gca peak Right_vessel = 0.57697 (60)
- gca peak Right_choroid_plexus = 0.10278 (48)
- gca peak Fifth_Ventricle = 0.45329 (19)
- gca peak WM_hypointensities = 0.17565 (83)
- gca peak non_WM_hypointensities = 0.12126 (54)
- gca peak Optic_Chiasm = 0.34858 (76)
- not using caudate to estimate GM means
- estimating mean gm scale to be 1.01 x + 0.0
- estimating mean wm scale to be 1.00 x + 0.0
- estimating mean csf scale to be 0.79 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
- 11399 gm and wm labels changed (%13 to gray, %87 to white out of all changed labels)
- 235 hippocampal voxels changed.
- 3 amygdala voxels changed.
- pass 1: 82810 changed. image ll: -2.173, PF=1.000
- pass 2: 15046 changed. image ll: -2.171, PF=1.000
- pass 3: 5577 changed.
- pass 4: 2485 changed.
- writing labeled volume to aseg.auto_noCCseg.mgz...
- auto-labeling took 19 minutes and 15 seconds.
- mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/cc_up.lta sub020
- 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/sub020/mri/transforms/cc_up.lta
- reading aseg from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/aseg.auto_noCCseg.mgz
- reading norm from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/norm.mgz
- 45277 voxels in left wm, 79193 in right wm, xrange [116, 131]
- searching rotation angles z=[-7 7], y=[-10 4]
-
searching scale 1 Z rot -7.3
searching scale 1 Z rot -7.0
searching scale 1 Z rot -6.8
searching scale 1 Z rot -6.5
searching scale 1 Z rot -6.3
searching scale 1 Z rot -6.0
searching scale 1 Z rot -5.8
searching scale 1 Z rot -5.5
searching scale 1 Z rot -5.3
searching scale 1 Z rot -5.0
searching scale 1 Z rot -4.8
searching scale 1 Z rot -4.5
searching scale 1 Z rot -4.3
searching scale 1 Z rot -4.0
searching scale 1 Z rot -3.8
searching scale 1 Z rot -3.5
searching scale 1 Z rot -3.3
searching scale 1 Z rot -3.0
searching scale 1 Z rot -2.8
searching scale 1 Z rot -2.5
searching scale 1 Z rot -2.3
searching scale 1 Z rot -2.0
searching scale 1 Z rot -1.8
searching scale 1 Z rot -1.5
searching scale 1 Z rot -1.3
searching scale 1 Z rot -1.0
searching scale 1 Z rot -0.8
searching scale 1 Z rot -0.5
searching scale 1 Z rot -0.3
searching scale 1 Z rot -0.0
searching scale 1 Z rot 0.2
searching scale 1 Z rot 0.5
searching scale 1 Z rot 0.7
searching scale 1 Z rot 1.0
searching scale 1 Z rot 1.2
searching scale 1 Z rot 1.5
searching scale 1 Z rot 1.7
searching scale 1 Z rot 2.0
searching scale 1 Z rot 2.2
searching scale 1 Z rot 2.5
searching scale 1 Z rot 2.7
searching scale 1 Z rot 3.0
searching scale 1 Z rot 3.2
searching scale 1 Z rot 3.5
searching scale 1 Z rot 3.7
searching scale 1 Z rot 4.0
searching scale 1 Z rot 4.2
searching scale 1 Z rot 4.5
searching scale 1 Z rot 4.7
searching scale 1 Z rot 5.0
searching scale 1 Z rot 5.2
searching scale 1 Z rot 5.5
searching scale 1 Z rot 5.7
searching scale 1 Z rot 6.0
searching scale 1 Z rot 6.2
searching scale 1 Z rot 6.5 global minimum found at slice 124.3, rotations (-2.83, -0.29)
- final transformation (x=124.3, yr=-2.832, zr=-0.290):
- 0.999 0.005 -0.049 8.231;
- -0.005 1.000 0.000 45.605;
- 0.049 -0.000 0.999 23.976;
- 0.000 0.000 0.000 1.000;
- updating x range to be [126, 132] in xformed coordinates
- best xformed slice 130
- cc center is found at 130 148 132
- eigenvectors:
- -0.002 0.001 1.000;
- -0.117 -0.993 0.001;
- 0.993 -0.117 0.002;
- error in mid anterior detected - correcting...
- writing aseg with callosum to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/aseg.auto.mgz...
- corpus callosum matter segmentation took 1.5 minutes
- #--------------------------------------
- #@# Merge ASeg Thu Aug 8 17:57:15 CEST 2013
- cp aseg.auto.mgz aseg.mgz
- #--------------------------------------------
- #@# Intensity Normalization2 Thu Aug 8 17:57:15 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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...
- 2323 control points removed
- Building bias image
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 0...
- Smoothing with sigma 8
- Applying bias correction
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Iterating 2 times
- ---------------------------------
- 3d normalization pass 1 of 2
- white matter peak found at 111
- white matter peak found at 109
- gm peak at 56 (56), valley at 30 (30)
- csf peak at 28, setting threshold to 46
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- ---------------------------------
- 3d normalization pass 2 of 2
- white matter peak found at 111
- white matter peak found at 110
- gm peak at 58 (58), valley at 23 (23)
- csf peak at 29, setting threshold to 48
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Done iterating ---------------------------------
- writing output to brain.mgz
- 3D bias adjustment took 4 minutes and 18 seconds.
- #--------------------------------------------
- #@# Mask BFS Thu Aug 8 18:01:35 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri
- mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
- threshold mask volume at 5
- DoAbs = 0
- Found 1510514 voxels in mask (pct= 9.00)
- Writing masked volume to brain.finalsurfs.mgz...done.
- #--------------------------------------------
- #@# WM Segmentation Thu Aug 8 18:01:37 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): 107.3 +- 4.9 [80.0 --> 125.0]
- GM (68.0) : 67.4 +- 9.5 [30.0 --> 96.0]
- setting bottom of white matter range to 76.8
- setting top of gray matter range to 86.3
- 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...
- 6324 sparsely connected voxels removed...
- thickening thin strands....
- 20 segments, 4923 filled
- 106 bright non-wm voxels segmented.
- 3276 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...
- 31 voxels added to wm to prevent paths from MTL structures to cortex
- 1454 additional wm voxels added
- 0 additional wm voxels added
- SEG EDIT: 52599 voxels turned on, 41050 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+): 8 found - 8 modified | TOTAL: 8
- pass 2 (xy+): 0 found - 8 modified | TOTAL: 8
- pass 1 (xy-): 17 found - 17 modified | TOTAL: 25
- pass 2 (xy-): 0 found - 17 modified | TOTAL: 25
- pass 1 (yz+): 40 found - 40 modified | TOTAL: 65
- pass 2 (yz+): 0 found - 40 modified | TOTAL: 65
- pass 1 (yz-): 20 found - 20 modified | TOTAL: 85
- pass 2 (yz-): 0 found - 20 modified | TOTAL: 85
- pass 1 (xz+): 27 found - 27 modified | TOTAL: 112
- pass 2 (xz+): 0 found - 27 modified | TOTAL: 112
- pass 1 (xz-): 24 found - 24 modified | TOTAL: 136
- pass 2 (xz-): 0 found - 24 modified | TOTAL: 136
- Iteration Number : 1
- pass 1 (+++): 5 found - 5 modified | TOTAL: 5
- pass 2 (+++): 0 found - 5 modified | TOTAL: 5
- pass 1 (+++): 5 found - 5 modified | TOTAL: 10
- pass 2 (+++): 0 found - 5 modified | TOTAL: 10
- pass 1 (+++): 9 found - 9 modified | TOTAL: 19
- pass 2 (+++): 0 found - 9 modified | TOTAL: 19
- pass 1 (+++): 6 found - 6 modified | TOTAL: 25
- pass 2 (+++): 0 found - 6 modified | TOTAL: 25
- Iteration Number : 1
- pass 1 (++): 89 found - 89 modified | TOTAL: 89
- pass 2 (++): 0 found - 89 modified | TOTAL: 89
- pass 1 (+-): 91 found - 91 modified | TOTAL: 180
- pass 2 (+-): 0 found - 91 modified | TOTAL: 180
- pass 1 (--): 93 found - 93 modified | TOTAL: 273
- pass 2 (--): 0 found - 93 modified | TOTAL: 273
- pass 1 (-+): 101 found - 101 modified | TOTAL: 374
- pass 2 (-+): 0 found - 101 modified | TOTAL: 374
- Iteration Number : 2
- pass 1 (xy+): 1 found - 1 modified | TOTAL: 1
- pass 2 (xy+): 0 found - 1 modified | TOTAL: 1
- pass 1 (xy-): 1 found - 1 modified | TOTAL: 2
- pass 2 (xy-): 0 found - 1 modified | TOTAL: 2
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 2
- pass 1 (yz-): 5 found - 5 modified | TOTAL: 7
- pass 2 (yz-): 0 found - 5 modified | TOTAL: 7
- pass 1 (xz+): 1 found - 1 modified | TOTAL: 8
- pass 2 (xz+): 0 found - 1 modified | TOTAL: 8
- pass 1 (xz-): 1 found - 1 modified | TOTAL: 9
- pass 2 (xz-): 0 found - 1 modified | TOTAL: 9
- 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 (++): 1 found - 1 modified | TOTAL: 1
- pass 2 (++): 0 found - 1 modified | TOTAL: 1
- pass 1 (+-): 0 found - 0 modified | TOTAL: 1
- pass 1 (--): 2 found - 2 modified | TOTAL: 3
- pass 2 (--): 0 found - 2 modified | TOTAL: 3
- pass 1 (-+): 1 found - 1 modified | TOTAL: 4
- pass 2 (-+): 0 found - 1 modified | TOTAL: 4
- Iteration Number : 3
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 1 found - 1 modified | TOTAL: 1
- pass 2 (xy-): 0 found - 1 modified | TOTAL: 1
- pass 1 (yz+): 2 found - 2 modified | TOTAL: 3
- pass 2 (yz+): 0 found - 2 modified | TOTAL: 3
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 3
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 3
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 3
- 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 = 551 (out of 568853: 0.096862)
- binarizing input wm segmentation...
- Ambiguous edge configurations...
- mri_pretess done
- #--------------------------------------------
- #@# Fill Thu Aug 8 18:04:06 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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
- 1.084 -0.050 -0.040 -2.782;
- 0.053 1.140 0.305 -34.316;
- 0.007 -0.268 0.999 19.431;
- 0.000 0.000 0.000 1.000;
- voxel to talairach voxel transform
- 1.084 -0.050 -0.040 -2.782;
- 0.053 1.140 0.305 -34.316;
- 0.007 -0.268 0.999 19.431;
- 0.000 0.000 0.000 1.000;
- reading segmented volume aseg.auto_noCCseg.mgz...
- Looking for area (min, max) = (350, 1400)
- area[0] = 2894 (min = 350, max = 1400), aspect = 1.32 (min = 0.10, max = 0.75)
- need search nearby
- using seed (127, 119, 147), TAL = (1.0, 19.0, 9.0)
- talairach voxel to voxel transform
- 0.920 0.046 0.023 3.682;
- -0.038 0.816 -0.250 32.772;
- -0.017 0.219 0.933 -10.663;
- 0.000 0.000 0.000 1.000;
- segmentation indicates cc at (127, 119, 147) --> (1.0, 19.0, 9.0)
- done.
- writing output to filled.mgz...
- filling took 0.9 minutes
- talairach cc position changed to (1.00, 19.00, 9.00)
- Erasing brainstem...done.
- seed_search_size = 9, min_neighbors = 5
- search rh wm seed point around talairach space:(19.00, 19.00, 9.00) SRC: (112.86, 88.93, 150.75)
- search lh wm seed point around talairach space (-17.00, 19.00, 9.00), SRC: (145.99, 87.56, 150.15)
- compute mri_fill using aseg
- Erasing Brain Stem and Cerebellum ...
- Define left and right masks using aseg:
- Building Voronoi diagram ...
- Using the Voronoi diagram to separate WM into two hemispheres ...
- Find the largest connected component for each hemisphere ...
- #--------------------------------------------
- #@# Tessellate lh Thu Aug 8 18:05:01 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/scripts
- mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz
- Iteration Number : 1
- pass 1 (xy+): 2 found - 2 modified | TOTAL: 2
- pass 2 (xy+): 0 found - 2 modified | TOTAL: 2
- pass 1 (xy-): 1 found - 1 modified | TOTAL: 3
- pass 2 (xy-): 0 found - 1 modified | TOTAL: 3
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 3
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 3
- pass 1 (xz+): 2 found - 2 modified | TOTAL: 5
- pass 2 (xz+): 0 found - 2 modified | TOTAL: 5
- pass 1 (xz-): 2 found - 2 modified | TOTAL: 7
- pass 2 (xz-): 0 found - 2 modified | TOTAL: 7
- Iteration Number : 1
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 1
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Total Number of Modified Voxels = 7 (out of 276130: 0.002535)
- 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: 1606 vertices, 1785 faces
- slice 50: 8814 vertices, 9160 faces
- slice 60: 19181 vertices, 19563 faces
- slice 70: 30618 vertices, 31021 faces
- slice 80: 42361 vertices, 42780 faces
- slice 90: 53413 vertices, 53775 faces
- slice 100: 64659 vertices, 65036 faces
- slice 110: 75761 vertices, 76121 faces
- slice 120: 86252 vertices, 86631 faces
- slice 130: 96333 vertices, 96697 faces
- slice 140: 105913 vertices, 106260 faces
- slice 150: 114452 vertices, 114732 faces
- slice 160: 121583 vertices, 121836 faces
- slice 170: 127543 vertices, 127741 faces
- slice 180: 132686 vertices, 132859 faces
- slice 190: 136116 vertices, 136232 faces
- slice 200: 136804 vertices, 136826 faces
- slice 210: 136804 vertices, 136826 faces
- slice 220: 136804 vertices, 136826 faces
- slice 230: 136804 vertices, 136826 faces
- slice 240: 136804 vertices, 136826 faces
- slice 250: 136804 vertices, 136826 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...
- 136804 voxel in cpt #1: X=-22 [v=136804,e=410478,f=273652] located at (-24.266279, -22.935061, 36.761734)
- For the whole surface: X=-22 [v=136804,e=410478,f=273652]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Smooth1 lh Thu Aug 8 18:05:08 CEST 2013
- mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/scripts
- setting seed for random number generator to 1234
- smoothing surface tessellation for 10 iterations...
- smoothing complete - recomputing first and second fundamental forms...
- #--------------------------------------------
- #@# Inflation1 lh Thu Aug 8 18:05:13 CEST 2013
- mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/scripts
- avg radius = 47.9 mm, total surface area = 72661 mm^2
- writing inflated surface to ../surf/lh.inflated.nofix
- inflation took 0.5 minutes
- Not saving sulc
-
step 000: RMS=0.098 (target=0.015)
step 005: RMS=0.072 (target=0.015)
step 010: RMS=0.053 (target=0.015)
step 015: RMS=0.044 (target=0.015)
step 020: RMS=0.037 (target=0.015)
step 025: RMS=0.032 (target=0.015)
step 030: RMS=0.029 (target=0.015)
step 035: RMS=0.027 (target=0.015)
step 040: RMS=0.025 (target=0.015)
step 045: RMS=0.024 (target=0.015)
step 050: RMS=0.023 (target=0.015)
step 055: RMS=0.023 (target=0.015)
step 060: RMS=0.023 (target=0.015)
- inflation complete.
- Not saving sulc
- #--------------------------------------------
- #@# QSphere lh Thu Aug 8 18:05:44 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 0.99 +- 0.57 (0.00-->6.08) (max @ vno 103761 --> 103762)
- face area 0.03 +- 0.03 (-0.12-->0.55)
- scaling brain by 0.318...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=175.868, avgs=0
- 005/300: dt: 0.9000, rms radial error=175.612, avgs=0
- 010/300: dt: 0.9000, rms radial error=175.062, avgs=0
- 015/300: dt: 0.9000, rms radial error=174.338, avgs=0
- 020/300: dt: 0.9000, rms radial error=173.508, avgs=0
- 025/300: dt: 0.9000, rms radial error=172.616, avgs=0
- 030/300: dt: 0.9000, rms radial error=171.692, avgs=0
- 035/300: dt: 0.9000, rms radial error=170.757, avgs=0
- 040/300: dt: 0.9000, rms radial error=169.813, avgs=0
- 045/300: dt: 0.9000, rms radial error=168.867, avgs=0
- 050/300: dt: 0.9000, rms radial error=167.921, avgs=0
- 055/300: dt: 0.9000, rms radial error=166.978, avgs=0
- 060/300: dt: 0.9000, rms radial error=166.038, avgs=0
- 065/300: dt: 0.9000, rms radial error=165.104, avgs=0
- 070/300: dt: 0.9000, rms radial error=164.175, avgs=0
- 075/300: dt: 0.9000, rms radial error=163.250, avgs=0
- 080/300: dt: 0.9000, rms radial error=162.331, avgs=0
- 085/300: dt: 0.9000, rms radial error=161.416, avgs=0
- 090/300: dt: 0.9000, rms radial error=160.506, avgs=0
- 095/300: dt: 0.9000, rms radial error=159.601, avgs=0
- 100/300: dt: 0.9000, rms radial error=158.701, avgs=0
- 105/300: dt: 0.9000, rms radial error=157.806, avgs=0
- 110/300: dt: 0.9000, rms radial error=156.915, avgs=0
- 115/300: dt: 0.9000, rms radial error=156.030, avgs=0
- 120/300: dt: 0.9000, rms radial error=155.150, avgs=0
- 125/300: dt: 0.9000, rms radial error=154.274, avgs=0
- 130/300: dt: 0.9000, rms radial error=153.404, avgs=0
- 135/300: dt: 0.9000, rms radial error=152.540, avgs=0
- 140/300: dt: 0.9000, rms radial error=151.680, avgs=0
- 145/300: dt: 0.9000, rms radial error=150.826, avgs=0
- 150/300: dt: 0.9000, rms radial error=149.975, avgs=0
- 155/300: dt: 0.9000, rms radial error=149.130, avgs=0
- 160/300: dt: 0.9000, rms radial error=148.289, avgs=0
- 165/300: dt: 0.9000, rms radial error=147.452, avgs=0
- 170/300: dt: 0.9000, rms radial error=146.621, avgs=0
- 175/300: dt: 0.9000, rms radial error=145.793, avgs=0
- 180/300: dt: 0.9000, rms radial error=144.971, avgs=0
- 185/300: dt: 0.9000, rms radial error=144.152, avgs=0
- 190/300: dt: 0.9000, rms radial error=143.339, avgs=0
- 195/300: dt: 0.9000, rms radial error=142.529, avgs=0
- 200/300: dt: 0.9000, rms radial error=141.725, avgs=0
- 205/300: dt: 0.9000, rms radial error=140.924, avgs=0
- 210/300: dt: 0.9000, rms radial error=140.128, avgs=0
- 215/300: dt: 0.9000, rms radial error=139.337, avgs=0
- 220/300: dt: 0.9000, rms radial error=138.550, avgs=0
- 225/300: dt: 0.9000, rms radial error=137.767, avgs=0
- 230/300: dt: 0.9000, rms radial error=136.989, avgs=0
- 235/300: dt: 0.9000, rms radial error=136.215, avgs=0
- 240/300: dt: 0.9000, rms radial error=135.445, avgs=0
- 245/300: dt: 0.9000, rms radial error=134.680, avgs=0
- 250/300: dt: 0.9000, rms radial error=133.919, avgs=0
- 255/300: dt: 0.9000, rms radial error=133.163, avgs=0
- 260/300: dt: 0.9000, rms radial error=132.410, avgs=0
- 265/300: dt: 0.9000, rms radial error=131.663, avgs=0
- 270/300: dt: 0.9000, rms radial error=130.919, avgs=0
- 275/300: dt: 0.9000, rms radial error=130.179, avgs=0
- 280/300: dt: 0.9000, rms radial error=129.444, avgs=0
- 285/300: dt: 0.9000, rms radial error=128.713, avgs=0
- 290/300: dt: 0.9000, rms radial error=127.986, avgs=0
- 295/300: dt: 0.9000, rms radial error=127.264, avgs=0
- 300/300: dt: 0.9000, rms radial error=126.545, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 15869.91
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00017
- epoch 2 (K=40.0), pass 1, starting sse = 2607.20
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00012
- epoch 3 (K=160.0), pass 1, starting sse = 258.68
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.07/11 = 0.00654
- epoch 4 (K=640.0), pass 1, starting sse = 15.09
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.06/12 = 0.00525
- final writing spherical brain to ../surf/lh.qsphere.nofix
- spherical transformation took 0.08 hours
- distance error %100000.00
- #--------------------------------------------
- #@# Fix Topology lh Thu Aug 8 18:10:24 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/sub020/scripts
- mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub020 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=-22 (nv=136804, nf=273652, ne=410478, g=12)
- using quasi-homeomorphic spherical map to tessellate cortical surface...
- Correction of the Topology
- Finding true center and radius of Spherical Surface...done
- Surface centered at (0,0,0) with radius 100.0 in 9 iterations
- marking ambiguous vertices...
- 3059 ambiguous faces found in tessellation
- segmenting defects...
- 15 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- 15 defects to be corrected
- 0 vertices coincident
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/lh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -9.6063 (-4.8032)
- -vertex loglikelihood: -6.6134 (-3.3067)
- -normal dot loglikelihood: -3.6536 (-3.6536)
- -quad curv loglikelihood: -6.1968 (-3.0984)
- Total Loglikelihood : -26.0702
- CORRECTING DEFECT 0 (vertices=363, convex hull=73)
- After retessellation of defect 0, euler #=-11 (135068,404801,269722) : difference with theory (-12) = -1
- CORRECTING DEFECT 1 (vertices=21, convex hull=54)
- After retessellation of defect 1, euler #=-10 (135078,404851,269763) : difference with theory (-11) = -1
- CORRECTING DEFECT 2 (vertices=52, convex hull=50)
- After retessellation of defect 2, euler #=-9 (135087,404901,269805) : difference with theory (-10) = -1
- CORRECTING DEFECT 3 (vertices=6, convex hull=24)
- After retessellation of defect 3, euler #=-8 (135089,404912,269815) : difference with theory (-9) = -1
- CORRECTING DEFECT 4 (vertices=818, convex hull=233)
- After retessellation of defect 4, euler #=-7 (135149,405212,270056) : difference with theory (-8) = -1
- CORRECTING DEFECT 5 (vertices=6, convex hull=11)
- After retessellation of defect 5, euler #=-6 (135149,405214,270059) : difference with theory (-7) = -1
- CORRECTING DEFECT 6 (vertices=53, convex hull=75)
- After retessellation of defect 6, euler #=-5 (135164,405292,270123) : difference with theory (-6) = -1
- CORRECTING DEFECT 7 (vertices=191, convex hull=143)
- After retessellation of defect 7, euler #=-5 (135201,405480,270274) : difference with theory (-5) = 0
- CORRECTING DEFECT 8 (vertices=16, convex hull=29)
- After retessellation of defect 8, euler #=-4 (135205,405499,270290) : difference with theory (-4) = 0
- CORRECTING DEFECT 9 (vertices=80, convex hull=71)
- After retessellation of defect 9, euler #=-3 (135214,405559,270342) : difference with theory (-3) = 0
- CORRECTING DEFECT 10 (vertices=43, convex hull=55)
- After retessellation of defect 10, euler #=-2 (135224,405609,270383) : difference with theory (-2) = 0
- CORRECTING DEFECT 11 (vertices=9, convex hull=25)
- After retessellation of defect 11, euler #=-1 (135226,405623,270396) : difference with theory (-1) = 0
- CORRECTING DEFECT 12 (vertices=44, convex hull=33)
- After retessellation of defect 12, euler #=0 (135230,405646,270416) : difference with theory (0) = 0
- CORRECTING DEFECT 13 (vertices=22, convex hull=57)
- After retessellation of defect 13, euler #=1 (135241,405701,270461) : difference with theory (1) = 0
- CORRECTING DEFECT 14 (vertices=22, convex hull=49)
- After retessellation of defect 14, euler #=2 (135248,405738,270492) : 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-->6.27) (max @ vno 39231 --> 45010)
- 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-->6.27) (max @ vno 39231 --> 45010)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 59 mutations (34.3%), 113 crossovers (65.7%), 187 vertices were eliminated
- building final representation...
- 1556 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=135248, nf=270492, ne=405738, g=0)
- writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/lh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 19.6 minutes
- 0 defective edges
- removing intersecting faces
- 000: 153 intersecting
- 001: 4 intersecting
- mris_euler_number ../surf/lh.orig
- euler # = v-e+f = 2g-2: 135248 - 405738 + 270492 = 2 --> 0 holes
- F =2V-4: 270492 = 270496-4 (0)
- 2E=3F: 811476 = 811476 (0)
- total defect index = 0
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/scripts
- mris_remove_intersection ../surf/lh.orig ../surf/lh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 43 intersecting
- 001: 3 intersecting
- writing corrected surface to ../surf/lh.orig
- rm ../surf/lh.inflated
- #--------------------------------------------
- #@# Make White Surf lh Thu Aug 8 18:30:06 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/scripts
- mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub020 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/sub020/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/wm.mgz...
- 20443 bright wm thresholded.
- 144 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/lh.orig...
- computing class statistics...
- border white: 255703 voxels (1.52%)
- border gray 281220 voxels (1.68%)
- WM (94.0): 94.7 +- 9.7 [70.0 --> 110.0]
- GM (77.0) : 75.5 +- 13.0 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 49.0 (was 70)
- setting MAX_BORDER_WHITE to 115.7 (was 105)
- setting MIN_BORDER_WHITE to 62.0 (was 85)
- setting MAX_CSF to 36.1 (was 40)
- setting MAX_GRAY to 96.3 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 55.5 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 23.1 (was 40)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.82 +- 0.21 (0.03-->2.80) (max @ vno 76633 --> 80883)
- face area 0.28 +- 0.12 (0.00-->2.20)
- mean absolute distance = 0.67 +- 0.86
- 2731 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 = 94.2, mean outside = 70.5
- smoothing surface for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- removing 3 vertex label from ripped group
- mean border=74.9, 34 (34) missing vertices, mean dist 0.3 [0.6 (%31.9)->0.7 (%68.1))]
- %70 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.91 +- 0.25 (0.10-->3.94) (max @ vno 109297 --> 110154)
- face area 0.28 +- 0.13 (0.00-->2.06)
- mean absolute distance = 0.34 +- 0.52
- 3445 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=6810441.0, rms=13.19
- 001: dt: 0.5000, sse=6827142.0, rms=9.391 (0.000%)
- 002: dt: 0.5000, sse=6961564.0, rms=7.081 (0.000%)
- 003: dt: 0.5000, sse=7200937.0, rms=5.657 (0.000%)
- 004: dt: 0.5000, sse=7418772.5, rms=4.876 (0.000%)
- 005: dt: 0.5000, sse=7588355.5, rms=4.512 (0.000%)
- 006: dt: 0.5000, sse=7655199.5, rms=4.331 (0.000%)
- 007: dt: 0.5000, sse=7647406.0, rms=4.249 (0.000%)
- 008: dt: 0.5000, sse=7670905.5, rms=4.188 (0.000%)
- rms = 4.16, time step reduction 1 of 3 to 0.250...
- 009: dt: 0.5000, sse=7629357.5, rms=4.161 (0.000%)
- 010: dt: 0.2500, sse=4677944.0, rms=2.810 (0.000%)
- 011: dt: 0.2500, sse=4244866.5, rms=2.343 (0.000%)
- 012: dt: 0.2500, sse=3989221.8, rms=2.225 (0.000%)
- 013: dt: 0.2500, sse=3913503.8, rms=2.136 (0.000%)
- rms = 2.10, time step reduction 2 of 3 to 0.125...
- 014: dt: 0.2500, sse=3833318.8, rms=2.102 (0.000%)
- 015: dt: 0.1250, sse=3636921.0, rms=1.874 (0.000%)
- rms = 1.85, time step reduction 3 of 3 to 0.062...
- 016: dt: 0.1250, sse=3598783.0, rms=1.847 (0.000%)
- positioning took 1.9 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 1 vertex label from ripped group
- mean border=79.9, 20 (2) missing vertices, mean dist -0.3 [0.4 (%80.6)->0.2 (%19.4))]
- %83 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.90 +- 0.24 (0.09-->4.16) (max @ vno 71071 --> 71070)
- face area 0.35 +- 0.16 (0.00-->2.67)
- mean absolute distance = 0.21 +- 0.32
- 3474 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4690865.0, rms=6.44
- 017: dt: 0.5000, sse=4692018.0, rms=4.237 (0.000%)
- rms = 4.44, time step reduction 1 of 3 to 0.250...
- 018: dt: 0.2500, sse=4257104.5, rms=3.144 (0.000%)
- 019: dt: 0.2500, sse=4073331.8, rms=2.476 (0.000%)
- 020: dt: 0.2500, sse=4004546.8, rms=2.013 (0.000%)
- 021: dt: 0.2500, sse=3975618.0, rms=1.883 (0.000%)
- 022: dt: 0.2500, sse=3909592.8, rms=1.728 (0.000%)
- rms = 1.70, time step reduction 2 of 3 to 0.125...
- 023: dt: 0.2500, sse=3925263.5, rms=1.698 (0.000%)
- 024: dt: 0.1250, sse=3791804.8, rms=1.508 (0.000%)
- rms = 1.49, time step reduction 3 of 3 to 0.062...
- 025: dt: 0.1250, sse=3752537.5, rms=1.487 (0.000%)
- positioning took 1.1 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 1 vertex label from ripped group
- mean border=83.1, 17 (2) missing vertices, mean dist -0.1 [0.2 (%77.9)->0.2 (%22.1))]
- %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.89 +- 0.24 (0.10-->4.33) (max @ vno 71071 --> 71070)
- face area 0.34 +- 0.16 (0.00-->2.69)
- mean absolute distance = 0.16 +- 0.25
- 2253 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4109970.0, rms=4.13
- 026: dt: 0.5000, sse=4467671.5, rms=4.058 (0.000%)
- rms = 4.15, time step reduction 1 of 3 to 0.250...
- 027: dt: 0.2500, sse=4004331.8, rms=2.536 (0.000%)
- 028: dt: 0.2500, sse=3874276.2, rms=2.004 (0.000%)
- 029: dt: 0.2500, sse=3941353.2, rms=1.638 (0.000%)
- rms = 1.67, time step reduction 2 of 3 to 0.125...
- 030: dt: 0.1250, sse=3881539.8, rms=1.511 (0.000%)
- 031: dt: 0.1250, sse=3800929.0, rms=1.329 (0.000%)
- rms = 1.31, time step reduction 3 of 3 to 0.062...
- 032: dt: 0.1250, sse=3765311.5, rms=1.310 (0.000%)
- positioning took 0.9 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 1 vertex label from ripped group
- removing 2 vertex label from ripped group
- mean border=84.1, 19 (2) missing vertices, mean dist -0.0 [0.2 (%58.7)->0.1 (%41.3))]
- %92 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- writing white matter surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/lh.white...
- writing smoothed curvature to lh.curv
- 000: dt: 0.0000, sse=3792510.5, rms=1.78
- rms = 2.55, time step reduction 1 of 3 to 0.250...
- 033: dt: 0.2500, sse=3850580.2, rms=1.176 (0.000%)
- 034: dt: 0.2500, sse=3953266.8, rms=0.998 (0.000%)
- rms = 1.00, time step reduction 2 of 3 to 0.125...
- rms = 0.99, time step reduction 3 of 3 to 0.062...
- 035: dt: 0.1250, sse=3951035.8, rms=0.986 (0.000%)
- positioning took 0.5 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- generating cortex label...
- 23 non-cortical segments detected
- only using segment with 2096 vertices
- erasing segment 1 (vno[0] = 59077)
- erasing segment 2 (vno[0] = 84682)
- erasing segment 3 (vno[0] = 88675)
- erasing segment 4 (vno[0] = 90626)
- erasing segment 5 (vno[0] = 92576)
- erasing segment 6 (vno[0] = 98291)
- erasing segment 7 (vno[0] = 98310)
- erasing segment 8 (vno[0] = 99247)
- erasing segment 9 (vno[0] = 101269)
- erasing segment 10 (vno[0] = 101515)
- erasing segment 11 (vno[0] = 103140)
- erasing segment 12 (vno[0] = 103194)
- erasing segment 13 (vno[0] = 104991)
- erasing segment 14 (vno[0] = 106774)
- erasing segment 15 (vno[0] = 106789)
- erasing segment 16 (vno[0] = 108525)
- erasing segment 17 (vno[0] = 109412)
- erasing segment 18 (vno[0] = 111099)
- erasing segment 19 (vno[0] = 111814)
- erasing segment 20 (vno[0] = 111850)
- erasing segment 21 (vno[0] = 135179)
- erasing segment 22 (vno[0] = 135194)
- writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/label/lh.cortex.label...
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/lh.curv
- writing smoothed area to lh.area
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/lh.area
- vertex spacing 0.89 +- 0.25 (0.05-->4.36) (max @ vno 71071 --> 71070)
- face area 0.33 +- 0.15 (0.00-->2.68)
- refinement took 6.6 minutes
- #--------------------------------------------
- #@# Smooth2 lh Thu Aug 8 18:36:43 CEST 2013
- mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/scripts
- smoothing for 3 iterations
- setting seed for random number generator to 1234
- smoothing surface tessellation for 3 iterations...
- smoothing complete - recomputing first and second fundamental forms...
- #--------------------------------------------
- #@# Inflation2 lh Thu Aug 8 18:36:47 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/scripts
- mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated
- avg radius = 48.1 mm, total surface area = 82091 mm^2
- writing inflated surface to ../surf/lh.inflated
- writing sulcal depths to ../surf/lh.sulc
-
step 000: RMS=0.112 (target=0.015)
step 005: RMS=0.077 (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=0.030 (target=0.015)
step 030: RMS=0.025 (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/lh.inflated
- normalizing curvature values.
- averaging curvature patterns 5 times.
- sampling 10 neighbors out to a distance of 10 mm
- 150 vertices thresholded to be in k1 ~ [-0.48 0.30], k2 ~ [-0.17 0.17]
- total integrated curvature = 0.640*4pi (8.044) --> 0 handles
- ICI = 1.7, FI = 11.7, variation=194.062
- 113 vertices thresholded to be in [-0.04 0.01]
- writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level
- curvature mean = 0.000, std = 0.002
- 104 vertices thresholded to be in [-0.14 0.13]
- done.
- writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.017, std = 0.025
- done.
- #-----------------------------------------
- #@# Curvature Stats lh Thu Aug 8 18:38:59 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub020 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 [ sub020/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 [ 206 ]
- Gb_filter = 0
- WARN: S lookup min: -0.931088
- WARN: S explicit min: 0.000000 vertex = 261
- #--------------------------------------------
- #@# Sphere lh Thu Aug 8 18:39:03 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 0.299...
- 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 %19.97
- pass 1: epoch 2 of 3 starting distance error %19.92
- unfolding complete - removing small folds...
- starting distance error %19.82
- removing remaining folds...
- final distance error %19.84
- MRISunfold() return, current seed 1234
- writing spherical brain to ../surf/lh.sphere
- spherical transformation took 0.84 hours
- #--------------------------------------------
- #@# Surf Reg lh Thu Aug 8 19:29:22 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 = 0.564
- curvature mean = 0.041, std = 0.937
- curvature mean = 0.024, std = 0.846
- Starting MRISrigidBodyAlignGlobal()
- d=64.00 min @ (0.00, -16.00, 0.00) sse = 341676.8, tmin=1.2556
- d=32.00 min @ (8.00, 8.00, -8.00) sse = 222731.3, tmin=2.5144
- d=16.00 min @ (0.00, 0.00, 4.00) sse = 219960.7, tmin=3.7944
- d=8.00 min @ (-2.00, 0.00, -2.00) sse = 213106.8, tmin=5.0845
- d=4.00 min @ (1.00, 0.00, 0.00) sse = 211550.7, tmin=6.4025
- d=2.00 min @ (0.00, 0.50, 0.50) sse = 210717.6, tmin=7.7350
- d=0.50 min @ (0.00, 0.00, -0.12) sse = 210684.3, tmin=10.3979
- 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 10.40 min
- curvature mean = 0.004, std = 0.948
- curvature mean = 0.013, std = 0.935
- curvature mean = 0.003, std = 0.961
- curvature mean = 0.006, std = 0.971
- curvature mean = 0.002, std = 0.963
- curvature mean = 0.002, std = 0.988
- 2 Reading smoothwm
- curvature mean = -0.023, std = 0.283
- curvature mean = 0.003, std = 0.067
- curvature mean = 0.067, std = 0.347
- curvature mean = 0.003, std = 0.078
- curvature mean = 0.027, std = 0.541
- curvature mean = 0.003, std = 0.084
- curvature mean = 0.014, std = 0.680
- curvature mean = 0.003, std = 0.087
- curvature mean = 0.004, std = 0.787
- MRISregister() return, current seed 0
- writing registered surface to ../surf/lh.sphere.reg...
- expanding nbhd size to 1
- #--------------------------------------------
- #@# Jacobian white lh Thu Aug 8 19:59:43 CEST 2013
- mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white
- reading surface from ../surf/lh.white...
- writing curvature file ../surf/lh.jacobian_white
- #--------------------------------------------
- #@# AvgCurv lh Thu Aug 8 19:59:45 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/scripts
- mrisp_paint -a 5 /opt/freesurfer/5.3.0/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv
- averaging curvature patterns 5 times...
- reading surface from ../surf/lh.sphere.reg...
- reading template parameterization from /opt/freesurfer/5.3.0/average/lh.average.curvature.filled.buckner40.tif...
- writing curvature file to ../surf/lh.avg_curv...
- #-----------------------------------------
- #@# Cortical Parc lh Thu Aug 8 19:59:47 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub020 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...
- 842 labels changed using aseg
- relabeling using gibbs priors...
- 000: 3192 changed, 135248 examined...
- 001: 759 changed, 13263 examined...
- 002: 199 changed, 4107 examined...
- 003: 90 changed, 1209 examined...
- 004: 42 changed, 533 examined...
- 005: 16 changed, 237 examined...
- 006: 10 changed, 103 examined...
- 007: 0 changed, 37 examined...
- 238 labels changed using aseg
- 000: 130 total segments, 90 labels (368 vertices) changed
- 001: 41 total segments, 2 labels (4 vertices) changed
- 002: 39 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...
- 973 vertices marked for relabeling...
- 973 labels changed in reclassification.
- writing output to ../label/lh.aparc.annot...
- classification took 1 minutes and 0 seconds.
- #--------------------------------------------
- #@# Make Pial Surf lh Thu Aug 8 20:00:47 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/scripts
- mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub020 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/sub020/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/wm.mgz...
- 20443 bright wm thresholded.
- 144 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/lh.orig...
- computing class statistics...
- border white: 255703 voxels (1.52%)
- border gray 281220 voxels (1.68%)
- WM (94.0): 94.7 +- 9.7 [70.0 --> 110.0]
- GM (77.0) : 75.5 +- 13.0 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 49.0 (was 70)
- setting MAX_BORDER_WHITE to 115.7 (was 105)
- setting MIN_BORDER_WHITE to 62.0 (was 85)
- setting MAX_CSF to 36.1 (was 40)
- setting MAX_GRAY to 96.3 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 55.5 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 23.1 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=106, GM=62
- mean inside = 94.2, 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/sub020/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.82 +- 0.21 (0.03-->2.80) (max @ vno 76633 --> 80883)
- face area 0.28 +- 0.12 (0.00-->2.20)
- mean absolute distance = 0.67 +- 0.87
- 2767 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 6 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 4 with 5 points - only 0.00% unknown
- deleting segment 5 with 634 points - only 0.00% unknown
- deleting segment 6 with 18 points - only 0.00% unknown
- deleting segment 9 with 13 points - only 0.00% unknown
- mean border=74.9, 34 (34) missing vertices, mean dist 0.3 [0.6 (%31.9)->0.7 (%68.1))]
- %71 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.91 +- 0.25 (0.10-->3.94) (max @ vno 109297 --> 110154)
- face area 0.28 +- 0.13 (0.00-->2.06)
- mean absolute distance = 0.34 +- 0.52
- 3465 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=6829905.0, rms=13.17
- 001: dt: 0.5000, sse=6854322.5, rms=9.378 (0.000%)
- 002: dt: 0.5000, sse=6986286.5, rms=7.070 (0.000%)
- 003: dt: 0.5000, sse=7236090.5, rms=5.649 (0.000%)
- 004: dt: 0.5000, sse=7452088.5, rms=4.869 (0.000%)
- 005: dt: 0.5000, sse=7630396.0, rms=4.508 (0.000%)
- 006: dt: 0.5000, sse=7690806.0, rms=4.326 (0.000%)
- 007: dt: 0.5000, sse=7689138.0, rms=4.246 (0.000%)
- 008: dt: 0.5000, sse=7707624.0, rms=4.185 (0.000%)
- rms = 4.16, time step reduction 1 of 3 to 0.250...
- 009: dt: 0.5000, sse=7671862.5, rms=4.159 (0.000%)
- 010: dt: 0.2500, sse=4697146.0, rms=2.808 (0.000%)
- 011: dt: 0.2500, sse=4262858.0, rms=2.341 (0.000%)
- 012: dt: 0.2500, sse=4006653.2, rms=2.224 (0.000%)
- 013: dt: 0.2500, sse=3932228.0, rms=2.135 (0.000%)
- rms = 2.10, time step reduction 2 of 3 to 0.125...
- 014: dt: 0.2500, sse=3850114.0, rms=2.102 (0.000%)
- 015: dt: 0.1250, sse=3654377.0, rms=1.875 (0.000%)
- rms = 1.85, time step reduction 3 of 3 to 0.062...
- 016: dt: 0.1250, sse=3616242.8, rms=1.848 (0.000%)
- positioning took 1.9 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- deleting segment 0 with 2 points - only 0.00% unknown
- deleting segment 1 with 6 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- removing 4 vertex label from ripped group
- deleting segment 5 with 477 points - only 0.00% unknown
- deleting segment 7 with 27 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 9 with 6 points - only 0.00% unknown
- deleting segment 13 with 18 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 14 with 3 points - only 0.00% unknown
- deleting segment 16 with 15 points - only 0.00% unknown
- mean border=79.8, 20 (2) missing vertices, mean dist -0.3 [0.4 (%80.6)->0.2 (%19.4))]
- %83 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.90 +- 0.24 (0.09-->4.16) (max @ vno 71071 --> 71070)
- face area 0.35 +- 0.16 (0.00-->2.67)
- mean absolute distance = 0.21 +- 0.32
- 2690 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4713921.5, rms=6.43
- 017: dt: 0.5000, sse=4719222.0, rms=4.229 (0.000%)
- rms = 4.43, time step reduction 1 of 3 to 0.250...
- 018: dt: 0.2500, sse=4282661.0, rms=3.139 (0.000%)
- 019: dt: 0.2500, sse=4095209.8, rms=2.473 (0.000%)
- 020: dt: 0.2500, sse=4026054.2, rms=2.012 (0.000%)
- 021: dt: 0.2500, sse=3997756.8, rms=1.883 (0.000%)
- 022: dt: 0.2500, sse=3931773.8, rms=1.729 (0.000%)
- rms = 1.70, time step reduction 2 of 3 to 0.125...
- 023: dt: 0.2500, sse=3945843.0, rms=1.698 (0.000%)
- 024: dt: 0.1250, sse=3812629.8, rms=1.509 (0.000%)
- rms = 1.49, time step reduction 3 of 3 to 0.062...
- 025: dt: 0.1250, sse=3773701.5, rms=1.488 (0.000%)
- positioning took 1.1 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- deleting segment 0 with 2 points - only 0.00% unknown
- deleting segment 1 with 5 points - only 0.00% unknown
- deleting segment 3 with 504 points - only 0.00% unknown
- deleting segment 4 with 28 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 7 with 14 points - only 0.00% unknown
- deleting segment 8 with 6 points - only 0.00% unknown
- deleting segment 10 with 15 points - only 0.00% unknown
- mean border=83.1, 19 (2) missing vertices, mean dist -0.1 [0.2 (%77.8)->0.2 (%22.2))]
- %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.89 +- 0.24 (0.10-->4.33) (max @ vno 71071 --> 71070)
- face area 0.34 +- 0.15 (0.00-->2.69)
- mean absolute distance = 0.16 +- 0.25
- 2262 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4130833.2, rms=4.12
- 026: dt: 0.5000, sse=4489973.5, rms=4.052 (0.000%)
- rms = 4.15, time step reduction 1 of 3 to 0.250...
- 027: dt: 0.2500, sse=4026188.0, rms=2.533 (0.000%)
- 028: dt: 0.2500, sse=3896845.5, rms=2.002 (0.000%)
- 029: dt: 0.2500, sse=3964422.2, rms=1.637 (0.000%)
- rms = 1.67, time step reduction 2 of 3 to 0.125...
- 030: dt: 0.1250, sse=3904344.8, rms=1.511 (0.000%)
- 031: dt: 0.1250, sse=3822548.8, rms=1.329 (0.000%)
- rms = 1.31, time step reduction 3 of 3 to 0.062...
- 032: dt: 0.1250, sse=3786476.2, rms=1.310 (0.000%)
- positioning took 0.9 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- deleting segment 0 with 2 points - only 0.00% unknown
- deleting segment 1 with 6 points - only 0.00% unknown
- deleting segment 2 with 511 points - only 0.00% unknown
- deleting segment 3 with 29 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 6 with 14 points - only 0.00% unknown
- deleting segment 7 with 9 points - only 0.00% unknown
- deleting segment 9 with 15 points - only 0.00% unknown
- mean border=84.1, 22 (2) missing vertices, mean dist -0.0 [0.2 (%58.6)->0.1 (%41.4))]
- %92 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- repositioning cortical surface to gray/csf boundary.
- smoothing T1 volume with sigma = 2.000
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=3813613.5, rms=1.77
- rms = 2.55, time step reduction 1 of 3 to 0.250...
- 033: dt: 0.2500, sse=3873246.2, rms=1.175 (0.000%)
- 034: dt: 0.2500, sse=3975384.5, rms=0.996 (0.000%)
- rms = 1.00, time step reduction 2 of 3 to 0.125...
- rms = 0.99, time step reduction 3 of 3 to 0.062...
- 035: dt: 0.1250, sse=3973434.5, rms=0.985 (0.000%)
- positioning took 0.5 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- smoothing surface for 5 iterations...
- mean border=51.5, 51 (51) missing vertices, mean dist 1.8 [0.1 (%0.0)->2.2 (%100.0))]
- %18 local maxima, %58 large gradients and %21 min vals, 1022 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=29661960.0, rms=32.36
- 001: dt: 0.5000, sse=21311736.0, rms=26.902 (0.000%)
- 002: dt: 0.5000, sse=15484765.0, rms=22.344 (0.000%)
- 003: dt: 0.5000, sse=11647855.0, rms=18.669 (0.000%)
- 004: dt: 0.5000, sse=9326069.0, rms=15.787 (0.000%)
- 005: dt: 0.5000, sse=8000544.0, rms=13.571 (0.000%)
- 006: dt: 0.5000, sse=7190648.0, rms=11.798 (0.000%)
- 007: dt: 0.5000, sse=6659011.0, rms=10.190 (0.000%)
- 008: dt: 0.5000, sse=6280474.0, rms=8.675 (0.000%)
- 009: dt: 0.5000, sse=6101816.5, rms=7.272 (0.000%)
- 010: dt: 0.5000, sse=6097923.5, rms=6.055 (0.000%)
- 011: dt: 0.5000, sse=6151258.0, rms=5.171 (0.000%)
- 012: dt: 0.5000, sse=6357881.5, rms=4.665 (0.000%)
- 013: dt: 0.5000, sse=6499634.0, rms=4.390 (0.000%)
- 014: dt: 0.5000, sse=6616610.0, rms=4.231 (0.000%)
- 015: dt: 0.5000, sse=6669723.0, rms=4.117 (0.000%)
- 016: dt: 0.5000, sse=6707777.5, rms=4.055 (0.000%)
- 017: dt: 0.5000, sse=6726900.5, rms=3.995 (0.000%)
- rms = 3.98, time step reduction 1 of 3 to 0.250...
- 018: dt: 0.5000, sse=6728921.5, rms=3.979 (0.000%)
- 019: dt: 0.2500, sse=4585510.5, rms=3.120 (0.000%)
- 020: dt: 0.2500, sse=4407923.5, rms=2.905 (0.000%)
- rms = 2.90, time step reduction 2 of 3 to 0.125...
- 021: dt: 0.2500, sse=4284707.0, rms=2.899 (0.000%)
- 022: dt: 0.1250, sse=4048423.0, rms=2.675 (0.000%)
- rms = 2.65, time step reduction 3 of 3 to 0.062...
- 023: dt: 0.1250, sse=4016132.8, rms=2.647 (0.000%)
- positioning took 2.6 minutes
- mean border=48.6, 697 (15) missing vertices, mean dist 0.2 [0.2 (%46.0)->0.6 (%54.0))]
- %35 local maxima, %43 large gradients and %17 min vals, 366 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=4773917.5, rms=5.28
- 024: dt: 0.5000, sse=4983242.5, rms=4.341 (0.000%)
- 025: dt: 0.5000, sse=6493481.0, rms=4.248 (0.000%)
- rms = 4.22, time step reduction 1 of 3 to 0.250...
- 026: dt: 0.5000, sse=6414279.5, rms=4.220 (0.000%)
- 027: dt: 0.2500, sse=4986874.0, rms=3.175 (0.000%)
- 028: dt: 0.2500, sse=4882686.0, rms=2.838 (0.000%)
- rms = 2.85, time step reduction 2 of 3 to 0.125...
- 029: dt: 0.1250, sse=4754148.0, rms=2.724 (0.000%)
- 030: dt: 0.1250, sse=4543004.5, rms=2.561 (0.000%)
- rms = 2.53, time step reduction 3 of 3 to 0.062...
- 031: dt: 0.1250, sse=4487251.0, rms=2.526 (0.000%)
- positioning took 1.0 minutes
- mean border=45.9, 839 (13) missing vertices, mean dist 0.1 [0.2 (%36.7)->0.4 (%63.3))]
- %56 local maxima, %22 large gradients and %17 min vals, 406 gradients ignored
- tol=1.0e-04, sigma=0.5, host=snake, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4846734.0, rms=4.39
- 032: dt: 0.5000, sse=4985756.5, rms=4.163 (0.000%)
- rms = 4.16, time step reduction 1 of 3 to 0.250...
- 033: dt: 0.5000, sse=6680401.5, rms=4.163 (0.000%)
- 034: dt: 0.2500, sse=4852842.0, rms=3.049 (0.000%)
- 035: dt: 0.2500, sse=5028732.5, rms=2.735 (0.000%)
- rms = 2.78, time step reduction 2 of 3 to 0.125...
- 036: dt: 0.1250, sse=4883438.5, rms=2.591 (0.000%)
- 037: dt: 0.1250, sse=4645600.5, rms=2.387 (0.000%)
- rms = 2.35, time step reduction 3 of 3 to 0.062...
- 038: dt: 0.1250, sse=4588248.0, rms=2.354 (0.000%)
- positioning took 0.9 minutes
- mean border=44.7, 1691 (10) missing vertices, mean dist 0.0 [0.2 (%44.7)->0.3 (%55.3))]
- %59 local maxima, %19 large gradients and %17 min vals, 316 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/sub020/surf/lh.pial...
- writing smoothed curvature to lh.curv.pial
- 000: dt: 0.0000, sse=4651571.0, rms=2.85
- rms = 3.80, time step reduction 1 of 3 to 0.250...
- 039: dt: 0.2500, sse=4494846.0, rms=2.499 (0.000%)
- 040: dt: 0.2500, sse=4626353.0, rms=2.410 (0.000%)
- rms = 2.42, time step reduction 2 of 3 to 0.125...
- rms = 2.37, time step reduction 3 of 3 to 0.062...
- 041: dt: 0.1250, sse=4572453.0, rms=2.366 (0.000%)
- positioning took 0.5 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/lh.curv.pial
- writing smoothed area to lh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/lh.area.pial
- vertex spacing 1.00 +- 0.41 (0.11-->7.77) (max @ vno 95684 --> 94761)
- face area 0.40 +- 0.29 (0.00-->8.29)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 135248 vertices processed
- 25000 of 135248 vertices processed
- 50000 of 135248 vertices processed
- 75000 of 135248 vertices processed
- 100000 of 135248 vertices processed
- 125000 of 135248 vertices processed
- 0 of 135248 vertices processed
- 25000 of 135248 vertices processed
- 50000 of 135248 vertices processed
- 75000 of 135248 vertices processed
- 100000 of 135248 vertices processed
- 125000 of 135248 vertices processed
- thickness calculation complete, 331:571 truncations.
- 33374 vertices at 0 distance
- 101022 vertices at 1 distance
- 84343 vertices at 2 distance
- 29818 vertices at 3 distance
- 7822 vertices at 4 distance
- 2057 vertices at 5 distance
- 576 vertices at 6 distance
- 217 vertices at 7 distance
- 90 vertices at 8 distance
- 62 vertices at 9 distance
- 24 vertices at 10 distance
- 18 vertices at 11 distance
- 14 vertices at 12 distance
- 8 vertices at 13 distance
- 6 vertices at 14 distance
- 6 vertices at 15 distance
- 3 vertices at 16 distance
- 2 vertices at 17 distance
- 2 vertices at 18 distance
- 2 vertices at 19 distance
- 6 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/lh.thickness
- positioning took 12.9 minutes
- #--------------------------------------------
- #@# Surf Volume lh Thu Aug 8 20:13:40 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf
- mris_calc -o lh.area.mid lh.area add lh.area.pial
- Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o lh.area.mid lh.area.mid div 2
- Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o lh.volume lh.area.mid mul lh.thickness
- Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ]
- #-----------------------------------------
- #@# WM/GM Contrast lh Thu Aug 8 20:13:40 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/scripts
- pctsurfcon --s sub020 --lh-only
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/scripts/pctsurfcon.log
- Thu Aug 8 20:13:40 CEST 2013
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/scripts
- /opt/freesurfer/5.3.0/bin/pctsurfcon
- $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $
- Linux snake6 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
- FREESURFER_HOME /opt/freesurfer/5.3.0
- mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/tmp.pctsurfcon.8938/lh.wm.mgh --regheader sub020 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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/sub020/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/label/lh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 = 105040
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/label/lh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/tmp.pctsurfcon.8938/lh.wm.mgh
- Dim: 135248 1 1
- mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/tmp.pctsurfcon.8938/lh.gm.mgh --projfrac 0.3 --regheader sub020 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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/sub020/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/label/lh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/lh.white
- Done reading source surface
- Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 = 120541
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/label/lh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/tmp.pctsurfcon.8938/lh.gm.mgh
- Dim: 135248 1 1
- mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/tmp.pctsurfcon.8938/lh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/tmp.pctsurfcon.8938/lh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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/sub020/surf/lh.w-g.pct.mgh
- mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/lh.w-g.pct.mgh --annot sub020 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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/sub020/surf/lh.w-g.pct.mgh --annot sub020 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/stats/lh.w-g.pct.stats --snr
- sysname Linux
- hostname snake6
- machine x86_64
- user fkaule
- UseRobust 0
- Constructing seg from annotation
- Reading annotation
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
- Seg base 1000
- Loading /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/lh.w-g.pct.mgh
- Vertex Area is 0.659815 mm^3
- Generating list of segmentation ids
- Found 36 segmentations
- Computing statistics for each segmentation
- 0 1000 unknown 0 0.000
- 1 1001 bankssts 1296 906.378
- 2 1002 caudalanteriorcingulate 790 545.621
- 3 1003 caudalmiddlefrontal 3642 2464.030
- 4 1004 corpuscallosum 0 0.000
- 5 1005 cuneus 2193 1421.663
- 6 1006 entorhinal 696 470.627
- 7 1007 fusiform 4684 3103.549
- 8 1008 inferiorparietal 6388 4242.716
- 9 1009 inferiortemporal 4877 3245.670
- 10 1010 isthmuscingulate 1625 1054.245
- 11 1011 lateraloccipital 8481 5409.865
- 12 1012 lateralorbitofrontal 3368 2250.251
- 13 1013 lingual 4600 2999.097
- 14 1014 medialorbitofrontal 2099 1388.502
- 15 1015 middletemporal 4211 2917.102
- 16 1016 parahippocampal 1130 743.088
- 17 1017 paracentral 2361 1501.160
- 18 1018 parsopercularis 2236 1521.886
- 19 1019 parsorbitalis 974 645.524
- 20 1020 parstriangularis 1437 966.584
- 21 1021 pericalcarine 1883 1281.285
- 22 1022 postcentral 6374 4115.595
- 23 1023 posteriorcingulate 1697 1145.847
- 24 1024 precentral 7954 4873.109
- 25 1025 precuneus 5645 3795.903
- 26 1026 rostralanteriorcingulate 1258 836.469
- 27 1027 rostralmiddlefrontal 9336 6216.244
- 28 1028 superiorfrontal 11685 7965.146
- 29 1029 superiorparietal 7646 5027.424
- 30 1030 superiortemporal 5562 3786.643
- 31 1031 supramarginal 6139 4128.002
- 32 1032 frontalpole 241 160.821
- 33 1033 temporalpole 706 482.521
- 34 1034 transversetemporal 967 545.626
- 35 1035 insula 3133 2041.708
- Reporting on 34 segmentations
- mri_segstats done
- Cleaning up
- #-----------------------------------------
- #@# Parcellation Stats lh Thu Aug 8 20:13:54 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 sub020 lh white
- computing statistics for each annotation in ../label/lh.aparc.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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
- 1296 906 2096 2.284 0.361 0.123 0.038 14 2.0 bankssts
- 790 546 1605 2.453 0.518 0.131 0.035 11 1.2 caudalanteriorcingulate
- 3642 2464 6611 2.552 0.366 0.130 0.039 41 5.5 caudalmiddlefrontal
- 2193 1422 3263 2.067 0.435 0.171 0.064 46 6.1 cuneus
- 696 471 2261 3.369 0.979 0.141 0.364 56 2.2 entorhinal
- 4684 3104 10170 2.869 0.523 0.153 0.055 90 10.2 fusiform
- 6388 4243 11347 2.393 0.397 0.133 0.051 113 12.3 inferiorparietal
- 4877 3246 10556 2.728 0.691 0.142 0.051 85 10.4 inferiortemporal
- 1625 1054 2976 2.598 0.576 0.155 0.228 121 5.1 isthmuscingulate
- 8481 5410 12588 2.136 0.445 0.151 0.057 154 18.9 lateraloccipital
- 3368 2250 6383 2.471 0.683 0.152 0.068 59 8.4 lateralorbitofrontal
- 4600 2999 7628 2.336 0.569 0.166 0.076 100 12.9 lingual
- 2099 1389 3663 2.256 0.717 0.173 0.122 111 10.0 medialorbitofrontal
- 4211 2917 9062 2.615 0.646 0.142 0.049 69 8.1 middletemporal
- 1130 743 2180 2.532 0.532 0.104 0.026 9 1.2 parahippocampal
- 2361 1501 4303 2.535 0.473 0.128 0.042 28 4.4 paracentral
- 2236 1522 4556 2.623 0.373 0.140 0.045 34 4.3 parsopercularis
- 974 646 2266 2.665 0.617 0.150 0.051 21 1.8 parsorbitalis
- 1437 967 2618 2.412 0.383 0.143 0.044 24 2.6 parstriangularis
- 1883 1281 2141 1.888 0.402 0.164 0.061 28 4.8 pericalcarine
- 6374 4116 9843 2.075 0.511 0.121 0.036 74 9.7 postcentral
- 1697 1146 3114 2.509 0.444 0.146 0.053 32 3.7 posteriorcingulate
- 7954 4873 14232 2.648 0.503 0.116 0.058 148 16.6 precentral
- 5645 3796 9878 2.383 0.439 0.143 0.058 114 15.0 precuneus
- 1258 836 2538 2.438 0.629 0.149 0.064 26 3.4 rostralanteriorcingulate
- 9336 6216 16528 2.287 0.459 0.148 0.055 179 19.0 rostralmiddlefrontal
- 11685 7965 24052 2.604 0.560 0.133 0.039 145 18.4 superiorfrontal
- 7646 5027 12244 2.225 0.412 0.135 0.047 246 15.5 superiorparietal
- 5562 3787 12207 2.858 0.560 0.124 0.034 60 8.0 superiortemporal
- 6139 4128 11698 2.523 0.428 0.142 0.046 91 11.7 supramarginal
- 241 161 518 2.352 0.664 0.205 0.073 7 0.7 frontalpole
- 706 483 2709 3.783 0.637 0.137 0.057 10 1.3 temporalpole
- 967 546 1604 2.528 0.326 0.116 0.066 13 1.9 transversetemporal
- 3133 2042 6445 3.033 0.762 0.123 0.056 57 6.7 insula
- #-----------------------------------------
- #@# Cortical Parc 2 lh Thu Aug 8 20:14:12 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub020 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...
- 108 labels changed using aseg
- relabeling using gibbs priors...
- 000: 9174 changed, 135248 examined...
- 001: 2199 changed, 35624 examined...
- 002: 702 changed, 11314 examined...
- 003: 291 changed, 3853 examined...
- 004: 137 changed, 1682 examined...
- 005: 59 changed, 804 examined...
- 006: 30 changed, 357 examined...
- 007: 18 changed, 186 examined...
- 008: 10 changed, 106 examined...
- 009: 4 changed, 53 examined...
- 010: 2 changed, 17 examined...
- 011: 2 changed, 12 examined...
- 012: 2 changed, 10 examined...
- 013: 0 changed, 7 examined...
- 21 labels changed using aseg
- 000: 283 total segments, 201 labels (2890 vertices) changed
- 001: 97 total segments, 16 labels (34 vertices) changed
- 002: 81 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 122 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 502 vertices marked for relabeling...
- 502 labels changed in reclassification.
- writing output to ../label/lh.aparc.a2009s.annot...
- classification took 1 minutes and 9 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 2 lh Thu Aug 8 20:15:20 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 sub020 lh white
- computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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
- 1394 925 2195 2.044 0.483 0.165 0.080 34 3.8 G_and_S_frontomargin
- 1605 1050 2866 2.434 0.409 0.157 0.050 29 3.3 G_and_S_occipital_inf
- 1930 1115 3420 2.479 0.498 0.128 0.065 59 6.0 G_and_S_paracentral
- 1653 1126 3251 2.452 0.441 0.142 0.046 26 3.4 G_and_S_subcentral
- 595 413 1099 2.184 0.480 0.185 0.066 17 1.7 G_and_S_transv_frontopol
- 2406 1658 4685 2.461 0.558 0.143 0.053 39 5.5 G_and_S_cingul-Ant
- 1149 797 2139 2.491 0.487 0.126 0.032 12 1.6 G_and_S_cingul-Mid-Ant
- 1581 1058 2697 2.474 0.434 0.133 0.040 22 2.6 G_and_S_cingul-Mid-Post
- 578 385 1352 2.880 0.405 0.159 0.068 13 1.7 G_cingul-Post-dorsal
- 361 216 642 2.416 0.782 0.148 0.071 7 0.9 G_cingul-Post-ventral
- 1987 1295 3105 2.043 0.460 0.175 0.072 45 6.0 G_cuneus
- 1270 838 3017 2.769 0.351 0.154 0.052 26 2.8 G_front_inf-Opercular
- 277 168 623 2.933 0.406 0.171 0.074 6 0.8 G_front_inf-Orbital
- 958 654 2211 2.598 0.325 0.169 0.059 24 2.6 G_front_inf-Triangul
- 5431 3628 11510 2.529 0.408 0.155 0.054 109 11.1 G_front_middle
- 7943 5356 18171 2.727 0.578 0.139 0.045 113 14.1 G_front_sup
- 653 413 1330 3.017 0.520 0.134 0.074 11 1.7 G_Ins_lg_and_S_cent_ins
- 675 421 2164 3.763 0.669 0.139 0.103 34 2.7 G_insular_short
- 2187 1385 4418 2.445 0.444 0.157 0.064 49 5.3 G_occipital_middle
- 1546 974 2452 2.224 0.355 0.159 0.058 29 3.9 G_occipital_sup
- 1949 1217 4602 2.961 0.479 0.172 0.066 52 5.3 G_oc-temp_lat-fusifor
- 3062 1981 5330 2.300 0.604 0.180 0.088 79 10.1 G_oc-temp_med-Lingual
- 1134 743 3012 2.912 0.855 0.104 0.026 9 1.2 G_oc-temp_med-Parahip
- 2466 1583 5886 2.735 0.637 0.176 0.098 74 7.9 G_orbital
- 2523 1628 5162 2.487 0.364 0.153 0.067 71 6.2 G_pariet_inf-Angular
- 3121 2109 7142 2.690 0.426 0.151 0.050 53 6.4 G_pariet_inf-Supramar
- 3016 1990 5888 2.383 0.442 0.139 0.048 52 5.8 G_parietal_sup
- 2404 1473 4234 2.247 0.441 0.125 0.038 32 3.7 G_postcentral
- 3280 1835 7065 2.943 0.398 0.116 0.046 58 6.3 G_precentral
- 2515 1662 5477 2.553 0.438 0.167 0.087 87 10.7 G_precuneus
- 765 490 1684 2.483 0.511 0.197 0.116 56 2.5 G_rectus
- 317 204 550 2.543 0.881 0.230 0.359 40 5.7 G_subcallosal
- 725 389 1354 2.637 0.385 0.122 0.080 12 1.7 G_temp_sup-G_T_transv
- 2010 1331 5768 3.138 0.507 0.156 0.051 38 4.1 G_temp_sup-Lateral
- 477 341 1286 3.542 0.449 0.103 0.040 4 1.0 G_temp_sup-Plan_polar
- 1184 798 2423 2.639 0.430 0.128 0.044 15 2.2 G_temp_sup-Plan_tempo
- 2887 1858 7022 2.798 0.681 0.158 0.065 69 7.9 G_temporal_inf
- 2554 1747 6404 2.716 0.657 0.162 0.065 60 6.3 G_temporal_middle
- 261 178 437 2.433 0.352 0.095 0.023 1 0.2 Lat_Fis-ant-Horizont
- 273 198 443 2.207 0.308 0.104 0.022 1 0.3 Lat_Fis-ant-Vertical
- 1214 838 1673 2.420 0.328 0.127 0.034 10 1.8 Lat_Fis-post
- 2612 1620 3275 1.879 0.407 0.165 0.081 64 8.2 Pole_occipital
- 1962 1338 6433 3.420 0.718 0.149 0.165 77 4.7 Pole_temporal
- 2539 1711 3183 2.126 0.520 0.151 0.051 32 5.5 S_calcarine
- 3250 2154 3964 2.024 0.611 0.112 0.067 40 5.4 S_central
- 1243 848 1804 2.259 0.327 0.114 0.028 9 1.5 S_cingul-Marginalis
- 525 352 939 3.017 0.608 0.124 0.040 5 0.9 S_circular_insula_ant
- 1500 1022 2524 2.737 0.572 0.091 0.018 7 1.2 S_circular_insula_inf
- 1566 1061 2275 2.476 0.427 0.114 0.030 10 2.0 S_circular_insula_sup
- 1161 808 1996 2.692 0.529 0.105 0.026 8 1.2 S_collat_transv_ant
- 356 241 455 2.226 0.334 0.131 0.038 3 0.5 S_collat_transv_post
- 2233 1493 3136 2.231 0.371 0.114 0.029 17 2.6 S_front_inf
- 2018 1341 2880 2.138 0.379 0.117 0.031 18 2.6 S_front_middle
- 2769 1904 4463 2.380 0.379 0.120 0.031 28 3.6 S_front_sup
- 765 494 932 2.167 0.272 0.096 0.020 3 0.7 S_interm_prim-Jensen
- 3205 2144 4470 2.239 0.314 0.125 0.041 168 6.2 S_intrapariet_and_P_trans
- 1882 1227 2402 2.094 0.327 0.132 0.038 20 2.9 S_oc_middle_and_Lunatus
- 1325 867 1672 2.129 0.376 0.130 0.039 14 2.1 S_oc_sup_and_transversal
- 738 495 921 2.035 0.440 0.111 0.026 6 0.8 S_occipital_ant
- 740 490 1093 2.603 0.619 0.160 0.062 13 1.7 S_oc-temp_lat
- 2129 1471 3472 2.495 0.396 0.127 0.043 24 3.1 S_oc-temp_med_and_Lingual
- 490 333 752 2.219 0.467 0.128 0.031 5 0.7 S_orbital_lateral
- 411 311 680 2.004 0.610 0.113 0.027 3 0.5 S_orbital_med-olfact
- 1201 836 1701 1.973 0.507 0.137 0.039 14 2.0 S_orbital-H_Shaped
- 2083 1434 2811 2.137 0.430 0.144 0.043 27 3.8 S_parieto_occipital
- 837 523 1219 2.451 0.624 0.175 0.404 111 3.6 S_pericallosal
- 2427 1613 3061 2.045 0.344 0.117 0.033 22 3.2 S_postcentral
- 1522 1025 2352 2.466 0.379 0.116 0.031 12 2.0 S_precentral-inf-part
- 1132 786 1686 2.399 0.456 0.105 0.023 6 1.2 S_precentral-sup-part
- 678 444 913 2.059 0.797 0.139 0.051 9 1.2 S_suborbital
- 1157 774 1730 2.307 0.387 0.116 0.032 8 1.5 S_subparietal
- 1424 991 2303 2.496 0.715 0.122 0.030 12 2.0 S_temporal_inf
- 4680 3268 7580 2.390 0.421 0.114 0.031 41 6.0 S_temporal_sup
- 438 311 616 2.437 0.287 0.113 0.026 3 0.5 S_temporal_transverse
- #-----------------------------------------
- #@# Cortical Parc 3 lh Thu Aug 8 20:15:38 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub020 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...
- 967 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2695 changed, 135248 examined...
- 001: 595 changed, 11313 examined...
- 002: 158 changed, 3188 examined...
- 003: 52 changed, 932 examined...
- 004: 19 changed, 337 examined...
- 005: 16 changed, 127 examined...
- 006: 9 changed, 88 examined...
- 007: 5 changed, 45 examined...
- 008: 6 changed, 34 examined...
- 009: 3 changed, 28 examined...
- 010: 2 changed, 24 examined...
- 011: 3 changed, 8 examined...
- 012: 2 changed, 13 examined...
- 013: 3 changed, 11 examined...
- 014: 2 changed, 11 examined...
- 015: 2 changed, 11 examined...
- 016: 0 changed, 12 examined...
- 124 labels changed using aseg
- 000: 84 total segments, 51 labels (259 vertices) changed
- 001: 34 total segments, 1 labels (1 vertices) changed
- 002: 33 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 59 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 381 vertices marked for relabeling...
- 381 labels changed in reclassification.
- writing output to ../label/lh.aparc.DKTatlas40.annot...
- classification took 1 minutes and 0 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 3 lh Thu Aug 8 20:16:38 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 sub020 lh white
- computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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
- 1374 941 2586 2.483 0.588 0.125 0.032 16 1.8 caudalanteriorcingulate
- 3676 2488 6699 2.558 0.368 0.129 0.038 40 5.5 caudalmiddlefrontal
- 3072 2016 4496 2.044 0.423 0.163 0.058 59 7.7 cuneus
- 641 439 2064 3.350 0.982 0.116 0.034 5 1.0 entorhinal
- 4151 2736 8711 2.843 0.504 0.153 0.056 81 9.2 fusiform
- 6360 4199 11180 2.384 0.395 0.134 0.052 114 12.5 inferiorparietal
- 5207 3463 11425 2.735 0.681 0.146 0.093 140 11.8 inferiortemporal
- 1614 1044 2946 2.599 0.578 0.157 0.230 121 5.2 isthmuscingulate
- 8601 5484 12711 2.125 0.446 0.152 0.057 158 19.2 lateraloccipital
- 3489 2316 6602 2.370 0.694 0.158 0.080 74 9.5 lateralorbitofrontal
- 4572 2979 7581 2.338 0.569 0.167 0.076 100 12.9 lingual
- 1766 1165 3174 2.274 0.718 0.174 0.120 94 8.3 medialorbitofrontal
- 5284 3660 11061 2.603 0.650 0.136 0.046 79 9.6 middletemporal
- 1175 777 2259 2.523 0.532 0.104 0.026 9 1.2 parahippocampal
- 2633 1687 4802 2.535 0.463 0.126 0.041 30 4.6 paracentral
- 1901 1289 3820 2.625 0.372 0.141 0.046 30 3.7 parsopercularis
- 894 591 1902 2.703 0.588 0.140 0.043 14 1.6 parsorbitalis
- 2009 1348 3476 2.364 0.426 0.139 0.043 30 3.4 parstriangularis
- 1877 1275 2131 1.891 0.400 0.163 0.060 27 4.7 pericalcarine
- 6881 4467 10677 2.092 0.513 0.122 0.037 79 10.5 postcentral
- 1793 1213 3228 2.507 0.444 0.146 0.052 32 3.9 posteriorcingulate
- 7916 4840 14107 2.649 0.501 0.117 0.059 149 16.7 precentral
- 5499 3706 9888 2.399 0.431 0.143 0.059 114 14.9 precuneus
- 1667 1103 3143 2.392 0.646 0.153 0.075 44 5.2 rostralanteriorcingulate
- 6320 4213 11951 2.386 0.461 0.145 0.052 114 12.2 rostralmiddlefrontal
- 13635 9268 27443 2.524 0.563 0.139 0.043 199 23.6 superiorfrontal
- 6131 4009 9883 2.261 0.403 0.134 0.046 224 12.6 superiorparietal
- 7315 5011 16850 2.889 0.645 0.129 0.040 90 12.0 superiortemporal
- 6008 4040 11338 2.522 0.427 0.141 0.044 84 11.0 supramarginal
- 951 534 1578 2.526 0.326 0.116 0.066 13 1.9 transversetemporal
- 2902 1900 6171 3.082 0.743 0.118 0.054 53 6.0 insula
- #--------------------------------------------
- #@# Tessellate rh Thu Aug 8 20:16:54 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/scripts
- mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz
- Iteration Number : 1
- pass 1 (xy+): 3 found - 3 modified | TOTAL: 3
- pass 2 (xy+): 0 found - 3 modified | TOTAL: 3
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 3
- pass 1 (yz+): 2 found - 2 modified | TOTAL: 5
- pass 2 (yz+): 0 found - 2 modified | TOTAL: 5
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 5
- pass 1 (xz+): 2 found - 2 modified | TOTAL: 7
- pass 2 (xz+): 0 found - 2 modified | TOTAL: 7
- pass 1 (xz-): 5 found - 5 modified | TOTAL: 12
- pass 2 (xz-): 0 found - 5 modified | TOTAL: 12
- Iteration Number : 1
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 1
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 2 found - 2 modified | TOTAL: 2
- pass 2 (--): 0 found - 2 modified | TOTAL: 2
- pass 1 (-+): 4 found - 4 modified | TOTAL: 6
- pass 2 (-+): 0 found - 4 modified | TOTAL: 6
- Iteration Number : 2
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Total Number of Modified Voxels = 18 (out of 270409: 0.006657)
- 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: 356 vertices, 421 faces
- slice 50: 4892 vertices, 5106 faces
- slice 60: 13510 vertices, 13891 faces
- slice 70: 24863 vertices, 25256 faces
- slice 80: 36651 vertices, 37101 faces
- slice 90: 48436 vertices, 48803 faces
- slice 100: 60369 vertices, 60782 faces
- slice 110: 72015 vertices, 72389 faces
- slice 120: 82769 vertices, 83148 faces
- slice 130: 93391 vertices, 93788 faces
- slice 140: 103684 vertices, 104052 faces
- slice 150: 113125 vertices, 113421 faces
- slice 160: 120954 vertices, 121177 faces
- slice 170: 127252 vertices, 127485 faces
- slice 180: 132781 vertices, 132964 faces
- slice 190: 136426 vertices, 136570 faces
- slice 200: 137292 vertices, 137308 faces
- slice 210: 137292 vertices, 137308 faces
- slice 220: 137292 vertices, 137308 faces
- slice 230: 137292 vertices, 137308 faces
- slice 240: 137292 vertices, 137308 faces
- slice 250: 137292 vertices, 137308 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...
- 137284 voxel in cpt #1: X=-18 [v=137284,e=411906,f=274604] located at (30.285721, -19.334991, 36.066875)
- 8 voxel in cpt #2: X=2 [v=8,e=18,f=12] located at (1.000000, 16.000000, 34.000000)
- For the whole surface: X=-16 [v=137292,e=411924,f=274616]
- 2 components have been found
- keeping component #1 with 137284 vertices
- done
- #--------------------------------------------
- #@# Smooth1 rh Thu Aug 8 20:17:02 CEST 2013
- mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/scripts
- setting seed for random number generator to 1234
- smoothing surface tessellation for 10 iterations...
- smoothing complete - recomputing first and second fundamental forms...
- #--------------------------------------------
- #@# Inflation1 rh Thu Aug 8 20:17:06 CEST 2013
- mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/scripts
- avg radius = 46.3 mm, total surface area = 72738 mm^2
- writing inflated surface to ../surf/rh.inflated.nofix
- inflation took 0.5 minutes
- Not saving sulc
-
step 000: RMS=0.098 (target=0.015)
step 005: RMS=0.071 (target=0.015)
step 010: RMS=0.051 (target=0.015)
step 015: RMS=0.042 (target=0.015)
step 020: RMS=0.036 (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=0.023 (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 rh Thu Aug 8 20:17:39 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/scripts
- mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix
- doing quick spherical unfolding.
- setting seed for random number genererator to 1234
- $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading original vertex positions...
- unfolding cortex into spherical form...
- surface projected - minimizing metric distortion...
- vertex spacing 1.00 +- 0.55 (0.00-->6.37) (max @ vno 57504 --> 58735)
- face area 0.03 +- 0.03 (-0.04-->0.81)
- scaling brain by 0.321...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=176.219, avgs=0
- 005/300: dt: 0.9000, rms radial error=175.962, avgs=0
- 010/300: dt: 0.9000, rms radial error=175.411, avgs=0
- 015/300: dt: 0.9000, rms radial error=174.685, avgs=0
- 020/300: dt: 0.9000, rms radial error=173.856, avgs=0
- 025/300: dt: 0.9000, rms radial error=172.970, avgs=0
- 030/300: dt: 0.9000, rms radial error=172.051, avgs=0
- 035/300: dt: 0.9000, rms radial error=171.114, avgs=0
- 040/300: dt: 0.9000, rms radial error=170.169, avgs=0
- 045/300: dt: 0.9000, rms radial error=169.222, avgs=0
- 050/300: dt: 0.9000, rms radial error=168.275, avgs=0
- 055/300: dt: 0.9000, rms radial error=167.331, avgs=0
- 060/300: dt: 0.9000, rms radial error=166.391, avgs=0
- 065/300: dt: 0.9000, rms radial error=165.455, avgs=0
- 070/300: dt: 0.9000, rms radial error=164.524, avgs=0
- 075/300: dt: 0.9000, rms radial error=163.598, avgs=0
- 080/300: dt: 0.9000, rms radial error=162.677, avgs=0
- 085/300: dt: 0.9000, rms radial error=161.761, avgs=0
- 090/300: dt: 0.9000, rms radial error=160.850, avgs=0
- 095/300: dt: 0.9000, rms radial error=159.943, avgs=0
- 100/300: dt: 0.9000, rms radial error=159.042, avgs=0
- 105/300: dt: 0.9000, rms radial error=158.146, avgs=0
- 110/300: dt: 0.9000, rms radial error=157.255, avgs=0
- 115/300: dt: 0.9000, rms radial error=156.368, avgs=0
- 120/300: dt: 0.9000, rms radial error=155.486, avgs=0
- 125/300: dt: 0.9000, rms radial error=154.610, avgs=0
- 130/300: dt: 0.9000, rms radial error=153.738, avgs=0
- 135/300: dt: 0.9000, rms radial error=152.871, avgs=0
- 140/300: dt: 0.9000, rms radial error=152.009, avgs=0
- 145/300: dt: 0.9000, rms radial error=151.152, avgs=0
- 150/300: dt: 0.9000, rms radial error=150.300, avgs=0
- 155/300: dt: 0.9000, rms radial error=149.452, avgs=0
- 160/300: dt: 0.9000, rms radial error=148.609, avgs=0
- 165/300: dt: 0.9000, rms radial error=147.771, avgs=0
- 170/300: dt: 0.9000, rms radial error=146.940, avgs=0
- 175/300: dt: 0.9000, rms radial error=146.113, avgs=0
- 180/300: dt: 0.9000, rms radial error=145.290, avgs=0
- 185/300: dt: 0.9000, rms radial error=144.473, avgs=0
- 190/300: dt: 0.9000, rms radial error=143.660, avgs=0
- 195/300: dt: 0.9000, rms radial error=142.851, avgs=0
- 200/300: dt: 0.9000, rms radial error=142.047, avgs=0
- 205/300: dt: 0.9000, rms radial error=141.247, avgs=0
- 210/300: dt: 0.9000, rms radial error=140.452, avgs=0
- 215/300: dt: 0.9000, rms radial error=139.661, avgs=0
- 220/300: dt: 0.9000, rms radial error=138.874, avgs=0
- 225/300: dt: 0.9000, rms radial error=138.092, avgs=0
- 230/300: dt: 0.9000, rms radial error=137.315, avgs=0
- 235/300: dt: 0.9000, rms radial error=136.541, avgs=0
- 240/300: dt: 0.9000, rms radial error=135.772, avgs=0
- 245/300: dt: 0.9000, rms radial error=135.007, avgs=0
- 250/300: dt: 0.9000, rms radial error=134.247, avgs=0
- 255/300: dt: 0.9000, rms radial error=133.491, avgs=0
- 260/300: dt: 0.9000, rms radial error=132.738, avgs=0
- 265/300: dt: 0.9000, rms radial error=131.991, avgs=0
- 270/300: dt: 0.9000, rms radial error=131.247, avgs=0
- 275/300: dt: 0.9000, rms radial error=130.507, avgs=0
- 280/300: dt: 0.9000, rms radial error=129.771, avgs=0
- 285/300: dt: 0.9000, rms radial error=129.040, avgs=0
- 290/300: dt: 0.9000, rms radial error=128.312, avgs=0
- 295/300: dt: 0.9000, rms radial error=127.589, avgs=0
- 300/300: dt: 0.9000, rms radial error=126.869, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 15867.47
- 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 = 2568.14
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00015
- epoch 3 (K=160.0), pass 1, starting sse = 240.26
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.12/13 = 0.00961
- epoch 4 (K=640.0), pass 1, starting sse = 11.41
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.43/22 = 0.01951
- final writing spherical brain to ../surf/rh.qsphere.nofix
- spherical transformation took 0.09 hours
- distance error %100000.00
- #--------------------------------------------
- #@# Fix Topology rh Thu Aug 8 20:23:10 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/sub020/scripts
- mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub020 rh
- reading spherical homeomorphism from 'qsphere.nofix'
- using genetic algorithm with optimized parameters
- setting seed for random number genererator to 1234
- *************************************************************
- Topology Correction Parameters
- retessellation mode: genetic search
- number of patches/generation : 10
- number of generations : 10
- surface mri loglikelihood coefficient : 1.0
- volume mri loglikelihood coefficient : 10.0
- normal dot loglikelihood coefficient : 1.0
- quadratic curvature loglikelihood coefficient : 1.0
- volume resolution : 2
- eliminate vertices during search : 1
- initial patch selection : 1
- select all defect vertices : 0
- ordering dependant retessellation: 0
- use precomputed edge table : 0
- smooth retessellated patch : 2
- match retessellated patch : 1
- verbose mode : 0
- *************************************************************
- INFO: assuming .mgz format
- $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- before topology correction, eno=-18 (nv=137284, nf=274604, ne=411906, g=10)
- using quasi-homeomorphic spherical map to tessellate cortical surface...
- Correction of the Topology
- Finding true center and radius of Spherical Surface...done
- Surface centered at (0,0,0) with radius 100.0 in 8 iterations
- marking ambiguous vertices...
- 1200 ambiguous faces found in tessellation
- segmenting defects...
- 17 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- 17 defects to be corrected
- 0 vertices coincident
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/rh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -9.7267 (-4.8633)
- -vertex loglikelihood: -6.6431 (-3.3216)
- -normal dot loglikelihood: -3.6827 (-3.6827)
- -quad curv loglikelihood: -6.4023 (-3.2011)
- Total Loglikelihood : -26.4548
- CORRECTING DEFECT 0 (vertices=15, convex hull=31)
- After retessellation of defect 0, euler #=-14 (136539,409315,272762) : difference with theory (-14) = 0
- CORRECTING DEFECT 1 (vertices=157, convex hull=51)
- After retessellation of defect 1, euler #=-13 (136556,409387,272818) : difference with theory (-13) = 0
- CORRECTING DEFECT 2 (vertices=34, convex hull=61)
- After retessellation of defect 2, euler #=-12 (136573,409462,272877) : difference with theory (-12) = 0
- CORRECTING DEFECT 3 (vertices=24, convex hull=42)
- After retessellation of defect 3, euler #=-11 (136584,409509,272914) : difference with theory (-11) = 0
- CORRECTING DEFECT 4 (vertices=29, convex hull=59)
- After retessellation of defect 4, euler #=-10 (136594,409569,272965) : difference with theory (-10) = 0
- CORRECTING DEFECT 5 (vertices=176, convex hull=105)
- After retessellation of defect 5, euler #=-9 (136644,409763,273110) : difference with theory (-9) = 0
- CORRECTING DEFECT 6 (vertices=33, convex hull=58)
- After retessellation of defect 6, euler #=-8 (136654,409817,273155) : difference with theory (-8) = 0
- CORRECTING DEFECT 7 (vertices=34, convex hull=64)
- After retessellation of defect 7, euler #=-7 (136671,409892,273214) : difference with theory (-7) = 0
- CORRECTING DEFECT 8 (vertices=58, convex hull=29)
- After retessellation of defect 8, euler #=-6 (136680,409932,273246) : difference with theory (-6) = 0
- CORRECTING DEFECT 9 (vertices=14, convex hull=26)
- After retessellation of defect 9, euler #=-5 (136681,409944,273258) : difference with theory (-5) = 0
- CORRECTING DEFECT 10 (vertices=8, convex hull=32)
- Warning - incorrect dp selected!!!!(-74.921190 >= -74.921192 )
- After retessellation of defect 10, euler #=-4 (136684,409963,273275) : difference with theory (-4) = 0
- CORRECTING DEFECT 11 (vertices=10, convex hull=23)
- After retessellation of defect 11, euler #=-3 (136685,409973,273285) : difference with theory (-3) = 0
- CORRECTING DEFECT 12 (vertices=32, convex hull=33)
- After retessellation of defect 12, euler #=-2 (136688,409992,273302) : difference with theory (-2) = 0
- CORRECTING DEFECT 13 (vertices=48, convex hull=33)
- After retessellation of defect 13, euler #=-1 (136695,410021,273325) : difference with theory (-1) = 0
- CORRECTING DEFECT 14 (vertices=20, convex hull=41)
- After retessellation of defect 14, euler #=0 (136706,410069,273363) : difference with theory (0) = 0
- CORRECTING DEFECT 15 (vertices=25, convex hull=57)
- After retessellation of defect 15, euler #=1 (136718,410123,273406) : difference with theory (1) = 0
- CORRECTING DEFECT 16 (vertices=31, convex hull=57)
- After retessellation of defect 16, euler #=2 (136728,410178,273452) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.88 +- 0.21 (0.09-->5.28) (max @ vno 125370 --> 125419)
- 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 (0.09-->5.28) (max @ vno 125370 --> 125419)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 64 mutations (38.1%), 104 crossovers (61.9%), 17 vertices were eliminated
- building final representation...
- 556 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=136728, nf=273452, ne=410178, g=0)
- writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/rh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 9.2 minutes
- 0 defective edges
- removing intersecting faces
- 000: 82 intersecting
- mris_euler_number ../surf/rh.orig
- euler # = v-e+f = 2g-2: 136728 - 410178 + 273452 = 2 --> 0 holes
- F =2V-4: 273452 = 273456-4 (0)
- 2E=3F: 820356 = 820356 (0)
- total defect index = 0
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/scripts
- mris_remove_intersection ../surf/rh.orig ../surf/rh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 18 intersecting
- 001: 2 intersecting
- writing corrected surface to ../surf/rh.orig
- rm ../surf/rh.inflated
- #--------------------------------------------
- #@# Make White Surf rh Thu Aug 8 20:32:29 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/scripts
- mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub020 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/sub020/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/wm.mgz...
- 19247 bright wm thresholded.
- 144 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/rh.orig...
- computing class statistics...
- border white: 255703 voxels (1.52%)
- border gray 281220 voxels (1.68%)
- WM (94.0): 94.7 +- 9.7 [70.0 --> 110.0]
- GM (77.0) : 75.3 +- 13.1 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 47.9 (was 70)
- setting MAX_BORDER_WHITE to 115.7 (was 105)
- setting MIN_BORDER_WHITE to 61.0 (was 85)
- setting MAX_CSF to 34.7 (was 40)
- setting MAX_GRAY to 96.3 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 54.4 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 21.6 (was 40)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.82 +- 0.21 (0.03-->2.90) (max @ vno 125370 --> 125419)
- face area 0.28 +- 0.12 (0.00-->1.15)
- mean absolute distance = 0.66 +- 0.81
- 2828 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=61
- mean inside = 94.2, mean outside = 70.0
- smoothing surface for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 3 vertex label from ripped group
- mean border=74.5, 28 (28) missing vertices, mean dist 0.3 [0.5 (%31.4)->0.7 (%68.6))]
- %73 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.91 +- 0.25 (0.13-->3.54) (max @ vno 108810 --> 109670)
- face area 0.28 +- 0.13 (0.00-->1.63)
- mean absolute distance = 0.33 +- 0.50
- 3682 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=7117391.5, rms=13.54
- 001: dt: 0.5000, sse=6948846.0, rms=9.664 (0.000%)
- 002: dt: 0.5000, sse=7068480.0, rms=7.294 (0.000%)
- 003: dt: 0.5000, sse=7209422.0, rms=5.800 (0.000%)
- 004: dt: 0.5000, sse=7475855.0, rms=4.974 (0.000%)
- 005: dt: 0.5000, sse=7585069.5, rms=4.563 (0.000%)
- 006: dt: 0.5000, sse=7730280.0, rms=4.384 (0.000%)
- 007: dt: 0.5000, sse=7702772.5, rms=4.281 (0.000%)
- rms = 4.23, time step reduction 1 of 3 to 0.250...
- 008: dt: 0.5000, sse=7738444.5, rms=4.232 (0.000%)
- 009: dt: 0.2500, sse=4690324.5, rms=2.864 (0.000%)
- 010: dt: 0.2500, sse=4274975.5, rms=2.383 (0.000%)
- 011: dt: 0.2500, sse=4003269.0, rms=2.271 (0.000%)
- 012: dt: 0.2500, sse=3932503.0, rms=2.176 (0.000%)
- rms = 2.14, time step reduction 2 of 3 to 0.125...
- 013: dt: 0.2500, sse=3845526.2, rms=2.140 (0.000%)
- 014: dt: 0.1250, sse=3637315.0, rms=1.884 (0.000%)
- rms = 1.85, time step reduction 3 of 3 to 0.062...
- 015: dt: 0.1250, sse=3596996.2, rms=1.849 (0.000%)
- positioning took 1.8 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 3 vertex label from ripped group
- mean border=79.4, 15 (6) missing vertices, mean dist -0.2 [0.4 (%80.2)->0.2 (%19.8))]
- %85 local maxima, %10 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 (0.11-->3.44) (max @ vno 87257 --> 88211)
- face area 0.35 +- 0.16 (0.00-->2.09)
- mean absolute distance = 0.21 +- 0.30
- 3255 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4734324.0, rms=6.52
- 016: dt: 0.5000, sse=4763859.5, rms=4.363 (0.000%)
- rms = 4.53, time step reduction 1 of 3 to 0.250...
- 017: dt: 0.2500, sse=4295636.0, rms=3.240 (0.000%)
- 018: dt: 0.2500, sse=4091933.0, rms=2.519 (0.000%)
- 019: dt: 0.2500, sse=4028683.5, rms=2.040 (0.000%)
- 020: dt: 0.2500, sse=4005933.0, rms=1.897 (0.000%)
- 021: dt: 0.2500, sse=3935471.2, rms=1.760 (0.000%)
- rms = 1.73, time step reduction 2 of 3 to 0.125...
- 022: dt: 0.2500, sse=3950504.5, rms=1.734 (0.000%)
- 023: dt: 0.1250, sse=3802604.2, rms=1.520 (0.000%)
- rms = 1.50, time step reduction 3 of 3 to 0.062...
- 024: dt: 0.1250, sse=3763822.2, rms=1.499 (0.000%)
- positioning took 1.1 minutes
- 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 3 vertex label from ripped group
- mean border=82.6, 11 (2) missing vertices, mean dist -0.1 [0.2 (%77.4)->0.2 (%22.6))]
- %91 local maxima, % 4 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-->3.55) (max @ vno 87257 --> 88211)
- face area 0.33 +- 0.15 (0.00-->2.04)
- mean absolute distance = 0.16 +- 0.24
- 3311 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4135006.0, rms=4.18
- 025: dt: 0.5000, sse=4517550.5, rms=4.071 (0.000%)
- rms = 4.25, time step reduction 1 of 3 to 0.250...
- 026: dt: 0.2500, sse=4044220.0, rms=2.544 (0.000%)
- 027: dt: 0.2500, sse=3917622.5, rms=2.023 (0.000%)
- 028: dt: 0.2500, sse=3989302.2, rms=1.688 (0.000%)
- rms = 1.72, time step reduction 2 of 3 to 0.125...
- 029: dt: 0.1250, sse=3924294.5, rms=1.550 (0.000%)
- 030: dt: 0.1250, sse=3836767.0, rms=1.351 (0.000%)
- rms = 1.33, time step reduction 3 of 3 to 0.062...
- 031: dt: 0.1250, sse=3801765.8, rms=1.328 (0.000%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 3 vertex label from ripped group
- mean border=83.6, 11 (2) missing vertices, mean dist -0.0 [0.2 (%58.5)->0.2 (%41.5))]
- %92 local maxima, % 2 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- writing white matter surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/rh.white...
- writing smoothed curvature to rh.curv
- 000: dt: 0.0000, sse=3826808.5, rms=1.74
- rms = 2.57, time step reduction 1 of 3 to 0.250...
- 032: dt: 0.2500, sse=3912167.0, rms=1.152 (0.000%)
- 033: dt: 0.2500, sse=4043820.5, rms=1.002 (0.000%)
- rms = 1.01, time step reduction 2 of 3 to 0.125...
- rms = 0.99, time step reduction 3 of 3 to 0.062...
- 034: dt: 0.1250, sse=4044467.8, rms=0.991 (0.000%)
- positioning took 0.5 minutes
- inhibiting deformation at non-cortical midline structures...
- generating cortex label...
- 11 non-cortical segments detected
- only using segment with 2250 vertices
- erasing segment 1 (vno[0] = 68261)
- erasing segment 2 (vno[0] = 82966)
- erasing segment 3 (vno[0] = 86282)
- erasing segment 4 (vno[0] = 87282)
- erasing segment 5 (vno[0] = 99720)
- erasing segment 6 (vno[0] = 105091)
- erasing segment 7 (vno[0] = 105107)
- erasing segment 8 (vno[0] = 106917)
- erasing segment 9 (vno[0] = 108821)
- erasing segment 10 (vno[0] = 108844)
- writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/label/rh.cortex.label...
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/rh.curv
- writing smoothed area to rh.area
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/rh.area
- vertex spacing 0.89 +- 0.24 (0.08-->3.58) (max @ vno 87257 --> 88211)
- face area 0.33 +- 0.15 (0.00-->2.03)
- refinement took 6.5 minutes
- #--------------------------------------------
- #@# Smooth2 rh Thu Aug 8 20:39:01 CEST 2013
- mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/scripts
- smoothing for 3 iterations
- setting seed for random number generator to 1234
- smoothing surface tessellation for 3 iterations...
- smoothing complete - recomputing first and second fundamental forms...
- #--------------------------------------------
- #@# Inflation2 rh Thu Aug 8 20:39:05 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/scripts
- mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated
- avg radius = 46.5 mm, total surface area = 82925 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=0.036 (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=0.020 (target=0.015)
step 045: RMS=0.018 (target=0.015)
step 050: RMS=0.016 (target=0.015)
step 055: RMS=0.015 (target=0.015)
- inflation complete.
- inflation took 0.5 minutes
- mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated
- normalizing curvature values.
- averaging curvature patterns 5 times.
- sampling 10 neighbors out to a distance of 10 mm
- 156 vertices thresholded to be in k1 ~ [-0.54 0.46], k2 ~ [-0.13 0.13]
- total integrated curvature = 0.550*4pi (6.915) --> 0 handles
- ICI = 1.6, FI = 11.0, variation=184.729
- 114 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
- 118 vertices thresholded to be in [-0.15 0.22]
- done.
- writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.015, std = 0.025
- done.
- #-----------------------------------------
- #@# Curvature Stats rh Thu Aug 8 20:41:18 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub020 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 [ sub020/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 [ 264 ]
- Gb_filter = 0
- WARN: S lookup min: -0.505221
- WARN: S explicit min: 0.000000 vertex = 1400
- #--------------------------------------------
- #@# Sphere rh Thu Aug 8 20:41:23 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/scripts
- mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere
- setting seed for random number genererator to 1234
- $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading original vertex positions...
- unfolding cortex into spherical form...
- surface projected - minimizing metric distortion...
- scaling brain by 0.300...
- MRISunfold() max_passes = 1 -------
- tol=5.0e-01, sigma=0.0, host=snake, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
- using quadratic fit line minimization
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 1.000000
- desired_rms_height -1.000000
- momentum 0.900000
- nbhd_size 7
- max_nbrs 8
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 1234
- --------------------
- mrisRemoveNegativeArea()
- pass 1: epoch 1 of 3 starting distance error %19.79
- pass 1: epoch 2 of 3 starting distance error %19.77
- unfolding complete - removing small folds...
- starting distance error %19.71
- removing remaining folds...
- final distance error %19.73
- MRISunfold() return, current seed 1234
- writing spherical brain to ../surf/rh.sphere
- spherical transformation took 0.82 hours
- #--------------------------------------------
- #@# Surf Reg rh Thu Aug 8 21:30:29 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 = 0.586
- curvature mean = 0.022, std = 0.939
- curvature mean = 0.022, std = 0.855
- Starting MRISrigidBodyAlignGlobal()
- d=64.00 min @ (16.00, 0.00, 0.00) sse = 321079.6, tmin=1.0896
- d=32.00 min @ (-8.00, 0.00, 0.00) sse = 251914.7, tmin=2.1835
- d=16.00 min @ (0.00, -4.00, 0.00) sse = 236139.9, tmin=3.2933
- d=8.00 min @ (0.00, 2.00, 0.00) sse = 233515.8, tmin=4.4154
- d=4.00 min @ (0.00, -1.00, 1.00) sse = 230169.5, tmin=5.5360
- d=2.00 min @ (0.50, 0.50, 0.00) sse = 229846.0, tmin=6.6694
- d=1.00 min @ (-0.25, -0.25, 0.00) sse = 229804.4, tmin=7.7978
- d=0.50 min @ (0.12, 0.12, 0.00) sse = 229781.5, tmin=8.9401
- tol=1.0e+00, sigma=0.5, host=snake, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
- using quadratic fit line minimization
- MRISrigidBodyAlignGlobal() done 8.94 min
- curvature mean = 0.006, std = 0.951
- curvature mean = 0.010, std = 0.939
- curvature mean = 0.002, std = 0.960
- curvature mean = 0.005, std = 0.973
- curvature mean = 0.000, std = 0.960
- curvature mean = 0.001, std = 0.988
- 2 Reading smoothwm
- curvature mean = -0.021, std = 0.268
- curvature mean = 0.005, std = 0.070
- curvature mean = 0.062, std = 0.369
- curvature mean = 0.005, std = 0.083
- curvature mean = 0.026, std = 0.574
- curvature mean = 0.006, std = 0.089
- curvature mean = 0.015, std = 0.715
- curvature mean = 0.006, std = 0.091
- curvature mean = 0.004, std = 0.823
- MRISregister() return, current seed 0
- writing registered surface to ../surf/rh.sphere.reg...
- expanding nbhd size to 1
- #--------------------------------------------
- #@# Jacobian white rh Thu Aug 8 21:57:06 CEST 2013
- mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white
- reading surface from ../surf/rh.white...
- writing curvature file ../surf/rh.jacobian_white
- #--------------------------------------------
- #@# AvgCurv rh Thu Aug 8 21:57:13 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/scripts
- mrisp_paint -a 5 /opt/freesurfer/5.3.0/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv
- averaging curvature patterns 5 times...
- reading surface from ../surf/rh.sphere.reg...
- reading template parameterization from /opt/freesurfer/5.3.0/average/rh.average.curvature.filled.buckner40.tif...
- writing curvature file to ../surf/rh.avg_curv...
- #-----------------------------------------
- #@# Cortical Parc rh Thu Aug 8 21:57:15 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub020 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...
- 1342 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2887 changed, 136728 examined...
- 001: 711 changed, 12400 examined...
- 002: 183 changed, 3990 examined...
- 003: 59 changed, 1076 examined...
- 004: 18 changed, 356 examined...
- 005: 7 changed, 108 examined...
- 006: 2 changed, 48 examined...
- 007: 2 changed, 14 examined...
- 008: 0 changed, 10 examined...
- 131 labels changed using aseg
- 000: 103 total segments, 65 labels (243 vertices) changed
- 001: 39 total segments, 1 labels (2 vertices) changed
- 002: 38 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 63 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 1461 vertices marked for relabeling...
- 1461 labels changed in reclassification.
- writing output to ../label/rh.aparc.annot...
- classification took 1 minutes and 3 seconds.
- #--------------------------------------------
- #@# Make Pial Surf rh Thu Aug 8 21:58:19 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/scripts
- mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub020 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/sub020/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/wm.mgz...
- 19247 bright wm thresholded.
- 144 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/rh.orig...
- computing class statistics...
- border white: 255703 voxels (1.52%)
- border gray 281220 voxels (1.68%)
- WM (94.0): 94.7 +- 9.7 [70.0 --> 110.0]
- GM (77.0) : 75.3 +- 13.1 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 47.9 (was 70)
- setting MAX_BORDER_WHITE to 115.7 (was 105)
- setting MIN_BORDER_WHITE to 61.0 (was 85)
- setting MAX_CSF to 34.7 (was 40)
- setting MAX_GRAY to 96.3 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 54.4 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 21.6 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=106, GM=61
- mean inside = 94.2, mean outside = 70.0
- smoothing surface for 5 iterations...
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.82 +- 0.21 (0.03-->2.90) (max @ vno 125370 --> 125419)
- face area 0.28 +- 0.12 (0.00-->1.15)
- mean absolute distance = 0.66 +- 0.82
- 2916 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- deleting segment 0 with 4 points - only 0.00% unknown
- deleting segment 1 with 5 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- removing 3 vertex label from ripped group
- deleting segment 6 with 34 points - only 0.00% unknown
- deleting segment 7 with 515 points - only 0.00% unknown
- deleting segment 8 with 8 points - only 0.00% unknown
- deleting segment 9 with 7 points - only 0.00% unknown
- deleting segment 11 with 5 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 12 with 4 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 13 with 3 points - only 0.00% unknown
- mean border=74.5, 28 (28) missing vertices, mean dist 0.3 [0.5 (%31.4)->0.7 (%68.6))]
- %74 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.91 +- 0.25 (0.13-->3.54) (max @ vno 108810 --> 109670)
- face area 0.28 +- 0.13 (0.00-->1.63)
- mean absolute distance = 0.33 +- 0.50
- 3712 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=7133935.0, rms=13.52
- 001: dt: 0.5000, sse=6975909.5, rms=9.654 (0.000%)
- 002: dt: 0.5000, sse=7095929.5, rms=7.287 (0.000%)
- 003: dt: 0.5000, sse=7243218.5, rms=5.795 (0.000%)
- 004: dt: 0.5000, sse=7511551.5, rms=4.971 (0.000%)
- 005: dt: 0.5000, sse=7625315.0, rms=4.561 (0.000%)
- 006: dt: 0.5000, sse=7768214.0, rms=4.382 (0.000%)
- 007: dt: 0.5000, sse=7743680.5, rms=4.279 (0.000%)
- rms = 4.23, time step reduction 1 of 3 to 0.250...
- 008: dt: 0.5000, sse=7778507.0, rms=4.230 (0.000%)
- 009: dt: 0.2500, sse=4715587.0, rms=2.864 (0.000%)
- 010: dt: 0.2500, sse=4298456.0, rms=2.385 (0.000%)
- 011: dt: 0.2500, sse=4025584.2, rms=2.273 (0.000%)
- 012: dt: 0.2500, sse=3954669.0, rms=2.179 (0.000%)
- rms = 2.14, time step reduction 2 of 3 to 0.125...
- 013: dt: 0.2500, sse=3867590.5, rms=2.142 (0.000%)
- 014: dt: 0.1250, sse=3659398.0, rms=1.888 (0.000%)
- rms = 1.85, time step reduction 3 of 3 to 0.062...
- 015: dt: 0.1250, sse=3619120.5, rms=1.853 (0.000%)
- positioning took 1.9 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 7 points - only 0.00% unknown
- deleting segment 1 with 7 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 3 with 3 points - only 0.00% unknown
- deleting segment 6 with 41 points - only 0.00% unknown
- deleting segment 7 with 345 points - only 0.00% unknown
- deleting segment 8 with 10 points - only 0.00% unknown
- deleting segment 9 with 48 points - only 0.00% unknown
- deleting segment 10 with 5 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- deleting segment 13 with 2 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 14 with 4 points - only 0.00% unknown
- deleting segment 15 with 6 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 16 with 3 points - only 0.00% unknown
- mean border=79.4, 15 (6) missing vertices, mean dist -0.2 [0.4 (%80.1)->0.2 (%19.9))]
- %85 local maxima, %10 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 (0.11-->3.09) (max @ vno 136664 --> 97853)
- face area 0.35 +- 0.16 (0.00-->2.09)
- mean absolute distance = 0.21 +- 0.30
- 3296 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4758129.5, rms=6.51
- 016: dt: 0.5000, sse=4790576.5, rms=4.358 (0.000%)
- rms = 4.52, time step reduction 1 of 3 to 0.250...
- 017: dt: 0.2500, sse=4321393.0, rms=3.237 (0.000%)
- 018: dt: 0.2500, sse=4117527.0, rms=2.519 (0.000%)
- 019: dt: 0.2500, sse=4054300.2, rms=2.043 (0.000%)
- 020: dt: 0.2500, sse=4032510.0, rms=1.900 (0.000%)
- 021: dt: 0.2500, sse=3961247.0, rms=1.764 (0.000%)
- rms = 1.74, time step reduction 2 of 3 to 0.125...
- 022: dt: 0.2500, sse=3973866.2, rms=1.738 (0.000%)
- 023: dt: 0.1250, sse=3826954.8, rms=1.524 (0.000%)
- rms = 1.50, time step reduction 3 of 3 to 0.062...
- 024: dt: 0.1250, sse=3787866.8, rms=1.504 (0.000%)
- positioning took 1.2 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 8 points - only 0.00% unknown
- deleting segment 1 with 7 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 4 with 34 points - only 0.00% unknown
- deleting segment 5 with 373 points - only 0.00% unknown
- deleting segment 7 with 11 points - only 0.00% unknown
- deleting segment 8 with 5 points - only 0.00% unknown
- deleting segment 9 with 74 points - only 0.00% unknown
- deleting segment 10 with 17 points - only 35.29% unknown
- removing 4 vertex label from ripped group
- deleting segment 11 with 4 points - only 0.00% unknown
- deleting segment 12 with 7 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 13 with 3 points - only 0.00% unknown
- mean border=82.6, 14 (2) missing vertices, mean dist -0.1 [0.2 (%77.4)->0.2 (%22.6))]
- %91 local maxima, % 4 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 (0.05-->3.23) (max @ vno 76776 --> 77855)
- face area 0.33 +- 0.15 (0.00-->2.04)
- mean absolute distance = 0.16 +- 0.25
- 3391 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4160654.8, rms=4.18
- 025: dt: 0.5000, sse=4547635.0, rms=4.069 (0.000%)
- rms = 4.25, time step reduction 1 of 3 to 0.250...
- 026: dt: 0.2500, sse=4072385.2, rms=2.546 (0.000%)
- 027: dt: 0.2500, sse=3948052.8, rms=2.025 (0.000%)
- 028: dt: 0.2500, sse=4017655.2, rms=1.691 (0.000%)
- rms = 1.72, time step reduction 2 of 3 to 0.125...
- 029: dt: 0.1250, sse=3952381.8, rms=1.554 (0.000%)
- 030: dt: 0.1250, sse=3866868.2, rms=1.356 (0.000%)
- rms = 1.33, time step reduction 3 of 3 to 0.062...
- 031: dt: 0.1250, sse=3828937.5, rms=1.333 (0.000%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 8 points - only 0.00% unknown
- deleting segment 1 with 7 points - only 0.00% unknown
- deleting segment 2 with 34 points - only 0.00% unknown
- deleting segment 3 with 359 points - only 0.00% unknown
- deleting segment 4 with 14 points - only 0.00% unknown
- deleting segment 5 with 5 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 7 with 74 points - only 0.00% unknown
- deleting segment 8 with 20 points - only 45.00% unknown
- deleting segment 9 with 5 points - only 0.00% unknown
- deleting segment 10 with 7 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 11 with 3 points - only 0.00% unknown
- mean border=83.5, 12 (2) missing vertices, mean dist -0.0 [0.2 (%58.5)->0.2 (%41.5))]
- %93 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- repositioning cortical surface to gray/csf boundary.
- smoothing T1 volume with sigma = 2.000
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=3855615.8, rms=1.75
- rms = 2.57, time step reduction 1 of 3 to 0.250...
- 032: dt: 0.2500, sse=3945283.5, rms=1.160 (0.000%)
- 033: dt: 0.2500, sse=4082589.2, rms=1.009 (0.000%)
- rms = 1.02, time step reduction 2 of 3 to 0.125...
- rms = 1.00, time step reduction 3 of 3 to 0.062...
- 034: dt: 0.1250, sse=4083164.8, rms=0.998 (0.000%)
- positioning took 0.5 minutes
- inhibiting deformation at non-cortical midline structures...
- smoothing surface for 5 iterations...
- mean border=50.5, 17 (17) missing vertices, mean dist 1.8 [0.0 (%0.0)->2.3 (%100.0))]
- %15 local maxima, %58 large gradients and %23 min vals, 1531 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=30556648.0, rms=32.73
- 001: dt: 0.5000, sse=21860996.0, rms=27.169 (0.000%)
- 002: dt: 0.5000, sse=15814784.0, rms=22.525 (0.000%)
- 003: dt: 0.5000, sse=11791920.0, rms=18.760 (0.000%)
- 004: dt: 0.5000, sse=9332565.0, rms=15.793 (0.000%)
- 005: dt: 0.5000, sse=7966546.0, rms=13.515 (0.000%)
- 006: dt: 0.5000, sse=7208453.5, rms=11.722 (0.000%)
- 007: dt: 0.5000, sse=6711477.0, rms=10.121 (0.000%)
- 008: dt: 0.5000, sse=6379755.0, rms=8.636 (0.000%)
- 009: dt: 0.5000, sse=6179826.5, rms=7.262 (0.000%)
- 010: dt: 0.5000, sse=6163926.0, rms=6.039 (0.000%)
- 011: dt: 0.5000, sse=6241837.5, rms=5.132 (0.000%)
- 012: dt: 0.5000, sse=6400384.5, rms=4.572 (0.000%)
- 013: dt: 0.5000, sse=6594946.0, rms=4.299 (0.000%)
- 014: dt: 0.5000, sse=6692684.0, rms=4.151 (0.000%)
- 015: dt: 0.5000, sse=6797784.5, rms=4.076 (0.000%)
- 016: dt: 0.5000, sse=6810150.5, rms=4.019 (0.000%)
- rms = 3.99, time step reduction 1 of 3 to 0.250...
- 017: dt: 0.5000, sse=6887906.5, rms=3.994 (0.000%)
- 018: dt: 0.2500, sse=4733983.5, rms=3.196 (0.000%)
- 019: dt: 0.2500, sse=4573727.0, rms=2.986 (0.000%)
- rms = 2.98, time step reduction 2 of 3 to 0.125...
- 020: dt: 0.2500, sse=4436115.0, rms=2.978 (0.000%)
- 021: dt: 0.1250, sse=4200251.5, rms=2.789 (0.000%)
- rms = 2.77, time step reduction 3 of 3 to 0.062...
- 022: dt: 0.1250, sse=4173370.5, rms=2.765 (0.000%)
- positioning took 2.7 minutes
- mean border=47.9, 746 (1) missing vertices, mean dist 0.2 [0.2 (%47.7)->0.6 (%52.3))]
- %33 local maxima, %43 large gradients and %19 min vals, 413 gradients ignored
- tol=1.0e-04, sigma=1.0, host=snake, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4858119.0, rms=5.07
- 023: dt: 0.5000, sse=5124526.0, rms=4.231 (0.000%)
- 024: dt: 0.5000, sse=6524816.0, rms=4.112 (0.000%)
- rms = 4.13, time step reduction 1 of 3 to 0.250...
- 025: dt: 0.2500, sse=5319450.5, rms=3.281 (0.000%)
- 026: dt: 0.2500, sse=4878609.5, rms=2.954 (0.000%)
- 027: dt: 0.2500, sse=4839185.5, rms=2.867 (0.000%)
- rms = 2.83, time step reduction 2 of 3 to 0.125...
- 028: dt: 0.2500, sse=4810943.0, rms=2.832 (0.000%)
- 029: dt: 0.1250, sse=4593558.0, rms=2.606 (0.000%)
- rms = 2.57, time step reduction 3 of 3 to 0.062...
- 030: dt: 0.1250, sse=4586477.0, rms=2.567 (0.000%)
- positioning took 1.1 minutes
- mean border=45.5, 952 (0) missing vertices, mean dist 0.1 [0.2 (%37.4)->0.4 (%62.6))]
- %55 local maxima, %21 large gradients and %19 min vals, 535 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=4892265.5, rms=4.16
- 031: dt: 0.5000, sse=5144366.0, rms=4.054 (0.000%)
- rms = 4.05, time step reduction 1 of 3 to 0.250...
- 032: dt: 0.5000, sse=6819236.0, rms=4.048 (0.000%)
- 033: dt: 0.2500, sse=5053637.5, rms=3.029 (0.000%)
- 034: dt: 0.2500, sse=5231069.5, rms=2.726 (0.000%)
- rms = 2.76, time step reduction 2 of 3 to 0.125...
- 035: dt: 0.1250, sse=5096027.5, rms=2.603 (0.000%)
- 036: dt: 0.1250, sse=4870017.5, rms=2.434 (0.000%)
- rms = 2.41, time step reduction 3 of 3 to 0.062...
- 037: dt: 0.1250, sse=4816853.5, rms=2.409 (0.000%)
- positioning took 1.0 minutes
- mean border=44.3, 2114 (0) missing vertices, mean dist 0.0 [0.2 (%45.3)->0.3 (%54.7))]
- %58 local maxima, %17 large gradients and %18 min vals, 406 gradients ignored
- tol=1.0e-04, sigma=0.2, host=snake, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- writing pial surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/rh.pial...
- writing smoothed curvature to rh.curv.pial
- 000: dt: 0.0000, sse=4874946.5, rms=2.83
- rms = 3.80, time step reduction 1 of 3 to 0.250...
- 038: dt: 0.2500, sse=4720697.5, rms=2.509 (0.000%)
- 039: dt: 0.2500, sse=4871129.0, rms=2.450 (0.000%)
- rms = 2.45, time step reduction 2 of 3 to 0.125...
- rms = 2.41, time step reduction 3 of 3 to 0.062...
- 040: dt: 0.1250, sse=4819515.5, rms=2.410 (0.000%)
- positioning took 0.6 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/rh.curv.pial
- writing smoothed area to rh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/rh.area.pial
- vertex spacing 1.00 +- 0.41 (0.07-->6.58) (max @ vno 93686 --> 94804)
- face area 0.40 +- 0.29 (0.00-->5.94)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 136728 vertices processed
- 25000 of 136728 vertices processed
- 50000 of 136728 vertices processed
- 75000 of 136728 vertices processed
- 100000 of 136728 vertices processed
- 125000 of 136728 vertices processed
- 0 of 136728 vertices processed
- 25000 of 136728 vertices processed
- 50000 of 136728 vertices processed
- 75000 of 136728 vertices processed
- 100000 of 136728 vertices processed
- 125000 of 136728 vertices processed
- thickness calculation complete, 187:621 truncations.
- 32949 vertices at 0 distance
- 100425 vertices at 1 distance
- 86491 vertices at 2 distance
- 30998 vertices at 3 distance
- 7728 vertices at 4 distance
- 1935 vertices at 5 distance
- 543 vertices at 6 distance
- 161 vertices at 7 distance
- 56 vertices at 8 distance
- 16 vertices at 9 distance
- 16 vertices at 10 distance
- 13 vertices at 11 distance
- 5 vertices at 12 distance
- 3 vertices at 13 distance
- 5 vertices at 14 distance
- 9 vertices at 15 distance
- 7 vertices at 16 distance
- 5 vertices at 17 distance
- 3 vertices at 18 distance
- 2 vertices at 19 distance
- 2 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/rh.thickness
- positioning took 13.8 minutes
- #--------------------------------------------
- #@# Surf Volume rh Thu Aug 8 22:12:08 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf
- mris_calc -o rh.area.mid rh.area add rh.area.pial
- Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o rh.area.mid rh.area.mid div 2
- Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o rh.volume rh.area.mid mul rh.thickness
- Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ]
- #-----------------------------------------
- #@# WM/GM Contrast rh Thu Aug 8 22:12:09 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/scripts
- pctsurfcon --s sub020 --rh-only
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/scripts/pctsurfcon.log
- Thu Aug 8 22:12:09 CEST 2013
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/scripts
- /opt/freesurfer/5.3.0/bin/pctsurfcon
- $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $
- Linux snake6 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
- FREESURFER_HOME /opt/freesurfer/5.3.0
- mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/tmp.pctsurfcon.18769/rh.wm.mgh --regheader sub020 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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/sub020/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/label/rh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 = 106733
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/label/rh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/tmp.pctsurfcon.18769/rh.wm.mgh
- Dim: 136728 1 1
- mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/tmp.pctsurfcon.18769/rh.gm.mgh --projfrac 0.3 --regheader sub020 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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/sub020/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/label/rh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/rh.white
- Done reading source surface
- Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 = 121778
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/label/rh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/tmp.pctsurfcon.18769/rh.gm.mgh
- Dim: 136728 1 1
- mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/tmp.pctsurfcon.18769/rh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/tmp.pctsurfcon.18769/rh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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/sub020/surf/rh.w-g.pct.mgh
- mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/rh.w-g.pct.mgh --annot sub020 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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/sub020/surf/rh.w-g.pct.mgh --annot sub020 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/stats/rh.w-g.pct.stats --snr
- sysname Linux
- hostname snake6
- machine x86_64
- user fkaule
- UseRobust 0
- Constructing seg from annotation
- Reading annotation
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
- Seg base 2000
- Loading /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/rh.w-g.pct.mgh
- Vertex Area is 0.65984 mm^3
- Generating list of segmentation ids
- Found 36 segmentations
- Computing statistics for each segmentation
- 0 2000 unknown 0 0.000
- 1 2001 bankssts 1460 1011.377
- 2 2002 caudalanteriorcingulate 1027 727.412
- 3 2003 caudalmiddlefrontal 2978 2016.214
- 4 2004 corpuscallosum 0 0.000
- 5 2005 cuneus 2451 1564.490
- 6 2006 entorhinal 507 367.742
- 7 2007 fusiform 3815 2537.211
- 8 2008 inferiorparietal 8481 5638.463
- 9 2009 inferiortemporal 4829 3285.833
- 10 2010 isthmuscingulate 1917 1256.303
- 11 2011 lateraloccipital 6509 4164.956
- 12 2012 lateralorbitofrontal 3526 2359.266
- 13 2013 lingual 5021 3359.140
- 14 2014 medialorbitofrontal 2255 1475.332
- 15 2015 middletemporal 5041 3473.833
- 16 2016 parahippocampal 844 562.135
- 17 2017 paracentral 2390 1470.547
- 18 2018 parsopercularis 1713 1129.400
- 19 2019 parsorbitalis 1013 679.792
- 20 2020 parstriangularis 2304 1569.481
- 21 2021 pericalcarine 2694 1816.383
- 22 2022 postcentral 6214 4017.607
- 23 2023 posteriorcingulate 1836 1209.421
- 24 2024 precentral 7305 4525.023
- 25 2025 precuneus 6158 4053.823
- 26 2026 rostralanteriorcingulate 1099 726.151
- 27 2027 rostralmiddlefrontal 9631 6519.294
- 28 2028 superiorfrontal 11473 7857.253
- 29 2029 superiorparietal 7100 4625.606
- 30 2030 superiortemporal 5577 3753.405
- 31 2031 supramarginal 6275 4157.746
- 32 2032 frontalpole 443 295.390
- 33 2033 temporalpole 501 361.103
- 34 2034 transversetemporal 736 400.594
- 35 2035 insula 3053 1997.466
- Reporting on 34 segmentations
- mri_segstats done
- Cleaning up
- #-----------------------------------------
- #@# Parcellation Stats rh Thu Aug 8 22:12:22 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 sub020 rh white
- computing statistics for each annotation in ../label/rh.aparc.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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
- 1460 1011 2770 2.587 0.519 0.128 0.036 16 2.1 bankssts
- 1027 727 1743 2.212 0.609 0.144 0.039 17 1.4 caudalanteriorcingulate
- 2978 2016 5762 2.586 0.376 0.126 0.034 29 4.3 caudalmiddlefrontal
- 2451 1564 3425 1.977 0.314 0.147 0.096 50 5.6 cuneus
- 507 368 1475 2.891 0.890 0.119 0.038 5 0.9 entorhinal
- 3815 2537 8009 2.691 0.556 0.146 0.048 66 7.8 fusiform
- 8481 5638 14397 2.294 0.467 0.141 0.047 133 16.1 inferiorparietal
- 4829 3286 9590 2.486 0.621 0.146 0.059 105 10.3 inferiortemporal
- 1917 1256 3466 2.449 0.784 0.154 0.059 36 4.4 isthmuscingulate
- 6509 4165 10472 2.275 0.452 0.153 0.056 111 14.7 lateraloccipital
- 3526 2359 6820 2.606 0.582 0.147 0.063 63 9.1 lateralorbitofrontal
- 5021 3359 7948 2.204 0.564 0.167 0.104 108 22.3 lingual
- 2255 1475 4002 2.319 0.712 0.160 0.093 66 7.1 medialorbitofrontal
- 5041 3474 11507 2.694 0.621 0.139 0.044 81 9.3 middletemporal
- 844 562 2193 3.198 0.746 0.125 0.041 13 1.3 parahippocampal
- 2390 1471 4094 2.491 0.417 0.128 0.050 48 6.1 paracentral
- 1713 1129 3306 2.580 0.402 0.134 0.045 27 3.3 parsopercularis
- 1013 680 2391 2.684 0.489 0.161 0.054 17 2.2 parsorbitalis
- 2304 1569 4338 2.393 0.415 0.138 0.083 75 4.4 parstriangularis
- 2694 1816 3000 1.761 0.381 0.169 0.070 44 7.5 pericalcarine
- 6214 4018 9601 2.100 0.514 0.120 0.037 75 10.0 postcentral
- 1836 1209 3007 2.294 0.774 0.159 0.056 35 4.1 posteriorcingulate
- 7305 4525 13371 2.687 0.507 0.119 0.173 525 27.5 precentral
- 6158 4054 10867 2.450 0.507 0.141 0.046 90 12.1 precuneus
- 1099 726 2231 2.702 0.618 0.162 0.076 31 3.6 rostralanteriorcingulate
- 9631 6519 16835 2.322 0.451 0.157 0.059 180 21.6 rostralmiddlefrontal
- 11473 7857 23971 2.626 0.484 0.134 0.041 139 18.8 superiorfrontal
- 7100 4626 11803 2.260 0.393 0.127 0.039 93 11.4 superiorparietal
- 5577 3753 12883 2.975 0.562 0.126 0.035 63 8.2 superiortemporal
- 6275 4158 11370 2.472 0.489 0.128 0.040 84 10.3 supramarginal
- 443 295 873 2.352 0.493 0.222 0.118 19 2.1 frontalpole
- 501 361 1892 3.731 0.602 0.194 0.078 12 1.7 temporalpole
- 736 401 1173 2.428 0.376 0.123 0.056 10 1.7 transversetemporal
- 3053 1997 6304 2.959 0.775 0.129 0.079 52 7.2 insula
- #-----------------------------------------
- #@# Cortical Parc 2 rh Thu Aug 8 22:12:42 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub020 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...
- 6 labels changed using aseg
- relabeling using gibbs priors...
- 000: 9937 changed, 136728 examined...
- 001: 2370 changed, 37718 examined...
- 002: 716 changed, 12126 examined...
- 003: 336 changed, 4047 examined...
- 004: 179 changed, 1867 examined...
- 005: 101 changed, 1003 examined...
- 006: 50 changed, 553 examined...
- 007: 32 changed, 305 examined...
- 008: 18 changed, 182 examined...
- 009: 9 changed, 90 examined...
- 010: 7 changed, 58 examined...
- 011: 7 changed, 38 examined...
- 012: 8 changed, 46 examined...
- 013: 6 changed, 34 examined...
- 014: 5 changed, 30 examined...
- 015: 3 changed, 22 examined...
- 016: 2 changed, 12 examined...
- 017: 2 changed, 11 examined...
- 018: 3 changed, 12 examined...
- 019: 0 changed, 10 examined...
- 4 labels changed using aseg
- 000: 269 total segments, 188 labels (2232 vertices) changed
- 001: 92 total segments, 11 labels (31 vertices) changed
- 002: 81 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 138 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 1019 vertices marked for relabeling...
- 1019 labels changed in reclassification.
- writing output to ../label/rh.aparc.a2009s.annot...
- classification took 1 minutes and 17 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 2 rh Thu Aug 8 22:14:01 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 sub020 rh white
- computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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
- 1017 688 1997 2.426 0.491 0.183 0.089 27 3.0 G_and_S_frontomargin
- 1255 817 2360 2.553 0.431 0.158 0.048 22 2.7 G_and_S_occipital_inf
- 1444 813 2343 2.369 0.454 0.131 0.055 39 3.7 G_and_S_paracentral
- 1424 972 2953 2.574 0.469 0.153 0.048 23 2.9 G_and_S_subcentral
- 1075 747 2061 2.307 0.375 0.193 0.090 32 3.8 G_and_S_transv_frontopol
- 3121 2119 6016 2.566 0.558 0.140 0.052 44 6.5 G_and_S_cingul-Ant
- 1517 1067 3085 2.659 0.487 0.133 0.039 19 2.5 G_and_S_cingul-Mid-Ant
- 1370 930 2647 2.578 0.449 0.144 0.044 20 2.4 G_and_S_cingul-Mid-Post
- 836 513 1875 2.945 0.715 0.180 0.078 21 2.8 G_cingul-Post-dorsal
- 327 207 857 2.951 0.503 0.157 0.055 6 0.7 G_cingul-Post-ventral
- 2412 1541 3346 1.944 0.341 0.156 0.104 53 6.0 G_cuneus
- 1134 751 2707 2.703 0.371 0.150 0.059 27 2.8 G_front_inf-Opercular
- 275 182 714 2.794 0.380 0.190 0.351 48 0.8 G_front_inf-Orbital
- 1044 725 2426 2.547 0.356 0.163 0.064 23 2.8 G_front_inf-Triangul
- 4476 2963 9476 2.506 0.454 0.158 0.057 92 10.2 G_front_middle
- 7468 5023 17087 2.718 0.478 0.147 0.054 126 15.6 G_front_sup
- 485 319 1071 3.027 0.646 0.127 0.057 8 1.1 G_Ins_lg_and_S_cent_ins
- 680 429 2135 3.551 0.796 0.154 0.079 18 2.2 G_insular_short
- 2092 1310 4204 2.519 0.357 0.163 0.067 48 5.2 G_occipital_middle
- 1632 1060 2881 2.228 0.359 0.139 0.047 27 3.1 G_occipital_sup
- 1260 774 2987 2.866 0.430 0.154 0.059 29 3.2 G_oc-temp_lat-fusifor
- 3292 2151 5791 2.301 0.599 0.184 0.119 87 15.1 G_oc-temp_med-Lingual
- 1284 877 3544 3.040 0.801 0.139 0.109 27 3.2 G_oc-temp_med-Parahip
- 2519 1671 6198 2.853 0.533 0.172 0.074 60 7.8 G_orbital
- 3367 2221 6920 2.451 0.527 0.156 0.058 71 7.9 G_pariet_inf-Angular
- 2938 1935 6595 2.701 0.448 0.143 0.050 54 5.9 G_pariet_inf-Supramar
- 2153 1395 4075 2.389 0.410 0.141 0.047 35 4.0 G_parietal_sup
- 2361 1446 4276 2.313 0.423 0.128 0.040 37 4.1 G_postcentral
- 3023 1730 6563 2.906 0.415 0.122 0.367 487 21.2 G_precentral
- 2554 1662 5782 2.645 0.446 0.157 0.054 52 5.7 G_precuneus
- 695 424 1267 2.211 0.589 0.199 0.145 36 4.1 G_rectus
- 383 253 795 2.778 1.088 0.106 0.047 8 0.7 G_subcallosal
- 608 307 1067 2.567 0.373 0.121 0.060 9 1.5 G_temp_sup-G_T_transv
- 1970 1326 6066 3.274 0.498 0.160 0.051 40 4.0 G_temp_sup-Lateral
- 705 493 1892 3.357 0.539 0.106 0.027 5 0.8 G_temp_sup-Plan_polar
- 1112 744 2144 2.626 0.442 0.104 0.026 6 1.2 G_temp_sup-Plan_tempo
- 2435 1662 5773 2.637 0.610 0.174 0.085 82 7.0 G_temporal_inf
- 2942 2037 7699 2.821 0.554 0.154 0.052 61 6.4 G_temporal_middle
- 548 366 816 2.202 0.403 0.111 0.041 4 0.7 Lat_Fis-ant-Horizont
- 207 150 360 2.174 0.427 0.156 0.051 3 0.4 Lat_Fis-ant-Vertical
- 1648 1087 2246 2.456 0.390 0.117 0.035 12 2.3 Lat_Fis-post
- 3185 2052 4354 2.001 0.464 0.163 0.067 56 8.4 Pole_occipital
- 1863 1290 5603 3.132 0.826 0.168 0.068 43 5.5 Pole_temporal
- 3126 2130 3884 2.010 0.591 0.159 0.079 54 12.2 S_calcarine
- 3164 2083 3786 2.018 0.674 0.107 0.031 18 4.2 S_central
- 1207 810 1819 2.322 0.391 0.119 0.033 10 1.6 S_cingul-Marginalis
- 581 389 940 2.616 0.487 0.105 0.028 3 0.7 S_circular_insula_ant
- 1289 840 2074 2.873 0.605 0.091 0.024 6 1.4 S_circular_insula_inf
- 1272 849 1753 2.360 0.378 0.107 0.027 6 1.5 S_circular_insula_sup
- 1222 876 2042 2.411 0.532 0.108 0.023 8 1.3 S_collat_transv_ant
- 533 340 689 2.053 0.303 0.134 0.049 6 1.0 S_collat_transv_post
- 1915 1312 2965 2.313 0.416 0.133 0.037 20 3.0 S_front_inf
- 2459 1690 3642 2.130 0.375 0.138 0.048 33 4.4 S_front_middle
- 2959 2047 4682 2.329 0.328 0.111 0.031 24 3.8 S_front_sup
- 719 473 843 1.883 0.405 0.112 0.034 8 1.0 S_interm_prim-Jensen
- 2687 1757 3738 2.123 0.352 0.113 0.029 24 3.3 S_intrapariet_and_P_trans
- 1078 744 1361 1.988 0.320 0.129 0.034 9 1.6 S_oc_middle_and_Lunatus
- 1270 854 1667 2.118 0.360 0.113 0.029 8 1.5 S_oc_sup_and_transversal
- 765 511 1187 2.286 0.375 0.115 0.032 7 1.1 S_occipital_ant
- 716 479 1137 2.404 0.424 0.125 0.031 8 0.8 S_oc-temp_lat
- 1397 962 2314 2.562 0.496 0.121 0.031 12 1.8 S_oc-temp_med_and_Lingual
- 501 328 656 2.116 0.350 0.116 0.036 3 0.8 S_orbital_lateral
- 667 479 939 2.042 0.577 0.121 0.036 6 1.0 S_orbital_med-olfact
- 1276 852 2096 2.500 0.469 0.146 0.053 20 2.8 S_orbital-H_Shaped
- 1916 1272 2636 2.319 0.383 0.121 0.034 15 2.9 S_parieto_occipital
- 1902 1220 1976 1.811 0.683 0.145 0.054 34 3.9 S_pericallosal
- 2768 1835 3556 2.100 0.327 0.106 0.027 18 3.3 S_postcentral
- 1636 1103 2535 2.643 0.325 0.114 0.028 12 1.9 S_precentral-inf-part
- 1071 742 1658 2.440 0.368 0.115 0.030 7 1.3 S_precentral-sup-part
- 47 32 50 1.384 0.349 0.160 0.042 0 0.1 S_suborbital
- 1814 1220 2674 2.229 0.454 0.136 0.042 24 3.1 S_subparietal
- 1596 1071 2247 2.289 0.652 0.122 0.035 14 2.3 S_temporal_inf
- 6171 4203 9833 2.413 0.483 0.125 0.036 66 8.7 S_temporal_sup
- 316 234 456 2.283 0.409 0.131 0.026 2 0.4 S_temporal_transverse
- #-----------------------------------------
- #@# Cortical Parc 3 rh Thu Aug 8 22:14:23 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub020 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...
- 717 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2689 changed, 136728 examined...
- 001: 609 changed, 11467 examined...
- 002: 149 changed, 3365 examined...
- 003: 55 changed, 900 examined...
- 004: 23 changed, 319 examined...
- 005: 15 changed, 148 examined...
- 006: 8 changed, 92 examined...
- 007: 2 changed, 55 examined...
- 008: 1 changed, 14 examined...
- 009: 1 changed, 7 examined...
- 010: 1 changed, 7 examined...
- 011: 2 changed, 4 examined...
- 012: 4 changed, 12 examined...
- 013: 5 changed, 15 examined...
- 014: 5 changed, 23 examined...
- 015: 5 changed, 24 examined...
- 016: 4 changed, 25 examined...
- 017: 1 changed, 16 examined...
- 018: 1 changed, 7 examined...
- 019: 0 changed, 6 examined...
- 119 labels changed using aseg
- 000: 65 total segments, 31 labels (218 vertices) changed
- 001: 35 total segments, 1 labels (1 vertices) changed
- 002: 34 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 69 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 874 vertices marked for relabeling...
- 874 labels changed in reclassification.
- writing output to ../label/rh.aparc.DKTatlas40.annot...
- classification took 1 minutes and 3 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 3 rh Thu Aug 8 22:15:27 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 sub020 rh white
- computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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
- 1015 720 1738 2.226 0.597 0.143 0.039 17 1.4 caudalanteriorcingulate
- 2963 2012 5739 2.580 0.384 0.127 0.034 29 4.4 caudalmiddlefrontal
- 2990 1930 4155 2.002 0.321 0.139 0.084 54 6.2 cuneus
- 527 381 1489 2.829 0.864 0.120 0.038 7 0.9 entorhinal
- 3271 2178 6773 2.689 0.514 0.142 0.046 52 6.1 fusiform
- 8157 5416 13855 2.302 0.473 0.143 0.047 129 15.6 inferiorparietal
- 5364 3642 10854 2.512 0.644 0.149 0.061 120 12.1 inferiortemporal
- 2004 1310 3585 2.437 0.773 0.153 0.058 37 4.6 isthmuscingulate
- 6868 4404 11097 2.273 0.448 0.152 0.055 115 15.2 lateraloccipital
- 3840 2599 7971 2.653 0.574 0.162 0.072 82 10.9 lateralorbitofrontal
- 4980 3333 7937 2.216 0.553 0.166 0.104 106 22.0 lingual
- 1830 1188 3263 2.245 0.759 0.166 0.109 61 6.6 medialorbitofrontal
- 5995 4120 13073 2.659 0.603 0.135 0.043 90 10.5 middletemporal
- 814 545 2123 3.211 0.748 0.124 0.039 9 1.3 parahippocampal
- 2496 1542 4290 2.497 0.420 0.128 0.050 49 6.3 paracentral
- 1874 1220 3558 2.569 0.391 0.134 0.048 31 3.8 parsopercularis
- 1146 767 2339 2.520 0.497 0.141 0.043 14 2.0 parsorbitalis
- 2346 1593 4301 2.370 0.422 0.137 0.080 74 4.2 parstriangularis
- 2658 1785 2921 1.744 0.392 0.172 0.071 46 7.6 pericalcarine
- 6846 4419 10604 2.135 0.524 0.120 0.037 81 11.0 postcentral
- 1948 1272 3171 2.318 0.767 0.157 0.055 37 4.3 posteriorcingulate
- 7058 4369 12950 2.692 0.505 0.119 0.177 523 27.2 precentral
- 6113 4037 10954 2.447 0.510 0.140 0.046 88 11.8 precuneus
- 1169 779 2397 2.699 0.634 0.163 0.075 32 3.7 rostralanteriorcingulate
- 6474 4368 11336 2.336 0.452 0.154 0.056 117 13.9 rostralmiddlefrontal
- 14779 10100 29716 2.554 0.491 0.139 0.045 207 26.9 superiorfrontal
- 5937 3849 9865 2.268 0.393 0.130 0.041 83 9.9 superiorparietal
- 7300 4939 17206 2.963 0.623 0.133 0.051 101 12.8 superiortemporal
- 5654 3775 10290 2.453 0.488 0.127 0.039 74 9.1 supramarginal
- 735 401 1169 2.425 0.376 0.125 0.056 10 1.8 transversetemporal
- 3025 1974 6172 2.947 0.768 0.126 0.051 41 6.2 insula
- #--------------------------------------------
- #@# Refine Pial Surfs w/ T2/FLAIR Thu Aug 8 22:15:45 CEST 2013
- bbregister --s sub020 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/T2raw.lta --init-fsl --T2
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/T2raw.dat.log
- Thu Aug 8 22:15:45 CEST 2013
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/scripts
- /opt/freesurfer/5.3.0/bin/bbregister --s sub020 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/T2raw.lta --init-fsl --T2
- $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $
- Linux snake6 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
- FREESURFER_HOME /opt/freesurfer/5.3.0
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/template.nii
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/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/sub020/mri/orig/T2raw.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.998287, -0.0504193, 0.0296894)
- j_ras = (-0.0475266, 0.9947, 0.0911741)
- k_ras = (0.034129, -0.0896069, 0.995392)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/template.nii...
- fslregister --s sub020 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/fslregister --dof 6 --fsvol brainmask.mgz
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/reg.init.dat.fslregister.log
- Thu Aug 8 22:15:50 CEST 2013
- --s sub020 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/fslregister --dof 6 --fsvol brainmask.mgz
- $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $
- snake6
- Linux snake6 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
- nIters 1
- --------------------------------------
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/scripts
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/fslregister/refvol.fslregister.nii
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/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/sub020/mri/brainmask.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, 6.98492e-09, -3.72529e-09)
- j_ras = (3.72529e-09, 0, -1)
- k_ras = (-1.00117e-08, 1, 7.45058e-09)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/fslregister/refvol.fslregister.nii...
- --------------------------------------
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/scripts
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/fslregister/movvol.fslregister.nii --frame 0
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/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/sub020/mri/transforms/tmp.bbregister.19082/template.nii...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.998287, -0.0504193, 0.0296894)
- j_ras = (-0.0475266, 0.9947, 0.0911741)
- k_ras = (0.034129, -0.0896069, 0.995392)
- keeping frame 0
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/fslregister/movvol.fslregister.nii...
- Mov determinant is -0.311079
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/scripts
- tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/fslregister/movvol.fslregister.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/fslregister/reg0.19121.dat --regheader --fslregout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/reg.init.dat.fsl.mat0 --s sub020 --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/sub020/mri/transforms/tmp.bbregister.19082/fslregister/movvol.fslregister.nii
- reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/fslregister/reg0.19121.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/sub020/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/sub020/mri/transforms/tmp.bbregister.19082/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) --------
- 0.998 0.050 -0.030 -0.000;
- 0.034 -0.090 0.995 0.000;
- 0.048 -0.995 -0.091 0.000;
- 0.000 0.000 0.000 1.000;
- ---------------------------------------
- ---- Input registration matrix --------
- 0.998 0.050 -0.030 -0.000;
- 0.034 -0.090 0.995 0.000;
- 0.048 -0.995 -0.091 0.000;
- 0.000 0.000 0.000 1.000;
- Determinant 1
- subject = sub020
- RegMat ---------------------------
- 0.998 0.050 -0.030 -0.000;
- 0.034 -0.090 0.995 0.000;
- 0.048 -0.995 -0.091 0.000;
- 0.000 0.000 0.000 1.000;
- FSLOUTPUTTYPE NIFTI
- tkreg2FSL: mov det = -0.311079, ref det = -1
- Thu Aug 8 22:15:58 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/scripts
- flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/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/sub020/mri/transforms/tmp.bbregister.19082/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/reg.init.dat.fsl.mat0
- Thu Aug 8 22:20:31 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/scripts
- flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/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/sub020/mri/transforms/tmp.bbregister.19082/reg.init.dat.fsl.mat -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/fslregister/fslmat0.trans.mat -schedule /opt/freesurfer/5.3.0/bin/flirt.newdefault.20080811.sch
- tkregister2_cmdl --s sub020 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/reg.init.dat --fslreg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/reg.init.dat.fsl.mat --noedit
- tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl
- ---- FSL registration matrix --------
- 0.998 0.048 -0.033 30.393;
- -0.029 -0.091 -0.995 271.146;
- -0.050 0.995 -0.090 16.219;
- 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/sub020/mri/transforms/tmp.bbregister.19082/template.nii
- reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/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/sub020/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/sub020/mri/transforms/tmp.bbregister.19082/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) --------
- 0.998 0.050 -0.029 -0.026;
- 0.033 -0.090 0.995 1.239;
- 0.048 -0.995 -0.091 -0.881;
- 0.000 0.000 0.000 1.000;
- ---------------------------------------
- ---- Input registration matrix --------
- 0.998 0.050 -0.029 -0.026;
- 0.033 -0.090 0.995 1.239;
- 0.048 -0.995 -0.091 -0.881;
- 0.000 0.000 0.000 1.000;
- Determinant 1
- subject = sub020
- RegMat ---------------------------
- 0.998 0.050 -0.029 -0.026;
- 0.033 -0.090 0.995 1.239;
- 0.048 -0.995 -0.091 -0.881;
- 0.000 0.000 0.000 1.000;
-
- Started at Thu Aug 8 22:15:50 CEST 2013
- Ended at Thu Aug 8 22:26:43 CEST 2013
-
- fslregister Done
-
- To check results, run:
- tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/reg.init.dat --surf orig
-
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/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/sub020/scripts
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5
- sysname Linux
- hostname snake6
- machine x86_64
- user fkaule
- movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/template.nii
- regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/reg.init.dat
- subject sub020
- dof 6
- outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/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 1376959936
- TransRandMax 0.000000
- RotRandMax 0.000000
- Translations 0.000000 0.000000 0.000000
- Rotations 0.000000 0.000000 0.000000
- Input reg
- 0.998 0.050 -0.029 -0.026;
- 0.033 -0.090 0.995 1.239;
- 0.048 -0.995 -0.091 -0.881;
- 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 1.009564
- 1 -25.0 -25.0 25.0 0.989784
- 2 -25.0 25.0 -25.0 0.998370
- 3 -25.0 25.0 25.0 1.044732
- 4 25.0 -25.0 -25.0 1.015749
- 5 25.0 -25.0 25.0 1.018151
- 6 25.0 25.0 -25.0 1.020733
- 7 25.0 25.0 25.0 1.002708
- REL: 8 0.289753 8.099791 1.012474 rel = 0.286183
- Initial costs ----------------
- Number of surface hits 2561
- WM Intensity 52.3774 +/- 7.4491
- Ctx Intensity 63.9203 +/- 10.2015
- Pct Contrast 19.3608 +/- 18.6507
- Cost 0.2898
- RelCost 0.2862
- ------------------------------------
- Brute force preopt -4 4 4, n = 729
- 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9893 0.9893 0.0
- 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.9767 0.9767 0.0
- 6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.9609 0.9609 0.0
- 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.8787 0.8787 0.0
- 21 -4.0000 -4.0000 -4.0000 4.0000 0.0000 -4.0000 0.8564 0.8564 0.0
- 39 -4.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.8233 0.8233 0.0
- 102 -4.0000 0.0000 -4.0000 4.0000 0.0000 -4.0000 0.7725 0.7725 0.0
- 120 -4.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.6807 0.6807 0.0
- 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.2898 0.2898 0.0
- Brute Force --------------------------
- Min cost was 0.289753
- Number of iterations 729
- Search time 3.750000 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
- 9 -0.090 0.000 0.000 0.000 0.000 0.000 0.2897133289
- 10 -0.047 0.000 0.000 0.000 0.000 0.000 0.2896632757
- 11 -0.052 0.000 0.000 0.000 0.000 0.000 0.2896421440
- 12 -0.065 0.000 0.000 0.000 0.000 0.000 0.2895030126
- 13 -0.075 0.000 0.000 0.000 0.000 0.000 0.2894471780
- 19 -0.075 -1.618 0.000 0.000 0.000 0.000 0.2674030719
- 20 -0.075 -0.895 0.000 0.000 0.000 0.000 0.2215231083
- 25 -0.075 -0.765 0.000 0.000 0.000 0.000 0.2195910650
- 26 -0.075 -0.782 0.000 0.000 0.000 0.000 0.2188661467
- 28 -0.075 -0.795 0.000 0.000 0.000 0.000 0.2186373520
- 33 -0.075 -0.795 1.000 0.000 0.000 0.000 0.1197352454
- 39 -0.075 -0.795 0.984 0.000 0.000 0.000 0.1197116263
- 42 -0.075 -0.795 0.985 0.000 0.000 0.000 0.1197115578
- 49 -0.075 -0.795 0.985 0.006 0.000 0.000 0.1194757737
- 50 -0.075 -0.795 0.985 0.073 0.000 0.000 0.1185802749
- 52 -0.075 -0.795 0.985 0.056 0.000 0.000 0.1183779642
- 54 -0.075 -0.795 0.985 0.057 0.000 0.000 0.1183773232
- 64 -0.075 -0.795 0.985 0.057 0.025 0.000 0.1182287058
- 65 -0.075 -0.795 0.985 0.057 0.021 0.000 0.1182084040
- 66 -0.075 -0.795 0.985 0.057 0.018 0.000 0.1182066430
- 68 -0.075 -0.795 0.985 0.057 0.019 0.000 0.1182064247
- 75 -0.075 -0.795 0.985 0.057 0.019 0.042 0.1162862375
- 76 -0.075 -0.795 0.985 0.057 0.019 0.140 0.1159126150
- 78 -0.075 -0.795 0.985 0.057 0.019 0.124 0.1157646068
- 79 -0.075 -0.795 0.985 0.057 0.019 0.103 0.1155614615
- 81 -0.075 -0.795 0.985 0.057 0.019 0.095 0.1155392746
- 83 -0.075 -0.795 0.985 0.057 0.019 0.096 0.1155390716
- 85 -0.075 -0.795 0.985 0.057 0.019 0.097 0.1155390022
- 95 -0.055 -0.795 0.985 0.057 0.019 0.097 0.1152808532
- 97 -0.053 -0.795 0.985 0.057 0.019 0.097 0.1152789001
- 105 -0.053 -0.814 0.985 0.057 0.019 0.097 0.1144369243
- 108 -0.053 -0.834 0.985 0.057 0.019 0.097 0.1141406839
- 110 -0.053 -0.833 0.985 0.057 0.019 0.097 0.1141394298
- 119 -0.053 -0.833 0.970 0.057 0.019 0.097 0.1140526486
- 121 -0.053 -0.833 0.971 0.057 0.019 0.097 0.1140517714
- 140 -0.053 -0.833 0.971 0.057 0.034 0.097 0.1138511865
- 141 -0.053 -0.833 0.971 0.057 0.037 0.097 0.1138506507
- 142 -0.053 -0.833 0.971 0.057 0.038 0.097 0.1138499119
- 144 -0.053 -0.833 0.971 0.057 0.041 0.097 0.1138485458
- 146 -0.053 -0.833 0.971 0.057 0.040 0.097 0.1138483746
- 155 -0.053 -0.833 0.971 0.057 0.040 0.123 0.1135440152
- 156 -0.053 -0.833 0.971 0.057 0.040 0.124 0.1135424953
- 157 -0.053 -0.833 0.971 0.057 0.040 0.126 0.1135406260
- 160 -0.053 -0.833 0.971 0.057 0.040 0.127 0.1135396864
- 171 -0.054 -0.833 0.971 0.057 0.040 0.127 0.1135367739
- 172 -0.056 -0.833 0.971 0.057 0.040 0.127 0.1135355177
- 183 -0.056 -0.831 0.971 0.057 0.040 0.127 0.1135331747
- 194 -0.056 -0.831 0.980 0.057 0.040 0.127 0.1135007806
- 196 -0.056 -0.831 0.979 0.057 0.040 0.127 0.1134999047
- 207 -0.056 -0.831 0.979 0.059 0.040 0.127 0.1134947058
- 216 -0.056 -0.831 0.979 0.059 0.045 0.127 0.1134266010
- 217 -0.056 -0.831 0.979 0.059 0.049 0.127 0.1134182977
- 229 -0.056 -0.831 0.979 0.059 0.049 0.133 0.1134129142
- 231 -0.056 -0.831 0.979 0.059 0.049 0.131 0.1134106662
- 239 -0.057 -0.830 0.982 0.060 0.052 0.132 0.1133981122
- 240 -0.057 -0.830 0.982 0.060 0.053 0.132 0.1133975152
- 242 -0.057 -0.830 0.982 0.060 0.053 0.132 0.1133972942
- 255 -0.063 -0.830 0.982 0.060 0.053 0.132 0.1133716336
- 275 -0.063 -0.830 0.978 0.060 0.053 0.132 0.1133716322
- 276 -0.063 -0.830 0.977 0.060 0.053 0.132 0.1133696908
- 277 -0.063 -0.830 0.976 0.060 0.053 0.132 0.1133684141
- 287 -0.063 -0.830 0.976 0.064 0.053 0.132 0.1133547938
- 292 -0.063 -0.830 0.976 0.065 0.053 0.132 0.1133540618
- 303 -0.063 -0.830 0.976 0.065 0.053 0.128 0.1133421952
- 304 -0.063 -0.830 0.976 0.065 0.053 0.127 0.1133421643
- 311 -0.064 -0.829 0.979 0.066 0.056 0.128 0.1133410216
- 312 -0.063 -0.829 0.977 0.066 0.055 0.128 0.1133394997
- 314 -0.063 -0.829 0.977 0.066 0.054 0.127 0.1133391143
- 320 -0.063 -0.829 0.977 0.066 0.054 0.127 0.1133390818
- 322 -0.063 -0.829 0.977 0.066 0.054 0.127 0.1133389740
- 323 -0.071 -0.828 0.975 0.072 0.059 0.124 0.1133331825
- 332 -0.067 -0.829 0.977 0.066 0.054 0.127 0.1133313437
- 342 -0.067 -0.827 0.977 0.066 0.054 0.127 0.1133297356
- 343 -0.067 -0.826 0.977 0.066 0.054 0.127 0.1133294073
- 351 -0.067 -0.826 0.969 0.066 0.054 0.127 0.1133195191
- 353 -0.067 -0.826 0.971 0.066 0.054 0.127 0.1133186516
- 377 -0.067 -0.826 0.971 0.066 0.054 0.124 0.1133117106
- 385 -0.068 -0.825 0.974 0.066 0.057 0.125 0.1133066911
- 387 -0.068 -0.825 0.974 0.066 0.057 0.125 0.1133065548
- 391 -0.068 -0.825 0.974 0.067 0.058 0.125 0.1133065333
- 392 -0.068 -0.825 0.974 0.066 0.058 0.125 0.1133065138
- 394 -0.068 -0.825 0.974 0.066 0.058 0.125 0.1133063039
- 396 -0.072 -0.821 0.972 0.067 0.061 0.123 0.1132722121
- 399 -0.080 -0.815 0.967 0.069 0.067 0.120 0.1132554500
- 400 -0.079 -0.816 0.968 0.068 0.066 0.121 0.1132532188
- 403 -0.078 -0.817 0.968 0.068 0.065 0.121 0.1132528868
- 404 -0.078 -0.817 0.968 0.068 0.065 0.121 0.1132528844
- 407 -0.078 -0.817 0.968 0.068 0.065 0.121 0.1132528798
- 412 -0.078 -0.817 0.968 0.068 0.065 0.121 0.1132528550
- 422 -0.083 -0.817 0.968 0.068 0.065 0.121 0.1132362651
- 431 -0.083 -0.818 0.968 0.068 0.065 0.121 0.1132294246
- 434 -0.083 -0.820 0.968 0.068 0.065 0.121 0.1132255578
- 443 -0.083 -0.820 0.968 0.068 0.065 0.120 0.1132235906
- 445 -0.082 -0.821 0.967 0.068 0.064 0.120 0.1132229610
- 448 -0.082 -0.821 0.967 0.068 0.064 0.120 0.1132228962
- 449 -0.082 -0.821 0.967 0.068 0.064 0.120 0.1132227859
- 461 -0.082 -0.821 0.967 0.074 0.064 0.120 0.1132118212
- 462 -0.082 -0.821 0.967 0.072 0.064 0.120 0.1132091714
- 474 -0.082 -0.821 0.967 0.072 0.064 0.119 0.1132053249
- 475 -0.082 -0.821 0.967 0.072 0.064 0.118 0.1132047668
- 478 -0.087 -0.817 0.964 0.073 0.068 0.116 0.1131824348
- 479 -0.095 -0.810 0.960 0.074 0.073 0.112 0.1131390998
- 482 -0.099 -0.807 0.958 0.075 0.077 0.110 0.1131119494
- 483 -0.102 -0.804 0.956 0.075 0.079 0.109 0.1131074225
- 499 -0.104 -0.804 0.956 0.075 0.079 0.109 0.1131014052
- 501 -0.105 -0.804 0.956 0.075 0.079 0.109 0.1131005014
- 511 -0.105 -0.808 0.956 0.075 0.079 0.109 0.1130846651
- 519 -0.106 -0.807 0.959 0.076 0.083 0.110 0.1130699390
- 536 -0.106 -0.807 0.959 0.084 0.083 0.110 0.1128816484
- 537 -0.106 -0.807 0.959 0.089 0.083 0.110 0.1128751056
- 538 -0.106 -0.807 0.959 0.087 0.083 0.110 0.1128676517
- 548 -0.106 -0.807 0.959 0.087 0.083 0.115 0.1128662636
- 549 -0.106 -0.807 0.959 0.087 0.083 0.113 0.1128602595
- 552 -0.110 -0.803 0.957 0.088 0.086 0.111 0.1128305572
- 557 -0.111 -0.803 0.956 0.088 0.087 0.111 0.1128294968
- 576 -0.108 -0.803 0.956 0.088 0.087 0.111 0.1128222835
- 587 -0.108 -0.805 0.956 0.088 0.087 0.111 0.1128171444
- 594 -0.107 -0.806 0.951 0.087 0.081 0.109 0.1127732266
- 595 -0.106 -0.807 0.948 0.086 0.078 0.107 0.1127692540
- 596 -0.106 -0.807 0.949 0.086 0.079 0.108 0.1127680820
- 611 -0.106 -0.807 0.949 0.088 0.079 0.108 0.1127574404
- 612 -0.106 -0.807 0.949 0.090 0.079 0.108 0.1127530221
- 623 -0.106 -0.807 0.949 0.090 0.079 0.109 0.1127478686
- 625 -0.106 -0.807 0.949 0.090 0.079 0.110 0.1127474919
- 627 -0.111 -0.803 0.947 0.090 0.082 0.108 0.1127104249
- 630 -0.114 -0.800 0.945 0.091 0.084 0.107 0.1127071319
- 632 -0.113 -0.801 0.945 0.091 0.084 0.107 0.1127064769
- 639 -0.113 -0.801 0.945 0.091 0.084 0.107 0.1127064125
- 642 -0.114 -0.799 0.935 0.094 0.081 0.104 0.1126431123
- 649 -0.115 -0.799 0.933 0.094 0.080 0.104 0.1126413567
- 652 -0.115 -0.799 0.933 0.094 0.080 0.104 0.1126413171
- 653 -0.115 -0.799 0.933 0.094 0.080 0.104 0.1126412457
- 655 -0.115 -0.799 0.933 0.094 0.080 0.104 0.1126411918
- 664 -0.113 -0.799 0.933 0.094 0.080 0.104 0.1126299976
- 667 -0.109 -0.799 0.933 0.094 0.080 0.104 0.1126176033
- 678 -0.109 -0.802 0.933 0.094 0.080 0.104 0.1126136576
- 679 -0.109 -0.801 0.933 0.094 0.080 0.104 0.1126133458
- 712 -0.109 -0.801 0.933 0.094 0.080 0.106 0.1126043608
- 714 -0.109 -0.801 0.933 0.094 0.080 0.107 0.1126020746
- 721 -0.109 -0.800 0.932 0.094 0.080 0.107 0.1126014395
- 722 -0.109 -0.800 0.932 0.094 0.080 0.107 0.1126014007
- 739 -0.107 -0.800 0.932 0.094 0.080 0.107 0.1125972864
- 758 -0.108 -0.800 0.932 0.095 0.080 0.107 0.1125966119
- 759 -0.108 -0.800 0.932 0.095 0.080 0.107 0.1125965534
- 761 -0.108 -0.800 0.932 0.095 0.080 0.107 0.1125962962
- 787 -0.108 -0.800 0.932 0.095 0.080 0.108 0.1125932688
- 789 -0.108 -0.800 0.932 0.095 0.080 0.109 0.1125928915
- Powell done niters = 9
- Computing relative cost
- 0 -25.0 -25.0 -25.0 1.020202
- 1 -25.0 -25.0 25.0 0.986642
- 2 -25.0 25.0 -25.0 1.020725
- 3 -25.0 25.0 25.0 0.994088
- 4 25.0 -25.0 -25.0 0.994992
- 5 25.0 -25.0 25.0 0.988573
- 6 25.0 25.0 -25.0 0.989970
- 7 25.0 25.0 25.0 1.033843
- REL: 8 0.112593 8.029034 1.003629 rel = 0.112186
- Number of iterations 9
- Min cost was 0.112593
- Number of FunctionCalls 806
- TolPowell 0.000100
- nMaxItersPowell 36
- OptimizationTime 2.751000 sec
- Parameters at optimum (transmm) -0.10783 -0.79971 0.93166
- Parameters at optimum (rotdeg) 0.09459 0.08050 0.10862
- Final costs ----------------
- Number of surface hits 2561
- WM Intensity 51.7578 +/- 6.4530
- Ctx Intensity 63.4173 +/- 7.4812
- Pct Contrast 20.1747 +/- 13.2974
- Cost 0.1126
- RelCost 0.2862
- Reg at min cost was
- 0.998 0.049 -0.031 -0.138;
- 0.035 -0.088 0.996 0.441;
- 0.046 -0.995 -0.089 0.053;
- 0.000 0.000 0.000 1.000;
- Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/bbr.pass1.dat, type = 14
- Original Reg
- 0.998 0.050 -0.029 -0.026;
- 0.033 -0.090 0.995 1.239;
- 0.048 -0.995 -0.091 -0.881;
- 0.000 0.000 0.000 1.000;
- Original Reg - Optimal Reg
- -0.000 0.001 0.002 0.111;
- -0.002 -0.002 -0.000 0.798;
- 0.001 0.000 -0.002 -0.934;
- 0.000 0.000 0.000 0.000;
- Computing change in lh position
- LH rmsDiffMean 1.369623
- Computing change in rh position
- Surface RMS Diff (mm) 1.306990 1.482164
- mri_segreg done
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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/sub020/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/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/sub020/scripts
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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/sub020/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5
- sysname Linux
- hostname snake6
- machine x86_64
- user fkaule
- movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/template.nii
- regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/tmp.bbregister.19082/bbr.pass1.dat
- subject sub020
- dof 6
- outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 1376035448
- TransRandMax 0.000000
- RotRandMax 0.000000
- Translations 0.000000 0.000000 0.000000
- Rotations 0.000000 0.000000 0.000000
- Input reg
- 0.998 0.049 -0.031 -0.138;
- 0.035 -0.088 0.996 0.441;
- 0.046 -0.995 -0.089 0.053;
- 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 1.013494
- 1 -25.0 -25.0 25.0 1.006108
- 2 -25.0 25.0 -25.0 0.997941
- 3 -25.0 25.0 25.0 1.011419
- 4 25.0 -25.0 -25.0 1.027242
- 5 25.0 -25.0 25.0 1.003605
- 6 25.0 25.0 -25.0 0.984781
- 7 25.0 25.0 25.0 1.015732
- REL: 8 0.129034 8.060323 1.007540 rel = 0.128068
- Initial costs ----------------
- Number of surface hits 255490
- WM Intensity 51.9075 +/- 7.0033
- Ctx Intensity 63.3654 +/- 7.6848
- Pct Contrast 19.8445 +/- 13.5786
- Cost 0.1290
- RelCost 0.1281
- ------------------------------------
- Brute force preopt -0.1 0.1 0.1, n = 729
- 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1259 0.1259 0.0
- 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.1220 0.1220 0.0
- 9 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 -0.1000 0.1209 0.1209 0.0
- 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.1187 0.1187 0.0
- 39 -0.1000 -0.1000 0.0000 0.0000 0.0000 -0.1000 0.1176 0.1176 0.0
- 103 -0.1000 0.0000 -0.1000 0.1000 0.0000 0.0000 0.1175 0.1175 0.0
- 120 -0.1000 0.0000 0.0000 0.0000 0.0000 -0.1000 0.1158 0.1158 0.0
- 337 0.0000 0.0000 -0.1000 0.0000 0.0000 0.0000 0.1152 0.1152 0.0
- 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1126 0.1126 0.0
- Brute Force --------------------------
- Min cost was 0.112593
- Number of iterations 729
- Search time 3.057000 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 0.164 0.000 0.000 0.000 0.000 0.000 0.1275259739
- 8 0.157 0.000 0.000 0.000 0.000 0.000 0.1275049393
- 9 0.142 0.000 0.000 0.000 0.000 0.000 0.1274834528
- 10 0.138 0.000 0.000 0.000 0.000 0.000 0.1274822781
- 11 0.137 0.000 0.000 0.000 0.000 0.000 0.1274819129
- 15 0.133 0.000 0.000 0.000 0.000 0.000 0.1274811044
- 24 0.133 0.005 0.000 0.000 0.000 0.000 0.1274772267
- 25 0.133 0.007 0.000 0.000 0.000 0.000 0.1274767438
- 26 0.133 0.008 0.000 0.000 0.000 0.000 0.1274765522
- 34 0.133 0.008 -0.017 0.000 0.000 0.000 0.1274134958
- 35 0.133 0.008 -0.037 0.000 0.000 0.000 0.1273929401
- 36 0.133 0.008 -0.034 0.000 0.000 0.000 0.1273906993
- 37 0.133 0.008 -0.032 0.000 0.000 0.000 0.1273902753
- 48 0.133 0.008 -0.032 0.001 0.000 0.000 0.1273900855
- 56 0.133 0.008 -0.032 0.001 -0.080 0.000 0.1262505055
- 57 0.133 0.008 -0.032 0.001 -0.134 0.000 0.1262437089
- 58 0.133 0.008 -0.032 0.001 -0.107 0.000 0.1261645037
- 60 0.133 0.008 -0.032 0.001 -0.108 0.000 0.1261643550
- 69 0.133 0.008 -0.032 0.001 -0.108 -0.098 0.1256937495
- 70 0.133 0.008 -0.032 0.001 -0.108 -0.077 0.1256835779
- 71 0.133 0.008 -0.032 0.001 -0.108 -0.084 0.1256831582
- 72 0.133 0.008 -0.032 0.001 -0.108 -0.081 0.1256830059
- 74 0.133 0.008 -0.032 0.001 -0.108 -0.080 0.1256829118
- 98 0.133 -0.001 -0.032 0.001 -0.108 -0.080 0.1256736232
- 100 0.133 -0.003 -0.032 0.001 -0.108 -0.080 0.1256732318
- 109 0.133 -0.004 -0.033 0.001 -0.108 -0.080 0.1256693110
- 110 0.133 -0.004 -0.064 0.001 -0.108 -0.080 0.1256062685
- 112 0.133 -0.004 -0.066 0.001 -0.108 -0.080 0.1256062499
- 121 0.133 -0.004 -0.066 0.007 -0.108 -0.080 0.1255985866
- 122 0.133 -0.004 -0.066 0.008 -0.108 -0.080 0.1255984469
- 131 0.133 -0.004 -0.066 0.008 -0.134 -0.080 0.1255457980
- 133 0.133 -0.004 -0.066 0.008 -0.130 -0.080 0.1255446129
- 134 0.133 -0.004 -0.066 0.008 -0.131 -0.080 0.1255444568
- 142 0.133 -0.004 -0.066 0.008 -0.131 -0.096 0.1255422605
- 143 0.133 -0.004 -0.066 0.008 -0.131 -0.089 0.1255369565
- 145 0.133 -0.004 -0.066 0.008 -0.131 -0.090 0.1255369215
- 157 0.136 -0.004 -0.066 0.008 -0.131 -0.090 0.1255360611
- 177 0.136 -0.004 -0.064 0.008 -0.131 -0.090 0.1255360562
- 179 0.136 -0.004 -0.065 0.008 -0.131 -0.090 0.1255358859
- 188 0.136 -0.004 -0.065 0.011 -0.131 -0.090 0.1255352140
- 190 0.136 -0.004 -0.065 0.012 -0.131 -0.090 0.1255351838
- 200 0.136 -0.004 -0.065 0.012 -0.132 -0.090 0.1255348151
- 211 0.136 -0.004 -0.065 0.012 -0.132 -0.089 0.1255347148
- 221 0.137 -0.004 -0.065 0.012 -0.132 -0.089 0.1255345964
- 230 0.137 -0.003 -0.065 0.012 -0.132 -0.089 0.1255344417
- 231 0.137 -0.002 -0.065 0.012 -0.132 -0.089 0.1255343620
- 242 0.137 -0.002 -0.067 0.012 -0.132 -0.089 0.1255339338
- 243 0.137 -0.002 -0.068 0.012 -0.132 -0.089 0.1255339324
- 253 0.137 -0.002 -0.068 0.013 -0.132 -0.089 0.1255337315
- 274 0.137 -0.002 -0.068 0.013 -0.132 -0.088 0.1255335548
- 294 0.137 -0.001 -0.068 0.013 -0.132 -0.088 0.1255335233
- 334 0.137 -0.001 -0.068 0.013 -0.132 -0.087 0.1255335115
- 344 0.138 -0.001 -0.068 0.013 -0.132 -0.087 0.1255333964
- Powell done niters = 6
- Computing relative cost
- 0 -25.0 -25.0 -25.0 1.013858
- 1 -25.0 -25.0 25.0 1.005302
- 2 -25.0 25.0 -25.0 0.998067
- 3 -25.0 25.0 25.0 1.012334
- 4 25.0 -25.0 -25.0 1.027999
- 5 25.0 -25.0 25.0 1.002595
- 6 25.0 25.0 -25.0 0.985033
- 7 25.0 25.0 25.0 1.016447
- REL: 8 0.125533 8.061634 1.007704 rel = 0.124574
- Number of iterations 6
- Min cost was 0.125533
- Number of FunctionCalls 457
- TolPowell 0.000000
- nMaxItersPowell 36
- OptimizationTime 57.502000 sec
- Parameters at optimum (transmm) 0.13841 -0.00092 -0.06751
- Parameters at optimum (rotdeg) 0.01267 -0.13233 -0.08668
- Final costs ----------------
- Number of surface hits 255490
- WM Intensity 51.9007 +/- 6.9972
- Ctx Intensity 63.3499 +/- 7.6561
- Pct Contrast 19.8367 +/- 13.5063
- Cost 0.1255
- RelCost 0.1281
- Reg at min cost was
- 0.998 0.051 -0.029 0.001;
- 0.033 -0.088 0.996 0.440;
- 0.049 -0.995 -0.089 -0.015;
- 0.000 0.000 0.000 1.000;
- Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/T2raw.dat, type = 14
- Original Reg
- 0.998 0.049 -0.031 -0.138;
- 0.035 -0.088 0.996 0.441;
- 0.046 -0.995 -0.089 0.053;
- 0.000 0.000 0.000 1.000;
- Original Reg - Optimal Reg
- 0.000 -0.002 -0.002 -0.139;
- 0.002 -0.000 -0.000 0.001;
- -0.002 -0.000 -0.000 0.068;
- 0.000 0.000 0.000 0.000;
- Computing change in lh position
- LH rmsDiffMean 0.215691
- Computing change in rh position
- Surface RMS Diff (mm) 0.196734 0.385326
- mri_segreg done
- tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/T2raw.dat --noedit --ltaout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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/sub020/mri/orig/T2raw.mgz
- reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/T2raw.dat
- LoadVol 0
- ZeroCRAS 0
- $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
- Diagnostic Level -1
- ---- Input registration matrix --------
- 0.998 0.051 -0.029 0.001;
- 0.033 -0.088 0.996 0.440;
- 0.049 -0.995 -0.089 -0.015;
- 0.000 0.000 0.000 1.000;
- float2int = 0
- ---------------------------------------
- INFO: loading target /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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/sub020/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 --------
- 0.998 0.051 -0.029 0.001;
- 0.033 -0.088 0.996 0.440;
- 0.049 -0.995 -0.089 -0.015;
- 0.000 0.000 0.000 1.000;
- Determinant 1
- subject = sub020
- RegMat ---------------------------
- 0.998 0.051 -0.029 0.001;
- 0.033 -0.088 0.996 0.440;
- 0.049 -0.995 -0.089 -0.015;
- 0.000 0.000 0.000 1.000;
- transformed matrix:
- 1.000 -0.001 -0.001 -0.001;
- 0.001 1.000 0.002 0.066;
- 0.001 -0.002 1.000 -0.380;
- 0.000 0.000 0.000 1.000;
- transformed matrix:
- 0.699 0.032 -0.022 30.355;
- -0.020 -0.060 -0.664 270.085;
- -0.036 0.663 -0.058 16.840;
- 0.000 0.000 0.000 1.000;
- Cleaning up
-
- Started at Thu Aug 8 22:15:45 CEST 2013
- Ended at Thu Aug 8 22:28:45 CEST 2013
- BBR-Run-Time-Sec 780
-
- bbregister Done
- To check results, run:
- tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/T2raw.dat --surf
-
- mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/T2.mgz
- mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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/sub020/mri/orig/T2raw.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.998287, -0.0504193, 0.0296894)
- j_ras = (-0.0475266, 0.9947, 0.0911741)
- k_ras = (0.034129, -0.0896069, 0.995392)
- INFO: Reading transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/T2raw.lta...
- Reading transform with LTAreadEx()
- reading extra input line subject sub020
- reading extra input line fscale 0.150000
- reading template info from volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/orig.mgz...
- INFO: Applying transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/transforms/T2raw.lta...
- ---------------------------------
- INFO: Transform Matrix (linear_ras_to_ras)
- 1.000 -0.001 -0.001 -0.001;
- 0.001 1.000 0.002 0.066;
- 0.001 -0.002 1.000 -0.380;
- 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/sub020/mri/T2.mgz...
- mri_normalize -aseg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/aseg.mgz -sigma 4 -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/rh.white identity.nofile -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/lh.white identity.nofile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/T2.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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/sub020/mri/T2.mgz...
- computing distance transform
- computing distance transform
- computing nonmaximum suppression
- 14065 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/sub020/mri/T2.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/scripts
- cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/lh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/lh.woT2.pial
- `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/lh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/lh.woT2.pial'
- mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub020 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/sub020/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/wm.mgz...
- 20443 bright wm thresholded.
- 144 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/lh.orig...
- computing class statistics...
- border white: 255703 voxels (1.52%)
- border gray 281220 voxels (1.68%)
- WM (94.0): 94.7 +- 9.7 [70.0 --> 110.0]
- GM (77.0) : 75.5 +- 13.0 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 49.0 (was 70)
- setting MAX_BORDER_WHITE to 115.7 (was 105)
- setting MIN_BORDER_WHITE to 62.0 (was 85)
- setting MAX_CSF to 36.1 (was 40)
- setting MAX_GRAY to 96.3 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 55.5 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 23.1 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=106, GM=62
- mean inside = 94.2, 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/sub020/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.89 +- 0.25 (0.03-->4.36) (max @ vno 71070 --> 71071)
- face area 0.33 +- 0.15 (0.00-->2.67)
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- deleting segment 0 with 2 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 1 with 1 points - only 0.00% unknown
- deleting segment 2 with 6 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- removing 3 vertex label from ripped group
- deleting segment 6 with 5 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 7 with 1 points - only 0.00% unknown
- deleting segment 8 with 613 points - only 0.00% unknown
- deleting segment 9 with 18 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 10 with 2 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 14 with 1 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 15 with 3 points - only 0.00% unknown
- deleting segment 16 with 13 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 17 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 +- 0.24 (0.06-->4.36) (max @ vno 71071 --> 71070)
- face area 0.33 +- 0.15 (0.00-->2.67)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=3945287.2, rms=0.00
- rms = 1.26, time step reduction 1 of 3 to 0.250...
- rms = 0.32, time step reduction 2 of 3 to 0.125...
- rms = 0.04, time step reduction 3 of 3 to 0.062...
- 001: dt: 0.1250, sse=3945287.2, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- deleting segment 0 with 2 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 1 with 1 points - only 0.00% unknown
- deleting segment 2 with 6 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- removing 3 vertex label from ripped group
- deleting segment 5 with 5 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 6 with 1 points - only 0.00% unknown
- deleting segment 7 with 613 points - only 0.00% unknown
- deleting segment 8 with 18 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 9 with 2 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 10 with 1 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 11 with 3 points - only 0.00% unknown
- deleting segment 12 with 13 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=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-->4.36) (max @ vno 71071 --> 71070)
- face area 0.33 +- 0.15 (0.00-->2.67)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=3945287.2, rms=0.00
- rms = 1.26, time step reduction 1 of 3 to 0.250...
- rms = 0.32, time step reduction 2 of 3 to 0.125...
- rms = 0.04, time step reduction 3 of 3 to 0.062...
- 002: dt: 0.1250, sse=3945287.2, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- deleting segment 0 with 2 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 1 with 1 points - only 0.00% unknown
- deleting segment 2 with 6 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- removing 3 vertex label from ripped group
- deleting segment 5 with 5 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 6 with 1 points - only 0.00% unknown
- deleting segment 7 with 613 points - only 0.00% unknown
- deleting segment 8 with 18 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 9 with 2 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 10 with 1 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 11 with 3 points - only 0.00% unknown
- deleting segment 12 with 13 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=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-->4.36) (max @ vno 71071 --> 71070)
- face area 0.33 +- 0.15 (0.00-->2.67)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=3945287.2, rms=0.00
- rms = 1.26, time step reduction 1 of 3 to 0.250...
- rms = 0.32, time step reduction 2 of 3 to 0.125...
- rms = 0.04, time step reduction 3 of 3 to 0.062...
- 003: dt: 0.1250, sse=3945287.2, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- deleting segment 0 with 2 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 1 with 1 points - only 0.00% unknown
- deleting segment 2 with 6 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- removing 3 vertex label from ripped group
- deleting segment 5 with 5 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 6 with 1 points - only 0.00% unknown
- deleting segment 7 with 613 points - only 0.00% unknown
- deleting segment 8 with 18 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 9 with 2 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 10 with 1 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 11 with 3 points - only 0.00% unknown
- deleting segment 12 with 13 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=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=3945287.2, rms=0.00
- rms = 1.26, time step reduction 1 of 3 to 0.250...
- rms = 0.32, time step reduction 2 of 3 to 0.125...
- rms = 0.04, time step reduction 3 of 3 to 0.062...
- 004: dt: 0.1250, sse=3945287.2, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 1 vertex label from ripped group
- removing 3 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
- 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 [-9.60 303.60], gm=147.00+-52.20, and vertices in regions > 120.9
- 2936 surface locations found to contain inconsistent values (0 in, 2936 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=448622.2, rms=0.11
- 001: dt: 0.5000, sse=421773.6, rms=0.111 (0.000%)
- 002: dt: 0.5000, sse=403808.5, rms=0.108 (0.000%)
- 003: dt: 0.5000, sse=391810.8, rms=0.106 (0.000%)
- 004: dt: 0.5000, sse=383760.7, rms=0.105 (0.000%)
- 005: dt: 0.5000, sse=377721.3, rms=0.103 (0.000%)
- 006: dt: 0.5000, sse=372956.0, rms=0.102 (0.000%)
- 007: dt: 0.5000, sse=369217.5, rms=0.101 (0.000%)
- 008: dt: 0.5000, sse=366585.2, rms=0.100 (0.000%)
- 009: dt: 0.5000, sse=364246.2, rms=0.100 (0.000%)
- 010: dt: 0.5000, sse=362565.6, rms=0.099 (0.000%)
- 011: dt: 0.5000, sse=361019.3, rms=0.099 (0.000%)
- 012: dt: 0.5000, sse=360033.0, rms=0.099 (0.000%)
- 013: dt: 0.5000, sse=358636.0, rms=0.099 (0.000%)
- 014: dt: 0.5000, sse=357439.1, rms=0.099 (0.000%)
- 015: dt: 0.5000, sse=356010.5, rms=0.099 (0.000%)
- 016: dt: 0.5000, sse=355337.6, rms=0.100 (0.000%)
- 017: dt: 0.5000, sse=354239.6, rms=0.100 (0.000%)
- 018: dt: 0.5000, sse=353378.9, rms=0.101 (0.000%)
- 019: dt: 0.5000, sse=352369.9, rms=0.101 (0.000%)
- 020: dt: 0.5000, sse=351824.2, rms=0.102 (0.000%)
- 021: dt: 0.5000, sse=350482.3, rms=0.102 (0.000%)
- 022: dt: 0.5000, sse=349564.7, rms=0.103 (0.000%)
- 023: dt: 0.5000, sse=348534.0, rms=0.103 (0.000%)
- 024: dt: 0.5000, sse=347336.8, rms=0.104 (0.000%)
- 025: dt: 0.5000, sse=346549.5, rms=0.104 (0.000%)
- 026: dt: 0.5000, sse=345747.4, rms=0.105 (0.000%)
- 027: dt: 0.5000, sse=345011.6, rms=0.105 (0.000%)
- 028: dt: 0.5000, sse=343974.7, rms=0.106 (0.000%)
- 029: dt: 0.5000, sse=343574.9, rms=0.106 (0.000%)
- 030: dt: 0.5000, sse=342580.2, rms=0.107 (0.000%)
- positioning took 3.4 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [90.00 210.00], gm=150.00+-20.00, and vertices in regions > 140.0
- 44983 surface locations found to contain inconsistent values (4802 in, 40181 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=40809.9, rms=0.23
- 031: dt: 0.5000, sse=40018.1, rms=0.220 (0.000%)
- 032: dt: 0.5000, sse=38936.4, rms=0.202 (0.000%)
- 033: dt: 0.5000, sse=38626.3, rms=0.187 (0.000%)
- 034: dt: 0.5000, sse=38608.5, rms=0.174 (0.000%)
- 035: dt: 0.5000, sse=38863.4, rms=0.162 (0.000%)
- 036: dt: 0.5000, sse=39199.9, rms=0.152 (0.000%)
- 037: dt: 0.5000, sse=39647.6, rms=0.142 (0.000%)
- 038: dt: 0.5000, sse=40165.6, rms=0.134 (0.000%)
- 039: dt: 0.5000, sse=40777.6, rms=0.126 (0.000%)
- 040: dt: 0.5000, sse=41461.8, rms=0.119 (0.000%)
- 041: dt: 0.5000, sse=42233.0, rms=0.112 (0.000%)
- 042: dt: 0.5000, sse=42966.4, rms=0.106 (0.000%)
- 043: dt: 0.5000, sse=43697.5, rms=0.101 (0.000%)
- 044: dt: 0.5000, sse=44402.9, rms=0.096 (0.000%)
- 045: dt: 0.5000, sse=45111.8, rms=0.091 (0.000%)
- 046: dt: 0.5000, sse=45792.2, rms=0.087 (0.000%)
- 047: dt: 0.5000, sse=46448.0, rms=0.083 (0.000%)
- 048: dt: 0.5000, sse=47074.8, rms=0.080 (0.000%)
- 049: dt: 0.5000, sse=47676.6, rms=0.076 (0.000%)
- 050: dt: 0.5000, sse=48282.1, rms=0.073 (0.000%)
- 051: dt: 0.5000, sse=48869.0, rms=0.070 (0.000%)
- 052: dt: 0.5000, sse=49355.9, rms=0.068 (0.000%)
- 053: dt: 0.5000, sse=49834.7, rms=0.065 (0.000%)
- 054: dt: 0.5000, sse=50283.6, rms=0.063 (0.000%)
- 055: dt: 0.5000, sse=50686.1, rms=0.060 (0.000%)
- 056: dt: 0.5000, sse=51077.7, rms=0.058 (0.000%)
- 057: dt: 0.5000, sse=51440.6, rms=0.056 (0.000%)
- 058: dt: 0.5000, sse=51758.8, rms=0.055 (0.000%)
- 059: dt: 0.5000, sse=52049.8, rms=0.053 (0.000%)
- 060: dt: 0.5000, sse=52347.1, rms=0.052 (0.000%)
- positioning took 3.4 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [88.40 209.60], gm=149.00+-20.20, and vertices in regions > 138.9
- 36247 surface locations found to contain inconsistent values (1063 in, 35184 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=5828.3, rms=0.07
- 061: dt: 0.5000, sse=5807.2, rms=0.067 (0.000%)
- 062: dt: 0.5000, sse=5798.5, rms=0.062 (0.000%)
- 063: dt: 0.5000, sse=5800.1, rms=0.057 (0.000%)
- 064: dt: 0.5000, sse=5806.1, rms=0.054 (0.000%)
- 065: dt: 0.5000, sse=5803.0, rms=0.051 (0.000%)
- 066: dt: 0.5000, sse=5803.9, rms=0.048 (0.000%)
- 067: dt: 0.5000, sse=5800.6, rms=0.046 (0.000%)
- 068: dt: 0.5000, sse=5793.9, rms=0.044 (0.000%)
- 069: dt: 0.5000, sse=5787.5, rms=0.043 (0.000%)
- 070: dt: 0.5000, sse=5782.1, rms=0.041 (0.000%)
- 071: dt: 0.5000, sse=5779.9, rms=0.039 (0.000%)
- 072: dt: 0.5000, sse=5778.4, rms=0.038 (0.000%)
- 073: dt: 0.5000, sse=5779.8, rms=0.036 (0.000%)
- 074: dt: 0.5000, sse=5780.7, rms=0.035 (0.000%)
- 075: dt: 0.5000, sse=5780.9, rms=0.034 (0.000%)
- 076: dt: 0.5000, sse=5783.3, rms=0.033 (0.000%)
- 077: dt: 0.5000, sse=5785.9, rms=0.031 (0.000%)
- 078: dt: 0.5000, sse=5789.2, rms=0.030 (0.000%)
- 079: dt: 0.5000, sse=5792.7, rms=0.030 (0.000%)
- 080: dt: 0.5000, sse=5795.7, rms=0.029 (0.000%)
- 081: dt: 0.5000, sse=5801.8, rms=0.028 (0.000%)
- 082: dt: 0.5000, sse=5805.6, rms=0.027 (0.000%)
- 083: dt: 0.5000, sse=5810.1, rms=0.027 (0.000%)
- 084: dt: 0.5000, sse=5812.7, rms=0.026 (0.000%)
- 085: dt: 0.5000, sse=5816.2, rms=0.026 (0.000%)
- 086: dt: 0.5000, sse=5819.6, rms=0.026 (0.000%)
- 087: dt: 0.5000, sse=5822.4, rms=0.025 (0.000%)
- 088: dt: 0.5000, sse=5826.1, rms=0.025 (0.000%)
- 089: dt: 0.5000, sse=5829.1, rms=0.025 (0.000%)
- 090: dt: 0.5000, sse=5831.0, rms=0.024 (0.000%)
- positioning took 3.4 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [85.70 212.30], gm=149.00+-21.10, and vertices in regions > 138.4
- 39039 surface locations found to contain inconsistent values (45 in, 38994 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/sub020/surf/lh.pial...
- writing smoothed curvature to lh.curv.pial
- 000: dt: 0.0000, sse=826.6, rms=0.04
- 091: dt: 0.5000, sse=807.4, rms=0.042 (0.000%)
- 092: dt: 0.5000, sse=762.4, rms=0.036 (0.000%)
- 093: dt: 0.5000, sse=748.1, rms=0.034 (0.000%)
- 094: dt: 0.5000, sse=740.5, rms=0.032 (0.000%)
- 095: dt: 0.5000, sse=733.8, rms=0.031 (0.000%)
- 096: dt: 0.5000, sse=728.4, rms=0.030 (0.000%)
- 097: dt: 0.5000, sse=724.4, rms=0.029 (0.000%)
- 098: dt: 0.5000, sse=720.0, rms=0.029 (0.000%)
- 099: dt: 0.5000, sse=716.5, rms=0.028 (0.000%)
- 100: dt: 0.5000, sse=713.1, rms=0.027 (0.000%)
- 101: dt: 0.5000, sse=709.8, rms=0.027 (0.000%)
- 102: dt: 0.5000, sse=707.4, rms=0.026 (0.000%)
- 103: dt: 0.5000, sse=704.8, rms=0.026 (0.000%)
- 104: dt: 0.5000, sse=702.5, rms=0.026 (0.000%)
- 105: dt: 0.5000, sse=700.8, rms=0.025 (0.000%)
- 106: dt: 0.5000, sse=698.8, rms=0.025 (0.000%)
- 107: dt: 0.5000, sse=697.3, rms=0.025 (0.000%)
- 108: dt: 0.5000, sse=696.1, rms=0.025 (0.000%)
- 109: dt: 0.5000, sse=694.8, rms=0.024 (0.000%)
- 110: dt: 0.5000, sse=693.7, rms=0.024 (0.000%)
- 111: dt: 0.5000, sse=692.9, rms=0.024 (0.000%)
- 112: dt: 0.5000, sse=692.4, rms=0.024 (0.000%)
- 113: dt: 0.5000, sse=691.7, rms=0.024 (0.000%)
- 114: dt: 0.5000, sse=690.8, rms=0.024 (0.000%)
- 115: dt: 0.5000, sse=690.4, rms=0.024 (0.000%)
- 116: dt: 0.5000, sse=689.7, rms=0.023 (0.000%)
- 117: dt: 0.5000, sse=689.2, rms=0.023 (0.000%)
- 118: dt: 0.5000, sse=689.0, rms=0.023 (0.000%)
- 119: dt: 0.5000, sse=688.8, rms=0.023 (0.000%)
- 120: dt: 0.5000, sse=688.4, rms=0.023 (0.000%)
- positioning took 3.3 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/lh.curv.pial
- writing smoothed area to lh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/lh.area.pial
- vertex spacing 1.02 +- 0.42 (0.04-->7.03) (max @ vno 105865 --> 105858)
- face area 0.41 +- 0.30 (0.00-->6.51)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 135248 vertices processed
- 25000 of 135248 vertices processed
- 50000 of 135248 vertices processed
- 75000 of 135248 vertices processed
- 100000 of 135248 vertices processed
- 125000 of 135248 vertices processed
- 0 of 135248 vertices processed
- 25000 of 135248 vertices processed
- 50000 of 135248 vertices processed
- 75000 of 135248 vertices processed
- 100000 of 135248 vertices processed
- 125000 of 135248 vertices processed
- thickness calculation complete, 403:667 truncations.
- 32496 vertices at 0 distance
- 100375 vertices at 1 distance
- 84257 vertices at 2 distance
- 30869 vertices at 3 distance
- 8309 vertices at 4 distance
- 2190 vertices at 5 distance
- 622 vertices at 6 distance
- 212 vertices at 7 distance
- 90 vertices at 8 distance
- 50 vertices at 9 distance
- 24 vertices at 10 distance
- 14 vertices at 11 distance
- 10 vertices at 12 distance
- 9 vertices at 13 distance
- 4 vertices at 14 distance
- 7 vertices at 15 distance
- 4 vertices at 16 distance
- 1 vertices at 17 distance
- 3 vertices at 18 distance
- 3 vertices at 19 distance
- 5 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/lh.thickness
- positioning took 18.6 minutes
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/scripts
- cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/rh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/rh.woT2.pial
- `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/rh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/rh.woT2.pial'
- mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub020 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/sub020/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/wm.mgz...
- 19247 bright wm thresholded.
- 144 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/rh.orig...
- computing class statistics...
- border white: 255703 voxels (1.52%)
- border gray 281220 voxels (1.68%)
- WM (94.0): 94.7 +- 9.7 [70.0 --> 110.0]
- GM (77.0) : 75.3 +- 13.1 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 47.9 (was 70)
- setting MAX_BORDER_WHITE to 115.7 (was 105)
- setting MIN_BORDER_WHITE to 61.0 (was 85)
- setting MAX_CSF to 34.7 (was 40)
- setting MAX_GRAY to 96.3 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 54.4 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 21.6 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=106, GM=61
- mean inside = 94.2, mean outside = 70.0
- smoothing surface for 5 iterations...
- reading initial white vertex positions from white...
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.89 +- 0.25 (0.03-->3.58) (max @ vno 87257 --> 88211)
- face area 0.33 +- 0.15 (0.00-->2.02)
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 7 points - only 0.00% unknown
- deleting segment 1 with 5 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 3 with 1 points - only 0.00% unknown
- deleting segment 7 with 34 points - only 0.00% unknown
- deleting segment 8 with 505 points - only 0.00% unknown
- deleting segment 9 with 13 points - only 0.00% unknown
- deleting segment 10 with 7 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 11 with 1 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 13 with 1 points - only 0.00% unknown
- deleting segment 14 with 5 points - only 0.00% unknown
- deleting segment 15 with 6 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 16 with 3 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 17 with 1 points - only 0.00% unknown
- tol=1.0e-04, sigma=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 (0.08-->3.58) (max @ vno 87257 --> 88211)
- face area 0.33 +- 0.15 (0.00-->2.02)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4031820.5, rms=0.00
- rms = 1.43, time step reduction 1 of 3 to 0.250...
- rms = 0.35, time step reduction 2 of 3 to 0.125...
- rms = 0.04, time step reduction 3 of 3 to 0.062...
- 001: dt: 0.1250, sse=4031820.5, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 7 points - only 0.00% unknown
- deleting segment 1 with 5 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 2 with 1 points - only 0.00% unknown
- deleting segment 3 with 34 points - only 0.00% unknown
- deleting segment 4 with 505 points - only 0.00% unknown
- deleting segment 5 with 13 points - only 0.00% unknown
- deleting segment 6 with 7 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 7 with 1 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 8 with 1 points - only 0.00% unknown
- deleting segment 9 with 5 points - only 0.00% unknown
- deleting segment 10 with 6 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 11 with 3 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 12 with 1 points - only 0.00% unknown
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.89 +- 0.24 (0.08-->3.58) (max @ vno 87257 --> 88211)
- face area 0.33 +- 0.15 (0.00-->2.02)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4031820.5, rms=0.00
- rms = 1.43, time step reduction 1 of 3 to 0.250...
- rms = 0.35, time step reduction 2 of 3 to 0.125...
- rms = 0.04, time step reduction 3 of 3 to 0.062...
- 002: dt: 0.1250, sse=4031820.5, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 7 points - only 0.00% unknown
- deleting segment 1 with 5 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 2 with 1 points - only 0.00% unknown
- deleting segment 3 with 34 points - only 0.00% unknown
- deleting segment 4 with 505 points - only 0.00% unknown
- deleting segment 5 with 13 points - only 0.00% unknown
- deleting segment 6 with 7 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 7 with 1 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 8 with 1 points - only 0.00% unknown
- deleting segment 9 with 5 points - only 0.00% unknown
- deleting segment 10 with 6 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 11 with 3 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 12 with 1 points - only 0.00% unknown
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.89 +- 0.24 (0.08-->3.58) (max @ vno 87257 --> 88211)
- face area 0.33 +- 0.15 (0.00-->2.02)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4031820.5, rms=0.00
- rms = 1.43, time step reduction 1 of 3 to 0.250...
- rms = 0.35, time step reduction 2 of 3 to 0.125...
- rms = 0.04, time step reduction 3 of 3 to 0.062...
- 003: dt: 0.1250, sse=4031820.5, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 7 points - only 0.00% unknown
- deleting segment 1 with 5 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 2 with 1 points - only 0.00% unknown
- deleting segment 3 with 34 points - only 0.00% unknown
- deleting segment 4 with 505 points - only 0.00% unknown
- deleting segment 5 with 13 points - only 0.00% unknown
- deleting segment 6 with 7 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 7 with 1 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 8 with 1 points - only 0.00% unknown
- deleting segment 9 with 5 points - only 0.00% unknown
- deleting segment 10 with 6 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 11 with 3 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 12 with 1 points - only 0.00% unknown
- tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- repositioning cortical surface to gray/csf boundary.
- smoothing T1 volume with sigma = 2.000
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4031820.5, rms=0.00
- rms = 1.43, time step reduction 1 of 3 to 0.250...
- rms = 0.35, time step reduction 2 of 3 to 0.125...
- rms = 0.04, time step reduction 3 of 3 to 0.062...
- 004: dt: 0.1250, sse=4031820.5, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- smoothing surface for 5 iterations...
- reading initial pial vertex positions from woT2.pial...
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [89.80 212.20], gm=151.00+-20.40, and vertices in regions > 140.8
- 43304 surface locations found to contain inconsistent values (3039 in, 40265 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=472589.1, rms=0.21
- 001: dt: 0.5000, sse=442930.6, rms=0.201 (0.000%)
- 002: dt: 0.5000, sse=424664.2, rms=0.187 (0.000%)
- 003: dt: 0.5000, sse=412980.9, rms=0.178 (0.000%)
- 004: dt: 0.5000, sse=404367.9, rms=0.169 (0.000%)
- 005: dt: 0.5000, sse=398024.7, rms=0.162 (0.000%)
- 006: dt: 0.5000, sse=393622.5, rms=0.156 (0.000%)
- 007: dt: 0.5000, sse=389960.1, rms=0.151 (0.000%)
- 008: dt: 0.5000, sse=386780.6, rms=0.147 (0.000%)
- 009: dt: 0.5000, sse=384244.2, rms=0.144 (0.000%)
- 010: dt: 0.5000, sse=382337.8, rms=0.141 (0.000%)
- 011: dt: 0.5000, sse=380231.2, rms=0.139 (0.000%)
- 012: dt: 0.5000, sse=378558.3, rms=0.137 (0.000%)
- 013: dt: 0.5000, sse=376872.5, rms=0.136 (0.000%)
- 014: dt: 0.5000, sse=375305.4, rms=0.134 (0.000%)
- 015: dt: 0.5000, sse=373725.4, rms=0.134 (0.000%)
- 016: dt: 0.5000, sse=373002.6, rms=0.133 (0.000%)
- 017: dt: 0.5000, sse=371573.0, rms=0.132 (0.000%)
- 018: dt: 0.5000, sse=370231.6, rms=0.132 (0.000%)
- 019: dt: 0.5000, sse=368878.1, rms=0.132 (0.000%)
- 020: dt: 0.5000, sse=367731.4, rms=0.131 (0.000%)
- 021: dt: 0.5000, sse=366561.6, rms=0.131 (0.000%)
- 022: dt: 0.5000, sse=365618.6, rms=0.131 (0.000%)
- 023: dt: 0.5000, sse=364359.8, rms=0.131 (0.000%)
- 024: dt: 0.5000, sse=363329.5, rms=0.132 (0.000%)
- 025: dt: 0.5000, sse=362358.8, rms=0.132 (0.000%)
- 026: dt: 0.5000, sse=361414.3, rms=0.132 (0.000%)
- 027: dt: 0.5000, sse=360635.4, rms=0.132 (0.000%)
- 028: dt: 0.5000, sse=359845.7, rms=0.133 (0.000%)
- 029: dt: 0.5000, sse=359047.3, rms=0.133 (0.000%)
- 030: dt: 0.5000, sse=358239.5, rms=0.133 (0.000%)
- positioning took 3.8 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [91.00 217.00], gm=154.00+-21.00, and vertices in regions > 143.5
- 38459 surface locations found to contain inconsistent values (1134 in, 37325 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=37287.9, rms=0.12
- 031: dt: 0.5000, sse=36974.7, rms=0.115 (0.000%)
- 032: dt: 0.5000, sse=37851.8, rms=0.104 (0.000%)
- 033: dt: 0.5000, sse=38885.9, rms=0.096 (0.000%)
- 034: dt: 0.5000, sse=39757.1, rms=0.091 (0.000%)
- 035: dt: 0.5000, sse=40468.8, rms=0.087 (0.000%)
- 036: dt: 0.5000, sse=41159.2, rms=0.082 (0.000%)
- 037: dt: 0.5000, sse=41830.7, rms=0.079 (0.000%)
- 038: dt: 0.5000, sse=42462.8, rms=0.075 (0.000%)
- 039: dt: 0.5000, sse=43058.8, rms=0.072 (0.000%)
- 040: dt: 0.5000, sse=43648.8, rms=0.069 (0.000%)
- 041: dt: 0.5000, sse=44201.5, rms=0.066 (0.000%)
- 042: dt: 0.5000, sse=44708.7, rms=0.064 (0.000%)
- 043: dt: 0.5000, sse=45190.4, rms=0.061 (0.000%)
- 044: dt: 0.5000, sse=45658.9, rms=0.059 (0.000%)
- 045: dt: 0.5000, sse=46089.0, rms=0.057 (0.000%)
- 046: dt: 0.5000, sse=46494.2, rms=0.055 (0.000%)
- 047: dt: 0.5000, sse=46876.8, rms=0.054 (0.000%)
- 048: dt: 0.5000, sse=47222.6, rms=0.052 (0.000%)
- 049: dt: 0.5000, sse=47556.0, rms=0.051 (0.000%)
- 050: dt: 0.5000, sse=47885.2, rms=0.049 (0.000%)
- 051: dt: 0.5000, sse=48151.8, rms=0.048 (0.000%)
- 052: dt: 0.5000, sse=48421.7, rms=0.047 (0.000%)
- 053: dt: 0.5000, sse=48671.9, rms=0.046 (0.000%)
- 054: dt: 0.5000, sse=48900.7, rms=0.045 (0.000%)
- 055: dt: 0.5000, sse=49113.5, rms=0.044 (0.000%)
- 056: dt: 0.5000, sse=49311.8, rms=0.043 (0.000%)
- 057: dt: 0.5000, sse=49506.9, rms=0.042 (0.000%)
- 058: dt: 0.5000, sse=49675.1, rms=0.042 (0.000%)
- 059: dt: 0.5000, sse=49857.1, rms=0.041 (0.000%)
- 060: dt: 0.5000, sse=50011.9, rms=0.040 (0.000%)
- positioning took 3.8 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [98.00 206.00], gm=152.00+-18.00, and vertices in regions > 143.0
- 12866 surface locations found to contain inconsistent values (4928 in, 7938 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=6364.5, rms=0.10
- 061: dt: 0.5000, sse=6309.6, rms=0.100 (0.000%)
- 062: dt: 0.5000, sse=6131.4, rms=0.092 (0.000%)
- 063: dt: 0.5000, sse=6015.7, rms=0.086 (0.000%)
- 064: dt: 0.5000, sse=5940.1, rms=0.080 (0.000%)
- 065: dt: 0.5000, sse=5894.4, rms=0.075 (0.000%)
- 066: dt: 0.5000, sse=5867.5, rms=0.071 (0.000%)
- 067: dt: 0.5000, sse=5843.3, rms=0.068 (0.000%)
- 068: dt: 0.5000, sse=5821.2, rms=0.065 (0.000%)
- 069: dt: 0.5000, sse=5800.9, rms=0.062 (0.000%)
- 070: dt: 0.5000, sse=5789.1, rms=0.059 (0.000%)
- 071: dt: 0.5000, sse=5784.9, rms=0.057 (0.000%)
- 072: dt: 0.5000, sse=5785.2, rms=0.054 (0.000%)
- 073: dt: 0.5000, sse=5789.6, rms=0.052 (0.000%)
- 074: dt: 0.5000, sse=5795.9, rms=0.050 (0.000%)
- 075: dt: 0.5000, sse=5803.9, rms=0.048 (0.000%)
- 076: dt: 0.5000, sse=5813.0, rms=0.046 (0.000%)
- 077: dt: 0.5000, sse=5821.3, rms=0.044 (0.000%)
- 078: dt: 0.5000, sse=5833.3, rms=0.043 (0.000%)
- 079: dt: 0.5000, sse=5846.5, rms=0.041 (0.000%)
- 080: dt: 0.5000, sse=5859.2, rms=0.040 (0.000%)
- 081: dt: 0.5000, sse=5869.2, rms=0.038 (0.000%)
- 082: dt: 0.5000, sse=5881.7, rms=0.037 (0.000%)
- 083: dt: 0.5000, sse=5891.9, rms=0.036 (0.000%)
- 084: dt: 0.5000, sse=5906.0, rms=0.035 (0.000%)
- 085: dt: 0.5000, sse=5918.0, rms=0.034 (0.000%)
- 086: dt: 0.5000, sse=5927.7, rms=0.033 (0.000%)
- 087: dt: 0.5000, sse=5935.3, rms=0.032 (0.000%)
- 088: dt: 0.5000, sse=5942.8, rms=0.032 (0.000%)
- 089: dt: 0.5000, sse=5949.1, rms=0.031 (0.000%)
- 090: dt: 0.5000, sse=5955.9, rms=0.030 (0.000%)
- positioning took 3.6 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [97.40 206.60], gm=152.00+-18.20, and vertices in regions > 142.9
- 8819 surface locations found to contain inconsistent values (462 in, 8357 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/sub020/surf/rh.pial...
- writing smoothed curvature to rh.curv.pial
- 000: dt: 0.0000, sse=860.5, rms=0.05
- 091: dt: 0.5000, sse=853.5, rms=0.045 (0.000%)
- 092: dt: 0.5000, sse=826.7, rms=0.043 (0.000%)
- 093: dt: 0.5000, sse=807.4, rms=0.041 (0.000%)
- 094: dt: 0.5000, sse=790.4, rms=0.039 (0.000%)
- 095: dt: 0.5000, sse=775.4, rms=0.037 (0.000%)
- 096: dt: 0.5000, sse=764.0, rms=0.036 (0.000%)
- 097: dt: 0.5000, sse=754.5, rms=0.035 (0.000%)
- 098: dt: 0.5000, sse=746.6, rms=0.034 (0.000%)
- 099: dt: 0.5000, sse=738.4, rms=0.033 (0.000%)
- 100: dt: 0.5000, sse=730.8, rms=0.032 (0.000%)
- 101: dt: 0.5000, sse=724.0, rms=0.031 (0.000%)
- 102: dt: 0.5000, sse=717.3, rms=0.031 (0.000%)
- 103: dt: 0.5000, sse=711.4, rms=0.030 (0.000%)
- 104: dt: 0.5000, sse=705.9, rms=0.029 (0.000%)
- 105: dt: 0.5000, sse=701.7, rms=0.028 (0.000%)
- 106: dt: 0.5000, sse=697.7, rms=0.028 (0.000%)
- 107: dt: 0.5000, sse=693.7, rms=0.027 (0.000%)
- 108: dt: 0.5000, sse=690.4, rms=0.027 (0.000%)
- 109: dt: 0.5000, sse=687.4, rms=0.026 (0.000%)
- 110: dt: 0.5000, sse=685.0, rms=0.026 (0.000%)
- 111: dt: 0.5000, sse=682.6, rms=0.025 (0.000%)
- 112: dt: 0.5000, sse=681.2, rms=0.025 (0.000%)
- 113: dt: 0.5000, sse=679.4, rms=0.025 (0.000%)
- 114: dt: 0.5000, sse=678.0, rms=0.024 (0.000%)
- 115: dt: 0.5000, sse=676.6, rms=0.024 (0.000%)
- 116: dt: 0.5000, sse=675.5, rms=0.024 (0.000%)
- 117: dt: 0.5000, sse=674.6, rms=0.024 (0.000%)
- 118: dt: 0.5000, sse=673.8, rms=0.024 (0.000%)
- 119: dt: 0.5000, sse=672.8, rms=0.023 (0.000%)
- 120: dt: 0.5000, sse=672.1, rms=0.023 (0.000%)
- positioning took 3.5 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/rh.curv.pial
- writing smoothed area to rh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/rh.area.pial
- vertex spacing 1.02 +- 0.43 (0.03-->6.51) (max @ vno 93686 --> 94804)
- face area 0.40 +- 0.30 (0.00-->5.00)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 136728 vertices processed
- 25000 of 136728 vertices processed
- 50000 of 136728 vertices processed
- 75000 of 136728 vertices processed
- 100000 of 136728 vertices processed
- 125000 of 136728 vertices processed
- 0 of 136728 vertices processed
- 25000 of 136728 vertices processed
- 50000 of 136728 vertices processed
- 75000 of 136728 vertices processed
- 100000 of 136728 vertices processed
- 125000 of 136728 vertices processed
- thickness calculation complete, 144:755 truncations.
- 32444 vertices at 0 distance
- 99412 vertices at 1 distance
- 86452 vertices at 2 distance
- 31713 vertices at 3 distance
- 8259 vertices at 4 distance
- 2166 vertices at 5 distance
- 591 vertices at 6 distance
- 171 vertices at 7 distance
- 75 vertices at 8 distance
- 28 vertices at 9 distance
- 21 vertices at 10 distance
- 12 vertices at 11 distance
- 2 vertices at 12 distance
- 10 vertices at 13 distance
- 11 vertices at 14 distance
- 8 vertices at 15 distance
- 11 vertices at 16 distance
- 6 vertices at 17 distance
- 9 vertices at 18 distance
- 6 vertices at 19 distance
- 1 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/rh.thickness
- positioning took 18.3 minutes
- #--------------------------------------------
- #@# Surf Volume lh Thu Aug 8 23:07:28 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf
- mris_calc -o lh.area.mid lh.area add lh.area.pial
- Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o lh.area.mid lh.area.mid div 2
- Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o lh.volume lh.area.mid mul lh.thickness
- Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ]
- #--------------------------------------------
- #@# Surf Volume rh Thu Aug 8 23:07:29 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf
- mris_calc -o rh.area.mid rh.area add rh.area.pial
- Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o rh.area.mid rh.area.mid div 2
- Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o rh.volume rh.area.mid mul rh.thickness
- Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ]
- #--------------------------------------------
- #@# Cortical ribbon mask Thu Aug 8 23:07:30 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri
- mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon sub020
- 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 = 35
- writing volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/ribbon.mgz
- writing ribbon files
- #--------------------------------------------
- #@# ASeg Stats Thu Aug 8 23:22:05 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020
- 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 sub020
- $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 sub020
- sysname Linux
- hostname snake6
- machine x86_64
- user fkaule
- UseRobust 0
- atlas_icv (eTIV) = 1189215 mm^3 (det: 1.638144 )
- Computing euler number
- orig.nofix lheno = -22, rheno = -18
- orig.nofix lhholes = 12, rhholes = 10
- Loading mri/aseg.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 243626.505 242493.000 diff= 1133.5 pctdiff= 0.465
- rhCtxGM: 245076.316 243754.000 diff= 1322.3 pctdiff= 0.540
- lhCtxWM: 232702.934 232535.000 diff= 167.9 pctdiff= 0.072
- rhCtxWM: 233629.919 233637.000 diff= -7.1 pctdiff=-0.003
- SubCortGMVol 64321.000
- SupraTentVol 1039368.673 (1035974.000) diff=3394.673 pctdiff=0.327
- SupraTentVolNotVent 1020437.673 (1017043.000) diff=3394.673 pctdiff=0.333
- BrainSegVol 1153612.000 (1150540.000) diff=3072.000 pctdiff=0.266
- BrainSegVolNotVent 1130980.000 (1133331.673) diff=-2351.673 pctdiff=-0.208
- BrainSegVolNotVent 1130980.000
- CerebellumVol 113672.000
- VentChorVol 18931.000
- 3rd4th5thCSF 3701.000
- CSFVol 651.000, OptChiasmVol 243.000
- MaskVol 1600687.000
- 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 10350 10349.553
- 4 5 Left-Inf-Lat-Vent 532 531.982
- 5 7 Left-Cerebellum-White-Matter 14951 14950.855
- 6 8 Left-Cerebellum-Cortex 42655 42654.559
- 7 10 Left-Thalamus-Proper 7875 7875.376
- 8 11 Left-Caudate 3600 3599.688
- 9 12 Left-Putamen 6050 6050.024
- 10 13 Left-Pallidum 2350 2350.297
- 11 14 3rd-Ventricle 957 956.663
- 12 15 4th-Ventricle 2312 2312.331
- 13 16 Brain-Stem 23342 23342.322
- 14 17 Left-Hippocampus 3867 3867.381
- 15 18 Left-Amygdala 1599 1598.899
- 16 24 CSF 687 687.051
- 17 26 Left-Accumbens-area 754 753.627
- 18 28 Left-VentralDC 4171 4171.196
- 19 30 Left-vessel 112 112.486
- 20 31 Left-choroid-plexus 1151 1150.828
- 23 43 Right-Lateral-Ventricle 4594 4593.949
- 24 44 Right-Inf-Lat-Vent 568 567.502
- 25 46 Right-Cerebellum-White-Matter 15291 15290.651
- 26 47 Right-Cerebellum-Cortex 42978 42978.051
- 27 49 Right-Thalamus-Proper 8107 8107.405
- 28 50 Right-Caudate 3975 3975.128
- 29 51 Right-Putamen 6454 6453.916
- 30 52 Right-Pallidum 2228 2228.198
- 31 53 Right-Hippocampus 4347 4346.928
- 32 54 Right-Amygdala 2027 2026.955
- 33 58 Right-Accumbens-area 697 696.642
- 34 60 Right-VentralDC 4007 4006.571
- 35 62 Right-vessel 156 156.231
- 36 63 Right-choroid-plexus 1757 1756.655
- 37 72 5th-Ventricle 0 0.000
- 38 77 WM-hypointensities 1411 1410.651
- 39 78 Left-WM-hypointensities 0 0.000
- 40 79 Right-WM-hypointensities 0 0.000
- 41 80 non-WM-hypointensities 15 14.591
- 42 81 Left-non-WM-hypointensities 0 0.000
- 43 82 Right-non-WM-hypointensities 0 0.000
- 44 85 Optic-Chiasm 241 241.365
- 45 251 CC_Posterior 661 661.093
- 46 252 CC_Mid_Posterior 371 371.185
- 47 253 CC_Central 350 350.120
- 48 254 CC_Mid_Anterior 395 394.599
- 49 255 CC_Anterior 746 745.828
- Reporting on 45 segmentations
- mri_segstats done
- #-----------------------------------------
- #@# AParc-to-ASeg Thu Aug 8 23:25:05 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020
- mri_aparc2aseg --s sub020 --volmask
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- subject sub020
- outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/aparc+aseg.mgz
- useribbon 0
- baseoffset 0
- RipUnknown 0
- Reading lh white surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/lh.white
- Reading lh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/lh.pial
- Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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/sub020/surf/rh.white
- Reading rh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/rh.pial
- Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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/sub020/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/sub020/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 = 483790
- Used brute-force search on 0 voxels
- Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/aparc+aseg.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020
- mri_aparc2aseg --s sub020 --volmask --a2009s
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- subject sub020
- outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/aparc.a2009s+aseg.mgz
- useribbon 0
- baseoffset 10100
- RipUnknown 0
- Reading lh white surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/lh.white
- Reading lh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/lh.pial
- Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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/sub020/surf/rh.white
- Reading rh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/rh.pial
- Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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/sub020/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/sub020/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 = 483790
- Used brute-force search on 0 voxels
- Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/aparc.a2009s+aseg.mgz
- #-----------------------------------------
- #@# WMParc Thu Aug 8 23:29:32 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020
- mri_aparc2aseg --s sub020 --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 sub020
- 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/sub020/mri/aparc+aseg.mgz
- Reading lh white surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/lh.white
- Reading lh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/lh.pial
- Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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/sub020/surf/rh.white
- Reading rh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/rh.pial
- Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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/sub020/mri/ribbon.mgz
- Loading filled from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/filled.mgz
- Ripping vertices labeled as unkown
- Ripped 7934 vertices from left hemi
- Ripped 8552 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/sub020/mri/aseg.mgz
- Loading Ctx Seg File /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 = 949843
- Used brute-force search on 294 voxels
- Fixing Parahip LH WM
- Found 13 clusters
- 0 k 1.000000
- 1 k 2.000000
- 2 k 19.000000
- 3 k 1.000000
- 4 k 1.000000
- 5 k 5.000000
- 6 k 4.000000
- 7 k 1671.000000
- 8 k 1.000000
- 9 k 8.000000
- 10 k 1.000000
- 11 k 1.000000
- 12 k 1.000000
- Fixing Parahip RH WM
- Found 5 clusters
- 0 k 1432.000000
- 1 k 1.000000
- 2 k 1.000000
- 3 k 35.000000
- 4 k 1.000000
- Writing output aseg to mri/wmparc.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020
- 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 sub020 --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 sub020 --surf-wm-vol --ctab /opt/freesurfer/5.3.0/WMParcStatsLUT.txt --etiv
- sysname Linux
- hostname snake6
- machine x86_64
- user fkaule
- UseRobust 0
- atlas_icv (eTIV) = 1189215 mm^3 (det: 1.638144 )
- Loading mri/wmparc.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 243626.505 242493.000 diff= 1133.5 pctdiff= 0.465
- rhCtxGM: 245076.316 243754.000 diff= 1322.3 pctdiff= 0.540
- lhCtxWM: 232702.934 232535.000 diff= 167.9 pctdiff= 0.072
- rhCtxWM: 233629.919 233637.000 diff= -7.1 pctdiff=-0.003
- SubCortGMVol 64321.000
- SupraTentVol 1039368.673 (1035974.000) diff=3394.673 pctdiff=0.327
- SupraTentVolNotVent 1020437.673 (1017043.000) diff=3394.673 pctdiff=0.333
- BrainSegVol 1153612.000 (1150540.000) diff=3072.000 pctdiff=0.266
- BrainSegVolNotVent 1130980.000 (1133331.673) diff=-2351.673 pctdiff=-0.208
- BrainSegVolNotVent 1130980.000
- CerebellumVol 113672.000
- VentChorVol 18931.000
- 3rd4th5thCSF 3701.000
- CSFVol 651.000, OptChiasmVol 243.000
- MaskVol 1600687.000
- 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 2401 2401.069
- 2 3002 wm-lh-caudalanteriorcingulate 2375 2375.337
- 3 3003 wm-lh-caudalmiddlefrontal 8274 8273.741
- 4 3004 wm-lh-corpuscallosum 0 0.000
- 5 3005 wm-lh-cuneus 2290 2290.403
- 6 3006 wm-lh-entorhinal 1144 1143.960
- 7 3007 wm-lh-fusiform 6688 6688.168
- 8 3008 wm-lh-inferiorparietal 8820 8819.961
- 9 3009 wm-lh-inferiortemporal 5663 5662.702
- 10 3010 wm-lh-isthmuscingulate 3875 3874.894
- 11 3011 wm-lh-lateraloccipital 11177 11176.998
- 12 3012 wm-lh-lateralorbitofrontal 6162 6161.910
- 13 3013 wm-lh-lingual 5083 5083.311
- 14 3014 wm-lh-medialorbitofrontal 2888 2888.162
- 15 3015 wm-lh-middletemporal 5429 5429.046
- 16 3016 wm-lh-parahippocampal 1723 1722.894
- 17 3017 wm-lh-paracentral 4399 4398.985
- 18 3018 wm-lh-parsopercularis 3440 3439.649
- 19 3019 wm-lh-parsorbitalis 887 886.574
- 20 3020 wm-lh-parstriangularis 2573 2573.346
- 21 3021 wm-lh-pericalcarine 2778 2777.504
- 22 3022 wm-lh-postcentral 7555 7555.304
- 23 3023 wm-lh-posteriorcingulate 4034 4033.842
- 24 3024 wm-lh-precentral 14285 14285.295
- 25 3025 wm-lh-precuneus 8485 8484.810
- 26 3026 wm-lh-rostralanteriorcingulate 3030 3030.228
- 27 3027 wm-lh-rostralmiddlefrontal 13786 13786.477
- 28 3028 wm-lh-superiorfrontal 21732 21732.143
- 29 3029 wm-lh-superiorparietal 11851 11851.019
- 30 3030 wm-lh-superiortemporal 8423 8423.245
- 31 3031 wm-lh-supramarginal 9609 9608.732
- 32 3032 wm-lh-frontalpole 129 129.265
- 33 3033 wm-lh-temporalpole 652 651.978
- 34 3034 wm-lh-transversetemporal 837 837.059
- 35 3035 wm-lh-insula 8294 8294.047
- 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 2773 2772.666
- 120 4002 wm-rh-caudalanteriorcingulate 3157 3157.345
- 121 4003 wm-rh-caudalmiddlefrontal 6362 6362.414
- 122 4004 wm-rh-corpuscallosum 0 0.000
- 123 4005 wm-rh-cuneus 2601 2601.081
- 124 4006 wm-rh-entorhinal 947 946.719
- 125 4007 wm-rh-fusiform 5673 5672.772
- 126 4008 wm-rh-inferiorparietal 12399 12398.517
- 127 4009 wm-rh-inferiortemporal 6300 6300.169
- 128 4010 wm-rh-isthmuscingulate 3679 3678.719
- 129 4011 wm-rh-lateraloccipital 8247 8246.771
- 130 4012 wm-rh-lateralorbitofrontal 5914 5913.527
- 131 4013 wm-rh-lingual 5853 5852.833
- 132 4014 wm-rh-medialorbitofrontal 3345 3344.653
- 133 4015 wm-rh-middletemporal 6047 6047.475
- 134 4016 wm-rh-parahippocampal 1495 1495.263
- 135 4017 wm-rh-paracentral 4650 4650.045
- 136 4018 wm-rh-parsopercularis 2558 2558.149
- 137 4019 wm-rh-parsorbitalis 1085 1084.763
- 138 4020 wm-rh-parstriangularis 3608 3607.619
- 139 4021 wm-rh-pericalcarine 3980 3979.763
- 140 4022 wm-rh-postcentral 8215 8214.576
- 141 4023 wm-rh-posteriorcingulate 4503 4502.979
- 142 4024 wm-rh-precentral 13475 13474.939
- 143 4025 wm-rh-precuneus 10053 10053.125
- 144 4026 wm-rh-rostralanteriorcingulate 2225 2224.917
- 145 4027 wm-rh-rostralmiddlefrontal 15609 15609.217
- 146 4028 wm-rh-superiorfrontal 20723 20723.453
- 147 4029 wm-rh-superiorparietal 9763 9762.570
- 148 4030 wm-rh-superiortemporal 7601 7601.156
- 149 4031 wm-rh-supramarginal 9851 9851.104
- 150 4032 wm-rh-frontalpole 333 333.304
- 151 4033 wm-rh-temporalpole 545 545.181
- 152 4034 wm-rh-transversetemporal 601 600.900
- 153 4035 wm-rh-insula 7679 7679.114
- 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 32873 32873.477
- 237 5002 Right-UnsegmentedWhiteMatter 32659 32658.512
- 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/sub020/label
- #--------------------------------------------
- #@# BA Labels lh Thu Aug 8 23:40:50 CEST 2013
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 135248
- Number of reverse mapping hits = 287
- Checking for and removing duplicates
- Writing label file ./lh.BA1.label 4416
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 135248
- Number of reverse mapping hits = 327
- Checking for and removing duplicates
- Writing label file ./lh.BA2.label 8236
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 135248
- Number of reverse mapping hits = 220
- Checking for and removing duplicates
- Writing label file ./lh.BA3a.label 4297
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 135248
- Number of reverse mapping hits = 450
- Checking for and removing duplicates
- Writing label file ./lh.BA3b.label 6433
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 135248
- Number of reverse mapping hits = 740
- Checking for and removing duplicates
- Writing label file ./lh.BA4a.label 6524
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 135248
- Number of reverse mapping hits = 522
- Checking for and removing duplicates
- Writing label file ./lh.BA4p.label 4592
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 135248
- Number of reverse mapping hits = 1607
- Checking for and removing duplicates
- Writing label file ./lh.BA6.label 15196
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 135248
- Number of reverse mapping hits = 312
- Checking for and removing duplicates
- Writing label file ./lh.BA44.label 4493
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 135248
- Number of reverse mapping hits = 630
- Checking for and removing duplicates
- Writing label file ./lh.BA45.label 4052
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 135248
- Number of reverse mapping hits = 1474
- Checking for and removing duplicates
- Writing label file ./lh.V1.label 6115
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 135248
- Number of reverse mapping hits = 3522
- Checking for and removing duplicates
- Writing label file ./lh.V2.label 11636
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 135248
- Number of reverse mapping hits = 412
- Checking for and removing duplicates
- Writing label file ./lh.MT.label 2430
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.perirhinal.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 135248
- Number of reverse mapping hits = 169
- Checking for and removing duplicates
- Writing label file ./lh.perirhinal.label 1368
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.thresh.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 135248
- Number of reverse mapping hits = 40
- Checking for and removing duplicates
- Writing label file ./lh.BA1.thresh.label 1054
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.thresh.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 135248
- Number of reverse mapping hits = 92
- Checking for and removing duplicates
- Writing label file ./lh.BA2.thresh.label 2184
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.thresh.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 135248
- Number of reverse mapping hits = 20
- Checking for and removing duplicates
- Writing label file ./lh.BA3a.thresh.label 1524
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.thresh.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 135248
- Number of reverse mapping hits = 215
- Checking for and removing duplicates
- Writing label file ./lh.BA3b.thresh.label 2211
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.thresh.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 135248
- Number of reverse mapping hits = 411
- Checking for and removing duplicates
- Writing label file ./lh.BA4a.thresh.label 2730
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.thresh.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 135248
- Number of reverse mapping hits = 157
- Checking for and removing duplicates
- Writing label file ./lh.BA4p.thresh.label 1706
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.thresh.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 135248
- Number of reverse mapping hits = 782
- Checking for and removing duplicates
- Writing label file ./lh.BA6.thresh.label 7817
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.thresh.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 135248
- Number of reverse mapping hits = 98
- Checking for and removing duplicates
- Writing label file ./lh.BA44.thresh.label 2010
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.thresh.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 135248
- Number of reverse mapping hits = 289
- Checking for and removing duplicates
- Writing label file ./lh.BA45.thresh.label 1440
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.thresh.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 135248
- Number of reverse mapping hits = 953
- Checking for and removing duplicates
- Writing label file ./lh.V1.thresh.label 4358
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.thresh.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 135248
- Number of reverse mapping hits = 1750
- Checking for and removing duplicates
- Writing label file ./lh.V2.thresh.label 5084
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.thresh.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 135248
- Number of reverse mapping hits = 66
- Checking for and removing duplicates
- Writing label file ./lh.MT.thresh.label 579
- mri_label2label: Done
- mris_label2annot --s sub020 --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/sub020/label
- cmdline mris_label2annot --s sub020 --hemi lh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --l lh.perirhinal.label --a BA --maxstatwinner --noverbose
- sysname Linux
- hostname snake6
- machine x86_64
- user fkaule
- subject sub020
- 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/sub020/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 93111 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/label/lh.BA.annot
- mris_label2annot --s sub020 --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/sub020/label
- cmdline mris_label2annot --s sub020 --hemi lh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l lh.BA1.thresh.label --l lh.BA2.thresh.label --l lh.BA3a.thresh.label --l lh.BA3b.thresh.label --l lh.BA4a.thresh.label --l lh.BA4p.thresh.label --l lh.BA6.thresh.label --l lh.BA44.thresh.label --l lh.BA45.thresh.label --l lh.V1.thresh.label --l lh.V2.thresh.label --l lh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose
- sysname Linux
- hostname snake6
- machine x86_64
- user fkaule
- subject sub020
- 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/sub020/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 110648 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/label/lh.BA.thresh.annot
- mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab sub020 lh white
- computing statistics for each annotation in ./lh.BA.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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
- 1034 590 2151 2.554 0.322 0.144 0.053 20 2.0 BA1
- 3468 2323 5887 2.329 0.428 0.121 0.034 33 4.8 BA2
- 984 664 959 1.889 0.376 0.141 0.042 9 1.7 BA3a
- 2607 1686 3935 1.989 0.549 0.117 0.035 30 4.2 BA3b
- 2066 1089 4006 2.995 0.425 0.106 0.112 70 6.6 BA4a
- 1498 901 2578 2.843 0.508 0.112 0.049 33 3.8 BA4p
- 9874 6541 23337 2.872 0.539 0.124 0.037 109 14.7 BA6
- 2143 1449 4451 2.663 0.423 0.139 0.044 31 3.9 BA44
- 2956 1994 5813 2.497 0.408 0.136 0.042 42 5.1 BA45
- 3445 2254 4222 1.879 0.456 0.170 0.072 68 10.1 V1
- 8992 5820 13680 2.201 0.450 0.167 0.068 191 23.9 V2
- 1961 1280 3367 2.369 0.495 0.126 0.035 21 3.0 MT
- 1109 759 3069 3.007 0.872 0.130 0.234 59 2.3 perirhinal
- mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab sub020 lh white
- computing statistics for each annotation in ./lh.BA.thresh.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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
- 642 337 1350 2.612 0.363 0.156 0.050 13 1.3 BA1
- 1363 911 2422 2.345 0.349 0.108 0.027 11 1.6 BA2
- 764 519 700 1.850 0.353 0.145 0.044 7 1.4 BA3a
- 1682 1118 2166 1.781 0.366 0.095 0.023 10 1.6 BA3b
- 1997 1067 3915 3.062 0.416 0.100 0.104 37 5.6 BA4a
- 1145 695 1955 2.819 0.423 0.119 0.065 49 3.8 BA4p
- 5609 3585 13026 2.896 0.563 0.122 0.038 64 9.0 BA6
- 1339 912 2896 2.669 0.444 0.151 0.051 24 2.8 BA44
- 1255 841 2875 2.667 0.369 0.162 0.055 27 3.0 BA45
- 3664 2431 4613 1.895 0.475 0.171 0.074 81 11.3 V1
- 4671 2976 6753 2.131 0.455 0.174 0.074 98 13.3 V2
- 469 327 727 2.191 0.673 0.111 0.028 3 0.5 MT
- #--------------------------------------------
- #@# BA Labels rh Thu Aug 8 23:45:15 CEST 2013
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 136728
- Number of reverse mapping hits = 314
- Checking for and removing duplicates
- Writing label file ./rh.BA1.label 4276
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 136728
- Number of reverse mapping hits = 398
- Checking for and removing duplicates
- Writing label file ./rh.BA2.label 7085
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 136728
- Number of reverse mapping hits = 124
- Checking for and removing duplicates
- Writing label file ./rh.BA3a.label 4104
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 136728
- Number of reverse mapping hits = 331
- Checking for and removing duplicates
- Writing label file ./rh.BA3b.label 4853
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 136728
- Number of reverse mapping hits = 617
- Checking for and removing duplicates
- Writing label file ./rh.BA4a.label 6364
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 136728
- Number of reverse mapping hits = 413
- Checking for and removing duplicates
- Writing label file ./rh.BA4p.label 4886
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 136728
- Number of reverse mapping hits = 1257
- Checking for and removing duplicates
- Writing label file ./rh.BA6.label 13513
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 136728
- Number of reverse mapping hits = 687
- Checking for and removing duplicates
- Writing label file ./rh.BA44.label 7599
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 136728
- Number of reverse mapping hits = 1091
- Checking for and removing duplicates
- Writing label file ./rh.BA45.label 6446
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 136728
- Number of reverse mapping hits = 2032
- Checking for and removing duplicates
- Writing label file ./rh.V1.label 6759
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 136728
- Number of reverse mapping hits = 3197
- Checking for and removing duplicates
- Writing label file ./rh.V2.label 11213
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 136728
- Number of reverse mapping hits = 362
- Checking for and removing duplicates
- Writing label file ./rh.MT.label 2294
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.perirhinal.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 136728
- Number of reverse mapping hits = 96
- Checking for and removing duplicates
- Writing label file ./rh.perirhinal.label 848
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.thresh.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 136728
- Number of reverse mapping hits = 75
- Checking for and removing duplicates
- Writing label file ./rh.BA1.thresh.label 951
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.thresh.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 136728
- Number of reverse mapping hits = 164
- Checking for and removing duplicates
- Writing label file ./rh.BA2.thresh.label 2852
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.thresh.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 136728
- Number of reverse mapping hits = 25
- Checking for and removing duplicates
- Writing label file ./rh.BA3a.thresh.label 1723
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.thresh.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 136728
- Number of reverse mapping hits = 202
- Checking for and removing duplicates
- Writing label file ./rh.BA3b.thresh.label 2385
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.thresh.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 136728
- Number of reverse mapping hits = 207
- Checking for and removing duplicates
- Writing label file ./rh.BA4a.thresh.label 1595
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.thresh.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 136728
- Number of reverse mapping hits = 117
- Checking for and removing duplicates
- Writing label file ./rh.BA4p.thresh.label 1606
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.thresh.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 136728
- Number of reverse mapping hits = 516
- Checking for and removing duplicates
- Writing label file ./rh.BA6.thresh.label 7475
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.thresh.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 136728
- Number of reverse mapping hits = 88
- Checking for and removing duplicates
- Writing label file ./rh.BA44.thresh.label 1100
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.thresh.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 136728
- Number of reverse mapping hits = 193
- Checking for and removing duplicates
- Writing label file ./rh.BA45.thresh.label 1371
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.thresh.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 136728
- Number of reverse mapping hits = 1476
- Checking for and removing duplicates
- Writing label file ./rh.V1.thresh.label 4708
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.thresh.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 136728
- Number of reverse mapping hits = 1532
- Checking for and removing duplicates
- Writing label file ./rh.V2.thresh.label 4969
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.thresh.label --trgsubject sub020 --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 = sub020
- 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/sub020/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 136728
- 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 sub020 --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/sub020/label
- cmdline mris_label2annot --s sub020 --hemi rh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --l rh.perirhinal.label --a BA --maxstatwinner --noverbose
- sysname Linux
- hostname snake6
- machine x86_64
- user fkaule
- subject sub020
- 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/sub020/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 94215 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/label/rh.BA.annot
- mris_label2annot --s sub020 --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/sub020/label
- cmdline mris_label2annot --s sub020 --hemi rh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l rh.BA1.thresh.label --l rh.BA2.thresh.label --l rh.BA3a.thresh.label --l rh.BA3b.thresh.label --l rh.BA4a.thresh.label --l rh.BA4p.thresh.label --l rh.BA6.thresh.label --l rh.BA44.thresh.label --l rh.BA45.thresh.label --l rh.V1.thresh.label --l rh.V2.thresh.label --l rh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose
- sysname Linux
- hostname snake6
- machine x86_64
- user fkaule
- subject sub020
- 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/sub020/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 113200 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/label/rh.BA.thresh.annot
- mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab sub020 rh white
- computing statistics for each annotation in ./rh.BA.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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
- 953 537 2051 2.669 0.376 0.142 0.056 19 2.3 BA1
- 3372 2221 5439 2.348 0.386 0.110 0.028 29 4.1 BA2
- 959 660 952 1.894 0.464 0.136 0.043 9 1.7 BA3a
- 2151 1374 3162 1.935 0.511 0.114 0.038 25 3.7 BA3b
- 1893 982 3516 2.965 0.484 0.106 0.063 64 4.0 BA4a
- 1294 835 2262 2.781 0.528 0.111 0.036 9 2.0 BA4p
- 8328 5464 19724 2.941 0.512 0.128 0.152 512 29.9 BA6
- 3235 2156 6461 2.725 0.389 0.132 0.041 47 5.5 BA44
- 4500 3030 9309 2.534 0.417 0.150 0.069 116 9.2 BA45
- 4538 3035 5753 1.885 0.449 0.176 0.119 106 18.6 V1
- 8715 5661 13357 2.203 0.475 0.159 0.072 160 25.5 V2
- 1907 1269 3133 2.336 0.411 0.139 0.045 27 3.5 MT
- 668 479 2103 3.115 0.747 0.115 0.034 5 0.9 perirhinal
- mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab sub020 rh white
- computing statistics for each annotation in ./rh.BA.thresh.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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
- 593 327 1265 2.685 0.364 0.143 0.050 12 1.3 BA1
- 1979 1311 3518 2.414 0.432 0.105 0.028 17 2.3 BA2
- 827 557 758 1.882 0.440 0.135 0.040 7 1.4 BA3a
- 1760 1170 2305 1.801 0.439 0.103 0.030 14 2.2 BA3b
- 1124 539 2065 2.956 0.463 0.119 0.719 60 4.7 BA4a
- 1101 697 1881 2.780 0.546 0.110 0.038 8 1.8 BA4p
- 4999 3289 11892 2.941 0.519 0.128 0.075 404 23.0 BA6
- 738 499 1613 2.693 0.405 0.146 0.055 17 1.6 BA44
- 1097 772 2633 2.613 0.351 0.163 0.062 24 2.6 BA45
- 4368 2929 5445 1.870 0.451 0.175 0.120 101 18.1 V1
- 4642 3016 6976 2.134 0.465 0.168 0.091 96 16.9 V2
- 300 188 626 2.719 0.391 0.172 0.059 7 0.7 MT
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/label
- #--------------------------------------------
- #@# Ex-vivo Entorhinal Cortex Label lh Thu Aug 8 23:49:40 CEST 2013
- mris_spherical_average -erode 1 -orig white -t 0.4 -o sub020 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label
- painting output onto subject sub020.
- processing subject lh.EC_average...
- reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 1039 points to lh.entorhinal_exvivo.label...
- mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label sub020 lh white
- limiting computations to label ./lh.entorhinal_exvivo.label.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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
- 372 237 1312 3.221 0.866 0.114 3.381 10 0.5 ./lh.entorhinal_exvivo.label
- #--------------------------------------------
- #@# Ex-vivo Entorhinal Cortex Label rh Thu Aug 8 23:49:54 CEST 2013
- mris_spherical_average -erode 1 -orig white -t 0.4 -o sub020 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label
- painting output onto subject sub020.
- processing subject rh.EC_average...
- reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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 857 points to rh.entorhinal_exvivo.label...
- mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label sub020 rh white
- limiting computations to label ./rh.entorhinal_exvivo.label.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/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
- 320 210 1049 2.990 0.673 0.110 0.032 5 0.5 ./rh.entorhinal_exvivo.label
- #------------------------------------------
- Started at Thu Aug 8 10:54:16 CEST 2013
- Ended at Thu Aug 8 23:50:10 CEST 2013
- #@#%# recon-all-run-time-hours 12.932
- recon-all -s sub020 finished without error at Thu Aug 8 23:50:10 CEST 2013
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