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|
- Thu Aug 8 10:54:16 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016
- /opt/freesurfer/5.3.0/bin/recon-all
- -i /home/data/exppsy/forrest_gump/openfmri.org/sub016/anatomy/highres001.nii.gz -cw256 -all -T2 /home/data/exppsy/forrest_gump/openfmri.org/sub016/anatomy/other/t2w001.nii.gz -T2pial -subjid sub016 -sd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- subjid sub016
- 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 96978996 2222696 0 118440 94733872
- -/+ buffers/cache: 2126684 97075008
- 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/sub016
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub016/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig/001.mgz
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub016/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/anatomy/highres001.nii.gz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.999248, 0.0307568, 0.0236215)
- j_ras = (0.0317878, 0.9985, 0.0445881)
- k_ras = (0.0222147, -0.0453054, 0.998726)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig/001.mgz...
- #--------------------------------------------
- #@# T2/FLAIR Input Thu Aug 8 10:54:37 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub016/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig/T2raw.mgz
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub016/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/anatomy/other/t2w001.nii.gz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.999248, 0.0307568, 0.0236215)
- j_ras = (0.0317878, 0.9985, 0.0445881)
- k_ras = (0.0222147, -0.0453054, 0.998726)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig/T2raw.mgz...
- #--------------------------------------------
- #@# MotionCor Thu Aug 8 10:54:53 CEST 2013
- Found 1 runs
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/mri/orig/001.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/rawavg.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig.mgz --conform --cw256
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/mri/rawavg.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.999248, 0.0307568, 0.0236215)
- j_ras = (0.0317878, 0.9985, 0.0445881)
- k_ras = (0.0222147, -0.0453054, 0.998726)
- Original Data has (0.699898, 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/sub016/mri/orig.mgz...
- mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/talairach.xfm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Talairach Thu Aug 8 10:55:33 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 10:58:41 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri
- talairach_afd -T 0.005 -xfm transforms/talairach.xfm
- talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7652, pval=0.6675 >= threshold=0.0050)
- awk -f /opt/freesurfer/5.3.0/bin/extract_talairach_avi_QA.awk /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/talairach_avi.log
- tal_QC_AZS /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/talairach_avi.log
- TalAviQA: 0.96776
- z-score: -2
- #--------------------------------------------
- #@# Nu Intensity Correction Thu Aug 8 10:58:42 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/sub016/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 10:58:42 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.25504
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.25504/nu0.mnc -odt float
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.25504/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, 1.86265e-09, 3.72529e-09)
- j_ras = (1.86265e-09, 0, -1)
- k_ras = (-1.97906e-09, 1, -3.72529e-09)
- changing data type from uchar to float (noscale = 0)...
- writing to ./tmp.mri_nu_correct.mni.25504/nu0.mnc...
-
- --------------------------------------------------------
- Iteration 1 Thu Aug 8 10:58:46 CEST 2013
- nu_correct -clobber ./tmp.mri_nu_correct.mni.25504/nu0.mnc ./tmp.mri_nu_correct.mni.25504/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.25504/0/
- [fkaule@snake6:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/] [2013-08-08 10:58:46] 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.25504/0/ ./tmp.mri_nu_correct.mni.25504/nu0.mnc ./tmp.mri_nu_correct.mni.25504/nu1.imp
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Number of iterations: 50
- CV of field change: 0.00127909
- [fkaule@snake6:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/] [2013-08-08 10:59:52] running:
- /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.25504/nu0.mnc ./tmp.mri_nu_correct.mni.25504/0//template.mnc
- Transforming slices:......................................................................................Done
- Transforming slices:................................................................................................................................................................................................................................................................Done
-
-
- --------------------------------------------------------
- Iteration 2 Thu Aug 8 10:59:59 CEST 2013
- nu_correct -clobber ./tmp.mri_nu_correct.mni.25504/nu1.mnc ./tmp.mri_nu_correct.mni.25504/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.25504/1/
- [fkaule@snake6:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/] [2013-08-08 10:59:59] 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.25504/1/ ./tmp.mri_nu_correct.mni.25504/nu1.mnc ./tmp.mri_nu_correct.mni.25504/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
- 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: 36
- CV of field change: 0.000992739
- [fkaule@snake6:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/] [2013-08-08 11:00:35] running:
- /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.25504/nu1.mnc ./tmp.mri_nu_correct.mni.25504/1//template.mnc
- Transforming slices:......................................................................................Done
- Transforming slices:................................................................................................................................................................................................................................................................Done
-
-
-
- mri_binarize --i ./tmp.mri_nu_correct.mni.25504/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.25504/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/sub016/mri
- cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.25504/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.25504/ones.mgz
- sysname Linux
- hostname snake6
- machine x86_64
- user fkaule
- input ./tmp.mri_nu_correct.mni.25504/nu2.mnc
- frame 0
- nErode3d 0
- nErode2d 0
- output ./tmp.mri_nu_correct.mni.25504/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.25504/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.25504/sum.junk --avgwf ./tmp.mri_nu_correct.mni.25504/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.25504/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.25504/sum.junk --avgwf ./tmp.mri_nu_correct.mni.25504/input.mean.dat
- sysname Linux
- hostname snake6
- machine x86_64
- user fkaule
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.25504/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.25504/input.mean.dat
- mri_segstats done
- mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.25504/ones.mgz --i ./tmp.mri_nu_correct.mni.25504/nu2.mnc --sum ./tmp.mri_nu_correct.mni.25504/sum.junk --avgwf ./tmp.mri_nu_correct.mni.25504/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.25504/ones.mgz --i ./tmp.mri_nu_correct.mni.25504/nu2.mnc --sum ./tmp.mri_nu_correct.mni.25504/sum.junk --avgwf ./tmp.mri_nu_correct.mni.25504/output.mean.dat
- sysname Linux
- hostname snake6
- machine x86_64
- user fkaule
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.25504/ones.mgz
- Loading ./tmp.mri_nu_correct.mni.25504/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.25504/output.mean.dat
- mri_segstats done
- mris_calc -o ./tmp.mri_nu_correct.mni.25504/nu2.mnc ./tmp.mri_nu_correct.mni.25504/nu2.mnc mul .91902004648487725472
- Saving result to './tmp.mri_nu_correct.mni.25504/nu2.mnc' (type = MINC ) [ ok ]
- mri_convert ./tmp.mri_nu_correct.mni.25504/nu2.mnc nu.mgz --like orig.mgz
- mri_convert ./tmp.mri_nu_correct.mni.25504/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.25504/nu2.mnc...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, 1.86264e-09, 3.72529e-09)
- j_ras = (1.86265e-09, 0, -1)
- k_ras = (-1.97906e-09, 1, -3.72529e-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 (11, 145) to ( 3, 110)
-
-
- Thu Aug 8 11:01:18 CEST 2013
- mri_nu_correct.mni done
- mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/talairach.xfm nu.mgz nu.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Intensity Normalization Thu Aug 8 11:01:19 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri
- mri_normalize -g 1 nu.mgz T1.mgz
- using max gradient = 1.000
- reading from nu.mgz...
- normalizing image...
- talairach transform
- 1.058 -0.012 -0.029 2.523;
- 0.001 1.053 0.291 -44.522;
- 0.050 -0.333 1.154 -5.882;
- 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 = 18
- Starting OpenSpline(): npoints = 18
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Iterating 2 times
- ---------------------------------
- 3d normalization pass 1 of 2
- white matter peak found at 111
- white matter peak found at 108
- gm peak at 56 (56), valley at 38 (38)
- csf peak at 28, setting threshold to 46
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- ---------------------------------
- 3d normalization pass 2 of 2
- white matter peak found at 111
- white matter peak found at 110
- gm peak at 57 (57), valley at 37 (37)
- csf peak at 28, setting threshold to 47
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Done iterating ---------------------------------
- writing output to T1.mgz
- 3D bias adjustment took 2 minutes and 46 seconds.
- #--------------------------------------------
- #@# Skull Stripping Thu Aug 8 11:04:06 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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=10.0
- skull bounding box = (48, 13, 15) --> (205, 255, 204)
- using (100, 94, 110) as brain centroid...
- mean wm in atlas = 126, using box (81,64,87) --> (119, 123,133) to find MRI wm
- before smoothing, mri peak at 108
- after smoothing, mri peak at 108, scaling input intensities by 1.167
- scaling channel 0 by 1.16667
- initial log_p = -4.7
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -4.486263 @ (-9.091, 27.273, -9.091)
- max log p = -4.316039 @ (4.545, -4.545, -4.545)
- max log p = -4.208757 @ (2.273, -2.273, 6.818)
- max log p = -4.208757 @ (0.000, 0.000, 0.000)
- max log p = -4.208757 @ (0.000, 0.000, 0.000)
- max log p = -4.208757 @ (0.000, 0.000, 0.000)
- Found translation: (-2.3, 20.5, -6.8): log p = -4.209
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.2 (thresh=-4.2)
- 1.000 0.000 0.000 -2.273;
- 0.000 1.194 0.320 -35.195;
- 0.000 -0.239 0.893 29.301;
- 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)
- 1.000 0.000 0.000 -2.273;
- 0.000 1.194 0.320 -35.195;
- 0.000 -0.239 0.893 29.301;
- 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)
- 0.962 -0.003 0.027 -0.106;
- -0.002 1.201 0.292 -28.668;
- -0.037 -0.210 0.955 24.058;
- 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)
- 0.962 -0.003 0.027 -0.106;
- -0.002 1.201 0.292 -28.668;
- -0.037 -0.210 0.955 24.058;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.0625
- ****************************************
- Nine parameter search. iteration 4 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 0.966 -0.003 0.027 -0.575;
- -0.002 1.198 0.291 -28.306;
- -0.037 -0.210 0.958 24.199;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 5 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 0.966 -0.003 0.027 -0.575;
- -0.002 1.203 0.292 -28.832;
- -0.037 -0.210 0.957 24.295;
- 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)
- 0.966 -0.003 0.027 -0.575;
- -0.002 1.205 0.292 -29.183;
- -0.037 -0.210 0.956 24.391;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 7 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 0.966 -0.003 0.027 -0.575;
- -0.002 1.205 0.292 -29.183;
- -0.037 -0.210 0.956 24.391;
- 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
- 0.96553 -0.00330 0.02692 -0.57520;
- -0.00214 1.20541 0.29238 -29.18299;
- -0.03709 -0.20989 0.95579 24.39078;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 3481
- Quasinewton: input matrix
- 0.96553 -0.00330 0.02692 -0.57520;
- -0.00214 1.20541 0.29238 -29.18299;
- -0.03709 -0.20989 0.95579 24.39078;
- 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:
- 0.966 -0.003 0.027 -0.575;
- -0.002 1.205 0.292 -29.183;
- -0.037 -0.210 0.956 24.391;
- 0.000 0.000 0.000 1.000;
- pass 1, spacing 8: log(p) = -4.0 (old=-4.7)
- transform before final EM align:
- 0.966 -0.003 0.027 -0.575;
- -0.002 1.205 0.292 -29.183;
- -0.037 -0.210 0.956 24.391;
- 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
- 0.96553 -0.00330 0.02692 -0.57520;
- -0.00214 1.20541 0.29238 -29.18299;
- -0.03709 -0.20989 0.95579 24.39078;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 382743
- Quasinewton: input matrix
- 0.96553 -0.00330 0.02692 -0.57520;
- -0.00214 1.20541 0.29238 -29.18299;
- -0.03709 -0.20989 0.95579 24.39078;
- 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:
- 0.966 -0.003 0.027 -0.575;
- -0.002 1.205 0.292 -29.183;
- -0.037 -0.210 0.956 24.391;
- 0.000 0.000 0.000 1.000;
- writing output transformation to transforms/talairach_with_skull.lta...
- registration took 40 minutes and 24 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=128 y=86 z=118 r=96
- first estimation of the main basin volume: 3810863 voxels
- Looking for seedpoints
- 2 found in the cerebellum
- 18 found in the rest of the brain
- global maximum in x=165, y=88, z=85, 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=22582056777 voxels, voxel volume =1.000
- = 22582056777 mmm3 = 22582056.960 cm3
- done.
- PostAnalyze...Basin Prior
- 214 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=127,y=97, z=111, r=9970 iterations
- ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^
- GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 45424
- RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=12 , nb = -1033853503
- LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = 1101477547
- RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1079460279
- LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1082319012
- OTHER CSF_MIN=0, CSF_intensity=9, CSF_MAX=32 , nb = 1066689784
-
- CSF_MAX TRANSITION GM_MIN GM
- GLOBAL
- before analyzing : 4, 6, 36, 57
- after analyzing : 4, 26, 36, 33
- RIGHT_CER
- before analyzing : 12, 20, 39, 61
- after analyzing : 12, 32, 39, 39
- LEFT_CER
- before analyzing : 5, 7, 36, 70
- after analyzing : 5, 26, 36, 37
- RIGHT_BRAIN
- before analyzing : 4, 6, 35, 56
- after analyzing : 4, 25, 35, 32
- LEFT_BRAIN
- before analyzing : 4, 6, 36, 57
- after analyzing : 4, 26, 36, 33
- OTHER
- before analyzing : 32, 66, 80, 89
- after analyzing : 32, 75, 80, 78
- mri_strip_skull: done peeling brain
- highly tesselated surface with 10242 vertices
- matching...66 iterations
- *********************VALIDATION*********************
- curvature mean = -0.012, std = 0.011
- curvature mean = 73.306, std = 8.785
- No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
- before rotation: sse = 2.07, sigma = 3.40
- after rotation: sse = 2.07, sigma = 3.40
- Localization of inacurate regions: Erosion-Dilation steps
- the sse mean is 2.13, its var is 2.71
- before Erosion-Dilatation 0.01% 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...52 iterations
- mri_strip_skull: done peeling brain
- Brain Size = 1932674 voxels, voxel volume = 1.000 mm3
- = 1932674 mmm3 = 1932.674 cm3
- ******************************
- Saving brainmask.auto.mgz
- done
- cp brainmask.auto.mgz brainmask.mgz
- #-------------------------------------
- #@# EM Registration Thu Aug 8 11:45:00 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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=22.0
- skull bounding box = (56, 37, 33) --> (198, 176, 203)
- using (103, 83, 118) as brain centroid...
- mean wm in atlas = 107, using box (86,66,97) --> (120, 100,138) to find MRI wm
- before smoothing, mri peak at 106
- after smoothing, mri peak at 106, scaling input intensities by 1.009
- scaling channel 0 by 1.00943
- initial log_p = -4.5
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -4.052590 @ (-9.091, 27.273, -9.091)
- max log p = -3.920415 @ (4.545, -4.545, 4.545)
- max log p = -3.806407 @ (2.273, 2.273, -6.818)
- max log p = -3.742288 @ (1.136, -3.409, 3.409)
- max log p = -3.716874 @ (-1.705, -1.705, -0.568)
- max log p = -3.716874 @ (0.000, 0.000, 0.000)
- Found translation: (-2.8, 19.9, -8.5): log p = -3.717
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.6, old_max_log_p =-3.7 (thresh=-3.7)
- 1.000 0.000 0.000 -2.841;
- 0.000 1.050 0.156 -2.858;
- 0.000 -0.112 0.997 2.922;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.6, old_max_log_p =-3.6 (thresh=-3.6)
- 1.000 0.000 0.000 -2.841;
- 0.000 1.050 0.156 -2.858;
- 0.000 -0.112 0.997 2.922;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.2500
- ****************************************
- Nine parameter search. iteration 2 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.5, old_max_log_p =-3.6 (thresh=-3.6)
- 0.998 -0.045 0.052 -3.782;
- 0.036 1.092 0.268 -20.552;
- -0.063 -0.199 0.940 28.185;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 3 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.4, old_max_log_p =-3.5 (thresh=-3.5)
- 0.980 -0.039 0.020 3.232;
- 0.039 1.119 0.241 -22.394;
- -0.030 -0.167 0.967 15.950;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 4 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4)
- 0.980 -0.039 0.020 3.232;
- 0.039 1.119 0.241 -22.394;
- -0.030 -0.167 0.967 15.950;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.0625
- ****************************************
- Nine parameter search. iteration 5 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4)
- 0.981 -0.039 0.020 2.619;
- 0.039 1.121 0.242 -23.193;
- -0.030 -0.167 0.963 16.264;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 6 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4)
- 0.983 -0.021 0.024 0.151;
- 0.022 1.119 0.249 -21.700;
- -0.030 -0.176 0.960 17.535;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 7 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4)
- 0.983 -0.021 0.024 0.151;
- 0.022 1.116 0.249 -21.370;
- -0.030 -0.176 0.960 17.535;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 8 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4)
- 0.983 -0.021 0.024 0.151;
- 0.022 1.116 0.249 -21.370;
- -0.030 -0.176 0.960 17.535;
- 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
- 0.98311 -0.02089 0.02425 0.15113;
- 0.02232 1.11629 0.24862 -21.37015;
- -0.02989 -0.17573 0.96035 17.53523;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 2772
- Quasinewton: input matrix
- 0.98311 -0.02089 0.02425 0.15113;
- 0.02232 1.11629 0.24862 -21.37015;
- -0.02989 -0.17573 0.96035 17.53523;
- 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:
- 0.983 -0.021 0.024 0.151;
- 0.022 1.116 0.249 -21.370;
- -0.030 -0.176 0.960 17.535;
- 0.000 0.000 0.000 1.000;
- pass 1, spacing 8: log(p) = -3.4 (old=-4.5)
- transform before final EM align:
- 0.983 -0.021 0.024 0.151;
- 0.022 1.116 0.249 -21.370;
- -0.030 -0.176 0.960 17.535;
- 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
- 0.98311 -0.02089 0.02425 0.15113;
- 0.02232 1.11629 0.24862 -21.37015;
- -0.02989 -0.17573 0.96035 17.53523;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 312841
- Quasinewton: input matrix
- 0.98311 -0.02089 0.02425 0.15113;
- 0.02232 1.11629 0.24862 -21.37015;
- -0.02989 -0.17573 0.96035 17.53523;
- 0.00000 0.00000 0.00000 1.00000;
- dfp_em_step_func: 012: -log(p) = 3.9
- after pass:transform: ( 0.98, -0.02, 0.02, 0.15)
- ( 0.02, 1.12, 0.25, -21.37)
- ( -0.03, -0.18, 0.96, 17.54)
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization...
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 014: -log(p) = 3.9 tol 0.000000
- final transform:
- 0.983 -0.021 0.024 0.151;
- 0.022 1.116 0.249 -21.370;
- -0.030 -0.176 0.960 17.535;
- 0.000 0.000 0.000 1.000;
- writing output transformation to transforms/talairach.lta...
- registration took 34 minutes and 25 seconds.
- #--------------------------------------
- #@# CA Normalize Thu Aug 8 12:19:24 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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=22.0
- skull bounding box = (56, 37, 33) --> (198, 176, 203)
- using (103, 83, 118) as brain centroid...
- mean wm in atlas = 107, using box (86,66,97) --> (120, 100,138) to find MRI wm
- before smoothing, mri peak at 106
- after smoothing, mri peak at 106, scaling input intensities by 1.009
- scaling channel 0 by 1.00943
- using 244171 sample points...
- INFO: compute sample coordinates transform
- 0.983 -0.021 0.024 0.151;
- 0.022 1.116 0.249 -21.370;
- -0.030 -0.176 0.960 17.535;
- 0.000 0.000 0.000 1.000;
- INFO: transform used
- finding control points in Left_Cerebral_White_Matter....
- found 41584 control points for structure...
- bounding box (127, 38, 35) --> (195, 141, 204)
- Left_Cerebral_White_Matter: limiting intensities to 106.0 --> 177.0
- 0 of 11 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 40735 control points for structure...
- bounding box (62, 39, 34) --> (128, 139, 203)
- Right_Cerebral_White_Matter: limiting intensities to 101.0 --> 177.0
- 0 of 8 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3012 control points for structure...
- bounding box (130, 118, 63) --> (180, 157, 117)
- Left_Cerebellum_White_Matter: limiting intensities to 91.0 --> 177.0
- 0 of 7 (0.0%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2764 control points for structure...
- bounding box (82, 118, 59) --> (129, 158, 117)
- Right_Cerebellum_White_Matter: limiting intensities to 103.0 --> 177.0
- 2 of 7 (28.6%) samples deleted
- finding control points in Brain_Stem....
- found 3520 control points for structure...
- bounding box (111, 108, 97) --> (144, 170, 128)
- Brain_Stem: limiting intensities to 79.0 --> 177.0
- 0 of 13 (0.0%) samples deleted
- using 46 total control points for intensity normalization...
- bias field = 0.956 +- 0.064
- 0 of 44 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 41584 control points for structure...
- bounding box (127, 38, 35) --> (195, 141, 204)
- Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 169.0
- 0 of 91 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 40735 control points for structure...
- bounding box (62, 39, 34) --> (128, 139, 203)
- Right_Cerebral_White_Matter: limiting intensities to 99.0 --> 169.0
- 0 of 103 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3012 control points for structure...
- bounding box (130, 118, 63) --> (180, 157, 117)
- Left_Cerebellum_White_Matter: limiting intensities to 99.0 --> 169.0
- 26 of 39 (66.7%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2764 control points for structure...
- bounding box (82, 118, 59) --> (129, 158, 117)
- Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 169.0
- 0 of 35 (0.0%) samples deleted
- finding control points in Brain_Stem....
- found 3520 control points for structure...
- bounding box (111, 108, 97) --> (144, 170, 128)
- Brain_Stem: limiting intensities to 89.0 --> 169.0
- 28 of 58 (48.3%) samples deleted
- using 326 total control points for intensity normalization...
- bias field = 0.957 +- 0.070
- 0 of 272 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 41584 control points for structure...
- bounding box (127, 38, 35) --> (195, 141, 204)
- Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 154.0
- 3 of 220 (1.4%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 40735 control points for structure...
- bounding box (62, 39, 34) --> (128, 139, 203)
- Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 154.0
- 0 of 222 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3012 control points for structure...
- bounding box (130, 118, 63) --> (180, 157, 117)
- Left_Cerebellum_White_Matter: limiting intensities to 75.0 --> 154.0
- 0 of 41 (0.0%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2764 control points for structure...
- bounding box (82, 118, 59) --> (129, 158, 117)
- Right_Cerebellum_White_Matter: limiting intensities to 81.0 --> 154.0
- 3 of 38 (7.9%) samples deleted
- finding control points in Brain_Stem....
- found 3520 control points for structure...
- bounding box (111, 108, 97) --> (144, 170, 128)
- Brain_Stem: limiting intensities to 64.0 --> 154.0
- 0 of 58 (0.0%) samples deleted
- using 579 total control points for intensity normalization...
- bias field = 1.027 +- 0.060
- 0 of 573 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 12:21:28 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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) = 1.10 (predicted orig area = 7.3)
- 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=0.863, neg=0, invalid=96777
- 0001: dt=129.472000, rms=0.793 (8.133%), neg=0, invalid=96777
- 0002: dt=129.472000, rms=0.779 (1.805%), neg=0, invalid=96777
- 0003: dt=129.472000, rms=0.765 (1.709%), neg=0, invalid=96777
- 0004: dt=110.976000, rms=0.761 (0.564%), neg=0, invalid=96777
- 0005: dt=129.472000, rms=0.754 (0.867%), neg=0, invalid=96777
- 0006: dt=92.480000, rms=0.752 (0.262%), neg=0, invalid=96777
- 0007: dt=369.920000, rms=0.745 (1.036%), neg=0, invalid=96777
- 0008: dt=55.488000, rms=0.742 (0.371%), neg=0, invalid=96777
- 0009: dt=129.472000, rms=0.740 (0.210%), neg=0, invalid=96777
- 0010: dt=129.472000, rms=0.738 (0.377%), neg=0, invalid=96777
- 0011: dt=129.472000, rms=0.734 (0.468%), neg=0, invalid=96777
- 0012: dt=129.472000, rms=0.731 (0.457%), neg=0, invalid=96777
- 0013: dt=129.472000, rms=0.726 (0.656%), neg=0, invalid=96777
- 0014: dt=129.472000, rms=0.721 (0.643%), neg=0, invalid=96777
- 0015: dt=129.472000, rms=0.718 (0.499%), neg=0, invalid=96777
- 0016: dt=129.472000, rms=0.715 (0.405%), neg=0, invalid=96777
- 0017: dt=129.472000, rms=0.712 (0.450%), neg=0, invalid=96777
- 0018: dt=129.472000, rms=0.709 (0.398%), neg=0, invalid=96777
- 0019: dt=129.472000, rms=0.707 (0.305%), neg=0, invalid=96777
- 0020: dt=129.472000, rms=0.705 (0.276%), neg=0, invalid=96777
- 0021: dt=129.472000, rms=0.703 (0.283%), neg=0, invalid=96777
- 0022: dt=129.472000, rms=0.701 (0.246%), neg=0, invalid=96777
- 0023: dt=129.472000, rms=0.699 (0.222%), neg=0, invalid=96777
- 0024: dt=129.472000, rms=0.698 (0.223%), neg=0, invalid=96777
- 0025: dt=129.472000, rms=0.696 (0.235%), neg=0, invalid=96777
- 0026: dt=129.472000, rms=0.694 (0.254%), neg=0, invalid=96777
- 0027: dt=129.472000, rms=0.693 (0.228%), neg=0, invalid=96777
- 0028: dt=129.472000, rms=0.691 (0.190%), neg=0, invalid=96777
- 0029: dt=129.472000, rms=0.690 (0.216%), neg=0, invalid=96777
- 0030: dt=129.472000, rms=0.689 (0.202%), neg=0, invalid=96777
- 0031: dt=129.472000, rms=0.687 (0.192%), neg=0, invalid=96777
- 0032: dt=129.472000, rms=0.686 (0.154%), neg=0, invalid=96777
- 0033: dt=129.472000, rms=0.685 (0.132%), neg=0, invalid=96777
- 0034: dt=129.472000, rms=0.684 (0.162%), neg=0, invalid=96777
- 0035: dt=129.472000, rms=0.683 (0.136%), neg=0, invalid=96777
- 0036: dt=129.472000, rms=0.683 (0.108%), neg=0, invalid=96777
- 0037: dt=129.472000, rms=0.682 (0.141%), neg=0, invalid=96777
- 0038: dt=129.472000, rms=0.680 (0.167%), neg=0, invalid=96777
- 0039: dt=129.472000, rms=0.679 (0.143%), neg=0, invalid=96777
- 0040: dt=129.472000, rms=0.679 (0.109%), neg=0, invalid=96777
- 0041: dt=129.472000, rms=0.678 (0.150%), neg=0, invalid=96777
- 0042: dt=129.472000, rms=0.677 (0.167%), neg=0, invalid=96777
- 0043: dt=129.472000, rms=0.676 (0.107%), neg=0, invalid=96777
- 0044: dt=129.472000, rms=0.675 (0.065%), neg=0, invalid=96777
- 0045: dt=295.936000, rms=0.675 (0.069%), neg=0, invalid=96777
- 0046: dt=4.624000, rms=0.675 (-0.006%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.675, neg=0, invalid=96777
- 0047: dt=27.744000, rms=0.675 (0.009%), neg=0, invalid=96777
- 0048: dt=18.496000, rms=0.675 (0.005%), neg=0, invalid=96777
- 0049: dt=18.496000, rms=0.675 (0.006%), neg=0, invalid=96777
- 0050: dt=18.496000, rms=0.675 (0.001%), neg=0, invalid=96777
- 0051: dt=18.496000, rms=0.675 (-0.000%), neg=0, invalid=96777
- setting smoothness coefficient to 0.154
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.684, neg=0, invalid=96777
- 0052: dt=331.776000, rms=0.666 (2.583%), neg=0, invalid=96777
- 0053: dt=36.288000, rms=0.663 (0.424%), neg=0, invalid=96777
- 0054: dt=145.152000, rms=0.656 (1.150%), neg=0, invalid=96777
- 0055: dt=20.736000, rms=0.654 (0.263%), neg=0, invalid=96777
- 0056: dt=36.288000, rms=0.653 (0.116%), neg=0, invalid=96777
- 0057: dt=36.288000, rms=0.652 (0.227%), neg=0, invalid=96777
- 0058: dt=36.288000, rms=0.650 (0.299%), neg=0, invalid=96777
- 0059: dt=36.288000, rms=0.647 (0.341%), neg=0, invalid=96777
- 0060: dt=36.288000, rms=0.645 (0.435%), neg=0, invalid=96777
- 0061: dt=36.288000, rms=0.641 (0.555%), neg=0, invalid=96777
- 0062: dt=36.288000, rms=0.637 (0.575%), neg=0, invalid=96777
- 0063: dt=36.288000, rms=0.634 (0.491%), neg=0, invalid=96777
- 0064: dt=36.288000, rms=0.631 (0.437%), neg=0, invalid=96777
- 0065: dt=36.288000, rms=0.629 (0.393%), neg=0, invalid=96777
- 0066: dt=36.288000, rms=0.626 (0.403%), neg=0, invalid=96777
- 0067: dt=36.288000, rms=0.624 (0.368%), neg=0, invalid=96777
- 0068: dt=36.288000, rms=0.622 (0.297%), neg=0, invalid=96777
- 0069: dt=36.288000, rms=0.621 (0.261%), neg=0, invalid=96777
- 0070: dt=36.288000, rms=0.619 (0.301%), neg=0, invalid=96777
- 0071: dt=36.288000, rms=0.617 (0.291%), neg=0, invalid=96777
- 0072: dt=36.288000, rms=0.615 (0.239%), neg=0, invalid=96777
- 0073: dt=36.288000, rms=0.614 (0.186%), neg=0, invalid=96777
- 0074: dt=36.288000, rms=0.613 (0.163%), neg=0, invalid=96777
- 0075: dt=36.288000, rms=0.612 (0.169%), neg=0, invalid=96777
- 0076: dt=36.288000, rms=0.611 (0.149%), neg=0, invalid=96777
- 0077: dt=36.288000, rms=0.611 (0.104%), neg=0, invalid=96777
- 0078: dt=36.288000, rms=0.610 (0.063%), neg=0, invalid=96777
- 0079: dt=145.152000, rms=0.610 (0.082%), neg=0, invalid=96777
- 0080: dt=0.000000, rms=0.610 (-0.005%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.610, neg=0, invalid=96777
- 0081: dt=15.552000, rms=0.610 (0.015%), neg=0, invalid=96777
- 0082: dt=31.104000, rms=0.610 (0.019%), neg=0, invalid=96777
- 0083: dt=25.920000, rms=0.610 (0.013%), neg=0, invalid=96777
- 0084: dt=25.920000, rms=0.610 (-0.005%), neg=0, invalid=96777
- setting smoothness coefficient to 0.588
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.640, neg=0, invalid=96777
- 0085: dt=2.800000, rms=0.640 (0.023%), neg=0, invalid=96777
- 0086: dt=0.700000, rms=0.640 (0.001%), neg=0, invalid=96777
- 0087: dt=0.700000, rms=0.640 (0.001%), neg=0, invalid=96777
- 0088: dt=0.700000, rms=0.640 (-0.003%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.640, neg=0, invalid=96777
- 0089: dt=0.000000, rms=0.640 (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=0.725, neg=0, invalid=96777
- 0090: dt=5.393665, rms=0.700 (3.417%), neg=0, invalid=96777
- 0091: dt=3.456000, rms=0.699 (0.216%), neg=0, invalid=96777
- 0092: dt=3.456000, rms=0.699 (-0.021%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.699, neg=0, invalid=96777
- 0093: dt=0.000000, rms=0.699 (0.000%), neg=0, invalid=96777
- setting smoothness coefficient to 5.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.774, neg=0, invalid=96777
- 0094: dt=1.290672, rms=0.768 (0.749%), neg=0, invalid=96777
- 0095: dt=1.536000, rms=0.760 (0.999%), neg=0, invalid=96777
- 0096: dt=0.816964, rms=0.759 (0.172%), neg=0, invalid=96777
- 0097: dt=0.816964, rms=0.758 (0.146%), neg=0, invalid=96777
- 0098: dt=0.816964, rms=0.757 (0.157%), neg=0, invalid=96777
- 0099: dt=0.816964, rms=0.757 (0.021%), neg=0, invalid=96777
- 0100: dt=0.816964, rms=0.757 (-0.282%), neg=0, invalid=96777
- 0101: dt=1.024000, rms=0.757 (0.018%), neg=0, invalid=96777
- 0102: dt=1.792000, rms=0.756 (0.071%), neg=0, invalid=96777
- 0103: dt=0.384000, rms=0.756 (0.005%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.756, neg=0, invalid=96777
- 0104: dt=1.166667, rms=0.755 (0.103%), neg=0, invalid=96777
- 0105: dt=0.000000, rms=0.755 (0.003%), neg=0, invalid=96777
- 0106: dt=0.100000, rms=0.755 (-0.004%), 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=0.719, neg=0, invalid=96777
- 0107: dt=0.155548, rms=0.711 (1.144%), neg=0, invalid=96777
- 0108: dt=0.000000, rms=0.711 (0.002%), neg=0, invalid=96777
- 0109: dt=0.050000, rms=0.711 (-0.029%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.711, neg=0, invalid=96777
- 0110: dt=0.278195, rms=0.709 (0.339%), neg=0, invalid=96777
- 0111: dt=0.081926, rms=0.708 (0.125%), neg=0, invalid=96777
- 0112: dt=0.081926, rms=0.708 (0.024%), neg=0, invalid=96777
- 0113: dt=0.081926, rms=0.707 (0.049%), neg=0, invalid=96777
- 0114: dt=0.081926, rms=0.707 (0.086%), neg=0, invalid=96777
- 0115: dt=0.081926, rms=0.706 (0.117%), neg=0, invalid=96777
- 0116: dt=0.081926, rms=0.705 (0.125%), neg=0, invalid=96777
- 0117: dt=0.081926, rms=0.704 (0.115%), neg=0, invalid=96777
- 0118: dt=0.081926, rms=0.703 (0.098%), neg=0, invalid=96777
- 0119: dt=0.000000, rms=0.703 (-0.000%), neg=0, invalid=96777
- renormalizing by structure alignment....
- renormalizing input #0
- gca peak = 0.11725 (24)
- mri peak = 0.12699 ( 8)
- Left_Lateral_Ventricle (4): linear fit = 0.28 x + 0.0 (1441 voxels, overlap=0.154)
- Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (1441 voxels, peak = 7), gca=9.6
- gca peak = 0.14022 (22)
- mri peak = 0.16230 (10)
- Right_Lateral_Ventricle (43): linear fit = 0.28 x + 0.0 (1121 voxels, overlap=0.005)
- Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (1121 voxels, peak = 6), gca=8.8
- gca peak = 0.24234 (100)
- mri peak = 0.10576 (78)
- Right_Pallidum (52): linear fit = 0.81 x + 0.0 (420 voxels, overlap=0.039)
- Right_Pallidum (52): linear fit = 0.81 x + 0.0 (420 voxels, peak = 80), gca=80.5
- gca peak = 0.19192 (97)
- mri peak = 0.12456 (75)
- Left_Pallidum (13): linear fit = 0.77 x + 0.0 (275 voxels, overlap=0.036)
- Left_Pallidum (13): linear fit = 0.77 x + 0.0 (275 voxels, peak = 75), gca=75.2
- gca peak = 0.24007 (63)
- mri peak = 0.06338 (56)
- Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (563 voxels, overlap=0.562)
- Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (563 voxels, peak = 55), gca=55.1
- gca peak = 0.29892 (64)
- mri peak = 0.08085 (61)
- Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (753 voxels, overlap=0.931)
- Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (753 voxels, peak = 59), gca=59.2
- gca peak = 0.12541 (104)
- mri peak = 0.06872 (105)
- Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (71044 voxels, overlap=0.897)
- Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (71044 voxels, peak = 106), gca=105.6
- gca peak = 0.13686 (104)
- mri peak = 0.07761 (105)
- Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (73417 voxels, overlap=0.866)
- Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (73417 voxels, peak = 106), gca=105.6
- gca peak = 0.11691 (63)
- mri peak = 0.05348 (55)
- Left_Cerebral_Cortex (3): linear fit = 0.85 x + 0.0 (24106 voxels, overlap=0.379)
- Left_Cerebral_Cortex (3): linear fit = 0.85 x + 0.0 (24106 voxels, peak = 53), gca=53.2
- gca peak = 0.13270 (63)
- mri peak = 0.05168 (54)
- Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (24760 voxels, overlap=0.382)
- Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (24760 voxels, peak = 52), gca=52.0
- gca peak = 0.15182 (70)
- mri peak = 0.08942 (63)
- Right_Caudate (50): linear fit = 0.86 x + 0.0 (569 voxels, overlap=0.135)
- Right_Caudate (50): linear fit = 0.86 x + 0.0 (569 voxels, peak = 60), gca=59.9
- gca peak = 0.14251 (76)
- mri peak = 0.08017 (63)
- Left_Caudate (11): linear fit = 0.79 x + 0.0 (718 voxels, overlap=0.017)
- Left_Caudate (11): linear fit = 0.79 x + 0.0 (718 voxels, peak = 60), gca=59.7
- gca peak = 0.12116 (60)
- mri peak = 0.04645 (62)
- Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (10675 voxels, overlap=0.948)
- Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (10675 voxels, peak = 62), gca=61.5
- gca peak = 0.12723 (61)
- mri peak = 0.05533 (58)
- Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (12758 voxels, overlap=0.986)
- Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (12758 voxels, peak = 60), gca=60.1
- gca peak = 0.22684 (88)
- mri peak = 0.05304 (94)
- Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (7086 voxels, overlap=0.844)
- Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (7086 voxels, peak = 95), gca=95.5
- gca peak = 0.21067 (87)
- mri peak = 0.06032 (89)
- Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (6944 voxels, overlap=0.924)
- Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (6944 voxels, peak = 94), gca=93.5
- gca peak = 0.25455 (62)
- mri peak = 0.09078 (58)
- Left_Amygdala (18): linear fit = 0.88 x + 0.0 (357 voxels, overlap=0.846)
- Left_Amygdala (18): linear fit = 0.88 x + 0.0 (357 voxels, peak = 54), gca=54.2
- gca peak = 0.39668 (62)
- mri peak = 0.10542 (57)
- Right_Amygdala (54): linear fit = 0.90 x + 0.0 (359 voxels, overlap=0.771)
- Right_Amygdala (54): linear fit = 0.90 x + 0.0 (359 voxels, peak = 56), gca=56.1
- gca peak = 0.10129 (93)
- mri peak = 0.05544 (88)
- Left_Thalamus_Proper (10): linear fit = 0.94 x + 0.0 (5742 voxels, overlap=0.918)
- Left_Thalamus_Proper (10): linear fit = 0.94 x + 0.0 (5742 voxels, peak = 88), gca=87.9
- gca peak = 0.12071 (89)
- mri peak = 0.06385 (80)
- Right_Thalamus_Proper (49): linear fit = 0.94 x + 0.0 (4190 voxels, overlap=0.796)
- Right_Thalamus_Proper (49): linear fit = 0.94 x + 0.0 (4190 voxels, peak = 83), gca=83.2
- gca peak = 0.13716 (82)
- mri peak = 0.06132 (70)
- Left_Putamen (12): linear fit = 0.85 x + 0.0 (2017 voxels, overlap=0.082)
- Left_Putamen (12): linear fit = 0.85 x + 0.0 (2017 voxels, peak = 69), gca=69.3
- gca peak = 0.15214 (84)
- mri peak = 0.06152 (68)
- Right_Putamen (51): linear fit = 0.81 x + 0.0 (2255 voxels, overlap=0.096)
- Right_Putamen (51): linear fit = 0.81 x + 0.0 (2255 voxels, peak = 68), gca=67.6
- gca peak = 0.08983 (85)
- mri peak = 0.07352 (88)
- Brain_Stem (16): linear fit = 1.03 x + 0.0 (12104 voxels, overlap=0.777)
- Brain_Stem (16): linear fit = 1.03 x + 0.0 (12104 voxels, peak = 88), gca=88.0
- gca peak = 0.11809 (92)
- mri peak = 0.07851 (92)
- Right_VentralDC (60): linear fit = 0.96 x + 0.0 (922 voxels, overlap=0.901)
- Right_VentralDC (60): linear fit = 0.96 x + 0.0 (922 voxels, peak = 89), gca=88.8
- gca peak = 0.12914 (94)
- mri peak = 0.07596 (87)
- Left_VentralDC (28): linear fit = 0.95 x + 0.0 (1094 voxels, overlap=0.925)
- Left_VentralDC (28): linear fit = 0.95 x + 0.0 (1094 voxels, peak = 90), gca=89.8
- gca peak = 0.21100 (36)
- mri peak = 0.15915 (55)
- Third_Ventricle (14): linear fit = 1.50 x + 0.0 (68 voxels, overlap=0.039)
- Third_Ventricle (14): linear fit = 1.50 x + 0.0 (68 voxels, peak = 54), gca=53.8
- gca peak = 0.13542 (27)
- mri peak = 0.12095 ( 8)
- Fourth_Ventricle (15): linear fit = 0.32 x + 0.0 (239 voxels, overlap=0.022)
- Fourth_Ventricle (15): linear fit = 0.32 x + 0.0 (239 voxels, peak = 9), gca=8.8
- gca peak Unknown = 0.94427 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.21802 (40)
- gca peak Fourth_Ventricle = 0.13542 (27)
- gca peak CSF = 0.17123 (45)
- gca peak Left_Accumbens_area = 0.25875 (69)
- gca peak Left_undetermined = 0.96240 (36)
- gca peak Left_vessel = 0.33262 (65)
- gca peak Left_choroid_plexus = 0.09846 (46)
- gca peak Right_Inf_Lat_Vent = 0.28113 (34)
- gca peak Right_Accumbens_area = 0.27120 (72)
- gca peak Right_vessel = 0.61915 (60)
- gca peak Right_choroid_plexus = 0.12775 (51)
- gca peak Fifth_Ventricle = 0.45329 (44)
- gca peak WM_hypointensities = 0.11729 (81)
- gca peak non_WM_hypointensities = 0.10912 (56)
- gca peak Optic_Chiasm = 0.33287 (75)
- label assignment complete, 0 changed (0.00%)
- not using caudate to estimate GM means
- estimating mean gm scale to be 0.88 x + 0.0
- estimating mean wm scale to be 1.01 x + 0.0
- estimating mean csf scale to be 0.77 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=0.731, neg=0, invalid=96777
- 0120: dt=129.472000, rms=0.722 (1.153%), neg=0, invalid=96777
- 0121: dt=295.936000, rms=0.717 (0.792%), neg=0, invalid=96777
- 0122: dt=110.976000, rms=0.715 (0.267%), neg=0, invalid=96777
- 0123: dt=129.472000, rms=0.713 (0.248%), neg=0, invalid=96777
- 0124: dt=129.472000, rms=0.712 (0.150%), neg=0, invalid=96777
- 0125: dt=129.472000, rms=0.711 (0.163%), neg=0, invalid=96777
- 0126: dt=110.976000, rms=0.710 (0.112%), neg=0, invalid=96777
- 0127: dt=129.472000, rms=0.709 (0.126%), neg=0, invalid=96777
- 0128: dt=129.472000, rms=0.708 (0.083%), neg=0, invalid=96777
- 0129: dt=129.472000, rms=0.708 (0.110%), neg=0, invalid=96777
- 0130: dt=110.976000, rms=0.707 (0.074%), neg=0, invalid=96777
- 0131: dt=129.472000, rms=0.707 (0.093%), neg=0, invalid=96777
- 0132: dt=129.472000, rms=0.706 (0.069%), neg=0, invalid=96777
- 0133: dt=129.472000, rms=0.705 (0.080%), neg=0, invalid=96777
- 0134: dt=129.472000, rms=0.705 (0.064%), neg=0, invalid=96777
- 0135: dt=129.472000, rms=0.704 (0.075%), neg=0, invalid=96777
- 0136: dt=110.976000, rms=0.704 (0.047%), neg=0, invalid=96777
- 0137: dt=110.976000, rms=0.704 (0.063%), neg=0, invalid=96777
- 0138: dt=110.976000, rms=0.703 (0.085%), neg=0, invalid=96777
- 0139: dt=110.976000, rms=0.702 (0.118%), neg=0, invalid=96777
- 0140: dt=110.976000, rms=0.701 (0.121%), neg=0, invalid=96777
- 0141: dt=110.976000, rms=0.700 (0.158%), neg=0, invalid=96777
- 0142: dt=110.976000, rms=0.699 (0.145%), neg=0, invalid=96777
- 0143: dt=110.976000, rms=0.698 (0.165%), neg=0, invalid=96777
- 0144: dt=110.976000, rms=0.697 (0.131%), neg=0, invalid=96777
- 0145: dt=110.976000, rms=0.696 (0.130%), neg=0, invalid=96777
- 0146: dt=110.976000, rms=0.696 (0.090%), neg=0, invalid=96777
- 0147: dt=110.976000, rms=0.695 (0.109%), neg=0, invalid=96777
- 0148: dt=110.976000, rms=0.694 (0.080%), neg=0, invalid=96777
- 0149: dt=110.976000, rms=0.694 (0.105%), neg=0, invalid=96777
- 0150: dt=110.976000, rms=0.693 (0.091%), neg=0, invalid=96777
- 0151: dt=110.976000, rms=0.692 (0.097%), neg=0, invalid=96777
- 0152: dt=110.976000, rms=0.692 (0.103%), neg=0, invalid=96777
- 0153: dt=110.976000, rms=0.691 (0.083%), neg=0, invalid=96777
- 0154: dt=110.976000, rms=0.690 (0.102%), neg=0, invalid=96777
- 0155: dt=110.976000, rms=0.690 (0.095%), neg=0, invalid=96777
- 0156: dt=110.976000, rms=0.689 (0.096%), neg=0, invalid=96777
- 0157: dt=110.976000, rms=0.688 (0.082%), neg=0, invalid=96777
- 0158: dt=110.976000, rms=0.688 (0.100%), neg=0, invalid=96777
- 0159: dt=110.976000, rms=0.687 (0.096%), neg=0, invalid=96777
- 0160: dt=110.976000, rms=0.686 (0.099%), neg=0, invalid=96777
- 0161: dt=110.976000, rms=0.686 (0.078%), neg=0, invalid=96777
- 0162: dt=110.976000, rms=0.685 (0.106%), neg=0, invalid=96777
- 0163: dt=110.976000, rms=0.685 (0.095%), neg=0, invalid=96777
- 0164: dt=110.976000, rms=0.684 (0.079%), neg=0, invalid=96777
- 0165: dt=110.976000, rms=0.684 (0.067%), neg=0, invalid=96777
- 0166: dt=110.976000, rms=0.683 (0.090%), neg=0, invalid=96777
- 0167: dt=110.976000, rms=0.682 (0.079%), neg=0, invalid=96777
- 0168: dt=110.976000, rms=0.682 (0.068%), neg=0, invalid=96777
- 0169: dt=110.976000, rms=0.682 (0.057%), neg=0, invalid=96777
- 0170: dt=110.976000, rms=0.681 (0.069%), neg=0, invalid=96777
- 0171: dt=110.976000, rms=0.680 (0.084%), neg=0, invalid=96777
- 0172: dt=110.976000, rms=0.680 (0.073%), neg=0, invalid=96777
- 0173: dt=110.976000, rms=0.680 (0.059%), neg=0, invalid=96777
- 0174: dt=110.976000, rms=0.679 (0.049%), neg=0, invalid=96777
- 0175: dt=110.976000, rms=0.679 (0.062%), neg=0, invalid=96777
- 0176: dt=110.976000, rms=0.678 (0.065%), neg=0, invalid=96777
- 0177: dt=110.976000, rms=0.678 (0.054%), neg=0, invalid=96777
- 0178: dt=110.976000, rms=0.678 (0.040%), neg=0, invalid=96777
- 0179: dt=110.976000, rms=0.677 (0.054%), neg=0, invalid=96777
- 0180: dt=110.976000, rms=0.677 (0.055%), neg=0, invalid=96777
- 0181: dt=110.976000, rms=0.677 (0.059%), neg=0, invalid=96777
- 0182: dt=110.976000, rms=0.676 (0.048%), neg=0, invalid=96777
- 0183: dt=110.976000, rms=0.676 (0.044%), neg=0, invalid=96777
- 0184: dt=110.976000, rms=0.676 (0.037%), neg=0, invalid=96777
- 0185: dt=110.976000, rms=0.676 (0.027%), neg=0, invalid=96777
- 0186: dt=110.976000, rms=0.675 (0.037%), neg=0, invalid=96777
- 0187: dt=110.976000, rms=0.675 (0.038%), neg=0, invalid=96777
- 0188: dt=110.976000, rms=0.675 (0.052%), neg=0, invalid=96777
- 0189: dt=110.976000, rms=0.674 (0.042%), neg=0, invalid=96777
- 0190: dt=110.976000, rms=0.674 (0.028%), neg=0, invalid=96777
- 0191: dt=110.976000, rms=0.674 (0.029%), neg=0, invalid=96777
- 0192: dt=110.976000, rms=0.674 (0.031%), neg=0, invalid=96777
- 0193: dt=110.976000, rms=0.674 (0.033%), neg=0, invalid=96777
- 0194: dt=110.976000, rms=0.673 (0.036%), neg=0, invalid=96777
- 0195: dt=110.976000, rms=0.673 (0.032%), neg=0, invalid=96777
- 0196: dt=110.976000, rms=0.673 (0.022%), neg=0, invalid=96777
- 0197: dt=110.976000, rms=0.673 (0.020%), neg=0, invalid=96777
- 0198: dt=517.888000, rms=0.673 (0.045%), neg=0, invalid=96777
- 0199: dt=27.744000, rms=0.673 (0.003%), neg=0, invalid=96777
- 0200: dt=27.744000, rms=0.673 (-0.002%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.673, neg=0, invalid=96777
- 0201: dt=73.984000, rms=0.672 (0.035%), neg=0, invalid=96777
- 0202: dt=129.472000, rms=0.672 (0.056%), neg=0, invalid=96777
- 0203: dt=517.888000, rms=0.671 (0.128%), neg=0, invalid=96777
- 0204: dt=221.952000, rms=0.671 (0.070%), neg=0, invalid=96777
- 0205: dt=92.480000, rms=0.670 (0.019%), neg=0, invalid=96777
- 0206: dt=92.480000, rms=0.670 (0.015%), neg=0, invalid=96777
- 0207: dt=92.480000, rms=0.670 (0.019%), neg=0, invalid=96777
- 0208: dt=92.480000, rms=0.670 (0.028%), neg=0, invalid=96777
- 0209: dt=92.480000, rms=0.670 (0.035%), neg=0, invalid=96777
- 0210: dt=92.480000, rms=0.670 (0.038%), neg=0, invalid=96777
- 0211: dt=92.480000, rms=0.669 (0.039%), neg=0, invalid=96777
- 0212: dt=92.480000, rms=0.669 (0.037%), neg=0, invalid=96777
- 0213: dt=92.480000, rms=0.669 (0.028%), neg=0, invalid=96777
- 0214: dt=92.480000, rms=0.669 (0.021%), neg=0, invalid=96777
- 0215: dt=92.480000, rms=0.669 (0.023%), neg=0, invalid=96777
- 0216: dt=92.480000, rms=0.668 (0.023%), neg=0, invalid=96777
- 0217: dt=221.952000, rms=0.668 (0.011%), neg=0, invalid=96777
- 0218: dt=221.952000, rms=0.668 (-0.017%), neg=0, invalid=96777
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.670, neg=0, invalid=96777
- 0219: dt=124.416000, rms=0.665 (0.803%), neg=0, invalid=96777
- 0220: dt=36.288000, rms=0.663 (0.199%), neg=0, invalid=96777
- 0221: dt=103.680000, rms=0.659 (0.685%), neg=0, invalid=96777
- 0222: dt=15.552000, rms=0.657 (0.221%), neg=0, invalid=96777
- 0223: dt=82.944000, rms=0.656 (0.265%), neg=0, invalid=96777
- 0224: dt=36.288000, rms=0.653 (0.434%), neg=0, invalid=96777
- 0225: dt=36.288000, rms=0.652 (0.098%), neg=0, invalid=96777
- 0226: dt=145.152000, rms=0.647 (0.697%), neg=0, invalid=96777
- 0227: dt=15.552000, rms=0.647 (0.136%), neg=0, invalid=96777
- 0228: dt=36.288000, rms=0.646 (0.108%), neg=0, invalid=96777
- 0229: dt=331.776000, rms=0.641 (0.822%), neg=0, invalid=96777
- 0230: dt=25.920000, rms=0.637 (0.561%), neg=0, invalid=96777
- 0231: dt=248.832000, rms=0.634 (0.468%), neg=0, invalid=96777
- 0232: dt=36.288000, rms=0.632 (0.367%), neg=0, invalid=96777
- 0233: dt=25.920000, rms=0.631 (0.101%), neg=0, invalid=96777
- 0234: dt=580.608000, rms=0.626 (0.761%), neg=0, invalid=96777
- 0235: dt=20.736000, rms=0.624 (0.438%), neg=0, invalid=96777
- 0236: dt=25.920000, rms=0.623 (0.093%), neg=0, invalid=96777
- 0237: dt=124.416000, rms=0.621 (0.265%), neg=0, invalid=96777
- 0238: dt=15.552000, rms=0.621 (0.069%), neg=0, invalid=96777
- 0239: dt=62.208000, rms=0.620 (0.061%), neg=0, invalid=96777
- 0240: dt=103.680000, rms=0.619 (0.188%), neg=0, invalid=96777
- 0241: dt=9.072000, rms=0.619 (0.037%), neg=0, invalid=96777
- 0242: dt=9.072000, rms=0.619 (0.020%), neg=0, invalid=96777
- 0243: dt=9.072000, rms=0.619 (0.001%), neg=0, invalid=96777
- 0244: dt=9.072000, rms=0.619 (0.010%), neg=0, invalid=96777
- 0245: dt=9.072000, rms=0.619 (0.025%), neg=0, invalid=96777
- 0246: dt=9.072000, rms=0.618 (0.063%), neg=0, invalid=96777
- 0247: dt=9.072000, rms=0.618 (0.089%), neg=0, invalid=96777
- 0248: dt=9.072000, rms=0.617 (0.088%), neg=0, invalid=96777
- 0249: dt=9.072000, rms=0.617 (0.075%), neg=0, invalid=96777
- 0250: dt=9.072000, rms=0.616 (0.071%), neg=0, invalid=96777
- 0251: dt=9.072000, rms=0.616 (0.076%), neg=0, invalid=96777
- 0252: dt=9.072000, rms=0.615 (0.067%), neg=0, invalid=96777
- 0253: dt=9.072000, rms=0.615 (0.068%), neg=0, invalid=96777
- 0254: dt=9.072000, rms=0.615 (0.078%), neg=0, invalid=96777
- 0255: dt=9.072000, rms=0.614 (0.086%), neg=0, invalid=96777
- 0256: dt=9.072000, rms=0.613 (0.097%), neg=0, invalid=96777
- 0257: dt=9.072000, rms=0.613 (0.012%), neg=0, invalid=96777
- 0258: dt=9.072000, rms=0.613 (0.027%), neg=0, invalid=96777
- 0259: dt=9.072000, rms=0.613 (0.034%), neg=0, invalid=96777
- 0260: dt=9.072000, rms=0.613 (0.033%), neg=0, invalid=96777
- 0261: dt=9.072000, rms=0.613 (0.042%), neg=0, invalid=96777
- 0262: dt=9.072000, rms=0.612 (0.043%), neg=0, invalid=96777
- 0263: dt=9.072000, rms=0.612 (0.049%), neg=0, invalid=96777
- 0264: dt=9.072000, rms=0.612 (0.053%), neg=0, invalid=96777
- 0265: dt=9.072000, rms=0.611 (0.057%), neg=0, invalid=96777
- 0266: dt=9.072000, rms=0.611 (0.060%), neg=0, invalid=96777
- 0267: dt=9.072000, rms=0.611 (0.065%), neg=0, invalid=96777
- 0268: dt=9.072000, rms=0.610 (0.068%), neg=0, invalid=96777
- 0269: dt=9.072000, rms=0.610 (0.010%), neg=0, invalid=96777
- 0270: dt=9.072000, rms=0.610 (0.017%), neg=0, invalid=96777
- 0271: dt=9.072000, rms=0.610 (0.021%), neg=0, invalid=96777
- 0272: dt=1.134000, rms=0.610 (0.000%), neg=0, invalid=96777
- 0273: dt=0.567000, rms=0.610 (0.001%), neg=0, invalid=96777
- 0274: dt=0.567000, rms=0.610 (0.001%), neg=0, invalid=96777
- 0275: dt=0.035437, rms=0.610 (0.000%), neg=0, invalid=96777
- 0276: dt=0.001107, rms=0.610 (0.000%), neg=0, invalid=96777
- 0277: dt=0.000277, rms=0.610 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.610, neg=0, invalid=96777
- 0278: dt=124.416000, rms=0.608 (0.325%), neg=0, invalid=96777
- 0279: dt=103.680000, rms=0.606 (0.324%), neg=0, invalid=96777
- 0280: dt=15.552000, rms=0.606 (0.051%), neg=0, invalid=96777
- 0281: dt=25.920000, rms=0.605 (0.029%), neg=0, invalid=96777
- 0282: dt=25.920000, rms=0.605 (0.028%), neg=0, invalid=96777
- 0283: dt=25.920000, rms=0.605 (0.052%), neg=0, invalid=96777
- 0284: dt=25.920000, rms=0.604 (0.087%), neg=0, invalid=96777
- 0285: dt=25.920000, rms=0.604 (0.116%), neg=0, invalid=96777
- 0286: dt=25.920000, rms=0.603 (0.139%), neg=0, invalid=96777
- 0287: dt=25.920000, rms=0.602 (0.137%), neg=0, invalid=96777
- 0288: dt=25.920000, rms=0.601 (0.132%), neg=0, invalid=96777
- 0289: dt=25.920000, rms=0.600 (0.127%), neg=0, invalid=96777
- 0290: dt=25.920000, rms=0.600 (0.124%), neg=0, invalid=96777
- 0291: dt=25.920000, rms=0.599 (0.118%), neg=0, invalid=96777
- 0292: dt=25.920000, rms=0.598 (0.126%), neg=0, invalid=96777
- 0293: dt=25.920000, rms=0.597 (0.130%), neg=0, invalid=96777
- 0294: dt=25.920000, rms=0.597 (0.131%), neg=0, invalid=96777
- 0295: dt=25.920000, rms=0.596 (0.121%), neg=0, invalid=96777
- 0296: dt=25.920000, rms=0.595 (0.121%), neg=0, invalid=96777
- 0297: dt=25.920000, rms=0.595 (0.121%), neg=0, invalid=96777
- 0298: dt=25.920000, rms=0.594 (0.123%), neg=0, invalid=96777
- 0299: dt=25.920000, rms=0.593 (0.130%), neg=0, invalid=96777
- 0300: dt=25.920000, rms=0.592 (0.115%), neg=0, invalid=96777
- 0301: dt=25.920000, rms=0.592 (0.109%), neg=0, invalid=96777
- 0302: dt=25.920000, rms=0.591 (0.109%), neg=0, invalid=96777
- 0303: dt=25.920000, rms=0.590 (0.113%), neg=0, invalid=96777
- 0304: dt=25.920000, rms=0.590 (0.114%), neg=0, invalid=96777
- 0305: dt=25.920000, rms=0.589 (0.107%), neg=0, invalid=96777
- 0306: dt=25.920000, rms=0.588 (0.110%), neg=0, invalid=96777
- 0307: dt=25.920000, rms=0.588 (0.095%), neg=0, invalid=96777
- 0308: dt=25.920000, rms=0.587 (0.091%), neg=0, invalid=96777
- 0309: dt=25.920000, rms=0.587 (0.091%), neg=0, invalid=96777
- 0310: dt=25.920000, rms=0.586 (0.092%), neg=0, invalid=96777
- 0311: dt=25.920000, rms=0.586 (0.095%), neg=0, invalid=96777
- 0312: dt=25.920000, rms=0.585 (0.084%), neg=0, invalid=96777
- 0313: dt=25.920000, rms=0.585 (0.088%), neg=0, invalid=96777
- 0314: dt=25.920000, rms=0.584 (0.069%), neg=0, invalid=96777
- 0315: dt=25.920000, rms=0.584 (0.068%), neg=0, invalid=96777
- 0316: dt=25.920000, rms=0.583 (0.078%), neg=0, invalid=96777
- 0317: dt=25.920000, rms=0.583 (0.080%), neg=0, invalid=96777
- 0318: dt=25.920000, rms=0.583 (0.068%), neg=0, invalid=96777
- 0319: dt=25.920000, rms=0.582 (0.063%), neg=0, invalid=96777
- 0320: dt=25.920000, rms=0.582 (0.066%), neg=0, invalid=96777
- 0321: dt=25.920000, rms=0.582 (0.052%), neg=0, invalid=96777
- 0322: dt=25.920000, rms=0.581 (0.061%), neg=0, invalid=96777
- 0323: dt=25.920000, rms=0.581 (0.059%), neg=0, invalid=96777
- 0324: dt=25.920000, rms=0.580 (0.057%), neg=0, invalid=96777
- 0325: dt=25.920000, rms=0.580 (0.059%), neg=0, invalid=96777
- 0326: dt=25.920000, rms=0.580 (0.058%), neg=0, invalid=96777
- 0327: dt=25.920000, rms=0.580 (0.053%), neg=0, invalid=96777
- 0328: dt=25.920000, rms=0.579 (0.050%), neg=0, invalid=96777
- 0329: dt=25.920000, rms=0.579 (0.046%), neg=0, invalid=96777
- 0330: dt=25.920000, rms=0.579 (0.045%), neg=0, invalid=96777
- 0331: dt=25.920000, rms=0.578 (0.045%), neg=0, invalid=96777
- 0332: dt=25.920000, rms=0.578 (0.044%), neg=0, invalid=96777
- 0333: dt=25.920000, rms=0.578 (0.048%), neg=0, invalid=96777
- 0334: dt=25.920000, rms=0.578 (0.042%), neg=0, invalid=96777
- 0335: dt=25.920000, rms=0.577 (0.037%), neg=0, invalid=96777
- 0336: dt=25.920000, rms=0.577 (0.036%), neg=0, invalid=96777
- 0337: dt=25.920000, rms=0.577 (0.041%), neg=0, invalid=96777
- 0338: dt=25.920000, rms=0.577 (0.042%), neg=0, invalid=96777
- 0339: dt=25.920000, rms=0.576 (0.045%), neg=0, invalid=96777
- 0340: dt=25.920000, rms=0.576 (0.038%), neg=0, invalid=96777
- 0341: dt=25.920000, rms=0.576 (0.037%), neg=0, invalid=96777
- 0342: dt=25.920000, rms=0.576 (0.032%), neg=0, invalid=96777
- 0343: dt=25.920000, rms=0.576 (0.035%), neg=0, invalid=96777
- 0344: dt=25.920000, rms=0.575 (0.034%), neg=0, invalid=96777
- 0345: dt=25.920000, rms=0.575 (0.034%), neg=0, invalid=96777
- 0346: dt=25.920000, rms=0.575 (0.034%), neg=0, invalid=96777
- 0347: dt=25.920000, rms=0.575 (0.032%), neg=0, invalid=96777
- 0348: dt=25.920000, rms=0.575 (0.035%), neg=0, invalid=96777
- 0349: dt=25.920000, rms=0.575 (0.033%), neg=0, invalid=96777
- 0350: dt=25.920000, rms=0.574 (0.029%), neg=0, invalid=96777
- 0351: dt=25.920000, rms=0.574 (0.026%), neg=0, invalid=96777
- 0352: dt=25.920000, rms=0.574 (0.028%), neg=0, invalid=96777
- 0353: dt=25.920000, rms=0.574 (0.033%), neg=0, invalid=96777
- 0354: dt=25.920000, rms=0.574 (0.029%), neg=0, invalid=96777
- 0355: dt=25.920000, rms=0.574 (0.027%), neg=0, invalid=96777
- 0356: dt=25.920000, rms=0.573 (0.029%), neg=0, invalid=96777
- 0357: dt=25.920000, rms=0.573 (0.024%), neg=0, invalid=96777
- 0358: dt=25.920000, rms=0.573 (0.027%), neg=0, invalid=96777
- 0359: dt=25.920000, rms=0.573 (0.031%), neg=0, invalid=96777
- 0360: dt=25.920000, rms=0.573 (0.029%), neg=0, invalid=96777
- 0361: dt=25.920000, rms=0.573 (0.036%), neg=0, invalid=96777
- 0362: dt=25.920000, rms=0.572 (0.024%), neg=0, invalid=96777
- 0363: dt=25.920000, rms=0.572 (0.030%), neg=0, invalid=96777
- 0364: dt=25.920000, rms=0.572 (0.018%), neg=0, invalid=96777
- 0365: dt=25.920000, rms=0.572 (0.029%), neg=0, invalid=96777
- 0366: dt=25.920000, rms=0.572 (0.027%), neg=0, invalid=96777
- 0367: dt=25.920000, rms=0.572 (0.026%), neg=0, invalid=96777
- 0368: dt=25.920000, rms=0.571 (0.027%), neg=0, invalid=96777
- 0369: dt=25.920000, rms=0.571 (0.025%), neg=0, invalid=96777
- 0370: dt=25.920000, rms=0.571 (0.023%), neg=0, invalid=96777
- 0371: dt=25.920000, rms=0.571 (0.022%), neg=0, invalid=96777
- 0372: dt=31.104000, rms=0.571 (0.003%), neg=0, invalid=96777
- 0373: dt=31.104000, rms=0.571 (0.006%), neg=0, invalid=96777
- 0374: dt=31.104000, rms=0.571 (0.005%), neg=0, invalid=96777
- 0375: dt=31.104000, rms=0.571 (0.003%), neg=0, invalid=96777
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.580, neg=0, invalid=96777
- 0376: dt=32.000000, rms=0.577 (0.526%), neg=0, invalid=96777
- 0377: dt=11.200000, rms=0.576 (0.180%), neg=0, invalid=96777
- 0378: dt=102.400000, rms=0.572 (0.734%), neg=0, invalid=96777
- 0379: dt=7.463259, rms=0.570 (0.303%), neg=0, invalid=96777
- 0380: dt=44.800000, rms=0.566 (0.646%), neg=0, invalid=96777
- 0381: dt=8.000000, rms=0.565 (0.206%), neg=0, invalid=96777
- 0382: dt=76.800000, rms=0.562 (0.546%), neg=0, invalid=96777
- 0383: dt=2.800000, rms=0.561 (0.150%), neg=0, invalid=96777
- 0384: dt=2.800000, rms=0.561 (0.107%), neg=0, invalid=96777
- 0385: dt=2.800000, rms=0.560 (0.056%), neg=0, invalid=96777
- 0386: dt=19.200000, rms=0.559 (0.134%), neg=0, invalid=96777
- 0387: dt=11.200000, rms=0.559 (0.147%), neg=0, invalid=96777
- 0388: dt=11.200000, rms=0.558 (0.049%), neg=0, invalid=96777
- 0389: dt=11.200000, rms=0.558 (0.114%), neg=0, invalid=96777
- 0390: dt=11.200000, rms=0.557 (0.147%), neg=0, invalid=96777
- 0391: dt=11.200000, rms=0.556 (0.203%), neg=0, invalid=96777
- 0392: dt=11.200000, rms=0.554 (0.249%), neg=0, invalid=96777
- 0393: dt=11.200000, rms=0.553 (0.304%), neg=0, invalid=96777
- 0394: dt=11.200000, rms=0.551 (0.307%), neg=0, invalid=96777
- 0395: dt=11.200000, rms=0.549 (0.301%), neg=0, invalid=96777
- 0396: dt=11.200000, rms=0.548 (0.296%), neg=0, invalid=96777
- 0397: dt=11.200000, rms=0.546 (0.309%), neg=0, invalid=96777
- 0398: dt=11.200000, rms=0.544 (0.283%), neg=0, invalid=96777
- 0399: dt=11.200000, rms=0.543 (0.262%), neg=0, invalid=96777
- 0400: dt=11.200000, rms=0.542 (0.236%), neg=0, invalid=96777
- 0401: dt=11.200000, rms=0.541 (0.231%), neg=0, invalid=96777
- 0402: dt=11.200000, rms=0.539 (0.213%), neg=0, invalid=96777
- 0403: dt=11.200000, rms=0.538 (0.186%), neg=0, invalid=96777
- 0404: dt=11.200000, rms=0.537 (0.170%), neg=0, invalid=96777
- 0405: dt=11.200000, rms=0.537 (0.151%), neg=0, invalid=96777
- 0406: dt=11.200000, rms=0.536 (0.163%), neg=0, invalid=96777
- 0407: dt=11.200000, rms=0.535 (0.132%), neg=0, invalid=96777
- 0408: dt=11.200000, rms=0.534 (0.122%), neg=0, invalid=96777
- 0409: dt=11.200000, rms=0.534 (0.115%), neg=0, invalid=96777
- 0410: dt=11.200000, rms=0.533 (0.126%), neg=0, invalid=96777
- 0411: dt=11.200000, rms=0.533 (0.106%), neg=0, invalid=96777
- 0412: dt=11.200000, rms=0.532 (0.102%), neg=0, invalid=96777
- 0413: dt=11.200000, rms=0.532 (0.093%), neg=0, invalid=96777
- 0414: dt=11.200000, rms=0.531 (0.098%), neg=0, invalid=96777
- 0415: dt=11.200000, rms=0.531 (0.093%), neg=0, invalid=96777
- 0416: dt=11.200000, rms=0.530 (0.081%), neg=0, invalid=96777
- 0417: dt=11.200000, rms=0.530 (0.067%), neg=0, invalid=96777
- 0418: dt=11.200000, rms=0.529 (0.064%), neg=0, invalid=96777
- 0419: dt=11.200000, rms=0.529 (0.079%), neg=0, invalid=96777
- 0420: dt=11.200000, rms=0.529 (0.065%), neg=0, invalid=96777
- 0421: dt=11.200000, rms=0.528 (0.050%), neg=0, invalid=96777
- 0422: dt=11.200000, rms=0.528 (0.058%), neg=0, invalid=96777
- 0423: dt=11.200000, rms=0.528 (0.066%), neg=0, invalid=96777
- 0424: dt=11.200000, rms=0.527 (0.058%), neg=0, invalid=96777
- 0425: dt=11.200000, rms=0.527 (0.050%), neg=0, invalid=96777
- 0426: dt=11.200000, rms=0.527 (0.042%), neg=0, invalid=96777
- 0427: dt=11.200000, rms=0.527 (0.068%), neg=0, invalid=96777
- 0428: dt=11.200000, rms=0.526 (0.058%), neg=0, invalid=96777
- 0429: dt=11.200000, rms=0.526 (0.047%), neg=0, invalid=96777
- 0430: dt=11.200000, rms=0.526 (0.045%), neg=0, invalid=96777
- 0431: dt=11.200000, rms=0.526 (0.053%), neg=0, invalid=96777
- 0432: dt=11.200000, rms=0.525 (0.046%), neg=0, invalid=96777
- 0433: dt=11.200000, rms=0.525 (0.037%), neg=0, invalid=96777
- 0434: dt=11.200000, rms=0.525 (0.034%), neg=0, invalid=96777
- 0435: dt=11.200000, rms=0.525 (0.036%), neg=0, invalid=96777
- 0436: dt=11.200000, rms=0.524 (0.040%), neg=0, invalid=96777
- 0437: dt=11.200000, rms=0.524 (0.042%), neg=0, invalid=96777
- 0438: dt=11.200000, rms=0.524 (0.042%), neg=0, invalid=96777
- 0439: dt=11.200000, rms=0.524 (0.038%), neg=0, invalid=96777
- 0440: dt=11.200000, rms=0.524 (0.038%), neg=0, invalid=96777
- 0441: dt=11.200000, rms=0.523 (0.045%), neg=0, invalid=96777
- 0442: dt=11.200000, rms=0.523 (0.036%), neg=0, invalid=96777
- 0443: dt=11.200000, rms=0.523 (0.017%), neg=0, invalid=96777
- 0444: dt=11.200000, rms=0.523 (0.031%), neg=0, invalid=96777
- 0445: dt=11.200000, rms=0.523 (0.034%), neg=0, invalid=96777
- 0446: dt=11.200000, rms=0.523 (0.028%), neg=0, invalid=96777
- 0447: dt=11.200000, rms=0.523 (0.023%), neg=0, invalid=96777
- 0448: dt=11.200000, rms=0.522 (0.020%), neg=0, invalid=96777
- 0449: dt=11.200000, rms=0.522 (0.014%), neg=0, invalid=96777
- 0450: dt=11.200000, rms=0.522 (-0.004%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.522, neg=0, invalid=96777
- 0451: dt=32.000000, rms=0.521 (0.240%), neg=0, invalid=96777
- 0452: dt=19.200000, rms=0.520 (0.140%), neg=0, invalid=96777
- 0453: dt=2.800000, rms=0.520 (0.002%), neg=0, invalid=96777
- 0454: dt=2.800000, rms=0.520 (0.012%), neg=0, invalid=96777
- 0455: dt=2.800000, rms=0.520 (0.005%), neg=0, invalid=96777
- 0456: dt=2.800000, rms=0.520 (0.006%), neg=0, invalid=96777
- 0457: dt=2.800000, rms=0.520 (0.012%), neg=0, invalid=96777
- 0458: dt=2.800000, rms=0.520 (0.016%), neg=0, invalid=96777
- 0459: dt=2.800000, rms=0.520 (0.026%), neg=0, invalid=96777
- 0460: dt=2.800000, rms=0.520 (0.019%), neg=0, invalid=96777
- 0461: dt=2.800000, rms=0.520 (0.004%), neg=0, invalid=96777
- 0462: dt=2.800000, rms=0.520 (0.005%), neg=0, invalid=96777
- 0463: dt=6.400000, rms=0.520 (-0.003%), neg=0, invalid=96777
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.548, neg=0, invalid=96777
- 0464: dt=0.000000, rms=0.548 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.548, neg=0, invalid=96777
- 0465: dt=0.000000, rms=0.548 (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=0.604, neg=0, invalid=96777
- 0466: dt=1.454774, rms=0.597 (1.103%), neg=0, invalid=96777
- 0467: dt=0.384000, rms=0.597 (0.030%), neg=0, invalid=96777
- 0468: dt=0.384000, rms=0.597 (-0.013%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.597, neg=0, invalid=96777
- 0469: dt=0.527778, rms=0.596 (0.090%), neg=0, invalid=96777
- 0470: dt=0.384000, rms=0.596 (0.020%), neg=0, invalid=96777
- 0471: dt=0.384000, rms=0.596 (-0.015%), 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=0.540, neg=0, invalid=96777
- 0472: dt=0.171000, rms=0.532 (1.388%), neg=0, invalid=96777
- 0473: dt=0.142562, rms=0.528 (0.791%), neg=0, invalid=96777
- 0474: dt=0.127083, rms=0.525 (0.529%), neg=0, invalid=96777
- 0475: dt=0.116667, rms=0.523 (0.384%), neg=0, invalid=96777
- 0476: dt=0.112069, rms=0.522 (0.307%), neg=0, invalid=96777
- 0477: dt=0.448000, rms=0.516 (1.006%), neg=0, invalid=96777
- 0478: dt=0.028000, rms=0.516 (0.025%), neg=0, invalid=96777
- 0479: dt=0.028000, rms=0.516 (0.026%), neg=0, invalid=96777
- 0480: dt=0.028000, rms=0.516 (0.046%), neg=0, invalid=96777
- 0481: dt=0.028000, rms=0.516 (0.066%), neg=0, invalid=96777
- 0482: dt=0.028000, rms=0.515 (0.077%), neg=0, invalid=96777
- 0483: dt=0.028000, rms=0.515 (0.088%), neg=0, invalid=96777
- 0484: dt=0.028000, rms=0.514 (0.100%), neg=0, invalid=96777
- 0485: dt=0.028000, rms=0.514 (0.105%), neg=0, invalid=96777
- 0486: dt=0.028000, rms=0.513 (0.109%), neg=0, invalid=96777
- 0487: dt=0.028000, rms=0.513 (0.109%), neg=0, invalid=96777
- 0488: dt=0.028000, rms=0.512 (0.112%), neg=0, invalid=96777
- 0489: dt=0.028000, rms=0.511 (0.107%), neg=0, invalid=96777
- 0490: dt=0.028000, rms=0.511 (0.099%), neg=0, invalid=96777
- 0491: dt=0.028000, rms=0.510 (0.098%), neg=0, invalid=96777
- 0492: dt=0.028000, rms=0.510 (0.004%), neg=0, invalid=96777
- 0493: dt=0.028000, rms=0.510 (0.009%), neg=0, invalid=96777
- 0494: dt=0.028000, rms=0.510 (0.009%), neg=0, invalid=96777
- 0495: dt=0.448000, rms=0.510 (0.065%), neg=0, invalid=96777
- 0496: dt=0.007000, rms=0.510 (-0.003%), neg=0, invalid=96777
- 0497: dt=0.007000, rms=0.510 (0.001%), neg=0, invalid=96777
- 0498: dt=0.007000, rms=0.510 (0.002%), neg=0, invalid=96777
- 0499: dt=0.007000, rms=0.510 (0.004%), neg=0, invalid=96777
- 0500: dt=0.007000, rms=0.510 (0.003%), neg=0, invalid=96777
- 0501: dt=0.007000, rms=0.510 (0.004%), neg=0, invalid=96777
- 0502: dt=0.007000, rms=0.510 (0.007%), neg=0, invalid=96777
- 0503: dt=0.007000, rms=0.510 (0.004%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.510, neg=0, invalid=96777
- 0504: dt=0.112000, rms=0.508 (0.289%), neg=0, invalid=96777
- 0505: dt=0.112000, rms=0.507 (0.217%), neg=0, invalid=96777
- 0506: dt=0.112000, rms=0.506 (0.166%), neg=0, invalid=96777
- 0507: dt=0.112000, rms=0.506 (0.129%), neg=0, invalid=96777
- 0508: dt=0.384000, rms=0.504 (0.333%), neg=0, invalid=96777
- 0509: dt=0.112000, rms=0.504 (0.017%), neg=0, invalid=96777
- 0510: dt=0.112000, rms=0.504 (0.028%), neg=0, invalid=96777
- 0511: dt=0.112000, rms=0.504 (0.034%), neg=0, invalid=96777
- 0512: dt=0.007000, rms=0.504 (0.003%), neg=0, invalid=96777
- 0513: dt=0.007000, rms=0.504 (0.002%), neg=0, invalid=96777
- 0514: dt=0.020000, rms=0.504 (0.002%), neg=0, invalid=96777
- 0515: dt=0.020000, rms=0.504 (0.004%), neg=0, invalid=96777
- 0516: dt=0.020000, rms=0.504 (0.004%), neg=0, invalid=96777
- 0517: dt=0.020000, rms=0.504 (0.001%), neg=0, invalid=96777
- 0518: dt=0.020000, rms=0.504 (0.006%), neg=0, invalid=96777
- 0519: dt=0.020000, rms=0.504 (0.007%), neg=0, invalid=96777
- 0520: dt=0.020000, rms=0.504 (0.010%), neg=0, invalid=96777
- 0521: dt=0.020000, rms=0.503 (0.009%), 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=0.501, neg=0, invalid=96777
- 0522: dt=73.984000, rms=0.501 (0.013%), neg=0, invalid=96777
- 0523: dt=73.984000, rms=0.501 (-0.002%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.501, neg=0, invalid=96777
- 0524: dt=129.472000, rms=0.501 (0.116%), neg=0, invalid=96777
- 0525: dt=32.368000, rms=0.501 (0.019%), neg=0, invalid=96777
- 0526: dt=32.368000, rms=0.501 (0.002%), neg=0, invalid=96777
- 0527: dt=32.368000, rms=0.501 (0.015%), neg=0, invalid=96777
- 0528: dt=32.368000, rms=0.500 (0.022%), neg=0, invalid=96777
- 0529: dt=32.368000, rms=0.500 (0.029%), neg=0, invalid=96777
- 0530: dt=32.368000, rms=0.500 (0.029%), neg=0, invalid=96777
- 0531: dt=32.368000, rms=0.500 (0.026%), neg=0, invalid=96777
- 0532: dt=32.368000, rms=0.500 (0.027%), neg=0, invalid=96777
- 0533: dt=32.368000, rms=0.500 (0.027%), neg=0, invalid=96777
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.500, neg=0, invalid=96777
- 0534: dt=36.288000, rms=0.499 (0.186%), neg=0, invalid=96777
- 0535: dt=36.288000, rms=0.498 (0.083%), neg=0, invalid=96777
- 0536: dt=36.288000, rms=0.498 (0.070%), neg=0, invalid=96777
- 0537: dt=36.288000, rms=0.498 (0.052%), neg=0, invalid=96777
- 0538: dt=36.288000, rms=0.498 (-0.027%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.498, neg=0, invalid=96777
- 0539: dt=82.944000, rms=0.496 (0.368%), neg=0, invalid=96777
- 0540: dt=36.288000, rms=0.495 (0.153%), neg=0, invalid=96777
- 0541: dt=36.288000, rms=0.495 (0.085%), neg=0, invalid=96777
- 0542: dt=36.288000, rms=0.494 (0.127%), neg=0, invalid=96777
- 0543: dt=36.288000, rms=0.493 (0.170%), neg=0, invalid=96777
- 0544: dt=36.288000, rms=0.493 (0.161%), neg=0, invalid=96777
- 0545: dt=36.288000, rms=0.492 (0.146%), neg=0, invalid=96777
- 0546: dt=36.288000, rms=0.491 (0.141%), neg=0, invalid=96777
- 0547: dt=36.288000, rms=0.491 (0.113%), neg=0, invalid=96777
- 0548: dt=36.288000, rms=0.490 (0.103%), neg=0, invalid=96777
- 0549: dt=25.920000, rms=0.490 (0.025%), neg=0, invalid=96777
- 0550: dt=25.920000, rms=0.490 (0.014%), neg=0, invalid=96777
- 0551: dt=25.920000, rms=0.490 (0.014%), neg=0, invalid=96777
- 0552: dt=25.920000, rms=0.490 (0.029%), neg=0, invalid=96777
- 0553: dt=25.920000, rms=0.490 (0.034%), neg=0, invalid=96777
- 0554: dt=25.920000, rms=0.489 (0.043%), neg=0, invalid=96777
- 0555: dt=25.920000, rms=0.489 (0.041%), neg=0, invalid=96777
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.489, neg=0, invalid=96777
- iter 0, gcam->neg = 3
- after 0 iterations, nbhd size=0, neg = 0
- 0556: dt=44.800000, rms=0.485 (0.830%), neg=0, invalid=96777
- iter 0, gcam->neg = 8
- after 8 iterations, nbhd size=1, neg = 0
- 0557: dt=25.600000, rms=0.484 (0.306%), neg=0, invalid=96777
- 0558: dt=8.000000, rms=0.483 (0.249%), neg=0, invalid=96777
- 0559: dt=8.000000, rms=0.482 (0.124%), neg=0, invalid=96777
- 0560: dt=8.000000, rms=0.481 (0.162%), neg=0, invalid=96777
- 0561: dt=8.000000, rms=0.480 (0.234%), neg=0, invalid=96777
- 0562: dt=8.000000, rms=0.479 (0.240%), neg=0, invalid=96777
- 0563: dt=8.000000, rms=0.478 (0.236%), neg=0, invalid=96777
- 0564: dt=8.000000, rms=0.477 (0.239%), neg=0, invalid=96777
- 0565: dt=8.000000, rms=0.476 (0.200%), neg=0, invalid=96777
- 0566: dt=8.000000, rms=0.475 (0.193%), neg=0, invalid=96777
- 0567: dt=8.000000, rms=0.474 (0.174%), neg=0, invalid=96777
- 0568: dt=8.000000, rms=0.473 (0.164%), neg=0, invalid=96777
- 0569: dt=8.000000, rms=0.473 (0.157%), neg=0, invalid=96777
- 0570: dt=8.000000, rms=0.472 (0.128%), neg=0, invalid=96777
- 0571: dt=8.000000, rms=0.471 (0.144%), neg=0, invalid=96777
- 0572: dt=8.000000, rms=0.471 (0.156%), neg=0, invalid=96777
- 0573: dt=8.000000, rms=0.470 (0.132%), neg=0, invalid=96777
- 0574: dt=8.000000, rms=0.469 (0.125%), neg=0, invalid=96777
- 0575: dt=8.000000, rms=0.469 (0.109%), neg=0, invalid=96777
- 0576: dt=11.200000, rms=0.469 (0.030%), neg=0, invalid=96777
- 0577: dt=11.200000, rms=0.469 (0.012%), neg=0, invalid=96777
- 0578: dt=11.200000, rms=0.468 (0.033%), neg=0, invalid=96777
- 0579: dt=11.200000, rms=0.468 (0.040%), neg=0, invalid=96777
- 0580: dt=11.200000, rms=0.468 (0.041%), neg=0, invalid=96777
- 0581: dt=11.200000, rms=0.468 (0.035%), neg=0, invalid=96777
- 0582: dt=11.200000, rms=0.468 (0.051%), neg=0, invalid=96777
- 0583: dt=11.200000, rms=0.467 (0.052%), neg=0, invalid=96777
- 0584: dt=11.200000, rms=0.467 (0.050%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.467, neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0585: dt=44.800000, rms=0.464 (0.584%), neg=0, invalid=96777
- 0586: dt=11.200000, rms=0.464 (0.195%), neg=0, invalid=96777
- 0587: dt=11.200000, rms=0.463 (0.078%), neg=0, invalid=96777
- 0588: dt=11.200000, rms=0.463 (0.108%), neg=0, invalid=96777
- 0589: dt=11.200000, rms=0.462 (0.163%), neg=0, invalid=96777
- 0590: dt=11.200000, rms=0.461 (0.118%), neg=0, invalid=96777
- 0591: dt=11.200000, rms=0.461 (0.089%), neg=0, invalid=96777
- 0592: dt=32.000000, rms=0.461 (0.046%), neg=0, invalid=96777
- 0593: dt=32.000000, rms=0.461 (-0.269%), neg=0, invalid=96777
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.467, neg=0, invalid=96777
- 0594: dt=2.304000, rms=0.466 (0.032%), neg=0, invalid=96777
- 0595: dt=1.008000, rms=0.466 (0.008%), neg=0, invalid=96777
- 0596: dt=1.008000, rms=0.466 (0.006%), neg=0, invalid=96777
- 0597: dt=1.008000, rms=0.466 (-0.011%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.466, neg=0, invalid=96777
- 0598: dt=4.032000, rms=0.466 (0.045%), neg=0, invalid=96777
- 0599: dt=4.032000, rms=0.466 (0.024%), neg=0, invalid=96777
- 0600: dt=4.032000, rms=0.466 (0.009%), neg=0, invalid=96777
- 0601: dt=4.032000, rms=0.466 (-0.022%), neg=0, invalid=96777
- setting smoothness coefficient to 1.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.473, neg=0, invalid=96777
- 0602: dt=0.000000, rms=0.473 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.473, neg=0, invalid=96777
- 0603: dt=0.064000, rms=0.473 (0.000%), neg=0, invalid=96777
- 0604: dt=0.064000, rms=0.473 (0.001%), neg=0, invalid=96777
- 0605: dt=0.020000, rms=0.473 (0.002%), neg=0, invalid=96777
- 0606: dt=0.016000, rms=0.473 (-0.001%), neg=0, invalid=96777
- resetting metric properties...
- setting smoothness coefficient to 2.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.461, neg=0, invalid=96777
- iter 0, gcam->neg = 751
- after 19 iterations, nbhd size=2, neg = 0
- 0607: dt=1.925076, rms=0.419 (9.275%), neg=0, invalid=96777
- 0608: dt=0.000109, rms=0.419 (0.003%), neg=0, invalid=96777
- 0609: dt=0.000109, rms=0.419 (-0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.419, neg=0, invalid=96777
- 0610: dt=0.000375, rms=0.419 (0.000%), neg=0, invalid=96777
- 0611: dt=0.000000, rms=0.419 (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=0.401, neg=0, invalid=96777
- 0612: dt=0.000000, rms=0.402 (-0.257%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.402, neg=0, invalid=96777
- 0613: dt=18.496000, rms=0.402 (0.001%), neg=0, invalid=96777
- 0614: dt=0.022578, rms=0.402 (0.000%), neg=0, invalid=96777
- 0615: dt=0.022578, rms=0.402 (-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=0.403, neg=0, invalid=96777
- 0616: dt=0.000000, rms=0.403 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.403, neg=0, invalid=96777
- 0617: dt=25.920000, rms=0.403 (0.015%), neg=0, invalid=96777
- 0618: dt=20.736000, rms=0.403 (0.003%), neg=0, invalid=96777
- 0619: dt=20.736000, rms=0.403 (0.001%), neg=0, invalid=96777
- 0620: dt=20.736000, rms=0.403 (-0.003%), neg=0, invalid=96777
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.403, neg=0, invalid=96777
- 0621: dt=11.200000, rms=0.403 (0.085%), neg=0, invalid=96777
- 0622: dt=6.400000, rms=0.403 (0.013%), neg=0, invalid=96777
- 0623: dt=6.400000, rms=0.403 (0.012%), neg=0, invalid=96777
- 0624: dt=6.400000, rms=0.403 (-0.007%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.403, neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0625: dt=38.400000, rms=0.402 (0.326%), neg=0, invalid=96777
- 0626: dt=11.200000, rms=0.401 (0.048%), neg=0, invalid=96777
- 0627: dt=11.200000, rms=0.401 (0.086%), neg=0, invalid=96777
- 0628: dt=11.200000, rms=0.400 (0.128%), neg=0, invalid=96777
- 0629: dt=11.200000, rms=0.400 (0.134%), neg=0, invalid=96777
- iter 0, gcam->neg = 11
- after 15 iterations, nbhd size=2, neg = 0
- 0630: dt=11.200000, rms=0.399 (0.124%), neg=0, invalid=96777
- 0631: dt=11.200000, rms=0.399 (0.073%), neg=0, invalid=96777
- iter 0, gcam->neg = 14
- after 17 iterations, nbhd size=2, neg = 0
- 0632: dt=76.800000, rms=0.399 (0.140%), neg=0, invalid=96777
- 0633: dt=2.800000, rms=0.399 (0.004%), neg=0, invalid=96777
- 0634: dt=2.800000, rms=0.399 (0.010%), neg=0, invalid=96777
- 0635: dt=2.800000, rms=0.398 (0.017%), neg=0, invalid=96777
- 0636: dt=2.800000, rms=0.398 (0.022%), neg=0, invalid=96777
- 0637: dt=2.800000, rms=0.398 (0.023%), neg=0, invalid=96777
- 0638: dt=2.800000, rms=0.398 (0.024%), neg=0, invalid=96777
- 0639: dt=2.800000, rms=0.398 (0.024%), neg=0, invalid=96777
- 0640: dt=2.800000, rms=0.398 (0.024%), neg=0, invalid=96777
- 0641: dt=2.800000, rms=0.398 (0.025%), neg=0, invalid=96777
- 0642: dt=2.800000, rms=0.398 (0.025%), neg=0, invalid=96777
- 0643: dt=2.800000, rms=0.398 (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=0.401, neg=0, invalid=96777
- iter 0, gcam->neg = 11
- after 9 iterations, nbhd size=1, neg = 0
- 0644: dt=4.032000, rms=0.401 (0.061%), neg=0, invalid=96777
- 0645: dt=0.006750, rms=0.401 (0.000%), neg=0, invalid=96777
- 0646: dt=0.006750, rms=0.401 (0.000%), neg=0, invalid=96777
- 0647: dt=0.006750, rms=0.401 (0.000%), neg=0, invalid=96777
- 0648: dt=0.006750, rms=0.401 (0.000%), neg=0, invalid=96777
- 0649: dt=0.006750, rms=0.401 (0.000%), neg=0, invalid=96777
- 0650: dt=0.006750, rms=0.401 (0.000%), neg=0, invalid=96777
- 0651: dt=0.006750, rms=0.401 (0.000%), neg=0, invalid=96777
- 0652: dt=0.006750, rms=0.401 (0.000%), neg=0, invalid=96777
- 0653: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777
- 0654: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777
- 0655: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777
- 0656: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777
- 0657: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777
- 0658: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777
- 0659: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777
- 0660: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777
- 0661: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777
- 0662: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777
- 0663: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777
- 0664: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777
- 0665: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777
- 0666: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777
- 0667: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777
- 0668: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777
- 0669: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777
- 0670: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777
- 0671: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777
- 0672: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777
- 0673: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.401, neg=0, invalid=96777
- iter 0, gcam->neg = 83
- after 38 iterations, nbhd size=3, neg = 0
- 0674: dt=16.128000, rms=0.399 (0.351%), neg=0, invalid=96777
- 0675: dt=0.003938, rms=0.399 (0.000%), neg=0, invalid=96777
- 0676: dt=0.003938, rms=0.399 (0.000%), neg=0, invalid=96777
- 0677: dt=0.003938, rms=0.399 (-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=0.405, neg=0, invalid=96777
- 0678: dt=0.000000, rms=0.405 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.405, neg=0, invalid=96777
- 0679: dt=0.000000, rms=0.405 (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=0.395, neg=0, invalid=96777
- iter 0, gcam->neg = 565
- after 34 iterations, nbhd size=3, neg = 0
- 0680: dt=0.910140, rms=0.380 (3.668%), neg=0, invalid=96777
- 0681: dt=0.000000, rms=0.380 (0.000%), neg=0, invalid=96777
- iter 0, gcam->neg = 693
- after 11 iterations, nbhd size=1, neg = 0
- 0682: dt=0.050000, rms=0.380 (-0.343%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.380, neg=0, invalid=96777
- 0683: dt=0.000000, rms=0.380 (-0.000%), neg=0, invalid=96777
- writing output transformation to transforms/talairach.m3z...
- GCAMwrite
- registration took 4 hours, 5 minutes and 53 seconds.
- #--------------------------------------
- #@# CA Reg Inv Thu Aug 8 16:27:21 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 16:28:41 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...
- 10717596 nonbrain voxels erased
- writing output to nu_noneck.mgz...
- nonbrain removal took 1 minutes and 23 seconds.
- #--------------------------------------
- #@# SkullLTA Thu Aug 8 16:30:04 CEST 2013
- mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta
- ======= NUMBER OF OPENMP THREADS = 1 =======
- aligning to atlas containing skull, setting unknown_nbr_spacing = 5
- using previously computed transform transforms/talairach.lta
- reading 1 input volumes...
- logging results to talairach_with_skull_2.log
- reading '/opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca'...
- average std = 23.1 using min determinant for regularization = 53.4
- 0 singular and 5702 ill-conditioned covariance matrices regularized
- reading 'nu_noneck.mgz'...
- freeing gibbs priors...done.
- bounding unknown intensity as < 20.2 or > 943.7
- total sample mean = 92.0 (1443 zeros)
- ************************************************
- spacing=8, using 3481 sample points, tol=1.00e-05...
- ************************************************
- register_mri: find_optimal_transform
- find_optimal_transform: nsamples 3481, passno 0, spacing 8
- resetting wm mean[0]: 117 --> 126
- resetting gm mean[0]: 74 --> 74
- input volume #1 is the most T1-like
- using real data threshold=11.0
- skull bounding box = (41, 13, 12) --> (213, 203, 219)
- using (98, 76, 116) as brain centroid...
- mean wm in atlas = 126, using box (77,53,90) --> (119, 99,141) 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)
- 0.983 -0.021 0.024 0.151;
- 0.024 1.200 0.267 -32.056;
- -0.030 -0.176 0.960 17.535;
- 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)
- 0.983 -0.021 0.024 0.151;
- 0.022 1.110 0.247 -20.569;
- -0.030 -0.176 0.960 17.535;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 2 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 0.983 -0.021 0.024 0.151;
- 0.022 1.110 0.247 -20.569;
- -0.030 -0.176 0.960 17.535;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.2500
- ****************************************
- Nine parameter search. iteration 3 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 0.983 -0.021 0.024 0.151;
- 0.022 1.124 0.282 -24.015;
- -0.031 -0.213 0.951 24.267;
- 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)
- 0.983 -0.021 0.024 0.151;
- 0.022 1.124 0.282 -24.015;
- -0.031 -0.213 0.951 24.267;
- 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)
- 0.981 -0.023 0.032 -0.221;
- 0.022 1.125 0.283 -24.185;
- -0.039 -0.213 0.952 25.667;
- 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)
- 0.981 -0.023 0.032 -0.221;
- 0.022 1.122 0.282 -23.844;
- -0.039 -0.213 0.950 25.855;
- 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
- 0.98052 -0.02259 0.03199 -0.22081;
- 0.02160 1.12247 0.28205 -23.84424;
- -0.03859 -0.21289 0.95010 25.85537;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 3481
- Quasinewton: input matrix
- 0.98052 -0.02259 0.03199 -0.22081;
- 0.02160 1.12247 0.28205 -23.84424;
- -0.03859 -0.21289 0.95010 25.85537;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 0.981 -0.023 0.032 -0.221;
- 0.022 1.122 0.282 -23.844;
- -0.039 -0.213 0.950 25.855;
- 0.000 0.000 0.000 1.000;
- pass 1, spacing 8: log(p) = -4.0 (old=-4.1)
- transform before final EM align:
- 0.981 -0.023 0.032 -0.221;
- 0.022 1.122 0.282 -23.844;
- -0.039 -0.213 0.950 25.855;
- 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
- 0.98052 -0.02259 0.03199 -0.22081;
- 0.02160 1.12247 0.28205 -23.84424;
- -0.03859 -0.21289 0.95010 25.85537;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 382743
- Quasinewton: input matrix
- 0.98052 -0.02259 0.03199 -0.22081;
- 0.02160 1.12247 0.28205 -23.84424;
- -0.03859 -0.21289 0.95010 25.85537;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = 4.4 tol 0.000000
- final transform:
- 0.981 -0.023 0.032 -0.221;
- 0.022 1.122 0.282 -23.844;
- -0.039 -0.213 0.950 25.855;
- 0.000 0.000 0.000 1.000;
- writing output transformation to transforms/talairach_with_skull_2.lta...
- registration took 36 minutes and 21 seconds.
- #--------------------------------------
- #@# SubCort Seg Thu Aug 8 17:06:25 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/sub016/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 = 0.09683 ( 8)
- Left_Lateral_Ventricle (4): linear fit = 0.25 x + 0.0 (650 voxels, overlap=0.008)
- Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (650 voxels, peak = 7), gca=10.8
- gca peak = 0.14982 (20)
- mri peak = 0.10375 (10)
- Right_Lateral_Ventricle (43): linear fit = 0.31 x + 0.0 (1059 voxels, overlap=0.010)
- Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (1059 voxels, peak = 6), gca=8.0
- gca peak = 0.28003 (97)
- mri peak = 0.10452 (80)
- Right_Pallidum (52): linear fit = 0.81 x + 0.0 (366 voxels, overlap=0.052)
- Right_Pallidum (52): linear fit = 0.81 x + 0.0 (366 voxels, peak = 79), gca=79.1
- gca peak = 0.18160 (96)
- mri peak = 0.08193 (80)
- Left_Pallidum (13): linear fit = 0.83 x + 0.0 (446 voxels, overlap=0.054)
- Left_Pallidum (13): linear fit = 0.83 x + 0.0 (446 voxels, peak = 80), gca=80.2
- gca peak = 0.27536 (62)
- mri peak = 0.07808 (56)
- Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (626 voxels, overlap=0.354)
- Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (626 voxels, peak = 54), gca=54.2
- gca peak = 0.32745 (63)
- mri peak = 0.07985 (60)
- Left_Hippocampus (17): linear fit = 0.89 x + 0.0 (798 voxels, overlap=0.998)
- Left_Hippocampus (17): linear fit = 0.89 x + 0.0 (798 voxels, peak = 56), gca=56.4
- gca peak = 0.08597 (105)
- mri peak = 0.06779 (107)
- Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (42590 voxels, overlap=0.786)
- Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (42590 voxels, peak = 107), gca=106.6
- gca peak = 0.09209 (106)
- mri peak = 0.07226 (107)
- Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (41902 voxels, overlap=0.750)
- Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (41902 voxels, peak = 109), gca=108.6
- gca peak = 0.07826 (63)
- mri peak = 0.05031 (56)
- Left_Cerebral_Cortex (3): linear fit = 0.86 x + 0.0 (19158 voxels, overlap=0.523)
- Left_Cerebral_Cortex (3): linear fit = 0.86 x + 0.0 (19158 voxels, peak = 54), gca=53.9
- gca peak = 0.08598 (64)
- mri peak = 0.05205 (51)
- Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (19561 voxels, overlap=0.343)
- Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (19561 voxels, peak = 53), gca=52.8
- gca peak = 0.24164 (71)
- mri peak = 0.09348 (63)
- Right_Caudate (50): linear fit = 0.88 x + 0.0 (921 voxels, overlap=0.027)
- Right_Caudate (50): linear fit = 0.88 x + 0.0 (921 voxels, peak = 62), gca=62.1
- gca peak = 0.18227 (75)
- mri peak = 0.09183 (63)
- Left_Caudate (11): linear fit = 0.81 x + 0.0 (1188 voxels, overlap=0.028)
- Left_Caudate (11): linear fit = 0.81 x + 0.0 (1188 voxels, peak = 61), gca=61.1
- gca peak = 0.10629 (62)
- mri peak = 0.05931 (62)
- Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (9466 voxels, overlap=0.988)
- Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (9466 voxels, peak = 64), gca=63.5
- gca peak = 0.11668 (59)
- mri peak = 0.06138 (61)
- Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (10220 voxels, overlap=0.998)
- Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (10220 voxels, peak = 58), gca=58.1
- gca peak = 0.17849 (88)
- mri peak = 0.06123 (94)
- Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (4512 voxels, overlap=0.922)
- Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (4512 voxels, peak = 95), gca=94.6
- gca peak = 0.16819 (86)
- mri peak = 0.06784 (93)
- Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (4332 voxels, overlap=0.945)
- Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (4332 voxels, peak = 92), gca=91.6
- gca peak = 0.41688 (64)
- mri peak = 0.08973 (59)
- Left_Amygdala (18): linear fit = 0.90 x + 0.0 (434 voxels, overlap=1.037)
- Left_Amygdala (18): linear fit = 0.90 x + 0.0 (434 voxels, peak = 58), gca=57.9
- gca peak = 0.42394 (62)
- mri peak = 0.09194 (61)
- Right_Amygdala (54): linear fit = 0.88 x + 0.0 (450 voxels, overlap=1.041)
- Right_Amygdala (54): linear fit = 0.88 x + 0.0 (450 voxels, peak = 55), gca=54.9
- gca peak = 0.10041 (96)
- mri peak = 0.07166 (85)
- Left_Thalamus_Proper (10): linear fit = 0.90 x + 0.0 (3745 voxels, overlap=0.469)
- Left_Thalamus_Proper (10): linear fit = 0.90 x + 0.0 (3745 voxels, peak = 87), gca=86.9
- gca peak = 0.13978 (88)
- mri peak = 0.07968 (81)
- Right_Thalamus_Proper (49): linear fit = 0.93 x + 0.0 (3812 voxels, overlap=0.625)
- Right_Thalamus_Proper (49): linear fit = 0.93 x + 0.0 (3812 voxels, peak = 81), gca=81.4
- gca peak = 0.08514 (81)
- mri peak = 0.07115 (70)
- Left_Putamen (12): linear fit = 0.81 x + 0.0 (1920 voxels, overlap=0.234)
- Left_Putamen (12): linear fit = 0.81 x + 0.0 (1920 voxels, peak = 66), gca=66.0
- gca peak = 0.09624 (82)
- mri peak = 0.07615 (71)
- Right_Putamen (51): linear fit = 0.82 x + 0.0 (1787 voxels, overlap=0.023)
- Right_Putamen (51): linear fit = 0.82 x + 0.0 (1787 voxels, peak = 68), gca=67.7
- gca peak = 0.07543 (88)
- mri peak = 0.07619 (88)
- Brain_Stem (16): linear fit = 1.01 x + 0.0 (11427 voxels, overlap=0.765)
- Brain_Stem (16): linear fit = 1.01 x + 0.0 (11427 voxels, peak = 89), gca=89.3
- gca peak = 0.12757 (95)
- mri peak = 0.07479 (89)
- Right_VentralDC (60): linear fit = 0.94 x + 0.0 (936 voxels, overlap=0.827)
- Right_VentralDC (60): linear fit = 0.94 x + 0.0 (936 voxels, peak = 90), gca=89.8
- gca peak = 0.17004 (92)
- mri peak = 0.07026 (87)
- Left_VentralDC (28): linear fit = 0.95 x + 0.0 (918 voxels, overlap=0.804)
- Left_VentralDC (28): linear fit = 0.95 x + 0.0 (918 voxels, peak = 88), gca=87.9
- gca peak = 0.21361 (36)
- mri peak = 0.08496 (15)
- gca peak = 0.26069 (23)
- mri peak = 0.13778 (11)
- Fourth_Ventricle (15): linear fit = 0.44 x + 0.0 (98 voxels, overlap=0.031)
- Fourth_Ventricle (15): linear fit = 0.44 x + 0.0 (98 voxels, peak = 10), gca=10.0
- gca peak Unknown = 0.94427 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.31795 (35)
- gca peak Third_Ventricle = 0.21361 (36)
- gca peak Fourth_Ventricle = 0.26069 (23)
- gca peak CSF = 0.14367 (38)
- gca peak Left_Accumbens_area = 0.57033 (70)
- gca peak Left_undetermined = 1.00000 (35)
- gca peak Left_vessel = 0.65201 (62)
- gca peak Left_choroid_plexus = 0.09084 (48)
- gca peak Right_Inf_Lat_Vent = 0.31129 (32)
- gca peak Right_Accumbens_area = 0.30219 (72)
- gca peak Right_vessel = 0.83418 (60)
- gca peak Right_choroid_plexus = 0.10189 (48)
- gca peak Fifth_Ventricle = 0.72939 (42)
- gca peak WM_hypointensities = 0.14821 (82)
- gca peak non_WM_hypointensities = 0.10354 (53)
- gca peak Optic_Chiasm = 0.34849 (76)
- not using caudate to estimate GM means
- estimating mean gm scale to be 0.87 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 = 0.09683 ( 8)
- Left_Lateral_Ventricle (4): linear fit = 0.70 x + 0.0 (650 voxels, overlap=0.989)
- Left_Lateral_Ventricle (4): linear fit = 0.70 x + 0.0 (650 voxels, peak = 8), gca=7.8
- gca peak = 0.29325 ( 9)
- mri peak = 0.10375 (10)
- Right_Lateral_Ventricle (43): linear fit = 0.79 x + 0.0 (1059 voxels, overlap=1.001)
- Right_Lateral_Ventricle (43): linear fit = 0.79 x + 0.0 (1059 voxels, peak = 7), gca=7.1
- gca peak = 0.26534 (80)
- mri peak = 0.10452 (80)
- Right_Pallidum (52): linear fit = 1.00 x + 0.0 (366 voxels, overlap=1.012)
- Right_Pallidum (52): linear fit = 1.00 x + 0.0 (366 voxels, peak = 80), gca=80.0
- gca peak = 0.20119 (80)
- mri peak = 0.08193 (80)
- Left_Pallidum (13): linear fit = 1.00 x + 0.0 (446 voxels, overlap=1.013)
- Left_Pallidum (13): linear fit = 1.00 x + 0.0 (446 voxels, peak = 80), gca=80.0
- gca peak = 0.31053 (54)
- mri peak = 0.07808 (56)
- Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (626 voxels, overlap=1.005)
- Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (626 voxels, peak = 53), gca=53.2
- gca peak = 0.26447 (56)
- mri peak = 0.07985 (60)
- Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (798 voxels, overlap=1.010)
- Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (798 voxels, peak = 57), gca=57.4
- gca peak = 0.08540 (107)
- mri peak = 0.06779 (107)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (42590 voxels, overlap=0.834)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (42590 voxels, peak = 107), gca=107.0
- gca peak = 0.08534 (108)
- mri peak = 0.07226 (107)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (41902 voxels, overlap=0.796)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (41902 voxels, peak = 107), gca=107.5
- gca peak = 0.09232 (54)
- mri peak = 0.05031 (56)
- Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (19158 voxels, overlap=0.991)
- Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (19158 voxels, peak = 54), gca=54.0
- gca peak = 0.10550 (53)
- mri peak = 0.05205 (51)
- Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (19561 voxels, overlap=0.984)
- Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (19561 voxels, peak = 53), gca=53.0
- gca peak = 0.23948 (64)
- mri peak = 0.09348 (63)
- Right_Caudate (50): linear fit = 1.00 x + 0.0 (921 voxels, overlap=1.004)
- Right_Caudate (50): linear fit = 1.00 x + 0.0 (921 voxels, peak = 64), gca=64.0
- gca peak = 0.18470 (61)
- mri peak = 0.09183 (63)
- Left_Caudate (11): linear fit = 0.99 x + 0.0 (1188 voxels, overlap=0.998)
- Left_Caudate (11): linear fit = 0.99 x + 0.0 (1188 voxels, peak = 60), gca=60.1
- gca peak = 0.10027 (62)
- mri peak = 0.05931 (62)
- Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (9466 voxels, overlap=0.997)
- Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (9466 voxels, peak = 61), gca=61.1
- gca peak = 0.12025 (59)
- mri peak = 0.06138 (61)
- Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (10220 voxels, overlap=0.997)
- Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (10220 voxels, peak = 60), gca=60.5
- gca peak = 0.17137 (94)
- mri peak = 0.06123 (94)
- Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4512 voxels, overlap=1.000)
- Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4512 voxels, peak = 94), gca=93.5
- gca peak = 0.16068 (92)
- mri peak = 0.06784 (93)
- Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (4332 voxels, overlap=1.000)
- Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (4332 voxels, peak = 91), gca=90.6
- gca peak = 0.40361 (58)
- mri peak = 0.08973 (59)
- Left_Amygdala (18): linear fit = 1.04 x + 0.0 (434 voxels, overlap=1.027)
- Left_Amygdala (18): linear fit = 1.04 x + 0.0 (434 voxels, peak = 61), gca=60.6
- gca peak = 0.57399 (55)
- mri peak = 0.09194 (61)
- Right_Amygdala (54): linear fit = 1.04 x + 0.0 (450 voxels, overlap=1.027)
- Right_Amygdala (54): linear fit = 1.04 x + 0.0 (450 voxels, peak = 57), gca=57.5
- gca peak = 0.11982 (87)
- mri peak = 0.07166 (85)
- Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3745 voxels, overlap=0.999)
- Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3745 voxels, peak = 87), gca=86.6
- gca peak = 0.11701 (81)
- mri peak = 0.07968 (81)
- Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (3812 voxels, overlap=0.980)
- Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (3812 voxels, peak = 80), gca=79.8
- gca peak = 0.09700 (71)
- mri peak = 0.07115 (70)
- Left_Putamen (12): linear fit = 1.03 x + 0.0 (1920 voxels, overlap=1.000)
- Left_Putamen (12): linear fit = 1.03 x + 0.0 (1920 voxels, peak = 73), gca=73.5
- gca peak = 0.10658 (68)
- mri peak = 0.07615 (71)
- Right_Putamen (51): linear fit = 0.99 x + 0.0 (1787 voxels, overlap=0.991)
- Right_Putamen (51): linear fit = 0.99 x + 0.0 (1787 voxels, peak = 67), gca=67.0
- gca peak = 0.07507 (87)
- mri peak = 0.07619 (88)
- Brain_Stem (16): linear fit = 1.00 x + 0.0 (11427 voxels, overlap=0.798)
- Brain_Stem (16): linear fit = 1.00 x + 0.0 (11427 voxels, peak = 87), gca=86.6
- gca peak = 0.12974 (86)
- mri peak = 0.07479 (89)
- Right_VentralDC (60): linear fit = 1.02 x + 0.0 (936 voxels, overlap=0.817)
- Right_VentralDC (60): linear fit = 1.02 x + 0.0 (936 voxels, peak = 88), gca=88.2
- gca peak = 0.15097 (88)
- mri peak = 0.07026 (87)
- Left_VentralDC (28): linear fit = 1.00 x + 0.0 (918 voxels, overlap=0.943)
- Left_VentralDC (28): linear fit = 1.00 x + 0.0 (918 voxels, peak = 88), gca=87.6
- gca peak = 0.35640 (14)
- mri peak = 0.08496 (15)
- gca peak = 0.33827 ( 9)
- mri peak = 0.13778 (11)
- Fourth_Ventricle (15): linear fit = 1.14 x + 0.0 (98 voxels, overlap=0.976)
- Fourth_Ventricle (15): linear fit = 1.14 x + 0.0 (98 voxels, peak = 10), gca=10.3
- gca peak Unknown = 0.94427 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.23697 (32)
- gca peak Third_Ventricle = 0.35640 (14)
- gca peak CSF = 0.30128 (18)
- gca peak Left_Accumbens_area = 0.68092 (57)
- gca peak Left_undetermined = 1.00000 (35)
- gca peak Left_vessel = 0.42552 (62)
- gca peak Left_choroid_plexus = 0.09084 (48)
- gca peak Right_Inf_Lat_Vent = 0.33086 (28)
- gca peak Right_Accumbens_area = 0.31091 (63)
- gca peak Right_vessel = 0.57322 (60)
- gca peak Right_choroid_plexus = 0.10278 (48)
- gca peak Fifth_Ventricle = 0.45329 (19)
- gca peak WM_hypointensities = 0.17567 (83)
- gca peak non_WM_hypointensities = 0.12171 (54)
- gca peak Optic_Chiasm = 0.34843 (76)
- not using caudate to estimate GM means
- estimating mean gm scale to be 1.02 x + 0.0
- estimating mean wm scale to be 1.00 x + 0.0
- estimating mean csf scale to be 0.88 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
- 13374 gm and wm labels changed (%13 to gray, %87 to white out of all changed labels)
- 310 hippocampal voxels changed.
- 13 amygdala voxels changed.
- pass 1: 98944 changed. image ll: -2.251, PF=1.000
- pass 2: 18094 changed. image ll: -2.249, PF=1.000
- pass 3: 6959 changed.
- pass 4: 3144 changed.
- writing labeled volume to aseg.auto_noCCseg.mgz...
- auto-labeling took 18 minutes and 5 seconds.
- mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/cc_up.lta sub016
- 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/sub016/mri/transforms/cc_up.lta
- reading aseg from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/aseg.auto_noCCseg.mgz
- reading norm from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/norm.mgz
- 24264 voxels in left wm, 26205 in right wm, xrange [124, 131]
- searching rotation angles z=[-6 8], y=[-6 8]
-
searching scale 1 Z rot -5.5
searching scale 1 Z rot -5.3
searching scale 1 Z rot -5.0
searching scale 1 Z rot -4.8
searching scale 1 Z rot -4.5
searching scale 1 Z rot -4.3
searching scale 1 Z rot -4.0
searching scale 1 Z rot -3.8
searching scale 1 Z rot -3.5
searching scale 1 Z rot -3.3
searching scale 1 Z rot -3.0
searching scale 1 Z rot -2.8
searching scale 1 Z rot -2.5
searching scale 1 Z rot -2.3
searching scale 1 Z rot -2.0
searching scale 1 Z rot -1.8
searching scale 1 Z rot -1.5
searching scale 1 Z rot -1.3
searching scale 1 Z rot -1.0
searching scale 1 Z rot -0.8
searching scale 1 Z rot -0.5
searching scale 1 Z rot -0.3
searching scale 1 Z rot -0.0
searching scale 1 Z rot 0.2
searching scale 1 Z rot 0.5
searching scale 1 Z rot 0.7
searching scale 1 Z rot 1.0
searching scale 1 Z rot 1.2
searching scale 1 Z rot 1.5
searching scale 1 Z rot 1.7
searching scale 1 Z rot 2.0
searching scale 1 Z rot 2.2
searching scale 1 Z rot 2.5
searching scale 1 Z rot 2.7
searching scale 1 Z rot 3.0
searching scale 1 Z rot 3.2
searching scale 1 Z rot 3.5
searching scale 1 Z rot 3.7
searching scale 1 Z rot 4.0
searching scale 1 Z rot 4.2
searching scale 1 Z rot 4.5
searching scale 1 Z rot 4.7
searching scale 1 Z rot 5.0
searching scale 1 Z rot 5.2
searching scale 1 Z rot 5.5
searching scale 1 Z rot 5.7
searching scale 1 Z rot 6.0
searching scale 1 Z rot 6.2
searching scale 1 Z rot 6.5
searching scale 1 Z rot 6.7
searching scale 1 Z rot 7.0
searching scale 1 Z rot 7.2
searching scale 1 Z rot 7.5
searching scale 1 Z rot 7.7
searching scale 1 Z rot 8.0
searching scale 1 Z rot 8.2 global minimum found at slice 127.2, rotations (0.87, 1.46)
- final transformation (x=127.2, yr=0.866, zr=1.458):
- 1.000 -0.025 0.015 1.292;
- 0.025 1.000 0.000 44.748;
- -0.015 -0.000 1.000 26.935;
- 0.000 0.000 0.000 1.000;
- updating x range to be [125, 131] in xformed coordinates
- best xformed slice 128
- cc center is found at 128 147 116
- eigenvectors:
- -0.000 0.001 1.000;
- -0.073 -0.997 0.001;
- 0.997 -0.073 0.001;
- error in mid anterior detected - correcting...
- writing aseg with callosum to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/aseg.auto.mgz...
- corpus callosum matter segmentation took 0.7 minutes
- #--------------------------------------
- #@# Merge ASeg Thu Aug 8 17:25:11 CEST 2013
- cp aseg.auto.mgz aseg.mgz
- #--------------------------------------------
- #@# Intensity Normalization2 Thu Aug 8 17:25:11 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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...
- 3712 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 57 (57), valley at 30 (30)
- csf peak at 28, setting threshold to 47
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- ---------------------------------
- 3d normalization pass 2 of 2
- white matter peak found at 111
- white matter peak found at 110
- gm peak at 58 (58), valley at 30 (30)
- 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 10 seconds.
- #--------------------------------------------
- #@# Mask BFS Thu Aug 8 17:29:23 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri
- mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
- threshold mask volume at 5
- DoAbs = 0
- Found 1767582 voxels in mask (pct= 10.54)
- Writing masked volume to brain.finalsurfs.mgz...done.
- #--------------------------------------------
- #@# WM Segmentation Thu Aug 8 17:29:25 CEST 2013
- mri_segment brain.mgz wm.seg.mgz
- doing initial intensity segmentation...
- using local statistics to label ambiguous voxels...
- computing class statistics for intensity windows...
- WM (107.0): 107.1 +- 5.1 [80.0 --> 125.0]
- GM (68.0) : 67.4 +- 9.2 [30.0 --> 96.0]
- setting bottom of white matter range to 76.6
- setting top of gray matter range to 85.7
- doing initial intensity segmentation...
- using local statistics to label ambiguous voxels...
- using local geometry to label remaining ambiguous voxels...
- reclassifying voxels using Gaussian border classifier...
- removing voxels with positive offset direction...
- smoothing T1 volume with sigma = 0.250
- removing 1-dimensional structures...
- 10649 sparsely connected voxels removed...
- thickening thin strands....
- 20 segments, 5279 filled
- 312 bright non-wm voxels segmented.
- 5168 diagonally connected voxels added...
- white matter segmentation took 1.9 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 0.65 minutes
- reading wm segmentation from wm.seg.mgz...
- 70 voxels added to wm to prevent paths from MTL structures to cortex
- 1160 additional wm voxels added
- 0 additional wm voxels added
- SEG EDIT: 51272 voxels turned on, 46916 voxels turned off.
- propagating editing to output volume from wm.seg.mgz
- 115,126,128 old 86 new 86
- 115,126,128 old 86 new 86
- writing edited volume to wm.asegedit.mgz....
- mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz
- Iteration Number : 1
- pass 1 (xy+): 28 found - 28 modified | TOTAL: 28
- pass 2 (xy+): 0 found - 28 modified | TOTAL: 28
- pass 1 (xy-): 25 found - 25 modified | TOTAL: 53
- pass 2 (xy-): 0 found - 25 modified | TOTAL: 53
- pass 1 (yz+): 32 found - 32 modified | TOTAL: 85
- pass 2 (yz+): 0 found - 32 modified | TOTAL: 85
- pass 1 (yz-): 23 found - 23 modified | TOTAL: 108
- pass 2 (yz-): 0 found - 23 modified | TOTAL: 108
- pass 1 (xz+): 18 found - 18 modified | TOTAL: 126
- pass 2 (xz+): 0 found - 18 modified | TOTAL: 126
- pass 1 (xz-): 23 found - 23 modified | TOTAL: 149
- pass 2 (xz-): 0 found - 23 modified | TOTAL: 149
- Iteration Number : 1
- pass 1 (+++): 6 found - 6 modified | TOTAL: 6
- pass 2 (+++): 0 found - 6 modified | TOTAL: 6
- pass 1 (+++): 27 found - 27 modified | TOTAL: 33
- pass 2 (+++): 0 found - 27 modified | TOTAL: 33
- pass 1 (+++): 9 found - 9 modified | TOTAL: 42
- pass 2 (+++): 0 found - 9 modified | TOTAL: 42
- pass 1 (+++): 16 found - 16 modified | TOTAL: 58
- pass 2 (+++): 0 found - 16 modified | TOTAL: 58
- Iteration Number : 1
- pass 1 (++): 204 found - 204 modified | TOTAL: 204
- pass 2 (++): 0 found - 204 modified | TOTAL: 204
- pass 1 (+-): 188 found - 188 modified | TOTAL: 392
- pass 2 (+-): 0 found - 188 modified | TOTAL: 392
- pass 1 (--): 178 found - 178 modified | TOTAL: 570
- pass 2 (--): 0 found - 178 modified | TOTAL: 570
- pass 1 (-+): 166 found - 166 modified | TOTAL: 736
- pass 2 (-+): 0 found - 166 modified | TOTAL: 736
- Iteration Number : 2
- pass 1 (xy+): 9 found - 9 modified | TOTAL: 9
- pass 2 (xy+): 0 found - 9 modified | TOTAL: 9
- pass 1 (xy-): 7 found - 7 modified | TOTAL: 16
- pass 2 (xy-): 0 found - 7 modified | TOTAL: 16
- pass 1 (yz+): 2 found - 2 modified | TOTAL: 18
- pass 2 (yz+): 0 found - 2 modified | TOTAL: 18
- pass 1 (yz-): 8 found - 8 modified | TOTAL: 26
- pass 2 (yz-): 0 found - 8 modified | TOTAL: 26
- pass 1 (xz+): 3 found - 3 modified | TOTAL: 29
- pass 2 (xz+): 0 found - 3 modified | TOTAL: 29
- pass 1 (xz-): 2 found - 2 modified | TOTAL: 31
- pass 2 (xz-): 0 found - 2 modified | TOTAL: 31
- 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 (+++): 0 found - 0 modified | TOTAL: 1
- pass 1 (+++): 1 found - 1 modified | TOTAL: 2
- pass 2 (+++): 0 found - 1 modified | TOTAL: 2
- Iteration Number : 2
- pass 1 (++): 3 found - 3 modified | TOTAL: 3
- pass 2 (++): 0 found - 3 modified | TOTAL: 3
- pass 1 (+-): 1 found - 1 modified | TOTAL: 4
- pass 2 (+-): 0 found - 1 modified | TOTAL: 4
- pass 1 (--): 2 found - 2 modified | TOTAL: 6
- pass 2 (--): 0 found - 2 modified | TOTAL: 6
- pass 1 (-+): 0 found - 0 modified | TOTAL: 6
- 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+): 1 found - 1 modified | TOTAL: 2
- pass 2 (yz+): 0 found - 1 modified | TOTAL: 2
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 2
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 2
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 2
- Iteration Number : 3
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 1 found - 1 modified | TOTAL: 1
- pass 2 (+++): 0 found - 1 modified | TOTAL: 1
- pass 1 (+++): 0 found - 0 modified | TOTAL: 1
- pass 1 (+++): 0 found - 0 modified | TOTAL: 1
- Iteration Number : 3
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 1 found - 1 modified | TOTAL: 1
- pass 2 (+-): 0 found - 1 modified | TOTAL: 1
- pass 1 (--): 0 found - 0 modified | TOTAL: 1
- pass 1 (-+): 1 found - 1 modified | TOTAL: 2
- pass 2 (-+): 0 found - 1 modified | TOTAL: 2
- 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 = 987 (out of 622745: 0.158492)
- binarizing input wm segmentation...
- Ambiguous edge configurations...
- mri_pretess done
- #--------------------------------------------
- #@# Fill Thu Aug 8 17:32:05 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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
- 0.983 -0.021 0.024 0.151;
- 0.022 1.116 0.249 -21.370;
- -0.030 -0.176 0.960 17.535;
- 0.000 0.000 0.000 1.000;
- voxel to talairach voxel transform
- 0.983 -0.021 0.024 0.151;
- 0.022 1.116 0.249 -21.370;
- -0.030 -0.176 0.960 17.535;
- 0.000 0.000 0.000 1.000;
- reading segmented volume aseg.auto_noCCseg.mgz...
- Looking for area (min, max) = (350, 1400)
- area[0] = 1119 (min = 350, max = 1400), aspect = 0.38 (min = 0.10, max = 0.75)
- no need to search
- using seed (126, 121, 149), TAL = (2.0, 21.0, 7.0)
- talairach voxel to voxel transform
- 1.016 0.014 -0.029 0.669;
- -0.026 0.860 -0.222 22.285;
- 0.027 0.158 1.000 -14.161;
- 0.000 0.000 0.000 1.000;
- segmentation indicates cc at (126, 121, 149) --> (2.0, 21.0, 7.0)
- done.
- writing output to filled.mgz...
- filling took 0.9 minutes
- talairach cc position changed to (2.00, 21.00, 7.00)
- Erasing brainstem...done.
- seed_search_size = 9, min_neighbors = 5
- search rh wm seed point around talairach space:(20.00, 21.00, 7.00) SRC: (107.76, 90.46, 156.80)
- search lh wm seed point around talairach space (-16.00, 21.00, 7.00), SRC: (144.33, 89.52, 157.76)
- compute mri_fill using aseg
- Erasing Brain Stem and Cerebellum ...
- Define left and right masks using aseg:
- Building Voronoi diagram ...
- Using the Voronoi diagram to separate WM into two hemispheres ...
- Find the largest connected component for each hemisphere ...
- #--------------------------------------------
- #@# Tessellate lh Thu Aug 8 17:33:00 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts
- mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz
- Iteration Number : 1
- pass 1 (xy+): 3 found - 3 modified | TOTAL: 3
- pass 2 (xy+): 0 found - 3 modified | TOTAL: 3
- pass 1 (xy-): 1 found - 1 modified | TOTAL: 4
- pass 2 (xy-): 0 found - 1 modified | TOTAL: 4
- pass 1 (yz+): 2 found - 2 modified | TOTAL: 6
- pass 2 (yz+): 0 found - 2 modified | TOTAL: 6
- pass 1 (yz-): 1 found - 1 modified | TOTAL: 7
- pass 2 (yz-): 0 found - 1 modified | TOTAL: 7
- pass 1 (xz+): 1 found - 1 modified | TOTAL: 8
- pass 2 (xz+): 0 found - 1 modified | TOTAL: 8
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 8
- Iteration Number : 1
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 1
- pass 1 (++): 1 found - 1 modified | TOTAL: 1
- pass 2 (++): 0 found - 1 modified | TOTAL: 1
- pass 1 (+-): 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
- pass 1 (-+): 0 found - 0 modified | TOTAL: 4
- Iteration Number : 2
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Total Number of Modified Voxels = 12 (out of 296303: 0.004050)
- 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: 2247 vertices, 2412 faces
- slice 50: 10036 vertices, 10353 faces
- slice 60: 21453 vertices, 21827 faces
- slice 70: 33202 vertices, 33629 faces
- slice 80: 45185 vertices, 45605 faces
- slice 90: 57325 vertices, 57748 faces
- slice 100: 70349 vertices, 70817 faces
- slice 110: 83004 vertices, 83431 faces
- slice 120: 95002 vertices, 95456 faces
- slice 130: 107089 vertices, 107487 faces
- slice 140: 118705 vertices, 119157 faces
- slice 150: 129205 vertices, 129627 faces
- slice 160: 138040 vertices, 138350 faces
- slice 170: 146229 vertices, 146519 faces
- slice 180: 153318 vertices, 153599 faces
- slice 190: 158619 vertices, 158840 faces
- slice 200: 161732 vertices, 161843 faces
- slice 210: 161964 vertices, 162010 faces
- slice 220: 161964 vertices, 162010 faces
- slice 230: 161964 vertices, 162010 faces
- slice 240: 161964 vertices, 162010 faces
- slice 250: 161964 vertices, 162010 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...
- 161964 voxel in cpt #1: X=-46 [v=161964,e=486030,f=324020] located at (-28.711313, -18.458485, 37.919922)
- For the whole surface: X=-46 [v=161964,e=486030,f=324020]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Smooth1 lh Thu Aug 8 17:33:08 CEST 2013
- mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts
- setting seed for random number generator to 1234
- smoothing surface tessellation for 10 iterations...
- smoothing complete - recomputing first and second fundamental forms...
- #--------------------------------------------
- #@# Inflation1 lh Thu Aug 8 17:33:13 CEST 2013
- mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts
- avg radius = 49.2 mm, total surface area = 86006 mm^2
- writing inflated surface to ../surf/lh.inflated.nofix
- inflation took 0.8 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=0.033 (target=0.015)
step 030: RMS=0.029 (target=0.015)
step 035: RMS=0.026 (target=0.015)
step 040: RMS=0.024 (target=0.015)
step 045: RMS=0.022 (target=0.015)
step 050: RMS=0.021 (target=0.015)
step 055: RMS=0.021 (target=0.015)
step 060: RMS=0.021 (target=0.015)
- inflation complete.
- Not saving sulc
- #--------------------------------------------
- #@# QSphere lh Thu Aug 8 17:34:00 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 0.91 +- 0.54 (0.00-->6.75) (max @ vno 121685 --> 121686)
- face area 0.02 +- 0.03 (-0.18-->0.72)
- scaling brain by 0.291...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=176.656, avgs=0
- 005/300: dt: 0.9000, rms radial error=176.398, avgs=0
- 010/300: dt: 0.9000, rms radial error=175.843, avgs=0
- 015/300: dt: 0.9000, rms radial error=175.115, avgs=0
- 020/300: dt: 0.9000, rms radial error=174.285, avgs=0
- 025/300: dt: 0.9000, rms radial error=173.398, avgs=0
- 030/300: dt: 0.9000, rms radial error=172.480, avgs=0
- 035/300: dt: 0.9000, rms radial error=171.544, avgs=0
- 040/300: dt: 0.9000, rms radial error=170.601, avgs=0
- 045/300: dt: 0.9000, rms radial error=169.655, avgs=0
- 050/300: dt: 0.9000, rms radial error=168.709, avgs=0
- 055/300: dt: 0.9000, rms radial error=167.766, avgs=0
- 060/300: dt: 0.9000, rms radial error=166.826, avgs=0
- 065/300: dt: 0.9000, rms radial error=165.890, avgs=0
- 070/300: dt: 0.9000, rms radial error=164.959, avgs=0
- 075/300: dt: 0.9000, rms radial error=164.032, avgs=0
- 080/300: dt: 0.9000, rms radial error=163.111, avgs=0
- 085/300: dt: 0.9000, rms radial error=162.193, avgs=0
- 090/300: dt: 0.9000, rms radial error=161.281, avgs=0
- 095/300: dt: 0.9000, rms radial error=160.373, avgs=0
- 100/300: dt: 0.9000, rms radial error=159.471, avgs=0
- 105/300: dt: 0.9000, rms radial error=158.573, avgs=0
- 110/300: dt: 0.9000, rms radial error=157.680, avgs=0
- 115/300: dt: 0.9000, rms radial error=156.792, avgs=0
- 120/300: dt: 0.9000, rms radial error=155.909, avgs=0
- 125/300: dt: 0.9000, rms radial error=155.031, avgs=0
- 130/300: dt: 0.9000, rms radial error=154.157, avgs=0
- 135/300: dt: 0.9000, rms radial error=153.289, avgs=0
- 140/300: dt: 0.9000, rms radial error=152.425, avgs=0
- 145/300: dt: 0.9000, rms radial error=151.566, avgs=0
- 150/300: dt: 0.9000, rms radial error=150.711, avgs=0
- 155/300: dt: 0.9000, rms radial error=149.861, avgs=0
- 160/300: dt: 0.9000, rms radial error=149.016, avgs=0
- 165/300: dt: 0.9000, rms radial error=148.175, avgs=0
- 170/300: dt: 0.9000, rms radial error=147.339, avgs=0
- 175/300: dt: 0.9000, rms radial error=146.508, avgs=0
- 180/300: dt: 0.9000, rms radial error=145.681, avgs=0
- 185/300: dt: 0.9000, rms radial error=144.859, avgs=0
- 190/300: dt: 0.9000, rms radial error=144.042, avgs=0
- 195/300: dt: 0.9000, rms radial error=143.231, avgs=0
- 200/300: dt: 0.9000, rms radial error=142.425, avgs=0
- 205/300: dt: 0.9000, rms radial error=141.623, avgs=0
- 210/300: dt: 0.9000, rms radial error=140.825, avgs=0
- 215/300: dt: 0.9000, rms radial error=140.032, avgs=0
- 220/300: dt: 0.9000, rms radial error=139.244, avgs=0
- 225/300: dt: 0.9000, rms radial error=138.459, avgs=0
- 230/300: dt: 0.9000, rms radial error=137.679, avgs=0
- 235/300: dt: 0.9000, rms radial error=136.904, avgs=0
- 240/300: dt: 0.9000, rms radial error=136.132, avgs=0
- 245/300: dt: 0.9000, rms radial error=135.365, avgs=0
- 250/300: dt: 0.9000, rms radial error=134.602, avgs=0
- 255/300: dt: 0.9000, rms radial error=133.844, avgs=0
- 260/300: dt: 0.9000, rms radial error=133.090, avgs=0
- 265/300: dt: 0.9000, rms radial error=132.340, avgs=0
- 270/300: dt: 0.9000, rms radial error=131.595, avgs=0
- 275/300: dt: 0.9000, rms radial error=130.853, avgs=0
- 280/300: dt: 0.9000, rms radial error=130.116, avgs=0
- 285/300: dt: 0.9000, rms radial error=129.382, avgs=0
- 290/300: dt: 0.9000, rms radial error=128.653, avgs=0
- 295/300: dt: 0.9000, rms radial error=127.928, avgs=0
- 300/300: dt: 0.9000, rms radial error=127.207, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 19332.81
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00015
- epoch 2 (K=40.0), pass 1, starting sse = 3371.47
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00004
- epoch 3 (K=160.0), pass 1, starting sse = 367.24
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.05/11 = 0.00481
- epoch 4 (K=640.0), pass 1, starting sse = 23.51
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.09/12 = 0.00726
- final writing spherical brain to ../surf/lh.qsphere.nofix
- spherical transformation took 0.09 hours
- distance error %100000.00
- #--------------------------------------------
- #@# Fix Topology lh Thu Aug 8 17:39:17 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/sub016/scripts
- mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub016 lh
- reading spherical homeomorphism from 'qsphere.nofix'
- using genetic algorithm with optimized parameters
- setting seed for random number genererator to 1234
- *************************************************************
- Topology Correction Parameters
- retessellation mode: genetic search
- number of patches/generation : 10
- number of generations : 10
- surface mri loglikelihood coefficient : 1.0
- volume mri loglikelihood coefficient : 10.0
- normal dot loglikelihood coefficient : 1.0
- quadratic curvature loglikelihood coefficient : 1.0
- volume resolution : 2
- eliminate vertices during search : 1
- initial patch selection : 1
- select all defect vertices : 0
- ordering dependant retessellation: 0
- use precomputed edge table : 0
- smooth retessellated patch : 2
- match retessellated patch : 1
- verbose mode : 0
- *************************************************************
- INFO: assuming .mgz format
- $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- before topology correction, eno=-46 (nv=161964, nf=324020, ne=486030, g=24)
- using quasi-homeomorphic spherical map to tessellate cortical surface...
- Correction of the Topology
- Finding true center and radius of Spherical Surface...done
- Surface centered at (0,0,0) with radius 100.0 in 9 iterations
- marking ambiguous vertices...
- 3711 ambiguous faces found in tessellation
- segmenting defects...
- 26 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- 26 defects to be corrected
- 0 vertices coincident
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -9.8304 (-4.9152)
- -vertex loglikelihood: -6.5729 (-3.2864)
- -normal dot loglikelihood: -3.6792 (-3.6792)
- -quad curv loglikelihood: -6.4542 (-3.2271)
- Total Loglikelihood : -26.5366
- CORRECTING DEFECT 0 (vertices=25, convex hull=62)
- After retessellation of defect 0, euler #=-23 (159748,478470,318699) : difference with theory (-23) = 0
- CORRECTING DEFECT 1 (vertices=694, convex hull=338)
- After retessellation of defect 1, euler #=-22 (160043,479516,319451) : difference with theory (-22) = 0
- CORRECTING DEFECT 2 (vertices=33, convex hull=71)
- After retessellation of defect 2, euler #=-21 (160062,479601,319518) : difference with theory (-21) = 0
- CORRECTING DEFECT 3 (vertices=5, convex hull=21)
- After retessellation of defect 3, euler #=-20 (160063,479608,319525) : difference with theory (-20) = 0
- CORRECTING DEFECT 4 (vertices=40, convex hull=86)
- After retessellation of defect 4, euler #=-19 (160083,479704,319602) : difference with theory (-19) = 0
- CORRECTING DEFECT 5 (vertices=6, convex hull=25)
- After retessellation of defect 5, euler #=-18 (160085,479718,319615) : difference with theory (-18) = 0
- CORRECTING DEFECT 6 (vertices=152, convex hull=137)
- After retessellation of defect 6, euler #=-17 (160158,480004,319829) : difference with theory (-17) = 0
- CORRECTING DEFECT 7 (vertices=238, convex hull=105)
- After retessellation of defect 7, euler #=-16 (160221,480241,320004) : difference with theory (-16) = 0
- CORRECTING DEFECT 8 (vertices=31, convex hull=33)
- After retessellation of defect 8, euler #=-15 (160226,480266,320025) : difference with theory (-15) = 0
- CORRECTING DEFECT 9 (vertices=30, convex hull=61)
- After retessellation of defect 9, euler #=-14 (160242,480344,320088) : difference with theory (-14) = 0
- CORRECTING DEFECT 10 (vertices=179, convex hull=55)
- After retessellation of defect 10, euler #=-13 (160255,480404,320136) : difference with theory (-13) = 0
- CORRECTING DEFECT 11 (vertices=75, convex hull=78)
- After retessellation of defect 11, euler #=-12 (160266,480472,320194) : difference with theory (-12) = 0
- CORRECTING DEFECT 12 (vertices=12, convex hull=21)
- After retessellation of defect 12, euler #=-11 (160270,480488,320207) : difference with theory (-11) = 0
- CORRECTING DEFECT 13 (vertices=34, convex hull=76)
- After retessellation of defect 13, euler #=-10 (160279,480545,320256) : difference with theory (-10) = 0
- CORRECTING DEFECT 14 (vertices=5, convex hull=15)
- After retessellation of defect 14, euler #=-9 (160279,480548,320260) : difference with theory (-9) = 0
- CORRECTING DEFECT 15 (vertices=46, convex hull=75)
- After retessellation of defect 15, euler #=-8 (160295,480626,320323) : difference with theory (-8) = 0
- CORRECTING DEFECT 16 (vertices=175, convex hull=114)
- After retessellation of defect 16, euler #=-7 (160337,480802,320458) : difference with theory (-7) = 0
- CORRECTING DEFECT 17 (vertices=125, convex hull=60)
- After retessellation of defect 17, euler #=-6 (160345,480860,320509) : difference with theory (-6) = 0
- CORRECTING DEFECT 18 (vertices=123, convex hull=128)
- After retessellation of defect 18, euler #=-5 (160411,481113,320697) : difference with theory (-5) = 0
- CORRECTING DEFECT 19 (vertices=40, convex hull=38)
- After retessellation of defect 19, euler #=-4 (160420,481152,320728) : difference with theory (-4) = 0
- CORRECTING DEFECT 20 (vertices=34, convex hull=59)
- After retessellation of defect 20, euler #=-3 (160438,481227,320786) : difference with theory (-3) = 0
- CORRECTING DEFECT 21 (vertices=10, convex hull=27)
- After retessellation of defect 21, euler #=-2 (160440,481240,320798) : difference with theory (-2) = 0
- CORRECTING DEFECT 22 (vertices=22, convex hull=52)
- After retessellation of defect 22, euler #=-1 (160453,481299,320845) : difference with theory (-1) = 0
- CORRECTING DEFECT 23 (vertices=16, convex hull=32)
- After retessellation of defect 23, euler #=0 (160460,481331,320871) : difference with theory (0) = 0
- CORRECTING DEFECT 24 (vertices=42, convex hull=62)
- After retessellation of defect 24, euler #=1 (160469,481382,320914) : difference with theory (1) = 0
- CORRECTING DEFECT 25 (vertices=25, convex hull=55)
- After retessellation of defect 25, euler #=2 (160479,481431,320954) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.88 +- 0.22 (0.05-->6.34) (max @ vno 116804 --> 122752)
- face area 0.00 +- 0.00 (0.00-->0.00)
- performing soap bubble on retessellated vertices for 0 iterations...
- vertex spacing 0.88 +- 0.22 (0.05-->6.34) (max @ vno 116804 --> 122752)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 78 mutations (33.6%), 154 crossovers (66.4%), 79 vertices were eliminated
- building final representation...
- 1485 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=160479, nf=320954, ne=481431, g=0)
- writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 18.4 minutes
- 0 defective edges
- removing intersecting faces
- 000: 224 intersecting
- 001: 27 intersecting
- 002: 11 intersecting
- 003: 7 intersecting
- 004: 2 intersecting
- mris_euler_number ../surf/lh.orig
- euler # = v-e+f = 2g-2: 160479 - 481431 + 320954 = 2 --> 0 holes
- F =2V-4: 320954 = 320958-4 (0)
- 2E=3F: 962862 = 962862 (0)
- total defect index = 0
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts
- mris_remove_intersection ../surf/lh.orig ../surf/lh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 48 intersecting
- 001: 35 intersecting
- 002: 11 intersecting
- 003: 8 intersecting
- 004: 7 intersecting
- 005: 2 intersecting
- writing corrected surface to ../surf/lh.orig
- rm ../surf/lh.inflated
- #--------------------------------------------
- #@# Make White Surf lh Thu Aug 8 17:57:56 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts
- mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub016 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/sub016/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz...
- 22234 bright wm thresholded.
- 384 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.orig...
- computing class statistics...
- border white: 298969 voxels (1.78%)
- border gray 333863 voxels (1.99%)
- WM (93.0): 93.9 +- 9.8 [70.0 --> 110.0]
- GM (77.0) : 75.0 +- 12.6 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 49.4 (was 70)
- setting MAX_BORDER_WHITE to 115.8 (was 105)
- setting MIN_BORDER_WHITE to 62.0 (was 85)
- setting MAX_CSF to 36.9 (was 40)
- setting MAX_GRAY to 96.2 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 55.7 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 24.3 (was 40)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.82 +- 0.22 (0.05-->3.95) (max @ vno 159822 --> 160009)
- face area 0.28 +- 0.12 (0.00-->5.04)
- mean absolute distance = 0.65 +- 0.78
- 4287 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 = 93.8, mean outside = 70.2
- smoothing surface for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 3 vertex label from ripped group
- mean border=74.3, 64 (64) missing vertices, mean dist 0.4 [0.5 (%30.4)->0.7 (%69.6))]
- %68 local maxima, %27 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 +- 0.26 (0.07-->5.11) (max @ vno 160099 --> 160100)
- face area 0.28 +- 0.13 (0.00-->4.98)
- mean absolute distance = 0.35 +- 0.49
- 4695 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=7818525.5, rms=12.80
- 001: dt: 0.5000, sse=7902479.5, rms=9.064 (0.000%)
- 002: dt: 0.5000, sse=8193120.5, rms=6.997 (0.000%)
- 003: dt: 0.5000, sse=8398064.0, rms=5.733 (0.000%)
- 004: dt: 0.5000, sse=8678498.0, rms=4.997 (0.000%)
- 005: dt: 0.5000, sse=8757485.0, rms=4.599 (0.000%)
- 006: dt: 0.5000, sse=8878632.0, rms=4.381 (0.000%)
- 007: dt: 0.5000, sse=8860942.0, rms=4.270 (0.000%)
- 008: dt: 0.5000, sse=8900009.0, rms=4.192 (0.000%)
- rms = 4.15, time step reduction 1 of 3 to 0.250...
- 009: dt: 0.5000, sse=8836779.0, rms=4.152 (0.000%)
- 010: dt: 0.2500, sse=5476378.0, rms=2.827 (0.000%)
- 011: dt: 0.2500, sse=5013794.5, rms=2.398 (0.000%)
- 012: dt: 0.2500, sse=4718828.5, rms=2.294 (0.000%)
- 013: dt: 0.2500, sse=4647839.5, rms=2.209 (0.000%)
- rms = 2.18, time step reduction 2 of 3 to 0.125...
- 014: dt: 0.2500, sse=4549292.0, rms=2.177 (0.000%)
- 015: dt: 0.1250, sse=4309767.5, rms=1.938 (0.000%)
- rms = 1.90, time step reduction 3 of 3 to 0.062...
- 016: dt: 0.1250, sse=4266609.5, rms=1.905 (0.000%)
- positioning took 2.3 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 3 vertex label from ripped group
- mean border=79.4, 72 (44) missing vertices, mean dist -0.3 [0.4 (%81.0)->0.2 (%19.0))]
- %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 +- 0.25 (0.11-->4.72) (max @ vno 160104 --> 70416)
- face area 0.35 +- 0.16 (0.00-->6.21)
- mean absolute distance = 0.22 +- 0.31
- 4347 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5623246.0, rms=6.60
- 017: dt: 0.5000, sse=5578929.0, rms=4.370 (0.000%)
- rms = 4.49, time step reduction 1 of 3 to 0.250...
- 018: dt: 0.2500, sse=5083324.0, rms=3.327 (0.000%)
- 019: dt: 0.2500, sse=4849302.0, rms=2.589 (0.000%)
- 020: dt: 0.2500, sse=4754413.0, rms=2.103 (0.000%)
- 021: dt: 0.2500, sse=4719963.5, rms=1.946 (0.000%)
- 022: dt: 0.2500, sse=4634218.5, rms=1.791 (0.000%)
- rms = 1.75, time step reduction 2 of 3 to 0.125...
- 023: dt: 0.2500, sse=4638862.0, rms=1.752 (0.000%)
- 024: dt: 0.1250, sse=4476490.5, rms=1.555 (0.000%)
- rms = 1.53, time step reduction 3 of 3 to 0.062...
- 025: dt: 0.1250, sse=4435944.5, rms=1.528 (0.000%)
- positioning took 1.4 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 3 vertex label from ripped group
- mean border=82.6, 61 (33) missing vertices, mean dist -0.1 [0.2 (%76.4)->0.2 (%23.6))]
- %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 +- 0.25 (0.10-->4.81) (max @ vno 160104 --> 70416)
- face area 0.33 +- 0.16 (0.00-->5.67)
- mean absolute distance = 0.16 +- 0.26
- 2934 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4852385.5, rms=4.12
- 026: dt: 0.5000, sse=5274197.5, rms=3.988 (0.000%)
- rms = 4.18, time step reduction 1 of 3 to 0.250...
- 027: dt: 0.2500, sse=4756714.5, rms=2.523 (0.000%)
- 028: dt: 0.2500, sse=4627541.0, rms=1.989 (0.000%)
- 029: dt: 0.2500, sse=4676251.0, rms=1.663 (0.000%)
- rms = 1.68, time step reduction 2 of 3 to 0.125...
- 030: dt: 0.1250, sse=4608184.5, rms=1.537 (0.000%)
- 031: dt: 0.1250, sse=4516804.0, rms=1.356 (0.000%)
- rms = 1.34, time step reduction 3 of 3 to 0.062...
- 032: dt: 0.1250, sse=4478627.0, rms=1.335 (0.000%)
- positioning took 1.2 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 3 vertex label from ripped group
- mean border=83.5, 64 (27) missing vertices, mean dist -0.0 [0.2 (%57.9)->0.2 (%42.1))]
- %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/sub016/surf/lh.white...
- writing smoothed curvature to lh.curv
- 000: dt: 0.0000, sse=4507100.0, rms=1.72
- rms = 2.50, time step reduction 1 of 3 to 0.250...
- 033: dt: 0.2500, sse=4605772.0, rms=1.156 (0.000%)
- 034: dt: 0.2500, sse=4770604.0, rms=1.004 (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...
- 035: dt: 0.1250, sse=4772717.5, rms=0.995 (0.000%)
- positioning took 0.6 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- generating cortex label...
- 22 non-cortical segments detected
- only using segment with 2520 vertices
- erasing segment 1 (vno[0] = 73170)
- erasing segment 2 (vno[0] = 94623)
- erasing segment 3 (vno[0] = 99325)
- erasing segment 4 (vno[0] = 107577)
- erasing segment 5 (vno[0] = 110708)
- erasing segment 6 (vno[0] = 110734)
- erasing segment 7 (vno[0] = 112785)
- erasing segment 8 (vno[0] = 112886)
- erasing segment 9 (vno[0] = 114058)
- erasing segment 10 (vno[0] = 114341)
- erasing segment 11 (vno[0] = 115359)
- erasing segment 12 (vno[0] = 115383)
- erasing segment 13 (vno[0] = 116597)
- erasing segment 14 (vno[0] = 117688)
- erasing segment 15 (vno[0] = 117768)
- erasing segment 16 (vno[0] = 121659)
- erasing segment 17 (vno[0] = 122561)
- erasing segment 18 (vno[0] = 122612)
- erasing segment 19 (vno[0] = 124558)
- erasing segment 20 (vno[0] = 126720)
- erasing segment 21 (vno[0] = 128787)
- writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/label/lh.cortex.label...
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.curv
- writing smoothed area to lh.area
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.area
- vertex spacing 0.89 +- 0.25 (0.03-->4.83) (max @ vno 160104 --> 70416)
- face area 0.33 +- 0.16 (0.00-->5.70)
- refinement took 8.0 minutes
- #--------------------------------------------
- #@# Smooth2 lh Thu Aug 8 18:05:54 CEST 2013
- mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 18:05:59 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts
- mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated
- avg radius = 49.3 mm, total surface area = 97677 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=0.078 (target=0.015)
step 010: RMS=0.056 (target=0.015)
step 015: RMS=0.046 (target=0.015)
step 020: RMS=0.038 (target=0.015)
step 025: RMS=0.032 (target=0.015)
step 030: RMS=0.026 (target=0.015)
step 035: RMS=0.022 (target=0.015)
step 040: RMS=0.019 (target=0.015)
step 045: RMS=0.017 (target=0.015)
step 050: RMS=0.015 (target=0.015)
- inflation complete.
- inflation took 0.6 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
- 209 vertices thresholded to be in k1 ~ [-0.24 0.56], k2 ~ [-0.12 0.09]
- total integrated curvature = 0.392*4pi (4.931) --> 1 handles
- ICI = 1.8, FI = 13.8, variation=228.351
- 163 vertices thresholded to be in [-0.02 0.02]
- writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level
- curvature mean = 0.000, std = 0.001
- 155 vertices thresholded to be in [-0.13 0.23]
- done.
- writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.015, std = 0.025
- done.
- #-----------------------------------------
- #@# Curvature Stats lh Thu Aug 8 18:08:39 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub016 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 [ sub016/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 [ 306 ]
- Gb_filter = 0
- WARN: S lookup min: -0.080822
- WARN: S explicit min: 0.000000 vertex = 1040
- #--------------------------------------------
- #@# Sphere lh Thu Aug 8 18:08:44 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 0.273...
- MRISunfold() max_passes = 1 -------
- tol=5.0e-01, sigma=0.0, host=snake, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
- using quadratic fit line minimization
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 1.000000
- desired_rms_height -1.000000
- momentum 0.900000
- nbhd_size 7
- max_nbrs 8
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 1234
- --------------------
- mrisRemoveNegativeArea()
- pass 1: epoch 1 of 3 starting distance error %20.27
- pass 1: epoch 2 of 3 starting distance error %20.21
- unfolding complete - removing small folds...
- starting distance error %20.11
- removing remaining folds...
- final distance error %20.12
- MRISunfold() return, current seed 1234
- writing spherical brain to ../surf/lh.sphere
- spherical transformation took 1.24 hours
- #--------------------------------------------
- #@# Surf Reg lh Thu Aug 8 19:23:03 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 = 0.579
- curvature mean = 0.019, std = 0.933
- curvature mean = 0.026, std = 0.836
- Starting MRISrigidBodyAlignGlobal()
- d=32.00 min @ (0.00, -8.00, 0.00) sse = 346322.2, tmin=2.6324
- d=16.00 min @ (4.00, 0.00, 0.00) sse = 340851.3, tmin=4.0946
- d=8.00 min @ (-2.00, 0.00, 0.00) sse = 336519.5, tmin=5.5732
- d=4.00 min @ (0.00, 0.00, -1.00) sse = 335921.1, tmin=7.0874
- d=1.00 min @ (0.25, 0.00, 0.00) sse = 335842.9, tmin=10.1403
- d=0.50 min @ (0.00, 0.12, 0.00) sse = 335828.7, tmin=11.6717
- tol=1.0e+00, sigma=0.5, host=snake, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
- using quadratic fit line minimization
- MRISrigidBodyAlignGlobal() done 11.67 min
- curvature mean = 0.009, std = 0.939
- curvature mean = 0.012, std = 0.923
- curvature mean = 0.007, std = 0.950
- curvature mean = 0.006, std = 0.963
- curvature mean = 0.005, std = 0.950
- curvature mean = 0.002, std = 0.983
- 2 Reading smoothwm
- curvature mean = -0.024, std = 0.291
- curvature mean = 0.003, std = 0.066
- curvature mean = 0.072, std = 0.316
- curvature mean = 0.004, std = 0.078
- curvature mean = 0.035, std = 0.506
- curvature mean = 0.005, std = 0.084
- curvature mean = 0.019, std = 0.650
- curvature mean = 0.005, std = 0.086
- curvature mean = 0.007, std = 0.765
- MRISregister() return, current seed 0
- writing registered surface to ../surf/lh.sphere.reg...
- expanding nbhd size to 1
- #--------------------------------------------
- #@# Jacobian white lh Thu Aug 8 20:00:55 CEST 2013
- mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white
- reading surface from ../surf/lh.white...
- writing curvature file ../surf/lh.jacobian_white
- #--------------------------------------------
- #@# AvgCurv lh Thu Aug 8 20:00:58 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts
- mrisp_paint -a 5 /opt/freesurfer/5.3.0/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv
- averaging curvature patterns 5 times...
- reading surface from ../surf/lh.sphere.reg...
- reading template parameterization from /opt/freesurfer/5.3.0/average/lh.average.curvature.filled.buckner40.tif...
- writing curvature file to ../surf/lh.avg_curv...
- #-----------------------------------------
- #@# Cortical Parc lh Thu Aug 8 20:01:00 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub016 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...
- 1573 labels changed using aseg
- relabeling using gibbs priors...
- 000: 3403 changed, 160479 examined...
- 001: 803 changed, 14657 examined...
- 002: 213 changed, 4459 examined...
- 003: 72 changed, 1275 examined...
- 004: 23 changed, 437 examined...
- 005: 10 changed, 132 examined...
- 006: 3 changed, 65 examined...
- 007: 2 changed, 23 examined...
- 008: 2 changed, 11 examined...
- 009: 2 changed, 11 examined...
- 010: 1 changed, 10 examined...
- 011: 0 changed, 7 examined...
- 262 labels changed using aseg
- 000: 164 total segments, 119 labels (468 vertices) changed
- 001: 45 total segments, 4 labels (12 vertices) changed
- 002: 41 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...
- 1861 vertices marked for relabeling...
- 1861 labels changed in reclassification.
- writing output to ../label/lh.aparc.annot...
- classification took 1 minutes and 10 seconds.
- #--------------------------------------------
- #@# Make Pial Surf lh Thu Aug 8 20:02:11 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts
- mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub016 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/sub016/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz...
- 22234 bright wm thresholded.
- 384 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.orig...
- computing class statistics...
- border white: 298969 voxels (1.78%)
- border gray 333863 voxels (1.99%)
- WM (93.0): 93.9 +- 9.8 [70.0 --> 110.0]
- GM (77.0) : 75.0 +- 12.6 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 49.4 (was 70)
- setting MAX_BORDER_WHITE to 115.8 (was 105)
- setting MIN_BORDER_WHITE to 62.0 (was 85)
- setting MAX_CSF to 36.9 (was 40)
- setting MAX_GRAY to 96.2 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 55.7 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 24.3 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=106, GM=62
- mean inside = 93.8, mean outside = 70.2
- 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/sub016/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.82 +- 0.22 (0.05-->3.95) (max @ vno 159822 --> 160009)
- face area 0.28 +- 0.12 (0.00-->5.04)
- mean absolute distance = 0.65 +- 0.79
- 4390 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 247 points - only 4.05% unknown
- removing 4 vertex label from ripped group
- deleting segment 1 with 4 points - only 0.00% unknown
- deleting segment 3 with 5 points - only 0.00% unknown
- deleting segment 5 with 6 points - only 0.00% unknown
- deleting segment 6 with 840 points - only 0.00% unknown
- deleting segment 7 with 7 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 11 with 37 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 12 with 2 points - only 0.00% unknown
- deleting segment 13 with 8 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 14 with 3 points - only 0.00% unknown
- deleting segment 15 with 5 points - only 0.00% unknown
- mean border=74.3, 66 (65) missing vertices, mean dist 0.4 [0.5 (%30.4)->0.7 (%69.6))]
- %69 local maxima, %27 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 +- 0.26 (0.07-->5.11) (max @ vno 160099 --> 160100)
- face area 0.28 +- 0.13 (0.00-->4.98)
- mean absolute distance = 0.35 +- 0.49
- 4775 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=7844055.5, rms=12.77
- 001: dt: 0.5000, sse=7941564.5, rms=9.040 (0.000%)
- 002: dt: 0.5000, sse=8239249.0, rms=6.981 (0.000%)
- 003: dt: 0.5000, sse=8449724.0, rms=5.724 (0.000%)
- 004: dt: 0.5000, sse=8730856.0, rms=4.991 (0.000%)
- 005: dt: 0.5000, sse=8813873.0, rms=4.595 (0.000%)
- 006: dt: 0.5000, sse=8934122.0, rms=4.376 (0.000%)
- 007: dt: 0.5000, sse=8914619.0, rms=4.266 (0.000%)
- 008: dt: 0.5000, sse=8955723.0, rms=4.187 (0.000%)
- rms = 4.15, time step reduction 1 of 3 to 0.250...
- 009: dt: 0.5000, sse=8894941.0, rms=4.146 (0.000%)
- 010: dt: 0.2500, sse=5502699.5, rms=2.823 (0.000%)
- 011: dt: 0.2500, sse=5038612.0, rms=2.394 (0.000%)
- 012: dt: 0.2500, sse=4741387.5, rms=2.291 (0.000%)
- 013: dt: 0.2500, sse=4670505.5, rms=2.207 (0.000%)
- rms = 2.17, time step reduction 2 of 3 to 0.125...
- 014: dt: 0.2500, sse=4573283.5, rms=2.175 (0.000%)
- 015: dt: 0.1250, sse=4333563.5, rms=1.938 (0.000%)
- rms = 1.91, time step reduction 3 of 3 to 0.062...
- 016: dt: 0.1250, sse=4290018.5, rms=1.905 (0.000%)
- positioning took 2.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 276 points - only 3.62% unknown
- deleting segment 1 with 5 points - only 0.00% unknown
- deleting segment 2 with 9 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 3 with 2 points - only 0.00% unknown
- deleting segment 7 with 766 points - only 0.00% unknown
- deleting segment 11 with 14 points - only 7.14% unknown
- deleting segment 14 with 8 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 16 with 3 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 17 with 4 points - only 0.00% unknown
- mean border=79.4, 70 (43) missing vertices, mean dist -0.3 [0.4 (%80.9)->0.2 (%19.1))]
- %84 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 +- 0.25 (0.11-->4.72) (max @ vno 160104 --> 70416)
- face area 0.35 +- 0.16 (0.00-->6.21)
- mean absolute distance = 0.22 +- 0.31
- 4410 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5655265.0, rms=6.59
- 017: dt: 0.5000, sse=5613595.5, rms=4.364 (0.000%)
- rms = 4.49, time step reduction 1 of 3 to 0.250...
- 018: dt: 0.2500, sse=5116181.5, rms=3.326 (0.000%)
- 019: dt: 0.2500, sse=4883240.5, rms=2.592 (0.000%)
- 020: dt: 0.2500, sse=4788981.5, rms=2.110 (0.000%)
- 021: dt: 0.2500, sse=4754010.0, rms=1.954 (0.000%)
- 022: dt: 0.2500, sse=4670228.5, rms=1.801 (0.000%)
- rms = 1.76, time step reduction 2 of 3 to 0.125...
- 023: dt: 0.2500, sse=4675198.5, rms=1.763 (0.000%)
- 024: dt: 0.1250, sse=4512359.5, rms=1.569 (0.000%)
- rms = 1.54, time step reduction 3 of 3 to 0.062...
- 025: dt: 0.1250, sse=4471475.0, rms=1.543 (0.000%)
- positioning took 1.4 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 264 points - only 3.79% unknown
- deleting segment 1 with 5 points - only 0.00% unknown
- deleting segment 2 with 9 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 3 with 2 points - only 0.00% unknown
- deleting segment 5 with 862 points - only 0.00% unknown
- deleting segment 6 with 11 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 7 with 2 points - only 0.00% unknown
- deleting segment 10 with 10 points - only 10.00% unknown
- deleting segment 11 with 8 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 12 with 3 points - only 0.00% unknown
- deleting segment 13 with 5 points - only 0.00% unknown
- mean border=82.6, 68 (34) missing vertices, mean dist -0.1 [0.2 (%76.3)->0.2 (%23.7))]
- %91 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 +- 0.25 (0.10-->4.81) (max @ vno 160104 --> 70416)
- face area 0.33 +- 0.16 (0.00-->5.67)
- mean absolute distance = 0.16 +- 0.25
- 2994 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4889192.0, rms=4.12
- 026: dt: 0.5000, sse=5312165.5, rms=3.986 (0.000%)
- rms = 4.18, time step reduction 1 of 3 to 0.250...
- 027: dt: 0.2500, sse=4792344.5, rms=2.529 (0.000%)
- 028: dt: 0.2500, sse=4666050.5, rms=2.000 (0.000%)
- 029: dt: 0.2500, sse=4714949.5, rms=1.677 (0.000%)
- rms = 1.70, time step reduction 2 of 3 to 0.125...
- 030: dt: 0.1250, sse=4647289.0, rms=1.554 (0.000%)
- 031: dt: 0.1250, sse=4557666.0, rms=1.376 (0.000%)
- rms = 1.36, time step reduction 3 of 3 to 0.062...
- 032: dt: 0.1250, sse=4520176.0, rms=1.356 (0.000%)
- positioning took 1.1 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 281 points - only 3.56% unknown
- deleting segment 1 with 5 points - only 0.00% unknown
- deleting segment 2 with 9 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 3 with 2 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 4 with 4 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 6 with 870 points - only 0.00% unknown
- deleting segment 7 with 10 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 8 with 2 points - only 0.00% unknown
- deleting segment 9 with 10 points - only 10.00% unknown
- deleting segment 10 with 8 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 5 points - only 0.00% unknown
- mean border=83.5, 76 (27) missing vertices, mean dist -0.0 [0.2 (%57.8)->0.2 (%42.2))]
- %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=4548075.5, rms=1.73
- rms = 2.49, time step reduction 1 of 3 to 0.250...
- 033: dt: 0.2500, sse=4649222.5, rms=1.169 (0.000%)
- 034: dt: 0.2500, sse=4818127.0, rms=1.016 (0.000%)
- rms = 1.02, time step reduction 2 of 3 to 0.125...
- rms = 1.01, time step reduction 3 of 3 to 0.062...
- 035: dt: 0.1250, sse=4820042.5, rms=1.007 (0.000%)
- positioning took 0.6 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 18 points - only 33.33% unknown
- smoothing surface for 5 iterations...
- mean border=51.7, 111 (111) missing vertices, mean dist 1.8 [0.2 (%0.0)->2.3 (%100.0))]
- %18 local maxima, %57 large gradients and %21 min vals, 1813 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=33252602.0, rms=31.32
- 001: dt: 0.5000, sse=23820164.0, rms=25.953 (0.000%)
- 002: dt: 0.5000, sse=17428042.0, rms=21.590 (0.000%)
- 003: dt: 0.5000, sse=13329135.0, rms=18.138 (0.000%)
- 004: dt: 0.5000, sse=10853808.0, rms=15.436 (0.000%)
- 005: dt: 0.5000, sse=9436409.0, rms=13.377 (0.000%)
- 006: dt: 0.5000, sse=8574854.0, rms=11.795 (0.000%)
- 007: dt: 0.5000, sse=8032852.0, rms=10.429 (0.000%)
- 008: dt: 0.5000, sse=7625669.5, rms=9.155 (0.000%)
- 009: dt: 0.5000, sse=7400627.5, rms=7.980 (0.000%)
- 010: dt: 0.5000, sse=7328718.5, rms=6.933 (0.000%)
- 011: dt: 0.5000, sse=7340751.0, rms=6.028 (0.000%)
- 012: dt: 0.5000, sse=7462176.0, rms=5.310 (0.000%)
- 013: dt: 0.5000, sse=7615104.5, rms=4.789 (0.000%)
- 014: dt: 0.5000, sse=7788750.5, rms=4.487 (0.000%)
- 015: dt: 0.5000, sse=7951089.5, rms=4.297 (0.000%)
- 016: dt: 0.5000, sse=8027350.0, rms=4.190 (0.000%)
- 017: dt: 0.5000, sse=8091952.0, rms=4.094 (0.000%)
- rms = 4.05, time step reduction 1 of 3 to 0.250...
- 018: dt: 0.5000, sse=8099899.0, rms=4.053 (0.000%)
- 019: dt: 0.2500, sse=5641960.0, rms=3.259 (0.000%)
- 020: dt: 0.2500, sse=5457684.5, rms=3.050 (0.000%)
- rms = 3.02, time step reduction 2 of 3 to 0.125...
- 021: dt: 0.2500, sse=5298820.0, rms=3.016 (0.000%)
- 022: dt: 0.1250, sse=5029088.0, rms=2.837 (0.000%)
- rms = 2.81, time step reduction 3 of 3 to 0.062...
- 023: dt: 0.1250, sse=5006962.5, rms=2.811 (0.000%)
- positioning took 3.3 minutes
- mean border=48.8, 993 (28) missing vertices, mean dist 0.2 [0.2 (%43.3)->0.5 (%56.7))]
- %37 local maxima, %41 large gradients and %18 min vals, 574 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=5916018.5, rms=5.31
- 024: dt: 0.5000, sse=6209243.5, rms=4.414 (0.000%)
- 025: dt: 0.5000, sse=7797205.5, rms=4.261 (0.000%)
- rms = 4.30, time step reduction 1 of 3 to 0.250...
- 026: dt: 0.2500, sse=6394776.5, rms=3.436 (0.000%)
- 027: dt: 0.2500, sse=5863477.5, rms=3.090 (0.000%)
- 028: dt: 0.2500, sse=5800961.0, rms=2.998 (0.000%)
- 029: dt: 0.2500, sse=5753294.5, rms=2.948 (0.000%)
- rms = 2.93, time step reduction 2 of 3 to 0.125...
- 030: dt: 0.2500, sse=5763284.0, rms=2.930 (0.000%)
- 031: dt: 0.1250, sse=5501244.5, rms=2.698 (0.000%)
- rms = 2.66, time step reduction 3 of 3 to 0.062...
- 032: dt: 0.1250, sse=5479329.0, rms=2.658 (0.000%)
- positioning took 1.4 minutes
- mean border=46.1, 1229 (21) missing vertices, mean dist 0.1 [0.2 (%34.9)->0.4 (%65.1))]
- %56 local maxima, %22 large gradients and %17 min vals, 621 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=5883961.0, rms=4.40
- 033: dt: 0.5000, sse=6194537.5, rms=4.201 (0.000%)
- rms = 4.17, time step reduction 1 of 3 to 0.250...
- 034: dt: 0.5000, sse=8006900.0, rms=4.171 (0.000%)
- 035: dt: 0.2500, sse=6001242.5, rms=3.119 (0.000%)
- 036: dt: 0.2500, sse=6192814.5, rms=2.792 (0.000%)
- rms = 2.81, time step reduction 2 of 3 to 0.125...
- 037: dt: 0.1250, sse=6027948.5, rms=2.661 (0.000%)
- 038: dt: 0.1250, sse=5747886.5, rms=2.474 (0.000%)
- rms = 2.44, time step reduction 3 of 3 to 0.062...
- 039: dt: 0.1250, sse=5683501.0, rms=2.439 (0.000%)
- positioning took 1.2 minutes
- mean border=44.9, 2472 (16) missing vertices, mean dist 0.0 [0.2 (%43.8)->0.2 (%56.2))]
- %58 local maxima, %20 large gradients and %17 min vals, 447 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/sub016/surf/lh.pial...
- writing smoothed curvature to lh.curv.pial
- 000: dt: 0.0000, sse=5745762.5, rms=2.86
- rms = 3.79, time step reduction 1 of 3 to 0.250...
- 040: dt: 0.2500, sse=5579690.0, rms=2.540 (0.000%)
- 041: dt: 0.2500, sse=5757399.5, rms=2.466 (0.000%)
- rms = 2.48, time step reduction 2 of 3 to 0.125...
- rms = 2.42, time step reduction 3 of 3 to 0.062...
- 042: dt: 0.1250, sse=5697529.5, rms=2.425 (0.000%)
- positioning took 0.7 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.curv.pial
- writing smoothed area to lh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.area.pial
- vertex spacing 1.01 +- 0.43 (0.05-->7.37) (max @ vno 109705 --> 108677)
- face area 0.41 +- 0.31 (0.00-->7.60)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 160479 vertices processed
- 25000 of 160479 vertices processed
- 50000 of 160479 vertices processed
- 75000 of 160479 vertices processed
- 100000 of 160479 vertices processed
- 125000 of 160479 vertices processed
- 150000 of 160479 vertices processed
- 0 of 160479 vertices processed
- 25000 of 160479 vertices processed
- 50000 of 160479 vertices processed
- 75000 of 160479 vertices processed
- 100000 of 160479 vertices processed
- 125000 of 160479 vertices processed
- 150000 of 160479 vertices processed
- thickness calculation complete, 283:849 truncations.
- 38541 vertices at 0 distance
- 110303 vertices at 1 distance
- 101984 vertices at 2 distance
- 41552 vertices at 3 distance
- 11775 vertices at 4 distance
- 3027 vertices at 5 distance
- 822 vertices at 6 distance
- 267 vertices at 7 distance
- 118 vertices at 8 distance
- 49 vertices at 9 distance
- 29 vertices at 10 distance
- 21 vertices at 11 distance
- 18 vertices at 12 distance
- 14 vertices at 13 distance
- 14 vertices at 14 distance
- 13 vertices at 15 distance
- 17 vertices at 16 distance
- 10 vertices at 17 distance
- 8 vertices at 18 distance
- 7 vertices at 19 distance
- 15 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.thickness
- positioning took 16.2 minutes
- #--------------------------------------------
- #@# Surf Volume lh Thu Aug 8 20:18:20 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 20:18:21 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts
- pctsurfcon --s sub016 --lh-only
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts/pctsurfcon.log
- Thu Aug 8 20:18:21 CEST 2013
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/tmp.pctsurfcon.9267/lh.wm.mgh --regheader sub016 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/label/lh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 = 124623
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/label/lh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/tmp.pctsurfcon.9267/lh.wm.mgh
- Dim: 160479 1 1
- mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/tmp.pctsurfcon.9267/lh.gm.mgh --projfrac 0.3 --regheader sub016 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/label/lh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.white
- Done reading source surface
- Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 = 142718
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/label/lh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/tmp.pctsurfcon.9267/lh.gm.mgh
- Dim: 160479 1 1
- mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/tmp.pctsurfcon.9267/lh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/tmp.pctsurfcon.9267/lh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/surf/lh.w-g.pct.mgh
- mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.w-g.pct.mgh --annot sub016 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/surf/lh.w-g.pct.mgh --annot sub016 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/surf/lh.w-g.pct.mgh
- Vertex Area is 0.660622 mm^3
- Generating list of segmentation ids
- Found 36 segmentations
- Computing statistics for each segmentation
- 0 1000 unknown 0 0.000
- 1 1001 bankssts 1512 1056.612
- 2 1002 caudalanteriorcingulate 1250 846.357
- 3 1003 caudalmiddlefrontal 3443 2308.520
- 4 1004 corpuscallosum 0 0.000
- 5 1005 cuneus 2906 1843.261
- 6 1006 entorhinal 750 510.895
- 7 1007 fusiform 5411 3674.410
- 8 1008 inferiorparietal 8099 5476.500
- 9 1009 inferiortemporal 7888 5305.233
- 10 1010 isthmuscingulate 2079 1352.020
- 11 1011 lateraloccipital 8202 5319.603
- 12 1012 lateralorbitofrontal 4837 3217.664
- 13 1013 lingual 5239 3490.395
- 14 1014 medialorbitofrontal 3096 2007.213
- 15 1015 middletemporal 5955 4078.508
- 16 1016 parahippocampal 1473 959.961
- 17 1017 paracentral 2087 1225.595
- 18 1018 parsopercularis 3193 2112.798
- 19 1019 parsorbitalis 1216 781.607
- 20 1020 parstriangularis 2274 1526.439
- 21 1021 pericalcarine 2660 1943.400
- 22 1022 postcentral 7142 4493.574
- 23 1023 posteriorcingulate 2413 1614.474
- 24 1024 precentral 8460 5267.162
- 25 1025 precuneus 7244 4771.850
- 26 1026 rostralanteriorcingulate 1630 1076.536
- 27 1027 rostralmiddlefrontal 8850 6006.854
- 28 1028 superiorfrontal 12261 8237.140
- 29 1029 superiorparietal 10142 6578.766
- 30 1030 superiortemporal 6058 4059.571
- 31 1031 supramarginal 7259 4838.904
- 32 1032 frontalpole 293 200.763
- 33 1033 temporalpole 701 477.017
- 34 1034 transversetemporal 1015 612.610
- 35 1035 insula 4037 2649.110
- Reporting on 34 segmentations
- mri_segstats done
- Cleaning up
- #-----------------------------------------
- #@# Parcellation Stats lh Thu Aug 8 20:18:36 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 sub016 lh white
- computing statistics for each annotation in ../label/lh.aparc.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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
- 1512 1057 2788 2.484 0.577 0.109 0.030 16 1.9 bankssts
- 1250 846 2519 2.694 0.558 0.132 0.039 20 1.9 caudalanteriorcingulate
- 3443 2309 6884 2.643 0.506 0.124 0.038 42 5.3 caudalmiddlefrontal
- 2906 1843 4888 2.270 0.557 0.151 0.065 56 8.1 cuneus
- 750 511 1990 3.183 0.555 0.141 0.049 10 1.5 entorhinal
- 5411 3674 11873 2.829 0.552 0.145 0.064 104 12.7 fusiform
- 8099 5476 15082 2.452 0.454 0.136 0.048 147 15.8 inferiorparietal
- 7888 5305 17636 2.745 0.662 0.143 0.064 184 19.7 inferiortemporal
- 2079 1352 3419 2.358 0.806 0.147 0.068 58 5.9 isthmuscingulate
- 8202 5320 13729 2.285 0.508 0.154 0.062 165 20.3 lateraloccipital
- 4837 3218 9518 2.570 0.607 0.154 0.072 98 12.5 lateralorbitofrontal
- 5239 3490 8311 2.164 0.560 0.154 0.077 104 17.9 lingual
- 3096 2007 5386 2.231 0.752 0.164 0.091 112 10.3 medialorbitofrontal
- 5955 4078 14688 2.876 0.629 0.146 0.053 113 12.2 middletemporal
- 1473 960 3480 3.050 0.644 0.161 0.204 54 6.4 parahippocampal
- 2087 1226 3632 2.649 0.600 0.113 0.183 52 4.7 paracentral
- 3193 2113 6704 2.788 0.481 0.127 0.040 46 5.5 parsopercularis
- 1216 782 2883 2.875 0.687 0.148 0.053 24 2.5 parsorbitalis
- 2274 1526 4452 2.475 0.542 0.138 0.046 38 4.1 parstriangularis
- 2660 1943 3720 2.004 0.464 0.156 0.059 48 6.9 pericalcarine
- 7142 4494 11708 2.289 0.613 0.130 0.054 188 17.9 postcentral
- 2413 1614 4505 2.550 0.656 0.135 0.048 39 4.1 posteriorcingulate
- 8460 5267 16227 2.749 0.553 0.113 0.040 178 13.8 precentral
- 7244 4772 13273 2.573 0.506 0.139 0.050 113 14.9 precuneus
- 1630 1077 3658 2.643 0.838 0.156 0.058 30 3.8 rostralanteriorcingulate
- 8850 6007 16555 2.345 0.560 0.145 0.052 167 19.0 rostralmiddlefrontal
- 12261 8237 26422 2.723 0.604 0.130 0.040 150 20.3 superiorfrontal
- 10142 6579 17306 2.358 0.445 0.130 0.043 162 17.5 superiorparietal
- 6058 4060 14107 3.042 0.686 0.122 0.041 78 9.4 superiortemporal
- 7259 4839 14989 2.719 0.528 0.141 0.049 160 14.3 supramarginal
- 293 201 790 2.634 0.541 0.237 0.128 14 1.1 frontalpole
- 701 477 2545 3.779 0.688 0.160 0.063 13 1.9 temporalpole
- 1015 613 2006 2.729 0.354 0.150 0.130 37 6.9 transversetemporal
- 4037 2649 8630 3.118 0.753 0.118 0.076 80 11.0 insula
- #-----------------------------------------
- #@# Cortical Parc 2 lh Thu Aug 8 20:18:59 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub016 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...
- 27 labels changed using aseg
- relabeling using gibbs priors...
- 000: 11050 changed, 160479 examined...
- 001: 2709 changed, 41932 examined...
- 002: 839 changed, 13821 examined...
- 003: 359 changed, 4563 examined...
- 004: 198 changed, 1995 examined...
- 005: 85 changed, 1065 examined...
- 006: 45 changed, 501 examined...
- 007: 25 changed, 248 examined...
- 008: 15 changed, 139 examined...
- 009: 9 changed, 82 examined...
- 010: 4 changed, 50 examined...
- 011: 2 changed, 24 examined...
- 012: 0 changed, 12 examined...
- 1 labels changed using aseg
- 000: 326 total segments, 243 labels (2925 vertices) changed
- 001: 104 total segments, 22 labels (106 vertices) changed
- 002: 82 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 128 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 1047 vertices marked for relabeling...
- 1047 labels changed in reclassification.
- writing output to ../label/lh.aparc.a2009s.annot...
- classification took 1 minutes and 22 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 2 lh Thu Aug 8 20:20:20 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 sub016 lh white
- computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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
- 1398 965 2614 2.232 0.588 0.153 0.052 29 3.1 G_and_S_frontomargin
- 1188 747 1903 2.183 0.403 0.122 0.054 29 2.3 G_and_S_occipital_inf
- 1708 930 2996 2.566 0.594 0.121 0.058 57 4.0 G_and_S_paracentral
- 2065 1309 4502 2.929 0.542 0.147 0.052 37 4.4 G_and_S_subcentral
- 613 424 1429 2.417 0.542 0.185 0.096 23 2.0 G_and_S_transv_frontopol
- 3293 2209 6728 2.546 0.738 0.145 0.053 53 6.4 G_and_S_cingul-Ant
- 1399 982 2690 2.599 0.569 0.116 0.040 15 2.0 G_and_S_cingul-Mid-Ant
- 1557 1044 2801 2.580 0.491 0.108 0.033 13 2.2 G_and_S_cingul-Mid-Post
- 969 616 2176 3.017 0.624 0.162 0.068 22 2.2 G_cingul-Post-dorsal
- 459 275 659 2.140 0.767 0.148 0.074 8 1.3 G_cingul-Post-ventral
- 2693 1742 4781 2.164 0.562 0.165 0.073 62 8.6 G_cuneus
- 1741 1119 4314 2.985 0.434 0.143 0.053 35 4.0 G_front_inf-Opercular
- 318 193 833 3.056 0.457 0.161 0.065 8 0.8 G_front_inf-Orbital
- 1238 845 2870 2.667 0.472 0.161 0.056 30 2.8 G_front_inf-Triangul
- 4770 3234 11350 2.683 0.510 0.160 0.062 112 11.8 G_front_middle
- 8303 5409 19745 2.878 0.584 0.137 0.078 152 15.8 G_front_sup
- 585 383 1443 3.214 0.499 0.125 0.062 8 1.2 G_Ins_lg_and_S_cent_ins
- 936 587 3021 3.869 0.650 0.145 0.167 51 5.2 G_insular_short
- 2895 1870 6213 2.594 0.475 0.174 0.088 99 9.8 G_occipital_middle
- 1937 1278 3192 2.268 0.428 0.150 0.054 54 4.4 G_occipital_sup
- 1579 1020 4156 3.069 0.447 0.159 0.065 40 3.8 G_oc-temp_lat-fusifor
- 3433 2248 5849 2.169 0.597 0.175 0.100 92 15.6 G_oc-temp_med-Lingual
- 1862 1244 5210 3.285 0.548 0.165 0.180 61 7.5 G_oc-temp_med-Parahip
- 3134 2051 7575 2.779 0.609 0.172 0.094 92 10.2 G_orbital
- 2868 1900 6701 2.675 0.474 0.158 0.063 80 7.5 G_pariet_inf-Angular
- 3884 2581 9527 2.905 0.493 0.153 0.051 80 7.8 G_pariet_inf-Supramar
- 4289 2725 8589 2.487 0.475 0.137 0.048 76 7.9 G_parietal_sup
- 2584 1530 4729 2.368 0.475 0.139 0.077 133 10.3 G_postcentral
- 3137 1796 7414 3.066 0.425 0.117 0.050 102 6.0 G_precentral
- 3240 2129 7232 2.764 0.505 0.158 0.060 69 7.8 G_precuneus
- 1054 665 2367 2.432 0.724 0.185 0.106 41 4.6 G_rectus
- 528 336 942 2.619 0.925 0.201 0.167 42 2.7 G_subcallosal
- 806 476 1868 2.876 0.428 0.157 0.150 36 6.5 G_temp_sup-G_T_transv
- 2099 1376 6291 3.287 0.569 0.144 0.047 44 4.1 G_temp_sup-Lateral
- 797 546 2450 3.766 0.713 0.126 0.056 9 1.8 G_temp_sup-Plan_polar
- 1421 954 3002 2.826 0.481 0.111 0.036 14 2.0 G_temp_sup-Plan_tempo
- 4735 3150 12232 2.902 0.696 0.168 0.085 161 15.4 G_temporal_inf
- 4179 2835 11296 2.979 0.610 0.150 0.057 89 8.9 G_temporal_middle
- 601 392 970 2.301 0.556 0.122 0.037 6 0.9 Lat_Fis-ant-Horizont
- 405 278 716 2.510 0.515 0.108 0.027 3 0.5 Lat_Fis-ant-Vertical
- 1616 1063 2328 2.569 0.489 0.119 0.037 13 2.4 Lat_Fis-post
- 2348 1502 3846 2.180 0.536 0.168 0.075 51 7.6 Pole_occipital
- 2019 1388 5883 3.157 0.733 0.173 0.090 48 6.8 Pole_temporal
- 3836 2660 5170 2.087 0.521 0.135 0.049 53 8.1 S_calcarine
- 3491 2319 4297 2.050 0.529 0.113 0.030 25 4.6 S_central
- 1249 834 1902 2.301 0.389 0.108 0.028 11 1.4 S_cingul-Marginalis
- 635 424 1051 2.606 0.552 0.112 0.042 5 0.9 S_circular_insula_ant
- 1843 1225 3131 2.905 0.720 0.094 0.023 8 1.9 S_circular_insula_inf
- 2052 1380 3127 2.685 0.520 0.101 0.030 12 2.4 S_circular_insula_sup
- 1820 1250 3121 2.680 0.526 0.106 0.028 12 2.2 S_collat_transv_ant
- 372 259 470 2.203 0.330 0.125 0.030 3 0.5 S_collat_transv_post
- 2485 1659 3858 2.268 0.461 0.116 0.031 23 3.3 S_front_inf
- 1660 1114 2382 2.089 0.458 0.127 0.045 20 3.1 S_front_middle
- 3117 2120 5236 2.484 0.505 0.110 0.031 25 4.2 S_front_sup
- 270 183 415 2.394 0.436 0.148 0.056 3 0.8 S_interm_prim-Jensen
- 3972 2642 5744 2.295 0.389 0.114 0.032 34 5.3 S_intrapariet_and_P_trans
- 1315 888 1703 1.936 0.351 0.123 0.033 14 1.7 S_oc_middle_and_Lunatus
- 1148 802 1778 2.314 0.363 0.148 0.045 15 2.1 S_oc_sup_and_transversal
- 1147 777 1667 2.349 0.413 0.140 0.040 13 2.0 S_occipital_ant
- 1621 1128 2813 2.551 0.379 0.103 0.024 10 1.7 S_oc-temp_lat
- 2180 1493 3796 2.606 0.538 0.138 0.053 27 4.5 S_oc-temp_med_and_Lingual
- 500 338 636 2.086 0.492 0.101 0.024 2 0.6 S_orbital_lateral
- 783 545 1203 2.192 0.724 0.126 0.040 7 1.4 S_orbital_med-olfact
- 1897 1253 3345 2.495 0.628 0.147 0.056 31 4.5 S_orbital-H_Shaped
- 2790 1859 4345 2.493 0.510 0.124 0.040 28 4.6 S_parieto_occipital
- 1802 1186 2164 2.040 0.678 0.140 0.057 59 4.5 S_pericallosal
- 3177 2122 4456 2.276 0.407 0.119 0.037 62 4.5 S_postcentral
- 1723 1173 2589 2.390 0.429 0.106 0.026 11 2.0 S_precentral-inf-part
- 1504 1062 2365 2.535 0.502 0.096 0.023 6 1.5 S_precentral-sup-part
- 573 397 822 1.895 0.805 0.160 0.053 11 1.4 S_suborbital
- 1235 833 2058 2.471 0.397 0.133 0.044 16 2.3 S_subparietal
- 1969 1385 3100 2.384 0.510 0.111 0.027 13 2.4 S_temporal_inf
- 5778 3972 9464 2.394 0.469 0.113 0.034 64 7.8 S_temporal_sup
- 448 298 661 2.708 0.332 0.114 0.031 3 0.6 S_temporal_transverse
- #-----------------------------------------
- #@# Cortical Parc 3 lh Thu Aug 8 20:20:46 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub016 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...
- 1036 labels changed using aseg
- relabeling using gibbs priors...
- 000: 3290 changed, 160479 examined...
- 001: 797 changed, 13782 examined...
- 002: 203 changed, 4294 examined...
- 003: 71 changed, 1206 examined...
- 004: 42 changed, 397 examined...
- 005: 17 changed, 242 examined...
- 006: 9 changed, 105 examined...
- 007: 6 changed, 52 examined...
- 008: 3 changed, 34 examined...
- 009: 4 changed, 17 examined...
- 010: 1 changed, 15 examined...
- 011: 0 changed, 7 examined...
- 76 labels changed using aseg
- 000: 76 total segments, 43 labels (249 vertices) changed
- 001: 35 total segments, 2 labels (3 vertices) changed
- 002: 33 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 60 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 969 vertices marked for relabeling...
- 969 labels changed in reclassification.
- writing output to ../label/lh.aparc.DKTatlas40.annot...
- classification took 1 minutes and 12 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 3 lh Thu Aug 8 20:21:58 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 sub016 lh white
- computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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
- 1893 1283 3926 2.752 0.604 0.132 0.040 27 2.9 caudalanteriorcingulate
- 3593 2400 7209 2.654 0.505 0.125 0.039 46 5.6 caudalmiddlefrontal
- 4013 2602 6428 2.246 0.530 0.146 0.058 69 10.0 cuneus
- 735 502 1959 3.204 0.559 0.135 0.043 8 1.3 entorhinal
- 4879 3297 10290 2.812 0.529 0.142 0.058 91 10.7 fusiform
- 7514 5088 13954 2.440 0.456 0.139 0.049 141 15.0 inferiorparietal
- 7834 5269 17861 2.771 0.671 0.144 0.065 181 19.7 inferiortemporal
- 2094 1351 3494 2.388 0.796 0.150 0.070 61 6.3 isthmuscingulate
- 8527 5521 14461 2.289 0.509 0.155 0.063 194 21.8 lateraloccipital
- 5148 3450 10650 2.605 0.623 0.165 0.094 131 17.8 lateralorbitofrontal
- 5174 3449 8220 2.165 0.560 0.154 0.077 102 17.8 lingual
- 2650 1728 4923 2.253 0.765 0.166 0.090 89 8.4 medialorbitofrontal
- 8067 5546 18703 2.774 0.632 0.144 0.052 148 16.7 middletemporal
- 1449 947 3427 3.051 0.641 0.161 0.206 54 6.4 parahippocampal
- 2469 1480 4347 2.661 0.575 0.111 0.159 55 5.2 paracentral
- 2851 1869 6007 2.818 0.479 0.126 0.041 41 5.0 parsopercularis
- 1239 795 2574 2.679 0.729 0.130 0.040 16 2.0 parsorbitalis
- 2842 1915 5509 2.464 0.537 0.140 0.045 50 5.3 parstriangularis
- 2666 1939 3741 2.016 0.474 0.155 0.059 47 6.9 pericalcarine
- 7942 5036 12997 2.297 0.607 0.129 0.051 194 18.6 postcentral
- 2570 1728 4662 2.520 0.661 0.132 0.046 39 4.2 posteriorcingulate
- 8474 5275 16160 2.748 0.551 0.114 0.041 178 13.9 precentral
- 6877 4527 12820 2.568 0.515 0.138 0.050 108 13.9 precuneus
- 2140 1408 4323 2.557 0.819 0.158 0.071 58 5.8 rostralanteriorcingulate
- 6215 4195 12007 2.418 0.597 0.142 0.049 106 12.6 rostralmiddlefrontal
- 13430 9036 28222 2.631 0.617 0.134 0.043 190 23.9 superiorfrontal
- 8234 5309 14237 2.393 0.433 0.129 0.042 118 13.7 superiorparietal
- 8005 5378 18976 3.041 0.720 0.123 0.043 104 13.3 superiortemporal
- 7050 4696 14499 2.709 0.539 0.142 0.049 157 13.9 supramarginal
- 1007 606 1995 2.729 0.354 0.150 0.131 37 6.9 transversetemporal
- 3494 2295 7719 3.170 0.723 0.109 0.052 62 6.3 insula
- #--------------------------------------------
- #@# Tessellate rh Thu Aug 8 20:22:22 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts
- mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz
- Iteration Number : 1
- pass 1 (xy+): 1 found - 1 modified | TOTAL: 1
- pass 2 (xy+): 0 found - 1 modified | TOTAL: 1
- pass 1 (xy-): 1 found - 1 modified | TOTAL: 2
- pass 2 (xy-): 0 found - 1 modified | TOTAL: 2
- pass 1 (yz+): 4 found - 4 modified | TOTAL: 6
- pass 2 (yz+): 0 found - 4 modified | TOTAL: 6
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 6
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 6
- pass 1 (xz-): 3 found - 3 modified | TOTAL: 9
- pass 2 (xz-): 0 found - 3 modified | TOTAL: 9
- 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 (-+): 3 found - 3 modified | TOTAL: 3
- pass 2 (-+): 0 found - 3 modified | TOTAL: 3
- Iteration Number : 2
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Total Number of Modified Voxels = 12 (out of 303005: 0.003960)
- 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: 1681 vertices, 1847 faces
- slice 50: 9012 vertices, 9345 faces
- slice 60: 19700 vertices, 20123 faces
- slice 70: 32179 vertices, 32646 faces
- slice 80: 44565 vertices, 45009 faces
- slice 90: 57262 vertices, 57668 faces
- slice 100: 70063 vertices, 70480 faces
- slice 110: 82614 vertices, 83037 faces
- slice 120: 94695 vertices, 95131 faces
- slice 130: 106511 vertices, 106941 faces
- slice 140: 118494 vertices, 118916 faces
- slice 150: 129325 vertices, 129675 faces
- slice 160: 138302 vertices, 138625 faces
- slice 170: 146915 vertices, 147215 faces
- slice 180: 154406 vertices, 154657 faces
- slice 190: 159885 vertices, 160074 faces
- slice 200: 163409 vertices, 163504 faces
- slice 210: 163856 vertices, 163888 faces
- slice 220: 163856 vertices, 163888 faces
- slice 230: 163856 vertices, 163888 faces
- slice 240: 163856 vertices, 163888 faces
- slice 250: 163856 vertices, 163888 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...
- 163856 voxel in cpt #1: X=-32 [v=163856,e=491664,f=327776] located at (30.498199, -17.300087, 36.784977)
- For the whole surface: X=-32 [v=163856,e=491664,f=327776]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Smooth1 rh Thu Aug 8 20:22:30 CEST 2013
- mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 20:22:36 CEST 2013
- mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts
- avg radius = 49.6 mm, total surface area = 86888 mm^2
- writing inflated surface to ../surf/rh.inflated.nofix
- inflation took 0.7 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=0.038 (target=0.015)
step 025: RMS=0.033 (target=0.015)
step 030: RMS=0.030 (target=0.015)
step 035: RMS=0.028 (target=0.015)
step 040: RMS=0.027 (target=0.015)
step 045: RMS=0.025 (target=0.015)
step 050: RMS=0.024 (target=0.015)
step 055: RMS=0.024 (target=0.015)
step 060: RMS=0.023 (target=0.015)
- inflation complete.
- Not saving sulc
- #--------------------------------------------
- #@# QSphere rh Thu Aug 8 20:23:15 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts
- mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix
- doing quick spherical unfolding.
- setting seed for random number genererator to 1234
- $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading original vertex positions...
- unfolding cortex into spherical form...
- surface projected - minimizing metric distortion...
- vertex spacing 0.91 +- 0.54 (0.00-->8.07) (max @ vno 116886 --> 118105)
- face area 0.02 +- 0.03 (-0.28-->0.62)
- scaling brain by 0.290...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=176.534, avgs=0
- 005/300: dt: 0.9000, rms radial error=176.274, avgs=0
- 010/300: dt: 0.9000, rms radial error=175.718, avgs=0
- 015/300: dt: 0.9000, rms radial error=174.987, avgs=0
- 020/300: dt: 0.9000, rms radial error=174.154, avgs=0
- 025/300: dt: 0.9000, rms radial error=173.264, avgs=0
- 030/300: dt: 0.9000, rms radial error=172.342, avgs=0
- 035/300: dt: 0.9000, rms radial error=171.405, avgs=0
- 040/300: dt: 0.9000, rms radial error=170.459, avgs=0
- 045/300: dt: 0.9000, rms radial error=169.511, avgs=0
- 050/300: dt: 0.9000, rms radial error=168.565, avgs=0
- 055/300: dt: 0.9000, rms radial error=167.620, avgs=0
- 060/300: dt: 0.9000, rms radial error=166.680, avgs=0
- 065/300: dt: 0.9000, rms radial error=165.744, avgs=0
- 070/300: dt: 0.9000, rms radial error=164.813, avgs=0
- 075/300: dt: 0.9000, rms radial error=163.887, avgs=0
- 080/300: dt: 0.9000, rms radial error=162.965, avgs=0
- 085/300: dt: 0.9000, rms radial error=162.051, avgs=0
- 090/300: dt: 0.9000, rms radial error=161.141, avgs=0
- 095/300: dt: 0.9000, rms radial error=160.237, avgs=0
- 100/300: dt: 0.9000, rms radial error=159.337, avgs=0
- 105/300: dt: 0.9000, rms radial error=158.443, avgs=0
- 110/300: dt: 0.9000, rms radial error=157.553, avgs=0
- 115/300: dt: 0.9000, rms radial error=156.668, avgs=0
- 120/300: dt: 0.9000, rms radial error=155.788, avgs=0
- 125/300: dt: 0.9000, rms radial error=154.912, avgs=0
- 130/300: dt: 0.9000, rms radial error=154.042, avgs=0
- 135/300: dt: 0.9000, rms radial error=153.176, avgs=0
- 140/300: dt: 0.9000, rms radial error=152.315, avgs=0
- 145/300: dt: 0.9000, rms radial error=151.459, avgs=0
- 150/300: dt: 0.9000, rms radial error=150.607, avgs=0
- 155/300: dt: 0.9000, rms radial error=149.760, avgs=0
- 160/300: dt: 0.9000, rms radial error=148.918, avgs=0
- 165/300: dt: 0.9000, rms radial error=148.080, avgs=0
- 170/300: dt: 0.9000, rms radial error=147.247, avgs=0
- 175/300: dt: 0.9000, rms radial error=146.419, avgs=0
- 180/300: dt: 0.9000, rms radial error=145.595, avgs=0
- 185/300: dt: 0.9000, rms radial error=144.776, avgs=0
- 190/300: dt: 0.9000, rms radial error=143.961, avgs=0
- 195/300: dt: 0.9000, rms radial error=143.151, avgs=0
- 200/300: dt: 0.9000, rms radial error=142.345, avgs=0
- 205/300: dt: 0.9000, rms radial error=141.544, avgs=0
- 210/300: dt: 0.9000, rms radial error=140.747, avgs=0
- 215/300: dt: 0.9000, rms radial error=139.955, avgs=0
- 220/300: dt: 0.9000, rms radial error=139.167, avgs=0
- 225/300: dt: 0.9000, rms radial error=138.384, avgs=0
- 230/300: dt: 0.9000, rms radial error=137.605, avgs=0
- 235/300: dt: 0.9000, rms radial error=136.830, avgs=0
- 240/300: dt: 0.9000, rms radial error=136.060, avgs=0
- 245/300: dt: 0.9000, rms radial error=135.293, avgs=0
- 250/300: dt: 0.9000, rms radial error=134.532, avgs=0
- 255/300: dt: 0.9000, rms radial error=133.774, avgs=0
- 260/300: dt: 0.9000, rms radial error=133.021, avgs=0
- 265/300: dt: 0.9000, rms radial error=132.271, avgs=0
- 270/300: dt: 0.9000, rms radial error=131.526, avgs=0
- 275/300: dt: 0.9000, rms radial error=130.785, avgs=0
- 280/300: dt: 0.9000, rms radial error=130.049, avgs=0
- 285/300: dt: 0.9000, rms radial error=129.316, avgs=0
- 290/300: dt: 0.9000, rms radial error=128.588, avgs=0
- 295/300: dt: 0.9000, rms radial error=127.863, avgs=0
- 300/300: dt: 0.9000, rms radial error=127.143, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 19564.79
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00013
- epoch 2 (K=40.0), pass 1, starting sse = 3392.89
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00001
- epoch 3 (K=160.0), pass 1, starting sse = 370.22
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.05/11 = 0.00471
- epoch 4 (K=640.0), pass 1, starting sse = 25.03
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.06/11 = 0.00562
- final writing spherical brain to ../surf/rh.qsphere.nofix
- spherical transformation took 0.10 hours
- distance error %100000.00
- #--------------------------------------------
- #@# Fix Topology rh Thu Aug 8 20:29:05 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/sub016/scripts
- mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub016 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=-32 (nv=163856, nf=327776, ne=491664, g=17)
- 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...
- 3558 ambiguous faces found in tessellation
- segmenting defects...
- 34 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- 34 defects to be corrected
- 0 vertices coincident
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -9.8298 (-4.9149)
- -vertex loglikelihood: -6.6052 (-3.3026)
- -normal dot loglikelihood: -3.6164 (-3.6164)
- -quad curv loglikelihood: -6.3230 (-3.1615)
- Total Loglikelihood : -26.3744
- CORRECTING DEFECT 0 (vertices=51, convex hull=77)
- After retessellation of defect 0, euler #=-31 (161715,484343,322597) : difference with theory (-31) = 0
- CORRECTING DEFECT 1 (vertices=8, convex hull=27)
- After retessellation of defect 1, euler #=-30 (161716,484353,322607) : difference with theory (-30) = 0
- CORRECTING DEFECT 2 (vertices=8, convex hull=21)
- After retessellation of defect 2, euler #=-29 (161718,484364,322617) : difference with theory (-29) = 0
- CORRECTING DEFECT 3 (vertices=9, convex hull=23)
- After retessellation of defect 3, euler #=-28 (161719,484374,322627) : difference with theory (-28) = 0
- CORRECTING DEFECT 4 (vertices=25, convex hull=44)
- After retessellation of defect 4, euler #=-27 (161724,484404,322653) : difference with theory (-27) = 0
- CORRECTING DEFECT 5 (vertices=36, convex hull=89)
- After retessellation of defect 5, euler #=-26 (161743,484497,322728) : difference with theory (-26) = 0
- CORRECTING DEFECT 6 (vertices=44, convex hull=34)
- After retessellation of defect 6, euler #=-25 (161747,484522,322750) : difference with theory (-25) = 0
- CORRECTING DEFECT 7 (vertices=32, convex hull=57)
- After retessellation of defect 7, euler #=-24 (161756,484567,322787) : difference with theory (-24) = 0
- CORRECTING DEFECT 8 (vertices=448, convex hull=240)
- After retessellation of defect 8, euler #=-23 (161788,484784,322973) : difference with theory (-23) = 0
- CORRECTING DEFECT 9 (vertices=33, convex hull=32)
- After retessellation of defect 9, euler #=-22 (161793,484809,322994) : difference with theory (-22) = 0
- CORRECTING DEFECT 10 (vertices=15, convex hull=35)
- After retessellation of defect 10, euler #=-21 (161796,484831,323014) : difference with theory (-21) = 0
- CORRECTING DEFECT 11 (vertices=25, convex hull=59)
- After retessellation of defect 11, euler #=-20 (161807,484886,323059) : difference with theory (-20) = 0
- CORRECTING DEFECT 12 (vertices=58, convex hull=50)
- After retessellation of defect 12, euler #=-19 (161818,484939,323102) : difference with theory (-19) = 0
- CORRECTING DEFECT 13 (vertices=25, convex hull=45)
- After retessellation of defect 13, euler #=-18 (161835,485005,323152) : difference with theory (-18) = 0
- CORRECTING DEFECT 14 (vertices=88, convex hull=89)
- After retessellation of defect 14, euler #=-17 (161859,485121,323245) : difference with theory (-17) = 0
- CORRECTING DEFECT 15 (vertices=16, convex hull=43)
- After retessellation of defect 15, euler #=-16 (161868,485163,323279) : difference with theory (-16) = 0
- CORRECTING DEFECT 16 (vertices=437, convex hull=123)
- After retessellation of defect 16, euler #=-15 (161905,485336,323416) : difference with theory (-15) = 0
- CORRECTING DEFECT 17 (vertices=16, convex hull=26)
- After retessellation of defect 17, euler #=-14 (161910,485359,323435) : difference with theory (-14) = 0
- CORRECTING DEFECT 18 (vertices=21, convex hull=28)
- After retessellation of defect 18, euler #=-13 (161912,485378,323453) : difference with theory (-13) = 0
- CORRECTING DEFECT 19 (vertices=15, convex hull=17)
- After retessellation of defect 19, euler #=-12 (161914,485390,323464) : difference with theory (-12) = 0
- CORRECTING DEFECT 20 (vertices=81, convex hull=88)
- After retessellation of defect 20, euler #=-11 (161935,485483,323537) : difference with theory (-11) = 0
- CORRECTING DEFECT 21 (vertices=17, convex hull=10)
- After retessellation of defect 21, euler #=-10 (161935,485485,323540) : difference with theory (-10) = 0
- CORRECTING DEFECT 22 (vertices=33, convex hull=18)
- After retessellation of defect 22, euler #=-9 (161940,485504,323555) : difference with theory (-9) = 0
- CORRECTING DEFECT 23 (vertices=117, convex hull=135)
- After retessellation of defect 23, euler #=-8 (161991,485716,323717) : difference with theory (-8) = 0
- CORRECTING DEFECT 24 (vertices=90, convex hull=65)
- After retessellation of defect 24, euler #=-7 (162011,485798,323780) : difference with theory (-7) = 0
- CORRECTING DEFECT 25 (vertices=113, convex hull=61)
- After retessellation of defect 25, euler #=-6 (162019,485846,323821) : difference with theory (-6) = 0
- CORRECTING DEFECT 26 (vertices=6, convex hull=28)
- After retessellation of defect 26, euler #=-5 (162020,485857,323832) : difference with theory (-5) = 0
- CORRECTING DEFECT 27 (vertices=16, convex hull=31)
- After retessellation of defect 27, euler #=-4 (162022,485872,323846) : difference with theory (-4) = 0
- CORRECTING DEFECT 28 (vertices=93, convex hull=92)
- After retessellation of defect 28, euler #=-3 (162072,486063,323988) : difference with theory (-3) = 0
- CORRECTING DEFECT 29 (vertices=54, convex hull=87)
- After retessellation of defect 29, euler #=-2 (162096,486177,324079) : difference with theory (-2) = 0
- CORRECTING DEFECT 30 (vertices=55, convex hull=82)
- After retessellation of defect 30, euler #=-1 (162129,486310,324180) : difference with theory (-1) = 0
- CORRECTING DEFECT 31 (vertices=25, convex hull=82)
- After retessellation of defect 31, euler #=0 (162142,486381,324239) : difference with theory (0) = 0
- CORRECTING DEFECT 32 (vertices=8, convex hull=31)
- Warning - incorrect dp selected!!!!(-87.980212 >= -87.980213 )
- After retessellation of defect 32, euler #=1 (162143,486393,324251) : difference with theory (1) = 0
- CORRECTING DEFECT 33 (vertices=33, convex hull=78)
- After retessellation of defect 33, euler #=2 (162159,486471,324314) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.88 +- 0.23 (0.10-->11.94) (max @ vno 66835 --> 69415)
- face area 0.00 +- 0.00 (0.00-->0.00)
- performing soap bubble on retessellated vertices for 0 iterations...
- vertex spacing 0.88 +- 0.23 (0.10-->11.94) (max @ vno 66835 --> 69415)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 129 mutations (35.9%), 230 crossovers (64.1%), 190 vertices were eliminated
- building final representation...
- 1697 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=162159, nf=324314, ne=486471, g=0)
- writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 28.8 minutes
- 0 defective edges
- removing intersecting faces
- 000: 225 intersecting
- mris_euler_number ../surf/rh.orig
- euler # = v-e+f = 2g-2: 162159 - 486471 + 324314 = 2 --> 0 holes
- F =2V-4: 324314 = 324318-4 (0)
- 2E=3F: 972942 = 972942 (0)
- total defect index = 0
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts
- mris_remove_intersection ../surf/rh.orig ../surf/rh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 39 intersecting
- 001: 2 intersecting
- writing corrected surface to ../surf/rh.orig
- rm ../surf/rh.inflated
- #--------------------------------------------
- #@# Make White Surf rh Thu Aug 8 20:58:01 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts
- mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub016 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/sub016/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz...
- 23684 bright wm thresholded.
- 383 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.orig...
- computing class statistics...
- border white: 298969 voxels (1.78%)
- border gray 333863 voxels (1.99%)
- WM (93.0): 94.0 +- 9.8 [70.0 --> 110.0]
- GM (76.0) : 74.9 +- 12.7 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 47.3 (was 70)
- setting MAX_BORDER_WHITE to 114.8 (was 105)
- setting MIN_BORDER_WHITE to 60.0 (was 85)
- setting MAX_CSF to 34.5 (was 40)
- setting MAX_GRAY to 95.2 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 53.6 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 21.8 (was 40)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.82 +- 0.22 (0.03-->5.50) (max @ vno 65573 --> 70451)
- face area 0.28 +- 0.12 (0.00-->5.65)
- mean absolute distance = 0.66 +- 0.79
- 5111 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=105, GM=60
- mean inside = 93.5, mean outside = 69.7
- smoothing surface for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 3 vertex label from ripped group
- mean border=73.5, 62 (62) missing vertices, mean dist 0.4 [0.5 (%29.6)->0.7 (%70.4))]
- %73 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.91 +- 0.26 (0.11-->8.50) (max @ vno 70451 --> 68130)
- face area 0.28 +- 0.13 (0.00-->5.07)
- mean absolute distance = 0.36 +- 0.50
- 4632 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=8153363.5, rms=13.09
- 001: dt: 0.5000, sse=8206518.0, rms=9.369 (0.000%)
- 002: dt: 0.5000, sse=8371105.0, rms=7.213 (0.000%)
- 003: dt: 0.5000, sse=8617238.0, rms=5.862 (0.000%)
- 004: dt: 0.5000, sse=8847876.0, rms=5.082 (0.000%)
- 005: dt: 0.5000, sse=8998998.0, rms=4.631 (0.000%)
- 006: dt: 0.5000, sse=9049736.0, rms=4.420 (0.000%)
- 007: dt: 0.5000, sse=9107665.0, rms=4.280 (0.000%)
- 008: dt: 0.5000, sse=9068589.0, rms=4.220 (0.000%)
- 009: dt: 0.5000, sse=9084191.0, rms=4.148 (0.000%)
- rms = 4.13, time step reduction 1 of 3 to 0.250...
- 010: dt: 0.5000, sse=9032769.0, rms=4.134 (0.000%)
- 011: dt: 0.2500, sse=5589936.0, rms=2.796 (0.000%)
- 012: dt: 0.2500, sse=5133850.5, rms=2.355 (0.000%)
- 013: dt: 0.2500, sse=4815090.0, rms=2.251 (0.000%)
- 014: dt: 0.2500, sse=4742968.5, rms=2.161 (0.000%)
- rms = 2.13, time step reduction 2 of 3 to 0.125...
- 015: dt: 0.2500, sse=4631043.5, rms=2.131 (0.000%)
- 016: dt: 0.1250, sse=4418955.5, rms=1.928 (0.000%)
- rms = 1.90, time step reduction 3 of 3 to 0.062...
- 017: dt: 0.1250, sse=4371228.5, rms=1.900 (0.000%)
- positioning took 2.5 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 3 vertex label from ripped group
- mean border=78.9, 77 (16) missing vertices, mean dist -0.3 [0.4 (%82.3)->0.2 (%17.7))]
- %86 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 +- 0.25 (0.05-->9.31) (max @ vno 70451 --> 68130)
- face area 0.35 +- 0.17 (0.00-->6.95)
- mean absolute distance = 0.21 +- 0.29
- 3579 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5901340.5, rms=6.95
- 018: dt: 0.5000, sse=5746078.5, rms=4.582 (0.000%)
- rms = 4.63, time step reduction 1 of 3 to 0.250...
- 019: dt: 0.2500, sse=5250808.0, rms=3.566 (0.000%)
- 020: dt: 0.2500, sse=4974762.0, rms=2.789 (0.000%)
- 021: dt: 0.2500, sse=4867593.5, rms=2.265 (0.000%)
- 022: dt: 0.2500, sse=4830676.5, rms=2.073 (0.000%)
- 023: dt: 0.2500, sse=4749424.0, rms=1.885 (0.000%)
- 024: dt: 0.2500, sse=4768091.0, rms=1.810 (0.000%)
- 025: dt: 0.2500, sse=4708092.0, rms=1.748 (0.000%)
- rms = 1.72, time step reduction 2 of 3 to 0.125...
- 026: dt: 0.2500, sse=4736196.0, rms=1.725 (0.000%)
- 027: dt: 0.1250, sse=4562554.5, rms=1.541 (0.000%)
- rms = 1.53, time step reduction 3 of 3 to 0.062...
- 028: dt: 0.1250, sse=4521904.5, rms=1.529 (0.000%)
- positioning took 1.7 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 3 vertex label from ripped group
- mean border=82.1, 58 (7) missing vertices, mean dist -0.1 [0.2 (%76.9)->0.2 (%23.1))]
- %92 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 +- 0.25 (0.04-->9.68) (max @ vno 70451 --> 68130)
- face area 0.33 +- 0.16 (0.00-->6.87)
- mean absolute distance = 0.16 +- 0.23
- 3256 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4962088.0, rms=4.20
- 029: dt: 0.5000, sse=5376449.5, rms=4.009 (0.000%)
- rms = 4.18, time step reduction 1 of 3 to 0.250...
- 030: dt: 0.2500, sse=4837316.0, rms=2.522 (0.000%)
- 031: dt: 0.2500, sse=4704395.5, rms=1.988 (0.000%)
- 032: dt: 0.2500, sse=4748966.0, rms=1.651 (0.000%)
- rms = 1.68, time step reduction 2 of 3 to 0.125...
- 033: dt: 0.1250, sse=4679433.5, rms=1.528 (0.000%)
- 034: dt: 0.1250, sse=4588254.5, rms=1.352 (0.000%)
- rms = 1.33, time step reduction 3 of 3 to 0.062...
- 035: dt: 0.1250, sse=4547578.5, rms=1.333 (0.000%)
- positioning took 1.2 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 3 vertex label from ripped group
- mean border=83.0, 51 (4) missing vertices, mean dist -0.0 [0.2 (%58.0)->0.2 (%42.0))]
- %93 local maxima, % 2 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- writing white matter surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.white...
- writing smoothed curvature to rh.curv
- 000: dt: 0.0000, sse=4576333.0, rms=1.72
- rms = 2.52, time step reduction 1 of 3 to 0.250...
- 036: dt: 0.2500, sse=4675320.0, rms=1.142 (0.000%)
- 037: dt: 0.2500, sse=4840894.5, rms=1.004 (0.000%)
- rms = 1.01, time step reduction 2 of 3 to 0.125...
- rms = 1.00, time step reduction 3 of 3 to 0.062...
- 038: dt: 0.1250, sse=4841039.0, rms=0.995 (0.000%)
- positioning took 0.6 minutes
- inhibiting deformation at non-cortical midline structures...
- generating cortex label...
- 20 non-cortical segments detected
- only using segment with 2323 vertices
- erasing segment 1 (vno[0] = 103811)
- erasing segment 2 (vno[0] = 106145)
- erasing segment 3 (vno[0] = 109699)
- erasing segment 4 (vno[0] = 110811)
- erasing segment 5 (vno[0] = 113952)
- erasing segment 6 (vno[0] = 113958)
- erasing segment 7 (vno[0] = 114058)
- erasing segment 8 (vno[0] = 114087)
- erasing segment 9 (vno[0] = 115145)
- erasing segment 10 (vno[0] = 116433)
- erasing segment 11 (vno[0] = 116525)
- erasing segment 12 (vno[0] = 120936)
- erasing segment 13 (vno[0] = 121020)
- erasing segment 14 (vno[0] = 124279)
- erasing segment 15 (vno[0] = 124302)
- erasing segment 16 (vno[0] = 125188)
- erasing segment 17 (vno[0] = 125211)
- erasing segment 18 (vno[0] = 127009)
- erasing segment 19 (vno[0] = 127902)
- writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/label/rh.cortex.label...
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.curv
- writing smoothed area to rh.area
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.area
- vertex spacing 0.89 +- 0.25 (0.05-->9.83) (max @ vno 70451 --> 68130)
- face area 0.33 +- 0.16 (0.00-->6.86)
- refinement took 8.6 minutes
- #--------------------------------------------
- #@# Smooth2 rh Thu Aug 8 21:06:36 CEST 2013
- mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts
- smoothing for 3 iterations
- setting seed for random number generator to 1234
- smoothing surface tessellation for 3 iterations...
- smoothing complete - recomputing first and second fundamental forms...
- #--------------------------------------------
- #@# Inflation2 rh Thu Aug 8 21:06:41 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts
- mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated
- avg radius = 49.8 mm, total surface area = 98579 mm^2
- writing inflated surface to ../surf/rh.inflated
- writing sulcal depths to ../surf/rh.sulc
-
step 000: RMS=0.112 (target=0.015)
step 005: RMS=0.078 (target=0.015)
step 010: RMS=0.056 (target=0.015)
step 015: RMS=0.046 (target=0.015)
step 020: RMS=0.037 (target=0.015)
step 025: RMS=0.031 (target=0.015)
step 030: RMS=0.027 (target=0.015)
step 035: RMS=0.023 (target=0.015)
step 040: RMS=0.019 (target=0.015)
step 045: RMS=0.017 (target=0.015)
step 050: RMS=0.016 (target=0.015)
- inflation complete.
- inflation took 0.6 minutes
- mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated
- normalizing curvature values.
- averaging curvature patterns 5 times.
- sampling 10 neighbors out to a distance of 10 mm
- 212 vertices thresholded to be in k1 ~ [-0.61 0.39], k2 ~ [-0.21 0.11]
- total integrated curvature = 0.400*4pi (5.028) --> 1 handles
- ICI = 1.7, FI = 14.3, variation=232.796
- 169 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
- 134 vertices thresholded to be in [-0.18 0.19]
- done.
- writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.015, std = 0.026
- done.
- #-----------------------------------------
- #@# Curvature Stats rh Thu Aug 8 21:09:21 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub016 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 [ sub016/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 [ 318 ]
- Gb_filter = 0
- #--------------------------------------------
- #@# Sphere rh Thu Aug 8 21:09:27 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 0.271...
- 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 %19.61
- pass 1: epoch 2 of 3 starting distance error %19.56
- unfolding complete - removing small folds...
- starting distance error %19.45
- removing remaining folds...
- final distance error %19.46
- MRISunfold() return, current seed 1234
- writing spherical brain to ../surf/rh.sphere
- spherical transformation took 1.24 hours
- #--------------------------------------------
- #@# Surf Reg rh Thu Aug 8 22:23:50 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 = 0.583
- curvature mean = 0.026, std = 0.944
- curvature mean = 0.026, std = 0.838
- Starting MRISrigidBodyAlignGlobal()
- d=64.00 min @ (16.00, 0.00, 0.00) sse = 442935.7, tmin=1.3303
- d=32.00 min @ (-8.00, -8.00, 0.00) sse = 380528.0, tmin=2.6304
- d=16.00 min @ (0.00, 4.00, 4.00) sse = 335983.4, tmin=3.9825
- d=8.00 min @ (0.00, -2.00, 0.00) sse = 330664.6, tmin=5.3504
- d=2.00 min @ (0.00, 0.50, -0.50) sse = 330548.4, tmin=8.1105
- d=1.00 min @ (-0.25, -0.25, 0.25) sse = 330150.7, tmin=9.4755
- 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 10.87 min
- curvature mean = 0.002, std = 0.935
- curvature mean = 0.011, std = 0.927
- curvature mean = -0.004, std = 0.939
- curvature mean = 0.006, std = 0.965
- curvature mean = -0.007, std = 0.935
- curvature mean = 0.001, std = 0.983
- 2 Reading smoothwm
- curvature mean = -0.023, std = 0.289
- curvature mean = 0.004, std = 0.069
- curvature mean = 0.073, std = 0.319
- curvature mean = 0.005, std = 0.082
- curvature mean = 0.036, std = 0.504
- curvature mean = 0.005, std = 0.088
- curvature mean = 0.020, std = 0.646
- curvature mean = 0.006, std = 0.090
- curvature mean = 0.007, std = 0.759
- MRISregister() return, current seed 0
- writing registered surface to ../surf/rh.sphere.reg...
- expanding nbhd size to 1
- #--------------------------------------------
- #@# Jacobian white rh Thu Aug 8 22:59:28 CEST 2013
- mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white
- reading surface from ../surf/rh.white...
- writing curvature file ../surf/rh.jacobian_white
- #--------------------------------------------
- #@# AvgCurv rh Thu Aug 8 22:59:32 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts
- mrisp_paint -a 5 /opt/freesurfer/5.3.0/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv
- averaging curvature patterns 5 times...
- reading surface from ../surf/rh.sphere.reg...
- reading template parameterization from /opt/freesurfer/5.3.0/average/rh.average.curvature.filled.buckner40.tif...
- writing curvature file to ../surf/rh.avg_curv...
- #-----------------------------------------
- #@# Cortical Parc rh Thu Aug 8 22:59:35 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub016 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...
- 1118 labels changed using aseg
- relabeling using gibbs priors...
- 000: 3403 changed, 162159 examined...
- 001: 812 changed, 14508 examined...
- 002: 208 changed, 4507 examined...
- 003: 52 changed, 1249 examined...
- 004: 24 changed, 343 examined...
- 005: 12 changed, 145 examined...
- 006: 3 changed, 72 examined...
- 007: 1 changed, 19 examined...
- 008: 2 changed, 6 examined...
- 009: 1 changed, 10 examined...
- 010: 0 changed, 8 examined...
- 184 labels changed using aseg
- 000: 104 total segments, 64 labels (442 vertices) changed
- 001: 41 total segments, 1 labels (7 vertices) changed
- 002: 40 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 64 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 2159 vertices marked for relabeling...
- 2159 labels changed in reclassification.
- writing output to ../label/rh.aparc.annot...
- classification took 1 minutes and 15 seconds.
- #--------------------------------------------
- #@# Make Pial Surf rh Thu Aug 8 23:00:50 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts
- mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub016 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/sub016/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz...
- 23684 bright wm thresholded.
- 383 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.orig...
- computing class statistics...
- border white: 298969 voxels (1.78%)
- border gray 333863 voxels (1.99%)
- WM (93.0): 94.0 +- 9.8 [70.0 --> 110.0]
- GM (76.0) : 74.9 +- 12.7 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 47.3 (was 70)
- setting MAX_BORDER_WHITE to 114.8 (was 105)
- setting MIN_BORDER_WHITE to 60.0 (was 85)
- setting MAX_CSF to 34.5 (was 40)
- setting MAX_GRAY to 95.2 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 53.6 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 21.8 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=105, GM=60
- mean inside = 93.5, mean outside = 69.7
- 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/sub016/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.82 +- 0.22 (0.03-->5.50) (max @ vno 65573 --> 70451)
- face area 0.28 +- 0.12 (0.00-->5.65)
- mean absolute distance = 0.66 +- 0.79
- 5220 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 12 points - only 0.00% unknown
- deleting segment 1 with 23 points - only 0.00% unknown
- deleting segment 2 with 14 points - only 0.00% unknown
- deleting segment 4 with 5 points - only 0.00% unknown
- deleting segment 5 with 19 points - only 0.00% unknown
- deleting segment 7 with 20 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 8 with 3 points - only 0.00% unknown
- deleting segment 9 with 40 points - only 0.00% unknown
- deleting segment 10 with 504 points - only 0.00% unknown
- deleting segment 11 with 6 points - only 0.00% unknown
- deleting segment 13 with 115 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 16 with 4 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 17 with 4 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 18 with 3 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 19 with 3 points - only 0.00% unknown
- mean border=73.4, 65 (64) missing vertices, mean dist 0.4 [0.5 (%29.6)->0.7 (%70.4))]
- %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 +- 0.26 (0.11-->8.50) (max @ vno 70451 --> 68130)
- face area 0.28 +- 0.13 (0.00-->5.07)
- mean absolute distance = 0.36 +- 0.50
- 4697 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=8176584.0, rms=13.08
- 001: dt: 0.5000, sse=8234243.5, rms=9.358 (0.000%)
- 002: dt: 0.5000, sse=8408520.0, rms=7.207 (0.000%)
- 003: dt: 0.5000, sse=8659359.0, rms=5.858 (0.000%)
- 004: dt: 0.5000, sse=8894008.0, rms=5.080 (0.000%)
- 005: dt: 0.5000, sse=9050424.0, rms=4.630 (0.000%)
- 006: dt: 0.5000, sse=9104576.0, rms=4.419 (0.000%)
- 007: dt: 0.5000, sse=9161903.0, rms=4.280 (0.000%)
- 008: dt: 0.5000, sse=9124109.0, rms=4.218 (0.000%)
- 009: dt: 0.5000, sse=9137261.0, rms=4.148 (0.000%)
- rms = 4.13, time step reduction 1 of 3 to 0.250...
- 010: dt: 0.5000, sse=9089501.0, rms=4.133 (0.000%)
- 011: dt: 0.2500, sse=5633577.5, rms=2.799 (0.000%)
- 012: dt: 0.2500, sse=5175912.0, rms=2.359 (0.000%)
- 013: dt: 0.2500, sse=4855685.0, rms=2.257 (0.000%)
- 014: dt: 0.2500, sse=4781068.5, rms=2.168 (0.000%)
- rms = 2.14, time step reduction 2 of 3 to 0.125...
- 015: dt: 0.2500, sse=4670974.0, rms=2.137 (0.000%)
- 016: dt: 0.1250, sse=4458593.5, rms=1.936 (0.000%)
- rms = 1.91, time step reduction 3 of 3 to 0.062...
- 017: dt: 0.1250, sse=4409677.5, rms=1.908 (0.000%)
- positioning took 2.6 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 19 points - only 0.00% unknown
- deleting segment 1 with 28 points - only 0.00% unknown
- deleting segment 2 with 18 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 3 with 2 points - only 0.00% unknown
- deleting segment 4 with 8 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 6 with 23 points - only 0.00% unknown
- deleting segment 7 with 16 points - only 0.00% unknown
- deleting segment 10 with 33 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
- deleting segment 14 with 329 points - only 0.00% unknown
- deleting segment 15 with 5 points - only 0.00% unknown
- deleting segment 19 with 24 points - only 0.00% unknown
- deleting segment 20 with 24 points - only 0.00% unknown
- deleting segment 21 with 9 points - only 33.33% unknown
- deleting segment 22 with 12 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 23 with 3 points - only 0.00% unknown
- mean border=78.9, 88 (18) missing vertices, mean dist -0.3 [0.4 (%82.2)->0.2 (%17.8))]
- %86 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 +- 0.25 (0.05-->9.31) (max @ vno 70451 --> 68130)
- face area 0.35 +- 0.17 (0.00-->6.95)
- mean absolute distance = 0.21 +- 0.30
- 3652 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5945504.5, rms=6.94
- 018: dt: 0.5000, sse=5791920.5, rms=4.578 (0.000%)
- rms = 4.62, time step reduction 1 of 3 to 0.250...
- 019: dt: 0.2500, sse=5293300.5, rms=3.565 (0.000%)
- 020: dt: 0.2500, sse=5015019.0, rms=2.790 (0.000%)
- 021: dt: 0.2500, sse=4908255.0, rms=2.268 (0.000%)
- 022: dt: 0.2500, sse=4870418.0, rms=2.077 (0.000%)
- 023: dt: 0.2500, sse=4789291.0, rms=1.889 (0.000%)
- 024: dt: 0.2500, sse=4807856.0, rms=1.815 (0.000%)
- 025: dt: 0.2500, sse=4749047.0, rms=1.753 (0.000%)
- rms = 1.73, time step reduction 2 of 3 to 0.125...
- 026: dt: 0.2500, sse=4776147.5, rms=1.731 (0.000%)
- 027: dt: 0.1250, sse=4603768.0, rms=1.548 (0.000%)
- rms = 1.54, time step reduction 3 of 3 to 0.062...
- 028: dt: 0.1250, sse=4562413.5, rms=1.536 (0.000%)
- positioning took 1.7 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 19 points - only 0.00% unknown
- deleting segment 1 with 28 points - only 0.00% unknown
- deleting segment 2 with 20 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 3 with 2 points - only 0.00% unknown
- deleting segment 4 with 8 points - only 0.00% unknown
- deleting segment 5 with 21 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 6 with 4 points - only 0.00% unknown
- deleting segment 7 with 18 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 9 with 32 points - only 0.00% unknown
- deleting segment 10 with 352 points - only 0.00% unknown
- deleting segment 11 with 5 points - only 0.00% unknown
- deleting segment 12 with 29 points - only 0.00% unknown
- deleting segment 14 with 24 points - only 0.00% unknown
- deleting segment 15 with 37 points - only 0.00% unknown
- deleting segment 16 with 8 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 17 with 4 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 18 with 3 points - only 0.00% unknown
- mean border=82.1, 68 (9) missing vertices, mean dist -0.1 [0.2 (%76.8)->0.2 (%23.2))]
- %92 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 +- 0.25 (0.04-->9.68) (max @ vno 70451 --> 68130)
- face area 0.33 +- 0.16 (0.00-->6.87)
- mean absolute distance = 0.16 +- 0.23
- 3372 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5002988.5, rms=4.19
- 029: dt: 0.5000, sse=5418778.5, rms=4.003 (0.000%)
- rms = 4.17, time step reduction 1 of 3 to 0.250...
- 030: dt: 0.2500, sse=4876998.0, rms=2.521 (0.000%)
- 031: dt: 0.2500, sse=4744753.5, rms=1.990 (0.000%)
- 032: dt: 0.2500, sse=4789559.5, rms=1.655 (0.000%)
- rms = 1.68, time step reduction 2 of 3 to 0.125...
- 033: dt: 0.1250, sse=4719764.5, rms=1.533 (0.000%)
- 034: dt: 0.1250, sse=4626804.5, rms=1.358 (0.000%)
- rms = 1.34, time step reduction 3 of 3 to 0.062...
- 035: dt: 0.1250, sse=4588271.5, rms=1.340 (0.000%)
- positioning took 1.2 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 18 points - only 0.00% unknown
- deleting segment 1 with 23 points - only 0.00% unknown
- deleting segment 2 with 19 points - only 0.00% unknown
- deleting segment 3 with 6 points - only 0.00% unknown
- deleting segment 4 with 21 points - only 0.00% unknown
- deleting segment 5 with 17 points - only 0.00% unknown
- deleting segment 6 with 38 points - only 0.00% unknown
- deleting segment 7 with 346 points - only 0.00% unknown
- deleting segment 8 with 5 points - only 0.00% unknown
- deleting segment 9 with 36 points - only 0.00% unknown
- deleting segment 10 with 24 points - only 0.00% unknown
- deleting segment 11 with 51 points - only 0.00% unknown
- deleting segment 12 with 8 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 13 with 2 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 14 with 4 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 15 with 3 points - only 0.00% unknown
- mean border=83.0, 64 (6) missing vertices, mean dist -0.0 [0.2 (%58.0)->0.2 (%42.0))]
- %94 local maxima, % 2 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- repositioning cortical surface to gray/csf boundary.
- smoothing T1 volume with sigma = 2.000
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4617414.0, rms=1.73
- rms = 2.51, time step reduction 1 of 3 to 0.250...
- 036: dt: 0.2500, sse=4718826.5, rms=1.153 (0.000%)
- 037: dt: 0.2500, sse=4896739.0, rms=1.012 (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...
- 038: dt: 0.1250, sse=4889615.5, rms=1.003 (0.000%)
- positioning took 0.6 minutes
- inhibiting deformation at non-cortical midline structures...
- smoothing surface for 5 iterations...
- mean border=49.8, 100 (100) missing vertices, mean dist 1.8 [0.1 (%0.0)->2.4 (%100.0))]
- %15 local maxima, %57 large gradients and %24 min vals, 1971 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=36520256.0, rms=32.77
- 001: dt: 0.5000, sse=26287360.0, rms=27.276 (0.000%)
- 002: dt: 0.5000, sse=19262446.0, rms=22.771 (0.000%)
- 003: dt: 0.5000, sse=14590273.0, rms=19.190 (0.000%)
- 004: dt: 0.5000, sse=11692645.0, rms=16.407 (0.000%)
- 005: dt: 0.5000, sse=10083440.0, rms=14.299 (0.000%)
- 006: dt: 0.5000, sse=9162082.0, rms=12.662 (0.000%)
- 007: dt: 0.5000, sse=8570043.0, rms=11.251 (0.000%)
- 008: dt: 0.5000, sse=8137810.5, rms=9.926 (0.000%)
- 009: dt: 0.5000, sse=7807090.0, rms=8.653 (0.000%)
- 010: dt: 0.5000, sse=7590589.5, rms=7.412 (0.000%)
- 011: dt: 0.5000, sse=7568264.0, rms=6.315 (0.000%)
- 012: dt: 0.5000, sse=7606946.5, rms=5.423 (0.000%)
- 013: dt: 0.5000, sse=7820857.5, rms=4.870 (0.000%)
- 014: dt: 0.5000, sse=7968421.5, rms=4.535 (0.000%)
- 015: dt: 0.5000, sse=8149022.5, rms=4.367 (0.000%)
- 016: dt: 0.5000, sse=8199023.0, rms=4.246 (0.000%)
- rms = 4.21, time step reduction 1 of 3 to 0.250...
- 017: dt: 0.5000, sse=8339397.5, rms=4.210 (0.000%)
- 018: dt: 0.2500, sse=5771961.0, rms=3.380 (0.000%)
- 019: dt: 0.2500, sse=5591880.0, rms=3.164 (0.000%)
- rms = 3.15, time step reduction 2 of 3 to 0.125...
- 020: dt: 0.2500, sse=5431412.5, rms=3.154 (0.000%)
- 021: dt: 0.1250, sse=5119481.0, rms=2.926 (0.000%)
- rms = 2.90, time step reduction 3 of 3 to 0.062...
- 022: dt: 0.1250, sse=5087547.5, rms=2.895 (0.000%)
- positioning took 3.2 minutes
- mean border=47.4, 982 (23) missing vertices, mean dist 0.1 [0.2 (%47.6)->0.5 (%52.4))]
- %34 local maxima, %41 large gradients and %20 min vals, 595 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=5842710.5, rms=4.86
- 023: dt: 0.5000, sse=6254044.5, rms=4.286 (0.000%)
- rms = 4.24, time step reduction 1 of 3 to 0.250...
- 024: dt: 0.5000, sse=8056153.0, rms=4.242 (0.000%)
- 025: dt: 0.2500, sse=5984153.0, rms=3.279 (0.000%)
- 026: dt: 0.2500, sse=6065187.5, rms=3.020 (0.000%)
- rms = 3.00, time step reduction 2 of 3 to 0.125...
- 027: dt: 0.2500, sse=5908627.0, rms=2.998 (0.000%)
- 028: dt: 0.1250, sse=5647260.5, rms=2.720 (0.000%)
- rms = 2.68, time step reduction 3 of 3 to 0.062...
- 029: dt: 0.1250, sse=5628531.0, rms=2.676 (0.000%)
- positioning took 1.0 minutes
- mean border=44.9, 1247 (6) missing vertices, mean dist 0.1 [0.2 (%36.8)->0.3 (%63.2))]
- %54 local maxima, %21 large gradients and %20 min vals, 785 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=5971874.0, rms=4.17
- rms = 4.25, time step reduction 1 of 3 to 0.250...
- 030: dt: 0.2500, sse=5692742.0, rms=3.447 (0.000%)
- 031: dt: 0.2500, sse=5601804.0, rms=2.962 (0.000%)
- 032: dt: 0.2500, sse=5887626.0, rms=2.847 (0.000%)
- rms = 2.86, time step reduction 2 of 3 to 0.125...
- 033: dt: 0.1250, sse=5791303.0, rms=2.764 (0.000%)
- 034: dt: 0.1250, sse=5689471.0, rms=2.644 (0.000%)
- rms = 2.62, time step reduction 3 of 3 to 0.062...
- 035: dt: 0.1250, sse=5678918.0, rms=2.618 (0.000%)
- positioning took 1.1 minutes
- mean border=43.8, 2605 (4) missing vertices, mean dist 0.0 [0.2 (%45.3)->0.3 (%54.7))]
- %56 local maxima, %18 large gradients and %20 min vals, 612 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/sub016/surf/rh.pial...
- writing smoothed curvature to rh.curv.pial
- 000: dt: 0.0000, sse=5742438.0, rms=3.01
- rms = 3.94, time step reduction 1 of 3 to 0.250...
- 036: dt: 0.2500, sse=5610674.5, rms=2.712 (0.000%)
- 037: dt: 0.2500, sse=5872142.0, rms=2.638 (0.000%)
- rms = 2.63, time step reduction 2 of 3 to 0.125...
- 038: dt: 0.2500, sse=5959964.5, rms=2.632 (0.000%)
- 039: dt: 0.1250, sse=5855301.0, rms=2.482 (0.000%)
- rms = 2.46, time step reduction 3 of 3 to 0.062...
- 040: dt: 0.1250, sse=5874691.5, rms=2.456 (0.000%)
- positioning took 0.9 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.curv.pial
- writing smoothed area to rh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.area.pial
- vertex spacing 1.01 +- 0.42 (0.07-->10.54) (max @ vno 70451 --> 68130)
- face area 0.41 +- 0.30 (0.00-->8.44)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 162159 vertices processed
- 25000 of 162159 vertices processed
- 50000 of 162159 vertices processed
- 75000 of 162159 vertices processed
- 100000 of 162159 vertices processed
- 125000 of 162159 vertices processed
- 150000 of 162159 vertices processed
- 0 of 162159 vertices processed
- 25000 of 162159 vertices processed
- 50000 of 162159 vertices processed
- 75000 of 162159 vertices processed
- 100000 of 162159 vertices processed
- 125000 of 162159 vertices processed
- 150000 of 162159 vertices processed
- thickness calculation complete, 368:737 truncations.
- 38776 vertices at 0 distance
- 112698 vertices at 1 distance
- 103614 vertices at 2 distance
- 41260 vertices at 3 distance
- 11150 vertices at 4 distance
- 2941 vertices at 5 distance
- 936 vertices at 6 distance
- 295 vertices at 7 distance
- 133 vertices at 8 distance
- 81 vertices at 9 distance
- 42 vertices at 10 distance
- 24 vertices at 11 distance
- 18 vertices at 12 distance
- 13 vertices at 13 distance
- 13 vertices at 14 distance
- 14 vertices at 15 distance
- 14 vertices at 16 distance
- 7 vertices at 17 distance
- 7 vertices at 18 distance
- 17 vertices at 19 distance
- 15 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.thickness
- positioning took 16.8 minutes
- #--------------------------------------------
- #@# Surf Volume rh Thu Aug 8 23:17:38 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 23:17:40 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts
- pctsurfcon --s sub016 --rh-only
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts/pctsurfcon.log
- Thu Aug 8 23:17:40 CEST 2013
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/tmp.pctsurfcon.24216/rh.wm.mgh --regheader sub016 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/label/rh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 = 125587
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/label/rh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/tmp.pctsurfcon.24216/rh.wm.mgh
- Dim: 162159 1 1
- mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/tmp.pctsurfcon.24216/rh.gm.mgh --projfrac 0.3 --regheader sub016 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/label/rh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.white
- Done reading source surface
- Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 = 144176
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/label/rh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/tmp.pctsurfcon.24216/rh.gm.mgh
- Dim: 162159 1 1
- mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/tmp.pctsurfcon.24216/rh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/tmp.pctsurfcon.24216/rh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/surf/rh.w-g.pct.mgh
- mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.w-g.pct.mgh --annot sub016 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/surf/rh.w-g.pct.mgh --annot sub016 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/surf/rh.w-g.pct.mgh
- Vertex Area is 0.659965 mm^3
- Generating list of segmentation ids
- Found 36 segmentations
- Computing statistics for each segmentation
- 0 2000 unknown 0 0.000
- 1 2001 bankssts 1538 1060.178
- 2 2002 caudalanteriorcingulate 744 498.773
- 3 2003 caudalmiddlefrontal 3373 2197.764
- 4 2004 corpuscallosum 0 0.000
- 5 2005 cuneus 2869 1883.642
- 6 2006 entorhinal 690 475.663
- 7 2007 fusiform 5435 3635.177
- 8 2008 inferiorparietal 10204 6793.776
- 9 2009 inferiortemporal 6788 4625.739
- 10 2010 isthmuscingulate 2352 1535.103
- 11 2011 lateraloccipital 8661 5648.796
- 12 2012 lateralorbitofrontal 4716 3174.235
- 13 2013 lingual 5406 3594.387
- 14 2014 medialorbitofrontal 3155 2060.892
- 15 2015 middletemporal 6473 4426.597
- 16 2016 parahippocampal 1241 845.652
- 17 2017 paracentral 3127 1926.372
- 18 2018 parsopercularis 3195 2085.679
- 19 2019 parsorbitalis 1295 920.021
- 20 2020 parstriangularis 2843 1916.146
- 21 2021 pericalcarine 2969 1987.918
- 22 2022 postcentral 7380 4679.101
- 23 2023 posteriorcingulate 2178 1427.377
- 24 2024 precentral 8535 5212.754
- 25 2025 precuneus 6617 4442.093
- 26 2026 rostralanteriorcingulate 957 615.840
- 27 2027 rostralmiddlefrontal 9516 6459.534
- 28 2028 superiorfrontal 13925 9212.408
- 29 2029 superiorparietal 9031 5771.498
- 30 2030 superiortemporal 5912 4041.441
- 31 2031 supramarginal 6201 4178.135
- 32 2032 frontalpole 435 286.539
- 33 2033 temporalpole 695 510.966
- 34 2034 transversetemporal 724 436.670
- 35 2035 insula 4226 2783.282
- Reporting on 34 segmentations
- mri_segstats done
- Cleaning up
- #-----------------------------------------
- #@# Parcellation Stats rh Thu Aug 8 23:17:54 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 sub016 rh white
- computing statistics for each annotation in ../label/rh.aparc.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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
- 1538 1060 2781 2.609 0.461 0.113 0.025 12 1.5 bankssts
- 744 499 1460 2.758 0.537 0.137 0.031 10 0.9 caudalanteriorcingulate
- 3373 2198 7148 2.880 0.490 0.131 0.085 61 6.6 caudalmiddlefrontal
- 2869 1884 4653 2.212 0.457 0.156 0.063 53 7.6 cuneus
- 690 476 1929 3.237 0.729 0.138 0.053 8 1.6 entorhinal
- 5435 3635 11899 2.707 0.545 0.146 0.066 107 15.3 fusiform
- 10204 6794 19774 2.558 0.499 0.143 0.053 188 20.3 inferiorparietal
- 6788 4626 15324 2.720 0.628 0.148 0.058 183 15.4 inferiortemporal
- 2352 1535 3946 2.362 0.936 0.160 0.084 70 8.9 isthmuscingulate
- 8661 5649 15111 2.353 0.485 0.153 0.059 174 20.3 lateraloccipital
- 4716 3174 10076 2.788 0.666 0.154 0.069 132 14.5 lateralorbitofrontal
- 5406 3594 8505 2.179 0.597 0.164 0.114 129 16.7 lingual
- 3155 2061 6074 2.505 0.732 0.155 0.089 95 12.8 medialorbitofrontal
- 6473 4427 15580 2.785 0.728 0.137 0.047 118 12.9 middletemporal
- 1241 846 2556 2.650 0.566 0.140 0.050 20 2.6 parahippocampal
- 3127 1926 5458 2.595 0.490 0.118 0.037 34 5.3 paracentral
- 3195 2086 6449 2.742 0.484 0.113 0.041 33 4.2 parsopercularis
- 1295 920 3171 2.710 0.557 0.179 0.075 34 3.5 parsorbitalis
- 2843 1916 5723 2.549 0.555 0.131 0.070 90 4.4 parstriangularis
- 2969 1988 3908 2.060 0.409 0.147 0.059 45 7.0 pericalcarine
- 7380 4679 12299 2.251 0.549 0.115 0.101 112 11.4 postcentral
- 2178 1427 4317 2.694 0.719 0.148 0.055 40 5.5 posteriorcingulate
- 8535 5213 15798 2.770 0.601 0.111 0.143 327 60.1 precentral
- 6617 4442 12727 2.601 0.539 0.143 0.051 117 13.4 precuneus
- 957 616 1784 2.977 0.788 0.122 0.150 131 5.9 rostralanteriorcingulate
- 9516 6460 18680 2.468 0.516 0.151 0.052 180 19.9 rostralmiddlefrontal
- 13925 9212 30286 2.842 0.528 0.130 0.046 234 26.0 superiorfrontal
- 9031 5771 14961 2.320 0.425 0.128 0.057 174 21.9 superiorparietal
- 5912 4041 14092 3.032 0.644 0.132 0.039 73 9.8 superiortemporal
- 6201 4178 12336 2.627 0.535 0.137 0.089 169 10.6 supramarginal
- 435 287 1023 2.472 0.637 0.208 0.100 20 2.1 frontalpole
- 695 511 2594 3.604 0.666 0.145 0.054 11 1.7 temporalpole
- 724 437 1532 2.915 0.317 0.122 0.046 8 1.2 transversetemporal
- 4226 2783 9058 3.049 0.957 0.131 0.065 70 9.6 insula
- #-----------------------------------------
- #@# Cortical Parc 2 rh Thu Aug 8 23:18:19 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub016 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...
- 7 labels changed using aseg
- relabeling using gibbs priors...
- 000: 11017 changed, 162159 examined...
- 001: 2717 changed, 42462 examined...
- 002: 854 changed, 13815 examined...
- 003: 385 changed, 4642 examined...
- 004: 167 changed, 2104 examined...
- 005: 83 changed, 924 examined...
- 006: 62 changed, 468 examined...
- 007: 36 changed, 333 examined...
- 008: 8 changed, 185 examined...
- 009: 8 changed, 51 examined...
- 010: 9 changed, 47 examined...
- 011: 5 changed, 47 examined...
- 012: 1 changed, 26 examined...
- 013: 0 changed, 6 examined...
- 8 labels changed using aseg
- 000: 314 total segments, 229 labels (3312 vertices) changed
- 001: 99 total segments, 14 labels (43 vertices) changed
- 002: 85 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 190 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 1277 vertices marked for relabeling...
- 1277 labels changed in reclassification.
- writing output to ../label/rh.aparc.a2009s.annot...
- classification took 1 minutes and 22 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 2 rh Thu Aug 8 23:19:41 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 sub016 rh white
- computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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
- 1096 752 2031 2.274 0.613 0.168 0.064 29 3.2 G_and_S_frontomargin
- 1490 988 2829 2.438 0.528 0.143 0.046 22 2.8 G_and_S_occipital_inf
- 1927 1097 3660 2.663 0.500 0.125 0.047 29 3.8 G_and_S_paracentral
- 1882 1226 3765 2.615 0.447 0.143 0.045 30 3.4 G_and_S_subcentral
- 1332 919 2841 2.470 0.516 0.172 0.062 34 3.6 G_and_S_transv_frontopol
- 3701 2483 7190 2.739 0.578 0.123 0.038 41 6.0 G_and_S_cingul-Ant
- 1779 1209 3639 2.736 0.465 0.130 0.052 23 3.1 G_and_S_cingul-Mid-Ant
- 1893 1251 3748 2.869 0.514 0.128 0.044 23 3.8 G_and_S_cingul-Mid-Post
- 889 575 2307 3.096 0.550 0.180 0.065 23 2.3 G_cingul-Post-dorsal
- 478 311 1199 2.950 0.740 0.164 0.082 12 1.4 G_cingul-Post-ventral
- 2709 1774 4465 2.141 0.435 0.165 0.076 59 8.4 G_cuneus
- 2036 1331 4855 2.855 0.442 0.133 0.052 32 3.3 G_front_inf-Opercular
- 420 286 1196 2.985 0.301 0.179 0.274 63 1.1 G_front_inf-Orbital
- 1567 1044 4008 2.840 0.506 0.149 0.050 30 3.1 G_front_inf-Triangul
- 4421 2987 11147 2.808 0.493 0.160 0.092 116 11.2 G_front_middle
- 8623 5535 20666 2.939 0.542 0.136 0.051 185 19.0 G_front_sup
- 693 447 1467 3.083 1.136 0.149 0.101 20 2.3 G_Ins_lg_and_S_cent_ins
- 630 409 2384 3.973 0.807 0.170 0.114 14 2.2 G_insular_short
- 2805 1773 6473 2.725 0.438 0.176 0.080 91 8.7 G_occipital_middle
- 2014 1254 3540 2.341 0.430 0.154 0.094 63 10.1 G_occipital_sup
- 1879 1203 4450 2.753 0.523 0.157 0.079 45 6.7 G_oc-temp_lat-fusifor
- 3604 2365 5923 2.141 0.611 0.176 0.144 106 12.6 G_oc-temp_med-Lingual
- 1831 1249 4931 3.056 0.754 0.159 0.078 38 5.4 G_oc-temp_med-Parahip
- 3321 2254 8708 2.942 0.633 0.180 0.077 90 10.7 G_orbital
- 3908 2565 8611 2.601 0.538 0.158 0.069 97 9.1 G_pariet_inf-Angular
- 3482 2356 8290 2.762 0.530 0.153 0.134 146 6.9 G_pariet_inf-Supramar
- 2579 1667 5060 2.473 0.462 0.132 0.043 40 4.5 G_parietal_sup
- 2697 1571 4949 2.408 0.503 0.115 0.221 64 5.1 G_postcentral
- 3108 1654 7103 3.209 0.474 0.107 0.339 285 52.9 G_precentral
- 2531 1707 6237 2.769 0.493 0.154 0.058 56 6.0 G_precuneus
- 831 534 1873 2.531 0.702 0.207 0.198 59 7.7 G_rectus
- 720 485 1550 2.850 0.877 0.175 0.233 146 6.8 G_subcallosal
- 668 408 1559 2.984 0.349 0.139 0.053 10 1.3 G_temp_sup-G_T_transv
- 2006 1348 6337 3.307 0.557 0.160 0.053 40 4.5 G_temp_sup-Lateral
- 848 615 2421 3.453 0.688 0.123 0.039 7 1.4 G_temp_sup-Plan_polar
- 1067 715 2144 2.849 0.491 0.117 0.034 11 1.6 G_temp_sup-Plan_tempo
- 3975 2690 10435 2.865 0.619 0.168 0.072 149 11.1 G_temporal_inf
- 3685 2521 10596 3.003 0.710 0.147 0.051 83 7.7 G_temporal_middle
- 630 411 847 2.232 0.444 0.093 0.019 3 0.5 Lat_Fis-ant-Horizont
- 395 263 547 2.533 0.383 0.096 0.023 2 0.4 Lat_Fis-ant-Vertical
- 1732 1151 2400 2.383 0.561 0.119 0.034 13 2.5 Lat_Fis-post
- 3856 2540 6340 2.205 0.478 0.157 0.067 75 10.0 Pole_occipital
- 2199 1555 6553 2.987 0.896 0.159 0.074 50 6.9 Pole_temporal
- 3545 2377 4758 2.182 0.586 0.137 0.049 46 7.1 S_calcarine
- 3502 2325 4313 2.047 0.580 0.104 0.029 19 4.5 S_central
- 1702 1132 2575 2.381 0.384 0.111 0.031 13 2.2 S_cingul-Marginalis
- 715 454 1395 3.296 0.629 0.124 0.062 8 1.3 S_circular_insula_ant
- 1422 946 2353 2.876 0.648 0.100 0.025 7 1.5 S_circular_insula_inf
- 1874 1269 3079 2.632 0.547 0.105 0.030 12 2.5 S_circular_insula_sup
- 1613 1099 2899 2.641 0.492 0.107 0.030 14 2.0 S_collat_transv_ant
- 487 325 780 2.491 0.456 0.159 0.055 8 1.2 S_collat_transv_post
- 2003 1348 3072 2.351 0.469 0.112 0.029 14 2.6 S_front_inf
- 2655 1772 4046 2.340 0.430 0.135 0.048 35 4.6 S_front_middle
- 3026 2041 5273 2.633 0.460 0.120 0.033 30 4.2 S_front_sup
- 363 245 556 2.499 0.510 0.132 0.032 3 0.5 S_interm_prim-Jensen
- 3607 2342 5253 2.233 0.381 0.110 0.032 38 4.7 S_intrapariet_and_P_trans
- 1529 1035 2207 2.262 0.419 0.124 0.036 15 2.1 S_oc_middle_and_Lunatus
- 1889 1247 2824 2.294 0.370 0.136 0.038 22 3.1 S_oc_sup_and_transversal
- 1026 689 1491 2.324 0.402 0.131 0.049 14 2.2 S_occipital_ant
- 1031 721 1710 2.572 0.471 0.108 0.029 5 1.3 S_oc-temp_lat
- 1926 1310 3304 2.645 0.453 0.131 0.042 23 3.6 S_oc-temp_med_and_Lingual
- 607 397 748 2.132 0.415 0.136 0.040 8 0.9 S_orbital_lateral
- 908 629 1432 2.399 0.729 0.117 0.080 51 4.1 S_orbital_med-olfact
- 1809 1235 3281 2.498 0.577 0.147 0.049 28 3.6 S_orbital-H_Shaped
- 3013 2007 4711 2.508 0.468 0.136 0.043 45 5.1 S_parieto_occipital
- 1788 1129 1989 1.998 0.976 0.154 0.077 53 6.8 S_pericallosal
- 2867 1919 3863 2.227 0.347 0.102 0.051 44 4.8 S_postcentral
- 1452 960 2390 2.687 0.386 0.109 0.030 12 1.6 S_precentral-inf-part
- 1761 1207 2737 2.457 0.492 0.111 0.026 12 2.0 S_precentral-sup-part
- 426 276 571 2.092 0.733 0.116 0.036 5 0.7 S_suborbital
- 1218 831 2140 2.524 0.485 0.133 0.047 16 2.4 S_subparietal
- 2137 1470 3119 2.265 0.558 0.130 0.045 31 3.7 S_temporal_inf
- 7180 4873 12323 2.568 0.482 0.117 0.031 68 9.1 S_temporal_sup
- 388 264 552 2.681 0.398 0.115 0.024 2 0.4 S_temporal_transverse
- #-----------------------------------------
- #@# Cortical Parc 3 rh Thu Aug 8 23:20:05 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub016 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...
- 1104 labels changed using aseg
- relabeling using gibbs priors...
- 000: 3246 changed, 162159 examined...
- 001: 744 changed, 13762 examined...
- 002: 171 changed, 4059 examined...
- 003: 78 changed, 1021 examined...
- 004: 39 changed, 437 examined...
- 005: 18 changed, 219 examined...
- 006: 8 changed, 102 examined...
- 007: 9 changed, 52 examined...
- 008: 5 changed, 57 examined...
- 009: 5 changed, 33 examined...
- 010: 3 changed, 26 examined...
- 011: 3 changed, 21 examined...
- 012: 5 changed, 21 examined...
- 013: 6 changed, 29 examined...
- 014: 7 changed, 33 examined...
- 015: 6 changed, 39 examined...
- 016: 6 changed, 33 examined...
- 017: 4 changed, 30 examined...
- 018: 2 changed, 17 examined...
- 019: 3 changed, 10 examined...
- 020: 5 changed, 14 examined...
- 021: 2 changed, 19 examined...
- 022: 4 changed, 14 examined...
- 023: 5 changed, 19 examined...
- 024: 1 changed, 27 examined...
- 025: 1 changed, 8 examined...
- 026: 1 changed, 6 examined...
- 027: 1 changed, 7 examined...
- 028: 1 changed, 7 examined...
- 029: 1 changed, 7 examined...
- 030: 1 changed, 7 examined...
- 031: 0 changed, 7 examined...
- 223 labels changed using aseg
- 000: 72 total segments, 38 labels (218 vertices) changed
- 001: 34 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...
- 1230 vertices marked for relabeling...
- 1230 labels changed in reclassification.
- writing output to ../label/rh.aparc.DKTatlas40.annot...
- classification took 1 minutes and 10 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 3 rh Thu Aug 8 23:21:16 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 sub016 rh white
- computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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
- 825 539 1678 2.803 0.558 0.143 0.058 13 1.1 caudalanteriorcingulate
- 3459 2269 7161 2.846 0.509 0.130 0.082 59 6.4 caudalmiddlefrontal
- 3488 2305 5757 2.268 0.457 0.149 0.057 58 8.4 cuneus
- 719 499 1968 3.209 0.724 0.138 0.051 8 1.6 entorhinal
- 4652 3113 10238 2.740 0.517 0.144 0.063 88 12.7 fusiform
- 9665 6411 18366 2.536 0.502 0.144 0.054 176 19.6 inferiorparietal
- 7469 5086 16763 2.696 0.637 0.149 0.061 201 17.9 inferiortemporal
- 2357 1539 3956 2.365 0.939 0.161 0.084 70 8.9 isthmuscingulate
- 9192 5987 16108 2.350 0.476 0.154 0.067 204 26.9 lateraloccipital
- 5244 3537 11285 2.718 0.679 0.160 0.072 159 16.9 lateralorbitofrontal
- 5477 3641 8694 2.183 0.605 0.163 0.113 130 16.8 lingual
- 2886 1874 5726 2.500 0.771 0.157 0.116 106 13.0 medialorbitofrontal
- 7553 5192 17626 2.749 0.691 0.133 0.044 130 14.0 middletemporal
- 1246 851 2573 2.668 0.562 0.140 0.051 20 2.6 parahippocampal
- 3214 1977 5663 2.609 0.492 0.118 0.037 34 5.4 paracentral
- 3328 2163 6592 2.723 0.477 0.114 0.041 36 4.4 parsopercularis
- 1436 1011 3342 2.708 0.569 0.159 0.063 29 3.2 parsorbitalis
- 2973 2006 5940 2.518 0.579 0.132 0.068 92 4.8 parstriangularis
- 2921 1957 3836 2.062 0.403 0.147 0.059 45 6.8 pericalcarine
- 8046 5091 13212 2.250 0.539 0.117 0.127 195 12.4 postcentral
- 2270 1487 4441 2.686 0.708 0.146 0.055 41 5.7 posteriorcingulate
- 8099 4949 15152 2.780 0.605 0.110 0.149 323 59.6 precentral
- 6594 4411 12746 2.591 0.537 0.142 0.051 118 13.4 precuneus
- 1018 656 1863 3.000 0.735 0.120 0.082 126 5.4 rostralanteriorcingulate
- 5927 3980 11386 2.484 0.480 0.146 0.049 104 12.1 rostralmiddlefrontal
- 17813 11902 38228 2.763 0.558 0.136 0.047 313 34.8 superiorfrontal
- 7643 4886 12640 2.319 0.436 0.125 0.040 108 12.1 superiorparietal
- 7917 5409 19364 3.068 0.662 0.135 0.042 102 13.8 superiortemporal
- 5709 3860 11375 2.638 0.534 0.136 0.063 113 11.4 supramarginal
- 719 434 1520 2.912 0.320 0.122 0.046 8 1.2 transversetemporal
- 3547 2326 7814 3.148 0.923 0.130 0.063 53 8.1 insula
- #--------------------------------------------
- #@# Refine Pial Surfs w/ T2/FLAIR Thu Aug 8 23:21:39 CEST 2013
- bbregister --s sub016 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/T2raw.lta --init-fsl --T2
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/T2raw.dat.log
- Thu Aug 8 23:21:40 CEST 2013
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts
- /opt/freesurfer/5.3.0/bin/bbregister --s sub016 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/template.nii
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/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/sub016/mri/orig/T2raw.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.999248, 0.0307568, 0.0236215)
- j_ras = (0.0317878, 0.9985, 0.0445881)
- k_ras = (0.0222147, -0.0453054, 0.998726)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/template.nii...
- fslregister --s sub016 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/fslregister --dof 6 --fsvol brainmask.mgz
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/reg.init.dat.fslregister.log
- Thu Aug 8 23:21:45 CEST 2013
- --s sub016 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/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/sub016/scripts
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/fslregister/refvol.fslregister.nii
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/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/sub016/mri/brainmask.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, 1.86265e-09, 3.72529e-09)
- j_ras = (1.86265e-09, 0, -1)
- k_ras = (-1.97906e-09, 1, -3.72529e-09)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/fslregister/refvol.fslregister.nii...
- --------------------------------------
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/fslregister/movvol.fslregister.nii --frame 0
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/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/sub016/mri/transforms/tmp.bbregister.24421/template.nii...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.999248, 0.0307568, 0.0236215)
- j_ras = (0.0317878, 0.9985, 0.0445881)
- k_ras = (0.0222147, -0.0453054, 0.998726)
- keeping frame 0
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/fslregister/movvol.fslregister.nii...
- Mov determinant is -0.311066
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts
- tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/fslregister/movvol.fslregister.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/fslregister/reg0.24460.dat --regheader --fslregout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/reg.init.dat.fsl.mat0 --s sub016 --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/sub016/mri/transforms/tmp.bbregister.24421/fslregister/movvol.fslregister.nii
- reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/fslregister/reg0.24460.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/sub016/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/sub016/mri/transforms/tmp.bbregister.24421/fslregister/movvol.fslregister.nii
- Tmov: --------------------
- -0.700 0.000 0.000 95.886;
- 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) --------
- 0.999 -0.031 -0.024 -0.000;
- 0.022 -0.045 0.999 -0.000;
- -0.032 -0.998 -0.045 -0.000;
- 0.000 0.000 0.000 1.000;
- ---------------------------------------
- ---- Input registration matrix --------
- 0.999 -0.031 -0.024 -0.000;
- 0.022 -0.045 0.999 -0.000;
- -0.032 -0.998 -0.045 -0.000;
- 0.000 0.000 0.000 1.000;
- Determinant 1
- subject = sub016
- RegMat ---------------------------
- 0.999 -0.031 -0.024 -0.000;
- 0.022 -0.045 0.999 -0.000;
- -0.032 -0.998 -0.045 -0.000;
- 0.000 0.000 0.000 1.000;
- FSLOUTPUTTYPE NIFTI
- tkreg2FSL: mov det = -0.311066, ref det = -1
- Thu Aug 8 23:21:54 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts
- flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/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/sub016/mri/transforms/tmp.bbregister.24421/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/reg.init.dat.fsl.mat0
- Thu Aug 8 23:26:14 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts
- flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/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/sub016/mri/transforms/tmp.bbregister.24421/reg.init.dat.fsl.mat -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/fslregister/fslmat0.trans.mat -schedule /opt/freesurfer/5.3.0/bin/flirt.newdefault.20080811.sch
- tkregister2_cmdl --s sub016 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/reg.init.dat --fslreg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/reg.init.dat.fsl.mat --noedit
- tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl
- ---- FSL registration matrix --------
- 0.999 -0.033 -0.022 39.132;
- -0.023 -0.039 -0.999 265.314;
- 0.032 0.999 -0.040 0.697;
- 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/sub016/mri/transforms/tmp.bbregister.24421/template.nii
- reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/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/sub016/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/sub016/mri/transforms/tmp.bbregister.24421/template.nii
- Tmov: --------------------
- -0.700 0.000 0.000 95.886;
- 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 = -0.311066, ref det = -1
- ---- Input registration matrix (computed) --------
- 0.999 -0.032 -0.023 -0.073;
- 0.022 -0.040 0.999 2.189;
- -0.033 -0.999 -0.039 -1.621;
- 0.000 0.000 0.000 1.000;
- ---------------------------------------
- ---- Input registration matrix --------
- 0.999 -0.032 -0.023 -0.073;
- 0.022 -0.040 0.999 2.189;
- -0.033 -0.999 -0.039 -1.621;
- 0.000 0.000 0.000 1.000;
- Determinant 1
- subject = sub016
- RegMat ---------------------------
- 0.999 -0.032 -0.023 -0.073;
- 0.022 -0.040 0.999 2.189;
- -0.033 -0.999 -0.039 -1.621;
- 0.000 0.000 0.000 1.000;
-
- Started at Thu Aug 8 23:21:45 CEST 2013
- Ended at Thu Aug 8 23:31:55 CEST 2013
-
- fslregister Done
-
- To check results, run:
- tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/reg.init.dat --surf orig
-
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/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/sub016/scripts
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/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/sub016/mri/transforms/tmp.bbregister.24421/template.nii
- regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/reg.init.dat
- subject sub016
- dof 6
- outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/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 1376727398
- TransRandMax 0.000000
- RotRandMax 0.000000
- Translations 0.000000 0.000000 0.000000
- Rotations 0.000000 0.000000 0.000000
- Input reg
- 0.999 -0.032 -0.023 -0.073;
- 0.022 -0.040 0.999 2.189;
- -0.033 -0.999 -0.039 -1.621;
- 0.000 0.000 0.000 1.000;
- Loading mov
- Projecting LH Surfs
- Loading lh.white surf
- Loading lh.thickness for GM
- GM Proj: 1 0.500000 2.000000
- WM Proj: 0 0.500000 2.000000
- Projecting RH Surfs
- Loading rh.white surf
- Loading rh.thickness
- Projecting RH Surfs
- Computing relative cost
- 0 -25.0 -25.0 -25.0 0.991698
- 1 -25.0 -25.0 25.0 1.017919
- 2 -25.0 25.0 -25.0 1.014961
- 3 -25.0 25.0 25.0 1.012154
- 4 25.0 -25.0 -25.0 1.053511
- 5 25.0 -25.0 25.0 1.038265
- 6 25.0 25.0 -25.0 1.025332
- 7 25.0 25.0 25.0 1.040335
- REL: 8 0.497330 8.194174 1.024272 rel = 0.485545
- Initial costs ----------------
- Number of surface hits 3047
- WM Intensity 58.1412 +/- 8.4125
- Ctx Intensity 68.1580 +/- 13.9941
- Pct Contrast 14.7458 +/- 22.3937
- Cost 0.4973
- RelCost 0.4855
- ------------------------------------
- Brute force preopt -4 4 4, n = 729
- 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9706 0.9706 0.0
- 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.9683 0.9683 0.0
- 3 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 -4.0000 0.9651 0.9651 0.0
- 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.8698 0.8698 0.0
- 21 -4.0000 -4.0000 -4.0000 4.0000 0.0000 -4.0000 0.8503 0.8503 0.0
- 39 -4.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.8111 0.8111 0.0
- 120 -4.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.7265 0.7265 0.0
- 346 0.0000 0.0000 -4.0000 4.0000 0.0000 0.0000 0.7237 0.7237 0.0
- 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.4973 0.4973 0.0
- Brute Force --------------------------
- Min cost was 0.497330
- Number of iterations 729
- Search time 2.336000 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 0.058 0.000 0.000 0.000 0.000 0.000 0.4962479741
- 8 0.173 0.000 0.000 0.000 0.000 0.000 0.4956493570
- 9 0.150 0.000 0.000 0.000 0.000 0.000 0.4954339777
- 11 0.148 0.000 0.000 0.000 0.000 0.000 0.4954213621
- 12 0.144 0.000 0.000 0.000 0.000 0.000 0.4954030878
- 18 0.144 -1.618 0.000 0.000 0.000 0.000 0.3123496406
- 23 0.144 -1.481 0.000 0.000 0.000 0.000 0.3072172974
- 24 0.144 -1.427 0.000 0.000 0.000 0.000 0.3064682236
- 26 0.144 -1.443 0.000 0.000 0.000 0.000 0.3063398337
- 27 0.144 -1.442 0.000 0.000 0.000 0.000 0.3063332070
- 28 0.144 -1.439 0.000 0.000 0.000 0.000 0.3063242057
- 33 0.144 -1.439 1.000 0.000 0.000 0.000 0.1447468946
- 38 0.144 -1.439 1.258 0.000 0.000 0.000 0.1406853989
- 39 0.144 -1.439 1.242 0.000 0.000 0.000 0.1403118087
- 40 0.144 -1.439 1.178 0.000 0.000 0.000 0.1399896185
- 42 0.144 -1.439 1.199 0.000 0.000 0.000 0.1397496399
- 44 0.144 -1.439 1.200 0.000 0.000 0.000 0.1397479461
- 57 0.144 -1.439 1.200 0.009 0.000 0.000 0.1395871869
- 58 0.144 -1.439 1.200 0.011 0.000 0.000 0.1395814210
- 67 0.144 -1.439 1.200 0.011 -0.164 0.000 0.1379313531
- 68 0.144 -1.439 1.200 0.011 -0.132 0.000 0.1376534846
- 69 0.144 -1.439 1.200 0.011 -0.118 0.000 0.1373763056
- 71 0.144 -1.439 1.200 0.011 -0.103 0.000 0.1372832564
- 80 0.144 -1.439 1.200 0.011 -0.103 0.119 0.1361960394
- 81 0.144 -1.439 1.200 0.011 -0.103 0.101 0.1360196246
- 82 0.144 -1.439 1.200 0.011 -0.103 0.083 0.1359179116
- 84 0.144 -1.439 1.200 0.011 -0.103 0.079 0.1359153918
- 85 0.144 -1.439 1.200 0.011 -0.103 0.080 0.1359150338
- 97 0.151 -1.439 1.200 0.011 -0.103 0.080 0.1359105495
- 98 0.149 -1.439 1.200 0.011 -0.103 0.080 0.1359064688
- 99 0.148 -1.439 1.200 0.011 -0.103 0.080 0.1359061504
- 107 0.148 -1.462 1.200 0.011 -0.103 0.080 0.1354371527
- 109 0.148 -1.526 1.200 0.011 -0.103 0.080 0.1348476725
- 110 0.148 -1.545 1.200 0.011 -0.103 0.080 0.1346955371
- 111 0.148 -1.577 1.200 0.011 -0.103 0.080 0.1345269131
- 113 0.148 -1.565 1.200 0.011 -0.103 0.080 0.1345157736
- 114 0.148 -1.570 1.200 0.011 -0.103 0.080 0.1345017495
- 115 0.148 -1.571 1.200 0.011 -0.103 0.080 0.1345011534
- 124 0.148 -1.571 1.153 0.011 -0.103 0.080 0.1344975072
- 125 0.148 -1.571 1.176 0.011 -0.103 0.080 0.1343772027
- 127 0.148 -1.571 1.171 0.011 -0.103 0.080 0.1343579904
- 129 0.148 -1.571 1.169 0.011 -0.103 0.080 0.1343552516
- 141 0.148 -1.571 1.169 0.010 -0.103 0.080 0.1343542902
- 150 0.148 -1.571 1.169 0.010 -0.131 0.080 0.1339936964
- 152 0.148 -1.571 1.169 0.010 -0.132 0.080 0.1339928523
- 162 0.148 -1.571 1.169 0.010 -0.132 0.045 0.1339816050
- 163 0.148 -1.571 1.169 0.010 -0.132 0.062 0.1338638798
- 166 0.148 -1.571 1.169 0.010 -0.132 0.064 0.1338620199
- 175 0.141 -1.571 1.169 0.010 -0.132 0.064 0.1337887306
- 179 0.138 -1.571 1.169 0.010 -0.132 0.064 0.1337767557
- 191 0.138 -1.582 1.169 0.010 -0.132 0.064 0.1337187231
- 193 0.138 -1.581 1.169 0.010 -0.132 0.064 0.1337185913
- 206 0.138 -1.581 1.164 0.010 -0.132 0.064 0.1336990090
- 208 0.138 -1.581 1.163 0.010 -0.132 0.064 0.1336987668
- 218 0.138 -1.581 1.163 0.012 -0.132 0.064 0.1336981293
- 241 0.138 -1.581 1.163 0.012 -0.132 0.048 0.1336249538
- 244 0.128 -1.592 1.156 0.014 -0.132 0.033 0.1335438535
- 251 0.129 -1.591 1.157 0.014 -0.132 0.034 0.1335415787
- 252 0.129 -1.590 1.157 0.014 -0.132 0.035 0.1335407690
- 257 0.129 -1.590 1.157 0.014 -0.132 0.035 0.1335407147
- 261 0.129 -1.590 1.157 0.014 -0.132 0.035 0.1335406048
- 270 0.129 -1.590 1.157 0.014 -0.132 0.038 0.1335310703
- 272 0.129 -1.590 1.157 0.014 -0.132 0.040 0.1335282673
- 273 0.129 -1.590 1.157 0.014 -0.132 0.041 0.1335277339
- 282 0.129 -1.581 1.157 0.014 -0.132 0.041 0.1334871275
- 283 0.129 -1.579 1.157 0.014 -0.132 0.041 0.1334814295
- 287 0.129 -1.577 1.157 0.014 -0.132 0.041 0.1334805825
- 301 0.129 -1.577 1.152 0.014 -0.132 0.041 0.1334726852
- 312 0.129 -1.577 1.152 0.015 -0.132 0.041 0.1334665716
- 313 0.129 -1.577 1.152 0.017 -0.132 0.041 0.1334652903
- 324 0.129 -1.577 1.152 0.017 -0.135 0.041 0.1334594948
- 328 0.120 -1.588 1.146 0.019 -0.135 0.026 0.1334288625
- 332 0.123 -1.584 1.149 0.018 -0.135 0.031 0.1334217989
- 334 0.123 -1.584 1.148 0.018 -0.135 0.031 0.1334216584
- 339 0.123 -1.584 1.149 0.018 -0.135 0.031 0.1334215674
- 341 0.123 -1.584 1.149 0.018 -0.135 0.031 0.1334214761
- 344 0.109 -1.587 1.134 0.024 -0.137 0.014 0.1333468299
- 351 0.107 -1.588 1.133 0.025 -0.138 0.012 0.1333424901
- 352 0.106 -1.588 1.132 0.026 -0.138 0.011 0.1333423748
- 353 0.106 -1.588 1.132 0.025 -0.138 0.011 0.1333422128
- 354 0.106 -1.588 1.132 0.025 -0.138 0.011 0.1333421542
- 374 0.112 -1.581 1.136 0.024 -0.138 0.021 0.1333064110
- 380 0.112 -1.581 1.136 0.024 -0.138 0.021 0.1333063697
- 411 0.112 -1.581 1.136 0.022 -0.138 0.021 0.1332996639
- 421 0.112 -1.581 1.136 0.022 -0.137 0.021 0.1332967946
- 422 0.112 -1.581 1.136 0.022 -0.135 0.021 0.1332967036
- 430 0.107 -1.582 1.131 0.025 -0.136 0.014 0.1332811809
- 431 0.106 -1.582 1.130 0.025 -0.136 0.013 0.1332794866
- 434 0.106 -1.582 1.130 0.025 -0.136 0.013 0.1332792467
- 451 0.106 -1.582 1.130 0.025 -0.136 0.011 0.1332780862
- 459 0.108 -1.579 1.131 0.025 -0.136 0.015 0.1332721868
- 460 0.108 -1.580 1.131 0.025 -0.136 0.015 0.1332718205
- 461 0.108 -1.580 1.131 0.025 -0.136 0.014 0.1332717118
- 470 0.108 -1.580 1.131 0.025 -0.136 0.014 0.1332716711
- 482 0.108 -1.580 1.139 0.025 -0.136 0.014 0.1332685167
- 483 0.108 -1.580 1.135 0.025 -0.136 0.014 0.1332621981
- 494 0.108 -1.580 1.135 0.022 -0.136 0.014 0.1332613604
- 496 0.108 -1.580 1.135 0.023 -0.136 0.014 0.1332588580
- 508 0.108 -1.580 1.135 0.023 -0.137 0.014 0.1332585011
- 514 0.102 -1.581 1.130 0.025 -0.138 0.008 0.1332576465
- 515 0.105 -1.581 1.133 0.024 -0.138 0.011 0.1332523634
- 516 0.105 -1.581 1.133 0.024 -0.138 0.011 0.1332522537
- 518 0.105 -1.581 1.133 0.024 -0.138 0.011 0.1332522008
- 526 0.105 -1.579 1.136 0.023 -0.139 0.009 0.1332483876
- 586 0.106 -1.580 1.136 0.023 -0.135 0.013 0.1332471225
- 587 0.106 -1.580 1.136 0.023 -0.136 0.013 0.1332467187
- 594 0.103 -1.581 1.133 0.024 -0.137 0.010 0.1332410557
- Powell done niters = 6
- Computing relative cost
- 0 -25.0 -25.0 -25.0 0.987108
- 1 -25.0 -25.0 25.0 1.009174
- 2 -25.0 25.0 -25.0 0.994077
- 3 -25.0 25.0 25.0 1.024224
- 4 25.0 -25.0 -25.0 1.032857
- 5 25.0 -25.0 25.0 1.005481
- 6 25.0 25.0 -25.0 0.980632
- 7 25.0 25.0 25.0 1.024402
- REL: 8 0.133241 8.057954 1.007244 rel = 0.132283
- Number of iterations 6
- Min cost was 0.133241
- Number of FunctionCalls 602
- TolPowell 0.000100
- nMaxItersPowell 36
- OptimizationTime 1.771000 sec
- Parameters at optimum (transmm) 0.10308 -1.58084 1.13322
- Parameters at optimum (rotdeg) 0.02365 -0.13659 0.00979
- Final costs ----------------
- Number of surface hits 3047
- WM Intensity 56.4536 +/- 7.1833
- Ctx Intensity 67.5397 +/- 7.6173
- Pct Contrast 17.8999 +/- 12.3774
- Cost 0.1332
- RelCost 0.4855
- Reg at min cost was
- 0.999 -0.029 -0.023 0.034;
- 0.022 -0.039 0.999 0.608;
- -0.030 -0.999 -0.039 -0.487;
- 0.000 0.000 0.000 1.000;
- Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/bbr.pass1.dat, type = 14
- Original Reg
- 0.999 -0.032 -0.023 -0.073;
- 0.022 -0.040 0.999 2.189;
- -0.033 -0.999 -0.039 -1.621;
- 0.000 0.000 0.000 1.000;
- Original Reg - Optimal Reg
- -0.000 -0.002 0.000 -0.107;
- -0.000 -0.000 -0.000 1.580;
- -0.002 0.000 -0.000 -1.134;
- 0.000 0.000 0.000 0.000;
- Computing change in lh position
- LH rmsDiffMean 1.928128
- Computing change in rh position
- Surface RMS Diff (mm) 1.965314 2.053568
- mri_segreg done
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/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/sub016/scripts
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/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/sub016/mri/transforms/tmp.bbregister.24421/template.nii
- regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/bbr.pass1.dat
- subject sub016
- dof 6
- outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 1376990004
- TransRandMax 0.000000
- RotRandMax 0.000000
- Translations 0.000000 0.000000 0.000000
- Rotations 0.000000 0.000000 0.000000
- Input reg
- 0.999 -0.029 -0.023 0.034;
- 0.022 -0.039 0.999 0.608;
- -0.030 -0.999 -0.039 -0.487;
- 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 1.013674
- 1 -25.0 -25.0 25.0 0.994273
- 2 -25.0 25.0 -25.0 0.995462
- 3 -25.0 25.0 25.0 1.013802
- 4 25.0 -25.0 -25.0 1.027246
- 5 25.0 -25.0 25.0 1.007479
- 6 25.0 25.0 -25.0 0.998557
- 7 25.0 25.0 25.0 1.024932
- REL: 8 0.141688 8.075426 1.009428 rel = 0.140364
- Initial costs ----------------
- Number of surface hits 304481
- WM Intensity 56.5409 +/- 7.1624
- Ctx Intensity 67.6348 +/- 7.7629
- Pct Contrast 17.8592 +/- 12.5660
- Cost 0.1417
- RelCost 0.1404
- ------------------------------------
- Brute force preopt -0.1 0.1 0.1, n = 729
- 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1471 0.1471 0.0
- 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.1459 0.1459 0.0
- 9 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 -0.1000 0.1439 0.1439 0.0
- 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.1434 0.1434 0.0
- 13 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.1426 0.1426 0.0
- 22 -0.1000 -0.1000 -0.1000 0.1000 0.0000 0.0000 0.1399 0.1399 0.0
- 39 -0.1000 -0.1000 0.0000 0.0000 0.0000 -0.1000 0.1396 0.1396 0.0
- 40 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.0000 0.1377 0.1377 0.0
- 49 -0.1000 -0.1000 0.0000 0.1000 0.0000 0.0000 0.1362 0.1362 0.0
- 67 -0.1000 -0.1000 0.1000 0.0000 0.0000 0.0000 0.1344 0.1344 0.0
- 130 -0.1000 0.0000 0.0000 0.1000 0.0000 0.0000 0.1344 0.1344 0.0
- 148 -0.1000 0.0000 0.1000 0.0000 0.0000 0.0000 0.1342 0.1342 0.0
- 157 -0.1000 0.0000 0.1000 0.1000 0.0000 0.0000 0.1342 0.1342 0.0
- 211 -0.1000 0.1000 0.0000 0.1000 0.0000 0.0000 0.1332 0.1332 0.0
- Brute Force --------------------------
- Min cost was 0.133165
- Number of iterations 729
- Search time 2.128000 sec
- Parameters at best (transmm, rotdeg)
- -0.100 0.100 0.000 0.100 0.000 0.000
- --------------------------------------------
- Starting Powell Minimization
- Init Powel Params dof = 6
- 0 -0.1
- 1 0.1
- 2 0
- 3 0.1
- 4 0
- 5 0
- 7 -0.040 0.100 0.000 0.100 0.000 0.000 0.1383786066
- 8 -0.060 0.100 0.000 0.100 0.000 0.000 0.1383350291
- 10 -0.059 0.100 0.000 0.100 0.000 0.000 0.1383349480
- 19 -0.059 0.196 0.000 0.100 0.000 0.000 0.1372708911
- 28 -0.059 0.196 0.126 0.100 0.000 0.000 0.1360247476
- 29 -0.059 0.196 0.120 0.100 0.000 0.000 0.1360163550
- 30 -0.059 0.196 0.116 0.100 0.000 0.000 0.1360147204
- 39 -0.059 0.196 0.116 0.051 0.000 0.000 0.1354389563
- 40 -0.059 0.196 0.116 0.044 0.000 0.000 0.1354184637
- 41 -0.059 0.196 0.116 0.038 0.000 0.000 0.1354155472
- 42 -0.059 0.196 0.116 0.040 0.000 0.000 0.1354152911
- 50 -0.059 0.196 0.116 0.040 -0.061 0.000 0.1348322987
- 52 -0.059 0.196 0.116 0.040 -0.065 0.000 0.1348295650
- 53 -0.059 0.196 0.116 0.040 -0.064 0.000 0.1348295083
- 61 -0.059 0.196 0.116 0.040 -0.064 0.015 0.1348115263
- 62 -0.059 0.196 0.116 0.040 -0.064 0.013 0.1348100653
- 63 -0.059 0.196 0.116 0.040 -0.064 0.012 0.1348097944
- 72 -0.023 0.196 0.116 0.040 -0.064 0.012 0.1347987256
- 73 -0.039 0.196 0.116 0.040 -0.064 0.012 0.1347666581
- 83 -0.039 0.189 0.116 0.040 -0.064 0.012 0.1347613712
- 92 -0.039 0.189 0.182 0.040 -0.064 0.012 0.1345687690
- 93 -0.039 0.189 0.167 0.040 -0.064 0.012 0.1345484474
- 95 -0.039 0.189 0.162 0.040 -0.064 0.012 0.1345484171
- 97 -0.039 0.189 0.164 0.040 -0.064 0.012 0.1345479816
- 106 -0.039 0.189 0.164 0.026 -0.064 0.012 0.1344668773
- 107 -0.039 0.189 0.164 0.016 -0.064 0.012 0.1344402774
- 108 -0.039 0.189 0.164 0.012 -0.064 0.012 0.1344367260
- 117 -0.039 0.189 0.164 0.012 -0.067 0.012 0.1344335818
- 118 -0.039 0.189 0.164 0.012 -0.071 0.012 0.1344296615
- 120 -0.039 0.189 0.164 0.012 -0.076 0.012 0.1344282299
- 122 -0.039 0.189 0.164 0.012 -0.075 0.012 0.1344281565
- 130 -0.039 0.189 0.164 0.012 -0.075 0.026 0.1344084441
- 131 -0.039 0.189 0.164 0.012 -0.075 0.025 0.1344074875
- 132 -0.039 0.189 0.164 0.012 -0.075 0.023 0.1344071491
- 134 -0.019 0.182 0.212 -0.015 -0.085 0.035 0.1343182007
- 140 -0.027 0.185 0.194 -0.005 -0.081 0.030 0.1343139430
- 141 -0.024 0.184 0.201 -0.009 -0.083 0.032 0.1343115115
- 142 -0.024 0.184 0.201 -0.009 -0.082 0.032 0.1343114196
- 144 -0.024 0.184 0.200 -0.009 -0.082 0.032 0.1343114161
- 145 -0.024 0.184 0.201 -0.009 -0.082 0.032 0.1343113993
- 146 -0.024 0.184 0.201 -0.009 -0.082 0.032 0.1343113763
- 156 -0.023 0.184 0.201 -0.009 -0.082 0.032 0.1343113219
- 165 -0.023 0.168 0.201 -0.009 -0.082 0.032 0.1342921102
- 168 -0.023 0.169 0.201 -0.009 -0.082 0.032 0.1342919357
- 186 -0.023 0.169 0.201 -0.010 -0.082 0.032 0.1342918736
- 194 -0.023 0.169 0.201 -0.010 -0.077 0.032 0.1342895233
- 196 -0.023 0.169 0.201 -0.010 -0.076 0.032 0.1342893447
- 204 -0.016 0.167 0.219 -0.020 -0.080 0.036 0.1342801141
- 205 -0.017 0.167 0.215 -0.018 -0.079 0.035 0.1342795104
- 206 -0.017 0.167 0.215 -0.018 -0.079 0.035 0.1342794935
- 207 -0.017 0.167 0.215 -0.018 -0.079 0.035 0.1342794915
- 208 -0.017 0.167 0.215 -0.018 -0.079 0.035 0.1342794695
- 220 -0.018 0.167 0.215 -0.018 -0.079 0.035 0.1342793241
- 228 -0.018 0.166 0.215 -0.018 -0.079 0.035 0.1342780381
- 229 -0.018 0.163 0.215 -0.018 -0.079 0.035 0.1342773814
- 231 -0.018 0.164 0.215 -0.018 -0.079 0.035 0.1342773395
- 240 -0.018 0.164 0.215 -0.018 -0.079 0.034 0.1342769522
- 251 -0.018 0.164 0.215 -0.014 -0.079 0.034 0.1342747860
- 269 -0.017 0.163 0.219 -0.016 -0.080 0.035 0.1342731830
- 270 -0.016 0.163 0.220 -0.017 -0.080 0.035 0.1342730505
- 271 -0.016 0.163 0.220 -0.017 -0.080 0.035 0.1342730021
- 274 -0.016 0.163 0.221 -0.017 -0.080 0.036 0.1342729395
- 288 -0.018 0.163 0.221 -0.017 -0.080 0.036 0.1342724065
- 306 -0.018 0.163 0.221 -0.017 -0.080 0.034 0.1342722990
- 307 -0.018 0.163 0.221 -0.017 -0.080 0.033 0.1342721992
- 321 -0.018 0.163 0.221 -0.016 -0.080 0.033 0.1342720073
- 330 -0.018 0.163 0.221 -0.016 -0.078 0.033 0.1342712016
- 341 -0.018 0.163 0.222 -0.017 -0.078 0.033 0.1342711738
- 344 -0.018 0.163 0.222 -0.017 -0.078 0.033 0.1342711728
- 357 -0.020 0.163 0.222 -0.017 -0.078 0.033 0.1342708052
- 366 -0.020 0.164 0.222 -0.017 -0.078 0.033 0.1342707798
- 375 -0.020 0.164 0.222 -0.017 -0.078 0.032 0.1342707229
- 384 -0.020 0.164 0.222 -0.016 -0.078 0.032 0.1342706602
- 393 -0.020 0.164 0.222 -0.016 -0.077 0.032 0.1342704408
- 417 -0.021 0.164 0.222 -0.016 -0.077 0.032 0.1342703886
- 454 -0.021 0.164 0.222 -0.016 -0.076 0.032 0.1342703700
- 466 -0.021 0.164 0.222 -0.016 -0.076 0.032 0.1342703523
- Powell done niters = 7
- Computing relative cost
- 0 -25.0 -25.0 -25.0 1.014724
- 1 -25.0 -25.0 25.0 0.993885
- 2 -25.0 25.0 -25.0 0.993645
- 3 -25.0 25.0 25.0 1.012720
- 4 25.0 -25.0 -25.0 1.028029
- 5 25.0 -25.0 25.0 1.005782
- 6 25.0 25.0 -25.0 0.999341
- 7 25.0 25.0 25.0 1.024793
- REL: 8 0.134270 8.072920 1.009115 rel = 0.133058
- Number of iterations 7
- Min cost was 0.134270
- Number of FunctionCalls 527
- TolPowell 0.000000
- nMaxItersPowell 36
- OptimizationTime 69.051000 sec
- Parameters at optimum (transmm) -0.02074 0.16374 0.22181
- Parameters at optimum (rotdeg) -0.01581 -0.07641 0.03234
- Final costs ----------------
- Number of surface hits 304481
- WM Intensity 56.5318 +/- 7.1402
- Ctx Intensity 67.5968 +/- 7.7119
- Pct Contrast 17.8233 +/- 12.4061
- Cost 0.1343
- RelCost 0.1404
- Reg at min cost was
- 0.999 -0.028 -0.023 0.013;
- 0.022 -0.040 0.999 0.772;
- -0.029 -0.999 -0.039 -0.265;
- 0.000 0.000 0.000 1.000;
- Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/T2raw.dat, type = 14
- Original Reg
- 0.999 -0.029 -0.023 0.034;
- 0.022 -0.039 0.999 0.608;
- -0.030 -0.999 -0.039 -0.487;
- 0.000 0.000 0.000 1.000;
- Original Reg - Optimal Reg
- -0.000 -0.001 0.001 0.020;
- -0.001 0.000 0.000 -0.164;
- -0.001 0.000 0.000 -0.222;
- 0.000 0.000 0.000 0.000;
- Computing change in lh position
- LH rmsDiffMean 0.244708
- Computing change in rh position
- Surface RMS Diff (mm) 0.284066 0.379271
- mri_segreg done
- tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/T2raw.dat --noedit --ltaout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/mri/orig/T2raw.mgz
- reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 --------
- 0.999 -0.028 -0.023 0.013;
- 0.022 -0.040 0.999 0.772;
- -0.029 -0.999 -0.039 -0.265;
- 0.000 0.000 0.000 1.000;
- float2int = 0
- ---------------------------------------
- INFO: loading target /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/mri/orig/T2raw.mgz
- Tmov: --------------------
- -0.700 0.000 0.000 95.886;
- 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 --------
- 0.999 -0.028 -0.023 0.013;
- 0.022 -0.040 0.999 0.772;
- -0.029 -0.999 -0.039 -0.265;
- 0.000 0.000 0.000 1.000;
- Determinant 1
- subject = sub016
- RegMat ---------------------------
- 0.999 -0.028 -0.023 0.013;
- 0.022 -0.040 0.999 0.772;
- -0.029 -0.999 -0.039 -0.265;
- 0.000 0.000 0.000 1.000;
- transformed matrix:
- 1.000 -0.003 -0.000 0.059;
- 0.003 1.000 0.006 -0.142;
- 0.000 -0.006 1.000 -0.599;
- 0.000 0.000 0.000 1.000;
- transformed matrix:
- 0.699 -0.019 -0.015 38.752;
- -0.016 -0.026 -0.666 263.892;
- 0.020 0.666 -0.026 2.326;
- 0.000 0.000 0.000 1.000;
- Cleaning up
-
- Started at Thu Aug 8 23:21:39 CEST 2013
- Ended at Thu Aug 8 23:33:58 CEST 2013
- BBR-Run-Time-Sec 739
-
- bbregister Done
- To check results, run:
- tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/T2raw.dat --surf
-
- mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/T2.mgz
- mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/mri/orig/T2raw.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.999248, 0.0307568, 0.0236215)
- j_ras = (0.0317878, 0.9985, 0.0445881)
- k_ras = (0.0222147, -0.0453054, 0.998726)
- INFO: Reading transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/T2raw.lta...
- Reading transform with LTAreadEx()
- reading extra input line subject sub016
- reading extra input line fscale 0.150000
- reading template info from volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig.mgz...
- INFO: Applying transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/T2raw.lta...
- ---------------------------------
- INFO: Transform Matrix (linear_ras_to_ras)
- 1.000 -0.003 -0.000 0.059;
- 0.003 1.000 0.006 -0.142;
- 0.000 -0.006 1.000 -0.599;
- 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/sub016/mri/T2.mgz...
- mri_normalize -aseg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/aseg.mgz -sigma 4 -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.white identity.nofile -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.white identity.nofile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/T2.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/mri/T2.mgz...
- computing distance transform
- computing distance transform
- computing nonmaximum suppression
- 15456 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/sub016/mri/T2.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts
- cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.woT2.pial
- `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.woT2.pial'
- mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub016 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/sub016/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz...
- 22234 bright wm thresholded.
- 384 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.orig...
- computing class statistics...
- border white: 298969 voxels (1.78%)
- border gray 333863 voxels (1.99%)
- WM (93.0): 93.9 +- 9.8 [70.0 --> 110.0]
- GM (77.0) : 75.0 +- 12.6 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 49.4 (was 70)
- setting MAX_BORDER_WHITE to 115.8 (was 105)
- setting MIN_BORDER_WHITE to 62.0 (was 85)
- setting MAX_CSF to 36.9 (was 40)
- setting MAX_GRAY to 96.2 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 55.7 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 24.3 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=106, GM=62
- mean inside = 93.8, mean outside = 70.2
- 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/sub016/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.89 +- 0.26 (0.03-->5.11) (max @ vno 160099 --> 160100)
- face area 0.33 +- 0.16 (0.00-->5.68)
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 247 points - only 4.05% unknown
- deleting segment 1 with 5 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 3 with 2 points - only 0.00% unknown
- deleting segment 4 with 5 points - only 0.00% unknown
- deleting segment 6 with 6 points - only 0.00% unknown
- deleting segment 7 with 881 points - only 0.00% unknown
- deleting segment 8 with 7 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 9 with 2 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 12 with 37 points - only 0.00% unknown
- deleting segment 13 with 8 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 14 with 1 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 15 with 2 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 16 with 3 points - only 0.00% unknown
- deleting segment 17 with 5 points - only 0.00% unknown
- tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.89 +- 0.25 (0.03-->4.83) (max @ vno 160104 --> 70416)
- face area 0.33 +- 0.16 (0.00-->5.68)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4771560.0, rms=0.00
- rms = 1.14, time step reduction 1 of 3 to 0.250...
- rms = 0.29, time step reduction 2 of 3 to 0.125...
- rms = 0.04, time step reduction 3 of 3 to 0.062...
- 001: dt: 0.1250, sse=4771560.0, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 247 points - only 4.05% unknown
- deleting segment 1 with 5 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 2 with 2 points - only 0.00% unknown
- deleting segment 3 with 5 points - only 0.00% unknown
- deleting segment 4 with 6 points - only 0.00% unknown
- deleting segment 5 with 881 points - only 0.00% unknown
- deleting segment 6 with 7 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 7 with 2 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 9 with 37 points - only 0.00% unknown
- deleting segment 10 with 8 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 11 with 1 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 12 with 2 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 13 with 3 points - only 0.00% unknown
- deleting segment 14 with 5 points - only 0.00% unknown
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.89 +- 0.25 (0.03-->4.83) (max @ vno 160104 --> 70416)
- face area 0.33 +- 0.16 (0.00-->5.68)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4771560.0, rms=0.00
- rms = 1.14, time step reduction 1 of 3 to 0.250...
- rms = 0.29, time step reduction 2 of 3 to 0.125...
- rms = 0.04, time step reduction 3 of 3 to 0.062...
- 002: dt: 0.1250, sse=4771560.0, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 247 points - only 4.05% unknown
- deleting segment 1 with 5 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 2 with 2 points - only 0.00% unknown
- deleting segment 3 with 5 points - only 0.00% unknown
- deleting segment 4 with 6 points - only 0.00% unknown
- deleting segment 5 with 881 points - only 0.00% unknown
- deleting segment 6 with 7 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 7 with 2 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 9 with 37 points - only 0.00% unknown
- deleting segment 10 with 8 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 11 with 1 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 12 with 2 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 13 with 3 points - only 0.00% unknown
- deleting segment 14 with 5 points - only 0.00% unknown
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.89 +- 0.25 (0.03-->4.83) (max @ vno 160104 --> 70416)
- face area 0.33 +- 0.16 (0.00-->5.68)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4771560.0, rms=0.00
- rms = 1.14, time step reduction 1 of 3 to 0.250...
- rms = 0.29, time step reduction 2 of 3 to 0.125...
- rms = 0.04, time step reduction 3 of 3 to 0.062...
- 003: dt: 0.1250, sse=4771560.0, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 247 points - only 4.05% unknown
- deleting segment 1 with 5 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 2 with 2 points - only 0.00% unknown
- deleting segment 3 with 5 points - only 0.00% unknown
- deleting segment 4 with 6 points - only 0.00% unknown
- deleting segment 5 with 881 points - only 0.00% unknown
- deleting segment 6 with 7 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 7 with 2 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 9 with 37 points - only 0.00% unknown
- deleting segment 10 with 8 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 11 with 1 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 12 with 2 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 13 with 3 points - only 0.00% unknown
- deleting segment 14 with 5 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=4771560.0, rms=0.00
- rms = 1.14, time step reduction 1 of 3 to 0.250...
- rms = 0.29, time step reduction 2 of 3 to 0.125...
- rms = 0.04, time step reduction 3 of 3 to 0.062...
- 004: dt: 0.1250, sse=4771560.0, 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
- removing 1 vertex label from ripped group
- smoothing surface for 5 iterations...
- reading initial pial vertex positions from woT2.pial...
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [90.50 201.50], gm=146.00+-18.50, and vertices in regions > 136.7
- 54026 surface locations found to contain inconsistent values (5139 in, 48887 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=562411.2, rms=0.25
- 001: dt: 0.5000, sse=527796.3, rms=0.244 (0.000%)
- 002: dt: 0.5000, sse=506658.5, rms=0.230 (0.000%)
- 003: dt: 0.5000, sse=493634.9, rms=0.220 (0.000%)
- 004: dt: 0.5000, sse=483524.0, rms=0.210 (0.000%)
- 005: dt: 0.5000, sse=476287.5, rms=0.202 (0.000%)
- 006: dt: 0.5000, sse=470805.8, rms=0.195 (0.000%)
- 007: dt: 0.5000, sse=466676.5, rms=0.188 (0.000%)
- 008: dt: 0.5000, sse=463023.4, rms=0.183 (0.000%)
- 009: dt: 0.5000, sse=460242.7, rms=0.178 (0.000%)
- 010: dt: 0.5000, sse=457962.3, rms=0.174 (0.000%)
- 011: dt: 0.5000, sse=456483.0, rms=0.170 (0.000%)
- 012: dt: 0.5000, sse=454198.5, rms=0.166 (0.000%)
- 013: dt: 0.5000, sse=452938.7, rms=0.163 (0.000%)
- 014: dt: 0.5000, sse=451551.8, rms=0.161 (0.000%)
- 015: dt: 0.5000, sse=450075.8, rms=0.158 (0.000%)
- 016: dt: 0.5000, sse=448673.4, rms=0.156 (0.000%)
- 017: dt: 0.5000, sse=447105.9, rms=0.154 (0.000%)
- 018: dt: 0.5000, sse=445862.4, rms=0.152 (0.000%)
- 019: dt: 0.5000, sse=444415.1, rms=0.151 (0.000%)
- 020: dt: 0.5000, sse=442952.5, rms=0.149 (0.000%)
- 021: dt: 0.5000, sse=442219.8, rms=0.148 (0.000%)
- 022: dt: 0.5000, sse=440692.2, rms=0.147 (0.000%)
- 023: dt: 0.5000, sse=439257.3, rms=0.146 (0.000%)
- 024: dt: 0.5000, sse=438124.2, rms=0.145 (0.000%)
- 025: dt: 0.5000, sse=436748.1, rms=0.144 (0.000%)
- 026: dt: 0.5000, sse=435682.4, rms=0.144 (0.000%)
- 027: dt: 0.5000, sse=434302.8, rms=0.143 (0.000%)
- 028: dt: 0.5000, sse=433407.2, rms=0.143 (0.000%)
- 029: dt: 0.5000, sse=432330.4, rms=0.142 (0.000%)
- 030: dt: 0.5000, sse=431423.0, rms=0.142 (0.000%)
- positioning took 4.3 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [89.00 203.00], gm=146.00+-19.00, and vertices in regions > 136.5
- 45632 surface locations found to contain inconsistent values (2102 in, 43530 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=45237.0, rms=0.13
- 031: dt: 0.5000, sse=44966.7, rms=0.127 (0.000%)
- 032: dt: 0.5000, sse=46114.0, rms=0.117 (0.000%)
- 033: dt: 0.5000, sse=47380.2, rms=0.110 (0.000%)
- 034: dt: 0.5000, sse=48373.9, rms=0.105 (0.000%)
- 035: dt: 0.5000, sse=49166.3, rms=0.100 (0.000%)
- 036: dt: 0.5000, sse=49909.8, rms=0.095 (0.000%)
- 037: dt: 0.5000, sse=50589.5, rms=0.091 (0.000%)
- 038: dt: 0.5000, sse=51284.1, rms=0.087 (0.000%)
- 039: dt: 0.5000, sse=51925.8, rms=0.084 (0.000%)
- 040: dt: 0.5000, sse=52511.0, rms=0.080 (0.000%)
- 041: dt: 0.5000, sse=53114.1, rms=0.077 (0.000%)
- 042: dt: 0.5000, sse=53633.8, rms=0.074 (0.000%)
- 043: dt: 0.5000, sse=54133.5, rms=0.071 (0.000%)
- 044: dt: 0.5000, sse=54613.6, rms=0.069 (0.000%)
- 045: dt: 0.5000, sse=55071.5, rms=0.066 (0.000%)
- 046: dt: 0.5000, sse=55508.4, rms=0.064 (0.000%)
- 047: dt: 0.5000, sse=55901.6, rms=0.062 (0.000%)
- 048: dt: 0.5000, sse=56286.2, rms=0.060 (0.000%)
- 049: dt: 0.5000, sse=56608.5, rms=0.058 (0.000%)
- 050: dt: 0.5000, sse=56914.4, rms=0.056 (0.000%)
- 051: dt: 0.5000, sse=57187.7, rms=0.054 (0.000%)
- 052: dt: 0.5000, sse=57457.3, rms=0.053 (0.000%)
- 053: dt: 0.5000, sse=57711.3, rms=0.051 (0.000%)
- 054: dt: 0.5000, sse=57931.1, rms=0.050 (0.000%)
- 055: dt: 0.5000, sse=58145.2, rms=0.049 (0.000%)
- 056: dt: 0.5000, sse=58316.2, rms=0.048 (0.000%)
- 057: dt: 0.5000, sse=58474.2, rms=0.047 (0.000%)
- 058: dt: 0.5000, sse=58636.4, rms=0.045 (0.000%)
- 059: dt: 0.5000, sse=58802.0, rms=0.045 (0.000%)
- 060: dt: 0.5000, sse=58943.7, rms=0.044 (0.000%)
- positioning took 4.2 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [87.50 204.50], gm=146.00+-19.50, and vertices in regions > 136.2
- 44528 surface locations found to contain inconsistent values (409 in, 44119 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=6391.9, rms=0.06
- 061: dt: 0.5000, sse=6374.1, rms=0.056 (0.000%)
- 062: dt: 0.5000, sse=6430.7, rms=0.050 (0.000%)
- 063: dt: 0.5000, sse=6488.5, rms=0.047 (0.000%)
- 064: dt: 0.5000, sse=6531.4, rms=0.045 (0.000%)
- 065: dt: 0.5000, sse=6554.4, rms=0.043 (0.000%)
- 066: dt: 0.5000, sse=6563.4, rms=0.041 (0.000%)
- 067: dt: 0.5000, sse=6572.1, rms=0.040 (0.000%)
- 068: dt: 0.5000, sse=6573.9, rms=0.039 (0.000%)
- 069: dt: 0.5000, sse=6574.2, rms=0.038 (0.000%)
- 070: dt: 0.5000, sse=6576.4, rms=0.036 (0.000%)
- 071: dt: 0.5000, sse=6576.7, rms=0.035 (0.000%)
- 072: dt: 0.5000, sse=6579.1, rms=0.035 (0.000%)
- 073: dt: 0.5000, sse=6580.4, rms=0.034 (0.000%)
- 074: dt: 0.5000, sse=6582.4, rms=0.033 (0.000%)
- 075: dt: 0.5000, sse=6582.9, rms=0.032 (0.000%)
- 076: dt: 0.5000, sse=6584.1, rms=0.031 (0.000%)
- 077: dt: 0.5000, sse=6586.4, rms=0.031 (0.000%)
- 078: dt: 0.5000, sse=6588.9, rms=0.030 (0.000%)
- 079: dt: 0.5000, sse=6589.1, rms=0.030 (0.000%)
- 080: dt: 0.5000, sse=6590.0, rms=0.029 (0.000%)
- 081: dt: 0.5000, sse=6594.9, rms=0.029 (0.000%)
- 082: dt: 0.5000, sse=6596.0, rms=0.028 (0.000%)
- 083: dt: 0.5000, sse=6596.7, rms=0.028 (0.000%)
- 084: dt: 0.5000, sse=6599.7, rms=0.028 (0.000%)
- 085: dt: 0.5000, sse=6600.9, rms=0.027 (0.000%)
- 086: dt: 0.5000, sse=6604.3, rms=0.027 (0.000%)
- 087: dt: 0.5000, sse=6604.2, rms=0.027 (0.000%)
- 088: dt: 0.5000, sse=6605.7, rms=0.027 (0.000%)
- 089: dt: 0.5000, sse=6606.5, rms=0.026 (0.000%)
- 090: dt: 0.5000, sse=6611.2, rms=0.026 (0.000%)
- positioning took 4.3 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [87.50 204.50], gm=146.00+-19.50, and vertices in regions > 136.2
- 44069 surface locations found to contain inconsistent values (113 in, 43956 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/sub016/surf/lh.pial...
- writing smoothed curvature to lh.curv.pial
- 000: dt: 0.0000, sse=814.6, rms=0.03
- 091: dt: 0.5000, sse=813.8, rms=0.032 (0.000%)
- 092: dt: 0.5000, sse=803.1, rms=0.031 (0.000%)
- 093: dt: 0.5000, sse=793.9, rms=0.030 (0.000%)
- 094: dt: 0.5000, sse=786.1, rms=0.029 (0.000%)
- 095: dt: 0.5000, sse=779.1, rms=0.028 (0.000%)
- 096: dt: 0.5000, sse=773.7, rms=0.028 (0.000%)
- 097: dt: 0.5000, sse=769.7, rms=0.027 (0.000%)
- 098: dt: 0.5000, sse=767.7, rms=0.027 (0.000%)
- 099: dt: 0.5000, sse=764.6, rms=0.027 (0.000%)
- 100: dt: 0.5000, sse=761.1, rms=0.026 (0.000%)
- 101: dt: 0.5000, sse=759.5, rms=0.026 (0.000%)
- 102: dt: 0.5000, sse=758.9, rms=0.026 (0.000%)
- 103: dt: 0.5000, sse=755.6, rms=0.025 (0.000%)
- 104: dt: 0.5000, sse=752.5, rms=0.025 (0.000%)
- 105: dt: 0.5000, sse=750.5, rms=0.025 (0.000%)
- 106: dt: 0.5000, sse=748.2, rms=0.024 (0.000%)
- 107: dt: 0.5000, sse=746.3, rms=0.024 (0.000%)
- 108: dt: 0.5000, sse=744.5, rms=0.024 (0.000%)
- 109: dt: 0.5000, sse=745.6, rms=0.024 (0.000%)
- 110: dt: 0.5000, sse=743.9, rms=0.024 (0.000%)
- 111: dt: 0.5000, sse=742.1, rms=0.024 (0.000%)
- 112: dt: 0.5000, sse=742.7, rms=0.024 (0.000%)
- 113: dt: 0.5000, sse=743.1, rms=0.024 (0.000%)
- 114: dt: 0.5000, sse=742.2, rms=0.024 (0.000%)
- 115: dt: 0.5000, sse=740.9, rms=0.023 (0.000%)
- 116: dt: 0.5000, sse=739.1, rms=0.023 (0.000%)
- 117: dt: 0.5000, sse=738.5, rms=0.023 (0.000%)
- 118: dt: 0.5000, sse=739.1, rms=0.023 (0.000%)
- 119: dt: 0.5000, sse=738.0, rms=0.023 (0.000%)
- 120: dt: 0.5000, sse=740.1, rms=0.023 (0.000%)
- positioning took 4.2 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.curv.pial
- writing smoothed area to lh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.area.pial
- vertex spacing 1.02 +- 0.44 (0.05-->7.32) (max @ vno 103206 --> 104423)
- face area 0.41 +- 0.32 (0.00-->7.45)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 160479 vertices processed
- 25000 of 160479 vertices processed
- 50000 of 160479 vertices processed
- 75000 of 160479 vertices processed
- 100000 of 160479 vertices processed
- 125000 of 160479 vertices processed
- 150000 of 160479 vertices processed
- 0 of 160479 vertices processed
- 25000 of 160479 vertices processed
- 50000 of 160479 vertices processed
- 75000 of 160479 vertices processed
- 100000 of 160479 vertices processed
- 125000 of 160479 vertices processed
- 150000 of 160479 vertices processed
- thickness calculation complete, 355:897 truncations.
- 37984 vertices at 0 distance
- 109456 vertices at 1 distance
- 102099 vertices at 2 distance
- 42033 vertices at 3 distance
- 12152 vertices at 4 distance
- 3266 vertices at 5 distance
- 931 vertices at 6 distance
- 266 vertices at 7 distance
- 118 vertices at 8 distance
- 58 vertices at 9 distance
- 39 vertices at 10 distance
- 24 vertices at 11 distance
- 13 vertices at 12 distance
- 14 vertices at 13 distance
- 9 vertices at 14 distance
- 18 vertices at 15 distance
- 14 vertices at 16 distance
- 11 vertices at 17 distance
- 5 vertices at 18 distance
- 4 vertices at 19 distance
- 16 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.thickness
- positioning took 20.8 minutes
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts
- cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.woT2.pial
- `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.woT2.pial'
- mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub016 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/sub016/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz...
- 23684 bright wm thresholded.
- 383 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.orig...
- computing class statistics...
- border white: 298969 voxels (1.78%)
- border gray 333863 voxels (1.99%)
- WM (93.0): 94.0 +- 9.8 [70.0 --> 110.0]
- GM (76.0) : 74.9 +- 12.7 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 47.3 (was 70)
- setting MAX_BORDER_WHITE to 114.8 (was 105)
- setting MIN_BORDER_WHITE to 60.0 (was 85)
- setting MAX_CSF to 34.5 (was 40)
- setting MAX_GRAY to 95.2 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 53.6 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 21.8 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=105, GM=60
- mean inside = 93.5, mean outside = 69.7
- 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/sub016/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.89 +- 0.26 (0.03-->9.83) (max @ vno 68130 --> 70451)
- face area 0.33 +- 0.16 (0.00-->6.84)
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 12 points - only 0.00% unknown
- deleting segment 1 with 21 points - only 0.00% unknown
- deleting segment 2 with 14 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 4 with 1 points - only 0.00% unknown
- deleting segment 5 with 5 points - only 0.00% unknown
- deleting segment 6 with 19 points - only 0.00% unknown
- deleting segment 8 with 20 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 10 with 3 points - only 0.00% unknown
- deleting segment 11 with 40 points - only 0.00% unknown
- deleting segment 12 with 487 points - only 0.00% unknown
- deleting segment 13 with 6 points - only 0.00% unknown
- deleting segment 15 with 105 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- removing 4 vertex label from ripped group
- deleting segment 18 with 4 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 19 with 1 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 20 with 3 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 21 with 2 points - only 0.00% unknown
- tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.89 +- 0.25 (0.05-->9.83) (max @ vno 70451 --> 68130)
- face area 0.33 +- 0.16 (0.00-->6.84)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4833013.5, rms=0.00
- rms = 1.31, 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=4833013.5, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 12 points - only 0.00% unknown
- deleting segment 1 with 21 points - only 0.00% unknown
- deleting segment 2 with 14 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 3 with 1 points - only 0.00% unknown
- deleting segment 4 with 5 points - only 0.00% unknown
- deleting segment 5 with 19 points - only 0.00% unknown
- deleting segment 6 with 20 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 7 with 3 points - only 0.00% unknown
- deleting segment 8 with 40 points - only 0.00% unknown
- deleting segment 9 with 487 points - only 0.00% unknown
- deleting segment 10 with 6 points - only 0.00% unknown
- deleting segment 11 with 105 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- removing 4 vertex label from ripped group
- deleting segment 13 with 4 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
- removing 2 vertex label from ripped group
- deleting segment 16 with 2 points - only 0.00% unknown
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.89 +- 0.25 (0.05-->9.83) (max @ vno 70451 --> 68130)
- face area 0.33 +- 0.16 (0.00-->6.84)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4833013.5, rms=0.00
- rms = 1.33, time step reduction 1 of 3 to 0.250...
- rms = 0.33, time step reduction 2 of 3 to 0.125...
- rms = 0.04, time step reduction 3 of 3 to 0.062...
- 002: dt: 0.1250, sse=4833013.5, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 12 points - only 0.00% unknown
- deleting segment 1 with 21 points - only 0.00% unknown
- deleting segment 2 with 14 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 3 with 1 points - only 0.00% unknown
- deleting segment 4 with 5 points - only 0.00% unknown
- deleting segment 5 with 19 points - only 0.00% unknown
- deleting segment 6 with 20 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 7 with 3 points - only 0.00% unknown
- deleting segment 8 with 40 points - only 0.00% unknown
- deleting segment 9 with 487 points - only 0.00% unknown
- deleting segment 10 with 6 points - only 0.00% unknown
- deleting segment 11 with 105 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- removing 4 vertex label from ripped group
- deleting segment 13 with 4 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
- removing 2 vertex label from ripped group
- deleting segment 16 with 2 points - only 0.00% unknown
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.89 +- 0.25 (0.05-->9.83) (max @ vno 70451 --> 68130)
- face area 0.33 +- 0.16 (0.00-->6.84)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4833013.5, rms=0.00
- rms = 1.31, 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=4833013.5, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 12 points - only 0.00% unknown
- deleting segment 1 with 21 points - only 0.00% unknown
- deleting segment 2 with 14 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 3 with 1 points - only 0.00% unknown
- deleting segment 4 with 5 points - only 0.00% unknown
- deleting segment 5 with 19 points - only 0.00% unknown
- deleting segment 6 with 20 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 7 with 3 points - only 0.00% unknown
- deleting segment 8 with 40 points - only 0.00% unknown
- deleting segment 9 with 487 points - only 0.00% unknown
- deleting segment 10 with 6 points - only 0.00% unknown
- deleting segment 11 with 105 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- removing 4 vertex label from ripped group
- deleting segment 13 with 4 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
- removing 2 vertex label from ripped group
- deleting segment 16 with 2 points - only 0.00% unknown
- tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- repositioning cortical surface to gray/csf boundary.
- smoothing T1 volume with sigma = 2.000
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4833013.5, rms=0.00
- rms = 1.33, time step reduction 1 of 3 to 0.250...
- rms = 0.33, time step reduction 2 of 3 to 0.125...
- rms = 0.04, time step reduction 3 of 3 to 0.062...
- 004: dt: 0.1250, sse=4833013.5, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- smoothing surface for 5 iterations...
- reading initial pial vertex positions from woT2.pial...
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [92.30 205.70], gm=149.00+-18.90, and vertices in regions > 139.5
- 53781 surface locations found to contain inconsistent values (6053 in, 47728 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=577312.1, rms=0.22
- 001: dt: 0.5000, sse=540316.5, rms=0.215 (0.000%)
- 002: dt: 0.5000, sse=518240.6, rms=0.201 (0.000%)
- 003: dt: 0.5000, sse=504950.8, rms=0.190 (0.000%)
- 004: dt: 0.5000, sse=494329.2, rms=0.180 (0.000%)
- 005: dt: 0.5000, sse=487119.2, rms=0.172 (0.000%)
- 006: dt: 0.5000, sse=481500.6, rms=0.166 (0.000%)
- 007: dt: 0.5000, sse=476917.7, rms=0.160 (0.000%)
- 008: dt: 0.5000, sse=473099.1, rms=0.155 (0.000%)
- 009: dt: 0.5000, sse=470895.4, rms=0.151 (0.000%)
- 010: dt: 0.5000, sse=468088.1, rms=0.147 (0.000%)
- 011: dt: 0.5000, sse=466238.7, rms=0.144 (0.000%)
- 012: dt: 0.5000, sse=464480.7, rms=0.142 (0.000%)
- 013: dt: 0.5000, sse=463018.3, rms=0.140 (0.000%)
- 014: dt: 0.5000, sse=461407.7, rms=0.138 (0.000%)
- 015: dt: 0.5000, sse=460017.0, rms=0.137 (0.000%)
- 016: dt: 0.5000, sse=458620.0, rms=0.136 (0.000%)
- 017: dt: 0.5000, sse=457024.2, rms=0.135 (0.000%)
- 018: dt: 0.5000, sse=455395.4, rms=0.135 (0.000%)
- 019: dt: 0.5000, sse=453960.3, rms=0.135 (0.000%)
- 020: dt: 0.5000, sse=453225.4, rms=0.135 (0.000%)
- 021: dt: 0.5000, sse=452069.9, rms=0.135 (0.000%)
- 022: dt: 0.5000, sse=450405.6, rms=0.135 (0.000%)
- 023: dt: 0.5000, sse=449234.2, rms=0.135 (0.000%)
- 024: dt: 0.5000, sse=448341.0, rms=0.135 (0.000%)
- 025: dt: 0.5000, sse=446750.0, rms=0.135 (0.000%)
- 026: dt: 0.5000, sse=446009.4, rms=0.136 (0.000%)
- 027: dt: 0.5000, sse=444634.4, rms=0.136 (0.000%)
- 028: dt: 0.5000, sse=443450.3, rms=0.136 (0.000%)
- 029: dt: 0.5000, sse=442174.8, rms=0.137 (0.000%)
- 030: dt: 0.5000, sse=441035.6, rms=0.137 (0.000%)
- positioning took 4.3 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [89.80 206.20], gm=148.00+-19.40, and vertices in regions > 138.3
- 43282 surface locations found to contain inconsistent values (2125 in, 41157 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=45524.7, rms=0.11
- 031: dt: 0.5000, sse=45359.8, rms=0.109 (0.000%)
- 032: dt: 0.5000, sse=46338.8, rms=0.099 (0.000%)
- 033: dt: 0.5000, sse=47439.3, rms=0.093 (0.000%)
- 034: dt: 0.5000, sse=48338.7, rms=0.088 (0.000%)
- 035: dt: 0.5000, sse=49099.1, rms=0.084 (0.000%)
- 036: dt: 0.5000, sse=49763.9, rms=0.080 (0.000%)
- 037: dt: 0.5000, sse=50400.2, rms=0.076 (0.000%)
- 038: dt: 0.5000, sse=51024.8, rms=0.073 (0.000%)
- 039: dt: 0.5000, sse=51626.3, rms=0.069 (0.000%)
- 040: dt: 0.5000, sse=52250.5, rms=0.067 (0.000%)
- 041: dt: 0.5000, sse=52839.6, rms=0.064 (0.000%)
- 042: dt: 0.5000, sse=53378.6, rms=0.062 (0.000%)
- 043: dt: 0.5000, sse=53894.7, rms=0.059 (0.000%)
- 044: dt: 0.5000, sse=54327.8, rms=0.057 (0.000%)
- 045: dt: 0.5000, sse=54761.2, rms=0.056 (0.000%)
- 046: dt: 0.5000, sse=55220.6, rms=0.054 (0.000%)
- 047: dt: 0.5000, sse=55600.4, rms=0.052 (0.000%)
- 048: dt: 0.5000, sse=55980.4, rms=0.051 (0.000%)
- 049: dt: 0.5000, sse=56346.9, rms=0.050 (0.000%)
- 050: dt: 0.5000, sse=56656.5, rms=0.049 (0.000%)
- 051: dt: 0.5000, sse=56945.3, rms=0.047 (0.000%)
- 052: dt: 0.5000, sse=57205.8, rms=0.046 (0.000%)
- 053: dt: 0.5000, sse=57428.1, rms=0.045 (0.000%)
- 054: dt: 0.5000, sse=57662.9, rms=0.044 (0.000%)
- 055: dt: 0.5000, sse=57878.0, rms=0.044 (0.000%)
- 056: dt: 0.5000, sse=58036.0, rms=0.043 (0.000%)
- 057: dt: 0.5000, sse=58191.1, rms=0.042 (0.000%)
- 058: dt: 0.5000, sse=58353.2, rms=0.041 (0.000%)
- 059: dt: 0.5000, sse=58484.9, rms=0.041 (0.000%)
- 060: dt: 0.5000, sse=58627.5, rms=0.040 (0.000%)
- positioning took 4.3 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [89.50 206.50], gm=148.00+-19.50, and vertices in regions > 138.2
- 41413 surface locations found to contain inconsistent values (523 in, 40890 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=6252.5, rms=0.05
- 061: dt: 0.5000, sse=6250.9, rms=0.050 (0.000%)
- 062: dt: 0.5000, sse=6288.3, rms=0.046 (0.000%)
- 063: dt: 0.5000, sse=6318.4, rms=0.044 (0.000%)
- 064: dt: 0.5000, sse=6338.7, rms=0.042 (0.000%)
- 065: dt: 0.5000, sse=6347.6, rms=0.040 (0.000%)
- 066: dt: 0.5000, sse=6352.7, rms=0.038 (0.000%)
- 067: dt: 0.5000, sse=6353.5, rms=0.037 (0.000%)
- 068: dt: 0.5000, sse=6354.3, rms=0.036 (0.000%)
- 069: dt: 0.5000, sse=6355.8, rms=0.035 (0.000%)
- 070: dt: 0.5000, sse=6358.2, rms=0.034 (0.000%)
- 071: dt: 0.5000, sse=6364.1, rms=0.033 (0.000%)
- 072: dt: 0.5000, sse=6367.2, rms=0.033 (0.000%)
- 073: dt: 0.5000, sse=6371.2, rms=0.032 (0.000%)
- 074: dt: 0.5000, sse=6373.3, rms=0.031 (0.000%)
- 075: dt: 0.5000, sse=6375.0, rms=0.030 (0.000%)
- 076: dt: 0.5000, sse=6377.8, rms=0.030 (0.000%)
- 077: dt: 0.5000, sse=6379.8, rms=0.029 (0.000%)
- 078: dt: 0.5000, sse=6383.7, rms=0.028 (0.000%)
- 079: dt: 0.5000, sse=6387.8, rms=0.028 (0.000%)
- 080: dt: 0.5000, sse=6391.2, rms=0.028 (0.000%)
- 081: dt: 0.5000, sse=6395.9, rms=0.027 (0.000%)
- 082: dt: 0.5000, sse=6399.5, rms=0.027 (0.000%)
- 083: dt: 0.5000, sse=6405.0, rms=0.027 (0.000%)
- 084: dt: 0.5000, sse=6407.4, rms=0.027 (0.000%)
- 085: dt: 0.5000, sse=6411.0, rms=0.026 (0.000%)
- 086: dt: 0.5000, sse=6413.6, rms=0.026 (0.000%)
- 087: dt: 0.5000, sse=6416.7, rms=0.026 (0.000%)
- 088: dt: 0.5000, sse=6419.7, rms=0.026 (0.000%)
- 089: dt: 0.5000, sse=6420.7, rms=0.026 (0.000%)
- 090: dt: 0.5000, sse=6420.5, rms=0.026 (0.000%)
- positioning took 4.3 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [88.50 205.50], gm=147.00+-19.50, and vertices in regions > 137.2
- 34465 surface locations found to contain inconsistent values (509 in, 33956 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/sub016/surf/rh.pial...
- writing smoothed curvature to rh.curv.pial
- 000: dt: 0.0000, sse=924.1, rms=0.04
- 091: dt: 0.5000, sse=921.2, rms=0.043 (0.000%)
- 092: dt: 0.5000, sse=891.2, rms=0.041 (0.000%)
- 093: dt: 0.5000, sse=867.7, rms=0.039 (0.000%)
- 094: dt: 0.5000, sse=846.4, rms=0.037 (0.000%)
- 095: dt: 0.5000, sse=828.1, rms=0.035 (0.000%)
- 096: dt: 0.5000, sse=815.2, rms=0.034 (0.000%)
- 097: dt: 0.5000, sse=805.5, rms=0.033 (0.000%)
- 098: dt: 0.5000, sse=798.8, rms=0.032 (0.000%)
- 099: dt: 0.5000, sse=792.5, rms=0.032 (0.000%)
- 100: dt: 0.5000, sse=786.2, rms=0.031 (0.000%)
- 101: dt: 0.5000, sse=779.7, rms=0.030 (0.000%)
- 102: dt: 0.5000, sse=774.9, rms=0.030 (0.000%)
- 103: dt: 0.5000, sse=770.3, rms=0.029 (0.000%)
- 104: dt: 0.5000, sse=766.4, rms=0.029 (0.000%)
- 105: dt: 0.5000, sse=762.4, rms=0.028 (0.000%)
- 106: dt: 0.5000, sse=759.3, rms=0.028 (0.000%)
- 107: dt: 0.5000, sse=756.1, rms=0.027 (0.000%)
- 108: dt: 0.5000, sse=753.5, rms=0.027 (0.000%)
- 109: dt: 0.5000, sse=750.8, rms=0.026 (0.000%)
- 110: dt: 0.5000, sse=749.4, rms=0.026 (0.000%)
- 111: dt: 0.5000, sse=747.7, rms=0.026 (0.000%)
- 112: dt: 0.5000, sse=748.8, rms=0.026 (0.000%)
- 113: dt: 0.5000, sse=747.9, rms=0.026 (0.000%)
- 114: dt: 0.5000, sse=746.2, rms=0.026 (0.000%)
- 115: dt: 0.5000, sse=744.9, rms=0.025 (0.000%)
- 116: dt: 0.5000, sse=744.1, rms=0.025 (0.000%)
- 117: dt: 0.5000, sse=742.9, rms=0.025 (0.000%)
- 118: dt: 0.5000, sse=742.5, rms=0.025 (0.000%)
- 119: dt: 0.5000, sse=741.8, rms=0.025 (0.000%)
- 120: dt: 0.5000, sse=742.3, rms=0.025 (0.000%)
- positioning took 4.2 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.curv.pial
- writing smoothed area to rh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.area.pial
- vertex spacing 1.02 +- 0.43 (0.05-->10.65) (max @ vno 70451 --> 68130)
- face area 0.41 +- 0.31 (0.00-->8.47)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 162159 vertices processed
- 25000 of 162159 vertices processed
- 50000 of 162159 vertices processed
- 75000 of 162159 vertices processed
- 100000 of 162159 vertices processed
- 125000 of 162159 vertices processed
- 150000 of 162159 vertices processed
- 0 of 162159 vertices processed
- 25000 of 162159 vertices processed
- 50000 of 162159 vertices processed
- 75000 of 162159 vertices processed
- 100000 of 162159 vertices processed
- 125000 of 162159 vertices processed
- 150000 of 162159 vertices processed
- thickness calculation complete, 487:848 truncations.
- 38169 vertices at 0 distance
- 112062 vertices at 1 distance
- 103989 vertices at 2 distance
- 41599 vertices at 3 distance
- 11472 vertices at 4 distance
- 3120 vertices at 5 distance
- 962 vertices at 6 distance
- 336 vertices at 7 distance
- 162 vertices at 8 distance
- 95 vertices at 9 distance
- 65 vertices at 10 distance
- 30 vertices at 11 distance
- 19 vertices at 12 distance
- 22 vertices at 13 distance
- 14 vertices at 14 distance
- 19 vertices at 15 distance
- 22 vertices at 16 distance
- 15 vertices at 17 distance
- 9 vertices at 18 distance
- 11 vertices at 19 distance
- 14 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.thickness
- positioning took 20.9 minutes
- #--------------------------------------------
- #@# Surf Volume lh Fri Aug 9 00:17:18 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 Fri Aug 9 00:17:18 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 Fri Aug 9 00:17:19 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri
- mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon sub016
- 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 = 37
- writing volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/ribbon.mgz
- writing ribbon files
- #--------------------------------------------
- #@# ASeg Stats Fri Aug 9 00:39:03 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016
- 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 sub016
- $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 sub016
- sysname Linux
- hostname snake6
- machine x86_64
- user fkaule
- UseRobust 0
- atlas_icv (eTIV) = 1402840 mm^3 (det: 1.388687 )
- Computing euler number
- orig.nofix lheno = -46, rheno = -32
- orig.nofix lhholes = 24, rhholes = 17
- Loading mri/aseg.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 306260.490 305489.000 diff= 771.5 pctdiff= 0.252
- rhCtxGM: 309907.285 309138.000 diff= 769.3 pctdiff= 0.248
- lhCtxWM: 253268.933 253103.500 diff= 165.4 pctdiff= 0.065
- rhCtxWM: 258556.463 258667.500 diff= -111.0 pctdiff=-0.043
- SubCortGMVol 75858.000
- SupraTentVol 1220313.171 (1217624.000) diff=2689.171 pctdiff=0.220
- SupraTentVolNotVent 1205373.171 (1202684.000) diff=2689.171 pctdiff=0.223
- BrainSegVol 1369384.000 (1366874.000) diff=2510.000 pctdiff=0.183
- BrainSegVolNotVent 1350669.000 (1351917.171) diff=-1248.171 pctdiff=-0.092
- BrainSegVolNotVent 1350669.000
- CerebellumVol 147638.000
- VentChorVol 14940.000
- 3rd4th5thCSF 3775.000
- CSFVol 1308.000, OptChiasmVol 304.000
- MaskVol 1848686.000
- 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 5205 5204.545
- 4 5 Left-Inf-Lat-Vent 587 587.482
- 5 7 Left-Cerebellum-White-Matter 15848 15847.543
- 6 8 Left-Cerebellum-Cortex 57326 57326.152
- 7 10 Left-Thalamus-Proper 9388 9388.153
- 8 11 Left-Caudate 5055 5055.190
- 9 12 Left-Putamen 7345 7345.435
- 10 13 Left-Pallidum 2485 2484.961
- 11 14 3rd-Ventricle 878 878.457
- 12 15 4th-Ventricle 1789 1788.563
- 13 16 Brain-Stem 25619 25619.164
- 14 17 Left-Hippocampus 5163 5163.188
- 15 18 Left-Amygdala 1837 1837.226
- 16 24 CSF 1269 1268.591
- 17 26 Left-Accumbens-area 926 926.388
- 18 28 Left-VentralDC 4287 4287.005
- 19 30 Left-vessel 252 252.209
- 20 31 Left-choroid-plexus 1120 1119.660
- 23 43 Right-Lateral-Ventricle 6175 6175.496
- 24 44 Right-Inf-Lat-Vent 417 417.325
- 25 46 Right-Cerebellum-White-Matter 16511 16510.811
- 26 47 Right-Cerebellum-Cortex 60517 60517.289
- 27 49 Right-Thalamus-Proper 8712 8711.553
- 28 50 Right-Caudate 6116 6115.571
- 29 51 Right-Putamen 6870 6870.305
- 30 52 Right-Pallidum 2510 2509.738
- 31 53 Right-Hippocampus 4969 4968.664
- 32 54 Right-Amygdala 2274 2273.631
- 33 58 Right-Accumbens-area 1003 1003.480
- 34 60 Right-VentralDC 4570 4569.587
- 35 62 Right-vessel 123 123.374
- 36 63 Right-choroid-plexus 1462 1462.179
- 37 72 5th-Ventricle 0 0.000
- 38 77 WM-hypointensities 3867 3866.558
- 39 78 Left-WM-hypointensities 0 0.000
- 40 79 Right-WM-hypointensities 0 0.000
- 41 80 non-WM-hypointensities 39 39.195
- 42 81 Left-non-WM-hypointensities 0 0.000
- 43 82 Right-non-WM-hypointensities 0 0.000
- 44 85 Optic-Chiasm 301 300.605
- 45 251 CC_Posterior 857 856.593
- 46 252 CC_Mid_Posterior 412 411.740
- 47 253 CC_Central 428 427.937
- 48 254 CC_Mid_Anterior 500 499.593
- 49 255 CC_Anterior 905 904.610
- Reporting on 45 segmentations
- mri_segstats done
- #-----------------------------------------
- #@# AParc-to-ASeg Fri Aug 9 00:41:45 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016
- mri_aparc2aseg --s sub016 --volmask
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- subject sub016
- outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/aparc+aseg.mgz
- useribbon 0
- baseoffset 0
- RipUnknown 0
- Reading lh white surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.white
- Reading lh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.pial
- Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/surf/rh.white
- Reading rh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.pial
- Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/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/sub016/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 = 611610
- Used brute-force search on 0 voxels
- Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/aparc+aseg.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016
- mri_aparc2aseg --s sub016 --volmask --a2009s
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- subject sub016
- outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/aparc.a2009s+aseg.mgz
- useribbon 0
- baseoffset 10100
- RipUnknown 0
- Reading lh white surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.white
- Reading lh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.pial
- Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/surf/rh.white
- Reading rh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.pial
- Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/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/sub016/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 = 611610
- Used brute-force search on 0 voxels
- Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/aparc.a2009s+aseg.mgz
- #-----------------------------------------
- #@# WMParc Fri Aug 9 00:47:13 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016
- mri_aparc2aseg --s sub016 --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 sub016
- 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/sub016/mri/aparc+aseg.mgz
- Reading lh white surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.white
- Reading lh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.pial
- Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/surf/rh.white
- Reading rh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.pial
- Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/mri/ribbon.mgz
- Loading filled from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/filled.mgz
- Ripping vertices labeled as unkown
- Ripped 9404 vertices from left hemi
- Ripped 8753 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/sub016/mri/aseg.mgz
- Loading Ctx Seg File /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 = 1123151
- Used brute-force search on 127 voxels
- Fixing Parahip LH WM
- Found 8 clusters
- 0 k 2078.000000
- 1 k 1.000000
- 2 k 1.000000
- 3 k 1.000000
- 4 k 1.000000
- 5 k 12.000000
- 6 k 1.000000
- 7 k 12.000000
- Fixing Parahip RH WM
- Found 9 clusters
- 0 k 1.000000
- 1 k 1929.000000
- 2 k 1.000000
- 3 k 1.000000
- 4 k 1.000000
- 5 k 1.000000
- 6 k 1.000000
- 7 k 2.000000
- 8 k 1.000000
- Writing output aseg to mri/wmparc.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016
- 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 sub016 --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 sub016 --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) = 1402840 mm^3 (det: 1.388687 )
- Loading mri/wmparc.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 306260.490 305489.000 diff= 771.5 pctdiff= 0.252
- rhCtxGM: 309907.285 309138.000 diff= 769.3 pctdiff= 0.248
- lhCtxWM: 253268.933 253103.500 diff= 165.4 pctdiff= 0.065
- rhCtxWM: 258556.463 258667.500 diff= -111.0 pctdiff=-0.043
- SubCortGMVol 75858.000
- SupraTentVol 1220313.171 (1217624.000) diff=2689.171 pctdiff=0.220
- SupraTentVolNotVent 1205373.171 (1202684.000) diff=2689.171 pctdiff=0.223
- BrainSegVol 1369384.000 (1366874.000) diff=2510.000 pctdiff=0.183
- BrainSegVolNotVent 1350669.000 (1351917.171) diff=-1248.171 pctdiff=-0.092
- BrainSegVolNotVent 1350669.000
- CerebellumVol 147638.000
- VentChorVol 14940.000
- 3rd4th5thCSF 3775.000
- CSFVol 1308.000, OptChiasmVol 304.000
- MaskVol 1848686.000
- 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 2452 2451.532
- 2 3002 wm-lh-caudalanteriorcingulate 3946 3945.573
- 3 3003 wm-lh-caudalmiddlefrontal 6079 6078.784
- 4 3004 wm-lh-corpuscallosum 0 0.000
- 5 3005 wm-lh-cuneus 2961 2961.475
- 6 3006 wm-lh-entorhinal 1284 1284.438
- 7 3007 wm-lh-fusiform 7966 7965.979
- 8 3008 wm-lh-inferiorparietal 11257 11256.769
- 9 3009 wm-lh-inferiortemporal 9263 9262.991
- 10 3010 wm-lh-isthmuscingulate 4640 4639.525
- 11 3011 wm-lh-lateraloccipital 9338 9337.695
- 12 3012 wm-lh-lateralorbitofrontal 7724 7724.123
- 13 3013 wm-lh-lingual 6364 6364.017
- 14 3014 wm-lh-medialorbitofrontal 3724 3724.163
- 15 3015 wm-lh-middletemporal 7293 7293.097
- 16 3016 wm-lh-parahippocampal 2142 2141.513
- 17 3017 wm-lh-paracentral 3707 3707.155
- 18 3018 wm-lh-parsopercularis 4535 4534.863
- 19 3019 wm-lh-parsorbitalis 1171 1171.051
- 20 3020 wm-lh-parstriangularis 3172 3171.806
- 21 3021 wm-lh-pericalcarine 4592 4591.900
- 22 3022 wm-lh-postcentral 7609 7608.956
- 23 3023 wm-lh-posteriorcingulate 5355 5355.249
- 24 3024 wm-lh-precentral 14215 14214.800
- 25 3025 wm-lh-precuneus 11123 11122.730
- 26 3026 wm-lh-rostralanteriorcingulate 2619 2619.199
- 27 3027 wm-lh-rostralmiddlefrontal 12685 12685.373
- 28 3028 wm-lh-superiorfrontal 20937 20937.270
- 29 3029 wm-lh-superiorparietal 14351 14350.940
- 30 3030 wm-lh-superiortemporal 9641 9641.078
- 31 3031 wm-lh-supramarginal 10236 10236.092
- 32 3032 wm-lh-frontalpole 151 151.290
- 33 3033 wm-lh-temporalpole 731 730.634
- 34 3034 wm-lh-transversetemporal 929 928.537
- 35 3035 wm-lh-insula 10118 10118.451
- 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 2831 2831.255
- 120 4002 wm-rh-caudalanteriorcingulate 2638 2637.598
- 121 4003 wm-rh-caudalmiddlefrontal 5731 5730.535
- 122 4004 wm-rh-corpuscallosum 0 0.000
- 123 4005 wm-rh-cuneus 3045 3045.040
- 124 4006 wm-rh-entorhinal 1034 1033.776
- 125 4007 wm-rh-fusiform 7612 7611.993
- 126 4008 wm-rh-inferiorparietal 13814 13813.651
- 127 4009 wm-rh-inferiortemporal 8415 8414.678
- 128 4010 wm-rh-isthmuscingulate 5231 5230.636
- 129 4011 wm-rh-lateraloccipital 9901 9900.562
- 130 4012 wm-rh-lateralorbitofrontal 7480 7480.153
- 131 4013 wm-rh-lingual 6713 6712.950
- 132 4014 wm-rh-medialorbitofrontal 3751 3750.894
- 133 4015 wm-rh-middletemporal 7945 7944.837
- 134 4016 wm-rh-parahippocampal 1995 1995.037
- 135 4017 wm-rh-paracentral 6093 6093.256
- 136 4018 wm-rh-parsopercularis 5347 5346.578
- 137 4019 wm-rh-parsorbitalis 1301 1301.438
- 138 4020 wm-rh-parstriangularis 4404 4404.237
- 139 4021 wm-rh-pericalcarine 4362 4361.587
- 140 4022 wm-rh-postcentral 8380 8379.893
- 141 4023 wm-rh-posteriorcingulate 4716 4716.122
- 142 4024 wm-rh-precentral 14818 14817.553
- 143 4025 wm-rh-precuneus 10880 10879.696
- 144 4026 wm-rh-rostralanteriorcingulate 2748 2747.739
- 145 4027 wm-rh-rostralmiddlefrontal 12665 12665.396
- 146 4028 wm-rh-superiorfrontal 22764 22763.979
- 147 4029 wm-rh-superiorparietal 11638 11637.731
- 148 4030 wm-rh-superiortemporal 7994 7994.231
- 149 4031 wm-rh-supramarginal 9586 9586.322
- 150 4032 wm-rh-frontalpole 256 256.280
- 151 4033 wm-rh-temporalpole 654 653.627
- 152 4034 wm-rh-transversetemporal 747 747.147
- 153 4035 wm-rh-insula 10469 10468.917
- 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 30700 30700.072
- 237 5002 Right-UnsegmentedWhiteMatter 32089 32089.314
- 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/sub016/label
- #--------------------------------------------
- #@# BA Labels lh Fri Aug 9 00:59:53 CEST 2013
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
- Number of reverse mapping hits = 398
- Checking for and removing duplicates
- Writing label file ./lh.BA1.label 4527
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
- Number of reverse mapping hits = 926
- Checking for and removing duplicates
- Writing label file ./lh.BA2.label 8835
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
- Number of reverse mapping hits = 241
- Checking for and removing duplicates
- Writing label file ./lh.BA3a.label 4318
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
- Number of reverse mapping hits = 611
- Checking for and removing duplicates
- Writing label file ./lh.BA3b.label 6594
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
- Number of reverse mapping hits = 681
- Checking for and removing duplicates
- Writing label file ./lh.BA4a.label 6465
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
- Number of reverse mapping hits = 406
- Checking for and removing duplicates
- Writing label file ./lh.BA4p.label 4476
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
- Number of reverse mapping hits = 1787
- Checking for and removing duplicates
- Writing label file ./lh.BA6.label 15376
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
- Number of reverse mapping hits = 889
- Checking for and removing duplicates
- Writing label file ./lh.BA44.label 5070
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
- Number of reverse mapping hits = 1201
- Checking for and removing duplicates
- Writing label file ./lh.BA45.label 4623
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
- Number of reverse mapping hits = 2377
- Checking for and removing duplicates
- Writing label file ./lh.V1.label 7018
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
- Number of reverse mapping hits = 3898
- Checking for and removing duplicates
- Writing label file ./lh.V2.label 12012
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
- Number of reverse mapping hits = 833
- Checking for and removing duplicates
- Writing label file ./lh.MT.label 2851
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.perirhinal.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
- Number of reverse mapping hits = 351
- Checking for and removing duplicates
- Writing label file ./lh.perirhinal.label 1550
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.thresh.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
- Number of reverse mapping hits = 86
- Checking for and removing duplicates
- Writing label file ./lh.BA1.thresh.label 1100
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.thresh.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
- Number of reverse mapping hits = 166
- Checking for and removing duplicates
- Writing label file ./lh.BA2.thresh.label 2258
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.thresh.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
- Number of reverse mapping hits = 23
- Checking for and removing duplicates
- Writing label file ./lh.BA3a.thresh.label 1527
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.thresh.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
- Number of reverse mapping hits = 248
- Checking for and removing duplicates
- Writing label file ./lh.BA3b.thresh.label 2244
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.thresh.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
- Number of reverse mapping hits = 433
- Checking for and removing duplicates
- Writing label file ./lh.BA4a.thresh.label 2752
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.thresh.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
- 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 sub016 --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 = sub016
- 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/sub016/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
- Number of reverse mapping hits = 635
- Checking for and removing duplicates
- Writing label file ./lh.BA6.thresh.label 7670
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.thresh.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
- Number of reverse mapping hits = 512
- Checking for and removing duplicates
- Writing label file ./lh.BA44.thresh.label 2424
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.thresh.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
- Number of reverse mapping hits = 510
- Checking for and removing duplicates
- Writing label file ./lh.BA45.thresh.label 1661
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.thresh.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
- Number of reverse mapping hits = 1745
- Checking for and removing duplicates
- Writing label file ./lh.V1.thresh.label 5150
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.thresh.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
- Number of reverse mapping hits = 1781
- Checking for and removing duplicates
- Writing label file ./lh.V2.thresh.label 5115
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.thresh.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
- Number of reverse mapping hits = 271
- Checking for and removing duplicates
- Writing label file ./lh.MT.thresh.label 784
- mri_label2label: Done
- mris_label2annot --s sub016 --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/sub016/label
- cmdline mris_label2annot --s sub016 --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 sub016
- 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/sub016/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 112515 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/label/lh.BA.annot
- mris_label2annot --s sub016 --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/sub016/label
- cmdline mris_label2annot --s sub016 --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 sub016
- 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/sub016/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 132861 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/label/lh.BA.thresh.annot
- mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab sub016 lh white
- computing statistics for each annotation in ./lh.BA.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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
- 1149 613 2316 2.623 0.404 0.163 0.131 114 8.4 BA1
- 4525 2973 8268 2.566 0.464 0.121 0.034 50 6.3 BA2
- 983 673 962 1.921 0.366 0.143 0.049 10 2.0 BA3a
- 2836 1812 4720 2.242 0.614 0.120 0.037 35 4.4 BA3b
- 1949 1016 4013 3.077 0.491 0.110 0.210 60 5.3 BA4a
- 1569 944 2751 2.818 0.448 0.105 0.030 12 2.0 BA4p
- 10174 6679 25171 3.070 0.614 0.119 0.035 191 15.6 BA6
- 3033 1986 6744 2.844 0.490 0.120 0.038 40 5.0 BA44
- 3724 2528 7712 2.570 0.571 0.142 0.046 66 7.1 BA45
- 4613 3269 6851 2.042 0.462 0.156 0.067 92 13.4 V1
- 9425 6060 14706 2.214 0.545 0.158 0.071 208 29.0 V2
- 2623 1768 4380 2.381 0.448 0.140 0.049 43 4.9 MT
- 1361 949 3783 3.229 0.681 0.163 0.072 26 4.0 perirhinal
- mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab sub016 lh white
- computing statistics for each annotation in ./lh.BA.thresh.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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
- 701 335 1409 2.627 0.332 0.181 0.181 105 7.5 BA1
- 1576 1045 2963 2.516 0.433 0.116 0.030 15 1.9 BA2
- 781 533 718 1.886 0.361 0.155 0.051 8 1.7 BA3a
- 1753 1164 2431 1.925 0.344 0.102 0.028 15 1.8 BA3b
- 2046 1043 4172 3.119 0.492 0.111 0.208 149 6.3 BA4a
- 1224 760 1963 2.666 0.406 0.102 0.027 8 1.3 BA4p
- 5405 3525 13798 3.144 0.580 0.117 0.035 56 8.0 BA6
- 2112 1377 4634 2.831 0.460 0.126 0.041 32 3.8 BA44
- 1587 1072 3832 2.814 0.450 0.163 0.058 38 3.7 BA45
- 4860 3446 7264 2.031 0.465 0.157 0.073 100 16.5 V1
- 4822 3104 7146 2.140 0.516 0.169 0.081 108 16.2 V2
- 751 475 1281 2.497 0.423 0.144 0.052 12 1.5 MT
- #--------------------------------------------
- #@# BA Labels rh Fri Aug 9 01:04:52 CEST 2013
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
- Number of reverse mapping hits = 604
- Checking for and removing duplicates
- Writing label file ./rh.BA1.label 4566
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
- Number of reverse mapping hits = 676
- Checking for and removing duplicates
- Writing label file ./rh.BA2.label 7363
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
- Number of reverse mapping hits = 228
- Checking for and removing duplicates
- Writing label file ./rh.BA3a.label 4208
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
- Number of reverse mapping hits = 555
- Checking for and removing duplicates
- Writing label file ./rh.BA3b.label 5077
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
- Number of reverse mapping hits = 895
- Checking for and removing duplicates
- Writing label file ./rh.BA4a.label 6642
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
- Number of reverse mapping hits = 447
- Checking for and removing duplicates
- Writing label file ./rh.BA4p.label 4920
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
- Number of reverse mapping hits = 2322
- Checking for and removing duplicates
- Writing label file ./rh.BA6.label 14578
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
- Number of reverse mapping hits = 1756
- Checking for and removing duplicates
- Writing label file ./rh.BA44.label 8668
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
- Number of reverse mapping hits = 1802
- Checking for and removing duplicates
- Writing label file ./rh.BA45.label 7157
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
- Number of reverse mapping hits = 2730
- Checking for and removing duplicates
- Writing label file ./rh.V1.label 7457
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
- Number of reverse mapping hits = 4422
- Checking for and removing duplicates
- Writing label file ./rh.V2.label 12438
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
- Number of reverse mapping hits = 925
- Checking for and removing duplicates
- Writing label file ./rh.MT.label 2857
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.perirhinal.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
- Number of reverse mapping hits = 192
- Checking for and removing duplicates
- Writing label file ./rh.perirhinal.label 944
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.thresh.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
- Number of reverse mapping hits = 272
- Checking for and removing duplicates
- Writing label file ./rh.BA1.thresh.label 1148
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.thresh.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
- Number of reverse mapping hits = 194
- Checking for and removing duplicates
- Writing label file ./rh.BA2.thresh.label 2882
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.thresh.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
- Number of reverse mapping hits = 59
- Checking for and removing duplicates
- Writing label file ./rh.BA3a.thresh.label 1757
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.thresh.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
- Number of reverse mapping hits = 347
- Checking for and removing duplicates
- Writing label file ./rh.BA3b.thresh.label 2530
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.thresh.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
- Number of reverse mapping hits = 238
- Checking for and removing duplicates
- Writing label file ./rh.BA4a.thresh.label 1626
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.thresh.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
- Number of reverse mapping hits = 152
- Checking for and removing duplicates
- Writing label file ./rh.BA4p.thresh.label 1641
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.thresh.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
- Number of reverse mapping hits = 1149
- Checking for and removing duplicates
- Writing label file ./rh.BA6.thresh.label 8108
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.thresh.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
- Number of reverse mapping hits = 471
- Checking for and removing duplicates
- Writing label file ./rh.BA44.thresh.label 1483
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.thresh.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
- Number of reverse mapping hits = 568
- Checking for and removing duplicates
- Writing label file ./rh.BA45.thresh.label 1746
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.thresh.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
- Number of reverse mapping hits = 1953
- Checking for and removing duplicates
- Writing label file ./rh.V1.thresh.label 5185
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.thresh.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
- Number of reverse mapping hits = 2003
- Checking for and removing duplicates
- Writing label file ./rh.V2.thresh.label 5440
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.thresh.label --trgsubject sub016 --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 = sub016
- 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/sub016/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
- Number of reverse mapping hits = 127
- Checking for and removing duplicates
- Writing label file ./rh.MT.thresh.label 395
- mri_label2label: Done
- mris_label2annot --s sub016 --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/sub016/label
- cmdline mris_label2annot --s sub016 --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 sub016
- 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/sub016/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 111800 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/label/rh.BA.annot
- mris_label2annot --s sub016 --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/sub016/label
- cmdline mris_label2annot --s sub016 --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 sub016
- 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/sub016/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 133862 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/label/rh.BA.thresh.annot
- mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab sub016 rh white
- computing statistics for each annotation in ./rh.BA.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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
- 1234 622 2657 2.836 0.465 0.128 0.447 48 3.2 BA1
- 3411 2318 5760 2.412 0.397 0.101 0.026 26 3.6 BA2
- 1110 754 1172 1.983 0.380 0.131 0.038 9 1.8 BA3a
- 2380 1505 3726 2.079 0.543 0.106 0.031 23 3.0 BA3b
- 2154 1136 4370 3.141 0.553 0.104 0.294 211 47.9 BA4a
- 1389 887 2423 2.795 0.441 0.098 0.031 12 1.8 BA4p
- 10186 6414 23606 3.041 0.597 0.120 0.078 212 22.4 BA6
- 4529 2987 8799 2.749 0.447 0.113 0.036 42 5.6 BA44
- 5076 3432 11633 2.717 0.589 0.142 0.064 133 9.4 BA45
- 5217 3502 7631 2.067 0.413 0.155 0.071 97 15.4 V1
- 10109 6603 16061 2.250 0.529 0.161 0.092 238 31.4 V2
- 2738 1871 4700 2.415 0.459 0.142 0.055 51 5.9 MT
- 826 562 1993 3.049 0.765 0.149 0.064 11 2.1 perirhinal
- mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab sub016 rh white
- computing statistics for each annotation in ./rh.BA.thresh.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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
- 939 455 1971 2.804 0.481 0.129 0.576 46 2.7 BA1
- 1971 1324 3546 2.430 0.392 0.092 0.023 13 1.9 BA2
- 951 644 912 1.977 0.367 0.132 0.036 7 1.5 BA3a
- 1988 1285 2678 1.914 0.438 0.096 0.026 14 2.3 BA3b
- 1224 601 2317 3.155 0.551 0.099 0.044 16 2.6 BA4a
- 1173 746 2044 2.887 0.495 0.098 0.032 10 1.6 BA4p
- 6353 3964 14626 3.011 0.600 0.116 0.101 169 16.1 BA6
- 1412 937 3367 2.868 0.383 0.112 0.043 15 1.7 BA44
- 1662 1115 4315 2.933 0.476 0.138 0.043 28 3.0 BA45
- 5008 3350 7193 2.063 0.420 0.153 0.070 90 14.5 V1
- 5235 3453 7829 2.089 0.483 0.174 0.075 111 15.5 V2
- 381 250 753 2.535 0.449 0.144 0.051 8 0.8 MT
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/label
- #--------------------------------------------
- #@# Ex-vivo Entorhinal Cortex Label lh Fri Aug 9 01:09:53 CEST 2013
- mris_spherical_average -erode 1 -orig white -t 0.4 -o sub016 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label
- painting output onto subject sub016.
- processing subject lh.EC_average...
- reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 1259 points to lh.entorhinal_exvivo.label...
- mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label sub016 lh white
- limiting computations to label ./lh.entorhinal_exvivo.label.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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
- 470 298 1375 3.150 0.616 0.126 0.042 4 0.9 ./lh.entorhinal_exvivo.label
- #--------------------------------------------
- #@# Ex-vivo Entorhinal Cortex Label rh Fri Aug 9 01:10:09 CEST 2013
- mris_spherical_average -erode 1 -orig white -t 0.4 -o sub016 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label
- painting output onto subject sub016.
- processing subject rh.EC_average...
- reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 1079 points to rh.entorhinal_exvivo.label...
- mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label sub016 rh white
- limiting computations to label ./rh.entorhinal_exvivo.label.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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
- 447 289 1300 3.259 0.643 0.131 0.064 5 1.1 ./rh.entorhinal_exvivo.label
- #------------------------------------------
- Started at Thu Aug 8 10:54:16 CEST 2013
- Ended at Fri Aug 9 01:10:26 CEST 2013
- #@#%# recon-all-run-time-hours 14.269
- recon-all -s sub016 finished without error at Fri Aug 9 01:10:26 CEST 2013
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