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|
- Thu Aug 8 10:53:49 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017
- /opt/freesurfer/5.3.0/bin/recon-all
- -i /home/data/exppsy/forrest_gump/openfmri.org/sub017/anatomy/highres001.nii.gz -cw256 -all -T2 /home/data/exppsy/forrest_gump/openfmri.org/sub017/anatomy/other/t2w001.nii.gz -T2pial -subjid sub017 -sd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- subjid sub017
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- FREESURFER_HOME /opt/freesurfer/5.3.0
- Actual FREESURFER_HOME /opt/freesurfer/5.3.0
- build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
- Linux snake5 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
- cputime unlimited
- filesize unlimited
- datasize unlimited
- stacksize unlimited
- coredumpsize 0 kbytes
- memoryuse unlimited
- vmemoryuse unlimited
- descriptors 1024
- memorylocked 64 kbytes
- maxproc unlimited
- maxlocks unlimited
- maxsignal 16382
- maxmessage 819200
- maxnice 0
- maxrtprio 0
- maxrttime unlimited
- total used free shared buffers cached
- Mem: 99201692 96129736 3071956 0 177856 94375796
- -/+ buffers/cache: 1576084 97625608
- Swap: 25165780 3620 25162160
- ########################################
- program versions used
- $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
- $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
- mri_convert -all-info
- ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- FLIRT version 5.5
- $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
- mri_convert --version
- stable5
- ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- Program nu_correct, built from:
- Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
- ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ======= NUMBER OF OPENMP THREADS = 1 =======
- ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:53-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:53-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:53-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:53-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:53-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:53-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:53-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $
- ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:53-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $
- ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:53-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:54-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:54-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:54-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:54-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: fkaule Machine: snake5 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- #######################################
- GCADIR /opt/freesurfer/5.3.0/average
- GCA RB_all_2008-03-26.gca
- GCASkull RB_all_withskull_2008-03-26.gca
- AvgCurvTif average.curvature.filled.buckner40.tif
- GCSDIR /opt/freesurfer/5.3.0/average
- GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
- #######################################
- -cw256 option is now persistent (remove with -clean-cw256)
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub017/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/orig/001.mgz
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub017/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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/sub017/anatomy/highres001.nii.gz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.998353, -0.0379406, 0.0430326)
- j_ras = (-0.0315844, 0.989674, 0.139811)
- k_ras = (0.0478928, -0.138221, 0.989243)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/orig/001.mgz...
- #--------------------------------------------
- #@# T2/FLAIR Input Thu Aug 8 10:54:10 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub017/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/orig/T2raw.mgz
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub017/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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/sub017/anatomy/other/t2w001.nii.gz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.998353, -0.0379406, 0.0430326)
- j_ras = (-0.0315844, 0.989674, 0.139811)
- k_ras = (0.0478928, -0.138221, 0.989243)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/orig/T2raw.mgz...
- #--------------------------------------------
- #@# MotionCor Thu Aug 8 10:54:25 CEST 2013
- Found 1 runs
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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/sub017/mri/orig/001.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/rawavg.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/orig.mgz --conform --cw256
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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/sub017/mri/rawavg.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.998353, -0.0379406, 0.0430326)
- j_ras = (-0.0315844, 0.989674, 0.139811)
- k_ras = (0.0478928, -0.138221, 0.989243)
- Original Data has (0.699905, 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/sub017/mri/orig.mgz...
- mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/talairach.xfm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/orig.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Talairach Thu Aug 8 10:55:03 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri
- mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
- talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
- cp transforms/talairach.auto.xfm transforms/talairach.xfm
- #--------------------------------------------
- #@# Talairach Failure Detection Thu Aug 8 10:57:49 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri
- talairach_afd -T 0.005 -xfm transforms/talairach.xfm
- talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.5570, pval=0.2115 >= threshold=0.0050)
- awk -f /opt/freesurfer/5.3.0/bin/extract_talairach_avi_QA.awk /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/talairach_avi.log
- tal_QC_AZS /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/talairach_avi.log
- TalAviQA: 0.96293
- z-score: -3
- #--------------------------------------------
- #@# Nu Intensity Correction Thu Aug 8 10:57:49 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/sub017/mri
- /opt/freesurfer/5.3.0/bin/mri_nu_correct.mni
- --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
- nIters 2
- $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $
- Linux snake5 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
- Thu Aug 8 10:57:49 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.12094
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.12094/nu0.mnc -odt float
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.12094/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 = (1.49012e-08, -1.49012e-08, -1)
- k_ras = (2.32831e-09, 1, 1.49012e-08)
- changing data type from uchar to float (noscale = 0)...
- writing to ./tmp.mri_nu_correct.mni.12094/nu0.mnc...
-
- --------------------------------------------------------
- Iteration 1 Thu Aug 8 10:57:54 CEST 2013
- nu_correct -clobber ./tmp.mri_nu_correct.mni.12094/nu0.mnc ./tmp.mri_nu_correct.mni.12094/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.12094/0/
- [fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/] [2013-08-08 10:57:55] 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.12094/0/ ./tmp.mri_nu_correct.mni.12094/nu0.mnc ./tmp.mri_nu_correct.mni.12094/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
- Number of iterations: 29
- CV of field change: 0.000996562
- [fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/] [2013-08-08 10:58:33] running:
- /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.12094/nu0.mnc ./tmp.mri_nu_correct.mni.12094/0//template.mnc
- Transforming slices:......................................................................................Done
- Transforming slices:................................................................................................................................................................................................................................................................Done
-
-
- --------------------------------------------------------
- Iteration 2 Thu Aug 8 10:58:41 CEST 2013
- nu_correct -clobber ./tmp.mri_nu_correct.mni.12094/nu1.mnc ./tmp.mri_nu_correct.mni.12094/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.12094/1/
- [fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/] [2013-08-08 10:58:42] 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.12094/1/ ./tmp.mri_nu_correct.mni.12094/nu1.mnc ./tmp.mri_nu_correct.mni.12094/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
- Number of iterations: 24
- CV of field change: 0.000978413
- [fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/] [2013-08-08 10:59:21] running:
- /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.12094/nu1.mnc ./tmp.mri_nu_correct.mni.12094/1//template.mnc
- Transforming slices:......................................................................................Done
- Transforming slices:................................................................................................................................................................................................................................................................Done
-
-
-
- mri_binarize --i ./tmp.mri_nu_correct.mni.12094/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.12094/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/sub017/mri
- cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.12094/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.12094/ones.mgz
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- input ./tmp.mri_nu_correct.mni.12094/nu2.mnc
- frame 0
- nErode3d 0
- nErode2d 0
- output ./tmp.mri_nu_correct.mni.12094/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.12094/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.12094/sum.junk --avgwf ./tmp.mri_nu_correct.mni.12094/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.12094/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.12094/sum.junk --avgwf ./tmp.mri_nu_correct.mni.12094/input.mean.dat
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.12094/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.12094/input.mean.dat
- mri_segstats done
- mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.12094/ones.mgz --i ./tmp.mri_nu_correct.mni.12094/nu2.mnc --sum ./tmp.mri_nu_correct.mni.12094/sum.junk --avgwf ./tmp.mri_nu_correct.mni.12094/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.12094/ones.mgz --i ./tmp.mri_nu_correct.mni.12094/nu2.mnc --sum ./tmp.mri_nu_correct.mni.12094/sum.junk --avgwf ./tmp.mri_nu_correct.mni.12094/output.mean.dat
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.12094/ones.mgz
- Loading ./tmp.mri_nu_correct.mni.12094/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.12094/output.mean.dat
- mri_segstats done
- mris_calc -o ./tmp.mri_nu_correct.mni.12094/nu2.mnc ./tmp.mri_nu_correct.mni.12094/nu2.mnc mul .95861432503293635782
- Saving result to './tmp.mri_nu_correct.mni.12094/nu2.mnc' (type = MINC ) [ ok ]
- mri_convert ./tmp.mri_nu_correct.mni.12094/nu2.mnc nu.mgz --like orig.mgz
- mri_convert ./tmp.mri_nu_correct.mni.12094/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.12094/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 = (1.49012e-08, -1.49012e-08, -1)
- k_ras = (2.32831e-09, 1, 1.49012e-08)
- INFO: transform src into the like-volume: orig.mgz
- writing to nu.mgz...
- mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz
- type change took 0 minutes and 9 seconds.
- mapping ( 7, 189) to ( 3, 110)
-
-
- Thu Aug 8 11:00:14 CEST 2013
- mri_nu_correct.mni done
- mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/talairach.xfm nu.mgz nu.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Intensity Normalization Thu Aug 8 11:00:15 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri
- mri_normalize -g 1 nu.mgz T1.mgz
- using max gradient = 1.000
- reading from nu.mgz...
- normalizing image...
- talairach transform
- 1.151 0.079 -0.010 0.485;
- -0.053 1.150 0.363 -28.132;
- 0.036 -0.550 1.247 9.346;
- 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 = 16
- Starting OpenSpline(): npoints = 16
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Iterating 2 times
- ---------------------------------
- 3d normalization pass 1 of 2
- white matter peak found at 111
- white matter peak found at 109
- gm peak at 50 (50), valley at 35 (35)
- csf peak at 10, setting threshold to 36
- 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 52 (52), valley at 40 (40)
- csf peak at 11, setting threshold to 38
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Done iterating ---------------------------------
- writing output to T1.mgz
- 3D bias adjustment took 2 minutes and 45 seconds.
- #--------------------------------------------
- #@# Skull Stripping Thu Aug 8 11:03:01 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri
- mri_em_register -skull nu.mgz /opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta
- ======= NUMBER OF OPENMP THREADS = 1 =======
- aligning to atlas containing skull, setting unknown_nbr_spacing = 5
- reading 1 input volumes...
- logging results to talairach_with_skull.log
- reading '/opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca'...
- average std = 23.1 using min determinant for regularization = 53.4
- 0 singular and 5702 ill-conditioned covariance matrices regularized
- reading 'nu.mgz'...
- freeing gibbs priors...done.
- bounding unknown intensity as < 20.2 or > 943.7
- total sample mean = 92.0 (1443 zeros)
- ************************************************
- spacing=8, using 3481 sample points, tol=1.00e-05...
- ************************************************
- register_mri: find_optimal_transform
- find_optimal_transform: nsamples 3481, passno 0, spacing 8
- resetting wm mean[0]: 117 --> 126
- resetting gm mean[0]: 74 --> 74
- input volume #1 is the most T1-like
- using real data threshold=8.0
- skull bounding box = (52, 27, 27) --> (200, 255, 201)
- using (101, 103, 114) as brain centroid...
- mean wm in atlas = 126, using box (83,75,93) --> (119, 131,135) to find MRI wm
- before smoothing, mri peak at 110
- after smoothing, mri peak at 110, scaling input intensities by 1.145
- scaling channel 0 by 1.14545
- initial log_p = -4.8
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -4.627415 @ (-9.091, 9.091, -9.091)
- max log p = -4.517626 @ (4.545, 4.545, -4.545)
- max log p = -4.503724 @ (2.273, -2.273, -6.818)
- max log p = -4.492685 @ (1.136, 1.136, 5.682)
- max log p = -4.485390 @ (-3.977, 0.568, 1.705)
- max log p = -4.485390 @ (0.000, 0.000, 0.000)
- Found translation: (-5.1, 13.1, -13.1): log p = -4.485
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.5 (thresh=-4.5)
- 1.150 0.000 0.000 -24.745;
- 0.000 1.142 0.473 -51.137;
- 0.000 -0.440 1.062 34.541;
- 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)
- 1.150 0.000 0.000 -24.745;
- 0.000 1.142 0.473 -51.137;
- 0.000 -0.440 1.062 34.541;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.2500
- ****************************************
- Nine parameter search. iteration 2 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-4.1 (thresh=-4.1)
- 1.145 -0.046 -0.100 -4.419;
- 0.077 1.220 0.460 -65.965;
- 0.073 -0.377 1.016 21.604;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 3 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 1.145 -0.046 -0.100 -4.419;
- 0.077 1.220 0.460 -65.965;
- 0.073 -0.377 1.016 21.604;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.0625
- ****************************************
- Nine parameter search. iteration 4 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 1.147 -0.032 -0.076 -9.296;
- 0.058 1.218 0.460 -63.355;
- 0.055 -0.376 1.019 23.649;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 5 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 1.147 -0.032 -0.076 -9.296;
- 0.058 1.214 0.458 -62.707;
- 0.055 -0.377 1.021 23.456;
- 0.000 0.000 0.000 1.000;
- min search scale 0.025000 reached
- ***********************************************
- Computing MAP estimate using 3481 samples...
- ***********************************************
- dt = 5.00e-06, momentum=0.80, tol=1.00e-05
- l_intensity = 1.0000
- Aligning input volume to GCA...
- Transform matrix
- 1.14723 -0.03216 -0.07610 -9.29553;
- 0.05777 1.21359 0.45849 -62.70662;
- 0.05494 -0.37702 1.02142 23.45569;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 3481
- Quasinewton: input matrix
- 1.14723 -0.03216 -0.07610 -9.29553;
- 0.05777 1.21359 0.45849 -62.70662;
- 0.05494 -0.37702 1.02142 23.45569;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 1.147 -0.032 -0.076 -9.296;
- 0.058 1.214 0.458 -62.707;
- 0.055 -0.377 1.021 23.456;
- 0.000 0.000 0.000 1.000;
- pass 1, spacing 8: log(p) = -3.9 (old=-4.8)
- transform before final EM align:
- 1.147 -0.032 -0.076 -9.296;
- 0.058 1.214 0.458 -62.707;
- 0.055 -0.377 1.021 23.456;
- 0.000 0.000 0.000 1.000;
- **************************************************
- EM alignment process ...
- Computing final MAP estimate using 382743 samples.
- **************************************************
- dt = 5.00e-06, momentum=0.80, tol=1.00e-07
- l_intensity = 1.0000
- Aligning input volume to GCA...
- Transform matrix
- 1.14723 -0.03216 -0.07610 -9.29553;
- 0.05777 1.21359 0.45849 -62.70662;
- 0.05494 -0.37702 1.02142 23.45569;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 382743
- Quasinewton: input matrix
- 1.14723 -0.03216 -0.07610 -9.29553;
- 0.05777 1.21359 0.45849 -62.70662;
- 0.05494 -0.37702 1.02142 23.45569;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = 4.4 tol 0.000000
- final transform:
- 1.147 -0.032 -0.076 -9.296;
- 0.058 1.214 0.458 -62.707;
- 0.055 -0.377 1.021 23.456;
- 0.000 0.000 0.000 1.000;
- writing output transformation to transforms/talairach_with_skull.lta...
- registration took 29 minutes and 52 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=129 y=93 z=114 r=92
- first estimation of the main basin volume: 3356910 voxels
- Looking for seedpoints
- 2 found in the cerebellum
- 15 found in the rest of the brain
- global maximum in x=107, y=93, z=78, Imax=255
- CSF=12, WM_intensity=110, WM_VARIANCE=5
- WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110
- preflooding height equal to 10 percent
- done.
- Analyze...
- main basin size=19034827907 voxels, voxel volume =1.000
- = 19034827907 mmm3 = 19034828.800 cm3
- done.
- PostAnalyze...Basin Prior
- 47 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=102, z=112, r=9364 iterations
- ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^
- GLOBAL CSF_MIN=0, CSF_intensity=3, CSF_MAX=12 , nb = 45533
- RIGHT_CER CSF_MIN=0, CSF_intensity=4, CSF_MAX=21 , nb = -1030593733
- LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=20 , nb = 1090954993
- RIGHT_BRAIN CSF_MIN=0, CSF_intensity=3, CSF_MAX=12 , nb = -1085888621
- LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=12 , nb = 1076667256
- OTHER CSF_MIN=0, CSF_intensity=9, CSF_MAX=25 , nb = 1078999108
-
- CSF_MAX TRANSITION GM_MIN GM
- GLOBAL
- before analyzing : 12, 16, 28, 50
- after analyzing : 12, 24, 28, 30
- RIGHT_CER
- before analyzing : 21, 21, 23, 73
- after analyzing : 21, 23, 25, 35
- LEFT_CER
- before analyzing : 20, 22, 26, 61
- after analyzing : 20, 24, 26, 33
- RIGHT_BRAIN
- before analyzing : 12, 16, 28, 50
- after analyzing : 12, 24, 28, 30
- LEFT_BRAIN
- before analyzing : 12, 16, 27, 54
- after analyzing : 12, 23, 27, 30
- OTHER
- before analyzing : 25, 55, 81, 94
- after analyzing : 25, 72, 81, 77
- mri_strip_skull: done peeling brain
- highly tesselated surface with 10242 vertices
- matching...77 iterations
- *********************VALIDATION*********************
- curvature mean = -0.013, std = 0.013
- curvature mean = 66.379, std = 8.380
- No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
- before rotation: sse = 4.53, sigma = 9.04
- after rotation: sse = 4.53, sigma = 9.04
- Localization of inacurate regions: Erosion-Dilation steps
- the sse mean is 5.35, its var is 10.08
- before Erosion-Dilatation 2.77% of inacurate vertices
- after Erosion-Dilatation 3.86% 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...44 iterations
- mri_strip_skull: done peeling brain
- Brain Size = 1497928 voxels, voxel volume = 1.000 mm3
- = 1497928 mmm3 = 1497.928 cm3
- ******************************
- Saving brainmask.auto.mgz
- done
- cp brainmask.auto.mgz brainmask.mgz
- #-------------------------------------
- #@# EM Registration Thu Aug 8 11:33:23 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 = (62, 51, 42) --> (191, 177, 188)
- using (105, 93, 115) as brain centroid...
- mean wm in atlas = 107, using box (89,78,97) --> (120, 108,132) to find MRI wm
- before smoothing, mri peak at 109
- after smoothing, mri peak at 110, scaling input intensities by 0.973
- scaling channel 0 by 0.972727
- initial log_p = -4.4
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -4.126220 @ (-9.091, 9.091, -9.091)
- max log p = -3.908504 @ (4.545, 4.545, -4.545)
- max log p = -3.908504 @ (0.000, 0.000, 0.000)
- max log p = -3.901324 @ (-1.136, -1.136, 1.136)
- max log p = -3.880781 @ (1.705, 2.841, 0.568)
- max log p = -3.880781 @ (0.000, 0.000, 0.000)
- Found translation: (-4.0, 15.3, -11.9): log p = -3.881
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p =-3.9 (thresh=-3.9)
- 1.140 0.034 -0.126 -11.022;
- 0.000 1.194 0.320 -42.274;
- 0.150 -0.257 0.958 -0.035;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p =-3.5 (thresh=-3.5)
- 1.140 0.034 -0.126 -11.022;
- 0.000 1.194 0.320 -42.274;
- 0.150 -0.257 0.958 -0.035;
- 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=-3.4, old_max_log_p =-3.5 (thresh=-3.5)
- 1.106 0.001 -0.030 -14.393;
- 0.007 1.163 0.342 -40.699;
- 0.042 -0.311 0.989 18.082;
- 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 =-3.4 (thresh=-3.3)
- 1.106 0.001 -0.030 -14.393;
- 0.007 1.163 0.342 -40.699;
- 0.042 -0.311 0.989 18.082;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.0625
- ****************************************
- Nine parameter search. iteration 4 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.3, old_max_log_p =-3.4 (thresh=-3.3)
- 1.109 0.011 -0.027 -15.093;
- -0.002 1.160 0.350 -40.721;
- 0.042 -0.321 0.986 19.390;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 5 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3)
- 1.109 0.011 -0.027 -15.093;
- -0.002 1.160 0.350 -40.721;
- 0.042 -0.321 0.986 19.390;
- 0.000 0.000 0.000 1.000;
- min search scale 0.025000 reached
- ***********************************************
- Computing MAP estimate using 2772 samples...
- ***********************************************
- dt = 5.00e-06, momentum=0.80, tol=1.00e-05
- l_intensity = 1.0000
- Aligning input volume to GCA...
- Transform matrix
- 1.10906 0.01072 -0.02711 -15.09295;
- -0.00170 1.16029 0.35006 -40.72054;
- 0.04173 -0.32076 0.98640 19.39028;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 2772
- Quasinewton: input matrix
- 1.10906 0.01072 -0.02711 -15.09295;
- -0.00170 1.16029 0.35006 -40.72054;
- 0.04173 -0.32076 0.98640 19.39028;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 1.109 0.011 -0.027 -15.093;
- -0.002 1.160 0.350 -40.721;
- 0.042 -0.321 0.986 19.390;
- 0.000 0.000 0.000 1.000;
- pass 1, spacing 8: log(p) = -3.3 (old=-4.4)
- transform before final EM align:
- 1.109 0.011 -0.027 -15.093;
- -0.002 1.160 0.350 -40.721;
- 0.042 -0.321 0.986 19.390;
- 0.000 0.000 0.000 1.000;
- **************************************************
- EM alignment process ...
- Computing final MAP estimate using 312841 samples.
- **************************************************
- dt = 5.00e-06, momentum=0.80, tol=1.00e-07
- l_intensity = 1.0000
- Aligning input volume to GCA...
- Transform matrix
- 1.10906 0.01072 -0.02711 -15.09295;
- -0.00170 1.16029 0.35006 -40.72054;
- 0.04173 -0.32076 0.98640 19.39028;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 312841
- Quasinewton: input matrix
- 1.10906 0.01072 -0.02711 -15.09295;
- -0.00170 1.16029 0.35006 -40.72054;
- 0.04173 -0.32076 0.98640 19.39028;
- 0.00000 0.00000 0.00000 1.00000;
- dfp_em_step_func: 009: -log(p) = 3.9
- after pass:transform: ( 1.11, 0.01, -0.03, -15.09)
- ( -0.00, 1.16, 0.35, -40.72)
- ( 0.04, -0.32, 0.99, 19.39)
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization...
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = 3.9 tol 0.000000
- final transform:
- 1.109 0.011 -0.027 -15.093;
- -0.002 1.160 0.350 -40.721;
- 0.042 -0.321 0.986 19.390;
- 0.000 0.000 0.000 1.000;
- writing output transformation to transforms/talairach.lta...
- registration took 24 minutes and 54 seconds.
- #--------------------------------------
- #@# CA Normalize Thu Aug 8 11:58:17 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 = (62, 51, 42) --> (191, 177, 188)
- using (105, 93, 115) as brain centroid...
- mean wm in atlas = 107, using box (89,78,97) --> (120, 108,132) to find MRI wm
- before smoothing, mri peak at 109
- after smoothing, mri peak at 110, scaling input intensities by 0.973
- scaling channel 0 by 0.972727
- using 244171 sample points...
- INFO: compute sample coordinates transform
- 1.109 0.011 -0.027 -15.093;
- -0.002 1.160 0.350 -40.721;
- 0.042 -0.321 0.986 19.390;
- 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 (125, 48, 43) --> (188, 149, 199)
- Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 138.0
- 0 of 36 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 40735 control points for structure...
- bounding box (71, 47, 43) --> (130, 141, 201)
- Right_Cerebral_White_Matter: limiting intensities to 99.0 --> 138.0
- 0 of 22 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3012 control points for structure...
- bounding box (130, 124, 72) --> (173, 162, 122)
- Left_Cerebellum_White_Matter: limiting intensities to 87.0 --> 138.0
- 0 of 17 (0.0%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2764 control points for structure...
- bounding box (87, 124, 70) --> (128, 160, 125)
- Right_Cerebellum_White_Matter: limiting intensities to 92.0 --> 138.0
- 0 of 7 (0.0%) samples deleted
- finding control points in Brain_Stem....
- found 3520 control points for structure...
- bounding box (114, 113, 104) --> (143, 170, 133)
- Brain_Stem: limiting intensities to 95.0 --> 138.0
- 6 of 7 (85.7%) samples deleted
- using 89 total control points for intensity normalization...
- bias field = 0.997 +- 0.053
- 0 of 83 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 41584 control points for structure...
- bounding box (125, 48, 43) --> (188, 149, 199)
- Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0
- 0 of 70 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 40735 control points for structure...
- bounding box (71, 47, 43) --> (130, 141, 201)
- Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0
- 0 of 90 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3012 control points for structure...
- bounding box (130, 124, 72) --> (173, 162, 122)
- Left_Cerebellum_White_Matter: limiting intensities to 80.0 --> 132.0
- 0 of 50 (0.0%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2764 control points for structure...
- bounding box (87, 124, 70) --> (128, 160, 125)
- Right_Cerebellum_White_Matter: limiting intensities to 80.0 --> 132.0
- 0 of 34 (0.0%) samples deleted
- finding control points in Brain_Stem....
- found 3520 control points for structure...
- bounding box (114, 113, 104) --> (143, 170, 133)
- Brain_Stem: limiting intensities to 77.0 --> 132.0
- 0 of 57 (0.0%) samples deleted
- using 301 total control points for intensity normalization...
- bias field = 0.996 +- 0.057
- 0 of 301 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 41584 control points for structure...
- bounding box (125, 48, 43) --> (188, 149, 199)
- Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 134.0
- 0 of 203 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 40735 control points for structure...
- bounding box (71, 47, 43) --> (130, 141, 201)
- Right_Cerebral_White_Matter: limiting intensities to 93.0 --> 134.0
- 0 of 184 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3012 control points for structure...
- bounding box (130, 124, 72) --> (173, 162, 122)
- Left_Cerebellum_White_Matter: limiting intensities to 74.0 --> 134.0
- 0 of 45 (0.0%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2764 control points for structure...
- bounding box (87, 124, 70) --> (128, 160, 125)
- Right_Cerebellum_White_Matter: limiting intensities to 75.0 --> 134.0
- 0 of 34 (0.0%) samples deleted
- finding control points in Brain_Stem....
- found 3520 control points for structure...
- bounding box (114, 113, 104) --> (143, 170, 133)
- Brain_Stem: limiting intensities to 75.0 --> 134.0
- 0 of 72 (0.0%) samples deleted
- using 538 total control points for intensity normalization...
- bias field = 1.003 +- 0.047
- 1 of 538 control points discarded
- writing normalized volume to norm.mgz...
- writing control points to ctrl_pts.mgz
- freeing GCA...done.
- normalization took 2 minutes and 1 seconds.
- #--------------------------------------
- #@# CA Reg Thu Aug 8 12:00:19 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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) = 1.40 (predicted orig area = 5.7)
- 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=0.991, neg=0, invalid=96777
- 0001: dt=129.472000, rms=0.832 (16.125%), neg=0, invalid=96777
- 0002: dt=129.472000, rms=0.791 (4.865%), neg=0, invalid=96777
- 0003: dt=221.952000, rms=0.773 (2.238%), neg=0, invalid=96777
- 0004: dt=92.480000, rms=0.768 (0.646%), neg=0, invalid=96777
- 0005: dt=443.904000, rms=0.758 (1.392%), neg=0, invalid=96777
- 0006: dt=73.984000, rms=0.753 (0.612%), neg=0, invalid=96777
- 0007: dt=443.904000, rms=0.748 (0.682%), neg=0, invalid=96777
- 0008: dt=92.480000, rms=0.746 (0.313%), neg=0, invalid=96777
- 0009: dt=369.920000, rms=0.743 (0.392%), neg=0, invalid=96777
- 0010: dt=92.480000, rms=0.741 (0.220%), neg=0, invalid=96777
- 0011: dt=92.480000, rms=0.740 (0.145%), neg=0, invalid=96777
- 0012: dt=92.480000, rms=0.738 (0.203%), neg=0, invalid=96777
- 0013: dt=92.480000, rms=0.736 (0.261%), neg=0, invalid=96777
- 0014: dt=92.480000, rms=0.734 (0.313%), neg=0, invalid=96777
- 0015: dt=92.480000, rms=0.732 (0.362%), neg=0, invalid=96777
- 0016: dt=92.480000, rms=0.729 (0.356%), neg=0, invalid=96777
- 0017: dt=92.480000, rms=0.726 (0.339%), neg=0, invalid=96777
- 0018: dt=92.480000, rms=0.724 (0.337%), neg=0, invalid=96777
- 0019: dt=92.480000, rms=0.722 (0.304%), neg=0, invalid=96777
- 0020: dt=92.480000, rms=0.720 (0.288%), neg=0, invalid=96777
- 0021: dt=92.480000, rms=0.718 (0.298%), neg=0, invalid=96777
- 0022: dt=92.480000, rms=0.715 (0.305%), neg=0, invalid=96777
- 0023: dt=92.480000, rms=0.713 (0.285%), neg=0, invalid=96777
- 0024: dt=92.480000, rms=0.711 (0.263%), neg=0, invalid=96777
- 0025: dt=92.480000, rms=0.710 (0.205%), neg=0, invalid=96777
- 0026: dt=92.480000, rms=0.708 (0.240%), neg=0, invalid=96777
- 0027: dt=92.480000, rms=0.706 (0.257%), neg=0, invalid=96777
- 0028: dt=92.480000, rms=0.705 (0.203%), neg=0, invalid=96777
- 0029: dt=92.480000, rms=0.704 (0.170%), neg=0, invalid=96777
- 0030: dt=92.480000, rms=0.703 (0.163%), neg=0, invalid=96777
- 0031: dt=92.480000, rms=0.701 (0.211%), neg=0, invalid=96777
- 0032: dt=92.480000, rms=0.700 (0.208%), neg=0, invalid=96777
- 0033: dt=92.480000, rms=0.699 (0.164%), neg=0, invalid=96777
- 0034: dt=92.480000, rms=0.698 (0.126%), neg=0, invalid=96777
- 0035: dt=92.480000, rms=0.697 (0.133%), neg=0, invalid=96777
- 0036: dt=92.480000, rms=0.696 (0.173%), neg=0, invalid=96777
- 0037: dt=92.480000, rms=0.694 (0.176%), neg=0, invalid=96777
- 0038: dt=92.480000, rms=0.693 (0.129%), neg=0, invalid=96777
- 0039: dt=92.480000, rms=0.693 (0.100%), neg=0, invalid=96777
- 0040: dt=92.480000, rms=0.692 (0.115%), neg=0, invalid=96777
- 0041: dt=92.480000, rms=0.691 (0.131%), neg=0, invalid=96777
- 0042: dt=92.480000, rms=0.690 (0.121%), neg=0, invalid=96777
- 0043: dt=92.480000, rms=0.690 (0.095%), neg=0, invalid=96777
- 0044: dt=129.472000, rms=0.690 (0.001%), neg=0, invalid=96777
- 0045: dt=129.472000, rms=0.689 (0.022%), neg=0, invalid=96777
- 0046: dt=129.472000, rms=0.689 (0.029%), neg=0, invalid=96777
- 0047: dt=129.472000, rms=0.689 (0.010%), neg=0, invalid=96777
- 0048: dt=129.472000, rms=0.689 (0.043%), neg=0, invalid=96777
- 0049: dt=129.472000, rms=0.688 (0.058%), neg=0, invalid=96777
- 0050: dt=129.472000, rms=0.688 (0.038%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.688, neg=0, invalid=96777
- 0051: dt=73.984000, rms=0.688 (0.029%), neg=0, invalid=96777
- 0052: dt=369.920000, rms=0.687 (0.137%), neg=0, invalid=96777
- 0053: dt=443.904000, rms=0.686 (0.152%), neg=0, invalid=96777
- 0054: dt=0.000000, rms=0.686 (-0.001%), neg=0, invalid=96777
- setting smoothness coefficient to 0.154
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.694, neg=0, invalid=96777
- 0055: dt=145.152000, rms=0.685 (1.390%), neg=0, invalid=96777
- 0056: dt=145.152000, rms=0.675 (1.488%), neg=0, invalid=96777
- 0057: dt=14.808511, rms=0.672 (0.339%), neg=0, invalid=96777
- 0058: dt=15.552000, rms=0.672 (0.103%), neg=0, invalid=96777
- 0059: dt=15.552000, rms=0.671 (0.081%), neg=0, invalid=96777
- 0060: dt=15.552000, rms=0.670 (0.135%), neg=0, invalid=96777
- 0061: dt=15.552000, rms=0.669 (0.211%), neg=0, invalid=96777
- 0062: dt=15.552000, rms=0.667 (0.304%), neg=0, invalid=96777
- 0063: dt=15.552000, rms=0.664 (0.388%), neg=0, invalid=96777
- 0064: dt=15.552000, rms=0.661 (0.424%), neg=0, invalid=96777
- 0065: dt=15.552000, rms=0.658 (0.430%), neg=0, invalid=96777
- 0066: dt=15.552000, rms=0.656 (0.405%), neg=0, invalid=96777
- 0067: dt=15.552000, rms=0.653 (0.387%), neg=0, invalid=96777
- 0068: dt=15.552000, rms=0.651 (0.364%), neg=0, invalid=96777
- 0069: dt=15.552000, rms=0.648 (0.378%), neg=0, invalid=96777
- 0070: dt=15.552000, rms=0.646 (0.387%), neg=0, invalid=96777
- 0071: dt=15.552000, rms=0.643 (0.385%), neg=0, invalid=96777
- 0072: dt=15.552000, rms=0.641 (0.345%), neg=0, invalid=96777
- 0073: dt=15.552000, rms=0.639 (0.291%), neg=0, invalid=96777
- 0074: dt=15.552000, rms=0.638 (0.249%), neg=0, invalid=96777
- 0075: dt=15.552000, rms=0.636 (0.213%), neg=0, invalid=96777
- 0076: dt=15.552000, rms=0.635 (0.196%), neg=0, invalid=96777
- 0077: dt=15.552000, rms=0.634 (0.212%), neg=0, invalid=96777
- 0078: dt=15.552000, rms=0.632 (0.227%), neg=0, invalid=96777
- 0079: dt=15.552000, rms=0.631 (0.220%), neg=0, invalid=96777
- 0080: dt=15.552000, rms=0.630 (0.202%), neg=0, invalid=96777
- 0081: dt=15.552000, rms=0.629 (0.178%), neg=0, invalid=96777
- 0082: dt=15.552000, rms=0.628 (0.161%), neg=0, invalid=96777
- 0083: dt=15.552000, rms=0.627 (0.138%), neg=0, invalid=96777
- 0084: dt=15.552000, rms=0.626 (0.138%), neg=0, invalid=96777
- 0085: dt=15.552000, rms=0.625 (0.151%), neg=0, invalid=96777
- 0086: dt=15.552000, rms=0.624 (0.148%), neg=0, invalid=96777
- 0087: dt=15.552000, rms=0.623 (0.131%), neg=0, invalid=96777
- 0088: dt=15.552000, rms=0.622 (0.110%), neg=0, invalid=96777
- 0089: dt=15.552000, rms=0.622 (0.095%), neg=0, invalid=96777
- 0090: dt=62.208000, rms=0.622 (0.028%), neg=0, invalid=96777
- 0091: dt=62.208000, rms=0.621 (0.058%), neg=0, invalid=96777
- 0092: dt=62.208000, rms=0.621 (0.064%), neg=0, invalid=96777
- 0093: dt=62.208000, rms=0.621 (0.064%), neg=0, invalid=96777
- 0094: dt=62.208000, rms=0.620 (0.100%), neg=0, invalid=96777
- 0095: dt=62.208000, rms=0.619 (0.144%), neg=0, invalid=96777
- 0096: dt=62.208000, rms=0.618 (0.117%), neg=0, invalid=96777
- 0097: dt=62.208000, rms=0.617 (0.147%), neg=0, invalid=96777
- 0098: dt=62.208000, rms=0.616 (0.169%), neg=0, invalid=96777
- 0099: dt=62.208000, rms=0.615 (0.139%), neg=0, invalid=96777
- 0100: dt=62.208000, rms=0.614 (0.160%), neg=0, invalid=96777
- 0101: dt=62.208000, rms=0.613 (0.213%), neg=0, invalid=96777
- 0102: dt=62.208000, rms=0.612 (0.162%), neg=0, invalid=96777
- 0103: dt=62.208000, rms=0.611 (0.137%), neg=0, invalid=96777
- 0104: dt=62.208000, rms=0.610 (0.215%), neg=0, invalid=96777
- 0105: dt=62.208000, rms=0.609 (0.139%), neg=0, invalid=96777
- 0106: dt=62.208000, rms=0.608 (0.130%), neg=0, invalid=96777
- 0107: dt=62.208000, rms=0.607 (0.184%), neg=0, invalid=96777
- 0108: dt=62.208000, rms=0.606 (0.135%), neg=0, invalid=96777
- 0109: dt=62.208000, rms=0.606 (0.095%), neg=0, invalid=96777
- 0110: dt=62.208000, rms=0.605 (0.099%), neg=0, invalid=96777
- 0111: dt=62.208000, rms=0.604 (0.164%), neg=0, invalid=96777
- 0112: dt=62.208000, rms=0.604 (0.084%), neg=0, invalid=96777
- 0113: dt=62.208000, rms=0.604 (0.028%), neg=0, invalid=96777
- 0114: dt=82.944000, rms=0.603 (0.105%), neg=0, invalid=96777
- 0115: dt=0.567000, rms=0.603 (-0.006%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.603, neg=0, invalid=96777
- 0116: dt=15.552000, rms=0.603 (0.040%), neg=0, invalid=96777
- 0117: dt=36.288000, rms=0.602 (0.059%), neg=0, invalid=96777
- 0118: dt=103.680000, rms=0.602 (0.113%), neg=0, invalid=96777
- 0119: dt=0.000000, rms=0.602 (-0.004%), neg=0, invalid=96777
- setting smoothness coefficient to 0.588
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.633, neg=0, invalid=96777
- 0120: dt=0.000000, rms=0.633 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.633, neg=0, invalid=96777
- 0121: dt=0.000000, rms=0.633 (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=0.726, neg=0, invalid=96777
- 0122: dt=4.253707, rms=0.705 (2.894%), neg=0, invalid=96777
- 0123: dt=2.081301, rms=0.704 (0.147%), neg=0, invalid=96777
- 0124: dt=2.081301, rms=0.704 (-0.047%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.704, neg=0, invalid=96777
- 0125: dt=0.000000, rms=0.704 (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=0.799, neg=0, invalid=96777
- 0126: dt=1.555184, rms=0.788 (1.362%), neg=0, invalid=96777
- 0127: dt=1.694656, rms=0.782 (0.722%), neg=0, invalid=96777
- 0128: dt=0.571429, rms=0.781 (0.157%), neg=0, invalid=96777
- 0129: dt=0.571429, rms=0.781 (0.044%), neg=0, invalid=96777
- 0130: dt=0.571429, rms=0.781 (0.022%), neg=0, invalid=96777
- 0131: dt=0.571429, rms=0.781 (-0.049%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.781, neg=0, invalid=96777
- 0132: dt=1.536000, rms=0.779 (0.244%), neg=0, invalid=96777
- 0133: dt=0.000000, rms=0.779 (-0.002%), neg=0, invalid=96777
- resetting metric properties...
- setting smoothness coefficient to 10.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.709, neg=0, invalid=96777
- 0134: dt=0.158545, rms=0.700 (1.221%), neg=0, invalid=96777
- 0135: dt=0.000000, rms=0.700 (0.003%), neg=0, invalid=96777
- 0136: dt=0.050000, rms=0.700 (-0.018%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.700, neg=0, invalid=96777
- 0137: dt=0.305019, rms=0.697 (0.400%), neg=0, invalid=96777
- 0138: dt=0.082458, rms=0.696 (0.164%), neg=0, invalid=96777
- 0139: dt=0.082458, rms=0.696 (0.021%), neg=0, invalid=96777
- 0140: dt=0.082458, rms=0.695 (0.045%), neg=0, invalid=96777
- 0141: dt=0.082458, rms=0.695 (0.085%), neg=0, invalid=96777
- 0142: dt=0.082458, rms=0.694 (0.129%), neg=0, invalid=96777
- 0143: dt=0.082458, rms=0.693 (0.138%), neg=0, invalid=96777
- 0144: dt=0.082458, rms=0.692 (0.131%), neg=0, invalid=96777
- 0145: dt=0.082458, rms=0.691 (0.111%), neg=0, invalid=96777
- 0146: dt=0.082458, rms=0.691 (0.088%), neg=0, invalid=96777
- 0147: dt=0.000000, rms=0.691 (0.001%), neg=0, invalid=96777
- 0148: dt=0.050000, rms=0.691 (-0.002%), neg=0, invalid=96777
- renormalizing by structure alignment....
- renormalizing input #0
- gca peak = 0.11725 (24)
- mri peak = 0.12154 ( 8)
- Left_Lateral_Ventricle (4): linear fit = 0.25 x + 0.0 (1135 voxels, overlap=0.005)
- Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (1135 voxels, peak = 6), gca=9.6
- gca peak = 0.14022 (22)
- mri peak = 0.12885 ( 8)
- Right_Lateral_Ventricle (43): linear fit = 0.28 x + 0.0 (848 voxels, overlap=0.007)
- Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (848 voxels, peak = 6), gca=8.8
- gca peak = 0.24234 (100)
- mri peak = 0.12349 (84)
- Right_Pallidum (52): linear fit = 0.83 x + 0.0 (219 voxels, overlap=0.045)
- Right_Pallidum (52): linear fit = 0.83 x + 0.0 (219 voxels, peak = 84), gca=83.5
- gca peak = 0.19192 (97)
- mri peak = 0.09231 (75)
- Left_Pallidum (13): linear fit = 0.77 x + 0.0 (145 voxels, overlap=0.427)
- Left_Pallidum (13): linear fit = 0.77 x + 0.0 (145 voxels, peak = 75), gca=75.2
- gca peak = 0.24007 (63)
- mri peak = 0.07421 (57)
- Right_Hippocampus (53): linear fit = 0.86 x + 0.0 (388 voxels, overlap=0.877)
- Right_Hippocampus (53): linear fit = 0.86 x + 0.0 (388 voxels, peak = 54), gca=53.9
- gca peak = 0.29892 (64)
- mri peak = 0.08599 (59)
- Left_Hippocampus (17): linear fit = 0.90 x + 0.0 (549 voxels, overlap=0.854)
- Left_Hippocampus (17): linear fit = 0.90 x + 0.0 (549 voxels, peak = 58), gca=57.9
- gca peak = 0.12541 (104)
- mri peak = 0.08583 (107)
- Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (49998 voxels, overlap=0.696)
- Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (49998 voxels, peak = 108), gca=107.6
- gca peak = 0.13686 (104)
- mri peak = 0.08514 (107)
- Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (54991 voxels, overlap=0.651)
- Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (54991 voxels, peak = 109), gca=108.7
- gca peak = 0.11691 (63)
- mri peak = 0.05138 (56)
- Left_Cerebral_Cortex (3): linear fit = 0.85 x + 0.0 (14723 voxels, overlap=0.379)
- Left_Cerebral_Cortex (3): linear fit = 0.85 x + 0.0 (14723 voxels, peak = 53), gca=53.2
- gca peak = 0.13270 (63)
- mri peak = 0.05433 (51)
- Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (14864 voxels, overlap=0.178)
- Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (14864 voxels, peak = 52), gca=52.0
- gca peak = 0.15182 (70)
- mri peak = 0.07042 (61)
- Right_Caudate (50): linear fit = 0.86 x + 0.0 (329 voxels, overlap=0.369)
- Right_Caudate (50): linear fit = 0.86 x + 0.0 (329 voxels, peak = 60), gca=59.9
- gca peak = 0.14251 (76)
- mri peak = 0.04400 (59)
- Left_Caudate (11): linear fit = 0.80 x + 0.0 (477 voxels, overlap=0.022)
- Left_Caudate (11): linear fit = 0.80 x + 0.0 (477 voxels, peak = 60), gca=60.4
- gca peak = 0.12116 (60)
- mri peak = 0.04317 (63)
- Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (8518 voxels, overlap=0.948)
- Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (8518 voxels, peak = 62), gca=61.5
- gca peak = 0.12723 (61)
- mri peak = 0.03742 (61)
- Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (10904 voxels, overlap=0.957)
- Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (10904 voxels, peak = 63), gca=62.5
- gca peak = 0.22684 (88)
- mri peak = 0.06784 (90)
- Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (5152 voxels, overlap=0.843)
- Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (5152 voxels, peak = 91), gca=91.1
- gca peak = 0.21067 (87)
- mri peak = 0.06322 (90)
- Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (4428 voxels, overlap=0.868)
- Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (4428 voxels, peak = 90), gca=90.0
- gca peak = 0.25455 (62)
- mri peak = 0.05870 (58)
- Left_Amygdala (18): linear fit = 0.94 x + 0.0 (254 voxels, overlap=0.992)
- Left_Amygdala (18): linear fit = 0.94 x + 0.0 (254 voxels, peak = 58), gca=58.0
- gca peak = 0.39668 (62)
- mri peak = 0.17778 (50)
- Right_Amygdala (54): linear fit = 0.90 x + 0.0 (107 voxels, overlap=0.702)
- Right_Amygdala (54): linear fit = 0.90 x + 0.0 (107 voxels, peak = 56), gca=56.1
- gca peak = 0.10129 (93)
- mri peak = 0.05191 (91)
- Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4171 voxels, overlap=0.980)
- Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4171 voxels, peak = 93), gca=93.5
- gca peak = 0.12071 (89)
- mri peak = 0.04883 (88)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3115 voxels, overlap=0.983)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3115 voxels, peak = 89), gca=88.6
- gca peak = 0.13716 (82)
- mri peak = 0.07379 (72)
- Left_Putamen (12): linear fit = 0.90 x + 0.0 (1617 voxels, overlap=0.548)
- Left_Putamen (12): linear fit = 0.90 x + 0.0 (1617 voxels, peak = 74), gca=74.2
- gca peak = 0.15214 (84)
- mri peak = 0.07164 (72)
- Right_Putamen (51): linear fit = 0.87 x + 0.0 (1317 voxels, overlap=0.217)
- Right_Putamen (51): linear fit = 0.87 x + 0.0 (1317 voxels, peak = 73), gca=72.7
- gca peak = 0.08983 (85)
- mri peak = 0.07023 (88)
- Brain_Stem (16): linear fit = 1.08 x + 0.0 (7656 voxels, overlap=0.666)
- Brain_Stem (16): linear fit = 1.08 x + 0.0 (7656 voxels, peak = 91), gca=91.4
- gca peak = 0.11809 (92)
- mri peak = 0.05814 (91)
- Right_VentralDC (60): linear fit = 0.98 x + 0.0 (530 voxels, overlap=0.807)
- Right_VentralDC (60): linear fit = 0.98 x + 0.0 (530 voxels, peak = 90), gca=89.7
- gca peak = 0.12914 (94)
- mri peak = 0.06579 (103)
- Left_VentralDC (28): linear fit = 1.09 x + 0.0 (637 voxels, overlap=0.663)
- Left_VentralDC (28): linear fit = 1.09 x + 0.0 (637 voxels, peak = 102), gca=102.0
- gca peak = 0.21100 (36)
- mri peak = 0.25000 (52)
- gca peak = 0.13542 (27)
- mri peak = 0.17978 (10)
- Fourth_Ventricle (15): linear fit = 0.28 x + 0.0 (494 voxels, overlap=0.020)
- Fourth_Ventricle (15): linear fit = 0.28 x + 0.0 (494 voxels, peak = 7), gca=7.4
- gca peak Unknown = 0.94427 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.21802 (40)
- gca peak Third_Ventricle = 0.21100 (36)
- gca peak Fourth_Ventricle = 0.13542 (27)
- gca peak CSF = 0.17123 (45)
- gca peak Left_Accumbens_area = 0.25875 (69)
- gca peak Left_undetermined = 0.96240 (36)
- gca peak Left_vessel = 0.33262 (65)
- gca peak Left_choroid_plexus = 0.09846 (46)
- gca peak Right_Inf_Lat_Vent = 0.28113 (34)
- gca peak Right_Accumbens_area = 0.27120 (72)
- gca peak Right_vessel = 0.61915 (60)
- gca peak Right_choroid_plexus = 0.12775 (51)
- gca peak Fifth_Ventricle = 0.45329 (44)
- gca peak WM_hypointensities = 0.11729 (81)
- gca peak non_WM_hypointensities = 0.10912 (56)
- gca peak Optic_Chiasm = 0.33287 (75)
- label assignment complete, 0 changed (0.00%)
- not using caudate to estimate GM means
- estimating mean gm scale to be 0.88 x + 0.0
- estimating mean wm scale to be 1.04 x + 0.0
- estimating mean csf scale to be 0.40 x + 0.0
- saving intensity scales to 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=0.723, neg=0, invalid=96777
- 0149: dt=129.472000, rms=0.716 (0.894%), neg=0, invalid=96777
- 0150: dt=221.952000, rms=0.712 (0.567%), neg=0, invalid=96777
- 0151: dt=110.976000, rms=0.711 (0.151%), neg=0, invalid=96777
- 0152: dt=129.472000, rms=0.710 (0.160%), neg=0, invalid=96777
- 0153: dt=129.472000, rms=0.709 (0.128%), neg=0, invalid=96777
- 0154: dt=129.472000, rms=0.709 (0.084%), neg=0, invalid=96777
- 0155: dt=129.472000, rms=0.708 (0.114%), neg=0, invalid=96777
- 0156: dt=73.984000, rms=0.707 (0.065%), neg=0, invalid=96777
- 0157: dt=517.888000, rms=0.706 (0.213%), neg=0, invalid=96777
- 0158: dt=55.488000, rms=0.705 (0.121%), neg=0, invalid=96777
- 0159: dt=517.888000, rms=0.703 (0.201%), neg=0, invalid=96777
- 0160: dt=73.984000, rms=0.703 (0.086%), neg=0, invalid=96777
- 0161: dt=129.472000, rms=0.703 (0.027%), neg=0, invalid=96777
- 0162: dt=129.472000, rms=0.702 (0.071%), neg=0, invalid=96777
- 0163: dt=129.472000, rms=0.702 (0.093%), neg=0, invalid=96777
- 0164: dt=129.472000, rms=0.701 (0.084%), neg=0, invalid=96777
- 0165: dt=129.472000, rms=0.700 (0.145%), neg=0, invalid=96777
- 0166: dt=129.472000, rms=0.699 (0.135%), neg=0, invalid=96777
- 0167: dt=129.472000, rms=0.698 (0.133%), neg=0, invalid=96777
- 0168: dt=129.472000, rms=0.697 (0.149%), neg=0, invalid=96777
- 0169: dt=129.472000, rms=0.696 (0.122%), neg=0, invalid=96777
- 0170: dt=129.472000, rms=0.695 (0.100%), neg=0, invalid=96777
- 0171: dt=129.472000, rms=0.695 (0.116%), neg=0, invalid=96777
- 0172: dt=129.472000, rms=0.694 (0.134%), neg=0, invalid=96777
- 0173: dt=129.472000, rms=0.693 (0.104%), neg=0, invalid=96777
- 0174: dt=129.472000, rms=0.692 (0.076%), neg=0, invalid=96777
- 0175: dt=129.472000, rms=0.692 (0.081%), neg=0, invalid=96777
- 0176: dt=129.472000, rms=0.691 (0.108%), neg=0, invalid=96777
- 0177: dt=129.472000, rms=0.690 (0.125%), neg=0, invalid=96777
- 0178: dt=129.472000, rms=0.690 (0.107%), neg=0, invalid=96777
- 0179: dt=129.472000, rms=0.689 (0.096%), neg=0, invalid=96777
- 0180: dt=129.472000, rms=0.688 (0.084%), neg=0, invalid=96777
- 0181: dt=129.472000, rms=0.688 (0.099%), neg=0, invalid=96777
- 0182: dt=129.472000, rms=0.687 (0.110%), neg=0, invalid=96777
- 0183: dt=129.472000, rms=0.686 (0.117%), neg=0, invalid=96777
- 0184: dt=129.472000, rms=0.685 (0.090%), neg=0, invalid=96777
- 0185: dt=129.472000, rms=0.685 (0.056%), neg=0, invalid=96777
- 0186: dt=129.472000, rms=0.685 (0.071%), neg=0, invalid=96777
- 0187: dt=129.472000, rms=0.684 (0.101%), neg=0, invalid=96777
- 0188: dt=129.472000, rms=0.683 (0.085%), neg=0, invalid=96777
- 0189: dt=129.472000, rms=0.683 (0.061%), neg=0, invalid=96777
- 0190: dt=129.472000, rms=0.683 (0.045%), neg=0, invalid=96777
- 0191: dt=129.472000, rms=0.682 (0.075%), neg=0, invalid=96777
- 0192: dt=129.472000, rms=0.682 (0.070%), neg=0, invalid=96777
- 0193: dt=129.472000, rms=0.681 (0.056%), neg=0, invalid=96777
- 0194: dt=129.472000, rms=0.681 (0.042%), neg=0, invalid=96777
- 0195: dt=129.472000, rms=0.681 (0.056%), neg=0, invalid=96777
- 0196: dt=129.472000, rms=0.680 (0.044%), neg=0, invalid=96777
- 0197: dt=129.472000, rms=0.680 (0.044%), neg=0, invalid=96777
- 0198: dt=129.472000, rms=0.680 (0.060%), neg=0, invalid=96777
- 0199: dt=129.472000, rms=0.679 (0.042%), neg=0, invalid=96777
- 0200: dt=129.472000, rms=0.679 (0.024%), neg=0, invalid=96777
- 0201: dt=129.472000, rms=0.679 (0.031%), neg=0, invalid=96777
- 0202: dt=129.472000, rms=0.679 (0.055%), neg=0, invalid=96777
- 0203: dt=129.472000, rms=0.678 (0.042%), neg=0, invalid=96777
- 0204: dt=129.472000, rms=0.678 (0.027%), neg=0, invalid=96777
- 0205: dt=129.472000, rms=0.678 (0.059%), neg=0, invalid=96777
- 0206: dt=129.472000, rms=0.677 (0.032%), neg=0, invalid=96777
- 0207: dt=129.472000, rms=0.677 (0.015%), neg=0, invalid=96777
- 0208: dt=129.472000, rms=0.677 (0.025%), neg=0, invalid=96777
- 0209: dt=129.472000, rms=0.677 (0.061%), neg=0, invalid=96777
- 0210: dt=129.472000, rms=0.676 (0.041%), neg=0, invalid=96777
- 0211: dt=129.472000, rms=0.676 (0.018%), neg=0, invalid=96777
- 0212: dt=129.472000, rms=0.676 (0.028%), neg=0, invalid=96777
- 0213: dt=129.472000, rms=0.676 (0.035%), neg=0, invalid=96777
- 0214: dt=129.472000, rms=0.676 (0.036%), neg=0, invalid=96777
- 0215: dt=129.472000, rms=0.676 (0.025%), neg=0, invalid=96777
- 0216: dt=129.472000, rms=0.675 (0.021%), neg=0, invalid=96777
- 0217: dt=8.092000, rms=0.675 (0.001%), neg=0, invalid=96777
- 0218: dt=8.092000, rms=0.675 (-0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.675, neg=0, invalid=96777
- 0219: dt=295.936000, rms=0.673 (0.310%), neg=0, invalid=96777
- 0220: dt=73.984000, rms=0.673 (0.059%), neg=0, invalid=96777
- 0221: dt=129.472000, rms=0.673 (0.025%), neg=0, invalid=96777
- 0222: dt=129.472000, rms=0.672 (0.043%), neg=0, invalid=96777
- 0223: dt=129.472000, rms=0.672 (0.060%), neg=0, invalid=96777
- 0224: dt=129.472000, rms=0.672 (0.053%), neg=0, invalid=96777
- 0225: dt=129.472000, rms=0.671 (0.065%), neg=0, invalid=96777
- 0226: dt=129.472000, rms=0.671 (0.055%), neg=0, invalid=96777
- 0227: dt=129.472000, rms=0.670 (0.059%), neg=0, invalid=96777
- 0228: dt=129.472000, rms=0.670 (0.044%), neg=0, invalid=96777
- 0229: dt=129.472000, rms=0.670 (0.040%), neg=0, invalid=96777
- 0230: dt=129.472000, rms=0.670 (0.039%), neg=0, invalid=96777
- 0231: dt=129.472000, rms=0.669 (0.030%), neg=0, invalid=96777
- 0232: dt=129.472000, rms=0.669 (0.036%), neg=0, invalid=96777
- 0233: dt=129.472000, rms=0.669 (0.032%), neg=0, invalid=96777
- 0234: dt=129.472000, rms=0.669 (0.034%), neg=0, invalid=96777
- 0235: dt=129.472000, rms=0.669 (0.020%), neg=0, invalid=96777
- 0236: dt=129.472000, rms=0.668 (0.027%), neg=0, invalid=96777
- 0237: dt=129.472000, rms=0.668 (0.035%), neg=0, invalid=96777
- 0238: dt=129.472000, rms=0.668 (0.035%), neg=0, invalid=96777
- 0239: dt=129.472000, rms=0.668 (0.019%), neg=0, invalid=96777
- 0240: dt=129.472000, rms=0.668 (0.007%), neg=0, invalid=96777
- 0241: dt=369.920000, rms=0.668 (0.027%), neg=0, invalid=96777
- 0242: dt=55.488000, rms=0.668 (0.010%), neg=0, invalid=96777
- 0243: dt=55.488000, rms=0.668 (0.001%), neg=0, invalid=96777
- 0244: dt=55.488000, rms=0.668 (0.001%), neg=0, invalid=96777
- 0245: dt=55.488000, rms=0.668 (0.002%), neg=0, invalid=96777
- 0246: dt=55.488000, rms=0.667 (0.005%), neg=0, invalid=96777
- 0247: dt=55.488000, rms=0.667 (0.008%), neg=0, invalid=96777
- 0248: dt=55.488000, rms=0.667 (0.007%), neg=0, invalid=96777
- 0249: dt=55.488000, rms=0.667 (0.008%), neg=0, invalid=96777
- 0250: dt=55.488000, rms=0.667 (0.008%), neg=0, invalid=96777
- 0251: dt=55.488000, rms=0.667 (0.006%), neg=0, invalid=96777
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.668, neg=0, invalid=96777
- 0252: dt=124.416000, rms=0.664 (0.644%), neg=0, invalid=96777
- 0253: dt=145.152000, rms=0.658 (0.936%), neg=0, invalid=96777
- 0254: dt=31.104000, rms=0.654 (0.539%), neg=0, invalid=96777
- 0255: dt=25.920000, rms=0.653 (0.140%), neg=0, invalid=96777
- 0256: dt=248.832000, rms=0.649 (0.756%), neg=0, invalid=96777
- 0257: dt=20.736000, rms=0.645 (0.525%), neg=0, invalid=96777
- 0258: dt=145.152000, rms=0.640 (0.822%), neg=0, invalid=96777
- 0259: dt=36.288000, rms=0.639 (0.120%), neg=0, invalid=96777
- 0260: dt=124.416000, rms=0.637 (0.393%), neg=0, invalid=96777
- 0261: dt=36.288000, rms=0.636 (0.139%), neg=0, invalid=96777
- 0262: dt=36.288000, rms=0.635 (0.146%), neg=0, invalid=96777
- 0263: dt=145.152000, rms=0.633 (0.288%), neg=0, invalid=96777
- 0264: dt=9.072000, rms=0.632 (0.133%), neg=0, invalid=96777
- 0265: dt=9.072000, rms=0.632 (0.071%), neg=0, invalid=96777
- 0266: dt=9.072000, rms=0.631 (0.042%), neg=0, invalid=96777
- 0267: dt=2.268000, rms=0.631 (0.012%), neg=0, invalid=96777
- 0268: dt=1.134000, rms=0.631 (0.002%), neg=0, invalid=96777
- 0269: dt=0.283500, rms=0.631 (0.000%), neg=0, invalid=96777
- 0270: dt=0.141750, rms=0.631 (0.001%), neg=0, invalid=96777
- 0271: dt=0.121500, rms=0.631 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.631, neg=0, invalid=96777
- 0272: dt=0.004860, rms=0.631 (-0.000%), neg=0, invalid=96777
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.637, neg=0, invalid=96777
- 0273: dt=0.001500, rms=0.637 (0.000%), neg=0, invalid=96777
- 0274: dt=0.000000, rms=0.637 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.637, neg=0, invalid=96777
- 0275: dt=0.000000, rms=0.637 (0.000%), neg=0, invalid=96777
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.654, neg=0, invalid=96777
- 0276: dt=2.880000, rms=0.639 (2.304%), neg=0, invalid=96777
- 0277: dt=1.008000, rms=0.634 (0.676%), neg=0, invalid=96777
- 0278: dt=1.008000, rms=0.630 (0.632%), neg=0, invalid=96777
- 0279: dt=4.032000, rms=0.616 (2.325%), neg=0, invalid=96777
- 0280: dt=3.456000, rms=0.606 (1.521%), neg=0, invalid=96777
- 0281: dt=4.032000, rms=0.598 (1.432%), neg=0, invalid=96777
- 0282: dt=4.032000, rms=0.591 (1.117%), neg=0, invalid=96777
- 0283: dt=4.032000, rms=0.586 (0.899%), neg=0, invalid=96777
- 0284: dt=4.032000, rms=0.582 (0.699%), neg=0, invalid=96777
- 0285: dt=4.032000, rms=0.578 (0.594%), neg=0, invalid=96777
- 0286: dt=4.032000, rms=0.575 (0.478%), neg=0, invalid=96777
- 0287: dt=4.032000, rms=0.573 (0.404%), neg=0, invalid=96777
- 0288: dt=4.032000, rms=0.571 (0.338%), neg=0, invalid=96777
- 0289: dt=4.032000, rms=0.569 (0.303%), neg=0, invalid=96777
- 0290: dt=4.032000, rms=0.568 (0.242%), neg=0, invalid=96777
- 0291: dt=4.032000, rms=0.567 (0.219%), neg=0, invalid=96777
- 0292: dt=16.128000, rms=0.563 (0.724%), neg=0, invalid=96777
- 0293: dt=2.880000, rms=0.562 (0.086%), neg=0, invalid=96777
- 0294: dt=4.032000, rms=0.562 (0.110%), neg=0, invalid=96777
- 0295: dt=4.032000, rms=0.561 (0.094%), neg=0, invalid=96777
- 0296: dt=16.128000, rms=0.559 (0.326%), neg=0, invalid=96777
- 0297: dt=4.032000, rms=0.559 (0.066%), neg=0, invalid=96777
- 0298: dt=4.032000, rms=0.558 (0.080%), neg=0, invalid=96777
- 0299: dt=4.032000, rms=0.558 (0.056%), neg=0, invalid=96777
- 0300: dt=4.032000, rms=0.558 (0.062%), neg=0, invalid=96777
- 0301: dt=4.032000, rms=0.557 (0.054%), neg=0, invalid=96777
- 0302: dt=4.032000, rms=0.557 (0.059%), neg=0, invalid=96777
- 0303: dt=4.032000, rms=0.557 (0.048%), neg=0, invalid=96777
- 0304: dt=4.032000, rms=0.556 (0.051%), neg=0, invalid=96777
- 0305: dt=4.032000, rms=0.556 (0.099%), neg=0, invalid=96777
- 0306: dt=4.032000, rms=0.555 (0.127%), neg=0, invalid=96777
- 0307: dt=4.032000, rms=0.554 (0.148%), neg=0, invalid=96777
- 0308: dt=4.032000, rms=0.553 (0.176%), neg=0, invalid=96777
- 0309: dt=4.032000, rms=0.552 (0.172%), neg=0, invalid=96777
- 0310: dt=4.032000, rms=0.552 (0.159%), neg=0, invalid=96777
- 0311: dt=4.032000, rms=0.551 (0.143%), neg=0, invalid=96777
- 0312: dt=4.032000, rms=0.551 (0.016%), neg=0, invalid=96777
- 0313: dt=4.032000, rms=0.551 (0.018%), neg=0, invalid=96777
- 0314: dt=4.032000, rms=0.551 (0.014%), neg=0, invalid=96777
- 0315: dt=13.824000, rms=0.550 (0.035%), neg=0, invalid=96777
- 0316: dt=2.304000, rms=0.550 (0.000%), neg=0, invalid=96777
- 0317: dt=2.304000, rms=0.550 (0.016%), neg=0, invalid=96777
- 0318: dt=2.304000, rms=0.550 (0.014%), neg=0, invalid=96777
- 0319: dt=2.304000, rms=0.550 (0.030%), neg=0, invalid=96777
- 0320: dt=2.304000, rms=0.550 (0.023%), neg=0, invalid=96777
- 0321: dt=2.304000, rms=0.550 (0.036%), neg=0, invalid=96777
- 0322: dt=2.304000, rms=0.550 (0.029%), neg=0, invalid=96777
- 0323: dt=2.304000, rms=0.549 (0.039%), neg=0, invalid=96777
- 0324: dt=2.304000, rms=0.549 (0.038%), neg=0, invalid=96777
- 0325: dt=2.304000, rms=0.549 (0.043%), neg=0, invalid=96777
- 0326: dt=2.304000, rms=0.549 (0.005%), neg=0, invalid=96777
- 0327: dt=2.304000, rms=0.549 (0.010%), neg=0, invalid=96777
- 0328: dt=2.304000, rms=0.549 (0.011%), neg=0, invalid=96777
- 0329: dt=2.304000, rms=0.549 (0.013%), neg=0, invalid=96777
- 0330: dt=2.304000, rms=0.549 (0.017%), neg=0, invalid=96777
- 0331: dt=2.304000, rms=0.548 (0.021%), neg=0, invalid=96777
- 0332: dt=2.304000, rms=0.548 (0.024%), neg=0, invalid=96777
- 0333: dt=2.304000, rms=0.548 (0.031%), neg=0, invalid=96777
- 0334: dt=2.304000, rms=0.548 (0.029%), neg=0, invalid=96777
- 0335: dt=2.304000, rms=0.548 (0.030%), neg=0, invalid=96777
- 0336: dt=2.304000, rms=0.548 (0.032%), neg=0, invalid=96777
- 0337: dt=2.304000, rms=0.547 (0.034%), neg=0, invalid=96777
- 0338: dt=2.304000, rms=0.547 (0.032%), neg=0, invalid=96777
- 0339: dt=2.304000, rms=0.547 (0.037%), neg=0, invalid=96777
- 0340: dt=2.304000, rms=0.547 (0.036%), neg=0, invalid=96777
- 0341: dt=2.304000, rms=0.547 (0.027%), neg=0, invalid=96777
- 0342: dt=2.304000, rms=0.547 (0.029%), neg=0, invalid=96777
- 0343: dt=2.304000, rms=0.546 (0.029%), neg=0, invalid=96777
- 0344: dt=2.304000, rms=0.546 (0.033%), neg=0, invalid=96777
- 0345: dt=2.304000, rms=0.546 (0.026%), neg=0, invalid=96777
- 0346: dt=2.304000, rms=0.546 (0.028%), neg=0, invalid=96777
- 0347: dt=2.304000, rms=0.546 (0.025%), neg=0, invalid=96777
- 0348: dt=2.304000, rms=0.546 (0.016%), neg=0, invalid=96777
- 0349: dt=2.304000, rms=0.546 (0.020%), neg=0, invalid=96777
- 0350: dt=2.304000, rms=0.545 (0.031%), neg=0, invalid=96777
- 0351: dt=2.304000, rms=0.545 (0.030%), neg=0, invalid=96777
- 0352: dt=2.304000, rms=0.545 (0.021%), neg=0, invalid=96777
- 0353: dt=2.304000, rms=0.545 (0.022%), neg=0, invalid=96777
- 0354: dt=2.304000, rms=0.545 (0.015%), neg=0, invalid=96777
- 0355: dt=4.032000, rms=0.545 (0.005%), neg=0, invalid=96777
- 0356: dt=4.032000, rms=0.545 (0.005%), neg=0, invalid=96777
- 0357: dt=4.032000, rms=0.545 (0.000%), neg=0, invalid=96777
- 0358: dt=4.032000, rms=0.545 (0.015%), neg=0, invalid=96777
- 0359: dt=4.032000, rms=0.545 (0.004%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.545, neg=0, invalid=96777
- 0360: dt=0.000000, rms=0.545 (-0.004%), neg=0, invalid=96777
- setting smoothness coefficient to 1.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.567, neg=0, invalid=96777
- 0361: dt=0.000000, rms=0.567 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.567, neg=0, invalid=96777
- 0362: dt=0.000000, rms=0.567 (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=0.529, neg=0, invalid=96777
- 0363: dt=0.080000, rms=0.526 (0.690%), neg=0, invalid=96777
- 0364: dt=0.024000, rms=0.525 (0.177%), neg=0, invalid=96777
- 0365: dt=0.005000, rms=0.525 (0.034%), neg=0, invalid=96777
- 0366: dt=0.005000, rms=0.524 (0.035%), neg=0, invalid=96777
- 0367: dt=0.005000, rms=0.524 (0.066%), neg=0, invalid=96777
- 0368: dt=0.005000, rms=0.524 (0.093%), neg=0, invalid=96777
- 0369: dt=0.005000, rms=0.523 (0.117%), neg=0, invalid=96777
- 0370: dt=0.005000, rms=0.522 (0.140%), neg=0, invalid=96777
- 0371: dt=0.005000, rms=0.521 (0.152%), neg=0, invalid=96777
- 0372: dt=0.005000, rms=0.521 (0.167%), neg=0, invalid=96777
- 0373: dt=0.005000, rms=0.520 (0.176%), neg=0, invalid=96777
- 0374: dt=0.005000, rms=0.519 (0.188%), neg=0, invalid=96777
- 0375: dt=0.005000, rms=0.518 (0.194%), neg=0, invalid=96777
- 0376: dt=0.005000, rms=0.517 (0.196%), neg=0, invalid=96777
- 0377: dt=0.005000, rms=0.516 (0.199%), neg=0, invalid=96777
- 0378: dt=0.005000, rms=0.515 (0.195%), neg=0, invalid=96777
- 0379: dt=0.005000, rms=0.514 (0.192%), neg=0, invalid=96777
- 0380: dt=0.005000, rms=0.513 (0.191%), neg=0, invalid=96777
- 0381: dt=0.005000, rms=0.512 (0.183%), neg=0, invalid=96777
- 0382: dt=0.005000, rms=0.511 (0.180%), neg=0, invalid=96777
- 0383: dt=0.005000, rms=0.510 (0.174%), neg=0, invalid=96777
- 0384: dt=0.002500, rms=0.510 (0.005%), neg=0, invalid=96777
- 0385: dt=0.002500, rms=0.510 (0.006%), neg=0, invalid=96777
- 0386: dt=0.002500, rms=0.510 (0.009%), neg=0, invalid=96777
- 0387: dt=0.002500, rms=0.510 (0.014%), neg=0, invalid=96777
- 0388: dt=0.002500, rms=0.510 (0.015%), neg=0, invalid=96777
- 0389: dt=0.002500, rms=0.510 (0.023%), neg=0, invalid=96777
- 0390: dt=0.002500, rms=0.509 (0.023%), neg=0, invalid=96777
- 0391: dt=0.002500, rms=0.509 (0.026%), neg=0, invalid=96777
- 0392: dt=0.002500, rms=0.509 (0.027%), neg=0, invalid=96777
- 0393: dt=0.002500, rms=0.509 (0.030%), neg=0, invalid=96777
- 0394: dt=0.002500, rms=0.509 (0.032%), neg=0, invalid=96777
- 0395: dt=0.002500, rms=0.509 (0.035%), neg=0, invalid=96777
- 0396: dt=0.002500, rms=0.508 (0.033%), neg=0, invalid=96777
- 0397: dt=0.002500, rms=0.508 (0.033%), neg=0, invalid=96777
- 0398: dt=0.002500, rms=0.508 (0.036%), neg=0, invalid=96777
- 0399: dt=0.002500, rms=0.508 (0.037%), neg=0, invalid=96777
- 0400: dt=0.002500, rms=0.508 (0.034%), neg=0, invalid=96777
- 0401: dt=0.002500, rms=0.508 (0.037%), neg=0, invalid=96777
- 0402: dt=0.002500, rms=0.507 (0.035%), neg=0, invalid=96777
- 0403: dt=0.002500, rms=0.507 (0.037%), neg=0, invalid=96777
- 0404: dt=0.002500, rms=0.507 (0.037%), neg=0, invalid=96777
- 0405: dt=0.002500, rms=0.507 (0.036%), neg=0, invalid=96777
- 0406: dt=0.002500, rms=0.507 (0.036%), neg=0, invalid=96777
- 0407: dt=0.002500, rms=0.506 (0.037%), neg=0, invalid=96777
- 0408: dt=0.002500, rms=0.506 (0.034%), neg=0, invalid=96777
- 0409: dt=0.002500, rms=0.506 (0.035%), neg=0, invalid=96777
- 0410: dt=0.002500, rms=0.506 (0.035%), neg=0, invalid=96777
- 0411: dt=0.002500, rms=0.506 (0.035%), neg=0, invalid=96777
- 0412: dt=0.002500, rms=0.506 (0.032%), neg=0, invalid=96777
- 0413: dt=0.002500, rms=0.505 (0.032%), neg=0, invalid=96777
- 0414: dt=0.002500, rms=0.505 (0.032%), neg=0, invalid=96777
- 0415: dt=0.002500, rms=0.505 (0.033%), neg=0, invalid=96777
- 0416: dt=0.002500, rms=0.505 (0.030%), neg=0, invalid=96777
- 0417: dt=0.002500, rms=0.505 (0.030%), neg=0, invalid=96777
- 0418: dt=0.002500, rms=0.505 (0.028%), neg=0, invalid=96777
- 0419: dt=0.002500, rms=0.505 (0.028%), neg=0, invalid=96777
- 0420: dt=0.002500, rms=0.504 (0.028%), neg=0, invalid=96777
- 0421: dt=0.002500, rms=0.504 (0.030%), neg=0, invalid=96777
- 0422: dt=0.002500, rms=0.504 (0.026%), neg=0, invalid=96777
- 0423: dt=0.002500, rms=0.504 (0.025%), neg=0, invalid=96777
- 0424: dt=0.002500, rms=0.504 (0.024%), neg=0, invalid=96777
- 0425: dt=0.002500, rms=0.504 (0.021%), neg=0, invalid=96777
- 0426: dt=0.112000, rms=0.503 (0.084%), neg=0, invalid=96777
- 0427: dt=0.007000, rms=0.503 (0.006%), neg=0, invalid=96777
- 0428: dt=0.001750, rms=0.503 (0.001%), neg=0, invalid=96777
- 0429: dt=0.001750, rms=0.503 (0.001%), neg=0, invalid=96777
- 0430: dt=0.001750, rms=0.503 (0.002%), neg=0, invalid=96777
- 0431: dt=0.001750, rms=0.503 (0.003%), neg=0, invalid=96777
- 0432: dt=0.001750, rms=0.503 (0.003%), neg=0, invalid=96777
- 0433: dt=0.028000, rms=0.503 (0.019%), neg=0, invalid=96777
- 0434: dt=0.112000, rms=0.503 (0.076%), neg=0, invalid=96777
- 0435: dt=0.028000, rms=0.503 (0.015%), neg=0, invalid=96777
- 0436: dt=0.028000, rms=0.503 (0.016%), neg=0, invalid=96777
- 0437: dt=0.007000, rms=0.503 (0.004%), neg=0, invalid=96777
- 0438: dt=0.007000, rms=0.503 (0.004%), neg=0, invalid=96777
- 0439: dt=0.007000, rms=0.503 (0.009%), neg=0, invalid=96777
- 0440: dt=0.007000, rms=0.502 (0.012%), neg=0, invalid=96777
- 0441: dt=0.007000, rms=0.502 (0.015%), neg=0, invalid=96777
- 0442: dt=0.007000, rms=0.502 (0.015%), neg=0, invalid=96777
- 0443: dt=0.028000, rms=0.502 (0.013%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.502, neg=0, invalid=96777
- 0444: dt=0.028000, rms=0.502 (0.087%), neg=0, invalid=96777
- 0445: dt=0.007000, rms=0.502 (0.023%), neg=0, invalid=96777
- 0446: dt=0.007000, rms=0.502 (0.016%), neg=0, invalid=96777
- 0447: dt=0.007000, rms=0.501 (0.037%), neg=0, invalid=96777
- 0448: dt=0.007000, rms=0.501 (0.052%), neg=0, invalid=96777
- 0449: dt=0.007000, rms=0.501 (0.066%), neg=0, invalid=96777
- 0450: dt=0.007000, rms=0.500 (0.074%), neg=0, invalid=96777
- 0451: dt=0.007000, rms=0.500 (0.082%), neg=0, invalid=96777
- 0452: dt=0.001750, rms=0.500 (0.003%), neg=0, invalid=96777
- 0453: dt=0.001750, rms=0.500 (0.004%), neg=0, invalid=96777
- 0454: dt=0.001750, rms=0.500 (0.007%), neg=0, invalid=96777
- 0455: dt=0.001750, rms=0.500 (0.011%), neg=0, invalid=96777
- 0456: dt=0.001750, rms=0.500 (0.013%), neg=0, invalid=96777
- 0457: dt=0.001750, rms=0.500 (0.015%), neg=0, invalid=96777
- 0458: dt=0.001750, rms=0.500 (0.017%), neg=0, invalid=96777
- 0459: dt=0.001750, rms=0.500 (0.019%), neg=0, invalid=96777
- 0460: dt=0.001750, rms=0.500 (0.019%), neg=0, invalid=96777
- 0461: dt=0.028000, rms=0.499 (0.057%), neg=0, invalid=96777
- 0462: dt=0.028000, rms=0.499 (0.051%), neg=0, invalid=96777
- 0463: dt=0.000438, rms=0.499 (-0.001%), neg=0, invalid=96777
- 0464: dt=0.000438, rms=0.499 (0.001%), neg=0, invalid=96777
- 0465: dt=0.000438, rms=0.499 (0.001%), neg=0, invalid=96777
- 0466: dt=0.000438, rms=0.499 (0.003%), neg=0, invalid=96777
- 0467: dt=0.000438, rms=0.499 (0.003%), neg=0, invalid=96777
- 0468: dt=0.000438, rms=0.499 (0.003%), neg=0, invalid=96777
- 0469: dt=0.000438, rms=0.499 (0.005%), neg=0, invalid=96777
- 0470: dt=0.000438, rms=0.499 (0.003%), neg=0, invalid=96777
- label assignment complete, 0 changed (0.00%)
- *********************************************************************************************
- *********************************************************************************************
- *********************************************************************************************
- ********************* ALLOWING NEGATIVE NODES IN DEFORMATION ********************************
- *********************************************************************************************
- *********************************************************************************************
- *********************************************************************************************
- **************** pass 1 of 1 ************************
- setting smoothness coefficient to 0.008
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.497, neg=0, invalid=96777
- 0471: dt=8.092000, rms=0.497 (0.001%), neg=0, invalid=96777
- 0472: dt=5.780000, rms=0.497 (-0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.497, neg=0, invalid=96777
- 0473: dt=295.936000, rms=0.496 (0.158%), neg=0, invalid=96777
- 0474: dt=92.480000, rms=0.496 (0.051%), neg=0, invalid=96777
- 0475: dt=92.480000, rms=0.496 (0.035%), neg=0, invalid=96777
- 0476: dt=92.480000, rms=0.496 (0.033%), neg=0, invalid=96777
- 0477: dt=92.480000, rms=0.496 (0.038%), neg=0, invalid=96777
- 0478: dt=92.480000, rms=0.496 (0.033%), neg=0, invalid=96777
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.496, neg=0, invalid=96777
- 0479: dt=36.288000, rms=0.495 (0.176%), neg=0, invalid=96777
- 0480: dt=36.288000, rms=0.494 (0.095%), neg=0, invalid=96777
- 0481: dt=36.288000, rms=0.494 (0.101%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 5 iterations, nbhd size=1, neg = 0
- 0482: dt=36.288000, rms=0.493 (0.076%), neg=0, invalid=96777
- 0483: dt=36.288000, rms=0.493 (-0.016%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.493, neg=0, invalid=96777
- iter 0, gcam->neg = 3
- after 7 iterations, nbhd size=1, neg = 0
- 0484: dt=103.680000, rms=0.491 (0.531%), neg=0, invalid=96777
- 0485: dt=36.288000, rms=0.489 (0.246%), neg=0, invalid=96777
- 0486: dt=36.288000, rms=0.489 (0.003%), neg=0, invalid=96777
- 0487: dt=36.288000, rms=0.489 (0.157%), neg=0, invalid=96777
- iter 0, gcam->neg = 2
- after 5 iterations, nbhd size=1, neg = 0
- 0488: dt=36.288000, rms=0.488 (0.221%), neg=0, invalid=96777
- 0489: dt=36.288000, rms=0.487 (0.168%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0490: dt=36.288000, rms=0.486 (0.097%), neg=0, invalid=96777
- 0491: dt=36.288000, rms=0.485 (0.176%), neg=0, invalid=96777
- 0492: dt=36.288000, rms=0.485 (0.158%), neg=0, invalid=96777
- 0493: dt=36.288000, rms=0.484 (0.111%), neg=0, invalid=96777
- 0494: dt=36.288000, rms=0.484 (0.090%), neg=0, invalid=96777
- 0495: dt=25.920000, rms=0.483 (0.049%), neg=0, invalid=96777
- 0496: dt=25.920000, rms=0.483 (0.014%), neg=0, invalid=96777
- 0497: dt=25.920000, rms=0.483 (0.025%), neg=0, invalid=96777
- 0498: dt=25.920000, rms=0.483 (0.033%), neg=0, invalid=96777
- 0499: dt=25.920000, rms=0.483 (0.036%), neg=0, invalid=96777
- 0500: dt=25.920000, rms=0.483 (0.042%), neg=0, invalid=96777
- 0501: dt=25.920000, rms=0.483 (0.034%), neg=0, invalid=96777
- 0502: dt=25.920000, rms=0.482 (0.047%), neg=0, invalid=96777
- 0503: dt=25.920000, rms=0.482 (0.056%), neg=0, invalid=96777
- 0504: dt=25.920000, rms=0.482 (0.044%), neg=0, invalid=96777
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.482, neg=0, invalid=96777
- iter 0, gcam->neg = 16
- after 17 iterations, nbhd size=2, neg = 0
- 0505: dt=32.000000, rms=0.480 (0.503%), neg=0, invalid=96777
- iter 0, gcam->neg = 3
- after 7 iterations, nbhd size=1, neg = 0
- 0506: dt=10.494624, rms=0.479 (0.236%), neg=0, invalid=96777
- 0507: dt=10.494624, rms=0.478 (0.195%), neg=0, invalid=96777
- iter 0, gcam->neg = 3
- after 13 iterations, nbhd size=2, neg = 0
- 0508: dt=10.494624, rms=0.476 (0.292%), neg=0, invalid=96777
- iter 0, gcam->neg = 7
- after 24 iterations, nbhd size=3, neg = 0
- 0509: dt=10.494624, rms=0.475 (0.330%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 14 iterations, nbhd size=2, neg = 0
- 0510: dt=10.494624, rms=0.474 (0.240%), neg=0, invalid=96777
- iter 0, gcam->neg = 4
- after 6 iterations, nbhd size=1, neg = 0
- 0511: dt=10.494624, rms=0.472 (0.274%), neg=0, invalid=96777
- iter 0, gcam->neg = 3
- after 6 iterations, nbhd size=1, neg = 0
- 0512: dt=10.494624, rms=0.471 (0.236%), neg=0, invalid=96777
- 0513: dt=10.494624, rms=0.470 (0.326%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 12 iterations, nbhd size=2, neg = 0
- 0514: dt=10.494624, rms=0.469 (0.255%), neg=0, invalid=96777
- iter 0, gcam->neg = 5
- after 7 iterations, nbhd size=1, neg = 0
- 0515: dt=10.494624, rms=0.467 (0.268%), neg=0, invalid=96777
- iter 0, gcam->neg = 2
- after 8 iterations, nbhd size=1, neg = 0
- 0516: dt=10.494624, rms=0.466 (0.200%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 200 iterations, nbhd size=1, neg = 1
- starting rms=0.004, neg=1, removing folds in lattice....
- iter 1, dt=0.000055: new neg 0, old_neg 1, delta 1, rms=0.004 (6.062%)
- 0517: dt=10.494624, rms=0.465 (0.223%), neg=0, invalid=96777
- 0518: dt=10.494624, rms=0.465 (0.082%), neg=0, invalid=96777
- 0519: dt=10.494624, rms=0.464 (0.103%), neg=0, invalid=96777
- iter 0, gcam->neg = 5
- after 33 iterations, nbhd size=1, neg = 0
- 0520: dt=10.494624, rms=0.464 (0.031%), neg=0, invalid=96777
- 0521: dt=11.200000, rms=0.464 (0.034%), neg=0, invalid=96777
- iter 0, gcam->neg = 26
- after 50 iterations, nbhd size=4, neg = 0
- 0522: dt=44.800000, rms=0.464 (0.087%), neg=0, invalid=96777
- 0523: dt=0.700000, rms=0.464 (0.006%), neg=0, invalid=96777
- 0524: dt=0.700000, rms=0.464 (0.003%), neg=0, invalid=96777
- 0525: dt=0.700000, rms=0.464 (0.007%), neg=0, invalid=96777
- 0526: dt=0.700000, rms=0.464 (0.002%), neg=0, invalid=96777
- 0527: dt=0.700000, rms=0.464 (0.006%), neg=0, invalid=96777
- 0528: dt=0.700000, rms=0.464 (0.006%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.464, neg=0, invalid=96777
- iter 0, gcam->neg = 3
- after 25 iterations, nbhd size=3, neg = 0
- 0529: dt=44.800000, rms=0.459 (0.934%), neg=0, invalid=96777
- iter 0, gcam->neg = 2
- after 0 iterations, nbhd size=0, neg = 0
- 0530: dt=11.200000, rms=0.459 (0.069%), neg=0, invalid=96777
- 0531: dt=11.200000, rms=0.459 (0.103%), neg=0, invalid=96777
- 0532: dt=11.200000, rms=0.458 (0.148%), neg=0, invalid=96777
- iter 0, gcam->neg = 10
- after 200 iterations, nbhd size=3, neg = 2
- starting rms=0.003, neg=2, removing folds in lattice....
- iter 1, dt=0.000875: new neg 0, old_neg 2, delta 2, rms=0.002 (31.675%)
- 0533: dt=11.200000, rms=0.457 (0.127%), neg=0, invalid=96777
- iter 0, gcam->neg = 3
- after 0 iterations, nbhd size=0, neg = 0
- 0534: dt=11.200000, rms=0.457 (0.048%), neg=0, invalid=96777
- iter 0, gcam->neg = 6
- after 7 iterations, nbhd size=1, neg = 0
- 0535: dt=11.200000, rms=0.457 (0.076%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0536: dt=11.200000, rms=0.456 (0.090%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0537: dt=11.200000, rms=0.456 (0.109%), neg=0, invalid=96777
- 0538: dt=11.200000, rms=0.455 (0.104%), neg=0, invalid=96777
- 0539: dt=11.200000, rms=0.455 (0.007%), neg=0, invalid=96777
- 0540: dt=11.200000, rms=0.455 (0.052%), neg=0, invalid=96777
- 0541: dt=11.200000, rms=0.455 (0.044%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0542: dt=11.200000, rms=0.455 (0.065%), neg=0, invalid=96777
- iter 0, gcam->neg = 5
- after 63 iterations, nbhd size=1, neg = 0
- 0543: dt=11.200000, rms=0.454 (0.032%), neg=0, invalid=96777
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.459, neg=0, invalid=96777
- 0544: dt=0.432000, rms=0.459 (0.006%), neg=0, invalid=96777
- iter 0, gcam->neg = 2
- after 5 iterations, nbhd size=1, neg = 0
- 0545: dt=2.304000, rms=0.459 (0.027%), neg=0, invalid=96777
- 0546: dt=0.015750, rms=0.459 (-0.001%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.459, neg=0, invalid=96777
- iter 0, gcam->neg = 5
- after 23 iterations, nbhd size=3, neg = 0
- 0547: dt=2.880000, rms=0.459 (0.017%), neg=0, invalid=96777
- 0548: dt=1.008000, rms=0.459 (0.005%), neg=0, invalid=96777
- 0549: dt=1.008000, rms=0.459 (0.022%), neg=0, invalid=96777
- 0550: dt=1.008000, rms=0.459 (0.032%), neg=0, invalid=96777
- iter 0, gcam->neg = 2
- after 27 iterations, nbhd size=4, neg = 0
- 0551: dt=1.008000, rms=0.459 (0.018%), neg=0, invalid=96777
- iter 0, gcam->neg = 2
- after 22 iterations, nbhd size=3, neg = 0
- 0552: dt=1.008000, rms=0.459 (-0.009%), neg=0, invalid=96777
- setting smoothness coefficient to 1.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.466, neg=0, invalid=96777
- 0553: dt=0.000094, rms=0.466 (0.000%), neg=0, invalid=96777
- 0554: dt=0.000094, rms=0.466 (-0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.466, neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 5 iterations, nbhd size=1, neg = 0
- 0555: dt=0.112000, rms=0.466 (0.012%), neg=0, invalid=96777
- iter 0, gcam->neg = 9
- after 24 iterations, nbhd size=3, neg = 0
- 0556: dt=0.881119, rms=0.465 (0.070%), neg=0, invalid=96777
- 0557: dt=0.001000, rms=0.465 (0.002%), neg=0, invalid=96777
- 0558: dt=0.001000, rms=0.465 (0.000%), neg=0, invalid=96777
- 0559: dt=0.001000, rms=0.465 (0.000%), neg=0, invalid=96777
- 0560: dt=0.001000, rms=0.465 (-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=0.455, neg=0, invalid=96777
- iter 0, gcam->neg = 1198
- after 31 iterations, nbhd size=3, neg = 0
- 0561: dt=1.536000, rms=0.419 (8.039%), neg=0, invalid=96777
- 0562: dt=0.000047, rms=0.419 (0.000%), neg=0, invalid=96777
- 0563: dt=0.000047, rms=0.419 (0.000%), neg=0, invalid=96777
- 0564: dt=0.000047, rms=0.419 (0.000%), neg=0, invalid=96777
- 0565: dt=0.000047, 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
- 0566: dt=0.000078, rms=0.419 (0.000%), neg=0, invalid=96777
- 0567: 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=0.409, neg=0, invalid=96777
- 0568: dt=0.000000, rms=0.410 (-0.271%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.410, neg=0, invalid=96777
- 0569: dt=55.488000, rms=0.410 (0.010%), neg=0, invalid=96777
- 0570: dt=73.984000, rms=0.410 (0.003%), neg=0, invalid=96777
- 0571: dt=73.984000, rms=0.410 (0.001%), neg=0, invalid=96777
- 0572: dt=73.984000, rms=0.410 (-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=0.410, neg=0, invalid=96777
- 0573: dt=0.000000, rms=0.410 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.410, neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 12 iterations, nbhd size=2, neg = 0
- 0574: dt=36.288000, rms=0.410 (0.022%), neg=0, invalid=96777
- 0575: dt=9.072000, rms=0.410 (0.001%), neg=0, invalid=96777
- 0576: dt=9.072000, rms=0.410 (0.004%), neg=0, invalid=96777
- 0577: dt=9.072000, rms=0.410 (0.007%), neg=0, invalid=96777
- 0578: dt=9.072000, rms=0.410 (0.008%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 5 iterations, nbhd size=1, neg = 0
- 0579: dt=9.072000, rms=0.410 (0.007%), neg=0, invalid=96777
- 0580: dt=9.072000, rms=0.410 (-0.002%), neg=0, invalid=96777
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.410, neg=0, invalid=96777
- 0581: dt=0.300000, rms=0.410 (0.000%), neg=0, invalid=96777
- iter 0, gcam->neg = 4
- after 31 iterations, nbhd size=4, neg = 0
- 0582: dt=11.200000, rms=0.410 (0.024%), neg=0, invalid=96777
- 0583: dt=0.009375, rms=0.410 (0.000%), neg=0, invalid=96777
- 0584: dt=0.009375, rms=0.410 (0.000%), neg=0, invalid=96777
- 0585: dt=0.009375, rms=0.410 (0.000%), neg=0, invalid=96777
- 0586: dt=0.009375, rms=0.410 (0.000%), neg=0, invalid=96777
- 0587: dt=0.009375, rms=0.410 (0.000%), neg=0, invalid=96777
- 0588: dt=0.009375, rms=0.410 (0.000%), neg=0, invalid=96777
- 0589: dt=0.009375, rms=0.410 (0.000%), neg=0, invalid=96777
- 0590: dt=0.009375, rms=0.410 (0.000%), neg=0, invalid=96777
- 0591: dt=0.009375, rms=0.410 (0.000%), neg=0, invalid=96777
- 0592: dt=0.009375, rms=0.410 (0.000%), neg=0, invalid=96777
- 0593: dt=0.009375, rms=0.410 (0.000%), neg=0, invalid=96777
- 0594: dt=0.009375, rms=0.410 (0.000%), neg=0, invalid=96777
- 0595: dt=0.009375, rms=0.410 (0.000%), neg=0, invalid=96777
- 0596: dt=0.009375, rms=0.410 (0.000%), neg=0, invalid=96777
- 0597: dt=0.009375, rms=0.410 (0.000%), neg=0, invalid=96777
- 0598: dt=0.009375, rms=0.410 (0.000%), neg=0, invalid=96777
- 0599: dt=0.009375, rms=0.410 (0.000%), neg=0, invalid=96777
- 0600: dt=0.009375, rms=0.410 (0.000%), neg=0, invalid=96777
- 0601: dt=0.009375, rms=0.410 (0.000%), neg=0, invalid=96777
- 0602: dt=0.009375, rms=0.410 (0.000%), neg=0, invalid=96777
- 0603: dt=0.009375, rms=0.410 (0.000%), neg=0, invalid=96777
- 0604: dt=0.009375, rms=0.410 (0.000%), neg=0, invalid=96777
- 0605: dt=0.009375, rms=0.410 (0.000%), neg=0, invalid=96777
- 0606: dt=0.009375, rms=0.410 (0.000%), neg=0, invalid=96777
- 0607: dt=0.009375, rms=0.410 (0.000%), neg=0, invalid=96777
- 0608: dt=0.009375, rms=0.410 (0.000%), neg=0, invalid=96777
- 0609: dt=0.009375, rms=0.410 (0.000%), neg=0, invalid=96777
- 0610: dt=0.009375, rms=0.410 (0.000%), neg=0, invalid=96777
- 0611: dt=0.009375, rms=0.410 (0.000%), neg=0, invalid=96777
- 0612: dt=0.009375, rms=0.410 (0.000%), neg=0, invalid=96777
- 0613: dt=0.009375, rms=0.410 (0.000%), neg=0, invalid=96777
- 0614: dt=0.009375, rms=0.410 (0.000%), neg=0, invalid=96777
- 0615: dt=0.009375, rms=0.410 (0.000%), neg=0, invalid=96777
- 0616: dt=0.009375, rms=0.410 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.410, neg=0, invalid=96777
- iter 0, gcam->neg = 41
- after 200 iterations, nbhd size=2, neg = 1
- starting rms=0.003, neg=1, removing folds in lattice....
- iter 1, dt=0.000055: new neg 0, old_neg 1, delta 1, rms=0.002 (19.636%)
- 0617: dt=44.800000, rms=0.408 (0.403%), neg=0, invalid=96777
- iter 0, gcam->neg = 41
- after 200 iterations, nbhd size=4, neg = 4
- starting rms=0.005, neg=4, removing folds in lattice....
- iter 1, dt=0.000055: new neg 0, old_neg 4, delta 4, rms=0.003 (44.783%)
- 0618: dt=32.000000, rms=0.408 (0.097%), neg=0, invalid=96777
- iter 0, gcam->neg = 35
- after 200 iterations, nbhd size=1, neg = 6
- starting rms=0.007, neg=6, removing folds in lattice....
- iter 1, dt=0.000055: new neg 0, old_neg 6, delta 6, rms=0.003 (62.663%)
- 0619: dt=32.000000, rms=0.408 (-0.180%), neg=0, invalid=96777
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.410, neg=0, invalid=96777
- iter 0, gcam->neg = 11
- after 200 iterations, nbhd size=4, neg = 4
- starting rms=0.004, neg=4, removing folds in lattice....
- iter 1, dt=0.000047: new neg 0, old_neg 4, delta 4, rms=0.002 (53.373%)
- 0620: dt=1.008000, rms=0.409 (0.041%), neg=0, invalid=96777
- iter 0, gcam->neg = 63
- after 200 iterations, nbhd size=2, neg = 4
- starting rms=0.004, neg=4, removing folds in lattice....
- iter 1, dt=0.000080: new neg 0, old_neg 4, delta 4, rms=0.002 (47.776%)
- 0621: dt=3.536232, rms=0.408 (0.251%), neg=0, invalid=96777
- iter 0, gcam->neg = 22
- after 200 iterations, nbhd size=2, neg = 2
- starting rms=0.004, neg=2, removing folds in lattice....
- iter 1, dt=0.000080: new neg 0, old_neg 2, delta 2, rms=0.002 (49.584%)
- 0622: dt=1.875000, rms=0.408 (0.069%), neg=0, invalid=96777
- iter 0, gcam->neg = 23
- after 200 iterations, nbhd size=2, neg = 2
- starting rms=0.004, neg=2, removing folds in lattice....
- iter 1, dt=0.000080: new neg 0, old_neg 2, delta 2, rms=0.002 (51.484%)
- 0623: dt=1.875000, rms=0.408 (0.109%), neg=0, invalid=96777
- iter 0, gcam->neg = 9
- after 200 iterations, nbhd size=2, neg = 2
- starting rms=0.004, neg=2, removing folds in lattice....
- iter 1, dt=0.000080: new neg 0, old_neg 2, delta 2, rms=0.002 (52.925%)
- 0624: dt=1.875000, rms=0.407 (0.103%), neg=0, invalid=96777
- iter 0, gcam->neg = 10
- after 200 iterations, nbhd size=4, neg = 2
- starting rms=0.004, neg=2, removing folds in lattice....
- iter 1, dt=0.000080: new neg 0, old_neg 2, delta 2, rms=0.002 (50.999%)
- 0625: dt=1.875000, rms=0.407 (0.080%), neg=0, invalid=96777
- iter 0, gcam->neg = 44
- after 200 iterations, nbhd size=4, neg = 3
- starting rms=0.004, neg=3, removing folds in lattice....
- iter 1, dt=0.000047: new neg 0, old_neg 3, delta 3, rms=0.002 (46.053%)
- 0626: dt=3.456000, rms=0.407 (0.095%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0627: dt=0.720000, rms=0.407 (0.004%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.407, neg=0, invalid=96777
- 0628: dt=0.003938, rms=0.407 (0.000%), neg=0, invalid=96777
- iter 0, gcam->neg = 66
- after 37 iterations, nbhd size=3, neg = 0
- 0629: dt=4.894737, rms=0.405 (0.274%), neg=0, invalid=96777
- 0630: dt=0.003938, rms=0.405 (0.000%), neg=0, invalid=96777
- 0631: dt=0.003938, rms=0.405 (0.000%), neg=0, invalid=96777
- 0632: dt=0.003938, rms=0.405 (0.000%), neg=0, invalid=96777
- 0633: dt=0.003938, rms=0.405 (0.000%), neg=0, invalid=96777
- 0634: dt=0.003938, rms=0.405 (0.000%), neg=0, invalid=96777
- 0635: dt=0.003938, rms=0.405 (0.001%), neg=0, invalid=96777
- 0636: dt=0.003938, rms=0.405 (0.001%), neg=0, invalid=96777
- 0637: dt=0.003938, rms=0.405 (0.001%), neg=0, invalid=96777
- 0638: dt=0.003938, rms=0.405 (0.001%), neg=0, invalid=96777
- 0639: dt=0.003938, rms=0.405 (0.001%), neg=0, invalid=96777
- 0640: dt=0.003938, rms=0.405 (0.001%), neg=0, invalid=96777
- 0641: dt=0.003938, rms=0.405 (0.001%), neg=0, invalid=96777
- 0642: dt=0.003938, rms=0.405 (0.002%), neg=0, invalid=96777
- 0643: dt=0.003938, rms=0.405 (0.002%), neg=0, invalid=96777
- 0644: dt=0.003938, rms=0.405 (0.002%), neg=0, invalid=96777
- 0645: dt=0.003938, rms=0.405 (0.002%), neg=0, invalid=96777
- 0646: dt=0.003938, rms=0.405 (0.002%), neg=0, invalid=96777
- 0647: dt=0.003938, rms=0.405 (0.002%), neg=0, invalid=96777
- 0648: dt=0.003938, rms=0.405 (0.002%), neg=0, invalid=96777
- 0649: dt=0.003938, rms=0.405 (0.002%), neg=0, invalid=96777
- 0650: dt=0.003938, rms=0.405 (0.002%), neg=0, invalid=96777
- 0651: dt=0.003938, rms=0.405 (0.002%), neg=0, invalid=96777
- 0652: dt=0.003938, rms=0.405 (0.002%), neg=0, invalid=96777
- 0653: dt=0.003938, rms=0.405 (0.002%), neg=0, invalid=96777
- 0654: dt=0.003938, rms=0.405 (0.002%), neg=0, invalid=96777
- 0655: dt=0.003938, rms=0.405 (0.002%), neg=0, invalid=96777
- 0656: dt=0.003938, rms=0.405 (0.002%), neg=0, invalid=96777
- 0657: dt=0.003938, rms=0.405 (0.002%), neg=0, invalid=96777
- 0658: dt=0.003938, rms=0.405 (0.002%), neg=0, invalid=96777
- 0659: dt=0.003938, rms=0.405 (0.002%), neg=0, invalid=96777
- 0660: dt=0.003938, rms=0.405 (0.002%), neg=0, invalid=96777
- 0661: dt=0.003938, rms=0.405 (0.002%), neg=0, invalid=96777
- 0662: dt=0.003938, rms=0.405 (0.003%), neg=0, invalid=96777
- 0663: dt=0.003938, rms=0.405 (0.003%), neg=0, invalid=96777
- 0664: dt=0.003938, rms=0.405 (0.003%), neg=0, invalid=96777
- 0665: dt=0.003938, rms=0.405 (0.003%), neg=0, invalid=96777
- 0666: dt=0.003938, rms=0.405 (0.003%), neg=0, invalid=96777
- 0667: dt=0.003938, rms=0.405 (0.003%), neg=0, invalid=96777
- 0668: dt=0.003938, rms=0.405 (0.003%), neg=0, invalid=96777
- 0669: dt=0.003938, rms=0.405 (0.003%), neg=0, invalid=96777
- iter 0, gcam->neg = 115
- after 200 iterations, nbhd size=4, neg = 2
- starting rms=0.004, neg=2, removing folds in lattice....
- iter 1, dt=0.000125: new neg 0, old_neg 2, delta 2, rms=0.002 (37.201%)
- 0670: dt=9.513889, rms=0.404 (0.349%), neg=0, invalid=96777
- 0671: dt=0.063000, rms=0.404 (0.000%), neg=0, invalid=96777
- 0672: dt=0.063000, rms=0.404 (0.002%), neg=0, invalid=96777
- 0673: dt=0.063000, rms=0.404 (0.003%), neg=0, invalid=96777
- 0674: dt=0.063000, rms=0.404 (0.005%), neg=0, invalid=96777
- 0675: dt=0.063000, rms=0.404 (0.007%), neg=0, invalid=96777
- 0676: dt=0.063000, rms=0.404 (0.008%), neg=0, invalid=96777
- 0677: dt=0.063000, rms=0.404 (0.010%), neg=0, invalid=96777
- 0678: dt=0.063000, rms=0.403 (0.011%), neg=0, invalid=96777
- 0679: dt=0.063000, rms=0.403 (0.012%), neg=0, invalid=96777
- 0680: dt=0.063000, rms=0.403 (0.012%), neg=0, invalid=96777
- 0681: dt=0.063000, rms=0.403 (0.013%), neg=0, invalid=96777
- 0682: dt=0.063000, rms=0.403 (0.014%), neg=0, invalid=96777
- 0683: dt=0.063000, rms=0.403 (0.014%), neg=0, invalid=96777
- 0684: dt=0.063000, rms=0.403 (0.015%), neg=0, invalid=96777
- 0685: dt=0.063000, rms=0.403 (0.015%), neg=0, invalid=96777
- 0686: dt=0.063000, rms=0.403 (0.015%), neg=0, invalid=96777
- 0687: dt=0.063000, rms=0.403 (0.015%), neg=0, invalid=96777
- 0688: dt=0.063000, rms=0.403 (0.016%), neg=0, invalid=96777
- 0689: dt=0.063000, rms=0.403 (0.016%), neg=0, invalid=96777
- 0690: dt=0.063000, rms=0.403 (0.016%), neg=0, invalid=96777
- 0691: dt=0.063000, rms=0.403 (0.016%), neg=0, invalid=96777
- 0692: dt=0.063000, rms=0.403 (0.016%), neg=0, invalid=96777
- iter 0, gcam->neg = 33
- after 200 iterations, nbhd size=1, neg = 1
- starting rms=0.002, neg=1, removing folds in lattice....
- iter 1, dt=0.000047: new neg 0, old_neg 1, delta 1, rms=0.002 (22.698%)
- 0693: dt=4.769231, rms=0.402 (0.042%), neg=0, invalid=96777
- 0694: dt=0.252000, rms=0.402 (0.001%), neg=0, invalid=96777
- setting smoothness coefficient to 1.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.407, neg=0, invalid=96777
- 0695: dt=0.000000, rms=0.407 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.407, neg=0, invalid=96777
- 0696: dt=0.000000, rms=0.407 (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=0.400, neg=0, invalid=96777
- iter 0, gcam->neg = 262
- after 11 iterations, nbhd size=1, neg = 0
- 0697: dt=0.306306, rms=0.393 (1.560%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0698: dt=0.000012, rms=0.393 (0.002%), neg=0, invalid=96777
- 0699: dt=0.000012, rms=0.393 (0.000%), neg=0, invalid=96777
- 0700: dt=0.000012, rms=0.393 (0.000%), neg=0, invalid=96777
- 0701: dt=0.000012, rms=0.393 (0.000%), neg=0, invalid=96777
- 0702: dt=0.000012, rms=0.393 (0.000%), neg=0, invalid=96777
- iter 0, gcam->neg = 3
- after 7 iterations, nbhd size=1, neg = 0
- 0703: dt=0.006000, rms=0.393 (0.008%), neg=0, invalid=96777
- 0704: dt=0.000438, rms=0.393 (0.001%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.393, neg=0, invalid=96777
- iter 0, gcam->neg = 53
- after 11 iterations, nbhd size=1, neg = 0
- 0705: dt=0.079765, rms=0.392 (0.322%), neg=0, invalid=96777
- 0706: dt=0.000016, rms=0.392 (0.001%), neg=0, invalid=96777
- 0707: dt=0.000016, rms=0.392 (0.000%), neg=0, invalid=96777
- 0708: dt=0.000016, rms=0.392 (0.000%), neg=0, invalid=96777
- 0709: dt=0.000016, rms=0.392 (0.000%), neg=0, invalid=96777
- 0710: dt=0.000016, rms=0.392 (0.000%), neg=0, invalid=96777
- 0711: dt=0.000016, rms=0.392 (0.000%), neg=0, invalid=96777
- 0712: dt=0.000016, rms=0.392 (0.000%), neg=0, invalid=96777
- 0713: dt=0.000016, rms=0.392 (0.000%), neg=0, invalid=96777
- 0714: dt=0.000016, rms=0.392 (0.000%), neg=0, invalid=96777
- 0715: dt=0.000016, rms=0.392 (0.000%), neg=0, invalid=96777
- 0716: dt=0.000016, rms=0.392 (0.000%), neg=0, invalid=96777
- 0717: dt=0.000016, rms=0.392 (0.000%), neg=0, invalid=96777
- 0718: dt=0.000016, rms=0.392 (0.000%), neg=0, invalid=96777
- 0719: dt=0.000016, rms=0.392 (0.000%), neg=0, invalid=96777
- 0720: dt=0.000016, rms=0.392 (0.000%), neg=0, invalid=96777
- 0721: dt=0.000016, rms=0.392 (0.000%), neg=0, invalid=96777
- 0722: dt=0.000016, rms=0.392 (0.000%), neg=0, invalid=96777
- 0723: dt=0.000016, rms=0.392 (0.000%), neg=0, invalid=96777
- 0724: dt=0.000016, rms=0.392 (0.000%), neg=0, invalid=96777
- 0725: dt=0.000016, rms=0.392 (0.000%), neg=0, invalid=96777
- 0726: dt=0.000016, rms=0.392 (0.000%), neg=0, invalid=96777
- 0727: dt=0.000016, rms=0.392 (0.000%), neg=0, invalid=96777
- 0728: dt=0.000016, rms=0.392 (0.000%), neg=0, invalid=96777
- 0729: dt=0.000016, rms=0.392 (0.000%), neg=0, invalid=96777
- 0730: dt=0.000016, rms=0.392 (0.000%), neg=0, invalid=96777
- 0731: dt=0.000016, rms=0.392 (0.000%), neg=0, invalid=96777
- 0732: dt=0.000016, rms=0.392 (0.000%), neg=0, invalid=96777
- 0733: dt=0.000016, rms=0.392 (0.001%), neg=0, invalid=96777
- 0734: dt=0.000016, rms=0.392 (0.001%), neg=0, invalid=96777
- 0735: dt=0.000016, rms=0.392 (0.001%), neg=0, invalid=96777
- 0736: dt=0.000016, rms=0.392 (0.001%), neg=0, invalid=96777
- 0737: dt=0.000016, rms=0.392 (0.001%), neg=0, invalid=96777
- 0738: dt=0.000016, rms=0.392 (0.001%), neg=0, invalid=96777
- 0739: dt=0.000016, rms=0.392 (0.001%), neg=0, invalid=96777
- 0740: dt=0.000016, rms=0.392 (0.001%), neg=0, invalid=96777
- 0741: dt=0.000016, rms=0.392 (0.001%), neg=0, invalid=96777
- iter 0, gcam->neg = 161
- after 17 iterations, nbhd size=2, neg = 0
- 0742: dt=0.213208, rms=0.390 (0.650%), neg=0, invalid=96777
- 0743: dt=0.000040, rms=0.390 (0.001%), neg=0, invalid=96777
- 0744: dt=0.000040, rms=0.390 (0.000%), neg=0, invalid=96777
- 0745: dt=0.000040, rms=0.390 (0.000%), neg=0, invalid=96777
- 0746: dt=0.000040, rms=0.390 (0.000%), neg=0, invalid=96777
- 0747: dt=0.000040, rms=0.390 (0.000%), neg=0, invalid=96777
- 0748: dt=0.000040, rms=0.390 (0.000%), neg=0, invalid=96777
- 0749: dt=0.000040, rms=0.390 (0.000%), neg=0, invalid=96777
- 0750: dt=0.000040, rms=0.390 (0.000%), neg=0, invalid=96777
- 0751: dt=0.000040, rms=0.390 (0.000%), neg=0, invalid=96777
- 0752: dt=0.000040, rms=0.390 (0.000%), neg=0, invalid=96777
- 0753: dt=0.000040, rms=0.390 (0.000%), neg=0, invalid=96777
- 0754: dt=0.000040, rms=0.390 (0.000%), neg=0, invalid=96777
- 0755: dt=0.000040, rms=0.390 (0.001%), neg=0, invalid=96777
- 0756: dt=0.000040, rms=0.390 (0.001%), neg=0, invalid=96777
- 0757: dt=0.000040, rms=0.389 (0.001%), neg=0, invalid=96777
- 0758: dt=0.000040, rms=0.389 (0.001%), neg=0, invalid=96777
- 0759: dt=0.000040, rms=0.389 (0.001%), neg=0, invalid=96777
- 0760: dt=0.000040, rms=0.389 (0.001%), neg=0, invalid=96777
- 0761: dt=0.000040, rms=0.389 (0.001%), neg=0, invalid=96777
- 0762: dt=0.000040, rms=0.389 (0.001%), neg=0, invalid=96777
- 0763: dt=0.000040, rms=0.389 (0.001%), neg=0, invalid=96777
- 0764: dt=0.000040, rms=0.389 (0.001%), neg=0, invalid=96777
- 0765: dt=0.000040, rms=0.389 (0.001%), neg=0, invalid=96777
- 0766: dt=0.000040, rms=0.389 (0.001%), neg=0, invalid=96777
- 0767: dt=0.000040, rms=0.389 (0.001%), neg=0, invalid=96777
- 0768: dt=0.000040, rms=0.389 (0.001%), neg=0, invalid=96777
- 0769: dt=0.000040, rms=0.389 (0.001%), neg=0, invalid=96777
- 0770: dt=0.000040, rms=0.389 (0.001%), neg=0, invalid=96777
- 0771: dt=0.000040, rms=0.389 (0.001%), neg=0, invalid=96777
- 0772: dt=0.000040, rms=0.389 (0.001%), neg=0, invalid=96777
- 0773: dt=0.000040, rms=0.389 (0.001%), neg=0, invalid=96777
- 0774: dt=0.000040, rms=0.389 (0.001%), neg=0, invalid=96777
- 0775: dt=0.000040, rms=0.389 (0.001%), neg=0, invalid=96777
- 0776: dt=0.000040, rms=0.389 (0.001%), neg=0, invalid=96777
- 0777: dt=0.000040, rms=0.389 (0.001%), neg=0, invalid=96777
- 0778: dt=0.000040, rms=0.389 (0.001%), neg=0, invalid=96777
- 0779: dt=0.000040, rms=0.389 (0.001%), neg=0, invalid=96777
- 0780: dt=0.000040, rms=0.389 (0.001%), neg=0, invalid=96777
- 0781: dt=0.000040, rms=0.389 (0.001%), neg=0, invalid=96777
- 0782: dt=0.000040, rms=0.389 (0.001%), neg=0, invalid=96777
- 0783: dt=0.000040, rms=0.389 (0.001%), neg=0, invalid=96777
- 0784: dt=0.000040, rms=0.389 (0.001%), neg=0, invalid=96777
- iter 0, gcam->neg = 77
- after 16 iterations, nbhd size=2, neg = 0
- 0785: dt=0.112000, rms=0.389 (0.195%), neg=0, invalid=96777
- 0786: dt=0.000023, rms=0.389 (0.001%), neg=0, invalid=96777
- writing output transformation to transforms/talairach.m3z...
- GCAMwrite
- registration took 5 hours, 37 minutes and 56 seconds.
- #--------------------------------------
- #@# CA Reg Inv Thu Aug 8 17:38:15 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 17:39:45 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...
- 11710027 nonbrain voxels erased
- writing output to nu_noneck.mgz...
- nonbrain removal took 1 minutes and 31 seconds.
- #--------------------------------------
- #@# SkullLTA Thu Aug 8 17:41:17 CEST 2013
- mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta
- ======= NUMBER OF OPENMP THREADS = 1 =======
- aligning to atlas containing skull, setting unknown_nbr_spacing = 5
- using previously computed transform transforms/talairach.lta
- reading 1 input volumes...
- logging results to talairach_with_skull_2.log
- reading '/opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca'...
- average std = 23.1 using min determinant for regularization = 53.4
- 0 singular and 5702 ill-conditioned covariance matrices regularized
- reading 'nu_noneck.mgz'...
- freeing gibbs priors...done.
- bounding unknown intensity as < 20.2 or > 943.7
- total sample mean = 92.0 (1443 zeros)
- ************************************************
- spacing=8, using 3481 sample points, tol=1.00e-05...
- ************************************************
- register_mri: find_optimal_transform
- find_optimal_transform: nsamples 3481, passno 0, spacing 8
- resetting wm mean[0]: 117 --> 126
- resetting gm mean[0]: 74 --> 74
- input volume #1 is the most T1-like
- using real data threshold=7.0
- skull bounding box = (51, 26, 25) --> (206, 205, 198)
- using (103, 86, 112) as brain centroid...
- mean wm in atlas = 126, using box (84,64,91) --> (122, 108,133) to find MRI wm
- before smoothing, mri peak at 110
- after smoothing, mri peak at 110, scaling input intensities by 1.145
- scaling channel 0 by 1.14545
- ****************************************
- 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)
- 1.109 0.011 -0.027 -15.093;
- -0.002 1.160 0.350 -40.721;
- 0.042 -0.321 0.986 19.390;
- 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)
- 1.109 0.011 -0.027 -15.093;
- -0.002 1.160 0.350 -40.721;
- 0.042 -0.321 0.986 19.390;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.2500
- ****************************************
- Nine parameter search. iteration 2 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.1 (thresh=-4.1)
- 1.126 -0.013 -0.074 -9.029;
- 0.032 1.172 0.384 -48.505;
- 0.083 -0.370 1.010 18.491;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 3 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.126 -0.013 -0.074 -9.029;
- 0.032 1.172 0.384 -48.505;
- 0.083 -0.370 1.010 18.491;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.0625
- ****************************************
- Nine parameter search. iteration 4 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-4.0 (thresh=-4.0)
- 1.126 -0.033 -0.081 -5.298;
- 0.051 1.168 0.381 -49.148;
- 0.083 -0.369 1.006 18.798;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 5 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 1.126 -0.033 -0.081 -5.298;
- 0.051 1.168 0.381 -49.148;
- 0.083 -0.369 1.006 18.798;
- 0.000 0.000 0.000 1.000;
- min search scale 0.025000 reached
- ***********************************************
- Computing MAP estimate using 3481 samples...
- ***********************************************
- dt = 5.00e-06, momentum=0.80, tol=1.00e-05
- l_intensity = 1.0000
- Aligning input volume to GCA...
- Transform matrix
- 1.12562 -0.03267 -0.08075 -5.29821;
- 0.05062 1.16771 0.38147 -49.14754;
- 0.08306 -0.36901 1.00613 18.79837;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 3481
- Quasinewton: input matrix
- 1.12562 -0.03267 -0.08075 -5.29821;
- 0.05062 1.16771 0.38147 -49.14754;
- 0.08306 -0.36901 1.00613 18.79837;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 007: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 1.126 -0.033 -0.081 -5.298;
- 0.051 1.168 0.381 -49.148;
- 0.083 -0.369 1.006 18.798;
- 0.000 0.000 0.000 1.000;
- pass 1, spacing 8: log(p) = -3.9 (old=-4.2)
- transform before final EM align:
- 1.126 -0.033 -0.081 -5.298;
- 0.051 1.168 0.381 -49.148;
- 0.083 -0.369 1.006 18.798;
- 0.000 0.000 0.000 1.000;
- **************************************************
- EM alignment process ...
- Computing final MAP estimate using 382743 samples.
- **************************************************
- dt = 5.00e-06, momentum=0.80, tol=1.00e-07
- l_intensity = 1.0000
- Aligning input volume to GCA...
- Transform matrix
- 1.12562 -0.03267 -0.08075 -5.29821;
- 0.05062 1.16771 0.38147 -49.14754;
- 0.08306 -0.36901 1.00613 18.79837;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 382743
- Quasinewton: input matrix
- 1.12562 -0.03267 -0.08075 -5.29821;
- 0.05062 1.16771 0.38147 -49.14754;
- 0.08306 -0.36901 1.00613 18.79837;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = 4.4 tol 0.000000
- final transform:
- 1.126 -0.033 -0.081 -5.298;
- 0.051 1.168 0.381 -49.148;
- 0.083 -0.369 1.006 18.798;
- 0.000 0.000 0.000 1.000;
- writing output transformation to transforms/talairach_with_skull_2.lta...
- registration took 31 minutes and 56 seconds.
- #--------------------------------------
- #@# SubCort Seg Thu Aug 8 18:13:13 CEST 2013
- mri_ca_label -align norm.mgz transforms/talairach.m3z /opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz
- sysname Linux
- hostname snake5
- machine x86_64
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 = 0.14089 ( 8)
- Left_Lateral_Ventricle (4): linear fit = 0.25 x + 0.0 (1783 voxels, overlap=0.007)
- Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (1783 voxels, peak = 7), gca=10.8
- gca peak = 0.14982 (20)
- mri peak = 0.12155 ( 7)
- Right_Lateral_Ventricle (43): linear fit = 0.31 x + 0.0 (1071 voxels, overlap=0.008)
- Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (1071 voxels, peak = 6), gca=8.0
- gca peak = 0.28003 (97)
- mri peak = 0.09873 (94)
- Right_Pallidum (52): linear fit = 0.93 x + 0.0 (348 voxels, overlap=0.527)
- Right_Pallidum (52): linear fit = 0.93 x + 0.0 (348 voxels, peak = 90), gca=89.7
- gca peak = 0.18160 (96)
- mri peak = 0.07940 (86)
- Left_Pallidum (13): linear fit = 0.88 x + 0.0 (265 voxels, overlap=0.051)
- Left_Pallidum (13): linear fit = 0.88 x + 0.0 (265 voxels, peak = 84), gca=84.0
- gca peak = 0.27536 (62)
- mri peak = 0.09800 (57)
- Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (549 voxels, overlap=0.537)
- Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (549 voxels, peak = 55), gca=54.9
- gca peak = 0.32745 (63)
- mri peak = 0.09524 (62)
- Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (607 voxels, overlap=0.785)
- Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (607 voxels, peak = 59), gca=58.9
- gca peak = 0.08597 (105)
- mri peak = 0.08783 (108)
- Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (32242 voxels, overlap=0.653)
- Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (32242 voxels, peak = 108), gca=107.6
- gca peak = 0.09209 (106)
- mri peak = 0.08772 (110)
- Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (30281 voxels, overlap=0.613)
- Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (30281 voxels, peak = 110), gca=109.7
- gca peak = 0.07826 (63)
- mri peak = 0.05176 (56)
- Left_Cerebral_Cortex (3): linear fit = 0.85 x + 0.0 (10578 voxels, overlap=0.445)
- Left_Cerebral_Cortex (3): linear fit = 0.85 x + 0.0 (10578 voxels, peak = 53), gca=53.2
- gca peak = 0.08598 (64)
- mri peak = 0.05557 (51)
- Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (9651 voxels, overlap=0.266)
- Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (9651 voxels, peak = 53), gca=52.8
- gca peak = 0.24164 (71)
- mri peak = 0.10947 (65)
- Right_Caudate (50): linear fit = 0.88 x + 0.0 (475 voxels, overlap=0.428)
- Right_Caudate (50): linear fit = 0.88 x + 0.0 (475 voxels, peak = 62), gca=62.1
- gca peak = 0.18227 (75)
- mri peak = 0.08043 (69)
- Left_Caudate (11): linear fit = 0.86 x + 0.0 (742 voxels, overlap=0.028)
- Left_Caudate (11): linear fit = 0.86 x + 0.0 (742 voxels, peak = 64), gca=64.1
- gca peak = 0.10629 (62)
- mri peak = 0.05583 (63)
- Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (7321 voxels, overlap=0.992)
- Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (7321 voxels, peak = 64), gca=63.5
- gca peak = 0.11668 (59)
- mri peak = 0.05438 (62)
- Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (7742 voxels, overlap=0.999)
- Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (7742 voxels, peak = 60), gca=60.5
- gca peak = 0.17849 (88)
- mri peak = 0.08882 (90)
- Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (4040 voxels, overlap=0.921)
- Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (4040 voxels, peak = 91), gca=91.1
- gca peak = 0.16819 (86)
- mri peak = 0.08408 (90)
- Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (3898 voxels, overlap=0.944)
- Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (3898 voxels, peak = 89), gca=89.0
- gca peak = 0.41688 (64)
- mri peak = 0.11719 (62)
- Left_Amygdala (18): linear fit = 0.95 x + 0.0 (254 voxels, overlap=1.041)
- Left_Amygdala (18): linear fit = 0.95 x + 0.0 (254 voxels, peak = 61), gca=61.1
- gca peak = 0.42394 (62)
- mri peak = 0.13014 (62)
- Right_Amygdala (54): linear fit = 0.96 x + 0.0 (149 voxels, overlap=1.040)
- Right_Amygdala (54): linear fit = 0.96 x + 0.0 (149 voxels, peak = 60), gca=59.8
- gca peak = 0.10041 (96)
- mri peak = 0.06884 (91)
- Left_Thalamus_Proper (10): linear fit = 0.96 x + 0.0 (3023 voxels, overlap=0.909)
- Left_Thalamus_Proper (10): linear fit = 0.96 x + 0.0 (3023 voxels, peak = 93), gca=92.6
- gca peak = 0.13978 (88)
- mri peak = 0.06318 (88)
- Right_Thalamus_Proper (49): linear fit = 0.96 x + 0.0 (2766 voxels, overlap=0.920)
- Right_Thalamus_Proper (49): linear fit = 0.96 x + 0.0 (2766 voxels, peak = 85), gca=84.9
- gca peak = 0.08514 (81)
- mri peak = 0.08152 (72)
- Left_Putamen (12): linear fit = 0.88 x + 0.0 (1605 voxels, overlap=0.465)
- Left_Putamen (12): linear fit = 0.88 x + 0.0 (1605 voxels, peak = 71), gca=70.9
- gca peak = 0.09624 (82)
- mri peak = 0.08519 (71)
- Right_Putamen (51): linear fit = 0.88 x + 0.0 (1360 voxels, overlap=0.375)
- Right_Putamen (51): linear fit = 0.88 x + 0.0 (1360 voxels, peak = 73), gca=72.6
- gca peak = 0.07543 (88)
- mri peak = 0.07129 (88)
- Brain_Stem (16): linear fit = 1.03 x + 0.0 (8685 voxels, overlap=0.765)
- Brain_Stem (16): linear fit = 1.03 x + 0.0 (8685 voxels, peak = 91), gca=91.1
- gca peak = 0.12757 (95)
- mri peak = 0.06713 (95)
- Right_VentralDC (60): linear fit = 1.03 x + 0.0 (666 voxels, overlap=0.835)
- Right_VentralDC (60): linear fit = 1.03 x + 0.0 (666 voxels, peak = 98), gca=98.3
- gca peak = 0.17004 (92)
- mri peak = 0.06949 (95)
- Left_VentralDC (28): linear fit = 1.02 x + 0.0 (701 voxels, overlap=0.900)
- Left_VentralDC (28): linear fit = 1.02 x + 0.0 (701 voxels, peak = 94), gca=94.3
- gca peak = 0.21361 (36)
- mri peak = 0.17654 (10)
- gca peak = 0.26069 (23)
- mri peak = 0.12858 (11)
- Fourth_Ventricle (15): linear fit = 0.35 x + 0.0 (202 voxels, overlap=0.024)
- Fourth_Ventricle (15): linear fit = 0.35 x + 0.0 (202 voxels, peak = 8), gca=8.2
- gca peak Unknown = 0.94427 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.31795 (35)
- gca peak Third_Ventricle = 0.21361 (36)
- gca peak Fourth_Ventricle = 0.26069 (23)
- gca peak CSF = 0.14367 (38)
- gca peak Left_Accumbens_area = 0.57033 (70)
- gca peak Left_undetermined = 1.00000 (35)
- gca peak Left_vessel = 0.65201 (62)
- gca peak Left_choroid_plexus = 0.09084 (48)
- gca peak Right_Inf_Lat_Vent = 0.31129 (32)
- gca peak Right_Accumbens_area = 0.30219 (72)
- gca peak Right_vessel = 0.83418 (60)
- gca peak Right_choroid_plexus = 0.10189 (48)
- gca peak Fifth_Ventricle = 0.72939 (42)
- gca peak WM_hypointensities = 0.14821 (82)
- gca peak non_WM_hypointensities = 0.10354 (53)
- gca peak Optic_Chiasm = 0.34849 (76)
- not using caudate to estimate GM means
- estimating mean gm scale to be 0.90 x + 0.0
- estimating mean wm scale to be 1.03 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 = 0.14089 ( 8)
- Left_Lateral_Ventricle (4): linear fit = 0.70 x + 0.0 (1783 voxels, overlap=0.942)
- Left_Lateral_Ventricle (4): linear fit = 0.70 x + 0.0 (1783 voxels, peak = 8), gca=7.8
- gca peak = 0.29325 ( 9)
- mri peak = 0.12155 ( 7)
- Right_Lateral_Ventricle (43): linear fit = 0.80 x + 0.0 (1071 voxels, overlap=0.969)
- Right_Lateral_Ventricle (43): linear fit = 0.80 x + 0.0 (1071 voxels, peak = 7), gca=7.2
- gca peak = 0.32313 (90)
- mri peak = 0.09873 (94)
- Right_Pallidum (52): linear fit = 1.01 x + 0.0 (348 voxels, overlap=1.022)
- Right_Pallidum (52): linear fit = 1.01 x + 0.0 (348 voxels, peak = 91), gca=91.3
- gca peak = 0.19962 (84)
- mri peak = 0.07940 (86)
- Left_Pallidum (13): linear fit = 1.00 x + 0.0 (265 voxels, overlap=1.012)
- Left_Pallidum (13): linear fit = 1.00 x + 0.0 (265 voxels, peak = 84), gca=84.0
- gca peak = 0.31426 (55)
- mri peak = 0.09800 (57)
- Right_Hippocampus (53): linear fit = 1.02 x + 0.0 (549 voxels, overlap=1.007)
- Right_Hippocampus (53): linear fit = 1.02 x + 0.0 (549 voxels, peak = 56), gca=56.4
- gca peak = 0.35523 (59)
- mri peak = 0.09524 (62)
- Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (607 voxels, overlap=1.007)
- Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (607 voxels, peak = 59), gca=59.0
- gca peak = 0.08343 (108)
- mri peak = 0.08783 (108)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (32242 voxels, overlap=0.757)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (32242 voxels, peak = 109), gca=108.5
- gca peak = 0.08545 (110)
- mri peak = 0.08772 (110)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (30281 voxels, overlap=0.722)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (30281 voxels, peak = 110), gca=110.0
- gca peak = 0.09185 (53)
- mri peak = 0.05176 (56)
- Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (10578 voxels, overlap=0.993)
- Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (10578 voxels, peak = 53), gca=53.0
- gca peak = 0.10545 (53)
- mri peak = 0.05557 (51)
- Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (9651 voxels, overlap=0.991)
- Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (9651 voxels, peak = 52), gca=52.2
- gca peak = 0.24057 (64)
- mri peak = 0.10947 (65)
- Right_Caudate (50): linear fit = 1.01 x + 0.0 (475 voxels, overlap=1.003)
- Right_Caudate (50): linear fit = 1.01 x + 0.0 (475 voxels, peak = 65), gca=65.0
- gca peak = 0.18422 (64)
- mri peak = 0.08043 (69)
- Left_Caudate (11): linear fit = 0.99 x + 0.0 (742 voxels, overlap=0.961)
- Left_Caudate (11): linear fit = 0.99 x + 0.0 (742 voxels, peak = 63), gca=63.0
- gca peak = 0.10054 (62)
- mri peak = 0.05583 (63)
- Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (7321 voxels, overlap=0.997)
- Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (7321 voxels, peak = 61), gca=61.1
- gca peak = 0.12528 (61)
- mri peak = 0.05438 (62)
- Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (7742 voxels, overlap=0.992)
- Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (7742 voxels, peak = 60), gca=60.1
- gca peak = 0.16819 (91)
- mri peak = 0.08882 (90)
- Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4040 voxels, overlap=0.989)
- Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4040 voxels, peak = 91), gca=90.5
- gca peak = 0.16430 (89)
- mri peak = 0.08408 (90)
- Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (3898 voxels, overlap=0.995)
- Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (3898 voxels, peak = 89), gca=88.6
- gca peak = 0.46583 (61)
- mri peak = 0.11719 (62)
- Left_Amygdala (18): linear fit = 1.00 x + 0.0 (254 voxels, overlap=1.032)
- Left_Amygdala (18): linear fit = 1.00 x + 0.0 (254 voxels, peak = 61), gca=61.0
- gca peak = 0.50337 (60)
- mri peak = 0.13014 (62)
- Right_Amygdala (54): linear fit = 1.01 x + 0.0 (149 voxels, overlap=1.027)
- Right_Amygdala (54): linear fit = 1.01 x + 0.0 (149 voxels, peak = 61), gca=60.9
- gca peak = 0.10264 (91)
- mri peak = 0.06884 (91)
- Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (3023 voxels, overlap=0.978)
- Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (3023 voxels, peak = 90), gca=89.6
- gca peak = 0.13160 (85)
- mri peak = 0.06318 (88)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (2766 voxels, overlap=0.997)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (2766 voxels, peak = 85), gca=84.6
- gca peak = 0.09487 (72)
- mri peak = 0.08152 (72)
- Left_Putamen (12): linear fit = 1.00 x + 0.0 (1605 voxels, overlap=1.002)
- Left_Putamen (12): linear fit = 1.00 x + 0.0 (1605 voxels, peak = 72), gca=72.0
- gca peak = 0.12381 (67)
- mri peak = 0.08519 (71)
- Right_Putamen (51): linear fit = 1.00 x + 0.0 (1360 voxels, overlap=0.985)
- Right_Putamen (51): linear fit = 1.00 x + 0.0 (1360 voxels, peak = 67), gca=67.0
- gca peak = 0.07011 (88)
- mri peak = 0.07129 (88)
- Brain_Stem (16): linear fit = 1.01 x + 0.0 (8685 voxels, overlap=0.837)
- Brain_Stem (16): linear fit = 1.01 x + 0.0 (8685 voxels, peak = 89), gca=89.3
- gca peak = 0.13169 (98)
- mri peak = 0.06713 (95)
- Right_VentralDC (60): linear fit = 1.00 x + 0.0 (666 voxels, overlap=0.851)
- Right_VentralDC (60): linear fit = 1.00 x + 0.0 (666 voxels, peak = 98), gca=98.0
- gca peak = 0.15748 (95)
- mri peak = 0.06949 (95)
- Left_VentralDC (28): linear fit = 1.00 x + 0.0 (701 voxels, overlap=0.932)
- Left_VentralDC (28): linear fit = 1.00 x + 0.0 (701 voxels, peak = 95), gca=95.5
- gca peak = 0.35640 (14)
- mri peak = 0.17654 (10)
- gca peak = 0.33827 ( 9)
- mri peak = 0.12858 (11)
- Fourth_Ventricle (15): linear fit = 0.81 x + 0.0 (202 voxels, overlap=0.932)
- Fourth_Ventricle (15): linear fit = 0.81 x + 0.0 (202 voxels, peak = 7), gca=7.2
- gca peak Unknown = 0.94427 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.27816 (33)
- gca peak Third_Ventricle = 0.35640 (14)
- gca peak CSF = 0.30128 (18)
- gca peak Left_Accumbens_area = 0.51723 (60)
- gca peak Left_undetermined = 1.00000 (35)
- gca peak Left_vessel = 0.58372 (62)
- gca peak Left_choroid_plexus = 0.09087 (48)
- gca peak Right_Inf_Lat_Vent = 0.33369 (28)
- gca peak Right_Accumbens_area = 0.31095 (63)
- gca peak Right_vessel = 0.60220 (60)
- gca peak Right_choroid_plexus = 0.10278 (48)
- gca peak Fifth_Ventricle = 0.45329 (19)
- gca peak WM_hypointensities = 0.17622 (84)
- gca peak non_WM_hypointensities = 0.08722 (54)
- gca peak Optic_Chiasm = 0.34840 (76)
- not using caudate to estimate GM means
- estimating mean gm scale to be 1.00 x + 0.0
- estimating mean wm scale to be 1.00 x + 0.0
- estimating mean csf scale to be 0.77 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
- 9448 gm and wm labels changed (%12 to gray, %88 to white out of all changed labels)
- 192 hippocampal voxels changed.
- 1 amygdala voxels changed.
- pass 1: 73417 changed. image ll: -2.146, PF=1.000
- pass 2: 13007 changed. image ll: -2.144, PF=1.000
- pass 3: 4745 changed.
- writing labeled volume to aseg.auto_noCCseg.mgz...
- auto-labeling took 20 minutes and 25 seconds.
- mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/cc_up.lta sub017
- 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/sub017/mri/transforms/cc_up.lta
- reading aseg from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/aseg.auto_noCCseg.mgz
- reading norm from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/norm.mgz
- 30262 voxels in left wm, 46695 in right wm, xrange [120, 133]
- searching rotation angles z=[-9 5], y=[-11 3]
-
searching scale 1 Z rot -9.0
searching scale 1 Z rot -8.7
searching scale 1 Z rot -8.5
searching scale 1 Z rot -8.2
searching scale 1 Z rot -8.0
searching scale 1 Z rot -7.7
searching scale 1 Z rot -7.5
searching scale 1 Z rot -7.2
searching scale 1 Z rot -7.0
searching scale 1 Z rot -6.7
searching scale 1 Z rot -6.5
searching scale 1 Z rot -6.2
searching scale 1 Z rot -6.0
searching scale 1 Z rot -5.7
searching scale 1 Z rot -5.5
searching scale 1 Z rot -5.2
searching scale 1 Z rot -5.0
searching scale 1 Z rot -4.7
searching scale 1 Z rot -4.5
searching scale 1 Z rot -4.2
searching scale 1 Z rot -4.0
searching scale 1 Z rot -3.7
searching scale 1 Z rot -3.5
searching scale 1 Z rot -3.2
searching scale 1 Z rot -3.0
searching scale 1 Z rot -2.7
searching scale 1 Z rot -2.5
searching scale 1 Z rot -2.2
searching scale 1 Z rot -2.0
searching scale 1 Z rot -1.7
searching scale 1 Z rot -1.5
searching scale 1 Z rot -1.2
searching scale 1 Z rot -1.0
searching scale 1 Z rot -0.7
searching scale 1 Z rot -0.5
searching scale 1 Z rot -0.2
searching scale 1 Z rot 0.0
searching scale 1 Z rot 0.3
searching scale 1 Z rot 0.5
searching scale 1 Z rot 0.8
searching scale 1 Z rot 1.0
searching scale 1 Z rot 1.3
searching scale 1 Z rot 1.5
searching scale 1 Z rot 1.8
searching scale 1 Z rot 2.0
searching scale 1 Z rot 2.3
searching scale 1 Z rot 2.5
searching scale 1 Z rot 2.8
searching scale 1 Z rot 3.0
searching scale 1 Z rot 3.3
searching scale 1 Z rot 3.5
searching scale 1 Z rot 3.8
searching scale 1 Z rot 4.0
searching scale 1 Z rot 4.3
searching scale 1 Z rot 4.5
searching scale 1 Z rot 4.8
searching scale 1 Z rot 5.0
searching scale 1 Z rot 5.3 global minimum found at slice 127.0, rotations (-4.03, -1.50)
- final transformation (x=127.0, yr=-4.028, zr=-1.497):
- 0.997 0.026 -0.070 6.449;
- -0.026 1.000 0.002 41.147;
- 0.070 -0.000 0.998 13.340;
- 0.000 0.000 0.000 1.000;
- updating x range to be [127, 131] in xformed coordinates
- best xformed slice 129
- cc center is found at 129 146 113
- eigenvectors:
- 0.000 0.004 1.000;
- -0.233 -0.973 0.004;
- 0.973 -0.233 0.000;
- error in mid anterior detected - correcting...
- error in mid anterior detected - correcting...
- writing aseg with callosum to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/aseg.auto.mgz...
- corpus callosum matter segmentation took 1.1 minutes
- #--------------------------------------
- #@# Merge ASeg Thu Aug 8 18:34:47 CEST 2013
- cp aseg.auto.mgz aseg.mgz
- #--------------------------------------------
- #@# Intensity Normalization2 Thu Aug 8 18:34:47 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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...
- 1627 control points removed
- Building bias image
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 0...
- Smoothing with sigma 8
- Applying bias correction
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Iterating 2 times
- ---------------------------------
- 3d normalization pass 1 of 2
- white matter peak found at 111
- white matter peak found at 110
- gm peak at 56 (56), valley at 39 (39)
- 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 39 (39)
- csf peak at 28, setting threshold to 47
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Done iterating ---------------------------------
- writing output to brain.mgz
- 3D bias adjustment took 4 minutes and 25 seconds.
- #--------------------------------------------
- #@# Mask BFS Thu Aug 8 18:39:16 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri
- mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
- threshold mask volume at 5
- DoAbs = 0
- Found 1395743 voxels in mask (pct= 8.32)
- Writing masked volume to brain.finalsurfs.mgz...done.
- #--------------------------------------------
- #@# WM Segmentation Thu Aug 8 18:39:18 CEST 2013
- mri_segment brain.mgz wm.seg.mgz
- doing initial intensity segmentation...
- using local statistics to label ambiguous voxels...
- computing class statistics for intensity windows...
- WM (107.0): 107.0 +- 5.3 [80.0 --> 125.0]
- GM (68.0) : 66.5 +- 9.7 [30.0 --> 96.0]
- setting bottom of white matter range to 76.2
- setting top of gray matter range to 86.0
- doing initial intensity segmentation...
- using local statistics to label ambiguous voxels...
- using local geometry to label remaining ambiguous voxels...
- reclassifying voxels using Gaussian border classifier...
- removing voxels with positive offset direction...
- smoothing T1 volume with sigma = 0.250
- removing 1-dimensional structures...
- 6083 sparsely connected voxels removed...
- thickening thin strands....
- 20 segments, 5303 filled
- 184 bright non-wm voxels segmented.
- 3274 diagonally connected voxels added...
- white matter segmentation took 1.7 minutes
- writing output to wm.seg.mgz...
- mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz
- preserving editing changes in input volume...
- auto filling took 0.71 minutes
- reading wm segmentation from wm.seg.mgz...
- 108 voxels added to wm to prevent paths from MTL structures to cortex
- 1121 additional wm voxels added
- 0 additional wm voxels added
- SEG EDIT: 48897 voxels turned on, 34464 voxels turned off.
- propagating editing to output volume from wm.seg.mgz
- 115,126,128 old 0 new 0
- 115,126,128 old 0 new 0
- writing edited volume to wm.asegedit.mgz....
- mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz
- Iteration Number : 1
- pass 1 (xy+): 17 found - 17 modified | TOTAL: 17
- pass 2 (xy+): 0 found - 17 modified | TOTAL: 17
- pass 1 (xy-): 14 found - 14 modified | TOTAL: 31
- pass 2 (xy-): 0 found - 14 modified | TOTAL: 31
- pass 1 (yz+): 30 found - 30 modified | TOTAL: 61
- pass 2 (yz+): 0 found - 30 modified | TOTAL: 61
- pass 1 (yz-): 15 found - 15 modified | TOTAL: 76
- pass 2 (yz-): 0 found - 15 modified | TOTAL: 76
- pass 1 (xz+): 11 found - 11 modified | TOTAL: 87
- pass 2 (xz+): 0 found - 11 modified | TOTAL: 87
- pass 1 (xz-): 11 found - 11 modified | TOTAL: 98
- pass 2 (xz-): 0 found - 11 modified | TOTAL: 98
- Iteration Number : 1
- pass 1 (+++): 10 found - 10 modified | TOTAL: 10
- pass 2 (+++): 0 found - 10 modified | TOTAL: 10
- pass 1 (+++): 10 found - 10 modified | TOTAL: 20
- pass 2 (+++): 0 found - 10 modified | TOTAL: 20
- pass 1 (+++): 8 found - 8 modified | TOTAL: 28
- pass 2 (+++): 0 found - 8 modified | TOTAL: 28
- pass 1 (+++): 6 found - 6 modified | TOTAL: 34
- pass 2 (+++): 0 found - 6 modified | TOTAL: 34
- Iteration Number : 1
- pass 1 (++): 174 found - 174 modified | TOTAL: 174
- pass 2 (++): 0 found - 174 modified | TOTAL: 174
- pass 1 (+-): 102 found - 102 modified | TOTAL: 276
- pass 2 (+-): 0 found - 102 modified | TOTAL: 276
- pass 1 (--): 143 found - 143 modified | TOTAL: 419
- pass 2 (--): 0 found - 143 modified | TOTAL: 419
- pass 1 (-+): 136 found - 136 modified | TOTAL: 555
- pass 2 (-+): 0 found - 136 modified | TOTAL: 555
- Iteration Number : 2
- pass 1 (xy+): 3 found - 3 modified | TOTAL: 3
- pass 2 (xy+): 0 found - 3 modified | TOTAL: 3
- pass 1 (xy-): 3 found - 3 modified | TOTAL: 6
- pass 2 (xy-): 0 found - 3 modified | TOTAL: 6
- pass 1 (yz+): 2 found - 2 modified | TOTAL: 8
- pass 2 (yz+): 0 found - 2 modified | TOTAL: 8
- pass 1 (yz-): 2 found - 2 modified | TOTAL: 10
- pass 2 (yz-): 0 found - 2 modified | TOTAL: 10
- pass 1 (xz+): 4 found - 4 modified | TOTAL: 14
- pass 2 (xz+): 0 found - 4 modified | TOTAL: 14
- pass 1 (xz-): 5 found - 5 modified | TOTAL: 19
- pass 2 (xz-): 0 found - 5 modified | TOTAL: 19
- 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 (++): 2 found - 2 modified | TOTAL: 2
- pass 2 (++): 0 found - 2 modified | TOTAL: 2
- pass 1 (+-): 2 found - 2 modified | TOTAL: 4
- pass 2 (+-): 0 found - 2 modified | TOTAL: 4
- pass 1 (--): 0 found - 0 modified | TOTAL: 4
- pass 1 (-+): 1 found - 1 modified | TOTAL: 5
- pass 2 (-+): 0 found - 1 modified | TOTAL: 5
- Iteration Number : 3
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 1 found - 1 modified | TOTAL: 1
- pass 2 (yz+): 0 found - 1 modified | TOTAL: 1
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 1
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 1
- pass 1 (xz-): 1 found - 1 modified | TOTAL: 2
- pass 2 (xz-): 0 found - 1 modified | TOTAL: 2
- Iteration Number : 3
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 3
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 1 found - 1 modified | TOTAL: 1
- pass 2 (-+): 0 found - 1 modified | TOTAL: 1
- 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 = 714 (out of 465724: 0.153310)
- binarizing input wm segmentation...
- Ambiguous edge configurations...
- mri_pretess done
- #--------------------------------------------
- #@# Fill Thu Aug 8 18:41:48 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri
- mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz
- logging cutting plane coordinates to ../scripts/ponscc.cut.log...
- INFO: Using transforms/talairach.lta and its offset for Talairach volume ...
- using segmentation aseg.auto_noCCseg.mgz...
- reading input volume...done.
- searching for cutting planes...voxel to talairach voxel transform
- 1.109 0.011 -0.027 -15.093;
- -0.002 1.160 0.350 -40.721;
- 0.042 -0.321 0.986 19.390;
- 0.000 0.000 0.000 1.000;
- voxel to talairach voxel transform
- 1.109 0.011 -0.027 -15.093;
- -0.002 1.160 0.350 -40.721;
- 0.042 -0.321 0.986 19.390;
- 0.000 0.000 0.000 1.000;
- reading segmented volume aseg.auto_noCCseg.mgz...
- Looking for area (min, max) = (350, 1400)
- area[0] = 3044 (min = 350, max = 1400), aspect = 1.31 (min = 0.10, max = 0.75)
- need search nearby
- using seed (123, 108, 83), TAL = (5.0, -45.0, 20.0)
- talairach voxel to voxel transform
- 0.901 -0.001 0.025 13.050;
- 0.012 0.785 -0.278 37.530;
- -0.034 0.255 0.922 -8.006;
- 0.000 0.000 0.000 1.000;
- segmentation indicates cc at (123, 108, 83) --> (5.0, -45.0, 20.0)
- done.
- writing output to filled.mgz...
- filling took 1.0 minutes
- talairach cc position changed to (5.00, -45.00, 20.00)
- Erasing brainstem...done.
- seed_search_size = 9, min_neighbors = 5
- search rh wm seed point around talairach space:(23.00, -45.00, 20.00) SRC: (109.57, 100.43, 92.51)
- search lh wm seed point around talairach space (-13.00, -45.00, 20.00), SRC: (142.00, 100.85, 91.27)
- compute mri_fill using aseg
- Erasing Brain Stem and Cerebellum ...
- Define left and right masks using aseg:
- Building Voronoi diagram ...
- Using the Voronoi diagram to separate WM into two hemispheres ...
- Find the largest connected component for each hemisphere ...
- #--------------------------------------------
- #@# Tessellate lh Thu Aug 8 18:42:47 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/scripts
- mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz
- Iteration Number : 1
- 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+): 0 found - 0 modified | TOTAL: 1
- pass 1 (yz-): 1 found - 1 modified | TOTAL: 2
- pass 2 (yz-): 0 found - 1 modified | TOTAL: 2
- pass 1 (xz+): 2 found - 2 modified | TOTAL: 4
- pass 2 (xz+): 0 found - 2 modified | TOTAL: 4
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 4
- Iteration Number : 1
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 2 found - 2 modified | TOTAL: 2
- pass 2 (+++): 0 found - 2 modified | TOTAL: 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 2
- Iteration Number : 1
- 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 : 2
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Total Number of Modified Voxels = 7 (out of 224820: 0.003114)
- 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 50: 2671 vertices, 2841 faces
- slice 60: 10096 vertices, 10433 faces
- slice 70: 20390 vertices, 20764 faces
- slice 80: 31059 vertices, 31419 faces
- slice 90: 41487 vertices, 41828 faces
- slice 100: 51814 vertices, 52182 faces
- slice 110: 62019 vertices, 62329 faces
- slice 120: 71760 vertices, 72146 faces
- slice 130: 81958 vertices, 82311 faces
- slice 140: 91105 vertices, 91430 faces
- slice 150: 99699 vertices, 99978 faces
- slice 160: 107040 vertices, 107294 faces
- slice 170: 112432 vertices, 112630 faces
- slice 180: 116830 vertices, 116996 faces
- slice 190: 119579 vertices, 119655 faces
- slice 200: 119766 vertices, 119790 faces
- slice 210: 119766 vertices, 119790 faces
- slice 220: 119766 vertices, 119790 faces
- slice 230: 119766 vertices, 119790 faces
- slice 240: 119766 vertices, 119790 faces
- slice 250: 119766 vertices, 119790 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...
- 119766 voxel in cpt #1: X=-24 [v=119766,e=359370,f=239580] located at (-26.907269, -19.149984, 31.983994)
- For the whole surface: X=-24 [v=119766,e=359370,f=239580]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Smooth1 lh Thu Aug 8 18:42:56 CEST 2013
- mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/scripts
- setting seed for random number generator to 1234
- smoothing surface tessellation for 10 iterations...
- smoothing complete - recomputing first and second fundamental forms...
- #--------------------------------------------
- #@# Inflation1 lh Thu Aug 8 18:43:00 CEST 2013
- mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/scripts
- avg radius = 45.0 mm, total surface area = 62871 mm^2
- writing inflated surface to ../surf/lh.inflated.nofix
- inflation took 0.5 minutes
- Not saving sulc
-
step 000: RMS=0.099 (target=0.015)
step 005: RMS=0.072 (target=0.015)
step 010: RMS=0.052 (target=0.015)
step 015: RMS=0.043 (target=0.015)
step 020: RMS=0.037 (target=0.015)
step 025: RMS=0.032 (target=0.015)
step 030: RMS=0.028 (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=0.020 (target=0.015)
- inflation complete.
- Not saving sulc
- #--------------------------------------------
- #@# QSphere lh Thu Aug 8 18:43:33 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/scripts
- mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix
- doing quick spherical unfolding.
- setting seed for random number genererator to 1234
- $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading original vertex positions...
- unfolding cortex into spherical form...
- surface projected - minimizing metric distortion...
- vertex spacing 1.05 +- 0.58 (0.00-->7.34) (max @ vno 94484 --> 94485)
- face area 0.03 +- 0.04 (-0.05-->0.73)
- scaling brain by 0.339...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=175.755, avgs=0
- 005/300: dt: 0.9000, rms radial error=175.502, avgs=0
- 010/300: dt: 0.9000, rms radial error=174.958, avgs=0
- 015/300: dt: 0.9000, rms radial error=174.237, avgs=0
- 020/300: dt: 0.9000, rms radial error=173.406, avgs=0
- 025/300: dt: 0.9000, rms radial error=172.522, avgs=0
- 030/300: dt: 0.9000, rms radial error=171.607, avgs=0
- 035/300: dt: 0.9000, rms radial error=170.675, avgs=0
- 040/300: dt: 0.9000, rms radial error=169.735, avgs=0
- 045/300: dt: 0.9000, rms radial error=168.793, avgs=0
- 050/300: dt: 0.9000, rms radial error=167.852, avgs=0
- 055/300: dt: 0.9000, rms radial error=166.913, avgs=0
- 060/300: dt: 0.9000, rms radial error=165.978, avgs=0
- 065/300: dt: 0.9000, rms radial error=165.047, avgs=0
- 070/300: dt: 0.9000, rms radial error=164.120, avgs=0
- 075/300: dt: 0.9000, rms radial error=163.198, avgs=0
- 080/300: dt: 0.9000, rms radial error=162.281, avgs=0
- 085/300: dt: 0.9000, rms radial error=161.368, avgs=0
- 090/300: dt: 0.9000, rms radial error=160.460, avgs=0
- 095/300: dt: 0.9000, rms radial error=159.557, avgs=0
- 100/300: dt: 0.9000, rms radial error=158.659, avgs=0
- 105/300: dt: 0.9000, rms radial error=157.766, avgs=0
- 110/300: dt: 0.9000, rms radial error=156.877, avgs=0
- 115/300: dt: 0.9000, rms radial error=155.993, avgs=0
- 120/300: dt: 0.9000, rms radial error=155.114, avgs=0
- 125/300: dt: 0.9000, rms radial error=154.241, avgs=0
- 130/300: dt: 0.9000, rms radial error=153.372, avgs=0
- 135/300: dt: 0.9000, rms radial error=152.507, avgs=0
- 140/300: dt: 0.9000, rms radial error=151.648, avgs=0
- 145/300: dt: 0.9000, rms radial error=150.794, avgs=0
- 150/300: dt: 0.9000, rms radial error=149.944, avgs=0
- 155/300: dt: 0.9000, rms radial error=149.098, avgs=0
- 160/300: dt: 0.9000, rms radial error=148.258, avgs=0
- 165/300: dt: 0.9000, rms radial error=147.422, avgs=0
- 170/300: dt: 0.9000, rms radial error=146.591, avgs=0
- 175/300: dt: 0.9000, rms radial error=145.765, avgs=0
- 180/300: dt: 0.9000, rms radial error=144.944, avgs=0
- 185/300: dt: 0.9000, rms radial error=144.127, avgs=0
- 190/300: dt: 0.9000, rms radial error=143.314, avgs=0
- 195/300: dt: 0.9000, rms radial error=142.507, avgs=0
- 200/300: dt: 0.9000, rms radial error=141.704, avgs=0
- 205/300: dt: 0.9000, rms radial error=140.905, avgs=0
- 210/300: dt: 0.9000, rms radial error=140.111, avgs=0
- 215/300: dt: 0.9000, rms radial error=139.322, avgs=0
- 220/300: dt: 0.9000, rms radial error=138.536, avgs=0
- 225/300: dt: 0.9000, rms radial error=137.755, avgs=0
- 230/300: dt: 0.9000, rms radial error=136.979, avgs=0
- 235/300: dt: 0.9000, rms radial error=136.207, avgs=0
- 240/300: dt: 0.9000, rms radial error=135.438, avgs=0
- 245/300: dt: 0.9000, rms radial error=134.675, avgs=0
- 250/300: dt: 0.9000, rms radial error=133.915, avgs=0
- 255/300: dt: 0.9000, rms radial error=133.160, avgs=0
- 260/300: dt: 0.9000, rms radial error=132.409, avgs=0
- 265/300: dt: 0.9000, rms radial error=131.662, avgs=0
- 270/300: dt: 0.9000, rms radial error=130.919, avgs=0
- 275/300: dt: 0.9000, rms radial error=130.180, avgs=0
- 280/300: dt: 0.9000, rms radial error=129.446, avgs=0
- 285/300: dt: 0.9000, rms radial error=128.716, avgs=0
- 290/300: dt: 0.9000, rms radial error=127.990, avgs=0
- 295/300: dt: 0.9000, rms radial error=127.268, avgs=0
- 300/300: dt: 0.9000, rms radial error=126.550, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 13580.52
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00020
- epoch 2 (K=40.0), pass 1, starting sse = 2118.17
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00019
- epoch 3 (K=160.0), pass 1, starting sse = 195.47
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.17/13 = 0.01342
- epoch 4 (K=640.0), pass 1, starting sse = 8.11
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.30/25 = 0.01186
- final dwriting spherical brain to ../surf/lh.qsphere.nofix
- spherical transformation took 0.09 hours
- istance error %100000.00
- #--------------------------------------------
- #@# Fix Topology lh Thu Aug 8 18:48:48 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/sub017/scripts
- mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub017 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=-24 (nv=119766, nf=239580, ne=359370, g=13)
- using quasi-homeomorphic spherical map to tessellate cortical surface...
- Correction of the Topology
- Finding true center and radius of Spherical Surface...done
- Surface centered at (0,0,0) with radius 100.0 in 10 iterations
- marking ambiguous vertices...
- 1025 ambiguous faces found in tessellation
- segmenting defects...
- 17 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- -merging segment 6 into 4
- 16 defects to be corrected
- 0 vertices coincident
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/lh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -9.6221 (-4.8111)
- -vertex loglikelihood: -6.6958 (-3.3479)
- -normal dot loglikelihood: -3.6433 (-3.6433)
- -quad curv loglikelihood: -6.5232 (-3.2616)
- Total Loglikelihood : -26.4845
- CORRECTING DEFECT 0 (vertices=24, convex hull=62)
- After retessellation of defect 0, euler #=-14 (119114,356994,237866) : difference with theory (-13) = 1
- CORRECTING DEFECT 1 (vertices=110, convex hull=71)
- After retessellation of defect 1, euler #=-13 (119140,357100,237947) : difference with theory (-12) = 1
- CORRECTING DEFECT 2 (vertices=12, convex hull=14)
- After retessellation of defect 2, euler #=-12 (119140,357101,237949) : difference with theory (-11) = 1
- CORRECTING DEFECT 3 (vertices=18, convex hull=60)
- After retessellation of defect 3, euler #=-11 (119152,357162,237999) : difference with theory (-10) = 1
- CORRECTING DEFECT 4 (vertices=129, convex hull=108)
- After retessellation of defect 4, euler #=-9 (119216,357410,238185) : difference with theory (-9) = 0
- CORRECTING DEFECT 5 (vertices=18, convex hull=38)
- After retessellation of defect 5, euler #=-8 (119225,357450,238217) : difference with theory (-8) = 0
- CORRECTING DEFECT 6 (vertices=29, convex hull=67)
- After retessellation of defect 6, euler #=-7 (119234,357504,238263) : difference with theory (-7) = 0
- CORRECTING DEFECT 7 (vertices=30, convex hull=53)
- After retessellation of defect 7, euler #=-6 (119247,357563,238310) : difference with theory (-6) = 0
- CORRECTING DEFECT 8 (vertices=12, convex hull=26)
- After retessellation of defect 8, euler #=-5 (119251,357581,238325) : difference with theory (-5) = 0
- CORRECTING DEFECT 9 (vertices=78, convex hull=42)
- After retessellation of defect 9, euler #=-4 (119268,357649,238377) : difference with theory (-4) = 0
- CORRECTING DEFECT 10 (vertices=60, convex hull=87)
- After retessellation of defect 10, euler #=-3 (119279,357721,238439) : difference with theory (-3) = 0
- CORRECTING DEFECT 11 (vertices=17, convex hull=48)
- After retessellation of defect 11, euler #=-2 (119290,357770,238478) : difference with theory (-2) = 0
- CORRECTING DEFECT 12 (vertices=49, convex hull=43)
- After retessellation of defect 12, euler #=-1 (119301,357820,238518) : difference with theory (-1) = 0
- CORRECTING DEFECT 13 (vertices=38, convex hull=85)
- After retessellation of defect 13, euler #=0 (119320,357909,238589) : difference with theory (0) = 0
- CORRECTING DEFECT 14 (vertices=11, convex hull=28)
- After retessellation of defect 14, euler #=1 (119321,357922,238602) : difference with theory (1) = 0
- CORRECTING DEFECT 15 (vertices=34, convex hull=78)
- After retessellation of defect 15, euler #=2 (119336,358002,238668) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.88 +- 0.21 (0.07-->5.74) (max @ vno 68220 --> 73280)
- face area 0.00 +- 0.00 (0.00-->0.00)
- performing soap bubble on retessellated vertices for 0 iterations...
- vertex spacing 0.88 +- 0.21 (0.07-->5.74) (max @ vno 68220 --> 73280)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 52 mutations (35.1%), 96 crossovers (64.9%), 43 vertices were eliminated
- building final representation...
- 430 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=119336, nf=238668, ne=358002, g=0)
- writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/lh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 9.3 minutes
- 0 defective edges
- removing intersecting faces
- 000: 112 intersecting
- mris_euler_number ../surf/lh.orig
- euler # = v-e+f = 2g-2: 119336 - 358002 + 238668 = 2 --> 0 holes
- F =2V-4: 238668 = 238672-4 (0)
- 2E=3F: 716004 = 716004 (0)
- total defect index = 0
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/scripts
- mris_remove_intersection ../surf/lh.orig ../surf/lh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 31 intersecting
- writing corrected surface to ../surf/lh.orig
- rm ../surf/lh.inflated
- #--------------------------------------------
- #@# Make White Surf lh Thu Aug 8 18:58:09 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/scripts
- mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub017 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/sub017/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/wm.mgz...
- 15790 bright wm thresholded.
- 318 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/lh.orig...
- computing class statistics...
- border white: 215675 voxels (1.29%)
- border gray 245603 voxels (1.46%)
- WM (92.0): 93.4 +- 10.3 [70.0 --> 110.0]
- GM (75.0) : 73.5 +- 13.0 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 47.0 (was 70)
- setting MAX_BORDER_WHITE to 115.3 (was 105)
- setting MIN_BORDER_WHITE to 60.0 (was 85)
- setting MAX_CSF to 34.0 (was 40)
- setting MAX_GRAY to 94.7 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 53.5 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 21.0 (was 40)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.82 +- 0.22 (0.01-->2.98) (max @ vno 73280 --> 73302)
- face area 0.28 +- 0.12 (0.00-->1.64)
- mean absolute distance = 0.67 +- 0.78
- 3175 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 = 93.3, mean outside = 69.0
- smoothing surface for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- mean border=73.4, 63 (63) missing vertices, mean dist 0.4 [0.5 (%31.8)->0.8 (%68.2))]
- %67 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 0.92 +- 0.26 (0.12-->3.35) (max @ vno 64529 --> 64521)
- face area 0.28 +- 0.13 (0.00-->1.99)
- mean absolute distance = 0.33 +- 0.51
- 2465 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=6320182.0, rms=13.61
- 001: dt: 0.5000, sse=6275324.5, rms=9.776 (0.000%)
- 002: dt: 0.5000, sse=6507068.5, rms=7.558 (0.000%)
- 003: dt: 0.5000, sse=6569456.0, rms=6.130 (0.000%)
- 004: dt: 0.5000, sse=6786154.0, rms=5.295 (0.000%)
- 005: dt: 0.5000, sse=6824300.0, rms=4.836 (0.000%)
- 006: dt: 0.5000, sse=6954359.0, rms=4.607 (0.000%)
- 007: dt: 0.5000, sse=6902208.5, rms=4.478 (0.000%)
- 008: dt: 0.5000, sse=6946429.5, rms=4.404 (0.000%)
- 009: dt: 0.5000, sse=6881908.5, rms=4.347 (0.000%)
- rms = 4.32, time step reduction 1 of 3 to 0.250...
- 010: dt: 0.5000, sse=6908631.0, rms=4.316 (0.000%)
- 011: dt: 0.2500, sse=4313752.5, rms=2.947 (0.000%)
- 012: dt: 0.2500, sse=3944984.2, rms=2.487 (0.000%)
- 013: dt: 0.2500, sse=3722843.0, rms=2.392 (0.000%)
- 014: dt: 0.2500, sse=3654123.0, rms=2.311 (0.000%)
- rms = 2.29, time step reduction 2 of 3 to 0.125...
- 015: dt: 0.2500, sse=3575957.2, rms=2.285 (0.000%)
- 016: dt: 0.1250, sse=3375320.2, rms=2.010 (0.000%)
- rms = 1.98, time step reduction 3 of 3 to 0.062...
- 017: dt: 0.1250, sse=3336865.8, rms=1.976 (0.000%)
- positioning took 1.8 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 4 vertex label from ripped group
- mean border=78.2, 68 (23) missing vertices, mean dist -0.2 [0.4 (%79.2)->0.2 (%20.8))]
- %79 local maxima, %15 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-->3.56) (max @ vno 95784 --> 94861)
- face area 0.35 +- 0.16 (0.00-->2.84)
- mean absolute distance = 0.22 +- 0.32
- 2362 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4300418.0, rms=6.46
- 018: dt: 0.5000, sse=4357745.0, rms=4.392 (0.000%)
- rms = 4.60, time step reduction 1 of 3 to 0.250...
- 019: dt: 0.2500, sse=3958077.5, rms=3.306 (0.000%)
- 020: dt: 0.2500, sse=3773904.2, rms=2.600 (0.000%)
- 021: dt: 0.2500, sse=3704253.2, rms=2.108 (0.000%)
- 022: dt: 0.2500, sse=3672574.5, rms=1.961 (0.000%)
- 023: dt: 0.2500, sse=3623633.0, rms=1.816 (0.000%)
- rms = 1.80, time step reduction 2 of 3 to 0.125...
- 024: dt: 0.2500, sse=3630568.2, rms=1.803 (0.000%)
- 025: dt: 0.1250, sse=3501662.0, rms=1.582 (0.000%)
- rms = 1.56, time step reduction 3 of 3 to 0.062...
- 026: dt: 0.1250, sse=3468197.2, rms=1.562 (0.000%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 2 vertex label from ripped group
- mean border=81.5, 74 (11) missing vertices, mean dist -0.1 [0.2 (%75.6)->0.2 (%24.4))]
- %87 local maxima, % 7 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 (0.06-->3.71) (max @ vno 73067 --> 73072)
- face area 0.34 +- 0.16 (0.00-->2.90)
- mean absolute distance = 0.17 +- 0.26
- 2273 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=3777065.5, rms=4.14
- 027: dt: 0.5000, sse=4094618.0, rms=4.057 (0.000%)
- rms = 4.28, time step reduction 1 of 3 to 0.250...
- 028: dt: 0.2500, sse=3702728.0, rms=2.554 (0.000%)
- 029: dt: 0.2500, sse=3597801.8, rms=2.035 (0.000%)
- 030: dt: 0.2500, sse=3661721.0, rms=1.703 (0.000%)
- rms = 1.75, time step reduction 2 of 3 to 0.125...
- 031: dt: 0.1250, sse=3605576.5, rms=1.570 (0.000%)
- 032: dt: 0.1250, sse=3526393.8, rms=1.385 (0.000%)
- rms = 1.36, time step reduction 3 of 3 to 0.062...
- 033: dt: 0.1250, sse=3493777.5, rms=1.364 (0.000%)
- positioning took 0.9 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 2 vertex label from ripped group
- mean border=82.6, 76 (7) missing vertices, mean dist -0.0 [0.2 (%58.6)->0.2 (%41.4))]
- %89 local maxima, % 5 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/sub017/surf/lh.white...
- writing smoothed curvature to lh.curv
- 000: dt: 0.0000, sse=3520009.0, rms=1.84
- rms = 2.77, time step reduction 1 of 3 to 0.250...
- 034: dt: 0.2500, sse=3582631.0, rms=1.191 (0.000%)
- 035: dt: 0.2500, sse=3699686.0, rms=1.033 (0.000%)
- rms = 1.03, time step reduction 2 of 3 to 0.125...
- 036: dt: 0.2500, sse=3754240.0, rms=1.033 (0.000%)
- rms = 1.01, time step reduction 3 of 3 to 0.062...
- 037: dt: 0.1250, sse=3779300.8, rms=1.012 (0.000%)
- positioning took 0.5 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- generating cortex label...
- 10 non-cortical segments detected
- only using segment with 1947 vertices
- erasing segment 1 (vno[0] = 50129)
- erasing segment 2 (vno[0] = 78295)
- erasing segment 3 (vno[0] = 83914)
- erasing segment 4 (vno[0] = 86726)
- erasing segment 5 (vno[0] = 87624)
- erasing segment 6 (vno[0] = 88582)
- erasing segment 7 (vno[0] = 90298)
- erasing segment 8 (vno[0] = 96547)
- erasing segment 9 (vno[0] = 97375)
- writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/label/lh.cortex.label...
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/lh.curv
- writing smoothed area to lh.area
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/lh.area
- vertex spacing 0.89 +- 0.25 (0.07-->3.67) (max @ vno 94861 --> 95784)
- face area 0.33 +- 0.16 (0.00-->2.74)
- refinement took 6.2 minutes
- #--------------------------------------------
- #@# Smooth2 lh Thu Aug 8 19:04:23 CEST 2013
- mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 19:04:27 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/scripts
- mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated
- avg radius = 45.2 mm, total surface area = 72127 mm^2
- writing inflated surface to ../surf/lh.inflated
- writing sulcal depths to ../surf/lh.sulc
-
step 000: RMS=0.115 (target=0.015)
step 005: RMS=0.078 (target=0.015)
step 010: RMS=0.057 (target=0.015)
step 015: RMS=0.046 (target=0.015)
step 020: RMS=0.039 (target=0.015)
step 025: RMS=0.032 (target=0.015)
step 030: RMS=0.027 (target=0.015)
step 035: RMS=0.023 (target=0.015)
step 040: RMS=0.020 (target=0.015)
step 045: RMS=0.018 (target=0.015)
step 050: RMS=0.017 (target=0.015)
step 055: RMS=0.016 (target=0.015)
- inflation complete.
- inflation took 0.5 minutes
- mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated
- normalizing curvature values.
- averaging curvature patterns 5 times.
- sampling 10 neighbors out to a distance of 10 mm
- 133 vertices thresholded to be in k1 ~ [-0.83 0.39], k2 ~ [-0.27 0.17]
- total integrated curvature = 0.603*4pi (7.572) --> 0 handles
- ICI = 1.4, FI = 7.9, variation=139.325
- 111 vertices thresholded to be in [-0.07 0.02]
- writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level
- curvature mean = 0.000, std = 0.002
- 89 vertices thresholded to be in [-0.25 0.13]
- done.
- writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.018, std = 0.022
- done.
- #-----------------------------------------
- #@# Curvature Stats lh Thu Aug 8 19:06:29 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub017 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 [ sub017/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 [ 243 ]
- Gb_filter = 0
- WARN: S lookup min: -0.093160
- WARN: S explicit min: 0.000000 vertex = 28
- #--------------------------------------------
- #@# Sphere lh Thu Aug 8 19:06:34 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 0.316...
- 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 %40.81
- pass 1: epoch 2 of 3 starting distance error %18.75
- unfolding complete - removing small folds...
- starting distance error %18.67
- removing remaining folds...
- final distance error %18.69
- MRISunfold() return, current seed 1234
- writing spherical brain to ../surf/lh.sphere
- spherical transformation took 0.55 hours
- #--------------------------------------------
- #@# Surf Reg lh Thu Aug 8 19:39:23 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 = 0.580
- curvature mean = 0.030, std = 0.931
- curvature mean = 0.023, std = 0.866
- Starting MRISrigidBodyAlignGlobal()
- d=64.00 min @ (0.00, -16.00, 0.00) sse = 289234.1, tmin=0.9976
- d=32.00 min @ (0.00, 8.00, -8.00) sse = 215633.0, tmin=2.0034
- d=8.00 min @ (2.00, 0.00, 2.00) sse = 211183.2, tmin=3.9907
- d=4.00 min @ (-1.00, -1.00, -1.00) sse = 209434.7, tmin=4.9846
- d=2.00 min @ (0.50, 0.00, 0.00) sse = 209226.5, tmin=6.0188
- d=1.00 min @ (0.00, 0.25, 0.00) sse = 209217.8, tmin=7.0405
- d=0.50 min @ (0.00, -0.12, -0.12) sse = 209186.2, tmin=8.1162
- tol=1.0e+00, sigma=0.5, host=snake, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
- using quadratic fit line minimization
- MRISrigidBodyAlignGlobal() done 8.12 min
- curvature mean = 0.006, std = 0.962
- curvature mean = 0.010, std = 0.942
- curvature mean = 0.004, std = 0.975
- curvature mean = 0.005, std = 0.974
- curvature mean = 0.002, std = 0.978
- curvature mean = 0.001, std = 0.989
- 2 Reading smoothwm
- curvature mean = -0.026, std = 0.288
- curvature mean = 0.003, std = 0.068
- curvature mean = 0.072, std = 0.362
- curvature mean = 0.003, std = 0.080
- curvature mean = 0.029, std = 0.568
- curvature mean = 0.003, std = 0.086
- curvature mean = 0.016, std = 0.707
- curvature mean = 0.004, std = 0.088
- curvature mean = 0.006, std = 0.812
- MRISregister() return, current seed 0
- writing registered surface to ../surf/lh.sphere.reg...
- expanding nbhd size to 1
- #--------------------------------------------
- #@# Jacobian white lh Thu Aug 8 20:03:59 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 20:04:01 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 20:04:03 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub017 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...
- 1105 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2751 changed, 119336 examined...
- 001: 645 changed, 11866 examined...
- 002: 145 changed, 3545 examined...
- 003: 49 changed, 850 examined...
- 004: 10 changed, 300 examined...
- 005: 7 changed, 67 examined...
- 006: 2 changed, 45 examined...
- 007: 2 changed, 12 examined...
- 008: 2 changed, 10 examined...
- 009: 1 changed, 10 examined...
- 010: 0 changed, 7 examined...
- 207 labels changed using aseg
- 000: 107 total segments, 61 labels (270 vertices) changed
- 001: 47 total segments, 7 labels (21 vertices) changed
- 002: 40 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 41 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 1317 vertices marked for relabeling...
- 1317 labels changed in reclassification.
- writing output to ../label/lh.aparc.annot...
- classification took 0 minutes and 55 seconds.
- #--------------------------------------------
- #@# Make Pial Surf lh Thu Aug 8 20:04:58 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/scripts
- mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub017 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/sub017/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/wm.mgz...
- 15790 bright wm thresholded.
- 318 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/lh.orig...
- computing class statistics...
- border white: 215675 voxels (1.29%)
- border gray 245603 voxels (1.46%)
- WM (92.0): 93.4 +- 10.3 [70.0 --> 110.0]
- GM (75.0) : 73.5 +- 13.0 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 47.0 (was 70)
- setting MAX_BORDER_WHITE to 115.3 (was 105)
- setting MIN_BORDER_WHITE to 60.0 (was 85)
- setting MAX_CSF to 34.0 (was 40)
- setting MAX_GRAY to 94.7 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 53.5 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 21.0 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=105, GM=60
- mean inside = 93.3, mean outside = 69.0
- smoothing surface for 5 iterations...
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.82 +- 0.22 (0.01-->2.98) (max @ vno 73280 --> 73302)
- face area 0.28 +- 0.12 (0.00-->1.64)
- mean absolute distance = 0.67 +- 0.79
- 3223 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 1 with 572 points - only 0.00% unknown
- deleting segment 2 with 8 points - only 0.00% unknown
- deleting segment 4 with 7 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 6 with 20 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 7 with 2 points - only 0.00% unknown
- deleting segment 8 with 7 points - only 0.00% unknown
- deleting segment 9 with 7 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 10 with 2 points - only 0.00% unknown
- deleting segment 11 with 6 points - only 0.00% unknown
- mean border=73.3, 63 (63) missing vertices, mean dist 0.4 [0.5 (%31.8)->0.7 (%68.2))]
- %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 0.92 +- 0.26 (0.12-->3.35) (max @ vno 64529 --> 64521)
- face area 0.28 +- 0.13 (0.00-->1.99)
- mean absolute distance = 0.33 +- 0.51
- 2853 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=6338174.0, rms=13.59
- 001: dt: 0.5000, sse=6302630.0, rms=9.762 (0.000%)
- 002: dt: 0.5000, sse=6534926.0, rms=7.547 (0.000%)
- 003: dt: 0.5000, sse=6601434.5, rms=6.121 (0.000%)
- 004: dt: 0.5000, sse=6817251.0, rms=5.288 (0.000%)
- 005: dt: 0.5000, sse=6861866.0, rms=4.830 (0.000%)
- 006: dt: 0.5000, sse=6988628.0, rms=4.601 (0.000%)
- 007: dt: 0.5000, sse=6942937.5, rms=4.472 (0.000%)
- 008: dt: 0.5000, sse=6981966.5, rms=4.399 (0.000%)
- 009: dt: 0.5000, sse=6921806.5, rms=4.342 (0.000%)
- rms = 4.31, time step reduction 1 of 3 to 0.250...
- 010: dt: 0.5000, sse=6946981.0, rms=4.312 (0.000%)
- 011: dt: 0.2500, sse=4339017.5, rms=2.943 (0.000%)
- 012: dt: 0.2500, sse=3966491.8, rms=2.485 (0.000%)
- 013: dt: 0.2500, sse=3744591.0, rms=2.389 (0.000%)
- 014: dt: 0.2500, sse=3674467.2, rms=2.309 (0.000%)
- rms = 2.28, time step reduction 2 of 3 to 0.125...
- 015: dt: 0.2500, sse=3597409.2, rms=2.284 (0.000%)
- 016: dt: 0.1250, sse=3396452.0, rms=2.010 (0.000%)
- rms = 1.98, time step reduction 3 of 3 to 0.062...
- 017: dt: 0.1250, sse=3357792.0, rms=1.976 (0.000%)
- positioning took 1.8 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- deleting segment 3 with 2 points - only 0.00% unknown
- deleting segment 4 with 482 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 5 with 3 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 8 with 10 points - only 0.00% unknown
- deleting segment 9 with 7 points - only 0.00% unknown
- deleting segment 10 with 8 points - only 0.00% unknown
- deleting segment 11 with 9 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 12 with 4 points - only 0.00% unknown
- deleting segment 13 with 6 points - only 0.00% unknown
- mean border=78.2, 68 (23) missing vertices, mean dist -0.2 [0.4 (%79.2)->0.2 (%20.8))]
- %80 local maxima, %15 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 (0.12-->3.56) (max @ vno 95784 --> 94861)
- face area 0.35 +- 0.16 (0.00-->2.76)
- mean absolute distance = 0.22 +- 0.32
- 2358 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4324233.0, rms=6.45
- 018: dt: 0.5000, sse=4386262.5, rms=4.384 (0.000%)
- rms = 4.59, time step reduction 1 of 3 to 0.250...
- 019: dt: 0.2500, sse=3984624.8, rms=3.300 (0.000%)
- 020: dt: 0.2500, sse=3797671.5, rms=2.594 (0.000%)
- 021: dt: 0.2500, sse=3727418.0, rms=2.105 (0.000%)
- 022: dt: 0.2500, sse=3696714.0, rms=1.958 (0.000%)
- 023: dt: 0.2500, sse=3647330.8, rms=1.815 (0.000%)
- rms = 1.80, time step reduction 2 of 3 to 0.125...
- 024: dt: 0.2500, sse=3655530.8, rms=1.804 (0.000%)
- 025: dt: 0.1250, sse=3525477.2, rms=1.583 (0.000%)
- rms = 1.56, time step reduction 3 of 3 to 0.062...
- 026: dt: 0.1250, sse=3492127.2, rms=1.563 (0.000%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 1 with 490 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 7 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 5 with 13 points - only 0.00% unknown
- deleting segment 6 with 11 points - only 0.00% unknown
- deleting segment 7 with 7 points - only 0.00% unknown
- deleting segment 8 with 8 points - only 0.00% unknown
- deleting segment 9 with 9 points - only 0.00% unknown
- deleting segment 10 with 5 points - only 0.00% unknown
- deleting segment 11 with 6 points - only 0.00% unknown
- mean border=81.4, 74 (11) missing vertices, mean dist -0.1 [0.2 (%75.5)->0.2 (%24.5))]
- %87 local maxima, % 7 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 (0.06-->3.61) (max @ vno 95784 --> 94861)
- face area 0.34 +- 0.16 (0.00-->2.80)
- mean absolute distance = 0.17 +- 0.26
- 2275 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=3801815.2, rms=4.13
- 027: dt: 0.5000, sse=4122375.0, rms=4.053 (0.000%)
- rms = 4.28, time step reduction 1 of 3 to 0.250...
- 028: dt: 0.2500, sse=3729413.8, rms=2.552 (0.000%)
- 029: dt: 0.2500, sse=3623484.2, rms=2.035 (0.000%)
- 030: dt: 0.2500, sse=3687104.2, rms=1.702 (0.000%)
- rms = 1.75, time step reduction 2 of 3 to 0.125...
- 031: dt: 0.1250, sse=3630988.2, rms=1.570 (0.000%)
- 032: dt: 0.1250, sse=3551265.5, rms=1.386 (0.000%)
- rms = 1.37, time step reduction 3 of 3 to 0.062...
- 033: dt: 0.1250, sse=3518794.0, rms=1.365 (0.000%)
- positioning took 0.9 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 521 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 1 with 2 points - only 0.00% unknown
- deleting segment 2 with 7 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 4 with 13 points - only 0.00% unknown
- deleting segment 5 with 11 points - only 0.00% unknown
- deleting segment 6 with 9 points - only 0.00% unknown
- deleting segment 7 with 8 points - only 0.00% unknown
- deleting segment 8 with 6 points - only 0.00% unknown
- deleting segment 9 with 5 points - only 0.00% unknown
- deleting segment 10 with 7 points - only 0.00% unknown
- mean border=82.5, 76 (7) missing vertices, mean dist -0.0 [0.2 (%58.5)->0.2 (%41.5))]
- %90 local maxima, % 5 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=3544703.0, rms=1.84
- rms = 2.77, time step reduction 1 of 3 to 0.250...
- 034: dt: 0.2500, sse=3609648.8, rms=1.188 (0.000%)
- 035: dt: 0.2500, sse=3729493.2, rms=1.034 (0.000%)
- rms = 1.03, time step reduction 2 of 3 to 0.125...
- 036: dt: 0.2500, sse=3784473.0, rms=1.034 (0.000%)
- rms = 1.01, time step reduction 3 of 3 to 0.062...
- 037: dt: 0.1250, sse=3810771.5, rms=1.013 (0.000%)
- positioning took 0.5 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- smoothing surface for 5 iterations...
- mean border=49.4, 63 (63) missing vertices, mean dist 1.8 [0.1 (%0.0)->2.3 (%100.0))]
- %20 local maxima, %53 large gradients and %22 min vals, 1371 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=26432396.0, rms=32.60
- 001: dt: 0.5000, sse=19021812.0, rms=27.117 (0.000%)
- 002: dt: 0.5000, sse=13843794.0, rms=22.523 (0.000%)
- 003: dt: 0.5000, sse=10412680.0, rms=18.780 (0.000%)
- 004: dt: 0.5000, sse=8305641.5, rms=15.794 (0.000%)
- 005: dt: 0.5000, sse=7092010.0, rms=13.482 (0.000%)
- 006: dt: 0.5000, sse=6341183.0, rms=11.677 (0.000%)
- 007: dt: 0.5000, sse=5865799.0, rms=10.161 (0.000%)
- 008: dt: 0.5000, sse=5601116.0, rms=8.813 (0.000%)
- 009: dt: 0.5000, sse=5421429.5, rms=7.640 (0.000%)
- 010: dt: 0.5000, sse=5407250.0, rms=6.606 (0.000%)
- 011: dt: 0.5000, sse=5427131.0, rms=5.761 (0.000%)
- 012: dt: 0.5000, sse=5524452.0, rms=5.113 (0.000%)
- 013: dt: 0.5000, sse=5651371.0, rms=4.721 (0.000%)
- 014: dt: 0.5000, sse=5744738.5, rms=4.454 (0.000%)
- 015: dt: 0.5000, sse=5818331.0, rms=4.246 (0.000%)
- 016: dt: 0.5000, sse=5835450.5, rms=4.076 (0.000%)
- 017: dt: 0.5000, sse=5871650.0, rms=3.981 (0.000%)
- 018: dt: 0.5000, sse=5895409.5, rms=3.903 (0.000%)
- rms = 3.87, time step reduction 1 of 3 to 0.250...
- 019: dt: 0.5000, sse=5892195.5, rms=3.868 (0.000%)
- 020: dt: 0.2500, sse=4066720.8, rms=3.051 (0.000%)
- 021: dt: 0.2500, sse=3887526.0, rms=2.826 (0.000%)
- rms = 2.79, time step reduction 2 of 3 to 0.125...
- 022: dt: 0.2500, sse=3780223.0, rms=2.785 (0.000%)
- 023: dt: 0.1250, sse=3610056.5, rms=2.648 (0.000%)
- rms = 2.63, time step reduction 3 of 3 to 0.062...
- 024: dt: 0.1250, sse=3589597.2, rms=2.633 (0.000%)
- positioning took 2.5 minutes
- mean border=46.5, 710 (3) missing vertices, mean dist 0.2 [0.2 (%44.3)->0.6 (%55.7))]
- %38 local maxima, %40 large gradients and %16 min vals, 403 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=4280308.0, rms=5.34
- 025: dt: 0.5000, sse=4457945.0, rms=4.232 (0.000%)
- 026: dt: 0.5000, sse=5593645.5, rms=4.083 (0.000%)
- rms = 4.07, time step reduction 1 of 3 to 0.250...
- 027: dt: 0.5000, sse=5583298.5, rms=4.068 (0.000%)
- 028: dt: 0.2500, sse=4384364.0, rms=3.040 (0.000%)
- 029: dt: 0.2500, sse=4280034.5, rms=2.720 (0.000%)
- rms = 2.68, time step reduction 2 of 3 to 0.125...
- 030: dt: 0.2500, sse=4167959.8, rms=2.682 (0.000%)
- 031: dt: 0.1250, sse=3991309.8, rms=2.491 (0.000%)
- rms = 2.46, time step reduction 3 of 3 to 0.062...
- 032: dt: 0.1250, sse=3971281.0, rms=2.463 (0.000%)
- positioning took 0.9 minutes
- mean border=44.3, 780 (3) missing vertices, mean dist 0.1 [0.2 (%38.5)->0.4 (%61.5))]
- %56 local maxima, %22 large gradients and %16 min vals, 524 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=4195089.0, rms=3.85
- 033: dt: 0.5000, sse=4406748.0, rms=3.759 (0.000%)
- rms = 3.95, time step reduction 1 of 3 to 0.250...
- 034: dt: 0.2500, sse=4101359.8, rms=2.936 (0.000%)
- 035: dt: 0.2500, sse=4210353.5, rms=2.571 (0.000%)
- 036: dt: 0.2500, sse=4181279.5, rms=2.502 (0.000%)
- rms = 2.47, time step reduction 2 of 3 to 0.125...
- 037: dt: 0.2500, sse=4203573.5, rms=2.472 (0.000%)
- 038: dt: 0.1250, sse=4047600.8, rms=2.308 (0.000%)
- rms = 2.29, time step reduction 3 of 3 to 0.062...
- 039: dt: 0.1250, sse=4037600.5, rms=2.286 (0.000%)
- positioning took 0.8 minutes
- mean border=43.3, 1508 (2) missing vertices, mean dist 0.0 [0.2 (%46.9)->0.3 (%53.1))]
- %59 local maxima, %18 large gradients and %16 min vals, 401 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/sub017/surf/lh.pial...
- writing smoothed curvature to lh.curv.pial
- 000: dt: 0.0000, sse=4074773.5, rms=2.64
- rms = 3.27, time step reduction 1 of 3 to 0.250...
- 040: dt: 0.2500, sse=3987202.2, rms=2.362 (0.000%)
- 041: dt: 0.2500, sse=4104145.8, rms=2.280 (0.000%)
- rms = 2.26, time step reduction 2 of 3 to 0.125...
- 042: dt: 0.2500, sse=4151474.0, rms=2.264 (0.000%)
- 043: dt: 0.1250, sse=4076444.2, rms=2.160 (0.000%)
- rms = 2.15, time step reduction 3 of 3 to 0.062...
- 044: dt: 0.1250, sse=4080378.2, rms=2.147 (0.000%)
- positioning took 0.6 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/lh.curv.pial
- writing smoothed area to lh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/lh.area.pial
- vertex spacing 1.01 +- 0.41 (0.08-->7.27) (max @ vno 88716 --> 88699)
- face area 0.41 +- 0.29 (0.00-->6.57)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 119336 vertices processed
- 25000 of 119336 vertices processed
- 50000 of 119336 vertices processed
- 75000 of 119336 vertices processed
- 100000 of 119336 vertices processed
- 0 of 119336 vertices processed
- 25000 of 119336 vertices processed
- 50000 of 119336 vertices processed
- 75000 of 119336 vertices processed
- 100000 of 119336 vertices processed
- thickness calculation complete, 374:681 truncations.
- 24873 vertices at 0 distance
- 78364 vertices at 1 distance
- 77138 vertices at 2 distance
- 32934 vertices at 3 distance
- 9519 vertices at 4 distance
- 2660 vertices at 5 distance
- 904 vertices at 6 distance
- 339 vertices at 7 distance
- 112 vertices at 8 distance
- 65 vertices at 9 distance
- 38 vertices at 10 distance
- 22 vertices at 11 distance
- 9 vertices at 12 distance
- 10 vertices at 13 distance
- 4 vertices at 14 distance
- 4 vertices at 15 distance
- 5 vertices at 16 distance
- 2 vertices at 17 distance
- 1 vertices at 18 distance
- 2 vertices at 19 distance
- 3 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/lh.thickness
- positioning took 12.3 minutes
- #--------------------------------------------
- #@# Surf Volume lh Thu Aug 8 20:17:16 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 20:17:16 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/scripts
- pctsurfcon --s sub017 --lh-only
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/scripts/pctsurfcon.log
- Thu Aug 8 20:17:16 CEST 2013
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/scripts
- /opt/freesurfer/5.3.0/bin/pctsurfcon
- $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $
- Linux snake5 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
- FREESURFER_HOME /opt/freesurfer/5.3.0
- mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/tmp.pctsurfcon.3065/lh.wm.mgh --regheader sub017 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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/sub017/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/label/lh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 = 91531
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/label/lh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/tmp.pctsurfcon.3065/lh.wm.mgh
- Dim: 119336 1 1
- mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/tmp.pctsurfcon.3065/lh.gm.mgh --projfrac 0.3 --regheader sub017 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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/sub017/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/label/lh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/lh.white
- Done reading source surface
- Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 = 106126
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/label/lh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/tmp.pctsurfcon.3065/lh.gm.mgh
- Dim: 119336 1 1
- mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/tmp.pctsurfcon.3065/lh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/tmp.pctsurfcon.3065/lh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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/sub017/surf/lh.w-g.pct.mgh
- mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/lh.w-g.pct.mgh --annot sub017 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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/sub017/surf/lh.w-g.pct.mgh --annot sub017 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/stats/lh.w-g.pct.stats --snr
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- UseRobust 0
- Constructing seg from annotation
- Reading annotation
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
- Seg base 1000
- Loading /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/lh.w-g.pct.mgh
- Vertex Area is 0.659146 mm^3
- Generating list of segmentation ids
- Found 36 segmentations
- Computing statistics for each segmentation
- 0 1000 unknown 0 0.000
- 1 1001 bankssts 1211 858.092
- 2 1002 caudalanteriorcingulate 738 505.626
- 3 1003 caudalmiddlefrontal 2535 1678.862
- 4 1004 corpuscallosum 0 0.000
- 5 1005 cuneus 2185 1374.593
- 6 1006 entorhinal 759 510.086
- 7 1007 fusiform 3590 2391.461
- 8 1008 inferiorparietal 5560 3758.255
- 9 1009 inferiortemporal 4256 2814.966
- 10 1010 isthmuscingulate 1328 841.677
- 11 1011 lateraloccipital 6508 4174.945
- 12 1012 lateralorbitofrontal 3493 2292.059
- 13 1013 lingual 3478 2285.774
- 14 1014 medialorbitofrontal 2381 1538.295
- 15 1015 middletemporal 4063 2739.810
- 16 1016 parahippocampal 1043 668.826
- 17 1017 paracentral 1673 1080.053
- 18 1018 parsopercularis 2361 1576.593
- 19 1019 parsorbitalis 819 552.650
- 20 1020 parstriangularis 1572 1044.700
- 21 1021 pericalcarine 1791 1197.410
- 22 1022 postcentral 5921 3784.758
- 23 1023 posteriorcingulate 1641 1095.566
- 24 1024 precentral 6547 4248.576
- 25 1025 precuneus 4468 3019.229
- 26 1026 rostralanteriorcingulate 759 512.815
- 27 1027 rostralmiddlefrontal 7547 5114.418
- 28 1028 superiorfrontal 9020 6017.236
- 29 1029 superiorparietal 8655 5657.071
- 30 1030 superiortemporal 5596 3780.891
- 31 1031 supramarginal 5691 3814.875
- 32 1032 frontalpole 266 177.259
- 33 1033 temporalpole 661 446.565
- 34 1034 transversetemporal 621 377.095
- 35 1035 insula 2650 1749.433
- Reporting on 34 segmentations
- mri_segstats done
- Cleaning up
- #-----------------------------------------
- #@# Parcellation Stats lh Thu Aug 8 20:17:30 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 sub017 lh white
- computing statistics for each annotation in ../label/lh.aparc.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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
- 1211 858 2030 2.435 0.429 0.128 0.033 13 1.7 bankssts
- 738 506 1453 2.526 0.678 0.157 0.036 14 1.1 caudalanteriorcingulate
- 2535 1679 4800 2.669 0.460 0.131 0.036 29 3.8 caudalmiddlefrontal
- 2185 1375 3293 2.049 0.514 0.172 0.090 96 7.2 cuneus
- 759 510 2482 3.504 0.916 0.148 0.069 12 2.0 entorhinal
- 3590 2391 7651 2.829 0.596 0.144 0.049 59 7.1 fusiform
- 5560 3758 10788 2.576 0.538 0.147 0.051 101 11.1 inferiorparietal
- 4256 2815 9738 2.868 0.722 0.151 0.067 92 10.9 inferiortemporal
- 1328 842 2017 2.240 0.757 0.159 0.319 221 5.7 isthmuscingulate
- 6508 4175 9794 2.155 0.413 0.151 0.056 146 13.7 lateraloccipital
- 3493 2292 6975 2.598 0.620 0.159 0.078 83 11.3 lateralorbitofrontal
- 3478 2286 5635 2.209 0.525 0.161 0.084 125 10.5 lingual
- 2381 1538 4171 2.337 0.849 0.173 0.100 77 9.1 medialorbitofrontal
- 4063 2740 9556 2.926 0.620 0.160 0.068 94 9.5 middletemporal
- 1043 669 2427 3.146 0.899 0.129 0.055 14 1.9 parahippocampal
- 1673 1080 2816 2.327 0.555 0.123 0.041 18 3.0 paracentral
- 2361 1577 4679 2.592 0.392 0.126 0.035 30 3.3 parsopercularis
- 819 553 1815 2.603 0.653 0.167 0.065 23 2.3 parsorbitalis
- 1572 1045 2826 2.416 0.468 0.135 0.042 25 2.7 parstriangularis
- 1791 1197 2115 1.827 0.458 0.135 0.049 23 3.4 pericalcarine
- 5921 3785 9276 2.142 0.645 0.139 0.046 91 11.6 postcentral
- 1641 1096 2937 2.389 0.747 0.152 0.090 72 5.5 posteriorcingulate
- 6547 4249 12214 2.576 0.555 0.122 0.040 91 10.5 precentral
- 4468 3019 8133 2.391 0.558 0.141 0.049 75 9.5 precuneus
- 759 513 1801 2.830 0.609 0.170 0.067 17 2.2 rostralanteriorcingulate
- 7547 5114 13300 2.201 0.555 0.162 0.067 182 20.1 rostralmiddlefrontal
- 9020 6017 19075 2.734 0.509 0.133 0.041 121 15.0 superiorfrontal
- 8655 5657 13594 2.214 0.490 0.137 0.043 130 14.9 superiorparietal
- 5596 3781 12836 2.922 0.598 0.136 0.043 80 9.9 superiortemporal
- 5691 3815 11193 2.636 0.540 0.153 0.058 107 11.9 supramarginal
- 266 177 594 2.475 0.419 0.187 0.064 9 0.8 frontalpole
- 661 447 2666 3.950 0.607 0.148 0.072 37 2.4 temporalpole
- 621 377 1055 2.432 0.349 0.132 0.040 11 1.2 transversetemporal
- 2650 1749 5545 3.052 0.758 0.151 3.080 398 641.2 insula
- #-----------------------------------------
- #@# Cortical Parc 2 lh Thu Aug 8 20:17:47 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub017 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...
- 40 labels changed using aseg
- relabeling using gibbs priors...
- 000: 8335 changed, 119336 examined...
- 001: 2056 changed, 32187 examined...
- 002: 621 changed, 10593 examined...
- 003: 240 changed, 3517 examined...
- 004: 115 changed, 1344 examined...
- 005: 73 changed, 648 examined...
- 006: 41 changed, 382 examined...
- 007: 25 changed, 248 examined...
- 008: 13 changed, 139 examined...
- 009: 6 changed, 77 examined...
- 010: 5 changed, 33 examined...
- 011: 2 changed, 21 examined...
- 012: 0 changed, 10 examined...
- 15 labels changed using aseg
- 000: 279 total segments, 196 labels (1974 vertices) changed
- 001: 96 total segments, 15 labels (396 vertices) changed
- 002: 80 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 107 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 617 vertices marked for relabeling...
- 617 labels changed in reclassification.
- writing output to ../label/lh.aparc.a2009s.annot...
- classification took 1 minutes and 3 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 2 lh Thu Aug 8 20:18:50 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 sub017 lh white
- computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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
- 1220 801 1817 1.936 0.606 0.158 0.070 29 3.0 G_and_S_frontomargin
- 1240 825 2114 2.283 0.458 0.146 0.045 21 2.3 G_and_S_occipital_inf
- 1310 792 2373 2.308 0.631 0.126 0.046 19 2.5 G_and_S_paracentral
- 1340 893 2743 2.723 0.482 0.169 0.056 27 2.9 G_and_S_subcentral
- 887 606 1897 2.414 0.564 0.210 0.101 35 3.7 G_and_S_transv_frontopol
- 1726 1185 3428 2.569 0.679 0.140 0.053 25 3.7 G_and_S_cingul-Ant
- 1032 718 1992 2.690 0.508 0.133 0.037 11 1.5 G_and_S_cingul-Mid-Ant
- 1194 824 2113 2.385 0.541 0.135 0.042 17 1.9 G_and_S_cingul-Mid-Post
- 429 284 1028 2.754 0.643 0.184 0.092 13 1.2 G_cingul-Post-dorsal
- 250 144 377 2.239 0.756 0.144 0.059 5 0.6 G_cingul-Post-ventral
- 2063 1259 3036 1.971 0.564 0.179 0.102 98 7.7 G_cuneus
- 1373 921 3418 2.766 0.397 0.153 0.046 26 2.7 G_front_inf-Opercular
- 287 189 791 2.858 0.434 0.181 0.076 10 1.0 G_front_inf-Orbital
- 992 640 2129 2.594 0.398 0.145 0.052 23 2.2 G_front_inf-Triangul
- 2870 1928 6475 2.575 0.550 0.162 0.061 65 7.3 G_front_middle
- 6377 4219 14717 2.813 0.496 0.140 0.045 98 11.6 G_front_sup
- 422 279 1001 3.058 0.739 0.251 18.958 356 635.4 G_Ins_lg_and_S_cent_ins
- 563 375 1866 3.646 0.817 0.187 0.139 27 2.7 G_insular_short
- 2157 1380 4576 2.562 0.422 0.168 0.081 93 5.8 G_occipital_middle
- 1522 970 2371 2.094 0.484 0.157 0.052 27 3.1 G_occipital_sup
- 1172 750 2892 2.887 0.571 0.174 0.073 31 3.3 G_oc-temp_lat-fusifor
- 2122 1355 3732 2.271 0.543 0.185 0.112 90 7.8 G_oc-temp_med-Lingual
- 1568 1018 4489 3.348 0.926 0.142 0.067 27 3.8 G_oc-temp_med-Parahip
- 2273 1484 5389 2.757 0.629 0.175 0.097 73 9.1 G_orbital
- 1752 1162 4050 2.681 0.623 0.156 0.056 39 4.0 G_pariet_inf-Angular
- 2945 1995 6978 2.874 0.474 0.170 0.062 70 6.9 G_pariet_inf-Supramar
- 3385 2190 6100 2.303 0.501 0.141 0.047 60 6.2 G_parietal_sup
- 2341 1472 4062 2.206 0.554 0.153 0.058 46 5.9 G_postcentral
- 2640 1622 6017 2.847 0.459 0.129 0.053 58 5.3 G_precentral
- 2487 1656 5478 2.543 0.518 0.160 0.063 60 7.1 G_precuneus
- 893 544 1892 2.472 0.620 0.208 0.118 40 4.3 G_rectus
- 243 149 453 2.957 0.801 0.131 0.058 6 0.6 G_subcallosal
- 450 260 884 2.561 0.253 0.137 0.051 11 1.0 G_temp_sup-G_T_transv
- 2154 1406 6363 3.263 0.510 0.167 0.061 49 5.3 G_temp_sup-Lateral
- 542 385 1419 3.241 0.592 0.110 0.043 4 0.7 G_temp_sup-Plan_polar
- 1027 690 1908 2.428 0.436 0.120 0.042 14 1.9 G_temp_sup-Plan_tempo
- 2220 1469 6197 3.073 0.725 0.170 0.087 64 7.1 G_temporal_inf
- 2440 1649 6672 3.021 0.668 0.188 0.093 83 7.6 G_temporal_middle
- 294 198 375 2.068 0.344 0.103 0.021 2 0.2 Lat_Fis-ant-Horizont
- 275 192 398 2.410 0.329 0.092 0.022 1 0.2 Lat_Fis-ant-Vertical
- 1139 765 1517 2.551 0.487 0.136 0.068 12 1.8 Lat_Fis-post
- 2079 1265 2757 1.993 0.375 0.157 0.059 39 5.0 Pole_occipital
- 1471 999 5152 3.593 0.729 0.150 0.065 53 4.1 Pole_temporal
- 2168 1489 2857 2.042 0.616 0.131 0.043 44 4.0 S_calcarine
- 2620 1731 3097 1.919 0.608 0.102 0.025 13 2.8 S_central
- 1029 680 1373 2.147 0.631 0.109 0.030 8 1.3 S_cingul-Marginalis
- 492 328 876 2.817 0.525 0.110 0.032 3 0.6 S_circular_insula_ant
- 1283 856 2063 2.821 0.688 0.097 0.032 9 1.5 S_circular_insula_inf
- 1631 1093 2465 2.608 0.410 0.114 0.034 11 2.1 S_circular_insula_sup
- 1271 869 2224 2.865 0.393 0.105 0.025 8 1.4 S_collat_transv_ant
- 288 186 373 2.215 0.307 0.158 0.048 3 0.7 S_collat_transv_post
- 1915 1283 2898 2.257 0.460 0.130 0.036 23 2.8 S_front_inf
- 1709 1174 2889 2.159 0.479 0.175 0.079 52 5.3 S_front_middle
- 2337 1584 3823 2.370 0.479 0.118 0.031 20 3.1 S_front_sup
- 158 107 319 2.415 0.503 0.133 0.041 3 0.3 S_interm_prim-Jensen
- 3448 2326 4911 2.244 0.389 0.119 0.034 38 4.8 S_intrapariet_and_P_trans
- 1170 800 1460 1.987 0.354 0.140 0.041 13 2.0 S_oc_middle_and_Lunatus
- 1162 796 1696 2.231 0.372 0.136 0.038 12 1.8 S_oc_sup_and_transversal
- 532 348 680 2.343 0.314 0.128 0.039 5 0.8 S_occipital_ant
- 627 420 1146 2.828 0.476 0.151 0.048 11 1.2 S_oc-temp_lat
- 1759 1190 2757 2.420 0.503 0.114 0.028 12 2.1 S_oc-temp_med_and_Lingual
- 244 186 440 2.166 0.396 0.140 0.036 2 0.4 S_orbital_lateral
- 743 490 1277 2.587 1.093 0.141 0.076 15 2.6 S_orbital_med-olfact
- 1377 908 2184 2.275 0.522 0.153 0.057 24 3.1 S_orbital-H_Shaped
- 1457 1022 2047 2.155 0.510 0.129 0.037 17 2.2 S_parieto_occipital
- 1199 743 1113 1.853 0.668 0.170 0.387 262 7.3 S_pericallosal
- 3002 1968 3990 2.102 0.498 0.132 0.040 34 4.9 S_postcentral
- 1296 857 1854 2.431 0.449 0.104 0.026 9 1.3 S_precentral-inf-part
- 1203 824 1759 2.455 0.514 0.116 0.029 8 1.6 S_precentral-sup-part
- 545 367 766 1.943 0.609 0.187 0.103 20 2.2 S_suborbital
- 709 482 1053 2.296 0.507 0.118 0.027 5 0.8 S_subparietal
- 1287 851 1974 2.483 0.655 0.143 0.049 19 2.6 S_temporal_inf
- 5225 3580 9026 2.622 0.497 0.129 0.039 60 7.9 S_temporal_sup
- 335 240 455 2.274 0.503 0.120 0.023 2 0.4 S_temporal_transverse
- #-----------------------------------------
- #@# Cortical Parc 3 lh Thu Aug 8 20:19:10 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub017 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...
- 1126 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2573 changed, 119336 examined...
- 001: 607 changed, 11017 examined...
- 002: 168 changed, 3370 examined...
- 003: 59 changed, 953 examined...
- 004: 29 changed, 349 examined...
- 005: 11 changed, 159 examined...
- 006: 5 changed, 64 examined...
- 007: 3 changed, 30 examined...
- 008: 3 changed, 21 examined...
- 009: 1 changed, 15 examined...
- 010: 1 changed, 8 examined...
- 011: 1 changed, 5 examined...
- 012: 1 changed, 7 examined...
- 013: 2 changed, 6 examined...
- 014: 2 changed, 12 examined...
- 015: 3 changed, 13 examined...
- 016: 3 changed, 18 examined...
- 017: 2 changed, 16 examined...
- 018: 2 changed, 13 examined...
- 019: 5 changed, 14 examined...
- 020: 4 changed, 15 examined...
- 021: 5 changed, 20 examined...
- 022: 2 changed, 18 examined...
- 023: 2 changed, 10 examined...
- 024: 2 changed, 10 examined...
- 025: 2 changed, 10 examined...
- 026: 1 changed, 10 examined...
- 027: 1 changed, 7 examined...
- 028: 0 changed, 7 examined...
- 247 labels changed using aseg
- 000: 72 total segments, 39 labels (182 vertices) changed
- 001: 33 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 58 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 653 vertices marked for relabeling...
- 653 labels changed in reclassification.
- writing output to ../label/lh.aparc.DKTatlas40.annot...
- classification took 0 minutes and 56 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 3 lh Thu Aug 8 20:20:06 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 sub017 lh white
- computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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
- 1270 856 2307 2.671 0.663 0.138 0.035 17 1.8 caudalanteriorcingulate
- 2546 1684 4822 2.672 0.455 0.131 0.036 29 3.8 caudalmiddlefrontal
- 2802 1769 4127 2.041 0.521 0.164 0.079 105 8.2 cuneus
- 760 511 2406 3.439 0.931 0.144 0.068 12 2.0 entorhinal
- 3126 2077 6144 2.738 0.504 0.139 0.050 48 5.8 fusiform
- 5420 3657 10461 2.567 0.538 0.148 0.051 98 11.0 inferiorparietal
- 4580 3020 11028 2.935 0.757 0.155 0.068 103 12.3 inferiortemporal
- 1319 835 2014 2.244 0.756 0.159 0.321 221 5.6 isthmuscingulate
- 6733 4317 10104 2.139 0.428 0.152 0.057 151 14.3 lateraloccipital
- 3819 2503 7549 2.540 0.717 0.164 0.090 109 14.1 lateralorbitofrontal
- 3467 2280 5595 2.207 0.524 0.160 0.081 103 9.7 lingual
- 1813 1164 3271 2.263 0.723 0.180 0.094 56 6.6 medialorbitofrontal
- 5057 3439 11209 2.831 0.613 0.155 0.061 106 10.9 middletemporal
- 1005 653 2341 3.175 0.879 0.131 0.043 13 1.8 parahippocampal
- 1897 1222 3314 2.398 0.588 0.120 0.039 19 3.2 paracentral
- 2014 1343 4067 2.637 0.377 0.129 0.038 27 2.9 parsopercularis
- 974 658 2203 2.701 0.563 0.153 0.053 21 2.1 parsorbitalis
- 1976 1325 3546 2.385 0.445 0.134 0.041 31 3.4 parstriangularis
- 1808 1204 2138 1.825 0.457 0.136 0.055 45 4.2 pericalcarine
- 6661 4260 10288 2.147 0.644 0.138 0.045 99 12.6 postcentral
- 1760 1175 3061 2.371 0.734 0.149 0.086 73 5.6 posteriorcingulate
- 6550 4249 12211 2.581 0.550 0.123 0.041 93 10.8 precentral
- 4420 2986 8184 2.402 0.554 0.143 0.050 77 9.6 precuneus
- 1046 693 2214 2.711 0.664 0.172 0.080 33 3.6 rostralanteriorcingulate
- 4875 3287 8598 2.240 0.584 0.155 0.059 96 11.5 rostralmiddlefrontal
- 10696 7194 22062 2.590 0.559 0.144 0.051 192 22.3 superiorfrontal
- 7075 4659 11412 2.247 0.467 0.135 0.043 107 12.0 superiorparietal
- 7231 4901 17205 2.980 0.680 0.137 0.049 130 14.3 superiortemporal
- 5581 3741 11033 2.645 0.538 0.153 0.058 105 11.6 supramarginal
- 617 375 1048 2.429 0.345 0.130 0.040 11 1.1 transversetemporal
- 2489 1644 5315 3.063 0.762 0.146 3.263 389 639.3 insula
- #--------------------------------------------
- #@# Tessellate rh Thu Aug 8 20:20:22 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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-): 0 found - 0 modified | TOTAL: 1
- pass 1 (yz+): 2 found - 2 modified | TOTAL: 3
- pass 2 (yz+): 0 found - 2 modified | TOTAL: 3
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 3
- pass 1 (xz+): 1 found - 1 modified | TOTAL: 4
- pass 2 (xz+): 0 found - 1 modified | TOTAL: 4
- pass 1 (xz-): 4 found - 4 modified | TOTAL: 8
- pass 2 (xz-): 0 found - 4 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 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 2 found - 2 modified | TOTAL: 2
- pass 2 (+-): 0 found - 2 modified | TOTAL: 2
- pass 1 (--): 0 found - 0 modified | TOTAL: 2
- pass 1 (-+): 0 found - 0 modified | TOTAL: 2
- Iteration Number : 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 = 10 (out of 221580: 0.004513)
- Ambiguous edge configurations...
- mri_pretess done
- mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix
- $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- slice 50: 1001 vertices, 1106 faces
- slice 60: 6379 vertices, 6608 faces
- slice 70: 14550 vertices, 14905 faces
- slice 80: 25142 vertices, 25522 faces
- slice 90: 35005 vertices, 35351 faces
- slice 100: 45261 vertices, 45588 faces
- slice 110: 55766 vertices, 56120 faces
- slice 120: 65871 vertices, 66225 faces
- slice 130: 76439 vertices, 76813 faces
- slice 140: 86600 vertices, 86957 faces
- slice 150: 95854 vertices, 96167 faces
- slice 160: 103303 vertices, 103571 faces
- slice 170: 109598 vertices, 109791 faces
- slice 180: 114663 vertices, 114830 faces
- slice 190: 117905 vertices, 117981 faces
- slice 200: 118204 vertices, 118216 faces
- slice 210: 118204 vertices, 118216 faces
- slice 220: 118204 vertices, 118216 faces
- slice 230: 118204 vertices, 118216 faces
- slice 240: 118204 vertices, 118216 faces
- slice 250: 118204 vertices, 118216 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...
- 118204 voxel in cpt #1: X=-12 [v=118204,e=354648,f=236432] located at (29.245720, -14.658929, 32.749611)
- For the whole surface: X=-12 [v=118204,e=354648,f=236432]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Smooth1 rh Thu Aug 8 20:20:31 CEST 2013
- mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 20:20:35 CEST 2013
- mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/scripts
- avg radius = 43.7 mm, total surface area = 62170 mm^2
- writing inflated surface to ../surf/rh.inflated.nofix
- inflation took 0.5 minutes
- Not saving sulc
-
step 000: RMS=0.099 (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=0.029 (target=0.015)
step 035: RMS=0.027 (target=0.015)
step 040: RMS=0.024 (target=0.015)
step 045: RMS=0.023 (target=0.015)
step 050: RMS=0.022 (target=0.015)
step 055: RMS=0.022 (target=0.015)
step 060: RMS=0.021 (target=0.015)
- inflation complete.
- Not saving sulc
- #--------------------------------------------
- #@# QSphere rh Thu Aug 8 20:21:07 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/scripts
- mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix
- doing quick spherical unfolding.
- setting seed for random number genererator to 1234
- $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading original vertex positions...
- unfolding cortex into spherical form...
- surface projected - minimizing metric distortion...
- vertex spacing 1.06 +- 0.57 (0.00-->5.67) (max @ vno 91851 --> 91871)
- face area 0.03 +- 0.04 (-0.08-->0.59)
- scaling brain by 0.347...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=175.577, avgs=0
- 005/300: dt: 0.9000, rms radial error=175.318, avgs=0
- 010/300: dt: 0.9000, rms radial error=174.762, avgs=0
- 015/300: dt: 0.9000, rms radial error=174.030, avgs=0
- 020/300: dt: 0.9000, rms radial error=173.194, avgs=0
- 025/300: dt: 0.9000, rms radial error=172.300, avgs=0
- 030/300: dt: 0.9000, rms radial error=171.390, avgs=0
- 035/300: dt: 0.9000, rms radial error=170.463, avgs=0
- 040/300: dt: 0.9000, rms radial error=169.527, avgs=0
- 045/300: dt: 0.9000, rms radial error=168.589, avgs=0
- 050/300: dt: 0.9000, rms radial error=167.651, avgs=0
- 055/300: dt: 0.9000, rms radial error=166.715, avgs=0
- 060/300: dt: 0.9000, rms radial error=165.784, avgs=0
- 065/300: dt: 0.9000, rms radial error=164.857, avgs=0
- 070/300: dt: 0.9000, rms radial error=163.934, avgs=0
- 075/300: dt: 0.9000, rms radial error=163.016, avgs=0
- 080/300: dt: 0.9000, rms radial error=162.103, avgs=0
- 085/300: dt: 0.9000, rms radial error=161.194, avgs=0
- 090/300: dt: 0.9000, rms radial error=160.291, avgs=0
- 095/300: dt: 0.9000, rms radial error=159.392, avgs=0
- 100/300: dt: 0.9000, rms radial error=158.498, avgs=0
- 105/300: dt: 0.9000, rms radial error=157.609, avgs=0
- 110/300: dt: 0.9000, rms radial error=156.724, avgs=0
- 115/300: dt: 0.9000, rms radial error=155.845, avgs=0
- 120/300: dt: 0.9000, rms radial error=154.970, avgs=0
- 125/300: dt: 0.9000, rms radial error=154.100, avgs=0
- 130/300: dt: 0.9000, rms radial error=153.235, avgs=0
- 135/300: dt: 0.9000, rms radial error=152.375, avgs=0
- 140/300: dt: 0.9000, rms radial error=151.520, avgs=0
- 145/300: dt: 0.9000, rms radial error=150.670, avgs=0
- 150/300: dt: 0.9000, rms radial error=149.824, avgs=0
- 155/300: dt: 0.9000, rms radial error=148.983, avgs=0
- 160/300: dt: 0.9000, rms radial error=148.147, avgs=0
- 165/300: dt: 0.9000, rms radial error=147.315, avgs=0
- 170/300: dt: 0.9000, rms radial error=146.488, avgs=0
- 175/300: dt: 0.9000, rms radial error=145.666, avgs=0
- 180/300: dt: 0.9000, rms radial error=144.848, avgs=0
- 185/300: dt: 0.9000, rms radial error=144.035, avgs=0
- 190/300: dt: 0.9000, rms radial error=143.226, avgs=0
- 195/300: dt: 0.9000, rms radial error=142.422, avgs=0
- 200/300: dt: 0.9000, rms radial error=141.622, avgs=0
- 205/300: dt: 0.9000, rms radial error=140.826, avgs=0
- 210/300: dt: 0.9000, rms radial error=140.035, avgs=0
- 215/300: dt: 0.9000, rms radial error=139.249, avgs=0
- 220/300: dt: 0.9000, rms radial error=138.466, avgs=0
- 225/300: dt: 0.9000, rms radial error=137.688, avgs=0
- 230/300: dt: 0.9000, rms radial error=136.915, avgs=0
- 235/300: dt: 0.9000, rms radial error=136.146, avgs=0
- 240/300: dt: 0.9000, rms radial error=135.381, avgs=0
- 245/300: dt: 0.9000, rms radial error=134.620, avgs=0
- 250/300: dt: 0.9000, rms radial error=133.863, avgs=0
- 255/300: dt: 0.9000, rms radial error=133.111, avgs=0
- 260/300: dt: 0.9000, rms radial error=132.363, avgs=0
- 265/300: dt: 0.9000, rms radial error=131.619, avgs=0
- 270/300: dt: 0.9000, rms radial error=130.879, avgs=0
- 275/300: dt: 0.9000, rms radial error=130.143, avgs=0
- 280/300: dt: 0.9000, rms radial error=129.412, avgs=0
- 285/300: dt: 0.9000, rms radial error=128.684, avgs=0
- 290/300: dt: 0.9000, rms radial error=127.961, avgs=0
- 295/300: dt: 0.9000, rms radial error=127.241, avgs=0
- 300/300: dt: 0.9000, rms radial error=126.526, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 13260.69
- 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 = 2020.37
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00028
- epoch 3 (K=160.0), pass 1, starting sse = 175.42
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.13/12 = 0.01115
- epoch 4 (K=640.0), pass 1, starting sse = 6.71
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.13/14 = 0.00938
- final dwriting spherical brain to ../surf/rh.qsphere.nofix
- spherical transformation took 0.07 hours
- istance error %100000.00
- #--------------------------------------------
- #@# Fix Topology rh Thu Aug 8 20:25:34 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/sub017/scripts
- mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub017 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=-12 (nv=118204, nf=236432, ne=354648, g=7)
- 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 7 iterations
- marking ambiguous vertices...
- 934 ambiguous faces found in tessellation
- segmenting defects...
- 19 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- 19 defects to be corrected
- 0 vertices coincident
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/rh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -9.7431 (-4.8716)
- -vertex loglikelihood: -6.7296 (-3.3648)
- -normal dot loglikelihood: -3.6731 (-3.6731)
- -quad curv loglikelihood: -6.4679 (-3.2340)
- Total Loglikelihood : -26.6137
- CORRECTING DEFECT 0 (vertices=36, convex hull=77)
- After retessellation of defect 0, euler #=-16 (117606,352550,234928) : difference with theory (-16) = 0
- CORRECTING DEFECT 1 (vertices=8, convex hull=27)
- After retessellation of defect 1, euler #=-15 (117607,352562,234940) : difference with theory (-15) = 0
- CORRECTING DEFECT 2 (vertices=34, convex hull=67)
- After retessellation of defect 2, euler #=-14 (117625,352643,235004) : difference with theory (-14) = 0
- CORRECTING DEFECT 3 (vertices=12, convex hull=32)
- After retessellation of defect 3, euler #=-13 (117629,352670,235028) : difference with theory (-13) = 0
- CORRECTING DEFECT 4 (vertices=8, convex hull=18)
- After retessellation of defect 4, euler #=-12 (117631,352679,235036) : difference with theory (-12) = 0
- CORRECTING DEFECT 5 (vertices=46, convex hull=22)
- After retessellation of defect 5, euler #=-11 (117634,352693,235048) : difference with theory (-11) = 0
- CORRECTING DEFECT 6 (vertices=5, convex hull=18)
- After retessellation of defect 6, euler #=-10 (117634,352698,235054) : difference with theory (-10) = 0
- CORRECTING DEFECT 7 (vertices=28, convex hull=28)
- After retessellation of defect 7, euler #=-9 (117639,352722,235074) : difference with theory (-9) = 0
- CORRECTING DEFECT 8 (vertices=10, convex hull=18)
- After retessellation of defect 8, euler #=-8 (117641,352734,235085) : difference with theory (-8) = 0
- CORRECTING DEFECT 9 (vertices=5, convex hull=15)
- Warning - incorrect dp selected!!!!(-107.551795 >= -107.551798 )
- After retessellation of defect 9, euler #=-7 (117642,352739,235090) : difference with theory (-7) = 0
- CORRECTING DEFECT 10 (vertices=9, convex hull=25)
- After retessellation of defect 10, euler #=-6 (117643,352750,235101) : difference with theory (-6) = 0
- CORRECTING DEFECT 11 (vertices=82, convex hull=112)
- After retessellation of defect 11, euler #=-5 (117695,352956,235256) : difference with theory (-5) = 0
- CORRECTING DEFECT 12 (vertices=153, convex hull=52)
- After retessellation of defect 12, euler #=-4 (117702,352997,235291) : difference with theory (-4) = 0
- CORRECTING DEFECT 13 (vertices=7, convex hull=14)
- After retessellation of defect 13, euler #=-3 (117704,353007,235300) : difference with theory (-3) = 0
- CORRECTING DEFECT 14 (vertices=23, convex hull=27)
- After retessellation of defect 14, euler #=-2 (117710,353035,235323) : difference with theory (-2) = 0
- CORRECTING DEFECT 15 (vertices=27, convex hull=50)
- After retessellation of defect 15, euler #=-1 (117722,353090,235367) : difference with theory (-1) = 0
- CORRECTING DEFECT 16 (vertices=46, convex hull=26)
- After retessellation of defect 16, euler #=0 (117726,353110,235384) : difference with theory (0) = 0
- CORRECTING DEFECT 17 (vertices=35, convex hull=67)
- After retessellation of defect 17, euler #=1 (117737,353172,235436) : difference with theory (1) = 0
- CORRECTING DEFECT 18 (vertices=47, convex hull=76)
- After retessellation of defect 18, euler #=2 (117762,353280,235520) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.88 +- 0.21 (0.10-->5.00) (max @ vno 97006 --> 117866)
- face area 0.00 +- 0.00 (0.00-->0.00)
- performing soap bubble on retessellated vertices for 0 iterations...
- vertex spacing 0.88 +- 0.21 (0.10-->5.00) (max @ vno 97006 --> 117866)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 83 mutations (40.3%), 123 crossovers (59.7%), 20 vertices were eliminated
- building final representation...
- 442 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=117762, nf=235520, ne=353280, g=0)
- writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/rh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 8.6 minutes
- 0 defective edges
- removing intersecting faces
- 000: 49 intersecting
- mris_euler_number ../surf/rh.orig
- euler # = v-e+f = 2g-2: 117762 - 353280 + 235520 = 2 --> 0 holes
- F =2V-4: 235520 = 235524-4 (0)
- 2E=3F: 706560 = 706560 (0)
- total defect index = 0
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/scripts
- mris_remove_intersection ../surf/rh.orig ../surf/rh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 5 intersecting
- writing corrected surface to ../surf/rh.orig
- rm ../surf/rh.inflated
- #--------------------------------------------
- #@# Make White Surf rh Thu Aug 8 20:34:15 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/scripts
- mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub017 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/sub017/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/wm.mgz...
- 15434 bright wm thresholded.
- 321 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/rh.orig...
- computing class statistics...
- border white: 215675 voxels (1.29%)
- border gray 245603 voxels (1.46%)
- WM (92.0): 93.4 +- 10.1 [70.0 --> 110.0]
- GM (76.0) : 73.6 +- 13.3 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 44.7 (was 70)
- setting MAX_BORDER_WHITE to 115.1 (was 105)
- setting MIN_BORDER_WHITE to 58.0 (was 85)
- setting MAX_CSF to 31.4 (was 40)
- setting MAX_GRAY to 94.9 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 51.4 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 18.1 (was 40)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.82 +- 0.21 (0.02-->2.76) (max @ vno 97006 --> 117695)
- face area 0.28 +- 0.12 (0.00-->1.40)
- mean absolute distance = 0.67 +- 0.75
- 3220 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=58
- mean inside = 93.0, mean outside = 68.2
- smoothing surface for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- mean border=71.9, 19 (19) missing vertices, mean dist 0.4 [0.4 (%29.9)->0.8 (%70.1))]
- %72 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.92 +- 0.26 (0.13-->4.92) (max @ vno 117695 --> 88943)
- face area 0.28 +- 0.13 (0.00-->1.48)
- mean absolute distance = 0.33 +- 0.47
- 2537 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=6698471.5, rms=14.34
- 001: dt: 0.5000, sse=6499721.0, rms=10.409 (0.000%)
- 002: dt: 0.5000, sse=6572003.5, rms=8.031 (0.000%)
- 003: dt: 0.5000, sse=6609998.5, rms=6.453 (0.000%)
- 004: dt: 0.5000, sse=6825845.5, rms=5.537 (0.000%)
- 005: dt: 0.5000, sse=6883788.0, rms=5.003 (0.000%)
- 006: dt: 0.5000, sse=7008570.5, rms=4.750 (0.000%)
- 007: dt: 0.5000, sse=6998311.0, rms=4.582 (0.000%)
- 008: dt: 0.5000, sse=7060701.5, rms=4.509 (0.000%)
- 009: dt: 0.5000, sse=7004261.0, rms=4.440 (0.000%)
- rms = 4.41, time step reduction 1 of 3 to 0.250...
- 010: dt: 0.5000, sse=7026507.5, rms=4.410 (0.000%)
- 011: dt: 0.2500, sse=4432067.5, rms=3.058 (0.000%)
- 012: dt: 0.2500, sse=4065341.5, rms=2.603 (0.000%)
- 013: dt: 0.2500, sse=3824837.5, rms=2.502 (0.000%)
- 014: dt: 0.2500, sse=3763455.0, rms=2.406 (0.000%)
- rms = 2.37, time step reduction 2 of 3 to 0.125...
- 015: dt: 0.2500, sse=3676696.5, rms=2.371 (0.000%)
- 016: dt: 0.1250, sse=3484522.2, rms=2.131 (0.000%)
- rms = 2.10, time step reduction 3 of 3 to 0.062...
- 017: dt: 0.1250, sse=3448165.5, rms=2.098 (0.000%)
- positioning took 1.8 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- mean border=77.2, 22 (2) missing vertices, mean dist -0.2 [0.3 (%81.0)->0.2 (%19.0))]
- %83 local maxima, %11 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 (0.10-->5.20) (max @ vno 117695 --> 88943)
- face area 0.35 +- 0.16 (0.00-->1.92)
- mean absolute distance = 0.21 +- 0.29
- 2756 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4495651.5, rms=6.79
- 018: dt: 0.5000, sse=4469435.0, rms=4.414 (0.000%)
- rms = 4.67, time step reduction 1 of 3 to 0.250...
- 019: dt: 0.2500, sse=4068267.0, rms=3.301 (0.000%)
- 020: dt: 0.2500, sse=3884773.5, rms=2.622 (0.000%)
- 021: dt: 0.2500, sse=3832815.2, rms=2.165 (0.000%)
- 022: dt: 0.2500, sse=3812918.0, rms=2.043 (0.000%)
- 023: dt: 0.2500, sse=3750268.2, rms=1.908 (0.000%)
- rms = 1.89, time step reduction 2 of 3 to 0.125...
- 024: dt: 0.2500, sse=3773926.2, rms=1.890 (0.000%)
- 025: dt: 0.1250, sse=3629454.0, rms=1.677 (0.000%)
- rms = 1.66, time step reduction 3 of 3 to 0.062...
- 026: dt: 0.1250, sse=3590912.8, rms=1.657 (0.000%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 1 vertex label from ripped group
- mean border=80.5, 26 (2) missing vertices, mean dist -0.1 [0.2 (%76.1)->0.2 (%23.9))]
- %89 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.25 (0.10-->5.33) (max @ vno 117695 --> 88943)
- face area 0.34 +- 0.16 (0.00-->2.04)
- mean absolute distance = 0.17 +- 0.24
- 1962 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=3908779.8, rms=4.23
- rms = 4.19, time step reduction 1 of 3 to 0.250...
- 027: dt: 0.5000, sse=4252403.5, rms=4.195 (0.000%)
- 028: dt: 0.2500, sse=3704366.8, rms=2.472 (0.000%)
- 029: dt: 0.2500, sse=3894087.5, rms=1.874 (0.000%)
- rms = 1.94, time step reduction 2 of 3 to 0.125...
- 030: dt: 0.1250, sse=3802336.0, rms=1.706 (0.000%)
- 031: dt: 0.1250, sse=3675967.8, rms=1.460 (0.000%)
- rms = 1.43, time step reduction 3 of 3 to 0.062...
- 032: dt: 0.1250, sse=3638312.0, rms=1.427 (0.000%)
- positioning took 0.7 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- mean border=81.6, 22 (2) missing vertices, mean dist -0.0 [0.2 (%58.6)->0.2 (%41.4))]
- %91 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- writing white matter surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/rh.white...
- writing smoothed curvature to rh.curv
- 000: dt: 0.0000, sse=3664871.5, rms=1.89
- rms = 2.84, time step reduction 1 of 3 to 0.250...
- 033: dt: 0.2500, sse=3726689.0, rms=1.252 (0.000%)
- 034: dt: 0.2500, sse=3853331.8, rms=1.085 (0.000%)
- rms = 1.08, time step reduction 2 of 3 to 0.125...
- 035: dt: 0.2500, sse=3910066.0, rms=1.080 (0.000%)
- rms = 1.06, time step reduction 3 of 3 to 0.062...
- 036: dt: 0.1250, sse=3940308.8, rms=1.062 (0.000%)
- positioning took 0.5 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 4 vertex label from ripped group
- generating cortex label...
- 9 non-cortical segments detected
- only using segment with 1871 vertices
- erasing segment 1 (vno[0] = 76950)
- erasing segment 2 (vno[0] = 84948)
- erasing segment 3 (vno[0] = 85076)
- erasing segment 4 (vno[0] = 85940)
- erasing segment 5 (vno[0] = 86017)
- erasing segment 6 (vno[0] = 86046)
- erasing segment 7 (vno[0] = 91421)
- erasing segment 8 (vno[0] = 94255)
- writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/label/rh.cortex.label...
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/rh.curv
- writing smoothed area to rh.area
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/rh.area
- vertex spacing 0.89 +- 0.25 (0.07-->5.38) (max @ vno 117695 --> 88943)
- face area 0.34 +- 0.16 (0.00-->2.24)
- refinement took 6.0 minutes
- #--------------------------------------------
- #@# Smooth2 rh Thu Aug 8 20:40:15 CEST 2013
- mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/scripts
- smoothing for 3 iterations
- setting seed for random number generator to 1234
- smoothing surface tessellation for 3 iterations...
- smoothing complete - recomputing first and second fundamental forms...
- #--------------------------------------------
- #@# Inflation2 rh Thu Aug 8 20:40:20 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/scripts
- mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated
- avg radius = 43.9 mm, total surface area = 71837 mm^2
- writing inflated surface to ../surf/rh.inflated
- writing sulcal depths to ../surf/rh.sulc
-
step 000: RMS=0.116 (target=0.015)
step 005: RMS=0.080 (target=0.015)
step 010: RMS=0.058 (target=0.015)
step 015: RMS=0.048 (target=0.015)
step 020: RMS=0.040 (target=0.015)
step 025: RMS=0.033 (target=0.015)
step 030: RMS=0.028 (target=0.015)
step 035: RMS=0.024 (target=0.015)
step 040: RMS=0.021 (target=0.015)
step 045: RMS=0.019 (target=0.015)
step 050: RMS=0.017 (target=0.015)
step 055: RMS=0.016 (target=0.015)
step 060: RMS=0.015 (target=0.015)
- inflation complete.
- inflation took 0.6 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
- 147 vertices thresholded to be in k1 ~ [-0.24 3.74], k2 ~ [-0.16 0.19]
- total integrated curvature = 0.631*4pi (7.929) --> 0 handles
- ICI = 1.4, FI = 6.7, variation=123.250
- 89 vertices thresholded to be in [-0.08 0.01]
- writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level
- curvature mean = 0.000, std = 0.002
- 85 vertices thresholded to be in [-0.11 0.81]
- done.
- writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.017, std = 0.021
- done.
- #-----------------------------------------
- #@# Curvature Stats rh Thu Aug 8 20:42:28 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub017 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 [ sub017/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 [ 229 ]
- Gb_filter = 0
- WARN: S lookup min: -0.212768
- WARN: S explicit min: 0.000000 vertex = 183
- #--------------------------------------------
- #@# Sphere rh Thu Aug 8 20:42:33 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 0.322...
- 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 %39.21
- pass 1: epoch 2 of 3 starting distance error %19.73
- unfolding complete - removing small folds...
- starting distance error %19.55
- removing remaining folds...
- final distance error %19.57
- MRISunfold() return, current seed 1234
- writing spherical brain to ../surf/rh.sphere
- spherical transformation took 0.51 hours
- #--------------------------------------------
- #@# Surf Reg rh Thu Aug 8 21:13:26 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 = 0.606
- curvature mean = 0.035, std = 0.938
- curvature mean = 0.022, std = 0.875
- Starting MRISrigidBodyAlignGlobal()
- d=64.00 min @ (16.00, 0.00, 0.00) sse = 320024.3, tmin=0.9967
- d=32.00 min @ (0.00, -8.00, -8.00) sse = 254396.0, tmin=2.0383
- d=16.00 min @ (0.00, 0.00, 4.00) sse = 241248.1, tmin=3.2132
- d=8.00 min @ (0.00, 2.00, -2.00) sse = 239697.9, tmin=4.3647
- d=4.00 min @ (1.00, -1.00, 1.00) sse = 237577.1, tmin=5.4189
- d=2.00 min @ (0.00, 0.50, 0.00) sse = 237424.0, tmin=6.4604
- d=1.00 min @ (-0.25, -0.25, 0.00) sse = 237320.8, tmin=7.4830
- tol=1.0e+00, sigma=0.5, host=snake, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
- using quadratic fit line minimization
- MRISrigidBodyAlignGlobal() done 8.52 min
- curvature mean = 0.017, std = 0.957
- curvature mean = 0.009, std = 0.947
- curvature mean = 0.015, std = 0.969
- curvature mean = 0.004, std = 0.976
- curvature mean = 0.012, std = 0.971
- curvature mean = 0.001, std = 0.990
- 2 Reading smoothwm
- curvature mean = -0.026, std = 0.303
- curvature mean = 0.006, std = 0.070
- curvature mean = 0.070, std = 0.345
- curvature mean = 0.007, std = 0.084
- curvature mean = 0.028, std = 0.540
- curvature mean = 0.007, std = 0.090
- curvature mean = 0.015, std = 0.674
- curvature mean = 0.007, std = 0.093
- curvature mean = 0.006, std = 0.778
- MRISregister() return, current seed 0
- writing registered surface to ../surf/rh.sphere.reg...
- #--------------------------------------------
- #@# Jacobian white rh Thu Aug 8 21:40:16 CEST 2013
- mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white
- reading surface from ../surf/rh.white...
- writing curvature file ../surf/rh.jacobian_white
- #--------------------------------------------
- #@# AvgCurv rh Thu Aug 8 21:40:18 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/scripts
- mrisp_paint -a 5 /opt/freesurfer/5.3.0/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv
- averaging curvature patterns 5 times...
- reading surface from ../surf/rh.sphere.reg...
- reading template parameterization from /opt/freesurfer/5.3.0/average/rh.average.curvature.filled.buckner40.tif...
- writing curvature file to ../surf/rh.avg_curv...
- #-----------------------------------------
- #@# Cortical Parc rh Thu Aug 8 21:40:20 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub017 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...
- 1049 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2641 changed, 117762 examined...
- 001: 595 changed, 11338 examined...
- 002: 142 changed, 3289 examined...
- 003: 38 changed, 851 examined...
- 004: 14 changed, 232 examined...
- 005: 5 changed, 88 examined...
- 006: 2 changed, 29 examined...
- 007: 0 changed, 8 examined...
- 167 labels changed using aseg
- 000: 91 total segments, 50 labels (292 vertices) changed
- 001: 41 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 36 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 1195 vertices marked for relabeling...
- 1195 labels changed in reclassification.
- writing output to ../label/rh.aparc.annot...
- classification took 0 minutes and 53 seconds.
- #--------------------------------------------
- #@# Make Pial Surf rh Thu Aug 8 21:41:14 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/scripts
- mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub017 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/sub017/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/wm.mgz...
- 15434 bright wm thresholded.
- 321 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/rh.orig...
- computing class statistics...
- border white: 215675 voxels (1.29%)
- border gray 245603 voxels (1.46%)
- WM (92.0): 93.4 +- 10.1 [70.0 --> 110.0]
- GM (76.0) : 73.6 +- 13.3 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 44.7 (was 70)
- setting MAX_BORDER_WHITE to 115.1 (was 105)
- setting MIN_BORDER_WHITE to 58.0 (was 85)
- setting MAX_CSF to 31.4 (was 40)
- setting MAX_GRAY to 94.9 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 51.4 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 18.1 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=105, GM=58
- mean inside = 93.0, mean outside = 68.2
- 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/sub017/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.82 +- 0.21 (0.02-->2.76) (max @ vno 97006 --> 117695)
- face area 0.28 +- 0.12 (0.00-->1.40)
- mean absolute distance = 0.67 +- 0.75
- 3269 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 48 points - only 2.08% unknown
- deleting segment 2 with 11 points - only 0.00% unknown
- deleting segment 3 with 473 points - only 0.00% unknown
- deleting segment 4 with 6 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- mean border=71.9, 23 (20) missing vertices, mean dist 0.4 [0.4 (%29.8)->0.8 (%70.2))]
- %72 local maxima, %23 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.92 +- 0.26 (0.13-->4.92) (max @ vno 117695 --> 88943)
- face area 0.28 +- 0.13 (0.00-->1.47)
- mean absolute distance = 0.33 +- 0.47
- 2568 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=6726313.0, rms=14.34
- 001: dt: 0.5000, sse=6528773.0, rms=10.414 (0.000%)
- 002: dt: 0.5000, sse=6605241.0, rms=8.043 (0.000%)
- 003: dt: 0.5000, sse=6646003.0, rms=6.468 (0.000%)
- 004: dt: 0.5000, sse=6862689.0, rms=5.548 (0.000%)
- 005: dt: 0.5000, sse=6922486.0, rms=5.012 (0.000%)
- 006: dt: 0.5000, sse=7051169.5, rms=4.758 (0.000%)
- 007: dt: 0.5000, sse=7038659.5, rms=4.591 (0.000%)
- 008: dt: 0.5000, sse=7104245.0, rms=4.517 (0.000%)
- 009: dt: 0.5000, sse=7046586.5, rms=4.447 (0.000%)
- rms = 4.42, time step reduction 1 of 3 to 0.250...
- 010: dt: 0.5000, sse=7070882.5, rms=4.416 (0.000%)
- 011: dt: 0.2500, sse=4461682.0, rms=3.071 (0.000%)
- 012: dt: 0.2500, sse=4092160.5, rms=2.622 (0.000%)
- 013: dt: 0.2500, sse=3850245.5, rms=2.518 (0.000%)
- 014: dt: 0.2500, sse=3789335.5, rms=2.426 (0.000%)
- rms = 2.39, time step reduction 2 of 3 to 0.125...
- 015: dt: 0.2500, sse=3702597.0, rms=2.390 (0.000%)
- 016: dt: 0.1250, sse=3510067.8, rms=2.157 (0.000%)
- rms = 2.13, time step reduction 3 of 3 to 0.062...
- 017: dt: 0.1250, sse=3474006.8, rms=2.125 (0.000%)
- positioning took 1.9 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 14 points - only 0.00% unknown
- deleting segment 2 with 12 points - only 0.00% unknown
- deleting segment 3 with 250 points - only 0.00% unknown
- deleting segment 4 with 7 points - only 0.00% unknown
- deleting segment 5 with 5 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 6 with 2 points - only 0.00% unknown
- deleting segment 7 with 5 points - only 0.00% unknown
- deleting segment 8 with 34 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- mean border=77.2, 31 (2) missing vertices, mean dist -0.2 [0.3 (%81.0)->0.2 (%19.0))]
- %83 local maxima, %11 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 (0.10-->5.20) (max @ vno 117695 --> 88943)
- face area 0.35 +- 0.16 (0.00-->1.92)
- mean absolute distance = 0.21 +- 0.30
- 2795 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4523024.0, rms=6.78
- 018: dt: 0.5000, sse=4503270.5, rms=4.421 (0.000%)
- rms = 4.68, time step reduction 1 of 3 to 0.250...
- 019: dt: 0.2500, sse=4098494.5, rms=3.314 (0.000%)
- 020: dt: 0.2500, sse=3914408.2, rms=2.643 (0.000%)
- 021: dt: 0.2500, sse=3862796.0, rms=2.194 (0.000%)
- 022: dt: 0.2500, sse=3842185.2, rms=2.069 (0.000%)
- 023: dt: 0.2500, sse=3778999.2, rms=1.934 (0.000%)
- rms = 1.91, time step reduction 2 of 3 to 0.125...
- 024: dt: 0.2500, sse=3802416.5, rms=1.912 (0.000%)
- 025: dt: 0.1250, sse=3657222.2, rms=1.701 (0.000%)
- rms = 1.68, time step reduction 3 of 3 to 0.062...
- 026: dt: 0.1250, sse=3618896.8, rms=1.680 (0.000%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 20 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 1 with 3 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 3 with 9 points - only 0.00% unknown
- deleting segment 4 with 278 points - only 0.00% unknown
- deleting segment 5 with 7 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 6 with 3 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 7 with 2 points - only 0.00% unknown
- deleting segment 8 with 53 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- removing 1 vertex label from ripped group
- mean border=80.5, 37 (2) missing vertices, mean dist -0.1 [0.2 (%76.1)->0.2 (%23.9))]
- %89 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.25 (0.10-->5.33) (max @ vno 117695 --> 88943)
- face area 0.34 +- 0.16 (0.00-->2.04)
- mean absolute distance = 0.17 +- 0.25
- 2003 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=3937170.0, rms=4.23
- rms = 4.20, time step reduction 1 of 3 to 0.250...
- 027: dt: 0.5000, sse=4290213.5, rms=4.197 (0.000%)
- 028: dt: 0.2500, sse=3735624.5, rms=2.478 (0.000%)
- 029: dt: 0.2500, sse=3923201.2, rms=1.880 (0.000%)
- rms = 1.94, time step reduction 2 of 3 to 0.125...
- 030: dt: 0.1250, sse=3830997.0, rms=1.713 (0.000%)
- 031: dt: 0.1250, sse=3704102.8, rms=1.468 (0.000%)
- rms = 1.43, time step reduction 3 of 3 to 0.062...
- 032: dt: 0.1250, sse=3665470.2, rms=1.434 (0.000%)
- positioning took 0.7 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 16 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 1 with 3 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 15 points - only 0.00% unknown
- deleting segment 4 with 279 points - only 0.00% unknown
- deleting segment 5 with 8 points - only 0.00% unknown
- deleting segment 6 with 5 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 7 with 2 points - only 0.00% unknown
- deleting segment 8 with 53 points - only 0.00% unknown
- mean border=81.5, 39 (2) missing vertices, mean dist -0.0 [0.2 (%58.5)->0.2 (%41.5))]
- %91 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- repositioning cortical surface to gray/csf boundary.
- smoothing T1 volume with sigma = 2.000
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=3691902.5, rms=1.89
- rms = 2.85, time step reduction 1 of 3 to 0.250...
- 033: dt: 0.2500, sse=3756295.5, rms=1.258 (0.000%)
- 034: dt: 0.2500, sse=3886075.5, rms=1.095 (0.000%)
- rms = 1.09, time step reduction 2 of 3 to 0.125...
- 035: dt: 0.2500, sse=3943006.5, rms=1.089 (0.000%)
- rms = 1.07, time step reduction 3 of 3 to 0.062...
- 036: dt: 0.1250, sse=3974014.8, rms=1.070 (0.000%)
- positioning took 0.5 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 1 vertex label from ripped group
- deleting segment 0 with 1 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- smoothing surface for 5 iterations...
- mean border=47.5, 31 (31) missing vertices, mean dist 1.8 [1.2 (%0.0)->2.4 (%100.0))]
- %18 local maxima, %54 large gradients and %24 min vals, 1471 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=27560596.0, rms=33.54
- 001: dt: 0.5000, sse=19819224.0, rms=27.891 (0.000%)
- 002: dt: 0.5000, sse=14380023.0, rms=23.135 (0.000%)
- 003: dt: 0.5000, sse=10719927.0, rms=19.270 (0.000%)
- 004: dt: 0.5000, sse=8441991.0, rms=16.194 (0.000%)
- 005: dt: 0.5000, sse=7082390.5, rms=13.790 (0.000%)
- 006: dt: 0.5000, sse=6317685.0, rms=11.927 (0.000%)
- 007: dt: 0.5000, sse=5865697.0, rms=10.380 (0.000%)
- 008: dt: 0.5000, sse=5640754.5, rms=9.013 (0.000%)
- 009: dt: 0.5000, sse=5482483.0, rms=7.782 (0.000%)
- 010: dt: 0.5000, sse=5459445.5, rms=6.708 (0.000%)
- 011: dt: 0.5000, sse=5469343.0, rms=5.843 (0.000%)
- 012: dt: 0.5000, sse=5588697.5, rms=5.182 (0.000%)
- 013: dt: 0.5000, sse=5684153.5, rms=4.764 (0.000%)
- 014: dt: 0.5000, sse=5810358.0, rms=4.483 (0.000%)
- 015: dt: 0.5000, sse=5868559.5, rms=4.307 (0.000%)
- 016: dt: 0.5000, sse=5910909.0, rms=4.173 (0.000%)
- 017: dt: 0.5000, sse=5930435.0, rms=4.093 (0.000%)
- 018: dt: 0.5000, sse=5970468.0, rms=4.018 (0.000%)
- rms = 3.99, time step reduction 1 of 3 to 0.250...
- 019: dt: 0.5000, sse=5971282.0, rms=3.992 (0.000%)
- 020: dt: 0.2500, sse=4110312.0, rms=3.200 (0.000%)
- 021: dt: 0.2500, sse=3930397.5, rms=2.980 (0.000%)
- rms = 2.95, time step reduction 2 of 3 to 0.125...
- 022: dt: 0.2500, sse=3825724.2, rms=2.950 (0.000%)
- 023: dt: 0.1250, sse=3655379.2, rms=2.816 (0.000%)
- rms = 2.80, time step reduction 3 of 3 to 0.062...
- 024: dt: 0.1250, sse=3624809.8, rms=2.796 (0.000%)
- positioning took 2.6 minutes
- mean border=44.9, 617 (6) missing vertices, mean dist 0.2 [0.2 (%45.6)->0.5 (%54.4))]
- %36 local maxima, %40 large gradients and %18 min vals, 373 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=4218705.0, rms=5.05
- 025: dt: 0.5000, sse=4392650.5, rms=4.061 (0.000%)
- rms = 4.02, time step reduction 1 of 3 to 0.250...
- 026: dt: 0.5000, sse=5634630.0, rms=4.024 (0.000%)
- 027: dt: 0.2500, sse=4225175.5, rms=3.095 (0.000%)
- 028: dt: 0.2500, sse=4219224.5, rms=2.846 (0.000%)
- 029: dt: 0.2500, sse=4117670.5, rms=2.790 (0.000%)
- rms = 2.74, time step reduction 2 of 3 to 0.125...
- 030: dt: 0.2500, sse=4133514.0, rms=2.741 (0.000%)
- 031: dt: 0.1250, sse=3965867.5, rms=2.584 (0.000%)
- rms = 2.56, time step reduction 3 of 3 to 0.062...
- 032: dt: 0.1250, sse=3947632.0, rms=2.557 (0.000%)
- positioning took 0.9 minutes
- mean border=42.8, 774 (5) missing vertices, mean dist 0.1 [0.2 (%39.0)->0.3 (%61.0))]
- %54 local maxima, %22 large gradients and %18 min vals, 491 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=4144391.5, rms=3.79
- rms = 3.77, time step reduction 1 of 3 to 0.250...
- 033: dt: 0.5000, sse=4411617.5, rms=3.765 (0.000%)
- 034: dt: 0.2500, sse=4250122.5, rms=2.853 (0.000%)
- 035: dt: 0.2500, sse=4285001.5, rms=2.640 (0.000%)
- rms = 2.64, time step reduction 2 of 3 to 0.125...
- 036: dt: 0.2500, sse=4216176.5, rms=2.637 (0.000%)
- 037: dt: 0.1250, sse=4073304.8, rms=2.412 (0.000%)
- rms = 2.38, time step reduction 3 of 3 to 0.062...
- 038: dt: 0.1250, sse=4059844.5, rms=2.381 (0.000%)
- positioning took 0.6 minutes
- mean border=41.8, 1559 (5) missing vertices, mean dist 0.0 [0.2 (%47.4)->0.3 (%52.6))]
- %58 local maxima, %18 large gradients and %18 min vals, 380 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/sub017/surf/rh.pial...
- writing smoothed curvature to rh.curv.pial
- 000: dt: 0.0000, sse=4096735.5, rms=2.71
- rms = 3.40, time step reduction 1 of 3 to 0.250...
- 039: dt: 0.2500, sse=4003954.2, rms=2.454 (0.000%)
- rms = 2.41, time step reduction 2 of 3 to 0.125...
- 040: dt: 0.2500, sse=4123548.8, rms=2.405 (0.000%)
- 041: dt: 0.1250, sse=4041016.8, rms=2.328 (0.000%)
- rms = 2.30, time step reduction 3 of 3 to 0.062...
- 042: dt: 0.1250, sse=4067850.8, rms=2.297 (0.000%)
- positioning took 0.5 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/rh.curv.pial
- writing smoothed area to rh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/rh.area.pial
- vertex spacing 1.01 +- 0.42 (0.04-->8.27) (max @ vno 117695 --> 88943)
- face area 0.41 +- 0.30 (0.00-->4.96)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 117762 vertices processed
- 25000 of 117762 vertices processed
- 50000 of 117762 vertices processed
- 75000 of 117762 vertices processed
- 100000 of 117762 vertices processed
- 0 of 117762 vertices processed
- 25000 of 117762 vertices processed
- 50000 of 117762 vertices processed
- 75000 of 117762 vertices processed
- 100000 of 117762 vertices processed
- thickness calculation complete, 357:793 truncations.
- 24245 vertices at 0 distance
- 76687 vertices at 1 distance
- 75940 vertices at 2 distance
- 32986 vertices at 3 distance
- 9692 vertices at 4 distance
- 2834 vertices at 5 distance
- 978 vertices at 6 distance
- 349 vertices at 7 distance
- 118 vertices at 8 distance
- 75 vertices at 9 distance
- 37 vertices at 10 distance
- 27 vertices at 11 distance
- 26 vertices at 12 distance
- 21 vertices at 13 distance
- 15 vertices at 14 distance
- 5 vertices at 15 distance
- 2 vertices at 16 distance
- 6 vertices at 17 distance
- 2 vertices at 18 distance
- 2 vertices at 19 distance
- 9 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/rh.thickness
- positioning took 12.1 minutes
- #--------------------------------------------
- #@# Surf Volume rh Thu Aug 8 21:53:17 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf
- mris_calc -o rh.area.mid rh.area add rh.area.pial
- Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o rh.area.mid rh.area.mid div 2
- Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o rh.volume rh.area.mid mul rh.thickness
- Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ]
- #-----------------------------------------
- #@# WM/GM Contrast rh Thu Aug 8 21:53:18 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/scripts
- pctsurfcon --s sub017 --rh-only
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/scripts/pctsurfcon.log
- Thu Aug 8 21:53:18 CEST 2013
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/scripts
- /opt/freesurfer/5.3.0/bin/pctsurfcon
- $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $
- Linux snake5 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
- FREESURFER_HOME /opt/freesurfer/5.3.0
- mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/tmp.pctsurfcon.8274/rh.wm.mgh --regheader sub017 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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/sub017/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/label/rh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 = 90699
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/label/rh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/tmp.pctsurfcon.8274/rh.wm.mgh
- Dim: 117762 1 1
- mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/tmp.pctsurfcon.8274/rh.gm.mgh --projfrac 0.3 --regheader sub017 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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/sub017/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/label/rh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/rh.white
- Done reading source surface
- Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 = 104566
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/label/rh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/tmp.pctsurfcon.8274/rh.gm.mgh
- Dim: 117762 1 1
- mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/tmp.pctsurfcon.8274/rh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/tmp.pctsurfcon.8274/rh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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/sub017/surf/rh.w-g.pct.mgh
- mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/rh.w-g.pct.mgh --annot sub017 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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/sub017/surf/rh.w-g.pct.mgh --annot sub017 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/stats/rh.w-g.pct.stats --snr
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- UseRobust 0
- Constructing seg from annotation
- Reading annotation
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
- Seg base 2000
- Loading /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/rh.w-g.pct.mgh
- Vertex Area is 0.666774 mm^3
- Generating list of segmentation ids
- Found 36 segmentations
- Computing statistics for each segmentation
- 0 2000 unknown 0 0.000
- 1 2001 bankssts 1540 1056.977
- 2 2002 caudalanteriorcingulate 1270 810.921
- 3 2003 caudalmiddlefrontal 2766 1847.890
- 4 2004 corpuscallosum 0 0.000
- 5 2005 cuneus 1856 1281.071
- 6 2006 entorhinal 452 342.884
- 7 2007 fusiform 3556 2411.379
- 8 2008 inferiorparietal 7788 5223.516
- 9 2009 inferiortemporal 3445 2340.363
- 10 2010 isthmuscingulate 1152 768.567
- 11 2011 lateraloccipital 6879 4427.723
- 12 2012 lateralorbitofrontal 3237 2188.373
- 13 2013 lingual 3687 2599.632
- 14 2014 medialorbitofrontal 2151 1463.958
- 15 2015 middletemporal 4294 2942.172
- 16 2016 parahippocampal 996 643.499
- 17 2017 paracentral 1740 1108.394
- 18 2018 parsopercularis 1953 1321.087
- 19 2019 parsorbitalis 1006 651.402
- 20 2020 parstriangularis 2076 1356.458
- 21 2021 pericalcarine 1961 1348.334
- 22 2022 postcentral 5618 3662.802
- 23 2023 posteriorcingulate 1367 891.195
- 24 2024 precentral 6889 4478.403
- 25 2025 precuneus 4604 3127.770
- 26 2026 rostralanteriorcingulate 793 513.488
- 27 2027 rostralmiddlefrontal 7218 4908.438
- 28 2028 superiorfrontal 8233 5557.880
- 29 2029 superiorparietal 7804 5200.031
- 30 2030 superiortemporal 4796 3257.486
- 31 2031 supramarginal 4143 2800.206
- 32 2032 frontalpole 388 266.053
- 33 2033 temporalpole 653 454.437
- 34 2034 transversetemporal 487 301.050
- 35 2035 insula 2960 1920.696
- Reporting on 34 segmentations
- mri_segstats done
- Cleaning up
- #-----------------------------------------
- #@# Parcellation Stats rh Thu Aug 8 21:53:31 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 sub017 rh white
- computing statistics for each annotation in ../label/rh.aparc.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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
- 1540 1057 2849 2.730 0.419 0.135 0.036 20 2.3 bankssts
- 1270 811 2560 3.027 0.644 0.166 0.048 44 2.7 caudalanteriorcingulate
- 2766 1848 5370 2.640 0.394 0.118 0.033 27 3.9 caudalmiddlefrontal
- 1856 1281 2795 1.931 0.406 0.154 0.056 30 4.2 cuneus
- 452 343 1598 3.921 0.531 0.144 0.041 4 0.8 entorhinal
- 3556 2411 7915 2.697 0.684 0.143 0.054 86 7.4 fusiform
- 7788 5224 15290 2.624 0.496 0.150 0.049 138 15.5 inferiorparietal
- 3445 2340 7426 2.605 0.680 0.149 0.063 66 8.8 inferiortemporal
- 1152 769 1999 2.404 0.754 0.152 0.061 22 2.9 isthmuscingulate
- 6879 4428 10675 2.212 0.483 0.154 0.057 143 15.3 lateraloccipital
- 3237 2188 6273 2.565 0.672 0.152 0.070 66 8.4 lateralorbitofrontal
- 3687 2600 6525 2.298 0.517 0.184 0.094 105 14.5 lingual
- 2151 1464 4402 2.622 0.636 0.182 0.114 86 7.4 medialorbitofrontal
- 4294 2942 10603 2.867 0.726 0.147 0.053 80 9.2 middletemporal
- 996 643 2324 2.984 0.806 0.133 0.068 23 2.3 parahippocampal
- 1740 1108 3023 2.506 0.577 0.124 0.042 20 2.6 paracentral
- 1953 1321 3998 2.672 0.394 0.137 0.049 32 3.7 parsopercularis
- 1006 651 2245 2.672 0.532 0.162 0.059 21 2.6 parsorbitalis
- 2076 1356 3848 2.468 0.464 0.141 0.047 36 4.1 parstriangularis
- 1961 1348 2426 1.895 0.500 0.160 0.063 31 5.0 pericalcarine
- 5618 3663 8871 2.094 0.617 0.143 0.057 100 11.0 postcentral
- 1367 891 2484 2.603 0.667 0.139 0.040 21 2.2 posteriorcingulate
- 6889 4478 12728 2.580 0.496 0.118 0.035 82 10.3 precentral
- 4604 3128 8507 2.456 0.550 0.156 0.057 93 10.7 precuneus
- 793 513 1580 3.148 0.680 0.159 0.182 20 1.9 rostralanteriorcingulate
- 7218 4908 13494 2.439 0.522 0.162 0.065 157 17.8 rostralmiddlefrontal
- 8233 5558 18247 2.885 0.517 0.142 0.046 123 14.9 superiorfrontal
- 7804 5200 11955 2.104 0.453 0.141 0.045 120 14.2 superiorparietal
- 4796 3257 11305 2.972 0.573 0.141 0.051 81 9.3 superiortemporal
- 4143 2800 7962 2.547 0.482 0.136 0.048 65 7.9 supramarginal
- 388 266 966 2.668 0.512 0.210 0.144 14 1.5 frontalpole
- 653 454 2570 3.953 0.641 0.188 0.119 17 3.0 temporalpole
- 487 301 817 2.451 0.409 0.138 0.084 13 1.9 transversetemporal
- 2960 1921 5941 2.871 0.764 0.149 0.098 87 12.0 insula
- #-----------------------------------------
- #@# Cortical Parc 2 rh Thu Aug 8 21:53:45 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub017 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...
- 8 labels changed using aseg
- relabeling using gibbs priors...
- 000: 8665 changed, 117762 examined...
- 001: 2093 changed, 33224 examined...
- 002: 641 changed, 10846 examined...
- 003: 252 changed, 3549 examined...
- 004: 116 changed, 1438 examined...
- 005: 49 changed, 649 examined...
- 006: 17 changed, 275 examined...
- 007: 11 changed, 110 examined...
- 008: 8 changed, 71 examined...
- 009: 4 changed, 44 examined...
- 010: 2 changed, 25 examined...
- 011: 0 changed, 9 examined...
- 8 labels changed using aseg
- 000: 244 total segments, 159 labels (2222 vertices) changed
- 001: 100 total segments, 16 labels (284 vertices) changed
- 002: 84 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 140 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 744 vertices marked for relabeling...
- 744 labels changed in reclassification.
- writing output to ../label/rh.aparc.a2009s.annot...
- classification took 1 minutes and 2 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 2 rh Thu Aug 8 21:54:47 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 sub017 rh white
- computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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
- 955 666 1845 2.477 0.661 0.187 0.107 30 3.1 G_and_S_frontomargin
- 1219 840 2201 2.340 0.429 0.149 0.044 21 2.2 G_and_S_occipital_inf
- 1071 680 1953 2.308 0.607 0.140 0.042 18 1.8 G_and_S_paracentral
- 1148 759 2317 2.623 0.594 0.166 0.061 24 2.7 G_and_S_subcentral
- 902 622 1999 2.505 0.466 0.180 0.068 25 2.5 G_and_S_transv_frontopol
- 2137 1435 4200 2.906 0.591 0.151 0.092 45 4.6 G_and_S_cingul-Ant
- 1318 900 2662 3.019 0.498 0.138 0.035 22 1.9 G_and_S_cingul-Mid-Ant
- 1454 957 2718 2.724 0.443 0.128 0.036 16 2.3 G_and_S_cingul-Mid-Post
- 383 251 944 3.005 0.698 0.192 0.064 11 1.0 G_cingul-Post-dorsal
- 216 140 512 2.776 0.505 0.158 0.064 5 0.5 G_cingul-Post-ventral
- 1808 1261 2600 1.815 0.440 0.174 0.071 34 5.3 G_cuneus
- 1290 881 3104 2.755 0.364 0.146 0.052 26 2.7 G_front_inf-Opercular
- 345 216 841 2.733 0.296 0.170 0.060 9 0.9 G_front_inf-Orbital
- 1149 755 2645 2.683 0.374 0.166 0.061 30 2.9 G_front_inf-Triangul
- 3267 2196 7537 2.602 0.486 0.160 0.063 74 7.5 G_front_middle
- 5480 3627 13629 2.951 0.518 0.158 0.066 125 13.0 G_front_sup
- 453 291 1118 3.179 0.762 0.143 0.072 8 1.4 G_Ins_lg_and_S_cent_ins
- 514 346 1776 3.615 0.754 0.214 0.157 23 4.5 G_insular_short
- 2129 1419 4854 2.616 0.522 0.171 0.066 52 5.7 G_occipital_middle
- 2064 1330 3173 2.102 0.490 0.159 0.050 38 4.0 G_occipital_sup
- 1336 848 3108 2.841 0.503 0.160 0.074 43 3.1 G_oc-temp_lat-fusifor
- 2355 1645 4548 2.377 0.498 0.211 0.120 87 12.0 G_oc-temp_med-Lingual
- 1352 907 4141 3.514 0.789 0.166 0.091 38 4.9 G_oc-temp_med-Parahip
- 2397 1582 5795 2.734 0.668 0.179 0.091 72 8.1 G_orbital
- 2519 1696 5341 2.681 0.490 0.163 0.059 58 5.8 G_pariet_inf-Angular
- 2178 1480 5180 2.739 0.484 0.165 0.067 54 6.0 G_pariet_inf-Supramar
- 2192 1491 3690 2.122 0.466 0.138 0.048 37 4.3 G_parietal_sup
- 2075 1289 3725 2.234 0.495 0.148 0.055 42 4.4 G_postcentral
- 2512 1569 6024 2.845 0.383 0.131 0.048 50 5.0 G_precentral
- 2410 1597 5303 2.591 0.563 0.179 0.073 69 7.5 G_precuneus
- 538 369 1228 2.694 0.601 0.219 0.136 28 2.3 G_rectus
- 321 200 590 2.743 0.895 0.093 0.165 11 0.4 G_subcallosal
- 321 199 642 2.535 0.348 0.162 0.114 12 1.7 G_temp_sup-G_T_transv
- 1789 1173 5154 3.149 0.508 0.169 0.072 51 4.6 G_temp_sup-Lateral
- 686 476 1878 3.345 0.765 0.145 0.065 14 1.9 G_temp_sup-Plan_polar
- 545 390 1176 2.681 0.374 0.108 0.025 4 0.5 G_temp_sup-Plan_tempo
- 1954 1326 5110 2.772 0.726 0.178 0.085 56 7.0 G_temporal_inf
- 2504 1716 7415 3.104 0.716 0.161 0.064 59 6.4 G_temporal_middle
- 380 253 473 2.062 0.311 0.098 0.020 2 0.3 Lat_Fis-ant-Horizont
- 190 137 245 2.150 0.323 0.126 0.030 1 0.3 Lat_Fis-ant-Vertical
- 1283 851 1765 2.478 0.484 0.108 0.030 8 1.6 Lat_Fis-post
- 2981 1840 4152 1.986 0.493 0.163 0.072 83 8.4 Pole_occipital
- 1568 1087 5455 3.477 0.722 0.169 0.085 34 5.3 Pole_temporal
- 1821 1284 2406 2.020 0.504 0.141 0.055 27 4.1 S_calcarine
- 2870 1931 3404 1.901 0.596 0.104 0.026 16 3.2 S_central
- 1008 699 1560 2.221 0.467 0.115 0.029 8 1.2 S_cingul-Marginalis
- 485 330 832 2.744 0.431 0.125 0.039 4 0.8 S_circular_insula_ant
- 1005 660 1512 2.499 0.498 0.096 0.064 32 0.9 S_circular_insula_inf
- 1342 880 1945 2.468 0.473 0.122 0.057 14 3.6 S_circular_insula_sup
- 905 634 1383 2.298 0.488 0.093 0.018 4 0.7 S_collat_transv_ant
- 507 341 656 2.235 0.450 0.152 0.043 6 0.9 S_collat_transv_post
- 1584 1061 2406 2.349 0.397 0.135 0.050 21 3.0 S_front_inf
- 1819 1245 2820 2.363 0.459 0.146 0.049 28 3.6 S_front_middle
- 2516 1705 4227 2.583 0.466 0.129 0.036 26 3.9 S_front_sup
- 435 283 700 2.440 0.417 0.100 0.020 2 0.4 S_interm_prim-Jensen
- 2771 1865 4101 2.211 0.447 0.128 0.041 32 4.3 S_intrapariet_and_P_trans
- 1323 877 1759 2.243 0.368 0.138 0.042 15 2.2 S_oc_middle_and_Lunatus
- 1761 1157 2716 2.285 0.458 0.140 0.039 24 2.9 S_oc_sup_and_transversal
- 730 488 963 2.306 0.309 0.142 0.049 8 1.4 S_occipital_ant
- 568 378 885 2.162 0.559 0.127 0.057 23 1.2 S_oc-temp_lat
- 1559 1106 2549 2.476 0.448 0.116 0.029 12 1.9 S_oc-temp_med_and_Lingual
- 332 211 468 2.365 0.493 0.149 0.053 4 0.7 S_orbital_lateral
- 564 408 926 2.171 0.731 0.116 0.044 5 1.2 S_orbital_med-olfact
- 1230 831 2118 2.549 0.570 0.147 0.055 20 2.7 S_orbital-H_Shaped
- 1708 1167 2412 2.252 0.468 0.126 0.035 16 2.4 S_parieto_occipital
- 1402 868 1702 2.421 0.930 0.159 0.061 36 3.4 S_pericallosal
- 2238 1510 2938 2.079 0.441 0.131 0.062 32 3.6 S_postcentral
- 1623 1078 2566 2.588 0.415 0.106 0.025 10 1.8 S_precentral-inf-part
- 1302 870 1879 2.520 0.390 0.100 0.022 6 1.3 S_precentral-sup-part
- 159 110 262 2.619 0.353 0.162 0.045 2 0.4 S_suborbital
- 933 647 1583 2.395 0.564 0.132 0.035 9 1.2 S_subparietal
- 988 666 1269 2.166 0.522 0.132 0.035 9 1.4 S_temporal_inf
- 6270 4275 11354 2.672 0.491 0.130 0.035 74 9.1 S_temporal_sup
- 312 213 502 2.724 0.501 0.120 0.031 2 0.4 S_temporal_transverse
- #-----------------------------------------
- #@# Cortical Parc 3 rh Thu Aug 8 21:55:02 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub017 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...
- 1142 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2526 changed, 117762 examined...
- 001: 647 changed, 10810 examined...
- 002: 177 changed, 3452 examined...
- 003: 71 changed, 1066 examined...
- 004: 32 changed, 409 examined...
- 005: 16 changed, 195 examined...
- 006: 9 changed, 89 examined...
- 007: 7 changed, 64 examined...
- 008: 5 changed, 33 examined...
- 009: 4 changed, 25 examined...
- 010: 3 changed, 21 examined...
- 011: 3 changed, 21 examined...
- 012: 5 changed, 22 examined...
- 013: 3 changed, 21 examined...
- 014: 4 changed, 13 examined...
- 015: 5 changed, 19 examined...
- 016: 4 changed, 20 examined...
- 017: 1 changed, 17 examined...
- 018: 1 changed, 7 examined...
- 019: 2 changed, 7 examined...
- 020: 2 changed, 12 examined...
- 021: 2 changed, 11 examined...
- 022: 1 changed, 10 examined...
- 023: 1 changed, 7 examined...
- 024: 1 changed, 7 examined...
- 025: 1 changed, 7 examined...
- 026: 2 changed, 7 examined...
- 027: 1 changed, 10 examined...
- 028: 1 changed, 7 examined...
- 029: 1 changed, 7 examined...
- 030: 1 changed, 7 examined...
- 031: 1 changed, 7 examined...
- 032: 1 changed, 7 examined...
- 033: 1 changed, 7 examined...
- 034: 1 changed, 7 examined...
- 035: 1 changed, 7 examined...
- 036: 0 changed, 7 examined...
- 251 labels changed using aseg
- 000: 51 total segments, 18 labels (162 vertices) changed
- 001: 33 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 61 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 527 vertices marked for relabeling...
- 527 labels changed in reclassification.
- writing output to ../label/rh.aparc.DKTatlas40.annot...
- classification took 0 minutes and 54 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 3 rh Thu Aug 8 21:55:56 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 sub017 rh white
- computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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
- 1273 814 2561 3.019 0.645 0.165 0.047 44 2.7 caudalanteriorcingulate
- 2834 1900 5440 2.639 0.398 0.117 0.032 27 3.9 caudalmiddlefrontal
- 2433 1651 3627 1.957 0.419 0.153 0.055 40 5.5 cuneus
- 547 405 2038 3.954 0.526 0.147 0.045 7 1.1 entorhinal
- 3111 2112 6384 2.619 0.608 0.141 0.053 77 6.2 fusiform
- 7141 4772 13948 2.620 0.492 0.151 0.050 128 14.4 inferiorparietal
- 3959 2682 8997 2.666 0.727 0.152 0.066 79 10.7 inferiortemporal
- 1152 769 2008 2.411 0.757 0.152 0.061 22 2.9 isthmuscingulate
- 7097 4592 11116 2.206 0.483 0.154 0.056 146 15.6 lateraloccipital
- 3614 2446 7368 2.617 0.705 0.168 0.085 93 11.1 lateralorbitofrontal
- 3748 2647 6595 2.293 0.516 0.183 0.094 105 14.8 lingual
- 1737 1181 3605 2.554 0.659 0.190 0.147 83 6.9 medialorbitofrontal
- 5351 3694 12892 2.886 0.670 0.146 0.050 96 10.9 middletemporal
- 955 612 2153 2.954 0.802 0.132 0.070 22 2.3 parahippocampal
- 1830 1167 3210 2.515 0.575 0.124 0.043 22 2.8 paracentral
- 1970 1328 4008 2.671 0.392 0.136 0.048 32 3.6 parsopercularis
- 1158 758 2398 2.603 0.494 0.147 0.049 19 2.5 parsorbitalis
- 2146 1419 4032 2.465 0.464 0.144 0.050 40 4.4 parstriangularis
- 1937 1330 2401 1.904 0.500 0.158 0.062 30 4.6 pericalcarine
- 6073 3980 9580 2.094 0.615 0.143 0.057 106 12.0 postcentral
- 1464 954 2661 2.598 0.651 0.139 0.039 24 2.3 posteriorcingulate
- 6590 4285 12290 2.580 0.499 0.119 0.036 80 10.0 precentral
- 4655 3153 8681 2.453 0.559 0.157 0.058 97 11.3 precuneus
- 858 566 1762 3.157 0.618 0.162 0.164 20 2.0 rostralanteriorcingulate
- 4500 3041 8306 2.407 0.519 0.157 0.060 90 10.5 rostralmiddlefrontal
- 11123 7509 23607 2.785 0.540 0.147 0.049 179 21.4 superiorfrontal
- 6693 4475 10336 2.125 0.446 0.139 0.043 101 11.5 superiorparietal
- 6495 4414 15471 2.991 0.663 0.146 0.057 116 14.7 superiortemporal
- 4103 2760 7743 2.529 0.480 0.135 0.047 63 7.7 supramarginal
- 483 298 810 2.443 0.407 0.139 0.084 13 1.9 transversetemporal
- 2728 1760 5543 2.899 0.732 0.139 0.089 74 9.9 insula
- #--------------------------------------------
- #@# Refine Pial Surfs w/ T2/FLAIR Thu Aug 8 21:56:13 CEST 2013
- bbregister --s sub017 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/T2raw.lta --init-fsl --T2
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/T2raw.dat.log
- Thu Aug 8 21:56:13 CEST 2013
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/scripts
- /opt/freesurfer/5.3.0/bin/bbregister --s sub017 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/T2raw.lta --init-fsl --T2
- $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $
- Linux snake5 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
- FREESURFER_HOME /opt/freesurfer/5.3.0
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/template.nii
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/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/sub017/mri/orig/T2raw.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.998353, -0.0379406, 0.0430326)
- j_ras = (-0.0315844, 0.989674, 0.139811)
- k_ras = (0.0478928, -0.138221, 0.989243)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/template.nii...
- fslregister --s sub017 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/fslregister --dof 6 --fsvol brainmask.mgz
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/reg.init.dat.fslregister.log
- Thu Aug 8 21:56:18 CEST 2013
- --s sub017 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/fslregister --dof 6 --fsvol brainmask.mgz
- $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $
- snake5
- Linux snake5 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
- nIters 1
- --------------------------------------
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/scripts
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/fslregister/refvol.fslregister.nii
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/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/sub017/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 = (1.49012e-08, -1.49012e-08, -1)
- k_ras = (2.32831e-09, 1, 1.49012e-08)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/fslregister/refvol.fslregister.nii...
- --------------------------------------
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/scripts
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/fslregister/movvol.fslregister.nii --frame 0
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/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/sub017/mri/transforms/tmp.bbregister.8459/template.nii...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.998353, -0.0379406, 0.0430326)
- j_ras = (-0.0315844, 0.989674, 0.139811)
- k_ras = (0.0478928, -0.138221, 0.989243)
- keeping frame 0
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/fslregister/movvol.fslregister.nii...
- Mov determinant is -0.311069
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/scripts
- tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/fslregister/movvol.fslregister.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/fslregister/reg0.8516.dat --regheader --fslregout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/reg.init.dat.fsl.mat0 --s sub017 --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/sub017/mri/transforms/tmp.bbregister.8459/fslregister/movvol.fslregister.nii
- reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/fslregister/reg0.8516.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/sub017/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/sub017/mri/transforms/tmp.bbregister.8459/fslregister/movvol.fslregister.nii
- Tmov: --------------------
- -0.700 0.000 0.000 95.887;
- 0.000 0.000 0.667 -128.000;
- 0.000 -0.667 0.000 128.000;
- 0.000 0.000 0.000 1.000;
- mkheaderreg = 1, float2int = 0
- Computing reg from header (and possibly input matrix)
- ---- Input registration matrix (computed) --------
- 0.998 0.038 -0.043 -0.000;
- 0.048 -0.138 0.989 0.000;
- 0.032 -0.990 -0.140 -0.000;
- 0.000 0.000 0.000 1.000;
- ---------------------------------------
- ---- Input registration matrix --------
- 0.998 0.038 -0.043 -0.000;
- 0.048 -0.138 0.989 0.000;
- 0.032 -0.990 -0.140 -0.000;
- 0.000 0.000 0.000 1.000;
- Determinant 1
- subject = sub017
- RegMat ---------------------------
- 0.998 0.038 -0.043 -0.000;
- 0.048 -0.138 0.989 0.000;
- 0.032 -0.990 -0.140 -0.000;
- 0.000 0.000 0.000 1.000;
- FSLOUTPUTTYPE NIFTI
- tkreg2FSL: mov det = -0.311069, ref det = -1
- Thu Aug 8 21:56:28 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/scripts
- flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/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/sub017/mri/transforms/tmp.bbregister.8459/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/reg.init.dat.fsl.mat0
- Thu Aug 8 22:01:17 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/scripts
- flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/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/sub017/mri/transforms/tmp.bbregister.8459/reg.init.dat.fsl.mat -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/fslregister/fslmat0.trans.mat -schedule /opt/freesurfer/5.3.0/bin/flirt.newdefault.20080811.sch
- tkregister2_cmdl --s sub017 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/reg.init.dat --fslreg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/reg.init.dat.fsl.mat --noedit
- tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl
- ---- FSL registration matrix --------
- 0.999 0.030 -0.039 33.729;
- -0.036 -0.116 -0.993 275.031;
- -0.034 0.993 -0.115 18.156;
- 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/sub017/mri/transforms/tmp.bbregister.8459/template.nii
- reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/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/sub017/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/sub017/mri/transforms/tmp.bbregister.8459/template.nii
- Tmov: --------------------
- -0.700 0.000 0.000 95.887;
- 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 = -0.311069, ref det = -1
- ---- Input registration matrix (computed) --------
- 0.999 0.034 -0.036 0.219;
- 0.039 -0.115 0.993 1.568;
- 0.030 -0.993 -0.116 -0.960;
- 0.000 0.000 0.000 1.000;
- ---------------------------------------
- ---- Input registration matrix --------
- 0.999 0.034 -0.036 0.219;
- 0.039 -0.115 0.993 1.568;
- 0.030 -0.993 -0.116 -0.960;
- 0.000 0.000 0.000 1.000;
- Determinant 1
- subject = sub017
- RegMat ---------------------------
- 0.999 0.034 -0.036 0.219;
- 0.039 -0.115 0.993 1.568;
- 0.030 -0.993 -0.116 -0.960;
- 0.000 0.000 0.000 1.000;
-
- Started at Thu Aug 8 21:56:18 CEST 2013
- Ended at Thu Aug 8 22:07:49 CEST 2013
-
- fslregister Done
-
- To check results, run:
- tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/reg.init.dat --surf orig
-
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/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/sub017/scripts
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/template.nii
- regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/reg.init.dat
- subject sub017
- dof 6
- outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/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 1376304493
- TransRandMax 0.000000
- RotRandMax 0.000000
- Translations 0.000000 0.000000 0.000000
- Rotations 0.000000 0.000000 0.000000
- Input reg
- 0.999 0.034 -0.036 0.219;
- 0.039 -0.115 0.993 1.568;
- 0.030 -0.993 -0.116 -0.960;
- 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 1.028282
- 1 -25.0 -25.0 25.0 1.000585
- 2 -25.0 25.0 -25.0 1.045979
- 3 -25.0 25.0 25.0 1.008282
- 4 25.0 -25.0 -25.0 1.054541
- 5 25.0 -25.0 25.0 1.015765
- 6 25.0 25.0 -25.0 0.986006
- 7 25.0 25.0 25.0 1.024750
- REL: 8 0.550692 8.164190 1.020524 rel = 0.539617
- Initial costs ----------------
- Number of surface hits 2205
- WM Intensity 52.9625 +/- 10.8160
- Ctx Intensity 62.0532 +/- 15.1184
- Pct Contrast 14.7214 +/- 27.0568
- Cost 0.5507
- RelCost 0.5396
- ------------------------------------
- Brute force preopt -4 4 4, n = 729
- 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9776 0.9776 0.0
- 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.9549 0.9549 0.0
- 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.8590 0.8590 0.0
- 24 -4.0000 -4.0000 -4.0000 4.0000 4.0000 -4.0000 0.8472 0.8472 0.0
- 39 -4.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.7781 0.7781 0.0
- 57 -4.0000 -4.0000 4.0000 -4.0000 0.0000 -4.0000 0.7733 0.7733 0.0
- 102 -4.0000 0.0000 -4.0000 4.0000 0.0000 -4.0000 0.7728 0.7728 0.0
- 120 -4.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.7528 0.7528 0.0
- 283 0.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.6141 0.6141 0.0
- 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.5507 0.5507 0.0
- Brute Force --------------------------
- Min cost was 0.550692
- Number of iterations 729
- Search time 2.220000 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
- 5 -0.618 0.000 0.000 0.000 0.000 0.000 0.5361687536
- 7 -0.737 0.000 0.000 0.000 0.000 0.000 0.5360418766
- 10 -0.775 0.000 0.000 0.000 0.000 0.000 0.5349764039
- 12 -0.768 0.000 0.000 0.000 0.000 0.000 0.5348510747
- 14 -0.767 0.000 0.000 0.000 0.000 0.000 0.5348497513
- 18 -0.767 -1.618 0.000 0.000 0.000 0.000 0.2304467739
- 24 -0.767 -1.907 0.000 0.000 0.000 0.000 0.2142245028
- 25 -0.767 -1.922 0.000 0.000 0.000 0.000 0.2141102131
- 27 -0.767 -1.926 0.000 0.000 0.000 0.000 0.2140979706
- 28 -0.767 -1.927 0.000 0.000 0.000 0.000 0.2140977897
- 31 -0.767 -1.927 1.000 0.000 0.000 0.000 0.1502588225
- 35 -0.767 -1.927 0.618 0.000 0.000 0.000 0.1459456529
- 36 -0.767 -1.927 0.743 0.000 0.000 0.000 0.1455617406
- 37 -0.767 -1.927 0.708 0.000 0.000 0.000 0.1450994235
- 38 -0.767 -1.927 0.689 0.000 0.000 0.000 0.1450565031
- 41 -0.767 -1.927 0.687 0.000 0.000 0.000 0.1450560489
- 49 -0.767 -1.927 0.687 0.037 0.000 0.000 0.1449045493
- 50 -0.767 -1.927 0.687 0.031 0.000 0.000 0.1448347882
- 51 -0.767 -1.927 0.687 0.023 0.000 0.000 0.1448070609
- 52 -0.767 -1.927 0.687 0.024 0.000 0.000 0.1448068474
- 59 -0.767 -1.927 0.687 0.024 0.382 0.000 0.1365568241
- 60 -0.767 -1.927 0.687 0.024 0.303 0.000 0.1345924621
- 61 -0.767 -1.927 0.687 0.024 0.261 0.000 0.1338792093
- 63 -0.767 -1.927 0.687 0.024 0.250 0.000 0.1337778129
- 65 -0.767 -1.927 0.687 0.024 0.241 0.000 0.1337314292
- 66 -0.767 -1.927 0.687 0.024 0.240 0.000 0.1337271589
- 68 -0.767 -1.927 0.687 0.024 0.238 0.000 0.1337258159
- 69 -0.767 -1.927 0.687 0.024 0.237 0.000 0.1337255587
- 76 -0.767 -1.927 0.687 0.024 0.237 0.382 0.1291250195
- 77 -0.767 -1.927 0.687 0.024 0.237 0.247 0.1270069339
- 79 -0.767 -1.927 0.687 0.024 0.237 0.287 0.1265904075
- 81 -0.767 -1.927 0.687 0.024 0.237 0.289 0.1265900063
- 90 -0.385 -1.927 0.687 0.024 0.237 0.289 0.1149722025
- 92 -0.374 -1.927 0.687 0.024 0.237 0.289 0.1148803567
- 94 -0.273 -1.927 0.687 0.024 0.237 0.289 0.1131011727
- 96 -0.258 -1.927 0.687 0.024 0.237 0.289 0.1129973874
- 99 -0.264 -1.927 0.687 0.024 0.237 0.289 0.1129916409
- 111 -0.264 -1.917 0.687 0.024 0.237 0.289 0.1129533994
- 112 -0.264 -1.914 0.687 0.024 0.237 0.289 0.1129492400
- 124 -0.264 -1.914 0.702 0.024 0.237 0.289 0.1128266163
- 125 -0.264 -1.914 0.701 0.024 0.237 0.289 0.1128244485
- 126 -0.264 -1.914 0.700 0.024 0.237 0.289 0.1128240623
- 135 -0.264 -1.914 0.700 0.023 0.237 0.289 0.1127918203
- 137 -0.264 -1.914 0.700 -0.028 0.237 0.289 0.1126724443
- 138 -0.264 -1.914 0.700 -0.005 0.237 0.289 0.1124501671
- 141 -0.264 -1.914 0.700 -0.002 0.237 0.289 0.1124468414
- 150 -0.264 -1.914 0.700 -0.002 0.272 0.289 0.1118990841
- 152 -0.264 -1.914 0.700 -0.002 0.282 0.289 0.1118934618
- 153 -0.264 -1.914 0.700 -0.002 0.278 0.289 0.1118828098
- 154 -0.264 -1.914 0.700 -0.002 0.277 0.289 0.1118825292
- 162 -0.264 -1.914 0.700 -0.002 0.277 0.442 0.1097817247
- 163 -0.264 -1.914 0.700 -0.002 0.277 0.435 0.1097547639
- 164 -0.264 -1.914 0.700 -0.002 0.277 0.422 0.1097533257
- 166 -0.264 -1.914 0.700 -0.002 0.277 0.428 0.1097388431
- 167 -0.264 -1.914 0.700 -0.002 0.277 0.429 0.1097379822
- 176 -0.199 -1.914 0.700 -0.002 0.277 0.429 0.1095425285
- 179 -0.152 -1.914 0.700 -0.002 0.277 0.429 0.1093368986
- 180 -0.157 -1.914 0.700 -0.002 0.277 0.429 0.1093011175
- 181 -0.168 -1.914 0.700 -0.002 0.277 0.429 0.1092629880
- 190 -0.168 -1.915 0.700 -0.002 0.277 0.429 0.1092102924
- 193 -0.168 -1.949 0.700 -0.002 0.277 0.429 0.1083581778
- 194 -0.168 -1.948 0.700 -0.002 0.277 0.429 0.1083524431
- 195 -0.168 -1.946 0.700 -0.002 0.277 0.429 0.1083454811
- 207 -0.168 -1.946 0.715 -0.002 0.277 0.429 0.1079970624
- 208 -0.168 -1.946 0.724 -0.002 0.277 0.429 0.1079463003
- 209 -0.168 -1.946 0.723 -0.002 0.277 0.429 0.1079436597
- 210 -0.168 -1.946 0.722 -0.002 0.277 0.429 0.1079436548
- 221 -0.168 -1.946 0.722 -0.007 0.277 0.429 0.1079398826
- 222 -0.168 -1.946 0.722 -0.005 0.277 0.429 0.1079346279
- 230 -0.168 -1.946 0.722 -0.005 0.267 0.429 0.1077530032
- 233 -0.168 -1.946 0.722 -0.005 0.252 0.429 0.1076588349
- 234 -0.168 -1.946 0.722 -0.005 0.254 0.429 0.1076582464
- 244 -0.168 -1.946 0.722 -0.005 0.254 0.450 0.1075714928
- 245 -0.168 -1.946 0.722 -0.005 0.254 0.447 0.1075550909
- 246 -0.168 -1.946 0.722 -0.005 0.254 0.444 0.1075507605
- 258 -0.176 -1.946 0.722 -0.005 0.254 0.444 0.1075421319
- 259 -0.173 -1.946 0.722 -0.005 0.254 0.444 0.1075416305
- 261 -0.174 -1.946 0.722 -0.005 0.254 0.444 0.1075413206
- 271 -0.174 -1.950 0.722 -0.005 0.254 0.444 0.1075312875
- 284 -0.174 -1.950 0.733 -0.005 0.254 0.444 0.1074843337
- 285 -0.174 -1.950 0.730 -0.005 0.254 0.444 0.1074733323
- 296 -0.174 -1.950 0.730 -0.004 0.254 0.444 0.1074693599
- 307 -0.174 -1.950 0.730 -0.004 0.248 0.444 0.1074679211
- 308 -0.174 -1.950 0.730 -0.004 0.251 0.444 0.1074646247
- 319 -0.174 -1.950 0.730 -0.004 0.251 0.447 0.1074646171
- 321 -0.174 -1.950 0.730 -0.004 0.251 0.446 0.1074635789
- 322 -0.174 -1.950 0.730 -0.004 0.251 0.445 0.1074632194
- 331 -0.178 -1.950 0.730 -0.004 0.251 0.445 0.1074573426
- 332 -0.179 -1.950 0.730 -0.004 0.251 0.445 0.1074563949
- 333 -0.180 -1.950 0.730 -0.004 0.251 0.445 0.1074549366
- 345 -0.180 -1.951 0.730 -0.004 0.251 0.445 0.1074548934
- 366 -0.180 -1.951 0.730 -0.003 0.251 0.445 0.1074530480
- 378 -0.180 -1.951 0.730 -0.003 0.250 0.445 0.1074525345
- 388 -0.180 -1.951 0.730 -0.003 0.250 0.444 0.1074519949
- 400 -0.181 -1.951 0.730 -0.003 0.250 0.444 0.1074512319
- 411 -0.181 -1.950 0.730 -0.003 0.250 0.444 0.1074505724
- 424 -0.181 -1.950 0.729 -0.003 0.250 0.444 0.1074505429
- 434 -0.181 -1.950 0.729 -0.002 0.250 0.444 0.1074497259
- Powell done niters = 5
- Computing relative cost
- 0 -25.0 -25.0 -25.0 1.028480
- 1 -25.0 -25.0 25.0 1.013004
- 2 -25.0 25.0 -25.0 1.017399
- 3 -25.0 25.0 25.0 1.011364
- 4 25.0 -25.0 -25.0 0.972474
- 5 25.0 -25.0 25.0 1.036422
- 6 25.0 25.0 -25.0 0.999075
- 7 25.0 25.0 25.0 1.045767
- REL: 8 0.107450 8.123987 1.015498 rel = 0.10581
- Number of iterations 5
- Min cost was 0.107450
- Number of FunctionCalls 457
- TolPowell 0.000100
- nMaxItersPowell 36
- OptimizationTime 1.495000 sec
- Parameters at optimum (transmm) -0.18123 -1.94952 0.72860
- Parameters at optimum (rotdeg) -0.00156 0.24981 0.44429
- Final costs ----------------
- Number of surface hits 2205
- WM Intensity 49.9591 +/- 7.8273
- Ctx Intensity 62.4556 +/- 7.9503
- Pct Contrast 22.4663 +/- 14.3042
- Cost 0.1074
- RelCost 0.5396
- Reg at min cost was
- 0.999 0.031 -0.044 0.022;
- 0.047 -0.115 0.992 -0.380;
- 0.025 -0.993 -0.116 -0.232;
- 0.000 0.000 0.000 1.000;
- Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/bbr.pass1.dat, type = 14
- Original Reg
- 0.999 0.034 -0.036 0.219;
- 0.039 -0.115 0.993 1.568;
- 0.030 -0.993 -0.116 -0.960;
- 0.000 0.000 0.000 1.000;
- Original Reg - Optimal Reg
- 0.000 0.003 0.008 0.198;
- -0.008 -0.000 0.000 1.948;
- 0.004 0.000 -0.000 -0.728;
- 0.000 0.000 0.000 0.000;
- Computing change in lh position
- LH rmsDiffMean 2.378444
- Computing change in rh position
- Surface RMS Diff (mm) 2.140999 2.669006
- mri_segreg done
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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/sub017/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/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/sub017/scripts
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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/sub017/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/template.nii
- regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/tmp.bbregister.8459/bbr.pass1.dat
- subject sub017
- dof 6
- outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 1376496607
- TransRandMax 0.000000
- RotRandMax 0.000000
- Translations 0.000000 0.000000 0.000000
- Rotations 0.000000 0.000000 0.000000
- Input reg
- 0.999 0.031 -0.044 0.022;
- 0.047 -0.115 0.992 -0.380;
- 0.025 -0.993 -0.116 -0.232;
- 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 1.014637
- 1 -25.0 -25.0 25.0 0.993182
- 2 -25.0 25.0 -25.0 0.990056
- 3 -25.0 25.0 25.0 1.022656
- 4 25.0 -25.0 -25.0 1.020820
- 5 25.0 -25.0 25.0 1.034447
- 6 25.0 25.0 -25.0 1.009558
- 7 25.0 25.0 25.0 1.021155
- REL: 8 0.107301 8.106511 1.013314 rel = 0.105891
- Initial costs ----------------
- Number of surface hits 221145
- WM Intensity 49.8423 +/- 8.0083
- Ctx Intensity 62.5564 +/- 7.9976
- Pct Contrast 22.8763 +/- 14.3153
- Cost 0.1073
- RelCost 0.1059
- ------------------------------------
- Brute force preopt -0.1 0.1 0.1, n = 729
- 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1255 0.1255 0.0
- 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1249 0.1249 0.0
- 2 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.1235 0.1235 0.0
- 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.1208 0.1208 0.0
- 6 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 0.1197 0.1197 0.0
- 9 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 -0.1000 0.1189 0.1189 0.0
- 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.1161 0.1161 0.0
- 15 -0.1000 -0.1000 -0.1000 0.0000 0.1000 -0.1000 0.1159 0.1159 0.0
- 33 -0.1000 -0.1000 0.0000 -0.1000 0.1000 -0.1000 0.1154 0.1154 0.0
- 37 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.0000 0.1146 0.1146 0.0
- 39 -0.1000 -0.1000 0.0000 0.0000 0.0000 -0.1000 0.1139 0.1139 0.0
- 40 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.0000 0.1137 0.1137 0.0
- 42 -0.1000 -0.1000 0.0000 0.0000 0.1000 -0.1000 0.1133 0.1133 0.0
- 58 -0.1000 -0.1000 0.1000 -0.1000 0.0000 0.0000 0.1132 0.1132 0.0
- 64 -0.1000 -0.1000 0.1000 0.0000 -0.1000 0.0000 0.1127 0.1127 0.0
- 67 -0.1000 -0.1000 0.1000 0.0000 0.0000 0.0000 0.1121 0.1121 0.0
- 107 -0.1000 0.0000 -0.1000 0.1000 0.1000 0.1000 0.1113 0.1113 0.0
- 118 -0.1000 0.0000 0.0000 0.0000 -0.1000 0.0000 0.1109 0.1109 0.0
- 120 -0.1000 0.0000 0.0000 0.0000 0.0000 -0.1000 0.1104 0.1104 0.0
- 121 -0.1000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1091 0.1091 0.0
- 148 -0.1000 0.0000 0.1000 0.0000 0.0000 0.0000 0.1088 0.1088 0.0
- 149 -0.1000 0.0000 0.1000 0.0000 0.0000 0.1000 0.1078 0.1078 0.0
- 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1074 0.1074 0.0
- Brute Force --------------------------
- Min cost was 0.107450
- Number of iterations 729
- Search time 2.278000 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 -0.057 0.000 0.000 0.000 0.000 0.000 0.1068712475
- 8 -0.069 0.000 0.000 0.000 0.000 0.000 0.1068692403
- 9 -0.064 0.000 0.000 0.000 0.000 0.000 0.1068643614
- 18 -0.064 0.067 0.000 0.000 0.000 0.000 0.1067500730
- 19 -0.064 0.041 0.000 0.000 0.000 0.000 0.1066512273
- 20 -0.064 0.040 0.000 0.000 0.000 0.000 0.1066502908
- 21 -0.064 0.038 0.000 0.000 0.000 0.000 0.1066497443
- 30 -0.064 0.038 0.094 0.000 0.000 0.000 0.1057392862
- 31 -0.064 0.038 0.093 0.000 0.000 0.000 0.1057373894
- 32 -0.064 0.038 0.085 0.000 0.000 0.000 0.1057290241
- 35 -0.064 0.038 0.084 0.000 0.000 0.000 0.1057289980
- 55 -0.064 0.038 0.084 0.000 0.001 0.000 0.1057289056
- 62 -0.064 0.038 0.084 0.000 0.001 0.022 0.1056238860
- 63 -0.064 0.038 0.084 0.000 0.001 0.033 0.1056007118
- 64 -0.064 0.038 0.084 0.000 0.001 0.039 0.1055993128
- 65 -0.064 0.038 0.084 0.000 0.001 0.037 0.1055987166
- 76 -0.055 0.038 0.084 0.000 0.001 0.037 0.1055954948
- 77 -0.057 0.038 0.084 0.000 0.001 0.037 0.1055954153
- 78 -0.058 0.038 0.084 0.000 0.001 0.037 0.1055953744
- 88 -0.058 0.039 0.084 0.000 0.001 0.037 0.1055953030
- 106 -0.058 0.039 0.084 0.002 0.001 0.037 0.1055947262
- 107 -0.058 0.039 0.084 0.003 0.001 0.037 0.1055947261
- 115 -0.058 0.039 0.084 0.003 0.009 0.037 0.1055859792
- 116 -0.058 0.039 0.084 0.003 0.010 0.037 0.1055858223
- 125 -0.058 0.039 0.084 0.003 0.010 0.041 0.1055831028
- 126 -0.058 0.039 0.084 0.003 0.010 0.043 0.1055826027
- 137 -0.051 0.039 0.084 0.003 0.010 0.043 0.1055788859
- 138 -0.052 0.039 0.084 0.003 0.010 0.043 0.1055788374
- 147 -0.052 0.040 0.084 0.003 0.010 0.043 0.1055783017
- 148 -0.052 0.042 0.084 0.003 0.010 0.043 0.1055781114
- 158 -0.052 0.042 0.081 0.003 0.010 0.043 0.1055775445
- 159 -0.052 0.042 0.082 0.003 0.010 0.043 0.1055771796
- 168 -0.052 0.042 0.082 0.005 0.010 0.043 0.1055768000
- 185 -0.052 0.042 0.082 0.005 0.010 0.044 0.1055764201
- 186 -0.052 0.042 0.082 0.005 0.010 0.045 0.1055762041
- 195 -0.050 0.043 0.081 0.005 0.010 0.046 0.1055754896
- 199 -0.051 0.042 0.081 0.005 0.010 0.046 0.1055754787
- 200 -0.051 0.042 0.081 0.005 0.010 0.046 0.1055754639
- 201 -0.050 0.043 0.081 0.005 0.010 0.046 0.1055754598
- 204 -0.050 0.043 0.081 0.005 0.010 0.046 0.1055754590
- 205 -0.050 0.043 0.081 0.005 0.010 0.046 0.1055754545
- 225 -0.050 0.042 0.081 0.005 0.010 0.046 0.1055754529
- 260 -0.050 0.042 0.081 0.005 0.010 0.046 0.1055754521
- 261 -0.050 0.042 0.081 0.005 0.010 0.046 0.1055754386
- 319 -0.050 0.042 0.081 0.005 0.010 0.046 0.1055754357
- 322 -0.050 0.042 0.081 0.005 0.010 0.046 0.1055754255
- 377 -0.050 0.042 0.081 0.005 0.009 0.046 0.1055754246
- Powell done niters = 5
- Computing relative cost
- 0 -25.0 -25.0 -25.0 1.014696
- 1 -25.0 -25.0 25.0 0.993794
- 2 -25.0 25.0 -25.0 0.991808
- 3 -25.0 25.0 25.0 1.021216
- 4 25.0 -25.0 -25.0 1.021337
- 5 25.0 -25.0 25.0 1.033976
- 6 25.0 25.0 -25.0 1.009100
- 7 25.0 25.0 25.0 1.021647
- REL: 8 0.105575 8.107574 1.013447 rel = 0.104175
- Number of iterations 5
- Min cost was 0.105575
- Number of FunctionCalls 392
- TolPowell 0.000000
- nMaxItersPowell 36
- OptimizationTime 56.296000 sec
- Parameters at optimum (transmm) -0.04955 0.04193 0.08066
- Parameters at optimum (rotdeg) 0.00547 0.00923 0.04620
- Final costs ----------------
- Number of surface hits 221145
- WM Intensity 49.8381 +/- 8.0201
- Ctx Intensity 62.5469 +/- 7.9977
- Pct Contrast 22.8707 +/- 14.2956
- Cost 0.1056
- RelCost 0.1059
- Reg at min cost was
- 0.999 0.031 -0.045 -0.027;
- 0.048 -0.115 0.992 -0.338;
- 0.025 -0.993 -0.116 -0.152;
- 0.000 0.000 0.000 1.000;
- Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/T2raw.dat, type = 14
- Original Reg
- 0.999 0.031 -0.044 0.022;
- 0.047 -0.115 0.992 -0.380;
- 0.025 -0.993 -0.116 -0.232;
- 0.000 0.000 0.000 1.000;
- Original Reg - Optimal Reg
- 0.000 0.000 0.001 0.049;
- -0.001 -0.000 0.000 -0.042;
- 0.000 0.000 -0.000 -0.081;
- 0.000 0.000 0.000 0.000;
- Computing change in lh position
- LH rmsDiffMean 0.117739
- Computing change in rh position
- Surface RMS Diff (mm) 0.123056 0.155097
- mri_segreg done
- tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/T2raw.dat --noedit --ltaout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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/sub017/mri/orig/T2raw.mgz
- reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 0.031 -0.045 -0.027;
- 0.048 -0.115 0.992 -0.338;
- 0.025 -0.993 -0.116 -0.152;
- 0.000 0.000 0.000 1.000;
- float2int = 0
- ---------------------------------------
- INFO: loading target /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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/sub017/mri/orig/T2raw.mgz
- Tmov: --------------------
- -0.700 0.000 0.000 95.887;
- 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 0.031 -0.045 -0.027;
- 0.048 -0.115 0.992 -0.338;
- 0.025 -0.993 -0.116 -0.152;
- 0.000 0.000 0.000 1.000;
- Determinant 1
- subject = sub017
- RegMat ---------------------------
- 0.999 0.031 -0.045 -0.027;
- 0.048 -0.115 0.992 -0.338;
- 0.025 -0.993 -0.116 -0.152;
- 0.000 0.000 0.000 1.000;
- transformed matrix:
- 1.000 0.006 0.001 -0.060;
- -0.006 1.000 0.024 0.439;
- -0.001 -0.024 1.000 0.807;
- 0.000 0.000 0.000 1.000;
- transformed matrix:
- 0.699 0.017 -0.032 35.125;
- -0.031 -0.077 -0.661 273.846;
- -0.021 0.662 -0.077 18.350;
- 0.000 0.000 0.000 1.000;
- Cleaning up
-
- Started at Thu Aug 8 21:56:13 CEST 2013
- Ended at Thu Aug 8 22:09:44 CEST 2013
- BBR-Run-Time-Sec 811
-
- bbregister Done
- To check results, run:
- tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/T2raw.dat --surf
-
- mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/T2.mgz
- mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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/sub017/mri/orig/T2raw.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.998353, -0.0379406, 0.0430326)
- j_ras = (-0.0315844, 0.989674, 0.139811)
- k_ras = (0.0478928, -0.138221, 0.989243)
- INFO: Reading transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/T2raw.lta...
- Reading transform with LTAreadEx()
- reading extra input line subject sub017
- reading extra input line fscale 0.150000
- reading template info from volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/orig.mgz...
- INFO: Applying transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/transforms/T2raw.lta...
- ---------------------------------
- INFO: Transform Matrix (linear_ras_to_ras)
- 1.000 0.006 0.001 -0.060;
- -0.006 1.000 0.024 0.439;
- -0.001 -0.024 1.000 0.807;
- 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/sub017/mri/T2.mgz...
- mri_normalize -aseg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/aseg.mgz -sigma 4 -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/rh.white identity.nofile -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/lh.white identity.nofile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/T2.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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/sub017/mri/T2.mgz...
- computing distance transform
- computing distance transform
- computing nonmaximum suppression
- 12215 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/sub017/mri/T2.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/scripts
- cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/lh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/lh.woT2.pial
- `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/lh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/lh.woT2.pial'
- mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub017 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/sub017/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/wm.mgz...
- 15790 bright wm thresholded.
- 318 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/lh.orig...
- computing class statistics...
- border white: 215675 voxels (1.29%)
- border gray 245603 voxels (1.46%)
- WM (92.0): 93.4 +- 10.3 [70.0 --> 110.0]
- GM (75.0) : 73.5 +- 13.0 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 47.0 (was 70)
- setting MAX_BORDER_WHITE to 115.3 (was 105)
- setting MIN_BORDER_WHITE to 60.0 (was 85)
- setting MAX_CSF to 34.0 (was 40)
- setting MAX_GRAY to 94.7 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 53.5 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 21.0 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=105, GM=60
- mean inside = 93.3, mean outside = 69.0
- smoothing surface for 5 iterations...
- reading initial white vertex positions from white...
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.89 +- 0.25 (0.01-->3.67) (max @ vno 94861 --> 95784)
- face area 0.33 +- 0.15 (0.00-->2.73)
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 1 with 583 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 2 with 2 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 3 with 3 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 4 with 2 points - only 0.00% unknown
- deleting segment 5 with 8 points - only 0.00% unknown
- deleting segment 7 with 7 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 9 with 20 points - only 0.00% unknown
- deleting segment 10 with 10 points - only 0.00% unknown
- deleting segment 11 with 7 points - only 0.00% unknown
- deleting segment 12 with 9 points - only 0.00% unknown
- deleting segment 13 with 5 points - only 0.00% unknown
- deleting segment 14 with 6 points - only 0.00% unknown
- tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.89 +- 0.25 (0.07-->3.67) (max @ vno 95784 --> 94861)
- face area 0.33 +- 0.15 (0.00-->2.73)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=3773334.5, rms=0.00
- rms = 1.34, 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...
- 001: dt: 0.1250, sse=3773334.5, rms=0.000 (1.000%)
- positioning took 0.4 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 583 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 1 with 2 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 2 with 3 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 3 with 2 points - only 0.00% unknown
- deleting segment 4 with 8 points - only 0.00% unknown
- deleting segment 5 with 7 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 7 with 20 points - only 0.00% unknown
- deleting segment 8 with 10 points - only 0.00% unknown
- deleting segment 9 with 7 points - only 0.00% unknown
- deleting segment 10 with 9 points - only 0.00% unknown
- deleting segment 11 with 5 points - only 0.00% unknown
- deleting segment 12 with 6 points - only 0.00% unknown
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.89 +- 0.25 (0.07-->3.67) (max @ vno 95784 --> 94861)
- face area 0.33 +- 0.15 (0.00-->2.73)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=3773334.5, rms=0.00
- rms = 1.34, 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=3773334.5, rms=0.000 (1.000%)
- positioning took 0.4 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 583 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 1 with 2 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 2 with 3 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 3 with 2 points - only 0.00% unknown
- deleting segment 4 with 8 points - only 0.00% unknown
- deleting segment 5 with 7 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 7 with 20 points - only 0.00% unknown
- deleting segment 8 with 10 points - only 0.00% unknown
- deleting segment 9 with 7 points - only 0.00% unknown
- deleting segment 10 with 9 points - only 0.00% unknown
- deleting segment 11 with 5 points - only 0.00% unknown
- deleting segment 12 with 6 points - only 0.00% unknown
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.89 +- 0.25 (0.07-->3.67) (max @ vno 95784 --> 94861)
- face area 0.33 +- 0.15 (0.00-->2.73)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=3773334.5, rms=0.00
- rms = 1.34, 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...
- 003: dt: 0.1250, sse=3773334.5, rms=0.000 (1.000%)
- positioning took 0.4 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 583 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 1 with 2 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 2 with 3 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 3 with 2 points - only 0.00% unknown
- deleting segment 4 with 8 points - only 0.00% unknown
- deleting segment 5 with 7 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 7 with 20 points - only 0.00% unknown
- deleting segment 8 with 10 points - only 0.00% unknown
- deleting segment 9 with 7 points - only 0.00% unknown
- deleting segment 10 with 9 points - only 0.00% unknown
- deleting segment 11 with 5 points - only 0.00% unknown
- deleting segment 12 with 6 points - only 0.00% unknown
- tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- repositioning cortical surface to gray/csf boundary.
- smoothing T1 volume with sigma = 2.000
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=3773334.5, rms=0.00
- rms = 1.34, 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=3773334.5, rms=0.000 (1.000%)
- positioning took 0.4 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- smoothing surface for 5 iterations...
- reading initial pial vertex positions from woT2.pial...
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [111.00 201.00], gm=156.00+-15.00, and vertices in regions > 148.5
- 50355 surface locations found to contain inconsistent values (13998 in, 36357 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=407420.7, rms=0.29
- 001: dt: 0.5000, sse=384349.5, rms=0.281 (0.000%)
- 002: dt: 0.5000, sse=369277.6, rms=0.264 (0.000%)
- 003: dt: 0.5000, sse=361165.3, rms=0.252 (0.000%)
- 004: dt: 0.5000, sse=354374.2, rms=0.241 (0.000%)
- 005: dt: 0.5000, sse=349649.4, rms=0.231 (0.000%)
- 006: dt: 0.5000, sse=345841.7, rms=0.222 (0.000%)
- 007: dt: 0.5000, sse=343230.8, rms=0.215 (0.000%)
- 008: dt: 0.5000, sse=341201.4, rms=0.208 (0.000%)
- 009: dt: 0.5000, sse=339716.5, rms=0.202 (0.000%)
- 010: dt: 0.5000, sse=338450.3, rms=0.197 (0.000%)
- 011: dt: 0.5000, sse=337355.2, rms=0.192 (0.000%)
- 012: dt: 0.5000, sse=336475.9, rms=0.188 (0.000%)
- 013: dt: 0.5000, sse=335534.6, rms=0.184 (0.000%)
- 014: dt: 0.5000, sse=334895.5, rms=0.181 (0.000%)
- 015: dt: 0.5000, sse=334073.6, rms=0.178 (0.000%)
- 016: dt: 0.5000, sse=333400.4, rms=0.175 (0.000%)
- 017: dt: 0.5000, sse=332706.3, rms=0.173 (0.000%)
- 018: dt: 0.5000, sse=331827.4, rms=0.170 (0.000%)
- 019: dt: 0.5000, sse=330985.8, rms=0.169 (0.000%)
- 020: dt: 0.5000, sse=330534.4, rms=0.167 (0.000%)
- 021: dt: 0.5000, sse=329729.6, rms=0.165 (0.000%)
- 022: dt: 0.5000, sse=328781.6, rms=0.164 (0.000%)
- 023: dt: 0.5000, sse=328117.8, rms=0.163 (0.000%)
- 024: dt: 0.5000, sse=327307.7, rms=0.162 (0.000%)
- 025: dt: 0.5000, sse=326725.9, rms=0.161 (0.000%)
- 026: dt: 0.5000, sse=326126.5, rms=0.160 (0.000%)
- 027: dt: 0.5000, sse=325380.4, rms=0.160 (0.000%)
- 028: dt: 0.5000, sse=324650.2, rms=0.159 (0.000%)
- 029: dt: 0.5000, sse=323592.6, rms=0.159 (0.000%)
- 030: dt: 0.5000, sse=322882.1, rms=0.159 (0.000%)
- positioning took 4.0 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [105.90 206.10], gm=156.00+-16.70, and vertices in regions > 147.6
- 38162 surface locations found to contain inconsistent values (2689 in, 35473 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=33853.9, rms=0.13
- 031: dt: 0.5000, sse=33632.8, rms=0.130 (0.000%)
- 032: dt: 0.5000, sse=34381.2, rms=0.118 (0.000%)
- 033: dt: 0.5000, sse=35315.2, rms=0.110 (0.000%)
- 034: dt: 0.5000, sse=36065.2, rms=0.105 (0.000%)
- 035: dt: 0.5000, sse=36685.0, rms=0.100 (0.000%)
- 036: dt: 0.5000, sse=37316.2, rms=0.095 (0.000%)
- 037: dt: 0.5000, sse=37911.5, rms=0.091 (0.000%)
- 038: dt: 0.5000, sse=38481.2, rms=0.087 (0.000%)
- 039: dt: 0.5000, sse=39028.2, rms=0.083 (0.000%)
- 040: dt: 0.5000, sse=39566.7, rms=0.080 (0.000%)
- 041: dt: 0.5000, sse=40077.8, rms=0.077 (0.000%)
- 042: dt: 0.5000, sse=40564.4, rms=0.074 (0.000%)
- 043: dt: 0.5000, sse=41032.1, rms=0.071 (0.000%)
- 044: dt: 0.5000, sse=41453.8, rms=0.069 (0.000%)
- 045: dt: 0.5000, sse=41867.6, rms=0.066 (0.000%)
- 046: dt: 0.5000, sse=42233.9, rms=0.064 (0.000%)
- 047: dt: 0.5000, sse=42605.8, rms=0.062 (0.000%)
- 048: dt: 0.5000, sse=42942.6, rms=0.060 (0.000%)
- 049: dt: 0.5000, sse=43259.6, rms=0.059 (0.000%)
- 050: dt: 0.5000, sse=43559.9, rms=0.057 (0.000%)
- 051: dt: 0.5000, sse=43833.1, rms=0.056 (0.000%)
- 052: dt: 0.5000, sse=44085.2, rms=0.054 (0.000%)
- 053: dt: 0.5000, sse=44320.0, rms=0.053 (0.000%)
- 054: dt: 0.5000, sse=44536.7, rms=0.052 (0.000%)
- 055: dt: 0.5000, sse=44765.5, rms=0.050 (0.000%)
- 056: dt: 0.5000, sse=44955.2, rms=0.049 (0.000%)
- 057: dt: 0.5000, sse=45121.2, rms=0.049 (0.000%)
- 058: dt: 0.5000, sse=45287.4, rms=0.048 (0.000%)
- 059: dt: 0.5000, sse=45437.0, rms=0.047 (0.000%)
- 060: dt: 0.5000, sse=45576.7, rms=0.046 (0.000%)
- positioning took 3.2 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [104.10 207.90], gm=156.00+-17.30, and vertices in regions > 147.3
- 36530 surface locations found to contain inconsistent values (419 in, 36111 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=4935.0, rms=0.06
- 061: dt: 0.5000, sse=4920.3, rms=0.057 (0.000%)
- 062: dt: 0.5000, sse=4969.4, rms=0.050 (0.000%)
- 063: dt: 0.5000, sse=5029.0, rms=0.047 (0.000%)
- 064: dt: 0.5000, sse=5076.9, rms=0.045 (0.000%)
- 065: dt: 0.5000, sse=5108.3, rms=0.043 (0.000%)
- 066: dt: 0.5000, sse=5124.8, rms=0.041 (0.000%)
- 067: dt: 0.5000, sse=5138.2, rms=0.040 (0.000%)
- 068: dt: 0.5000, sse=5145.1, rms=0.039 (0.000%)
- 069: dt: 0.5000, sse=5152.3, rms=0.038 (0.000%)
- 070: dt: 0.5000, sse=5162.6, rms=0.037 (0.000%)
- 071: dt: 0.5000, sse=5170.1, rms=0.037 (0.000%)
- 072: dt: 0.5000, sse=5176.2, rms=0.036 (0.000%)
- 073: dt: 0.5000, sse=5187.0, rms=0.035 (0.000%)
- 074: dt: 0.5000, sse=5192.7, rms=0.034 (0.000%)
- 075: dt: 0.5000, sse=5198.0, rms=0.034 (0.000%)
- 076: dt: 0.5000, sse=5204.4, rms=0.033 (0.000%)
- 077: dt: 0.5000, sse=5206.7, rms=0.033 (0.000%)
- 078: dt: 0.5000, sse=5209.9, rms=0.032 (0.000%)
- 079: dt: 0.5000, sse=5213.0, rms=0.032 (0.000%)
- 080: dt: 0.5000, sse=5217.1, rms=0.031 (0.000%)
- 081: dt: 0.5000, sse=5220.0, rms=0.031 (0.000%)
- 082: dt: 0.5000, sse=5226.2, rms=0.031 (0.000%)
- 083: dt: 0.5000, sse=5227.1, rms=0.031 (0.000%)
- 084: dt: 0.5000, sse=5232.0, rms=0.031 (0.000%)
- 085: dt: 0.5000, sse=5236.1, rms=0.030 (0.000%)
- 086: dt: 0.5000, sse=5235.9, rms=0.030 (0.000%)
- 087: dt: 0.5000, sse=5236.3, rms=0.030 (0.000%)
- 088: dt: 0.5000, sse=5239.4, rms=0.030 (0.000%)
- 089: dt: 0.5000, sse=5239.6, rms=0.030 (0.000%)
- 090: dt: 0.5000, sse=5239.0, rms=0.029 (0.000%)
- positioning took 3.2 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [106.20 205.80], gm=156.00+-16.60, and vertices in regions > 147.7
- 27583 surface locations found to contain inconsistent values (869 in, 26714 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/sub017/surf/lh.pial...
- writing smoothed curvature to lh.curv.pial
- 000: dt: 0.0000, sse=744.9, rms=0.05
- 091: dt: 0.5000, sse=741.1, rms=0.045 (0.000%)
- 092: dt: 0.5000, sse=720.3, rms=0.042 (0.000%)
- 093: dt: 0.5000, sse=709.7, rms=0.041 (0.000%)
- 094: dt: 0.5000, sse=696.1, rms=0.040 (0.000%)
- 095: dt: 0.5000, sse=685.1, rms=0.038 (0.000%)
- 096: dt: 0.5000, sse=677.5, rms=0.037 (0.000%)
- 097: dt: 0.5000, sse=670.0, rms=0.036 (0.000%)
- 098: dt: 0.5000, sse=664.8, rms=0.036 (0.000%)
- 099: dt: 0.5000, sse=659.5, rms=0.035 (0.000%)
- 100: dt: 0.5000, sse=655.9, rms=0.034 (0.000%)
- 101: dt: 0.5000, sse=652.3, rms=0.034 (0.000%)
- 102: dt: 0.5000, sse=650.9, rms=0.034 (0.000%)
- 103: dt: 0.5000, sse=646.4, rms=0.033 (0.000%)
- 104: dt: 0.5000, sse=641.6, rms=0.032 (0.000%)
- 105: dt: 0.5000, sse=638.2, rms=0.032 (0.000%)
- 106: dt: 0.5000, sse=636.7, rms=0.032 (0.000%)
- 107: dt: 0.5000, sse=632.9, rms=0.031 (0.000%)
- 108: dt: 0.5000, sse=630.8, rms=0.031 (0.000%)
- 109: dt: 0.5000, sse=629.0, rms=0.030 (0.000%)
- 110: dt: 0.5000, sse=628.0, rms=0.030 (0.000%)
- 111: dt: 0.5000, sse=625.8, rms=0.030 (0.000%)
- 112: dt: 0.5000, sse=623.8, rms=0.030 (0.000%)
- 113: dt: 0.5000, sse=621.9, rms=0.029 (0.000%)
- 114: dt: 0.5000, sse=620.0, rms=0.029 (0.000%)
- 115: dt: 0.5000, sse=621.0, rms=0.029 (0.000%)
- 116: dt: 0.5000, sse=620.9, rms=0.029 (0.000%)
- 117: dt: 0.5000, sse=620.5, rms=0.029 (0.000%)
- 118: dt: 0.5000, sse=618.8, rms=0.029 (0.000%)
- 119: dt: 0.5000, sse=619.6, rms=0.029 (0.000%)
- 120: dt: 0.5000, sse=617.7, rms=0.028 (0.000%)
- positioning took 3.2 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/lh.curv.pial
- writing smoothed area to lh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/lh.area.pial
- vertex spacing 1.02 +- 0.43 (0.10-->7.00) (max @ vno 88716 --> 88699)
- face area 0.41 +- 0.30 (0.00-->6.15)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 119336 vertices processed
- 25000 of 119336 vertices processed
- 50000 of 119336 vertices processed
- 75000 of 119336 vertices processed
- 100000 of 119336 vertices processed
- 0 of 119336 vertices processed
- 25000 of 119336 vertices processed
- 50000 of 119336 vertices processed
- 75000 of 119336 vertices processed
- 100000 of 119336 vertices processed
- thickness calculation complete, 331:625 truncations.
- 24905 vertices at 0 distance
- 79011 vertices at 1 distance
- 77376 vertices at 2 distance
- 32315 vertices at 3 distance
- 9432 vertices at 4 distance
- 2653 vertices at 5 distance
- 851 vertices at 6 distance
- 322 vertices at 7 distance
- 97 vertices at 8 distance
- 57 vertices at 9 distance
- 33 vertices at 10 distance
- 20 vertices at 11 distance
- 12 vertices at 12 distance
- 12 vertices at 13 distance
- 11 vertices at 14 distance
- 5 vertices at 15 distance
- 9 vertices at 16 distance
- 3 vertices at 17 distance
- 3 vertices at 18 distance
- 3 vertices at 19 distance
- 2 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/lh.thickness
- positioning took 19.0 minutes
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/scripts
- cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/rh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/rh.woT2.pial
- `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/rh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/rh.woT2.pial'
- mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub017 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/sub017/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/wm.mgz...
- 15434 bright wm thresholded.
- 321 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/rh.orig...
- computing class statistics...
- border white: 215675 voxels (1.29%)
- border gray 245603 voxels (1.46%)
- WM (92.0): 93.4 +- 10.1 [70.0 --> 110.0]
- GM (76.0) : 73.6 +- 13.3 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 44.7 (was 70)
- setting MAX_BORDER_WHITE to 115.1 (was 105)
- setting MIN_BORDER_WHITE to 58.0 (was 85)
- setting MAX_CSF to 31.4 (was 40)
- setting MAX_GRAY to 94.9 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 51.4 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 18.1 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=105, GM=58
- mean inside = 93.0, mean outside = 68.2
- 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/sub017/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.89 +- 0.25 (0.03-->5.38) (max @ vno 88943 --> 117695)
- face area 0.33 +- 0.16 (0.00-->2.23)
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 46 points - only 2.17% unknown
- removing 2 vertex label from ripped group
- deleting segment 1 with 2 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 2 with 1 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 4 with 3 points - only 0.00% unknown
- deleting segment 5 with 11 points - only 0.00% unknown
- deleting segment 6 with 446 points - only 0.00% unknown
- deleting segment 7 with 6 points - only 0.00% unknown
- deleting segment 8 with 5 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 9 with 3 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 (0.07-->5.38) (max @ vno 117695 --> 88943)
- face area 0.33 +- 0.16 (0.00-->2.23)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=3931417.2, rms=0.00
- rms = 1.49, time step reduction 1 of 3 to 0.250...
- rms = 0.38, time step reduction 2 of 3 to 0.125...
- rms = 0.05, time step reduction 3 of 3 to 0.062...
- 001: dt: 0.1250, sse=3931417.2, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 46 points - only 2.17% unknown
- removing 2 vertex label from ripped group
- deleting segment 1 with 2 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 2 with 1 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 3 with 3 points - only 0.00% unknown
- deleting segment 4 with 11 points - only 0.00% unknown
- deleting segment 5 with 446 points - only 0.00% unknown
- deleting segment 6 with 6 points - only 0.00% unknown
- deleting segment 7 with 5 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 8 with 3 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 (0.07-->5.38) (max @ vno 117695 --> 88943)
- face area 0.33 +- 0.16 (0.00-->2.23)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=3931417.2, rms=0.00
- rms = 1.49, time step reduction 1 of 3 to 0.250...
- rms = 0.37, time step reduction 2 of 3 to 0.125...
- rms = 0.05, time step reduction 3 of 3 to 0.062...
- 002: dt: 0.1250, sse=3931417.2, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 46 points - only 2.17% unknown
- removing 2 vertex label from ripped group
- deleting segment 1 with 2 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 2 with 1 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 3 with 3 points - only 0.00% unknown
- deleting segment 4 with 11 points - only 0.00% unknown
- deleting segment 5 with 446 points - only 0.00% unknown
- deleting segment 6 with 6 points - only 0.00% unknown
- deleting segment 7 with 5 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 8 with 3 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 (0.07-->5.38) (max @ vno 117695 --> 88943)
- face area 0.33 +- 0.16 (0.00-->2.23)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=3931417.2, rms=0.00
- rms = 1.49, time step reduction 1 of 3 to 0.250...
- rms = 0.38, time step reduction 2 of 3 to 0.125...
- rms = 0.05, time step reduction 3 of 3 to 0.062...
- 003: dt: 0.1250, sse=3931417.2, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 46 points - only 2.17% unknown
- removing 2 vertex label from ripped group
- deleting segment 1 with 2 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 2 with 1 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 3 with 3 points - only 0.00% unknown
- deleting segment 4 with 11 points - only 0.00% unknown
- deleting segment 5 with 446 points - only 0.00% unknown
- deleting segment 6 with 6 points - only 0.00% unknown
- deleting segment 7 with 5 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 8 with 3 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=3931417.2, rms=0.00
- rms = 1.49, time step reduction 1 of 3 to 0.250...
- rms = 0.37, time step reduction 2 of 3 to 0.125...
- rms = 0.05, time step reduction 3 of 3 to 0.062...
- 004: dt: 0.1250, sse=3931417.2, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- deleting segment 0 with 4 points - only 0.00% unknown
- 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 [97.80 220.20], gm=159.00+-20.40, and vertices in regions > 148.8
- 44059 surface locations found to contain inconsistent values (4868 in, 39191 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=402573.1, rms=0.26
- 001: dt: 0.5000, sse=379618.1, rms=0.252 (0.000%)
- 002: dt: 0.5000, sse=364836.4, rms=0.236 (0.000%)
- 003: dt: 0.5000, sse=356688.0, rms=0.224 (0.000%)
- 004: dt: 0.5000, sse=349865.1, rms=0.212 (0.000%)
- 005: dt: 0.5000, sse=344907.9, rms=0.203 (0.000%)
- 006: dt: 0.5000, sse=341335.3, rms=0.194 (0.000%)
- 007: dt: 0.5000, sse=338651.5, rms=0.187 (0.000%)
- 008: dt: 0.5000, sse=336763.9, rms=0.181 (0.000%)
- 009: dt: 0.5000, sse=335181.8, rms=0.176 (0.000%)
- 010: dt: 0.5000, sse=334243.8, rms=0.171 (0.000%)
- 011: dt: 0.5000, sse=332987.5, rms=0.167 (0.000%)
- 012: dt: 0.5000, sse=332073.9, rms=0.164 (0.000%)
- 013: dt: 0.5000, sse=331172.4, rms=0.161 (0.000%)
- 014: dt: 0.5000, sse=330319.2, rms=0.158 (0.000%)
- 015: dt: 0.5000, sse=329298.5, rms=0.156 (0.000%)
- 016: dt: 0.5000, sse=328398.0, rms=0.155 (0.000%)
- 017: dt: 0.5000, sse=327529.6, rms=0.153 (0.000%)
- 018: dt: 0.5000, sse=326496.7, rms=0.152 (0.000%)
- 019: dt: 0.5000, sse=325753.5, rms=0.151 (0.000%)
- 020: dt: 0.5000, sse=324698.3, rms=0.150 (0.000%)
- 021: dt: 0.5000, sse=324110.7, rms=0.149 (0.000%)
- 022: dt: 0.5000, sse=323358.1, rms=0.148 (0.000%)
- 023: dt: 0.5000, sse=322595.8, rms=0.148 (0.000%)
- 024: dt: 0.5000, sse=321780.2, rms=0.147 (0.000%)
- 025: dt: 0.5000, sse=320916.3, rms=0.147 (0.000%)
- 026: dt: 0.5000, sse=319830.4, rms=0.147 (0.000%)
- 027: dt: 0.5000, sse=319499.8, rms=0.146 (0.000%)
- 028: dt: 0.5000, sse=318713.5, rms=0.146 (0.000%)
- 029: dt: 0.5000, sse=317998.7, rms=0.146 (0.000%)
- 030: dt: 0.5000, sse=317412.0, rms=0.146 (0.000%)
- positioning took 3.3 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [88.50 229.50], gm=159.00+-23.50, and vertices in regions > 147.2
- 37394 surface locations found to contain inconsistent values (694 in, 36700 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=33452.1, rms=0.14
- 031: dt: 0.5000, sse=33128.3, rms=0.130 (0.000%)
- 032: dt: 0.5000, sse=33732.1, rms=0.117 (0.000%)
- 033: dt: 0.5000, sse=34590.7, rms=0.108 (0.000%)
- 034: dt: 0.5000, sse=35343.2, rms=0.102 (0.000%)
- 035: dt: 0.5000, sse=36019.2, rms=0.096 (0.000%)
- 036: dt: 0.5000, sse=36704.5, rms=0.091 (0.000%)
- 037: dt: 0.5000, sse=37368.0, rms=0.086 (0.000%)
- 038: dt: 0.5000, sse=38022.5, rms=0.082 (0.000%)
- 039: dt: 0.5000, sse=38654.6, rms=0.078 (0.000%)
- 040: dt: 0.5000, sse=39257.6, rms=0.075 (0.000%)
- 041: dt: 0.5000, sse=39825.5, rms=0.072 (0.000%)
- 042: dt: 0.5000, sse=40368.1, rms=0.069 (0.000%)
- 043: dt: 0.5000, sse=40866.9, rms=0.066 (0.000%)
- 044: dt: 0.5000, sse=41342.8, rms=0.063 (0.000%)
- 045: dt: 0.5000, sse=41783.7, rms=0.061 (0.000%)
- 046: dt: 0.5000, sse=42213.8, rms=0.059 (0.000%)
- 047: dt: 0.5000, sse=42603.0, rms=0.057 (0.000%)
- 048: dt: 0.5000, sse=42952.4, rms=0.055 (0.000%)
- 049: dt: 0.5000, sse=43301.1, rms=0.053 (0.000%)
- 050: dt: 0.5000, sse=43642.7, rms=0.052 (0.000%)
- 051: dt: 0.5000, sse=43961.7, rms=0.050 (0.000%)
- 052: dt: 0.5000, sse=44243.0, rms=0.049 (0.000%)
- 053: dt: 0.5000, sse=44495.9, rms=0.047 (0.000%)
- 054: dt: 0.5000, sse=44709.6, rms=0.046 (0.000%)
- 055: dt: 0.5000, sse=44923.3, rms=0.045 (0.000%)
- 056: dt: 0.5000, sse=45119.6, rms=0.044 (0.000%)
- 057: dt: 0.5000, sse=45293.3, rms=0.043 (0.000%)
- 058: dt: 0.5000, sse=45460.6, rms=0.043 (0.000%)
- 059: dt: 0.5000, sse=45617.6, rms=0.042 (0.000%)
- 060: dt: 0.5000, sse=45768.6, rms=0.041 (0.000%)
- positioning took 3.4 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [87.00 231.00], gm=159.00+-24.00, and vertices in regions > 147.0
- 36465 surface locations found to contain inconsistent values (153 in, 36312 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=4884.7, rms=0.05
- 061: dt: 0.5000, sse=4870.9, rms=0.051 (0.000%)
- 062: dt: 0.5000, sse=4933.4, rms=0.045 (0.000%)
- 063: dt: 0.5000, sse=4992.8, rms=0.042 (0.000%)
- 064: dt: 0.5000, sse=5038.7, rms=0.040 (0.000%)
- 065: dt: 0.5000, sse=5068.0, rms=0.038 (0.000%)
- 066: dt: 0.5000, sse=5084.6, rms=0.037 (0.000%)
- 067: dt: 0.5000, sse=5094.3, rms=0.036 (0.000%)
- 068: dt: 0.5000, sse=5101.3, rms=0.035 (0.000%)
- 069: dt: 0.5000, sse=5107.2, rms=0.034 (0.000%)
- 070: dt: 0.5000, sse=5113.0, rms=0.033 (0.000%)
- 071: dt: 0.5000, sse=5119.8, rms=0.032 (0.000%)
- 072: dt: 0.5000, sse=5126.7, rms=0.031 (0.000%)
- 073: dt: 0.5000, sse=5132.6, rms=0.031 (0.000%)
- 074: dt: 0.5000, sse=5138.2, rms=0.030 (0.000%)
- 075: dt: 0.5000, sse=5141.5, rms=0.030 (0.000%)
- 076: dt: 0.5000, sse=5144.7, rms=0.029 (0.000%)
- 077: dt: 0.5000, sse=5148.3, rms=0.029 (0.000%)
- 078: dt: 0.5000, sse=5151.4, rms=0.028 (0.000%)
- 079: dt: 0.5000, sse=5153.5, rms=0.028 (0.000%)
- 080: dt: 0.5000, sse=5155.5, rms=0.028 (0.000%)
- 081: dt: 0.5000, sse=5158.5, rms=0.027 (0.000%)
- 082: dt: 0.5000, sse=5160.4, rms=0.027 (0.000%)
- 083: dt: 0.5000, sse=5162.4, rms=0.027 (0.000%)
- 084: dt: 0.5000, sse=5165.7, rms=0.027 (0.000%)
- 085: dt: 0.5000, sse=5167.4, rms=0.027 (0.000%)
- 086: dt: 0.5000, sse=5168.6, rms=0.027 (0.000%)
- 087: dt: 0.5000, sse=5170.1, rms=0.026 (0.000%)
- 088: dt: 0.5000, sse=5172.1, rms=0.026 (0.000%)
- 089: dt: 0.5000, sse=5173.6, rms=0.026 (0.000%)
- 090: dt: 0.5000, sse=5174.1, rms=0.026 (0.000%)
- positioning took 3.4 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [86.70 225.30], gm=156.00+-23.10, and vertices in regions > 144.4
- 12324 surface locations found to contain inconsistent values (569 in, 11755 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/sub017/surf/rh.pial...
- writing smoothed curvature to rh.curv.pial
- 000: dt: 0.0000, sse=884.4, rms=0.06
- 091: dt: 0.5000, sse=873.1, rms=0.057 (0.000%)
- 092: dt: 0.5000, sse=821.8, rms=0.053 (0.000%)
- 093: dt: 0.5000, sse=782.1, rms=0.049 (0.000%)
- 094: dt: 0.5000, sse=750.2, rms=0.046 (0.000%)
- 095: dt: 0.5000, sse=723.9, rms=0.043 (0.000%)
- 096: dt: 0.5000, sse=705.7, rms=0.041 (0.000%)
- 097: dt: 0.5000, sse=692.0, rms=0.039 (0.000%)
- 098: dt: 0.5000, sse=681.6, rms=0.038 (0.000%)
- 099: dt: 0.5000, sse=672.4, rms=0.037 (0.000%)
- 100: dt: 0.5000, sse=663.3, rms=0.036 (0.000%)
- 101: dt: 0.5000, sse=654.8, rms=0.034 (0.000%)
- 102: dt: 0.5000, sse=647.0, rms=0.033 (0.000%)
- 103: dt: 0.5000, sse=640.6, rms=0.032 (0.000%)
- 104: dt: 0.5000, sse=634.9, rms=0.031 (0.000%)
- 105: dt: 0.5000, sse=629.7, rms=0.030 (0.000%)
- 106: dt: 0.5000, sse=625.7, rms=0.029 (0.000%)
- 107: dt: 0.5000, sse=622.2, rms=0.029 (0.000%)
- 108: dt: 0.5000, sse=619.4, rms=0.028 (0.000%)
- 109: dt: 0.5000, sse=616.7, rms=0.028 (0.000%)
- 110: dt: 0.5000, sse=614.6, rms=0.027 (0.000%)
- 111: dt: 0.5000, sse=613.2, rms=0.027 (0.000%)
- 112: dt: 0.5000, sse=611.7, rms=0.026 (0.000%)
- 113: dt: 0.5000, sse=610.7, rms=0.026 (0.000%)
- 114: dt: 0.5000, sse=609.9, rms=0.026 (0.000%)
- 115: dt: 0.5000, sse=609.4, rms=0.026 (0.000%)
- 116: dt: 0.5000, sse=608.8, rms=0.026 (0.000%)
- 117: dt: 0.5000, sse=608.4, rms=0.025 (0.000%)
- 118: dt: 0.5000, sse=608.2, rms=0.025 (0.000%)
- 119: dt: 0.5000, sse=607.8, rms=0.025 (0.000%)
- 120: dt: 0.5000, sse=607.5, rms=0.025 (0.000%)
- positioning took 3.3 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/rh.curv.pial
- writing smoothed area to rh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/rh.area.pial
- vertex spacing 1.03 +- 0.44 (0.07-->8.20) (max @ vno 117695 --> 88943)
- face area 0.41 +- 0.31 (0.00-->5.39)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 117762 vertices processed
- 25000 of 117762 vertices processed
- 50000 of 117762 vertices processed
- 75000 of 117762 vertices processed
- 100000 of 117762 vertices processed
- 0 of 117762 vertices processed
- 25000 of 117762 vertices processed
- 50000 of 117762 vertices processed
- 75000 of 117762 vertices processed
- 100000 of 117762 vertices processed
- thickness calculation complete, 394:973 truncations.
- 23399 vertices at 0 distance
- 75690 vertices at 1 distance
- 76309 vertices at 2 distance
- 33657 vertices at 3 distance
- 10224 vertices at 4 distance
- 3039 vertices at 5 distance
- 1038 vertices at 6 distance
- 364 vertices at 7 distance
- 129 vertices at 8 distance
- 68 vertices at 9 distance
- 45 vertices at 10 distance
- 22 vertices at 11 distance
- 20 vertices at 12 distance
- 18 vertices at 13 distance
- 23 vertices at 14 distance
- 7 vertices at 15 distance
- 7 vertices at 16 distance
- 8 vertices at 17 distance
- 8 vertices at 18 distance
- 4 vertices at 19 distance
- 9 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/rh.thickness
- positioning took 18.2 minutes
- #--------------------------------------------
- #@# Surf Volume lh Thu Aug 8 22:48:51 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf
- mris_calc -o lh.area.mid lh.area add lh.area.pial
- Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o lh.area.mid lh.area.mid div 2
- Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o lh.volume lh.area.mid mul lh.thickness
- Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ]
- #--------------------------------------------
- #@# Surf Volume rh Thu Aug 8 22:48:52 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf
- mris_calc -o rh.area.mid rh.area add rh.area.pial
- Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o rh.area.mid rh.area.mid div 2
- Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o rh.volume rh.area.mid mul rh.thickness
- Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ]
- #--------------------------------------------
- #@# Cortical ribbon mask Thu Aug 8 22:49:03 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri
- mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon sub017
- 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 = 6
- writing volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/ribbon.mgz
- writing ribbon files
- #--------------------------------------------
- #@# ASeg Stats Thu Aug 8 23:02:51 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017
- 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 sub017
- $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 sub017
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- UseRobust 0
- atlas_icv (eTIV) = 1032834 mm^3 (det: 1.886175 )
- Computing euler number
- orig.nofix lheno = -24, rheno = -12
- orig.nofix lhholes = 13, rhholes = 7
- Loading mri/aseg.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 215196.141 214911.000 diff= 285.1 pctdiff= 0.133
- rhCtxGM: 222938.092 222234.000 diff= 704.1 pctdiff= 0.316
- lhCtxWM: 188462.721 188378.000 diff= 84.7 pctdiff= 0.045
- rhCtxWM: 189829.481 189791.000 diff= 38.5 pctdiff= 0.020
- SubCortGMVol 56059.000
- SupraTentVol 892279.435 (890339.000) diff=1940.435 pctdiff=0.217
- SupraTentVolNotVent 873534.435 (871594.000) diff=1940.435 pctdiff=0.222
- BrainSegVol 1007543.000 (1004562.000) diff=2981.000 pctdiff=0.296
- BrainSegVolNotVent 984840.000 (985689.435) diff=-849.435 pctdiff=-0.086
- BrainSegVolNotVent 984840.000
- CerebellumVol 112983.000
- VentChorVol 18745.000
- 3rd4th5thCSF 3958.000
- CSFVol 993.000, OptChiasmVol 247.000
- MaskVol 1491190.000
- 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 8670 8669.895
- 4 5 Left-Inf-Lat-Vent 313 312.717
- 5 7 Left-Cerebellum-White-Matter 12868 12868.347
- 6 8 Left-Cerebellum-Cortex 43693 43692.789
- 7 10 Left-Thalamus-Proper 7211 7211.264
- 8 11 Left-Caudate 3204 3203.923
- 9 12 Left-Putamen 5874 5874.365
- 10 13 Left-Pallidum 1994 1994.171
- 11 14 3rd-Ventricle 1070 1069.903
- 12 15 4th-Ventricle 2046 2045.684
- 13 16 Brain-Stem 20794 20793.734
- 14 17 Left-Hippocampus 3643 3643.101
- 15 18 Left-Amygdala 1556 1555.641
- 16 24 CSF 988 987.802
- 17 26 Left-Accumbens-area 630 629.849
- 18 28 Left-VentralDC 3554 3553.896
- 19 30 Left-vessel 115 115.305
- 20 31 Left-choroid-plexus 1036 1036.235
- 23 43 Right-Lateral-Ventricle 6866 6865.720
- 24 44 Right-Inf-Lat-Vent 530 529.840
- 25 46 Right-Cerebellum-White-Matter 13822 13821.636
- 26 47 Right-Cerebellum-Cortex 44742 44742.234
- 27 49 Right-Thalamus-Proper 6217 6216.692
- 28 50 Right-Caudate 3511 3510.915
- 29 51 Right-Putamen 5838 5838.277
- 30 52 Right-Pallidum 1755 1754.703
- 31 53 Right-Hippocampus 3670 3670.318
- 32 54 Right-Amygdala 1522 1522.274
- 33 58 Right-Accumbens-area 574 574.153
- 34 60 Right-VentralDC 3675 3674.643
- 35 62 Right-vessel 86 85.871
- 36 63 Right-choroid-plexus 1240 1239.725
- 37 72 5th-Ventricle 0 0.000
- 38 77 WM-hypointensities 841 841.465
- 39 78 Left-WM-hypointensities 0 0.000
- 40 79 Right-WM-hypointensities 0 0.000
- 41 80 non-WM-hypointensities 17 16.848
- 42 81 Left-non-WM-hypointensities 0 0.000
- 43 82 Right-non-WM-hypointensities 0 0.000
- 44 85 Optic-Chiasm 251 251.214
- 45 251 CC_Posterior 1072 1072.344
- 46 252 CC_Mid_Posterior 556 555.635
- 47 253 CC_Central 444 443.950
- 48 254 CC_Mid_Anterior 416 415.782
- 49 255 CC_Anterior 788 788.215
- Reporting on 45 segmentations
- mri_segstats done
- #-----------------------------------------
- #@# AParc-to-ASeg Thu Aug 8 23:06:38 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017
- mri_aparc2aseg --s sub017 --volmask
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- subject sub017
- outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/aparc+aseg.mgz
- useribbon 0
- baseoffset 0
- RipUnknown 0
- Reading lh white surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/lh.white
- Reading lh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/lh.pial
- Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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/sub017/surf/rh.white
- Reading rh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/rh.pial
- Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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/sub017/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/sub017/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 = 435441
- Used brute-force search on 0 voxels
- Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/aparc+aseg.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017
- mri_aparc2aseg --s sub017 --volmask --a2009s
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- subject sub017
- outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/aparc.a2009s+aseg.mgz
- useribbon 0
- baseoffset 10100
- RipUnknown 0
- Reading lh white surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/lh.white
- Reading lh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/lh.pial
- Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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/sub017/surf/rh.white
- Reading rh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/rh.pial
- Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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/sub017/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/sub017/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 = 435441
- Used brute-force search on 0 voxels
- Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/aparc.a2009s+aseg.mgz
- #-----------------------------------------
- #@# WMParc Thu Aug 8 23:11:01 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017
- mri_aparc2aseg --s sub017 --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 sub017
- 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/sub017/mri/aparc+aseg.mgz
- Reading lh white surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/lh.white
- Reading lh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/lh.pial
- Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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/sub017/surf/rh.white
- Reading rh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/rh.pial
- Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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/sub017/mri/ribbon.mgz
- Loading filled from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/filled.mgz
- Ripping vertices labeled as unkown
- Ripped 7949 vertices from left hemi
- Ripped 8004 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/sub017/mri/aseg.mgz
- Loading Ctx Seg File /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 = 812012
- Used brute-force search on 64 voxels
- Fixing Parahip LH WM
- Found 9 clusters
- 0 k 5.000000
- 1 k 7.000000
- 2 k 2.000000
- 3 k 1.000000
- 4 k 1380.000000
- 5 k 2.000000
- 6 k 1.000000
- 7 k 1.000000
- 8 k 1.000000
- Fixing Parahip RH WM
- Found 7 clusters
- 0 k 3.000000
- 1 k 4.000000
- 2 k 1445.000000
- 3 k 1.000000
- 4 k 1.000000
- 5 k 1.000000
- 6 k 1.000000
- Writing output aseg to mri/wmparc.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017
- 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 sub017 --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 sub017 --surf-wm-vol --ctab /opt/freesurfer/5.3.0/WMParcStatsLUT.txt --etiv
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- UseRobust 0
- atlas_icv (eTIV) = 1032834 mm^3 (det: 1.886175 )
- Loading mri/wmparc.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 215196.141 214911.000 diff= 285.1 pctdiff= 0.133
- rhCtxGM: 222938.092 222234.000 diff= 704.1 pctdiff= 0.316
- lhCtxWM: 188462.721 188378.000 diff= 84.7 pctdiff= 0.045
- rhCtxWM: 189829.481 189791.000 diff= 38.5 pctdiff= 0.020
- SubCortGMVol 56059.000
- SupraTentVol 892279.435 (890339.000) diff=1940.435 pctdiff=0.217
- SupraTentVolNotVent 873534.435 (871594.000) diff=1940.435 pctdiff=0.222
- BrainSegVol 1007543.000 (1004562.000) diff=2981.000 pctdiff=0.296
- BrainSegVolNotVent 984840.000 (985689.435) diff=-849.435 pctdiff=-0.086
- BrainSegVolNotVent 984840.000
- CerebellumVol 112983.000
- VentChorVol 18745.000
- 3rd4th5thCSF 3958.000
- CSFVol 993.000, OptChiasmVol 247.000
- MaskVol 1491190.000
- 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 2054 2053.989
- 2 3002 wm-lh-caudalanteriorcingulate 2117 2117.253
- 3 3003 wm-lh-caudalmiddlefrontal 5529 5529.437
- 4 3004 wm-lh-corpuscallosum 0 0.000
- 5 3005 wm-lh-cuneus 1898 1897.970
- 6 3006 wm-lh-entorhinal 840 840.011
- 7 3007 wm-lh-fusiform 5349 5348.910
- 8 3008 wm-lh-inferiorparietal 7403 7402.981
- 9 3009 wm-lh-inferiortemporal 4805 4804.625
- 10 3010 wm-lh-isthmuscingulate 3316 3315.540
- 11 3011 wm-lh-lateraloccipital 7816 7816.280
- 12 3012 wm-lh-lateralorbitofrontal 5666 5666.009
- 13 3013 wm-lh-lingual 3886 3886.289
- 14 3014 wm-lh-medialorbitofrontal 3238 3237.684
- 15 3015 wm-lh-middletemporal 4875 4874.749
- 16 3016 wm-lh-parahippocampal 1460 1459.591
- 17 3017 wm-lh-paracentral 2796 2795.613
- 18 3018 wm-lh-parsopercularis 3315 3314.705
- 19 3019 wm-lh-parsorbitalis 881 880.726
- 20 3020 wm-lh-parstriangularis 2491 2490.870
- 21 3021 wm-lh-pericalcarine 2229 2229.120
- 22 3022 wm-lh-postcentral 6441 6440.779
- 23 3023 wm-lh-posteriorcingulate 3834 3833.532
- 24 3024 wm-lh-precentral 11227 11226.994
- 25 3025 wm-lh-precuneus 6314 6314.002
- 26 3026 wm-lh-rostralanteriorcingulate 1963 1962.874
- 27 3027 wm-lh-rostralmiddlefrontal 10403 10402.612
- 28 3028 wm-lh-superiorfrontal 14737 14737.029
- 29 3029 wm-lh-superiorparietal 12534 12534.019
- 30 3030 wm-lh-superiortemporal 6516 6515.986
- 31 3031 wm-lh-supramarginal 7936 7935.712
- 32 3032 wm-lh-frontalpole 130 130.208
- 33 3033 wm-lh-temporalpole 498 498.127
- 34 3034 wm-lh-transversetemporal 534 534.030
- 35 3035 wm-lh-insula 6663 6662.521
- 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 3338 3337.948
- 120 4002 wm-rh-caudalanteriorcingulate 2582 2581.943
- 121 4003 wm-rh-caudalmiddlefrontal 4935 4934.551
- 122 4004 wm-rh-corpuscallosum 0 0.000
- 123 4005 wm-rh-cuneus 1910 1910.048
- 124 4006 wm-rh-entorhinal 600 599.546
- 125 4007 wm-rh-fusiform 4950 4949.613
- 126 4008 wm-rh-inferiorparietal 10889 10888.824
- 127 4009 wm-rh-inferiortemporal 4050 4050.255
- 128 4010 wm-rh-isthmuscingulate 2968 2968.035
- 129 4011 wm-rh-lateraloccipital 7769 7769.137
- 130 4012 wm-rh-lateralorbitofrontal 5551 5551.053
- 131 4013 wm-rh-lingual 4357 4356.592
- 132 4014 wm-rh-medialorbitofrontal 3159 3158.881
- 133 4015 wm-rh-middletemporal 4927 4926.894
- 134 4016 wm-rh-parahippocampal 1497 1496.826
- 135 4017 wm-rh-paracentral 3552 3551.526
- 136 4018 wm-rh-parsopercularis 2913 2912.725
- 137 4019 wm-rh-parsorbitalis 936 935.891
- 138 4020 wm-rh-parstriangularis 3078 3077.531
- 139 4021 wm-rh-pericalcarine 2278 2277.819
- 140 4022 wm-rh-postcentral 6297 6297.394
- 141 4023 wm-rh-posteriorcingulate 3734 3733.894
- 142 4024 wm-rh-precentral 12049 12048.565
- 143 4025 wm-rh-precuneus 6623 6623.351
- 144 4026 wm-rh-rostralanteriorcingulate 1834 1834.353
- 145 4027 wm-rh-rostralmiddlefrontal 10661 10661.457
- 146 4028 wm-rh-superiorfrontal 13466 13465.592
- 147 4029 wm-rh-superiorparietal 10920 10920.327
- 148 4030 wm-rh-superiortemporal 5168 5167.939
- 149 4031 wm-rh-supramarginal 6465 6464.501
- 150 4032 wm-rh-frontalpole 205 204.839
- 151 4033 wm-rh-temporalpole 631 630.754
- 152 4034 wm-rh-transversetemporal 508 507.577
- 153 4035 wm-rh-insula 7877 7877.193
- 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 27412 27411.617
- 237 5002 Right-UnsegmentedWhiteMatter 28464 28464.172
- 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/sub017/label
- #--------------------------------------------
- #@# BA Labels lh Thu Aug 8 23:22:39 CEST 2013
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 119336
- Number of reverse mapping hits = 314
- Checking for and removing duplicates
- Writing label file ./lh.BA1.label 4443
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 119336
- Number of reverse mapping hits = 472
- Checking for and removing duplicates
- Writing label file ./lh.BA2.label 8381
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 119336
- Number of reverse mapping hits = 104
- Checking for and removing duplicates
- Writing label file ./lh.BA3a.label 4181
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 119336
- Number of reverse mapping hits = 292
- Checking for and removing duplicates
- Writing label file ./lh.BA3b.label 6275
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 119336
- Number of reverse mapping hits = 214
- Checking for and removing duplicates
- Writing label file ./lh.BA4a.label 5998
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 119336
- Number of reverse mapping hits = 142
- Checking for and removing duplicates
- Writing label file ./lh.BA4p.label 4212
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 119336
- Number of reverse mapping hits = 672
- Checking for and removing duplicates
- Writing label file ./lh.BA6.label 14261
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 119336
- Number of reverse mapping hits = 313
- Checking for and removing duplicates
- Writing label file ./lh.BA44.label 4494
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 119336
- Number of reverse mapping hits = 455
- Checking for and removing duplicates
- Writing label file ./lh.BA45.label 3877
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 119336
- Number of reverse mapping hits = 1097
- Checking for and removing duplicates
- Writing label file ./lh.V1.label 5738
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 119336
- Number of reverse mapping hits = 2067
- Checking for and removing duplicates
- Writing label file ./lh.V2.label 10181
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 119336
- Number of reverse mapping hits = 292
- Checking for and removing duplicates
- Writing label file ./lh.MT.label 2310
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.perirhinal.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 119336
- Number of reverse mapping hits = 247
- Checking for and removing duplicates
- Writing label file ./lh.perirhinal.label 1446
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.thresh.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 119336
- Number of reverse mapping hits = 66
- Checking for and removing duplicates
- Writing label file ./lh.BA1.thresh.label 1080
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.thresh.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 119336
- Number of reverse mapping hits = 128
- Checking for and removing duplicates
- Writing label file ./lh.BA2.thresh.label 2220
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.thresh.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 119336
- Number of reverse mapping hits = 30
- Checking for and removing duplicates
- Writing label file ./lh.BA3a.thresh.label 1534
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.thresh.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 119336
- Number of reverse mapping hits = 97
- Checking for and removing duplicates
- Writing label file ./lh.BA3b.thresh.label 2093
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.thresh.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 119336
- Number of reverse mapping hits = 108
- Checking for and removing duplicates
- Writing label file ./lh.BA4a.thresh.label 2427
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.thresh.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 119336
- Number of reverse mapping hits = 29
- Checking for and removing duplicates
- Writing label file ./lh.BA4p.thresh.label 1578
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.thresh.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 119336
- Number of reverse mapping hits = 307
- Checking for and removing duplicates
- Writing label file ./lh.BA6.thresh.label 7342
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.thresh.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 119336
- Number of reverse mapping hits = 144
- Checking for and removing duplicates
- Writing label file ./lh.BA44.thresh.label 2056
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.thresh.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 119336
- Number of reverse mapping hits = 229
- Checking for and removing duplicates
- Writing label file ./lh.BA45.thresh.label 1380
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.thresh.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 119336
- Number of reverse mapping hits = 738
- Checking for and removing duplicates
- Writing label file ./lh.V1.thresh.label 4143
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.thresh.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 119336
- Number of reverse mapping hits = 1012
- Checking for and removing duplicates
- Writing label file ./lh.V2.thresh.label 4346
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.thresh.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 119336
- Number of reverse mapping hits = 63
- Checking for and removing duplicates
- Writing label file ./lh.MT.thresh.label 576
- mri_label2label: Done
- mris_label2annot --s sub017 --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/sub017/label
- cmdline mris_label2annot --s sub017 --hemi lh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --l lh.perirhinal.label --a BA --maxstatwinner --noverbose
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- subject sub017
- 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/sub017/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 82654 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/label/lh.BA.annot
- mris_label2annot --s sub017 --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/sub017/label
- cmdline mris_label2annot --s sub017 --hemi lh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l lh.BA1.thresh.label --l lh.BA2.thresh.label --l lh.BA3a.thresh.label --l lh.BA3b.thresh.label --l lh.BA4a.thresh.label --l lh.BA4p.thresh.label --l lh.BA6.thresh.label --l lh.BA44.thresh.label --l lh.BA45.thresh.label --l lh.V1.thresh.label --l lh.V2.thresh.label --l lh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- subject sub017
- 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/sub017/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 98106 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/label/lh.BA.thresh.annot
- mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab sub017 lh white
- computing statistics for each annotation in ./lh.BA.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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
- 1119 660 2372 2.593 0.471 0.160 0.065 26 3.1 BA1
- 3728 2455 6146 2.369 0.507 0.137 0.044 49 6.8 BA2
- 858 561 829 1.907 0.463 0.131 0.042 8 1.3 BA3a
- 2241 1491 3529 2.103 0.626 0.132 0.041 33 4.1 BA3b
- 1271 803 3010 2.895 0.502 0.114 0.032 13 1.8 BA4a
- 1109 727 2044 2.750 0.425 0.110 0.053 31 2.3 BA4p
- 8009 5236 18039 2.867 0.525 0.126 0.037 89 12.1 BA6
- 2395 1587 4711 2.616 0.399 0.126 0.035 29 3.4 BA44
- 2567 1733 5143 2.498 0.444 0.136 0.044 43 4.6 BA45
- 3182 2033 4138 1.905 0.507 0.149 0.080 105 9.8 V1
- 7244 4636 11028 2.168 0.480 0.165 0.070 192 18.7 V2
- 1785 1173 2968 2.408 0.450 0.151 0.052 34 3.5 MT
- 1174 765 3143 3.216 0.974 0.157 0.088 24 3.6 perirhinal
- mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab sub017 lh white
- computing statistics for each annotation in ./lh.BA.thresh.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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
- 662 374 1457 2.640 0.497 0.165 0.075 17 2.4 BA1
- 1441 945 2606 2.369 0.432 0.134 0.044 19 2.5 BA2
- 736 479 671 1.911 0.450 0.129 0.036 5 1.1 BA3a
- 1402 921 1841 1.816 0.436 0.104 0.027 12 1.6 BA3b
- 1322 806 2985 2.958 0.462 0.112 0.050 35 2.7 BA4a
- 844 587 1537 2.657 0.418 0.104 0.027 5 0.9 BA4p
- 4579 2950 10743 2.925 0.555 0.122 0.037 48 6.9 BA6
- 1530 1017 3150 2.630 0.384 0.124 0.035 20 2.1 BA44
- 1148 760 2623 2.657 0.377 0.142 0.047 23 2.3 BA45
- 3322 2147 4426 1.910 0.508 0.147 0.079 104 10.2 V1
- 3789 2401 5479 2.069 0.482 0.175 0.081 110 10.9 V2
- 455 307 638 2.227 0.377 0.128 0.034 5 0.6 MT
- #--------------------------------------------
- #@# BA Labels rh Thu Aug 8 23:26:43 CEST 2013
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 117762
- Number of reverse mapping hits = 180
- Checking for and removing duplicates
- Writing label file ./rh.BA1.label 4142
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 117762
- Number of reverse mapping hits = 285
- Checking for and removing duplicates
- Writing label file ./rh.BA2.label 6972
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 117762
- Number of reverse mapping hits = 111
- Checking for and removing duplicates
- Writing label file ./rh.BA3a.label 4091
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 117762
- Number of reverse mapping hits = 173
- Checking for and removing duplicates
- Writing label file ./rh.BA3b.label 4695
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 117762
- Number of reverse mapping hits = 135
- Checking for and removing duplicates
- Writing label file ./rh.BA4a.label 5882
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 117762
- Number of reverse mapping hits = 86
- Checking for and removing duplicates
- Writing label file ./rh.BA4p.label 4559
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 117762
- Number of reverse mapping hits = 534
- Checking for and removing duplicates
- Writing label file ./rh.BA6.label 12790
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 117762
- Number of reverse mapping hits = 620
- Checking for and removing duplicates
- Writing label file ./rh.BA44.label 7532
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 117762
- Number of reverse mapping hits = 676
- Checking for and removing duplicates
- Writing label file ./rh.BA45.label 6031
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 117762
- Number of reverse mapping hits = 1061
- Checking for and removing duplicates
- Writing label file ./rh.V1.label 5788
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 117762
- Number of reverse mapping hits = 2092
- Checking for and removing duplicates
- Writing label file ./rh.V2.label 10108
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 117762
- Number of reverse mapping hits = 626
- Checking for and removing duplicates
- Writing label file ./rh.MT.label 2558
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.perirhinal.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 117762
- Number of reverse mapping hits = 66
- Checking for and removing duplicates
- Writing label file ./rh.perirhinal.label 818
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.thresh.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 117762
- Number of reverse mapping hits = 44
- Checking for and removing duplicates
- Writing label file ./rh.BA1.thresh.label 920
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.thresh.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 117762
- Number of reverse mapping hits = 123
- Checking for and removing duplicates
- Writing label file ./rh.BA2.thresh.label 2811
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.thresh.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 117762
- Number of reverse mapping hits = 19
- Checking for and removing duplicates
- Writing label file ./rh.BA3a.thresh.label 1717
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.thresh.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 117762
- Number of reverse mapping hits = 125
- Checking for and removing duplicates
- Writing label file ./rh.BA3b.thresh.label 2308
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.thresh.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 117762
- Number of reverse mapping hits = 19
- Checking for and removing duplicates
- Writing label file ./rh.BA4a.thresh.label 1407
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.thresh.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 117762
- Number of reverse mapping hits = 55
- Checking for and removing duplicates
- Writing label file ./rh.BA4p.thresh.label 1544
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.thresh.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 117762
- Number of reverse mapping hits = 296
- Checking for and removing duplicates
- Writing label file ./rh.BA6.thresh.label 7255
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.thresh.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 117762
- Number of reverse mapping hits = 134
- Checking for and removing duplicates
- Writing label file ./rh.BA44.thresh.label 1146
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.thresh.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 117762
- Number of reverse mapping hits = 152
- Checking for and removing duplicates
- Writing label file ./rh.BA45.thresh.label 1330
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.thresh.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 117762
- Number of reverse mapping hits = 681
- Checking for and removing duplicates
- Writing label file ./rh.V1.thresh.label 3913
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.thresh.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 117762
- Number of reverse mapping hits = 968
- Checking for and removing duplicates
- Writing label file ./rh.V2.thresh.label 4405
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.thresh.label --trgsubject sub017 --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 = sub017
- 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/sub017/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 117762
- Number of reverse mapping hits = 108
- Checking for and removing duplicates
- Writing label file ./rh.MT.thresh.label 376
- mri_label2label: Done
- mris_label2annot --s sub017 --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/sub017/label
- cmdline mris_label2annot --s sub017 --hemi rh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --l rh.perirhinal.label --a BA --maxstatwinner --noverbose
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- subject sub017
- 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/sub017/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 81148 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/label/rh.BA.annot
- mris_label2annot --s sub017 --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/sub017/label
- cmdline mris_label2annot --s sub017 --hemi rh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l rh.BA1.thresh.label --l rh.BA2.thresh.label --l rh.BA3a.thresh.label --l rh.BA3b.thresh.label --l rh.BA4a.thresh.label --l rh.BA4p.thresh.label --l rh.BA6.thresh.label --l rh.BA44.thresh.label --l rh.BA45.thresh.label --l rh.V1.thresh.label --l rh.V2.thresh.label --l rh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- subject sub017
- 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/sub017/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 97812 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/label/rh.BA.thresh.annot
- mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab sub017 rh white
- computing statistics for each annotation in ./rh.BA.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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
- 769 464 1840 2.739 0.371 0.168 0.066 20 2.0 BA1
- 3067 2047 5611 2.415 0.514 0.136 0.061 48 5.4 BA2
- 943 624 970 1.929 0.491 0.126 0.035 8 1.5 BA3a
- 1822 1213 2854 1.963 0.505 0.127 0.041 26 2.9 BA3b
- 1205 752 2952 3.073 0.427 0.114 0.031 13 1.6 BA4a
- 1146 751 2130 2.746 0.465 0.101 0.041 22 2.2 BA4p
- 6720 4417 16544 3.058 0.532 0.126 0.038 75 10.0 BA6
- 3586 2372 7156 2.745 0.429 0.125 0.039 45 5.6 BA44
- 3811 2537 8018 2.618 0.501 0.154 0.055 75 8.7 BA45
- 3332 2292 4896 1.988 0.501 0.163 0.076 64 10.6 V1
- 7269 4843 11636 2.219 0.514 0.173 0.075 190 22.1 V2
- 2346 1566 3685 2.362 0.434 0.138 0.046 30 4.3 MT
- 598 439 2003 3.807 0.657 0.149 0.072 15 1.1 perirhinal
- mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab sub017 rh white
- computing statistics for each annotation in ./rh.BA.thresh.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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
- 523 280 1219 2.705 0.334 0.154 0.059 12 1.2 BA1
- 1771 1194 3433 2.455 0.549 0.137 0.074 29 3.1 BA2
- 817 548 795 1.879 0.429 0.121 0.031 5 1.1 BA3a
- 1519 1026 2023 1.800 0.387 0.115 0.033 18 2.3 BA3b
- 713 414 1718 3.183 0.395 0.116 0.032 7 0.9 BA4a
- 995 666 1897 2.816 0.452 0.099 0.044 21 2.0 BA4p
- 4347 2840 10376 3.030 0.516 0.123 0.037 46 6.3 BA6
- 929 626 2176 2.865 0.332 0.126 0.037 15 1.4 BA44
- 1057 713 2622 2.838 0.433 0.165 0.065 28 2.6 BA45
- 3157 2189 4571 1.979 0.506 0.157 0.069 53 9.2 V1
- 3761 2520 6031 2.117 0.522 0.187 0.093 105 13.7 V2
- 361 237 712 2.429 0.384 0.139 0.043 6 0.6 MT
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/label
- #--------------------------------------------
- #@# Ex-vivo Entorhinal Cortex Label lh Thu Aug 8 23:30:54 CEST 2013
- mris_spherical_average -erode 1 -orig white -t 0.4 -o sub017 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label
- painting output onto subject sub017.
- processing subject lh.EC_average...
- reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 1177 points to lh.entorhinal_exvivo.label...
- mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label sub017 lh white
- limiting computations to label ./lh.entorhinal_exvivo.label.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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
- 407 288 1091 3.344 0.573 0.116 0.035 3 0.6 ./lh.entorhinal_exvivo.label
- #--------------------------------------------
- #@# Ex-vivo Entorhinal Cortex Label rh Thu Aug 8 23:31:08 CEST 2013
- mris_spherical_average -erode 1 -orig white -t 0.4 -o sub017 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label
- painting output onto subject sub017.
- processing subject rh.EC_average...
- reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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 697 points to rh.entorhinal_exvivo.label...
- mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label sub017 rh white
- limiting computations to label ./rh.entorhinal_exvivo.label.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub017/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
- 226 175 611 3.464 0.538 0.166 0.039 3 0.5 ./rh.entorhinal_exvivo.label
- #------------------------------------------
- Started at Thu Aug 8 10:53:49 CEST 2013
- Ended at Thu Aug 8 23:31:23 CEST 2013
- #@#%# recon-all-run-time-hours 12.626
- recon-all -s sub017 finished without error at Thu Aug 8 23:31:23 CEST 2013
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