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- Thu Aug 8 10:53:55 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018
- /opt/freesurfer/5.3.0/bin/recon-all
- -i /home/data/exppsy/forrest_gump/openfmri.org/sub018/anatomy/highres001.nii.gz -cw256 -all -T2 /home/data/exppsy/forrest_gump/openfmri.org/sub018/anatomy/other/t2w001.nii.gz -T2pial -subjid sub018 -sd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- subjid sub018
- 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 96471788 2729904 0 177872 94401932
- -/+ buffers/cache: 1891984 97309708
- 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: 2013/08/08-08:53:56-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: 2013/08/08-08:53:56-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: 2013/08/08-08:53:56-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: 2013/08/08-08:53:56-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: 2013/08/08-08:53:56-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: 2013/08/08-08:53:56-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: 2013/08/08-08:53:56-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: 2013/08/08-08:53:56-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: 2013/08/08-08:53:57-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: 2013/08/08-08:53:57-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: 2013/08/08-08:53:57-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: 2013/08/08-08:53:57-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: 2013/08/08-08:53:57-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: 2013/08/08-08:53:57-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: 2013/08/08-08:53:57-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: 2013/08/08-08:53:57-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: 2013/08/08-08:53:57-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: 2013/08/08-08:53:57-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: 2013/08/08-08:53:58-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: 2013/08/08-08:53:58-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: 2013/08/08-08:53:58-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: 2013/08/08-08:53:58-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: 2013/08/08-08:53:58-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: 2013/08/08-08:53:58-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: 2013/08/08-08:53:58-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: 2013/08/08-08:53:58-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: 2013/08/08-08:53:58-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: 2013/08/08-08:53:58-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: 2013/08/08-08:53:59-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: 2013/08/08-08:53:59-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: 2013/08/08-08:53:59-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: 2013/08/08-08:53:59-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: 2013/08/08-08:53:59-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: 2013/08/08-08:53:59-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: 2013/08/08-08:53:59-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: 2013/08/08-08:53:59-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: 2013/08/08-08:53:59-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: 2013/08/08-08:53:59-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/sub018
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub018/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/orig/001.mgz
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub018/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/anatomy/highres001.nii.gz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.998519, 0.0146261, 0.052401)
- j_ras = (0.020019, 0.994384, 0.103917)
- k_ras = (0.0505869, -0.104812, 0.993205)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/orig/001.mgz...
- #--------------------------------------------
- #@# T2/FLAIR Input Thu Aug 8 10:54:16 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub018/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/orig/T2raw.mgz
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub018/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/anatomy/other/t2w001.nii.gz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.998519, 0.0146261, 0.052401)
- j_ras = (0.020019, 0.994384, 0.103917)
- k_ras = (0.0505869, -0.104812, 0.993205)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/orig/T2raw.mgz...
- #--------------------------------------------
- #@# MotionCor Thu Aug 8 10:54:32 CEST 2013
- Found 1 runs
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/mri/orig/001.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/rawavg.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/orig.mgz --conform --cw256
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/mri/rawavg.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.998519, 0.0146261, 0.052401)
- j_ras = (0.020019, 0.994384, 0.103917)
- k_ras = (0.0505869, -0.104812, 0.993205)
- Original Data has (0.699936, 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/sub018/mri/orig.mgz...
- mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/talairach.xfm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/orig.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Talairach Thu Aug 8 10:55:16 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri
- mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
- talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
- cp transforms/talairach.auto.xfm transforms/talairach.xfm
- #--------------------------------------------
- #@# Talairach Failure Detection Thu Aug 8 10:58:37 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri
- talairach_afd -T 0.005 -xfm transforms/talairach.xfm
- talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7211, pval=0.4932 >= threshold=0.0050)
- awk -f /opt/freesurfer/5.3.0/bin/extract_talairach_avi_QA.awk /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/talairach_avi.log
- tal_QC_AZS /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/talairach_avi.log
- TalAviQA: 0.96888
- z-score: -2
- #--------------------------------------------
- #@# Nu Intensity Correction Thu Aug 8 10:58:37 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/sub018/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 10:58:37 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.14649
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.14649/nu0.mnc -odt float
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.14649/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, 0)
- j_ras = (0, 2.23517e-08, -1)
- k_ras = (-9.31323e-10, 1, 7.45058e-09)
- changing data type from uchar to float (noscale = 0)...
- writing to ./tmp.mri_nu_correct.mni.14649/nu0.mnc...
-
- --------------------------------------------------------
- Iteration 1 Thu Aug 8 10:58:43 CEST 2013
- nu_correct -clobber ./tmp.mri_nu_correct.mni.14649/nu0.mnc ./tmp.mri_nu_correct.mni.14649/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.14649/0/
- [fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/] [2013-08-08 10:58:43] 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.14649/0/ ./tmp.mri_nu_correct.mni.14649/nu0.mnc ./tmp.mri_nu_correct.mni.14649/nu1.imp
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Number of iterations: 50
- CV of field change: 0.00113831
- [fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/] [2013-08-08 11:00:07] running:
- /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.14649/nu0.mnc ./tmp.mri_nu_correct.mni.14649/0//template.mnc
- Transforming slices:......................................................................................Done
- Transforming slices:................................................................................................................................................................................................................................................................Done
-
-
- --------------------------------------------------------
- Iteration 2 Thu Aug 8 11:00:13 CEST 2013
- nu_correct -clobber ./tmp.mri_nu_correct.mni.14649/nu1.mnc ./tmp.mri_nu_correct.mni.14649/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.14649/1/
- [fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/] [2013-08-08 11:00:13] 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.14649/1/ ./tmp.mri_nu_correct.mni.14649/nu1.mnc ./tmp.mri_nu_correct.mni.14649/nu2.imp
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
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- Processing:.................................................................Done
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- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Number of iterations: 50
- CV of field change: 0.000991634
- [fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/] [2013-08-08 11:01:19] running:
- /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.14649/nu1.mnc ./tmp.mri_nu_correct.mni.14649/1//template.mnc
- Transforming slices:......................................................................................Done
- Transforming slices:................................................................................................................................................................................................................................................................Done
-
-
-
- mri_binarize --i ./tmp.mri_nu_correct.mni.14649/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.14649/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/sub018/mri
- cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.14649/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.14649/ones.mgz
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- input ./tmp.mri_nu_correct.mni.14649/nu2.mnc
- frame 0
- nErode3d 0
- nErode2d 0
- output ./tmp.mri_nu_correct.mni.14649/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.14649/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.14649/sum.junk --avgwf ./tmp.mri_nu_correct.mni.14649/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.14649/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.14649/sum.junk --avgwf ./tmp.mri_nu_correct.mni.14649/input.mean.dat
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.14649/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.14649/input.mean.dat
- mri_segstats done
- mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.14649/ones.mgz --i ./tmp.mri_nu_correct.mni.14649/nu2.mnc --sum ./tmp.mri_nu_correct.mni.14649/sum.junk --avgwf ./tmp.mri_nu_correct.mni.14649/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.14649/ones.mgz --i ./tmp.mri_nu_correct.mni.14649/nu2.mnc --sum ./tmp.mri_nu_correct.mni.14649/sum.junk --avgwf ./tmp.mri_nu_correct.mni.14649/output.mean.dat
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.14649/ones.mgz
- Loading ./tmp.mri_nu_correct.mni.14649/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.14649/output.mean.dat
- mri_segstats done
- mris_calc -o ./tmp.mri_nu_correct.mni.14649/nu2.mnc ./tmp.mri_nu_correct.mni.14649/nu2.mnc mul .87816104870743779040
- Saving result to './tmp.mri_nu_correct.mni.14649/nu2.mnc' (type = MINC ) [ ok ]
- mri_convert ./tmp.mri_nu_correct.mni.14649/nu2.mnc nu.mgz --like orig.mgz
- mri_convert ./tmp.mri_nu_correct.mni.14649/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.14649/nu2.mnc...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, -1.86265e-09, 0)
- j_ras = (0, 2.23517e-08, -1)
- k_ras = (-9.31323e-10, 1, 7.45058e-09)
- INFO: transform src into the like-volume: orig.mgz
- writing to nu.mgz...
- mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz
- type change took 0 minutes and 7 seconds.
- mapping (13, 161) to ( 3, 110)
-
-
- Thu Aug 8 11:02:18 CEST 2013
- mri_nu_correct.mni done
- mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/talairach.xfm nu.mgz nu.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Intensity Normalization Thu Aug 8 11:02:20 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri
- mri_normalize -g 1 nu.mgz T1.mgz
- using max gradient = 1.000
- reading from nu.mgz...
- normalizing image...
- talairach transform
- 1.184 -0.017 -0.054 4.517;
- 0.038 1.079 0.328 -41.092;
- 0.050 -0.405 1.164 -1.179;
- 0.000 0.000 0.000 1.000;
- processing without aseg, no1d=0
- MRInormInit():
- INFO: Modifying talairach volume c_(r,a,s) based on average_305
- MRInormalize():
- MRIsplineNormalize(): npeaks = 17
- Starting OpenSpline(): npoints = 17
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Iterating 2 times
- ---------------------------------
- 3d normalization pass 1 of 2
- white matter peak found at 111
- white matter peak found at 108
- gm peak at 54 (54), valley at 37 (37)
- csf peak at 27, setting threshold to 45
- 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 39 (39)
- csf peak at 26, setting threshold to 43
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Done iterating ---------------------------------
- writing output to T1.mgz
- 3D bias adjustment took 3 minutes and 19 seconds.
- #--------------------------------------------
- #@# Skull Stripping Thu Aug 8 11:05:39 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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=9.0
- skull bounding box = (51, 10, 16) --> (201, 255, 204)
- using (101, 92, 110) as brain centroid...
- mean wm in atlas = 126, using box (83,62,87) --> (119, 122,133) to find MRI wm
- before smoothing, mri peak at 108
- after smoothing, mri peak at 108, scaling input intensities by 1.167
- scaling channel 0 by 1.16667
- initial log_p = -4.9
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -4.569289 @ (-9.091, 27.273, -9.091)
- max log p = -4.460065 @ (13.636, -4.545, -4.545)
- max log p = -4.410065 @ (-6.818, -2.273, 2.273)
- max log p = -4.391715 @ (3.409, 3.409, 1.136)
- max log p = -4.386332 @ (-2.841, -1.705, -0.568)
- max log p = -4.386332 @ (0.000, 0.000, 0.000)
- Found translation: (-1.7, 22.2, -10.8): log p = -4.386
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.4 (thresh=-4.4)
- 1.236 0.000 0.000 -31.818;
- 0.000 1.142 0.473 -39.679;
- 0.000 -0.473 1.142 26.911;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1)
- 1.236 0.000 0.000 -31.818;
- 0.000 1.284 0.344 -39.157;
- 0.000 -0.296 1.105 6.558;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 2 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1)
- 1.236 0.000 0.000 -31.818;
- 0.000 1.284 0.344 -39.157;
- 0.000 -0.296 1.105 6.558;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.2500
- ****************************************
- Nine parameter search. iteration 3 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.1 (thresh=-4.1)
- 1.167 -0.046 0.026 -19.806;
- 0.045 1.331 0.355 -52.556;
- -0.040 -0.299 1.125 11.331;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 4 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.188 -0.047 0.026 -22.536;
- 0.045 1.331 0.355 -52.556;
- -0.040 -0.304 1.146 9.555;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.0625
- ****************************************
- Nine parameter search. iteration 5 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.190 -0.052 0.045 -23.508;
- 0.045 1.336 0.357 -53.167;
- -0.060 -0.303 1.146 11.994;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 6 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.190 -0.052 0.045 -23.508;
- 0.045 1.336 0.357 -53.167;
- -0.060 -0.303 1.146 11.994;
- 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
- 1.19036 -0.05200 0.04499 -23.50809;
- 0.04517 1.33590 0.35668 -53.16697;
- -0.05976 -0.30345 1.14592 11.99424;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 3481
- Quasinewton: input matrix
- 1.19036 -0.05200 0.04499 -23.50809;
- 0.04517 1.33590 0.35668 -53.16697;
- -0.05976 -0.30345 1.14592 11.99424;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 4 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 1.190 -0.052 0.045 -23.508;
- 0.045 1.336 0.357 -53.167;
- -0.060 -0.303 1.146 11.994;
- 0.000 0.000 0.000 1.000;
- pass 1, spacing 8: log(p) = -4.0 (old=-4.9)
- transform before final EM align:
- 1.190 -0.052 0.045 -23.508;
- 0.045 1.336 0.357 -53.167;
- -0.060 -0.303 1.146 11.994;
- 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
- 1.19036 -0.05200 0.04499 -23.50809;
- 0.04517 1.33590 0.35668 -53.16697;
- -0.05976 -0.30345 1.14592 11.99424;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 382743
- Quasinewton: input matrix
- 1.19036 -0.05200 0.04499 -23.50809;
- 0.04517 1.33590 0.35668 -53.16697;
- -0.05976 -0.30345 1.14592 11.99424;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = 4.4 tol 0.000000
- final transform:
- 1.190 -0.052 0.045 -23.508;
- 0.045 1.336 0.357 -53.167;
- -0.060 -0.303 1.146 11.994;
- 0.000 0.000 0.000 1.000;
- writing output transformation to transforms/talairach_with_skull.lta...
- registration took 35 minutes and 23 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=125 y=83 z=117 r=94
- first estimation of the main basin volume: 3567053 voxels
- Looking for seedpoints
- 2 found in the cerebellum
- 12 found in the rest of the brain
- global maximum in x=108, y=81, z=85, Imax=255
- CSF=13, WM_intensity=110, WM_VARIANCE=5
- WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110
- preflooding height equal to 10 percent
- done.
- Analyze...
- main basin size=15872698844 voxels, voxel volume =1.000
- = 15872698844 mmm3 = 15872698.368 cm3
- done.
- PostAnalyze...Basin Prior
- 64 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=126,y=96, z=110, r=10261 iterations
- ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^
- GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 45532
- RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=11 , nb = -1032548792
- LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=10 , nb = 1100101065
- RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1075437826
- LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1081450114
- OTHER CSF_MIN=0, CSF_intensity=9, CSF_MAX=19 , nb = 1072930794
- (2) Problem with the least square interpolation in GM_MIN calculation.
-
- CSF_MAX TRANSITION GM_MIN GM
- GLOBAL
- before analyzing : 4, 6, 32, 50
- after analyzing : 4, 23, 32, 29
- RIGHT_CER
- before analyzing : 11, 16, 30, 50
- after analyzing : 11, 25, 30, 31
- LEFT_CER
- before analyzing : 10, 14, 30, 56
- after analyzing : 10, 24, 30, 32
- RIGHT_BRAIN
- before analyzing : 4, 6, 30, 50
- after analyzing : 4, 22, 30, 29
- LEFT_BRAIN
- before analyzing : 4, 6, 30, 50
- after analyzing : 4, 22, 30, 29
- OTHER
- before analyzing : 19, 48, 93, 108
- after analyzing : 19, 78, 93, 85
- mri_strip_skull: done peeling brain
- highly tesselated surface with 10242 vertices
- matching...70 iterations
- *********************VALIDATION*********************
- curvature mean = -0.013, std = 0.012
- curvature mean = 69.413, std = 7.854
- No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
- before rotation: sse = 1.67, sigma = 2.86
- after rotation: sse = 1.67, sigma = 2.86
- Localization of inacurate regions: Erosion-Dilation steps
- the sse mean is 1.71, its var is 2.52
- before Erosion-Dilatation 0.07% of inacurate vertices
- after Erosion-Dilatation 0.00% of inacurate vertices
- Validation of the shape of the surface done.
- Scaling of atlas fields onto current surface fields
- ********FINAL ITERATIVE TEMPLATE DEFORMATION********
- Compute Local values csf/gray
- Fine Segmentation...39 iterations
- mri_strip_skull: done peeling brain
- Brain Size = 1660037 voxels, voxel volume = 1.000 mm3
- = 1660037 mmm3 = 1660.037 cm3
- ******************************
- Saving brainmask.auto.mgz
- done
- cp brainmask.auto.mgz brainmask.mgz
- #-------------------------------------
- #@# EM Registration Thu Aug 8 11:41:31 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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=23.0
- skull bounding box = (60, 41, 38) --> (191, 173, 199)
- using (104, 85, 119) as brain centroid...
- mean wm in atlas = 107, using box (88,69,99) --> (120, 101,138) to find MRI wm
- before smoothing, mri peak at 106
- after smoothing, mri peak at 106, scaling input intensities by 1.009
- scaling channel 0 by 1.00943
- initial log_p = -4.5
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -4.098838 @ (-9.091, 27.273, -9.091)
- max log p = -3.886874 @ (4.545, -4.545, -4.545)
- max log p = -3.871808 @ (2.273, 2.273, -2.273)
- max log p = -3.835258 @ (1.136, -3.409, 3.409)
- max log p = -3.815219 @ (0.568, -0.568, -1.705)
- max log p = -3.815219 @ (0.000, 0.000, 0.000)
- Found translation: (-0.6, 21.0, -14.2): log p = -3.815
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.6, old_max_log_p =-3.8 (thresh=-3.8)
- 1.150 0.000 0.000 -19.675;
- 0.000 1.111 0.298 -17.897;
- 0.000 -0.236 0.883 30.466;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.6, old_max_log_p =-3.6 (thresh=-3.6)
- 1.055 -0.134 -0.036 8.983;
- 0.150 1.101 0.295 -35.847;
- 0.000 -0.272 1.015 19.236;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 2 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p =-3.6 (thresh=-3.6)
- 1.065 0.011 0.003 -10.203;
- 0.011 1.109 0.297 -19.144;
- 0.000 -0.272 1.015 19.236;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 3 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p =-3.5 (thresh=-3.5)
- 1.065 0.011 0.003 -10.203;
- 0.011 1.109 0.297 -19.144;
- 0.000 -0.272 1.015 19.236;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.2500
- ****************************************
- Nine parameter search. iteration 4 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.5 (thresh=-3.5)
- 1.104 -0.035 0.020 -12.843;
- 0.045 1.129 0.304 -28.083;
- -0.032 -0.262 0.996 24.176;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 5 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3)
- 1.104 -0.035 0.020 -12.843;
- 0.045 1.129 0.304 -28.083;
- -0.032 -0.262 0.996 24.176;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.0625
- ****************************************
- Nine parameter search. iteration 6 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3)
- 1.103 -0.074 0.018 -8.708;
- 0.081 1.119 0.320 -34.301;
- -0.042 -0.279 0.989 27.435;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 7 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3)
- 1.100 -0.074 0.018 -8.391;
- 0.081 1.119 0.320 -34.301;
- -0.042 -0.279 0.989 27.435;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 8 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3)
- 1.100 -0.074 0.018 -8.391;
- 0.081 1.119 0.320 -34.301;
- -0.042 -0.279 0.989 27.435;
- 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
- 1.10000 -0.07384 0.01772 -8.39068;
- 0.08076 1.11928 0.31996 -34.30147;
- -0.04177 -0.27917 0.98873 27.43496;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 2772
- Quasinewton: input matrix
- 1.10000 -0.07384 0.01772 -8.39068;
- 0.08076 1.11928 0.31996 -34.30147;
- -0.04177 -0.27917 0.98873 27.43496;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 1.100 -0.074 0.018 -8.391;
- 0.081 1.119 0.320 -34.301;
- -0.042 -0.279 0.989 27.435;
- 0.000 0.000 0.000 1.000;
- pass 1, spacing 8: log(p) = -3.3 (old=-4.5)
- transform before final EM align:
- 1.100 -0.074 0.018 -8.391;
- 0.081 1.119 0.320 -34.301;
- -0.042 -0.279 0.989 27.435;
- 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
- 1.10000 -0.07384 0.01772 -8.39068;
- 0.08076 1.11928 0.31996 -34.30147;
- -0.04177 -0.27917 0.98873 27.43496;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 312841
- Quasinewton: input matrix
- 1.10000 -0.07384 0.01772 -8.39068;
- 0.08076 1.11928 0.31996 -34.30147;
- -0.04177 -0.27917 0.98873 27.43496;
- 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: 013: -log(p) = 3.8 tol 0.000000
- final transform:
- 1.100 -0.074 0.018 -8.391;
- 0.081 1.119 0.320 -34.301;
- -0.042 -0.279 0.989 27.435;
- 0.000 0.000 0.000 1.000;
- writing output transformation to transforms/talairach.lta...
- registration took 35 minutes and 46 seconds.
- #--------------------------------------
- #@# CA Normalize Thu Aug 8 12:17:17 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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=23.0
- skull bounding box = (60, 41, 38) --> (191, 173, 200)
- using (104, 85, 119) as brain centroid...
- mean wm in atlas = 107, using box (88,69,99) --> (120, 101,138) to find MRI wm
- before smoothing, mri peak at 106
- after smoothing, mri peak at 106, scaling input intensities by 1.009
- scaling channel 0 by 1.00943
- using 244171 sample points...
- INFO: compute sample coordinates transform
- 1.100 -0.074 0.018 -8.391;
- 0.081 1.119 0.320 -34.301;
- -0.042 -0.279 0.989 27.435;
- 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 (126, 38, 39) --> (188, 141, 196)
- Left_Cerebral_White_Matter: limiting intensities to 104.0 --> 160.0
- 0 of 17 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 40735 control points for structure...
- bounding box (67, 39, 37) --> (127, 137, 197)
- Right_Cerebral_White_Matter: limiting intensities to 106.0 --> 160.0
- 1 of 8 (12.5%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3012 control points for structure...
- bounding box (130, 117, 68) --> (176, 154, 118)
- Left_Cerebellum_White_Matter: limiting intensities to 93.0 --> 160.0
- 0 of 16 (0.0%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2764 control points for structure...
- bounding box (89, 117, 64) --> (130, 157, 119)
- Right_Cerebellum_White_Matter: limiting intensities to 97.0 --> 160.0
- 1 of 7 (14.3%) samples deleted
- finding control points in Brain_Stem....
- found 3520 control points for structure...
- bounding box (114, 106, 99) --> (144, 166, 128)
- Brain_Stem: limiting intensities to 77.0 --> 160.0
- 0 of 7 (0.0%) samples deleted
- using 55 total control points for intensity normalization...
- bias field = 0.924 +- 0.069
- 0 of 53 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 41584 control points for structure...
- bounding box (126, 38, 39) --> (188, 141, 196)
- Left_Cerebral_White_Matter: limiting intensities to 93.0 --> 143.0
- 0 of 103 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 40735 control points for structure...
- bounding box (67, 39, 37) --> (127, 137, 197)
- Right_Cerebral_White_Matter: limiting intensities to 93.0 --> 143.0
- 0 of 99 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3012 control points for structure...
- bounding box (130, 117, 68) --> (176, 154, 118)
- Left_Cerebellum_White_Matter: limiting intensities to 83.0 --> 143.0
- 0 of 19 (0.0%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2764 control points for structure...
- bounding box (89, 117, 64) --> (130, 157, 119)
- finding control points in Brain_Stem....
- found 3520 control points for structure...
- bounding box (114, 106, 99) --> (144, 166, 128)
- Brain_Stem: limiting intensities to 85.0 --> 143.0
- 30 of 63 (47.6%) samples deleted
- using 284 total control points for intensity normalization...
- bias field = 1.000 +- 0.061
- 0 of 254 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 41584 control points for structure...
- bounding box (126, 38, 39) --> (188, 141, 196)
- Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 136.0
- 0 of 201 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 40735 control points for structure...
- bounding box (67, 39, 37) --> (127, 137, 197)
- Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 136.0
- 0 of 196 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3012 control points for structure...
- bounding box (130, 117, 68) --> (176, 154, 118)
- Left_Cerebellum_White_Matter: limiting intensities to 79.0 --> 136.0
- 0 of 8 (0.0%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2764 control points for structure...
- bounding box (89, 117, 64) --> (130, 157, 119)
- Right_Cerebellum_White_Matter: limiting intensities to 83.0 --> 136.0
- 1 of 12 (8.3%) samples deleted
- finding control points in Brain_Stem....
- found 3520 control points for structure...
- bounding box (114, 106, 99) --> (144, 166, 128)
- Brain_Stem: limiting intensities to 67.0 --> 136.0
- 0 of 70 (0.0%) samples deleted
- using 487 total control points for intensity normalization...
- bias field = 1.025 +- 0.062
- 0 of 486 control points discarded
- writing normalized volume to norm.mgz...
- writing control points to ctrl_pts.mgz
- freeing GCA...done.
- normalization took 2 minutes and 7 seconds.
- #--------------------------------------
- #@# CA Reg Thu Aug 8 12:19:24 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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) = 1.32 (predicted orig area = 6.0)
- label assignment complete, 0 changed (0.00%)
- freeing gibbs priors...done.
- average std[0] = 5.0
- **************** pass 1 of 1 ************************
- setting smoothness coefficient to 0.039
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.820, neg=0, invalid=96777
- 0001: dt=129.472000, rms=0.774 (5.632%), neg=0, invalid=96777
- 0002: dt=129.472000, rms=0.764 (1.319%), neg=0, invalid=96777
- 0003: dt=221.952000, rms=0.755 (1.188%), neg=0, invalid=96777
- 0004: dt=129.472000, rms=0.750 (0.682%), neg=0, invalid=96777
- 0005: dt=129.472000, rms=0.746 (0.442%), neg=0, invalid=96777
- 0006: dt=129.472000, rms=0.743 (0.489%), neg=0, invalid=96777
- 0007: dt=129.472000, rms=0.741 (0.291%), neg=0, invalid=96777
- 0008: dt=129.472000, rms=0.738 (0.398%), neg=0, invalid=96777
- 0009: dt=129.472000, rms=0.736 (0.244%), neg=0, invalid=96777
- 0010: dt=129.472000, rms=0.734 (0.292%), neg=0, invalid=96777
- 0011: dt=129.472000, rms=0.730 (0.448%), neg=0, invalid=96777
- 0012: dt=129.472000, rms=0.727 (0.480%), neg=0, invalid=96777
- 0013: dt=129.472000, rms=0.722 (0.600%), neg=0, invalid=96777
- 0014: dt=129.472000, rms=0.718 (0.587%), neg=0, invalid=96777
- 0015: dt=129.472000, rms=0.715 (0.500%), neg=0, invalid=96777
- 0016: dt=129.472000, rms=0.712 (0.407%), neg=0, invalid=96777
- 0017: dt=129.472000, rms=0.709 (0.451%), neg=0, invalid=96777
- 0018: dt=129.472000, rms=0.706 (0.398%), neg=0, invalid=96777
- 0019: dt=129.472000, rms=0.703 (0.328%), neg=0, invalid=96777
- 0020: dt=129.472000, rms=0.701 (0.278%), neg=0, invalid=96777
- 0021: dt=129.472000, rms=0.700 (0.267%), neg=0, invalid=96777
- 0022: dt=129.472000, rms=0.698 (0.242%), neg=0, invalid=96777
- 0023: dt=129.472000, rms=0.696 (0.250%), neg=0, invalid=96777
- 0024: dt=129.472000, rms=0.695 (0.213%), neg=0, invalid=96777
- 0025: dt=129.472000, rms=0.693 (0.236%), neg=0, invalid=96777
- 0026: dt=129.472000, rms=0.691 (0.226%), neg=0, invalid=96777
- 0027: dt=129.472000, rms=0.690 (0.240%), neg=0, invalid=96777
- 0028: dt=129.472000, rms=0.688 (0.211%), neg=0, invalid=96777
- 0029: dt=129.472000, rms=0.687 (0.205%), neg=0, invalid=96777
- 0030: dt=129.472000, rms=0.686 (0.184%), neg=0, invalid=96777
- 0031: dt=129.472000, rms=0.684 (0.188%), neg=0, invalid=96777
- 0032: dt=129.472000, rms=0.683 (0.149%), neg=0, invalid=96777
- 0033: dt=129.472000, rms=0.682 (0.128%), neg=0, invalid=96777
- 0034: dt=129.472000, rms=0.682 (0.125%), neg=0, invalid=96777
- 0035: dt=129.472000, rms=0.681 (0.130%), neg=0, invalid=96777
- 0036: dt=129.472000, rms=0.680 (0.111%), neg=0, invalid=96777
- 0037: dt=129.472000, rms=0.679 (0.096%), neg=0, invalid=96777
- 0038: dt=443.904000, rms=0.679 (0.056%), neg=0, invalid=96777
- 0039: dt=443.904000, rms=0.679 (-1.585%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.679, neg=0, invalid=96777
- 0040: dt=32.368000, rms=0.679 (0.041%), neg=0, invalid=96777
- 0041: dt=92.480000, rms=0.678 (0.043%), neg=0, invalid=96777
- 0042: dt=443.904000, rms=0.677 (0.201%), neg=0, invalid=96777
- 0043: dt=23.120000, rms=0.677 (-0.002%), neg=0, invalid=96777
- setting smoothness coefficient to 0.154
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.684, neg=0, invalid=96777
- 0044: dt=103.680000, rms=0.678 (0.909%), neg=0, invalid=96777
- 0045: dt=36.288000, rms=0.672 (0.804%), neg=0, invalid=96777
- 0046: dt=25.920000, rms=0.671 (0.214%), neg=0, invalid=96777
- 0047: dt=25.920000, rms=0.669 (0.318%), neg=0, invalid=96777
- 0048: dt=25.920000, rms=0.666 (0.471%), neg=0, invalid=96777
- 0049: dt=25.920000, rms=0.662 (0.592%), neg=0, invalid=96777
- 0050: dt=25.920000, rms=0.658 (0.646%), neg=0, invalid=96777
- 0051: dt=25.920000, rms=0.653 (0.698%), neg=0, invalid=96777
- 0052: dt=25.920000, rms=0.648 (0.721%), neg=0, invalid=96777
- 0053: dt=25.920000, rms=0.644 (0.663%), neg=0, invalid=96777
- 0054: dt=25.920000, rms=0.640 (0.599%), neg=0, invalid=96777
- 0055: dt=25.920000, rms=0.637 (0.536%), neg=0, invalid=96777
- 0056: dt=25.920000, rms=0.634 (0.490%), neg=0, invalid=96777
- 0057: dt=25.920000, rms=0.631 (0.455%), neg=0, invalid=96777
- 0058: dt=25.920000, rms=0.628 (0.424%), neg=0, invalid=96777
- 0059: dt=25.920000, rms=0.626 (0.369%), neg=0, invalid=96777
- 0060: dt=25.920000, rms=0.624 (0.335%), neg=0, invalid=96777
- 0061: dt=25.920000, rms=0.622 (0.295%), neg=0, invalid=96777
- 0062: dt=25.920000, rms=0.620 (0.278%), neg=0, invalid=96777
- 0063: dt=25.920000, rms=0.618 (0.257%), neg=0, invalid=96777
- 0064: dt=25.920000, rms=0.617 (0.225%), neg=0, invalid=96777
- 0065: dt=25.920000, rms=0.616 (0.192%), neg=0, invalid=96777
- 0066: dt=25.920000, rms=0.615 (0.154%), neg=0, invalid=96777
- 0067: dt=25.920000, rms=0.614 (0.138%), neg=0, invalid=96777
- 0068: dt=25.920000, rms=0.613 (0.136%), neg=0, invalid=96777
- 0069: dt=25.920000, rms=0.612 (0.116%), neg=0, invalid=96777
- 0070: dt=25.920000, rms=0.612 (0.092%), neg=0, invalid=96777
- 0071: dt=103.680000, rms=0.612 (0.032%), neg=0, invalid=96777
- 0072: dt=103.680000, rms=0.611 (0.113%), neg=0, invalid=96777
- 0073: dt=103.680000, rms=0.611 (-1.233%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.611, neg=0, invalid=96777
- 0074: dt=9.072000, rms=0.611 (0.066%), neg=0, invalid=96777
- 0075: dt=9.072000, rms=0.610 (0.035%), neg=0, invalid=96777
- 0076: dt=9.072000, rms=0.610 (0.020%), neg=0, invalid=96777
- 0077: dt=9.072000, rms=0.610 (0.010%), neg=0, invalid=96777
- 0078: dt=9.072000, rms=0.610 (0.002%), neg=0, invalid=96777
- setting smoothness coefficient to 0.588
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.636, neg=0, invalid=96777
- 0079: dt=6.372881, rms=0.636 (0.086%), neg=0, invalid=96777
- 0080: dt=1.200000, rms=0.636 (0.003%), neg=0, invalid=96777
- 0081: dt=1.200000, rms=0.636 (-0.001%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.636, neg=0, invalid=96777
- 0082: dt=0.500000, rms=0.636 (0.000%), neg=0, invalid=96777
- 0083: dt=0.125000, rms=0.636 (0.000%), neg=0, invalid=96777
- 0084: dt=0.125000, rms=0.636 (0.000%), neg=0, invalid=96777
- 0085: dt=0.125000, rms=0.636 (-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=0.705, neg=0, invalid=96777
- 0086: dt=5.310924, rms=0.686 (2.764%), neg=0, invalid=96777
- 0087: dt=2.880000, rms=0.685 (0.141%), neg=0, invalid=96777
- 0088: dt=2.880000, rms=0.685 (-0.002%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.685, neg=0, invalid=96777
- 0089: dt=0.000000, rms=0.685 (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=0.750, neg=0, invalid=96777
- 0090: dt=1.024000, rms=0.746 (0.510%), neg=0, invalid=96777
- 0091: dt=2.056180, rms=0.740 (0.796%), neg=0, invalid=96777
- 0092: dt=0.488095, rms=0.739 (0.084%), neg=0, invalid=96777
- 0093: dt=0.488095, rms=0.739 (0.065%), neg=0, invalid=96777
- 0094: dt=0.488095, rms=0.738 (0.072%), neg=0, invalid=96777
- 0095: dt=0.488095, rms=0.738 (0.046%), neg=0, invalid=96777
- 0096: dt=0.488095, rms=0.738 (-0.026%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.738, neg=0, invalid=96777
- 0097: dt=1.792000, rms=0.736 (0.296%), neg=0, invalid=96777
- 0098: dt=0.000000, rms=0.736 (-0.001%), neg=0, invalid=96777
- 0099: dt=0.100000, rms=0.736 (-0.007%), 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=0.699, neg=0, invalid=96777
- 0100: dt=0.448000, rms=0.679 (2.883%), neg=0, invalid=96777
- 0101: dt=0.000000, rms=0.679 (0.006%), neg=0, invalid=96777
- 0102: dt=0.050000, rms=0.679 (-0.503%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.679, neg=0, invalid=96777
- 0103: dt=0.000000, rms=0.679 (0.000%), neg=0, invalid=96777
- renormalizing by structure alignment....
- renormalizing input #0
- gca peak = 0.11725 (24)
- mri peak = 0.15967 ( 9)
- Left_Lateral_Ventricle (4): linear fit = 0.22 x + 0.0 (762 voxels, overlap=0.005)
- Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (762 voxels, peak = 5), gca=9.6
- gca peak = 0.14022 (22)
- mri peak = 0.20958 ( 8)
- Right_Lateral_Ventricle (43): linear fit = 0.28 x + 0.0 (565 voxels, overlap=0.005)
- Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (565 voxels, peak = 6), gca=8.8
- gca peak = 0.24234 (100)
- mri peak = 0.11045 (83)
- Right_Pallidum (52): linear fit = 0.83 x + 0.0 (381 voxels, overlap=0.049)
- Right_Pallidum (52): linear fit = 0.83 x + 0.0 (381 voxels, peak = 84), gca=83.5
- gca peak = 0.19192 (97)
- mri peak = 0.10127 (79)
- Left_Pallidum (13): linear fit = 0.83 x + 0.0 (265 voxels, overlap=0.061)
- Left_Pallidum (13): linear fit = 0.83 x + 0.0 (265 voxels, peak = 81), gca=81.0
- gca peak = 0.24007 (63)
- mri peak = 0.07595 (56)
- Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (408 voxels, overlap=0.301)
- Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (408 voxels, peak = 55), gca=55.1
- gca peak = 0.29892 (64)
- mri peak = 0.08306 (56)
- Left_Hippocampus (17): linear fit = 0.85 x + 0.0 (614 voxels, overlap=0.449)
- Left_Hippocampus (17): linear fit = 0.85 x + 0.0 (614 voxels, peak = 54), gca=54.1
- gca peak = 0.12541 (104)
- mri peak = 0.06587 (107)
- Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (60604 voxels, overlap=0.859)
- Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (60604 voxels, peak = 107), gca=106.6
- gca peak = 0.13686 (104)
- mri peak = 0.07229 (106)
- Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (62492 voxels, overlap=0.824)
- Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (62492 voxels, peak = 107), gca=106.6
- gca peak = 0.11691 (63)
- mri peak = 0.06072 (51)
- Left_Cerebral_Cortex (3): linear fit = 0.81 x + 0.0 (15397 voxels, overlap=0.274)
- Left_Cerebral_Cortex (3): linear fit = 0.81 x + 0.0 (15397 voxels, peak = 51), gca=51.3
- gca peak = 0.13270 (63)
- mri peak = 0.05634 (51)
- Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (15467 voxels, overlap=0.270)
- Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (15467 voxels, peak = 52), gca=52.0
- gca peak = 0.15182 (70)
- mri peak = 0.11664 (63)
- Right_Caudate (50): linear fit = 0.86 x + 0.0 (430 voxels, overlap=0.015)
- Right_Caudate (50): linear fit = 0.86 x + 0.0 (430 voxels, peak = 60), gca=59.9
- gca peak = 0.14251 (76)
- mri peak = 0.08069 (64)
- Left_Caudate (11): linear fit = 0.85 x + 0.0 (596 voxels, overlap=0.168)
- Left_Caudate (11): linear fit = 0.85 x + 0.0 (596 voxels, peak = 64), gca=64.2
- gca peak = 0.12116 (60)
- mri peak = 0.04818 (56)
- Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (8260 voxels, overlap=0.979)
- Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (8260 voxels, peak = 56), gca=56.1
- gca peak = 0.12723 (61)
- mri peak = 0.04496 (55)
- Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (10207 voxels, overlap=0.839)
- Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (10207 voxels, peak = 57), gca=57.0
- gca peak = 0.22684 (88)
- mri peak = 0.05895 (88)
- Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (5012 voxels, overlap=0.904)
- Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (5012 voxels, peak = 89), gca=89.3
- gca peak = 0.21067 (87)
- mri peak = 0.05106 (91)
- Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (4542 voxels, overlap=0.965)
- Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (4542 voxels, peak = 90), gca=90.0
- gca peak = 0.25455 (62)
- mri peak = 0.10453 (55)
- Left_Amygdala (18): linear fit = 0.86 x + 0.0 (316 voxels, overlap=0.404)
- Left_Amygdala (18): linear fit = 0.86 x + 0.0 (316 voxels, peak = 53), gca=53.0
- gca peak = 0.39668 (62)
- mri peak = 0.12132 (58)
- Right_Amygdala (54): linear fit = 0.85 x + 0.0 (308 voxels, overlap=0.244)
- Right_Amygdala (54): linear fit = 0.85 x + 0.0 (308 voxels, peak = 52), gca=52.4
- gca peak = 0.10129 (93)
- mri peak = 0.05714 (83)
- Left_Thalamus_Proper (10): linear fit = 0.92 x + 0.0 (4717 voxels, overlap=0.756)
- Left_Thalamus_Proper (10): linear fit = 0.92 x + 0.0 (4717 voxels, peak = 85), gca=85.1
- gca peak = 0.12071 (89)
- mri peak = 0.07686 (80)
- Right_Thalamus_Proper (49): linear fit = 0.94 x + 0.0 (3821 voxels, overlap=0.565)
- Right_Thalamus_Proper (49): linear fit = 0.94 x + 0.0 (3821 voxels, peak = 83), gca=83.2
- gca peak = 0.13716 (82)
- mri peak = 0.05967 (71)
- Left_Putamen (12): linear fit = 0.88 x + 0.0 (1644 voxels, overlap=0.415)
- Left_Putamen (12): linear fit = 0.88 x + 0.0 (1644 voxels, peak = 73), gca=72.6
- gca peak = 0.15214 (84)
- mri peak = 0.06344 (70)
- Right_Putamen (51): linear fit = 0.83 x + 0.0 (1899 voxels, overlap=0.159)
- Right_Putamen (51): linear fit = 0.83 x + 0.0 (1899 voxels, peak = 70), gca=70.1
- gca peak = 0.08983 (85)
- mri peak = 0.08139 (82)
- Brain_Stem (16): linear fit = 1.02 x + 0.0 (8892 voxels, overlap=0.777)
- Brain_Stem (16): linear fit = 1.02 x + 0.0 (8892 voxels, peak = 87), gca=87.1
- gca peak = 0.11809 (92)
- mri peak = 0.06918 (89)
- Right_VentralDC (60): linear fit = 0.96 x + 0.0 (684 voxels, overlap=0.675)
- Right_VentralDC (60): linear fit = 0.96 x + 0.0 (684 voxels, peak = 89), gca=88.8
- gca peak = 0.12914 (94)
- mri peak = 0.08774 (88)
- Left_VentralDC (28): linear fit = 0.94 x + 0.0 (952 voxels, overlap=0.652)
- Left_VentralDC (28): linear fit = 0.94 x + 0.0 (952 voxels, peak = 89), gca=88.8
- gca peak = 0.21100 (36)
- mri peak = 0.27273 (51)
- gca peak = 0.13542 (27)
- mri peak = 0.19745 ( 6)
- Fourth_Ventricle (15): linear fit = 0.32 x + 0.0 (366 voxels, overlap=0.024)
- Fourth_Ventricle (15): linear fit = 0.32 x + 0.0 (366 voxels, peak = 9), gca=8.8
- 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 0.84 x + 0.0
- estimating mean wm scale to be 1.02 x + 0.0
- estimating mean csf scale to be 0.40 x + 0.0
- saving intensity scales to talairach.label_intensities.txt
- **************** pass 1 of 1 ************************
- setting smoothness coefficient to 0.008
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.697, neg=0, invalid=96777
- 0104: dt=129.472000, rms=0.692 (0.715%), neg=0, invalid=96777
- 0105: dt=221.952000, rms=0.689 (0.488%), neg=0, invalid=96777
- 0106: dt=92.480000, rms=0.687 (0.228%), neg=0, invalid=96777
- 0107: dt=295.936000, rms=0.686 (0.240%), neg=0, invalid=96777
- 0108: dt=92.480000, rms=0.684 (0.199%), neg=0, invalid=96777
- 0109: dt=129.472000, rms=0.684 (0.091%), neg=0, invalid=96777
- 0110: dt=129.472000, rms=0.683 (0.107%), neg=0, invalid=96777
- 0111: dt=92.480000, rms=0.683 (0.057%), neg=0, invalid=96777
- 0112: dt=295.936000, rms=0.682 (0.137%), neg=0, invalid=96777
- 0113: dt=32.368000, rms=0.681 (0.084%), neg=0, invalid=96777
- 0114: dt=73.984000, rms=0.681 (0.032%), neg=0, invalid=96777
- 0115: dt=73.984000, rms=0.681 (0.042%), neg=0, invalid=96777
- 0116: dt=73.984000, rms=0.680 (0.078%), neg=0, invalid=96777
- 0117: dt=73.984000, rms=0.680 (0.095%), neg=0, invalid=96777
- 0118: dt=73.984000, rms=0.679 (0.099%), neg=0, invalid=96777
- 0119: dt=73.984000, rms=0.678 (0.119%), neg=0, invalid=96777
- 0120: dt=73.984000, rms=0.677 (0.120%), neg=0, invalid=96777
- 0121: dt=73.984000, rms=0.676 (0.120%), neg=0, invalid=96777
- 0122: dt=73.984000, rms=0.676 (0.117%), neg=0, invalid=96777
- 0123: dt=73.984000, rms=0.675 (0.117%), neg=0, invalid=96777
- 0124: dt=73.984000, rms=0.674 (0.118%), neg=0, invalid=96777
- 0125: dt=73.984000, rms=0.673 (0.098%), neg=0, invalid=96777
- 0126: dt=73.984000, rms=0.673 (0.075%), neg=0, invalid=96777
- 0127: dt=73.984000, rms=0.673 (0.057%), neg=0, invalid=96777
- 0128: dt=73.984000, rms=0.672 (0.057%), neg=0, invalid=96777
- 0129: dt=73.984000, rms=0.672 (0.071%), neg=0, invalid=96777
- 0130: dt=73.984000, rms=0.671 (0.072%), neg=0, invalid=96777
- 0131: dt=73.984000, rms=0.671 (0.069%), neg=0, invalid=96777
- 0132: dt=73.984000, rms=0.670 (0.053%), neg=0, invalid=96777
- 0133: dt=73.984000, rms=0.670 (0.047%), neg=0, invalid=96777
- 0134: dt=73.984000, rms=0.670 (0.052%), neg=0, invalid=96777
- 0135: dt=73.984000, rms=0.669 (0.053%), neg=0, invalid=96777
- 0136: dt=73.984000, rms=0.669 (0.063%), neg=0, invalid=96777
- 0137: dt=73.984000, rms=0.668 (0.065%), neg=0, invalid=96777
- 0138: dt=73.984000, rms=0.668 (0.059%), neg=0, invalid=96777
- 0139: dt=73.984000, rms=0.668 (0.055%), neg=0, invalid=96777
- 0140: dt=73.984000, rms=0.667 (0.042%), neg=0, invalid=96777
- 0141: dt=73.984000, rms=0.667 (0.039%), neg=0, invalid=96777
- 0142: dt=73.984000, rms=0.667 (0.042%), neg=0, invalid=96777
- 0143: dt=73.984000, rms=0.667 (0.045%), neg=0, invalid=96777
- 0144: dt=73.984000, rms=0.666 (0.046%), neg=0, invalid=96777
- 0145: dt=73.984000, rms=0.666 (0.046%), neg=0, invalid=96777
- 0146: dt=73.984000, rms=0.666 (0.038%), neg=0, invalid=96777
- 0147: dt=73.984000, rms=0.665 (0.037%), neg=0, invalid=96777
- 0148: dt=73.984000, rms=0.665 (0.032%), neg=0, invalid=96777
- 0149: dt=73.984000, rms=0.665 (0.034%), neg=0, invalid=96777
- 0150: dt=73.984000, rms=0.665 (0.039%), neg=0, invalid=96777
- 0151: dt=73.984000, rms=0.665 (0.045%), neg=0, invalid=96777
- 0152: dt=73.984000, rms=0.664 (0.042%), neg=0, invalid=96777
- 0153: dt=73.984000, rms=0.664 (0.037%), neg=0, invalid=96777
- 0154: dt=73.984000, rms=0.664 (0.028%), neg=0, invalid=96777
- 0155: dt=73.984000, rms=0.664 (0.019%), neg=0, invalid=96777
- 0156: dt=73.984000, rms=0.664 (0.023%), neg=0, invalid=96777
- 0157: dt=73.984000, rms=0.663 (0.033%), neg=0, invalid=96777
- 0158: dt=73.984000, rms=0.663 (0.036%), neg=0, invalid=96777
- 0159: dt=73.984000, rms=0.663 (0.039%), neg=0, invalid=96777
- 0160: dt=73.984000, rms=0.663 (0.027%), neg=0, invalid=96777
- 0161: dt=73.984000, rms=0.662 (0.018%), neg=0, invalid=96777
- 0162: dt=73.984000, rms=0.662 (0.017%), neg=0, invalid=96777
- 0163: dt=369.920000, rms=0.662 (0.014%), neg=0, invalid=96777
- 0164: dt=369.920000, rms=0.662 (-0.127%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.662, neg=0, invalid=96777
- 0165: dt=369.920000, rms=0.661 (0.243%), neg=0, invalid=96777
- 0166: dt=92.480000, rms=0.660 (0.059%), neg=0, invalid=96777
- 0167: dt=443.904000, rms=0.660 (0.068%), neg=0, invalid=96777
- 0168: dt=129.472000, rms=0.659 (0.057%), neg=0, invalid=96777
- 0169: dt=129.472000, rms=0.659 (0.028%), neg=0, invalid=96777
- 0170: dt=129.472000, rms=0.659 (0.007%), neg=0, invalid=96777
- 0171: dt=129.472000, rms=0.659 (0.043%), neg=0, invalid=96777
- 0172: dt=129.472000, rms=0.659 (0.053%), neg=0, invalid=96777
- 0173: dt=129.472000, rms=0.658 (0.041%), neg=0, invalid=96777
- 0174: dt=129.472000, rms=0.658 (0.042%), neg=0, invalid=96777
- 0175: dt=129.472000, rms=0.658 (0.051%), neg=0, invalid=96777
- 0176: dt=129.472000, rms=0.657 (0.050%), neg=0, invalid=96777
- 0177: dt=129.472000, rms=0.657 (0.038%), neg=0, invalid=96777
- 0178: dt=129.472000, rms=0.657 (0.041%), neg=0, invalid=96777
- 0179: dt=129.472000, rms=0.657 (0.042%), neg=0, invalid=96777
- 0180: dt=129.472000, rms=0.656 (0.027%), neg=0, invalid=96777
- 0181: dt=129.472000, rms=0.656 (0.023%), neg=0, invalid=96777
- 0182: dt=129.472000, rms=0.656 (0.039%), neg=0, invalid=96777
- 0183: dt=129.472000, rms=0.656 (0.040%), neg=0, invalid=96777
- 0184: dt=129.472000, rms=0.656 (0.029%), neg=0, invalid=96777
- 0185: dt=129.472000, rms=0.655 (0.019%), neg=0, invalid=96777
- 0186: dt=129.472000, rms=0.655 (0.016%), neg=0, invalid=96777
- 0187: dt=110.976000, rms=0.655 (0.004%), neg=0, invalid=96777
- 0188: dt=110.976000, rms=0.655 (0.003%), neg=0, invalid=96777
- 0189: dt=110.976000, rms=0.655 (0.001%), neg=0, invalid=96777
- 0190: dt=110.976000, rms=0.655 (0.006%), neg=0, invalid=96777
- 0191: dt=110.976000, rms=0.655 (0.013%), neg=0, invalid=96777
- 0192: dt=110.976000, rms=0.655 (0.017%), neg=0, invalid=96777
- 0193: dt=110.976000, rms=0.655 (0.012%), neg=0, invalid=96777
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.656, neg=0, invalid=96777
- 0194: dt=145.152000, rms=0.650 (0.849%), neg=0, invalid=96777
- 0195: dt=124.416000, rms=0.645 (0.731%), neg=0, invalid=96777
- 0196: dt=36.288000, rms=0.642 (0.511%), neg=0, invalid=96777
- 0197: dt=62.208000, rms=0.641 (0.218%), neg=0, invalid=96777
- 0198: dt=36.288000, rms=0.639 (0.246%), neg=0, invalid=96777
- 0199: dt=36.288000, rms=0.638 (0.146%), neg=0, invalid=96777
- 0200: dt=36.288000, rms=0.637 (0.211%), neg=0, invalid=96777
- 0201: dt=62.208000, rms=0.636 (0.180%), neg=0, invalid=96777
- 0202: dt=36.288000, rms=0.634 (0.219%), neg=0, invalid=96777
- 0203: dt=36.288000, rms=0.633 (0.117%), neg=0, invalid=96777
- 0204: dt=36.288000, rms=0.632 (0.189%), neg=0, invalid=96777
- 0205: dt=36.288000, rms=0.632 (0.114%), neg=0, invalid=96777
- 0206: dt=145.152000, rms=0.629 (0.362%), neg=0, invalid=96777
- 0207: dt=20.736000, rms=0.628 (0.212%), neg=0, invalid=96777
- 0208: dt=414.720000, rms=0.623 (0.728%), neg=0, invalid=96777
- 0209: dt=17.968883, rms=0.621 (0.427%), neg=0, invalid=96777
- 0210: dt=25.920000, rms=0.620 (0.070%), neg=0, invalid=96777
- 0211: dt=248.832000, rms=0.618 (0.370%), neg=0, invalid=96777
- 0212: dt=20.736000, rms=0.617 (0.168%), neg=0, invalid=96777
- 0213: dt=145.152000, rms=0.615 (0.252%), neg=0, invalid=96777
- 0214: dt=36.288000, rms=0.615 (0.101%), neg=0, invalid=96777
- 0215: dt=62.208000, rms=0.614 (0.106%), neg=0, invalid=96777
- 0216: dt=31.104000, rms=0.614 (0.057%), neg=0, invalid=96777
- 0217: dt=82.944000, rms=0.613 (0.123%), neg=0, invalid=96777
- 0218: dt=25.920000, rms=0.613 (0.058%), neg=0, invalid=96777
- 0219: dt=331.776000, rms=0.610 (0.357%), neg=0, invalid=96777
- 0220: dt=15.552000, rms=0.610 (0.155%), neg=0, invalid=96777
- 0221: dt=25.920000, rms=0.609 (0.045%), neg=0, invalid=96777
- 0222: dt=25.920000, rms=0.609 (0.051%), neg=0, invalid=96777
- 0223: dt=25.920000, rms=0.608 (0.071%), neg=0, invalid=96777
- 0224: dt=25.920000, rms=0.608 (0.084%), neg=0, invalid=96777
- 0225: dt=25.920000, rms=0.607 (0.098%), neg=0, invalid=96777
- 0226: dt=25.920000, rms=0.607 (0.134%), neg=0, invalid=96777
- 0227: dt=25.920000, rms=0.606 (0.159%), neg=0, invalid=96777
- 0228: dt=25.920000, rms=0.605 (0.160%), neg=0, invalid=96777
- 0229: dt=25.920000, rms=0.604 (0.165%), neg=0, invalid=96777
- 0230: dt=25.920000, rms=0.603 (0.158%), neg=0, invalid=96777
- 0231: dt=25.920000, rms=0.602 (0.163%), neg=0, invalid=96777
- 0232: dt=25.920000, rms=0.601 (0.181%), neg=0, invalid=96777
- 0233: dt=25.920000, rms=0.599 (0.190%), neg=0, invalid=96777
- 0234: dt=25.920000, rms=0.598 (0.164%), neg=0, invalid=96777
- 0235: dt=25.920000, rms=0.598 (0.148%), neg=0, invalid=96777
- 0236: dt=25.920000, rms=0.597 (0.163%), neg=0, invalid=96777
- 0237: dt=25.920000, rms=0.596 (0.176%), neg=0, invalid=96777
- 0238: dt=25.920000, rms=0.595 (0.164%), neg=0, invalid=96777
- 0239: dt=25.920000, rms=0.594 (0.130%), neg=0, invalid=96777
- 0240: dt=25.920000, rms=0.594 (0.003%), neg=0, invalid=96777
- 0241: dt=25.920000, rms=0.594 (0.020%), neg=0, invalid=96777
- 0242: dt=25.920000, rms=0.593 (0.034%), neg=0, invalid=96777
- 0243: dt=25.920000, rms=0.593 (0.050%), neg=0, invalid=96777
- 0244: dt=25.920000, rms=0.593 (0.053%), neg=0, invalid=96777
- 0245: dt=25.920000, rms=0.593 (0.053%), neg=0, invalid=96777
- 0246: dt=25.920000, rms=0.592 (0.050%), neg=0, invalid=96777
- 0247: dt=25.920000, rms=0.592 (0.060%), neg=0, invalid=96777
- 0248: dt=25.920000, rms=0.591 (0.088%), neg=0, invalid=96777
- 0249: dt=25.920000, rms=0.591 (0.081%), neg=0, invalid=96777
- 0250: dt=25.920000, rms=0.590 (0.075%), neg=0, invalid=96777
- 0251: dt=25.920000, rms=0.590 (0.077%), neg=0, invalid=96777
- 0252: dt=25.920000, rms=0.590 (0.077%), neg=0, invalid=96777
- 0253: dt=25.920000, rms=0.589 (0.084%), neg=0, invalid=96777
- 0254: dt=25.920000, rms=0.589 (0.090%), neg=0, invalid=96777
- 0255: dt=25.920000, rms=0.588 (0.085%), neg=0, invalid=96777
- 0256: dt=25.920000, rms=0.588 (0.067%), neg=0, invalid=96777
- 0257: dt=25.920000, rms=0.587 (0.060%), neg=0, invalid=96777
- 0258: dt=25.920000, rms=0.587 (0.076%), neg=0, invalid=96777
- 0259: dt=25.920000, rms=0.586 (0.091%), neg=0, invalid=96777
- 0260: dt=25.920000, rms=0.586 (0.081%), neg=0, invalid=96777
- 0261: dt=25.920000, rms=0.585 (0.076%), neg=0, invalid=96777
- 0262: dt=25.920000, rms=0.585 (0.071%), neg=0, invalid=96777
- 0263: dt=25.920000, rms=0.584 (0.091%), neg=0, invalid=96777
- 0264: dt=25.920000, rms=0.584 (0.070%), neg=0, invalid=96777
- 0265: dt=25.920000, rms=0.584 (0.031%), neg=0, invalid=96777
- 0266: dt=25.920000, rms=0.584 (0.048%), neg=0, invalid=96777
- 0267: dt=25.920000, rms=0.583 (0.066%), neg=0, invalid=96777
- 0268: dt=25.920000, rms=0.583 (0.074%), neg=0, invalid=96777
- 0269: dt=25.920000, rms=0.582 (0.064%), neg=0, invalid=96777
- 0270: dt=25.920000, rms=0.582 (0.054%), neg=0, invalid=96777
- 0271: dt=25.920000, rms=0.582 (0.045%), neg=0, invalid=96777
- 0272: dt=25.920000, rms=0.582 (0.048%), neg=0, invalid=96777
- 0273: dt=25.920000, rms=0.581 (0.046%), neg=0, invalid=96777
- 0274: dt=25.920000, rms=0.581 (0.057%), neg=0, invalid=96777
- 0275: dt=25.920000, rms=0.581 (0.041%), neg=0, invalid=96777
- 0276: dt=25.920000, rms=0.581 (0.030%), neg=0, invalid=96777
- 0277: dt=25.920000, rms=0.580 (0.040%), neg=0, invalid=96777
- 0278: dt=25.920000, rms=0.580 (0.050%), neg=0, invalid=96777
- 0279: dt=25.920000, rms=0.580 (0.057%), neg=0, invalid=96777
- 0280: dt=25.920000, rms=0.579 (0.047%), neg=0, invalid=96777
- 0281: dt=25.920000, rms=0.579 (0.037%), neg=0, invalid=96777
- 0282: dt=25.920000, rms=0.579 (0.043%), neg=0, invalid=96777
- 0283: dt=25.920000, rms=0.579 (0.045%), neg=0, invalid=96777
- 0284: dt=25.920000, rms=0.578 (0.048%), neg=0, invalid=96777
- 0285: dt=25.920000, rms=0.578 (0.040%), neg=0, invalid=96777
- 0286: dt=25.920000, rms=0.578 (0.035%), neg=0, invalid=96777
- 0287: dt=25.920000, rms=0.578 (0.038%), neg=0, invalid=96777
- 0288: dt=25.920000, rms=0.578 (0.035%), neg=0, invalid=96777
- 0289: dt=25.920000, rms=0.577 (0.040%), neg=0, invalid=96777
- 0290: dt=25.920000, rms=0.577 (0.028%), neg=0, invalid=96777
- 0291: dt=25.920000, rms=0.577 (0.036%), neg=0, invalid=96777
- 0292: dt=25.920000, rms=0.577 (0.030%), neg=0, invalid=96777
- 0293: dt=25.920000, rms=0.577 (0.026%), neg=0, invalid=96777
- 0294: dt=25.920000, rms=0.576 (0.027%), neg=0, invalid=96777
- 0295: dt=25.920000, rms=0.576 (0.032%), neg=0, invalid=96777
- 0296: dt=25.920000, rms=0.576 (0.041%), neg=0, invalid=96777
- 0297: dt=25.920000, rms=0.576 (0.040%), neg=0, invalid=96777
- 0298: dt=25.920000, rms=0.576 (0.028%), neg=0, invalid=96777
- 0299: dt=25.920000, rms=0.576 (0.021%), neg=0, invalid=96777
- 0300: dt=25.920000, rms=0.575 (0.025%), neg=0, invalid=96777
- 0301: dt=25.920000, rms=0.575 (0.032%), neg=0, invalid=96777
- 0302: dt=25.920000, rms=0.575 (0.030%), neg=0, invalid=96777
- 0303: dt=25.920000, rms=0.575 (0.024%), neg=0, invalid=96777
- 0304: dt=25.920000, rms=0.575 (0.036%), neg=0, invalid=96777
- 0305: dt=25.920000, rms=0.574 (0.034%), neg=0, invalid=96777
- 0306: dt=25.920000, rms=0.574 (0.015%), neg=0, invalid=96777
- 0307: dt=25.920000, rms=0.574 (-0.002%), neg=0, invalid=96777
- 0308: dt=9.072000, rms=0.574 (0.000%), neg=0, invalid=96777
- 0309: dt=36.288000, rms=0.574 (0.002%), neg=0, invalid=96777
- 0310: dt=20.736000, rms=0.574 (0.002%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.574, neg=0, invalid=96777
- 0311: dt=145.152000, rms=0.572 (0.413%), neg=0, invalid=96777
- 0312: dt=36.288000, rms=0.571 (0.108%), neg=0, invalid=96777
- 0313: dt=82.944000, rms=0.571 (0.050%), neg=0, invalid=96777
- 0314: dt=82.944000, rms=0.571 (0.066%), neg=0, invalid=96777
- 0315: dt=20.736000, rms=0.570 (0.063%), neg=0, invalid=96777
- 0316: dt=20.736000, rms=0.570 (0.039%), neg=0, invalid=96777
- 0317: dt=20.736000, rms=0.570 (0.040%), neg=0, invalid=96777
- 0318: dt=20.736000, rms=0.570 (0.040%), neg=0, invalid=96777
- 0319: dt=20.736000, rms=0.569 (0.039%), neg=0, invalid=96777
- 0320: dt=20.736000, rms=0.569 (0.040%), neg=0, invalid=96777
- 0321: dt=20.736000, rms=0.569 (0.061%), neg=0, invalid=96777
- 0322: dt=20.736000, rms=0.569 (0.056%), neg=0, invalid=96777
- 0323: dt=20.736000, rms=0.568 (0.066%), neg=0, invalid=96777
- 0324: dt=20.736000, rms=0.568 (0.050%), neg=0, invalid=96777
- 0325: dt=20.736000, rms=0.568 (0.035%), neg=0, invalid=96777
- 0326: dt=20.736000, rms=0.567 (0.040%), neg=0, invalid=96777
- 0327: dt=20.736000, rms=0.567 (0.041%), neg=0, invalid=96777
- 0328: dt=20.736000, rms=0.567 (0.052%), neg=0, invalid=96777
- 0329: dt=20.736000, rms=0.567 (0.036%), neg=0, invalid=96777
- 0330: dt=20.736000, rms=0.567 (0.028%), neg=0, invalid=96777
- 0331: dt=20.736000, rms=0.566 (0.025%), neg=0, invalid=96777
- 0332: dt=20.736000, rms=0.566 (0.028%), neg=0, invalid=96777
- 0333: dt=20.736000, rms=0.566 (0.039%), neg=0, invalid=96777
- 0334: dt=20.736000, rms=0.566 (0.046%), neg=0, invalid=96777
- 0335: dt=20.736000, rms=0.566 (0.032%), neg=0, invalid=96777
- 0336: dt=20.736000, rms=0.565 (0.023%), neg=0, invalid=96777
- 0337: dt=20.736000, rms=0.565 (0.021%), neg=0, invalid=96777
- 0338: dt=145.152000, rms=0.565 (0.052%), neg=0, invalid=96777
- 0339: dt=6.480000, rms=0.565 (0.002%), neg=0, invalid=96777
- 0340: dt=6.480000, rms=0.565 (-0.001%), neg=0, invalid=96777
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.573, neg=0, invalid=96777
- 0341: dt=2.800000, rms=0.573 (0.071%), neg=0, invalid=96777
- 0342: dt=2.800000, rms=0.572 (0.072%), neg=0, invalid=96777
- 0343: dt=11.200000, rms=0.571 (0.223%), neg=0, invalid=96777
- 0344: dt=44.800000, rms=0.568 (0.519%), neg=0, invalid=96777
- 0345: dt=11.200000, rms=0.567 (0.167%), neg=0, invalid=96777
- 0346: dt=38.400000, rms=0.564 (0.500%), neg=0, invalid=96777
- 0347: dt=5.757322, rms=0.563 (0.141%), neg=0, invalid=96777
- 0348: dt=32.000000, rms=0.562 (0.252%), neg=0, invalid=96777
- 0349: dt=11.200000, rms=0.560 (0.307%), neg=0, invalid=96777
- 0350: dt=11.200000, rms=0.560 (0.059%), neg=0, invalid=96777
- 0351: dt=32.000000, rms=0.558 (0.313%), neg=0, invalid=96777
- 0352: dt=3.523810, rms=0.558 (0.084%), neg=0, invalid=96777
- 0353: dt=8.000000, rms=0.557 (0.064%), neg=0, invalid=96777
- 0354: dt=44.800000, rms=0.555 (0.402%), neg=0, invalid=96777
- 0355: dt=4.800000, rms=0.555 (0.073%), neg=0, invalid=96777
- 0356: dt=11.200000, rms=0.554 (0.084%), neg=0, invalid=96777
- 0357: dt=44.800000, rms=0.552 (0.390%), neg=0, invalid=96777
- 0358: dt=2.800000, rms=0.552 (0.019%), neg=0, invalid=96777
- 0359: dt=2.800000, rms=0.552 (0.021%), neg=0, invalid=96777
- 0360: dt=2.800000, rms=0.552 (0.016%), neg=0, invalid=96777
- 0361: dt=2.800000, rms=0.552 (0.040%), neg=0, invalid=96777
- 0362: dt=2.800000, rms=0.551 (0.065%), neg=0, invalid=96777
- 0363: dt=2.800000, rms=0.551 (0.099%), neg=0, invalid=96777
- 0364: dt=2.800000, rms=0.550 (0.103%), neg=0, invalid=96777
- 0365: dt=2.800000, rms=0.549 (0.115%), neg=0, invalid=96777
- 0366: dt=2.800000, rms=0.549 (0.114%), neg=0, invalid=96777
- 0367: dt=2.800000, rms=0.548 (0.111%), neg=0, invalid=96777
- 0368: dt=2.800000, rms=0.548 (0.113%), neg=0, invalid=96777
- 0369: dt=2.800000, rms=0.547 (0.106%), neg=0, invalid=96777
- 0370: dt=2.800000, rms=0.546 (0.112%), neg=0, invalid=96777
- 0371: dt=2.800000, rms=0.546 (0.123%), neg=0, invalid=96777
- 0372: dt=2.800000, rms=0.545 (0.128%), neg=0, invalid=96777
- 0373: dt=2.800000, rms=0.544 (0.126%), neg=0, invalid=96777
- 0374: dt=2.800000, rms=0.544 (0.127%), neg=0, invalid=96777
- 0375: dt=2.800000, rms=0.543 (0.121%), neg=0, invalid=96777
- 0376: dt=2.800000, rms=0.542 (0.110%), neg=0, invalid=96777
- 0377: dt=2.800000, rms=0.542 (0.110%), neg=0, invalid=96777
- 0378: dt=2.800000, rms=0.541 (0.107%), neg=0, invalid=96777
- 0379: dt=2.800000, rms=0.541 (0.108%), neg=0, invalid=96777
- 0380: dt=2.800000, rms=0.540 (0.110%), neg=0, invalid=96777
- 0381: dt=2.800000, rms=0.539 (0.111%), neg=0, invalid=96777
- 0382: dt=2.800000, rms=0.539 (0.114%), neg=0, invalid=96777
- 0383: dt=2.800000, rms=0.538 (0.101%), neg=0, invalid=96777
- 0384: dt=2.800000, rms=0.538 (0.095%), neg=0, invalid=96777
- 0385: dt=2.800000, rms=0.537 (0.092%), neg=0, invalid=96777
- 0386: dt=2.800000, rms=0.537 (0.087%), neg=0, invalid=96777
- 0387: dt=2.800000, rms=0.536 (0.081%), neg=0, invalid=96777
- 0388: dt=2.800000, rms=0.536 (0.082%), neg=0, invalid=96777
- 0389: dt=2.800000, rms=0.535 (0.081%), neg=0, invalid=96777
- 0390: dt=2.800000, rms=0.535 (0.073%), neg=0, invalid=96777
- 0391: dt=2.800000, rms=0.535 (0.075%), neg=0, invalid=96777
- 0392: dt=2.800000, rms=0.534 (0.076%), neg=0, invalid=96777
- 0393: dt=2.800000, rms=0.534 (0.066%), neg=0, invalid=96777
- 0394: dt=2.800000, rms=0.534 (0.064%), neg=0, invalid=96777
- 0395: dt=2.800000, rms=0.533 (0.064%), neg=0, invalid=96777
- 0396: dt=2.800000, rms=0.533 (0.069%), neg=0, invalid=96777
- 0397: dt=2.800000, rms=0.533 (0.062%), neg=0, invalid=96777
- 0398: dt=2.800000, rms=0.532 (0.060%), neg=0, invalid=96777
- 0399: dt=2.800000, rms=0.532 (0.063%), neg=0, invalid=96777
- 0400: dt=2.800000, rms=0.532 (0.057%), neg=0, invalid=96777
- 0401: dt=2.800000, rms=0.531 (0.055%), neg=0, invalid=96777
- 0402: dt=2.800000, rms=0.531 (0.049%), neg=0, invalid=96777
- 0403: dt=2.800000, rms=0.531 (0.052%), neg=0, invalid=96777
- 0404: dt=2.800000, rms=0.530 (0.047%), neg=0, invalid=96777
- 0405: dt=2.800000, rms=0.530 (0.047%), neg=0, invalid=96777
- 0406: dt=2.800000, rms=0.530 (0.040%), neg=0, invalid=96777
- 0407: dt=2.800000, rms=0.530 (0.042%), neg=0, invalid=96777
- 0408: dt=2.800000, rms=0.530 (0.036%), neg=0, invalid=96777
- 0409: dt=2.800000, rms=0.529 (0.042%), neg=0, invalid=96777
- 0410: dt=2.800000, rms=0.529 (0.040%), neg=0, invalid=96777
- 0411: dt=2.800000, rms=0.529 (0.037%), neg=0, invalid=96777
- 0412: dt=2.800000, rms=0.529 (0.039%), neg=0, invalid=96777
- 0413: dt=2.800000, rms=0.529 (0.036%), neg=0, invalid=96777
- 0414: dt=2.800000, rms=0.528 (0.036%), neg=0, invalid=96777
- 0415: dt=2.800000, rms=0.528 (0.034%), neg=0, invalid=96777
- 0416: dt=2.800000, rms=0.528 (0.030%), neg=0, invalid=96777
- 0417: dt=2.800000, rms=0.528 (0.033%), neg=0, invalid=96777
- 0418: dt=2.800000, rms=0.528 (0.030%), neg=0, invalid=96777
- 0419: dt=2.800000, rms=0.528 (0.033%), neg=0, invalid=96777
- 0420: dt=2.800000, rms=0.527 (0.029%), neg=0, invalid=96777
- 0421: dt=2.800000, rms=0.527 (0.030%), neg=0, invalid=96777
- 0422: dt=2.800000, rms=0.527 (0.028%), neg=0, invalid=96777
- 0423: dt=2.800000, rms=0.527 (0.030%), neg=0, invalid=96777
- 0424: dt=2.800000, rms=0.527 (0.026%), neg=0, invalid=96777
- 0425: dt=2.800000, rms=0.527 (0.029%), neg=0, invalid=96777
- 0426: dt=2.800000, rms=0.527 (0.022%), neg=0, invalid=96777
- 0427: dt=2.800000, rms=0.526 (0.022%), neg=0, invalid=96777
- 0428: dt=44.800000, rms=0.526 (0.040%), neg=0, invalid=96777
- 0429: dt=2.400000, rms=0.526 (-0.002%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.526, neg=0, invalid=96777
- 0430: dt=32.000000, rms=0.524 (0.387%), neg=0, invalid=96777
- 0431: dt=11.200000, rms=0.523 (0.205%), neg=0, invalid=96777
- 0432: dt=6.400000, rms=0.523 (0.032%), neg=0, invalid=96777
- 0433: dt=6.400000, rms=0.523 (0.047%), neg=0, invalid=96777
- 0434: dt=6.400000, rms=0.522 (0.058%), neg=0, invalid=96777
- 0435: dt=6.400000, rms=0.522 (0.068%), neg=0, invalid=96777
- 0436: dt=6.400000, rms=0.522 (0.071%), neg=0, invalid=96777
- 0437: dt=6.400000, rms=0.521 (0.067%), neg=0, invalid=96777
- 0438: dt=6.400000, rms=0.521 (0.055%), neg=0, invalid=96777
- 0439: dt=6.400000, rms=0.521 (0.039%), neg=0, invalid=96777
- 0440: dt=6.400000, rms=0.521 (0.027%), neg=0, invalid=96777
- 0441: dt=6.400000, rms=0.521 (0.020%), neg=0, invalid=96777
- 0442: dt=6.400000, rms=0.520 (0.034%), neg=0, invalid=96777
- 0443: dt=6.400000, rms=0.520 (0.036%), neg=0, invalid=96777
- 0444: dt=6.400000, rms=0.520 (0.035%), neg=0, invalid=96777
- 0445: dt=6.400000, rms=0.520 (0.038%), neg=0, invalid=96777
- 0446: dt=6.400000, rms=0.520 (0.038%), neg=0, invalid=96777
- 0447: dt=6.400000, rms=0.519 (0.047%), neg=0, invalid=96777
- 0448: dt=6.400000, rms=0.519 (0.050%), neg=0, invalid=96777
- 0449: dt=6.400000, rms=0.519 (0.047%), neg=0, invalid=96777
- 0450: dt=6.400000, rms=0.519 (0.060%), neg=0, invalid=96777
- 0451: dt=6.400000, rms=0.518 (0.061%), neg=0, invalid=96777
- 0452: dt=6.400000, rms=0.518 (0.050%), neg=0, invalid=96777
- 0453: dt=6.400000, rms=0.518 (0.055%), neg=0, invalid=96777
- 0454: dt=6.400000, rms=0.517 (0.056%), neg=0, invalid=96777
- 0455: dt=6.400000, rms=0.517 (0.051%), neg=0, invalid=96777
- 0456: dt=6.400000, rms=0.517 (0.048%), neg=0, invalid=96777
- 0457: dt=6.400000, rms=0.517 (0.039%), neg=0, invalid=96777
- 0458: dt=6.400000, rms=0.517 (0.025%), neg=0, invalid=96777
- 0459: dt=6.400000, rms=0.516 (0.031%), neg=0, invalid=96777
- 0460: dt=6.400000, rms=0.516 (0.050%), neg=0, invalid=96777
- 0461: dt=6.400000, rms=0.516 (0.047%), neg=0, invalid=96777
- 0462: dt=6.400000, rms=0.516 (0.047%), neg=0, invalid=96777
- 0463: dt=6.400000, rms=0.516 (0.031%), neg=0, invalid=96777
- 0464: dt=6.400000, rms=0.515 (0.044%), neg=0, invalid=96777
- 0465: dt=6.400000, rms=0.515 (0.040%), neg=0, invalid=96777
- 0466: dt=6.400000, rms=0.515 (0.038%), neg=0, invalid=96777
- 0467: dt=6.400000, rms=0.515 (0.023%), neg=0, invalid=96777
- 0468: dt=6.400000, rms=0.515 (0.036%), neg=0, invalid=96777
- 0469: dt=6.400000, rms=0.514 (0.042%), neg=0, invalid=96777
- 0470: dt=6.400000, rms=0.514 (0.033%), neg=0, invalid=96777
- 0471: dt=6.400000, rms=0.514 (0.040%), neg=0, invalid=96777
- 0472: dt=6.400000, rms=0.514 (0.036%), neg=0, invalid=96777
- 0473: dt=6.400000, rms=0.514 (0.025%), neg=0, invalid=96777
- 0474: dt=6.400000, rms=0.514 (0.025%), neg=0, invalid=96777
- 0475: dt=6.400000, rms=0.513 (0.030%), neg=0, invalid=96777
- 0476: dt=6.400000, rms=0.513 (0.034%), neg=0, invalid=96777
- 0477: dt=6.400000, rms=0.513 (0.030%), neg=0, invalid=96777
- 0478: dt=6.400000, rms=0.513 (0.030%), neg=0, invalid=96777
- 0479: dt=6.400000, rms=0.513 (0.024%), neg=0, invalid=96777
- 0480: dt=6.400000, rms=0.513 (0.020%), neg=0, invalid=96777
- 0481: dt=11.200000, rms=0.513 (0.015%), neg=0, invalid=96777
- 0482: dt=11.200000, rms=0.513 (-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=0.531, neg=0, invalid=96777
- 0483: dt=0.000000, rms=0.531 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.531, neg=0, invalid=96777
- 0484: dt=0.000000, rms=0.531 (0.000%), neg=0, invalid=96777
- setting smoothness coefficient to 1.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.567, neg=0, invalid=96777
- 0485: dt=0.555556, rms=0.566 (0.177%), neg=0, invalid=96777
- 0486: dt=0.112000, rms=0.566 (0.009%), neg=0, invalid=96777
- 0487: dt=0.112000, rms=0.566 (0.001%), neg=0, invalid=96777
- 0488: dt=0.112000, rms=0.566 (-0.022%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.566, neg=0, invalid=96777
- 0489: dt=0.384000, rms=0.566 (0.035%), neg=0, invalid=96777
- 0490: dt=0.028000, rms=0.566 (0.001%), neg=0, invalid=96777
- 0491: dt=0.028000, rms=0.566 (0.001%), neg=0, invalid=96777
- 0492: dt=0.028000, rms=0.566 (-0.002%), 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=0.517, neg=0, invalid=96777
- 0493: dt=0.169643, rms=0.509 (1.367%), neg=0, invalid=96777
- 0494: dt=0.140625, rms=0.506 (0.752%), neg=0, invalid=96777
- 0495: dt=0.122863, rms=0.503 (0.491%), neg=0, invalid=96777
- 0496: dt=0.384000, rms=0.497 (1.179%), neg=0, invalid=96777
- 0497: dt=0.028000, rms=0.497 (0.031%), neg=0, invalid=96777
- 0498: dt=0.028000, rms=0.497 (0.030%), neg=0, invalid=96777
- 0499: dt=0.028000, rms=0.497 (0.055%), neg=0, invalid=96777
- 0500: dt=0.028000, rms=0.496 (0.080%), neg=0, invalid=96777
- 0501: dt=0.028000, rms=0.496 (0.097%), neg=0, invalid=96777
- 0502: dt=0.028000, rms=0.495 (0.108%), neg=0, invalid=96777
- 0503: dt=0.028000, rms=0.495 (0.115%), neg=0, invalid=96777
- 0504: dt=0.028000, rms=0.495 (0.012%), neg=0, invalid=96777
- 0505: dt=0.028000, rms=0.494 (0.033%), neg=0, invalid=96777
- 0506: dt=0.028000, rms=0.494 (0.040%), neg=0, invalid=96777
- 0507: dt=0.028000, rms=0.494 (0.051%), neg=0, invalid=96777
- 0508: dt=0.028000, rms=0.494 (0.057%), neg=0, invalid=96777
- 0509: dt=0.028000, rms=0.493 (0.060%), neg=0, invalid=96777
- 0510: dt=0.028000, rms=0.493 (0.066%), neg=0, invalid=96777
- 0511: dt=0.028000, rms=0.493 (0.066%), neg=0, invalid=96777
- 0512: dt=0.028000, rms=0.492 (0.071%), neg=0, invalid=96777
- 0513: dt=0.028000, rms=0.492 (0.065%), neg=0, invalid=96777
- 0514: dt=0.028000, rms=0.492 (0.064%), neg=0, invalid=96777
- 0515: dt=0.028000, rms=0.491 (0.064%), neg=0, invalid=96777
- 0516: dt=0.028000, rms=0.491 (0.056%), neg=0, invalid=96777
- 0517: dt=0.028000, rms=0.491 (0.047%), neg=0, invalid=96777
- 0518: dt=0.028000, rms=0.491 (0.045%), neg=0, invalid=96777
- 0519: dt=0.028000, rms=0.490 (0.045%), neg=0, invalid=96777
- 0520: dt=0.028000, rms=0.490 (0.034%), neg=0, invalid=96777
- 0521: dt=0.028000, rms=0.490 (0.030%), neg=0, invalid=96777
- 0522: dt=0.028000, rms=0.490 (0.030%), neg=0, invalid=96777
- 0523: dt=0.028000, rms=0.490 (0.027%), neg=0, invalid=96777
- 0524: dt=0.028000, rms=0.490 (0.019%), neg=0, invalid=96777
- 0525: dt=0.028000, rms=0.490 (0.017%), neg=0, invalid=96777
- 0526: dt=0.000000, rms=0.490 (-0.002%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.490, neg=0, invalid=96777
- 0527: dt=0.320000, rms=0.485 (0.895%), neg=0, invalid=96777
- 0528: dt=0.112000, rms=0.485 (0.087%), neg=0, invalid=96777
- 0529: dt=0.028000, rms=0.485 (0.015%), neg=0, invalid=96777
- 0530: dt=0.028000, rms=0.485 (0.016%), neg=0, invalid=96777
- 0531: dt=0.028000, rms=0.485 (0.028%), neg=0, invalid=96777
- 0532: dt=0.028000, rms=0.484 (0.038%), neg=0, invalid=96777
- 0533: dt=0.028000, rms=0.484 (0.044%), neg=0, invalid=96777
- 0534: dt=0.028000, rms=0.484 (0.044%), neg=0, invalid=96777
- 0535: dt=0.028000, rms=0.484 (0.046%), neg=0, invalid=96777
- 0536: dt=0.028000, rms=0.484 (0.001%), neg=0, invalid=96777
- 0537: dt=0.028000, rms=0.484 (0.003%), neg=0, invalid=96777
- 0538: dt=0.028000, rms=0.484 (0.007%), neg=0, invalid=96777
- 0539: dt=0.028000, rms=0.484 (0.003%), neg=0, invalid=96777
- 0540: dt=0.384000, rms=0.484 (0.007%), neg=0, invalid=96777
- 0541: dt=0.001250, rms=0.484 (-0.001%), 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=0.482, neg=0, invalid=96777
- 0542: dt=0.000000, rms=0.482 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.482, neg=0, invalid=96777
- 0543: dt=129.472000, rms=0.482 (0.014%), neg=0, invalid=96777
- 0544: dt=517.888000, rms=0.482 (0.043%), neg=0, invalid=96777
- 0545: dt=32.368000, rms=0.482 (0.000%), neg=0, invalid=96777
- 0546: dt=32.368000, rms=0.481 (0.002%), neg=0, invalid=96777
- 0547: dt=32.368000, rms=0.481 (0.001%), neg=0, invalid=96777
- 0548: dt=32.368000, rms=0.481 (0.003%), neg=0, invalid=96777
- 0549: dt=32.368000, rms=0.481 (0.006%), neg=0, invalid=96777
- 0550: dt=32.368000, rms=0.481 (0.011%), neg=0, invalid=96777
- 0551: dt=32.368000, rms=0.481 (0.008%), neg=0, invalid=96777
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.481, neg=0, invalid=96777
- 0552: dt=20.736000, rms=0.481 (0.027%), neg=0, invalid=96777
- 0553: dt=2.268000, rms=0.481 (-0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.481, neg=0, invalid=96777
- 0554: dt=145.152000, rms=0.480 (0.274%), neg=0, invalid=96777
- 0555: dt=31.104000, rms=0.480 (0.077%), neg=0, invalid=96777
- 0556: dt=31.104000, rms=0.479 (0.022%), neg=0, invalid=96777
- 0557: dt=31.104000, rms=0.479 (0.063%), neg=0, invalid=96777
- 0558: dt=31.104000, rms=0.479 (0.092%), neg=0, invalid=96777
- 0559: dt=31.104000, rms=0.478 (0.072%), neg=0, invalid=96777
- 0560: dt=31.104000, rms=0.478 (0.052%), neg=0, invalid=96777
- 0561: dt=36.288000, rms=0.478 (0.037%), neg=0, invalid=96777
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.478, neg=0, invalid=96777
- iter 0, gcam->neg = 4
- after 6 iterations, nbhd size=1, neg = 0
- 0562: dt=32.000000, rms=0.476 (0.348%), neg=0, invalid=96777
- 0563: dt=19.200000, rms=0.476 (0.193%), neg=0, invalid=96777
- iter 0, gcam->neg = 3
- after 6 iterations, nbhd size=1, neg = 0
- 0564: dt=19.200000, rms=0.476 (-0.129%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.476, neg=0, invalid=96777
- 0565: dt=11.200000, rms=0.474 (0.306%), neg=0, invalid=96777
- 0566: dt=11.200000, rms=0.473 (0.304%), neg=0, invalid=96777
- 0567: dt=9.600000, rms=0.472 (0.150%), neg=0, invalid=96777
- 0568: dt=9.600000, rms=0.471 (0.187%), neg=0, invalid=96777
- 0569: dt=9.600000, rms=0.470 (0.227%), neg=0, invalid=96777
- 0570: dt=9.600000, rms=0.469 (0.258%), neg=0, invalid=96777
- 0571: dt=9.600000, rms=0.468 (0.240%), neg=0, invalid=96777
- 0572: dt=9.600000, rms=0.466 (0.330%), neg=0, invalid=96777
- 0573: dt=9.600000, rms=0.465 (0.260%), neg=0, invalid=96777
- 0574: dt=9.600000, rms=0.464 (0.233%), neg=0, invalid=96777
- 0575: dt=9.600000, rms=0.463 (0.168%), neg=0, invalid=96777
- 0576: dt=9.600000, rms=0.462 (0.238%), neg=0, invalid=96777
- 0577: dt=9.600000, rms=0.461 (0.193%), neg=0, invalid=96777
- 0578: dt=9.600000, rms=0.460 (0.140%), neg=0, invalid=96777
- 0579: dt=9.600000, rms=0.460 (0.100%), neg=0, invalid=96777
- 0580: dt=9.600000, rms=0.459 (0.158%), neg=0, invalid=96777
- 0581: dt=9.600000, rms=0.459 (0.136%), neg=0, invalid=96777
- 0582: dt=9.600000, rms=0.458 (0.109%), neg=0, invalid=96777
- 0583: dt=9.600000, rms=0.458 (0.074%), neg=0, invalid=96777
- 0584: dt=11.200000, rms=0.457 (0.053%), neg=0, invalid=96777
- 0585: dt=11.200000, rms=0.457 (-0.003%), neg=0, invalid=96777
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.461, neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 6 iterations, nbhd size=1, neg = 0
- 0586: dt=5.076923, rms=0.460 (0.152%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 5 iterations, nbhd size=1, neg = 0
- 0587: dt=5.000000, rms=0.460 (0.104%), neg=0, invalid=96777
- iter 0, gcam->neg = 5
- after 7 iterations, nbhd size=1, neg = 0
- 0588: dt=5.000000, rms=0.460 (0.005%), neg=0, invalid=96777
- iter 0, gcam->neg = 5
- after 8 iterations, nbhd size=1, neg = 0
- 0589: dt=5.000000, rms=0.459 (-0.010%), 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 = 33
- after 4 iterations, nbhd size=0, neg = 0
- 0590: dt=7.721393, rms=0.458 (0.267%), neg=0, invalid=96777
- iter 0, gcam->neg = 2
- after 5 iterations, nbhd size=1, neg = 0
- 0591: dt=2.880000, rms=0.458 (0.047%), neg=0, invalid=96777
- 0592: dt=2.880000, rms=0.458 (0.105%), neg=0, invalid=96777
- iter 0, gcam->neg = 6
- after 0 iterations, nbhd size=0, neg = 0
- 0593: dt=2.880000, rms=0.457 (0.145%), neg=0, invalid=96777
- iter 0, gcam->neg = 5
- after 6 iterations, nbhd size=1, neg = 0
- 0594: dt=2.880000, rms=0.456 (0.156%), neg=0, invalid=96777
- iter 0, gcam->neg = 2
- after 0 iterations, nbhd size=0, neg = 0
- 0595: dt=2.880000, rms=0.456 (0.147%), neg=0, invalid=96777
- iter 0, gcam->neg = 4
- after 1 iterations, nbhd size=0, neg = 0
- 0596: dt=2.880000, rms=0.455 (0.149%), neg=0, invalid=96777
- iter 0, gcam->neg = 4
- after 8 iterations, nbhd size=1, neg = 0
- 0597: dt=2.880000, rms=0.454 (0.169%), neg=0, invalid=96777
- iter 0, gcam->neg = 3
- after 6 iterations, nbhd size=1, neg = 0
- 0598: dt=2.880000, rms=0.453 (0.193%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0599: dt=2.880000, rms=0.452 (0.237%), neg=0, invalid=96777
- iter 0, gcam->neg = 4
- after 6 iterations, nbhd size=1, neg = 0
- 0600: dt=2.880000, rms=0.451 (0.266%), neg=0, invalid=96777
- 0601: dt=2.880000, rms=0.450 (0.287%), neg=0, invalid=96777
- iter 0, gcam->neg = 6
- after 6 iterations, nbhd size=1, neg = 0
- 0602: dt=2.880000, rms=0.449 (0.236%), neg=0, invalid=96777
- iter 0, gcam->neg = 8
- after 7 iterations, nbhd size=1, neg = 0
- 0603: dt=2.880000, rms=0.448 (0.210%), neg=0, invalid=96777
- iter 0, gcam->neg = 9
- after 1 iterations, nbhd size=0, neg = 0
- 0604: dt=2.880000, rms=0.447 (0.187%), neg=0, invalid=96777
- iter 0, gcam->neg = 12
- after 2 iterations, nbhd size=0, neg = 0
- 0605: dt=2.880000, rms=0.446 (0.157%), neg=0, invalid=96777
- iter 0, gcam->neg = 14
- after 1 iterations, nbhd size=0, neg = 0
- 0606: dt=2.880000, rms=0.446 (0.099%), neg=0, invalid=96777
- iter 0, gcam->neg = 7
- after 2 iterations, nbhd size=0, neg = 0
- 0607: dt=2.880000, rms=0.445 (0.070%), neg=0, invalid=96777
- 0608: dt=0.000176, rms=0.445 (-0.006%), neg=0, invalid=96777
- setting smoothness coefficient to 1.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.450, neg=0, invalid=96777
- 0609: dt=0.000000, rms=0.450 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.450, neg=0, invalid=96777
- 0610: dt=0.000000, rms=0.450 (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=0.442, neg=0, invalid=96777
- iter 0, gcam->neg = 560
- after 50 iterations, nbhd size=2, neg = 0
- 0611: dt=1.894243, rms=0.404 (8.672%), neg=0, invalid=96777
- 0612: dt=0.000027, rms=0.404 (0.001%), neg=0, invalid=96777
- 0613: dt=0.000027, rms=0.404 (0.000%), neg=0, invalid=96777
- 0614: dt=0.000027, rms=0.404 (0.000%), neg=0, invalid=96777
- 0615: dt=0.000027, rms=0.404 (-0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.404, neg=0, invalid=96777
- 0616: dt=0.000313, rms=0.404 (0.000%), neg=0, invalid=96777
- 0617: dt=0.000000, rms=0.404 (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=0.389, neg=0, invalid=96777
- 0618: dt=8.092000, rms=0.390 (-0.351%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.390, neg=0, invalid=96777
- 0619: dt=18.496000, rms=0.390 (0.003%), neg=0, invalid=96777
- 0620: dt=0.003387, rms=0.390 (0.000%), neg=0, invalid=96777
- 0621: dt=0.003387, rms=0.390 (-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=0.390, neg=0, invalid=96777
- 0622: dt=5.184000, rms=0.390 (0.004%), neg=0, invalid=96777
- 0623: dt=0.567000, rms=0.390 (0.000%), neg=0, invalid=96777
- 0624: dt=0.567000, rms=0.390 (-0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.390, neg=0, invalid=96777
- 0625: dt=15.552000, rms=0.390 (0.008%), neg=0, invalid=96777
- 0626: dt=9.072000, rms=0.390 (0.001%), neg=0, invalid=96777
- 0627: dt=9.072000, rms=0.390 (0.000%), neg=0, invalid=96777
- 0628: dt=9.072000, rms=0.390 (-0.003%), neg=0, invalid=96777
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.391, neg=0, invalid=96777
- iter 0, gcam->neg = 2
- after 200 iterations, nbhd size=4, neg = 1
- starting rms=0.005, neg=1, removing folds in lattice....
- iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.005 (0.000%)
- ---------- unfolding failed - restoring original position --------------------
- 0629: dt=6.400000, rms=0.391 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.391, neg=0, invalid=96777
- iter 0, gcam->neg = 13
- after 200 iterations, nbhd size=1, neg = 2
- starting rms=0.006, neg=2, removing folds in lattice....
- iter 1, dt=0.000023: new neg 2, old_neg 2, delta 0, rms=0.004 (32.252%)
- iter 2, dt=0.000143: new neg 0, old_neg 2, delta 2, rms=0.002 (39.247%)
- 0630: dt=32.000000, rms=0.391 (0.060%), neg=0, invalid=96777
- iter 0, gcam->neg = 26
- after 200 iterations, nbhd size=1, neg = 4
- starting rms=0.009, neg=4, removing folds in lattice....
- iter 1, dt=0.000023: new neg 2, old_neg 4, delta 2, rms=0.005 (51.144%)
- iter 2, dt=0.000143: new neg 0, old_neg 2, delta 2, rms=0.003 (38.835%)
- 0631: dt=44.800000, rms=0.390 (0.160%), neg=0, invalid=96777
- iter 0, gcam->neg = 3
- after 200 iterations, nbhd size=4, neg = 1
- starting rms=0.005, neg=1, removing folds in lattice....
- iter 1, dt=0.000219: new neg 0, old_neg 1, delta 1, rms=0.002 (49.100%)
- 0632: dt=19.200000, rms=0.390 (0.041%), neg=0, invalid=96777
- iter 0, gcam->neg = 4
- after 200 iterations, nbhd size=3, neg = 3
- starting rms=0.009, neg=3, removing folds in lattice....
- iter 1, dt=0.000023: new neg 3, old_neg 3, delta 0, rms=0.004 (53.953%)
- iter 2, dt=0.000143: new neg 0, old_neg 3, delta 3, rms=0.002 (44.184%)
- 0633: dt=19.200000, rms=0.389 (0.062%), neg=0, invalid=96777
- iter 0, gcam->neg = 4
- after 200 iterations, nbhd size=3, neg = 3
- starting rms=0.010, neg=3, removing folds in lattice....
- iter 1, dt=0.000023: new neg 3, old_neg 3, delta 0, rms=0.004 (56.157%)
- iter 2, dt=0.000143: new neg 0, old_neg 3, delta 3, rms=0.002 (45.372%)
- 0634: dt=19.200000, rms=0.389 (0.047%), neg=0, invalid=96777
- iter 0, gcam->neg = 4
- after 200 iterations, nbhd size=3, neg = 3
- starting rms=0.010, neg=3, removing folds in lattice....
- iter 1, dt=0.000023: new neg 3, old_neg 3, delta 0, rms=0.004 (58.553%)
- iter 2, dt=0.000146: new neg 0, old_neg 3, delta 3, rms=0.002 (45.065%)
- 0635: dt=19.200000, rms=0.389 (0.040%), neg=0, invalid=96777
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.392, neg=0, invalid=96777
- iter 0, gcam->neg = 26
- after 200 iterations, nbhd size=1, neg = 4
- starting rms=0.010, neg=4, removing folds in lattice....
- iter 1, dt=0.000023: new neg 3, old_neg 4, delta 1, rms=0.004 (60.159%)
- iter 2, dt=0.000163: new neg 0, old_neg 3, delta 3, rms=0.002 (53.533%)
- 0636: dt=6.142857, rms=0.391 (0.135%), neg=0, invalid=96777
- iter 0, gcam->neg = 10
- after 200 iterations, nbhd size=3, neg = 2
- starting rms=0.005, neg=2, removing folds in lattice....
- iter 1, dt=0.000100: new neg 0, old_neg 2, delta 2, rms=0.002 (64.348%)
- 0637: dt=4.032000, rms=0.391 (0.043%), neg=0, invalid=96777
- iter 0, gcam->neg = 8
- after 200 iterations, nbhd size=2, neg = 3
- starting rms=0.010, neg=3, removing folds in lattice....
- iter 1, dt=0.000023: new neg 3, old_neg 3, delta 0, rms=0.004 (58.277%)
- iter 2, dt=0.000159: new neg 0, old_neg 3, delta 3, rms=0.002 (52.635%)
- 0638: dt=4.032000, rms=0.391 (0.036%), neg=0, invalid=96777
- iter 0, gcam->neg = 8
- after 200 iterations, nbhd size=2, neg = 1
- starting rms=0.005, neg=1, removing folds in lattice....
- iter 1, dt=0.000219: new neg 0, old_neg 1, delta 1, rms=0.002 (57.822%)
- 0639: dt=4.032000, rms=0.391 (-0.002%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.391, neg=0, invalid=96777
- iter 0, gcam->neg = 66
- after 200 iterations, nbhd size=1, neg = 3
- starting rms=0.008, neg=3, removing folds in lattice....
- iter 1, dt=0.000023: new neg 2, old_neg 3, delta 1, rms=0.004 (50.445%)
- iter 2, dt=0.000156: new neg 0, old_neg 2, delta 2, rms=0.002 (51.943%)
- 0640: dt=13.824000, rms=0.389 (0.429%), neg=0, invalid=96777
- iter 0, gcam->neg = 6
- after 200 iterations, nbhd size=3, neg = 2
- starting rms=0.007, neg=2, removing folds in lattice....
- iter 1, dt=0.000023: new neg 2, old_neg 2, delta 0, rms=0.004 (50.357%)
- iter 2, dt=0.000162: new neg 0, old_neg 2, delta 2, rms=0.001 (58.636%)
- 0641: dt=4.032000, rms=0.389 (0.042%), neg=0, invalid=96777
- iter 0, gcam->neg = 7
- after 200 iterations, nbhd size=3, neg = 2
- starting rms=0.007, neg=2, removing folds in lattice....
- iter 1, dt=0.000023: new neg 2, old_neg 2, delta 0, rms=0.004 (50.420%)
- iter 2, dt=0.000163: new neg 0, old_neg 2, delta 2, rms=0.001 (58.869%)
- 0642: dt=4.032000, rms=0.389 (0.084%), neg=0, invalid=96777
- iter 0, gcam->neg = 7
- after 200 iterations, nbhd size=4, neg = 2
- starting rms=0.007, neg=2, removing folds in lattice....
- iter 1, dt=0.000023: new neg 2, old_neg 2, delta 0, rms=0.003 (49.979%)
- iter 2, dt=0.000159: new neg 0, old_neg 2, delta 2, rms=0.001 (58.237%)
- 0643: dt=4.032000, rms=0.388 (0.064%), neg=0, invalid=96777
- iter 0, gcam->neg = 7
- after 200 iterations, nbhd size=3, neg = 2
- starting rms=0.007, neg=2, removing folds in lattice....
- iter 1, dt=0.000023: new neg 2, old_neg 2, delta 0, rms=0.004 (49.903%)
- iter 2, dt=0.000155: new neg 0, old_neg 2, delta 2, rms=0.002 (56.725%)
- 0644: dt=4.032000, rms=0.388 (0.050%), neg=0, invalid=96777
- iter 0, gcam->neg = 7
- after 200 iterations, nbhd size=3, neg = 2
- starting rms=0.007, neg=2, removing folds in lattice....
- iter 1, dt=0.000023: new neg 2, old_neg 2, delta 0, rms=0.004 (50.161%)
- iter 2, dt=0.000160: new neg 0, old_neg 2, delta 2, rms=0.001 (57.942%)
- 0645: dt=4.032000, rms=0.388 (0.034%), neg=0, invalid=96777
- setting smoothness coefficient to 1.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.393, neg=0, invalid=96777
- 0646: dt=0.000000, rms=0.393 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.393, neg=0, invalid=96777
- 0647: dt=0.000000, rms=0.393 (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=0.384, neg=0, invalid=96777
- iter 0, gcam->neg = 500
- after 32 iterations, nbhd size=3, neg = 0
- 0648: dt=1.020921, rms=0.370 (3.680%), neg=0, invalid=96777
- 0649: dt=0.000109, rms=0.370 (0.003%), neg=0, invalid=96777
- 0650: dt=0.000109, rms=0.370 (0.000%), neg=0, invalid=96777
- 0651: dt=0.000109, rms=0.370 (-0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.370, neg=0, invalid=96777
- 0652: dt=0.000375, rms=0.370 (0.000%), neg=0, invalid=96777
- 0653: dt=0.000000, rms=0.370 (0.000%), neg=0, invalid=96777
- writing output transformation to transforms/talairach.m3z...
- GCAMwrite
- registration took 5 hours, 3 minutes and 31 seconds.
- #--------------------------------------
- #@# CA Reg Inv Thu Aug 8 17:22:55 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 17:24:29 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...
- 11336786 nonbrain voxels erased
- writing output to nu_noneck.mgz...
- nonbrain removal took 1 minutes and 35 seconds.
- #--------------------------------------
- #@# SkullLTA Thu Aug 8 17:26:04 CEST 2013
- mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta
- ======= NUMBER OF OPENMP THREADS = 1 =======
- aligning to atlas containing skull, setting unknown_nbr_spacing = 5
- using previously computed transform transforms/talairach.lta
- reading 1 input volumes...
- logging results to talairach_with_skull_2.log
- reading '/opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca'...
- average std = 23.1 using min determinant for regularization = 53.4
- 0 singular and 5702 ill-conditioned covariance matrices regularized
- reading 'nu_noneck.mgz'...
- freeing gibbs priors...done.
- bounding unknown intensity as < 20.2 or > 943.7
- total sample mean = 92.0 (1443 zeros)
- ************************************************
- spacing=8, using 3481 sample points, tol=1.00e-05...
- ************************************************
- register_mri: find_optimal_transform
- find_optimal_transform: nsamples 3481, passno 0, spacing 8
- resetting wm mean[0]: 117 --> 126
- resetting gm mean[0]: 74 --> 74
- input volume #1 is the most T1-like
- using real data threshold=9.0
- skull bounding box = (47, 10, 15) --> (206, 201, 197)
- using (100, 74, 106) as brain centroid...
- mean wm in atlas = 126, using box (80,50,84) --> (119, 97,128) to find MRI wm
- before smoothing, mri peak at 108
- after smoothing, mri peak at 108, scaling input intensities by 1.167
- scaling channel 0 by 1.16667
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1)
- 1.100 -0.074 0.018 -8.391;
- 0.081 1.119 0.320 -34.301;
- -0.039 -0.258 0.915 33.330;
- 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)
- 1.100 -0.074 0.018 -8.391;
- 0.081 1.119 0.320 -34.301;
- -0.042 -0.278 0.983 27.877;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 2 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1)
- 1.100 -0.074 0.018 -8.391;
- 0.081 1.119 0.320 -34.301;
- -0.042 -0.278 0.983 27.877;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.2500
- ****************************************
- Nine parameter search. iteration 3 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.1 (thresh=-4.1)
- 1.081 -0.039 0.031 -10.858;
- 0.047 1.111 0.351 -34.627;
- -0.042 -0.320 0.990 31.306;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 4 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.081 -0.039 0.031 -10.858;
- 0.047 1.111 0.351 -34.627;
- -0.042 -0.320 0.990 31.306;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.0625
- ****************************************
- Nine parameter search. iteration 5 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.078 -0.054 0.017 -7.838;
- 0.065 1.111 0.351 -36.800;
- -0.033 -0.319 0.988 29.866;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 6 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.078 -0.054 0.017 -7.838;
- 0.065 1.111 0.351 -36.800;
- -0.033 -0.319 0.988 29.866;
- 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
- 1.07751 -0.05390 0.01694 -7.83754;
- 0.06476 1.11064 0.35119 -36.80036;
- -0.03333 -0.31928 0.98830 29.86566;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 3481
- Quasinewton: input matrix
- 1.07751 -0.05390 0.01694 -7.83754;
- 0.06476 1.11064 0.35119 -36.80036;
- -0.03333 -0.31928 0.98830 29.86566;
- 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:
- 1.078 -0.054 0.017 -7.838;
- 0.065 1.111 0.351 -36.800;
- -0.033 -0.319 0.988 29.866;
- 0.000 0.000 0.000 1.000;
- pass 1, spacing 8: log(p) = -4.0 (old=-4.1)
- transform before final EM align:
- 1.078 -0.054 0.017 -7.838;
- 0.065 1.111 0.351 -36.800;
- -0.033 -0.319 0.988 29.866;
- 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
- 1.07751 -0.05390 0.01694 -7.83754;
- 0.06476 1.11064 0.35119 -36.80036;
- -0.03333 -0.31928 0.98830 29.86566;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 382743
- Quasinewton: input matrix
- 1.07751 -0.05390 0.01694 -7.83754;
- 0.06476 1.11064 0.35119 -36.80036;
- -0.03333 -0.31928 0.98830 29.86566;
- 0.00000 0.00000 0.00000 1.00000;
- dfp_em_step_func: 009: -log(p) = 4.4
- after pass:transform: ( 1.08, -0.05, 0.02, -7.84)
- ( 0.06, 1.11, 0.35, -36.80)
- ( -0.03, -0.32, 0.99, 29.87)
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization...
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = 4.4 tol 0.000000
- final transform:
- 1.078 -0.054 0.017 -7.838;
- 0.065 1.111 0.351 -36.800;
- -0.033 -0.319 0.988 29.866;
- 0.000 0.000 0.000 1.000;
- writing output transformation to transforms/talairach_with_skull_2.lta...
- registration took 40 minutes and 25 seconds.
- #--------------------------------------
- #@# SubCort Seg Thu Aug 8 18:06:29 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/sub018/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 = 0.13981 ( 8)
- Left_Lateral_Ventricle (4): linear fit = 0.25 x + 0.0 (1031 voxels, overlap=0.007)
- Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (1031 voxels, peak = 7), gca=10.8
- gca peak = 0.14982 (20)
- mri peak = 0.15612 ( 8)
- Right_Lateral_Ventricle (43): linear fit = 0.31 x + 0.0 (686 voxels, overlap=0.007)
- Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (686 voxels, peak = 6), gca=8.0
- gca peak = 0.28003 (97)
- mri peak = 0.11525 (85)
- Right_Pallidum (52): linear fit = 0.87 x + 0.0 (300 voxels, overlap=0.049)
- Right_Pallidum (52): linear fit = 0.87 x + 0.0 (300 voxels, peak = 84), gca=83.9
- gca peak = 0.18160 (96)
- mri peak = 0.08915 (86)
- Left_Pallidum (13): linear fit = 0.85 x + 0.0 (272 voxels, overlap=0.058)
- Left_Pallidum (13): linear fit = 0.85 x + 0.0 (272 voxels, peak = 81), gca=81.1
- gca peak = 0.27536 (62)
- mri peak = 0.08966 (56)
- Right_Hippocampus (53): linear fit = 0.83 x + 0.0 (435 voxels, overlap=0.478)
- Right_Hippocampus (53): linear fit = 0.83 x + 0.0 (435 voxels, peak = 52), gca=51.8
- gca peak = 0.32745 (63)
- mri peak = 0.09177 (54)
- Left_Hippocampus (17): linear fit = 0.83 x + 0.0 (575 voxels, overlap=0.506)
- Left_Hippocampus (17): linear fit = 0.83 x + 0.0 (575 voxels, peak = 53), gca=52.6
- gca peak = 0.08597 (105)
- mri peak = 0.06693 (107)
- Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (36446 voxels, overlap=0.786)
- Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (36446 voxels, peak = 108), gca=107.6
- gca peak = 0.09209 (106)
- mri peak = 0.07390 (107)
- Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (37210 voxels, overlap=0.750)
- Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (37210 voxels, peak = 110), gca=109.7
- gca peak = 0.07826 (63)
- mri peak = 0.06130 (53)
- Left_Cerebral_Cortex (3): linear fit = 0.82 x + 0.0 (14531 voxels, overlap=0.307)
- Left_Cerebral_Cortex (3): linear fit = 0.82 x + 0.0 (14531 voxels, peak = 52), gca=52.0
- gca peak = 0.08598 (64)
- mri peak = 0.05382 (50)
- Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (13475 voxels, overlap=0.343)
- Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (13475 voxels, peak = 53), gca=52.8
- gca peak = 0.24164 (71)
- mri peak = 0.11916 (64)
- Right_Caudate (50): linear fit = 0.88 x + 0.0 (621 voxels, overlap=0.022)
- Right_Caudate (50): linear fit = 0.88 x + 0.0 (621 voxels, peak = 62), gca=62.1
- gca peak = 0.18227 (75)
- mri peak = 0.10624 (64)
- Left_Caudate (11): linear fit = 0.83 x + 0.0 (753 voxels, overlap=0.033)
- Left_Caudate (11): linear fit = 0.83 x + 0.0 (753 voxels, peak = 63), gca=62.6
- gca peak = 0.10629 (62)
- mri peak = 0.05693 (56)
- Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (7455 voxels, overlap=0.995)
- Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (7455 voxels, peak = 60), gca=59.8
- gca peak = 0.11668 (59)
- mri peak = 0.05915 (55)
- Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (7984 voxels, overlap=0.959)
- Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (7984 voxels, peak = 55), gca=55.2
- gca peak = 0.17849 (88)
- mri peak = 0.07214 (88)
- Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4066 voxels, overlap=0.980)
- Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4066 voxels, peak = 88), gca=87.6
- gca peak = 0.16819 (86)
- mri peak = 0.06366 (91)
- Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (3816 voxels, overlap=0.973)
- Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (3816 voxels, peak = 91), gca=90.7
- gca peak = 0.41688 (64)
- mri peak = 0.10417 (56)
- Left_Amygdala (18): linear fit = 0.88 x + 0.0 (353 voxels, overlap=0.347)
- Left_Amygdala (18): linear fit = 0.88 x + 0.0 (353 voxels, peak = 56), gca=56.0
- gca peak = 0.42394 (62)
- mri peak = 0.08871 (53)
- Right_Amygdala (54): linear fit = 0.83 x + 0.0 (285 voxels, overlap=0.626)
- Right_Amygdala (54): linear fit = 0.83 x + 0.0 (285 voxels, peak = 52), gca=51.8
- gca peak = 0.10041 (96)
- mri peak = 0.07617 (83)
- Left_Thalamus_Proper (10): linear fit = 0.89 x + 0.0 (3455 voxels, overlap=0.341)
- Left_Thalamus_Proper (10): linear fit = 0.89 x + 0.0 (3455 voxels, peak = 86), gca=85.9
- gca peak = 0.13978 (88)
- mri peak = 0.08348 (80)
- Right_Thalamus_Proper (49): linear fit = 0.93 x + 0.0 (3666 voxels, overlap=0.485)
- Right_Thalamus_Proper (49): linear fit = 0.93 x + 0.0 (3666 voxels, peak = 81), gca=81.4
- gca peak = 0.08514 (81)
- mri peak = 0.07058 (71)
- Left_Putamen (12): linear fit = 0.87 x + 0.0 (1815 voxels, overlap=0.463)
- Left_Putamen (12): linear fit = 0.87 x + 0.0 (1815 voxels, peak = 70), gca=70.1
- gca peak = 0.09624 (82)
- mri peak = 0.07984 (70)
- Right_Putamen (51): linear fit = 0.85 x + 0.0 (1569 voxels, overlap=0.264)
- Right_Putamen (51): linear fit = 0.85 x + 0.0 (1569 voxels, peak = 69), gca=69.3
- gca peak = 0.07543 (88)
- mri peak = 0.08096 (82)
- Brain_Stem (16): linear fit = 1.00 x + 0.0 (8414 voxels, overlap=0.764)
- Brain_Stem (16): linear fit = 1.00 x + 0.0 (8414 voxels, peak = 88), gca=87.6
- gca peak = 0.12757 (95)
- mri peak = 0.08039 (86)
- Right_VentralDC (60): linear fit = 0.94 x + 0.0 (835 voxels, overlap=0.549)
- Right_VentralDC (60): linear fit = 0.94 x + 0.0 (835 voxels, peak = 89), gca=88.8
- gca peak = 0.17004 (92)
- mri peak = 0.08398 (88)
- Left_VentralDC (28): linear fit = 0.94 x + 0.0 (958 voxels, overlap=0.646)
- Left_VentralDC (28): linear fit = 0.94 x + 0.0 (958 voxels, peak = 87), gca=86.9
- gca peak = 0.21361 (36)
- uniform distribution in MR - rejecting arbitrary fit
- gca peak = 0.26069 (23)
- mri peak = 0.11343 ( 9)
- Fourth_Ventricle (15): linear fit = 0.35 x + 0.0 (334 voxels, overlap=0.027)
- Fourth_Ventricle (15): linear fit = 0.35 x + 0.0 (334 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 0.84 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 = 0.13981 ( 8)
- Left_Lateral_Ventricle (4): linear fit = 0.62 x + 0.0 (1031 voxels, overlap=0.781)
- Left_Lateral_Ventricle (4): linear fit = 0.62 x + 0.0 (1031 voxels, peak = 7), gca=6.8
- gca peak = 0.29325 ( 9)
- mri peak = 0.15612 ( 8)
- Right_Lateral_Ventricle (43): linear fit = 0.75 x + 0.0 (686 voxels, overlap=0.829)
- Right_Lateral_Ventricle (43): linear fit = 0.75 x + 0.0 (686 voxels, peak = 7), gca=6.7
- gca peak = 0.26182 (84)
- mri peak = 0.11525 (85)
- Right_Pallidum (52): linear fit = 1.00 x + 0.0 (300 voxels, overlap=1.021)
- Right_Pallidum (52): linear fit = 1.00 x + 0.0 (300 voxels, peak = 84), gca=84.0
- gca peak = 0.22767 (81)
- mri peak = 0.08915 (86)
- Left_Pallidum (13): linear fit = 1.00 x + 0.0 (272 voxels, overlap=1.008)
- Left_Pallidum (13): linear fit = 1.00 x + 0.0 (272 voxels, peak = 81), gca=81.0
- gca peak = 0.32299 (52)
- mri peak = 0.08966 (56)
- Right_Hippocampus (53): linear fit = 1.01 x + 0.0 (435 voxels, overlap=1.007)
- Right_Hippocampus (53): linear fit = 1.01 x + 0.0 (435 voxels, peak = 53), gca=52.8
- gca peak = 0.28448 (53)
- mri peak = 0.09177 (54)
- Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (575 voxels, overlap=1.007)
- Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (575 voxels, peak = 55), gca=55.4
- gca peak = 0.08344 (108)
- mri peak = 0.06693 (107)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (36446 voxels, overlap=0.861)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (36446 voxels, peak = 108), gca=108.0
- gca peak = 0.08545 (110)
- mri peak = 0.07390 (107)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (37210 voxels, overlap=0.823)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (37210 voxels, peak = 109), gca=109.4
- gca peak = 0.09526 (52)
- mri peak = 0.06130 (53)
- Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (14531 voxels, overlap=0.974)
- Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (14531 voxels, peak = 52), gca=52.0
- gca peak = 0.10572 (53)
- mri peak = 0.05382 (50)
- Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (13475 voxels, overlap=0.992)
- Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (13475 voxels, peak = 52), gca=52.2
- gca peak = 0.24214 (64)
- mri peak = 0.11916 (64)
- Right_Caudate (50): linear fit = 0.99 x + 0.0 (621 voxels, overlap=1.001)
- Right_Caudate (50): linear fit = 0.99 x + 0.0 (621 voxels, peak = 63), gca=63.0
- gca peak = 0.17636 (62)
- mri peak = 0.10624 (64)
- Left_Caudate (11): linear fit = 1.00 x + 0.0 (753 voxels, overlap=0.983)
- Left_Caudate (11): linear fit = 1.00 x + 0.0 (753 voxels, peak = 62), gca=62.0
- gca peak = 0.10995 (60)
- mri peak = 0.05693 (56)
- Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (7455 voxels, overlap=0.999)
- Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (7455 voxels, peak = 62), gca=61.5
- gca peak = 0.13104 (56)
- mri peak = 0.05915 (55)
- Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (7984 voxels, overlap=1.000)
- Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (7984 voxels, peak = 55), gca=55.2
- gca peak = 0.18448 (87)
- mri peak = 0.07214 (88)
- Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (4066 voxels, overlap=0.977)
- Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (4066 voxels, peak = 88), gca=88.3
- gca peak = 0.16436 (91)
- mri peak = 0.06366 (91)
- Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (3816 voxels, overlap=1.000)
- Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (3816 voxels, peak = 90), gca=89.6
- gca peak = 0.54115 (56)
- mri peak = 0.10417 (56)
- Left_Amygdala (18): linear fit = 1.00 x + 0.0 (353 voxels, overlap=1.023)
- Left_Amygdala (18): linear fit = 1.00 x + 0.0 (353 voxels, peak = 56), gca=56.0
- gca peak = 0.63626 (52)
- mri peak = 0.08871 (53)
- Right_Amygdala (54): linear fit = 1.11 x + 0.0 (285 voxels, overlap=1.018)
- Right_Amygdala (54): linear fit = 1.11 x + 0.0 (285 voxels, peak = 57), gca=57.5
- gca peak = 0.11392 (86)
- mri peak = 0.07617 (83)
- Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (3455 voxels, overlap=0.983)
- Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (3455 voxels, peak = 85), gca=84.7
- gca peak = 0.11701 (81)
- mri peak = 0.08348 (80)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3666 voxels, overlap=0.950)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3666 voxels, peak = 81), gca=80.6
- gca peak = 0.09481 (74)
- mri peak = 0.07058 (71)
- Left_Putamen (12): linear fit = 0.99 x + 0.0 (1815 voxels, overlap=1.000)
- Left_Putamen (12): linear fit = 0.99 x + 0.0 (1815 voxels, peak = 73), gca=72.9
- gca peak = 0.12360 (64)
- mri peak = 0.07984 (70)
- Right_Putamen (51): linear fit = 1.00 x + 0.0 (1569 voxels, overlap=0.999)
- Right_Putamen (51): linear fit = 1.00 x + 0.0 (1569 voxels, peak = 64), gca=64.0
- gca peak = 0.07838 (85)
- mri peak = 0.08096 (82)
- Brain_Stem (16): linear fit = 1.00 x + 0.0 (8414 voxels, overlap=0.757)
- Brain_Stem (16): linear fit = 1.00 x + 0.0 (8414 voxels, peak = 85), gca=84.6
- gca peak = 0.11836 (85)
- mri peak = 0.08039 (86)
- Right_VentralDC (60): linear fit = 1.00 x + 0.0 (835 voxels, overlap=0.817)
- Right_VentralDC (60): linear fit = 1.00 x + 0.0 (835 voxels, peak = 85), gca=84.6
- gca peak = 0.15844 (87)
- mri peak = 0.08398 (88)
- Left_VentralDC (28): linear fit = 1.00 x + 0.0 (958 voxels, overlap=0.930)
- Left_VentralDC (28): linear fit = 1.00 x + 0.0 (958 voxels, peak = 87), gca=86.6
- gca peak = 0.35640 (14)
- uniform distribution in MR - rejecting arbitrary fit
- gca peak = 0.33827 ( 9)
- mri peak = 0.11343 ( 9)
- Fourth_Ventricle (15): linear fit = 0.88 x + 0.0 (334 voxels, overlap=0.870)
- Fourth_Ventricle (15): linear fit = 0.88 x + 0.0 (334 voxels, peak = 8), gca=8.0
- gca peak Unknown = 0.94427 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.24968 (29)
- gca peak Third_Ventricle = 0.35640 (14)
- gca peak CSF = 0.30128 (18)
- gca peak Left_Accumbens_area = 0.44849 (58)
- gca peak Left_undetermined = 1.00000 (35)
- gca peak Left_vessel = 0.44155 (61)
- gca peak Left_choroid_plexus = 0.09164 (48)
- gca peak Right_Inf_Lat_Vent = 0.30433 (27)
- gca peak Right_Accumbens_area = 0.31145 (63)
- gca peak Right_vessel = 0.57697 (60)
- gca peak Right_choroid_plexus = 0.10280 (48)
- gca peak Fifth_Ventricle = 0.45329 (19)
- gca peak WM_hypointensities = 0.17626 (84)
- gca peak non_WM_hypointensities = 0.08624 (54)
- gca peak Optic_Chiasm = 0.34843 (76)
- not using caudate to estimate GM means
- estimating mean gm scale to be 1.02 x + 0.0
- estimating mean wm scale to be 1.00 x + 0.0
- estimating mean csf scale to be 0.75 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
- 11056 gm and wm labels changed (%12 to gray, %88 to white out of all changed labels)
- 273 hippocampal voxels changed.
- 2 amygdala voxels changed.
- pass 1: 84602 changed. image ll: -2.194, PF=1.000
- pass 2: 15160 changed. image ll: -2.192, PF=1.000
- pass 3: 5407 changed.
- pass 4: 2374 changed.
- writing labeled volume to aseg.auto_noCCseg.mgz...
- auto-labeling took 19 minutes and 49 seconds.
- mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/cc_up.lta sub018
- 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/sub018/mri/transforms/cc_up.lta
- reading aseg from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/aseg.auto_noCCseg.mgz
- reading norm from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/norm.mgz
- 26739 voxels in left wm, 23098 in right wm, xrange [123, 130]
- searching rotation angles z=[-5 9], y=[-6 8]
-
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
searching scale 1 Z rot 5.5
searching scale 1 Z rot 5.8
searching scale 1 Z rot 6.0
searching scale 1 Z rot 6.3
searching scale 1 Z rot 6.5
searching scale 1 Z rot 6.8
searching scale 1 Z rot 7.0
searching scale 1 Z rot 7.3
searching scale 1 Z rot 7.5
searching scale 1 Z rot 7.8
searching scale 1 Z rot 8.0
searching scale 1 Z rot 8.3
searching scale 1 Z rot 8.5 global minimum found at slice 126.0, rotations (1.24, 1.77)
- final transformation (x=126.0, yr=1.237, zr=1.773):
- 0.999 -0.031 0.022 2.395;
- 0.031 1.000 0.001 43.073;
- -0.022 0.000 1.000 28.744;
- 0.000 0.000 0.000 1.000;
- updating x range to be [125, 130] in xformed coordinates
- best xformed slice 128
- cc center is found at 128 151 118
- eigenvectors:
- -0.001 0.005 1.000;
- -0.197 -0.980 0.005;
- 0.980 -0.197 0.002;
- error in mid anterior detected - correcting...
- writing aseg with callosum to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/aseg.auto.mgz...
- corpus callosum matter segmentation took 0.7 minutes
- #--------------------------------------
- #@# Merge ASeg Thu Aug 8 18:26:59 CEST 2013
- cp aseg.auto.mgz aseg.mgz
- #--------------------------------------------
- #@# Intensity Normalization2 Thu Aug 8 18:26:59 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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...
- 4822 control points removed
- Building bias image
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 0...
- Smoothing with sigma 8
- Applying bias correction
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Iterating 2 times
- ---------------------------------
- 3d normalization pass 1 of 2
- white matter peak found at 111
- white matter peak found at 109
- gm peak at 56 (56), valley at 29 (29)
- 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 30 (30)
- 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 35 seconds.
- #--------------------------------------------
- #@# Mask BFS Thu Aug 8 18:31:36 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri
- mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
- threshold mask volume at 5
- DoAbs = 0
- Found 1492386 voxels in mask (pct= 8.90)
- Writing masked volume to brain.finalsurfs.mgz...done.
- #--------------------------------------------
- #@# WM Segmentation Thu Aug 8 18:31:38 CEST 2013
- mri_segment brain.mgz wm.seg.mgz
- doing initial intensity segmentation...
- using local statistics to label ambiguous voxels...
- computing class statistics for intensity windows...
- WM (107.0): 107.1 +- 5.1 [80.0 --> 125.0]
- GM (67.0) : 66.2 +- 9.5 [30.0 --> 96.0]
- setting bottom of white matter range to 75.6
- setting top of gray matter range to 85.1
- 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...
- 6666 sparsely connected voxels removed...
- thickening thin strands....
- 20 segments, 5586 filled
- 304 bright non-wm voxels segmented.
- 4272 diagonally connected voxels added...
- white matter segmentation took 1.8 minutes
- writing output to wm.seg.mgz...
- mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz
- preserving editing changes in input volume...
- auto filling took 0.71 minutes
- reading wm segmentation from wm.seg.mgz...
- 85 voxels added to wm to prevent paths from MTL structures to cortex
- 989 additional wm voxels added
- 0 additional wm voxels added
- SEG EDIT: 48610 voxels turned on, 33564 voxels turned off.
- propagating editing to output volume from wm.seg.mgz
- 115,126,128 old 0 new 0
- 115,126,128 old 0 new 0
- writing edited volume to wm.asegedit.mgz....
- mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz
- Iteration Number : 1
- pass 1 (xy+): 19 found - 19 modified | TOTAL: 19
- pass 2 (xy+): 0 found - 19 modified | TOTAL: 19
- pass 1 (xy-): 14 found - 14 modified | TOTAL: 33
- pass 2 (xy-): 0 found - 14 modified | TOTAL: 33
- pass 1 (yz+): 30 found - 30 modified | TOTAL: 63
- pass 2 (yz+): 0 found - 30 modified | TOTAL: 63
- pass 1 (yz-): 22 found - 22 modified | TOTAL: 85
- pass 2 (yz-): 0 found - 22 modified | TOTAL: 85
- pass 1 (xz+): 19 found - 19 modified | TOTAL: 104
- pass 2 (xz+): 0 found - 19 modified | TOTAL: 104
- pass 1 (xz-): 15 found - 15 modified | TOTAL: 119
- pass 2 (xz-): 0 found - 15 modified | TOTAL: 119
- Iteration Number : 1
- pass 1 (+++): 10 found - 10 modified | TOTAL: 10
- pass 2 (+++): 0 found - 10 modified | TOTAL: 10
- pass 1 (+++): 12 found - 12 modified | TOTAL: 22
- pass 2 (+++): 0 found - 12 modified | TOTAL: 22
- pass 1 (+++): 6 found - 6 modified | TOTAL: 28
- pass 2 (+++): 0 found - 6 modified | TOTAL: 28
- pass 1 (+++): 13 found - 13 modified | TOTAL: 41
- pass 2 (+++): 0 found - 13 modified | TOTAL: 41
- Iteration Number : 1
- pass 1 (++): 246 found - 246 modified | TOTAL: 246
- pass 2 (++): 0 found - 246 modified | TOTAL: 246
- pass 1 (+-): 259 found - 259 modified | TOTAL: 505
- pass 2 (+-): 0 found - 259 modified | TOTAL: 505
- pass 1 (--): 249 found - 249 modified | TOTAL: 754
- pass 2 (--): 0 found - 249 modified | TOTAL: 754
- pass 1 (-+): 187 found - 187 modified | TOTAL: 941
- pass 2 (-+): 0 found - 187 modified | TOTAL: 941
- Iteration Number : 2
- pass 1 (xy+): 7 found - 7 modified | TOTAL: 7
- pass 2 (xy+): 0 found - 7 modified | TOTAL: 7
- pass 1 (xy-): 4 found - 4 modified | TOTAL: 11
- pass 2 (xy-): 0 found - 4 modified | TOTAL: 11
- pass 1 (yz+): 6 found - 6 modified | TOTAL: 17
- pass 2 (yz+): 0 found - 6 modified | TOTAL: 17
- pass 1 (yz-): 5 found - 5 modified | TOTAL: 22
- pass 2 (yz-): 0 found - 5 modified | TOTAL: 22
- pass 1 (xz+): 2 found - 2 modified | TOTAL: 24
- pass 2 (xz+): 0 found - 2 modified | TOTAL: 24
- pass 1 (xz-): 7 found - 7 modified | TOTAL: 31
- pass 2 (xz-): 0 found - 7 modified | TOTAL: 31
- Iteration Number : 2
- 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
- pass 1 (+++): 0 found - 0 modified | TOTAL: 2
- Iteration Number : 2
- pass 1 (++): 2 found - 2 modified | TOTAL: 2
- pass 2 (++): 0 found - 2 modified | TOTAL: 2
- pass 1 (+-): 1 found - 1 modified | TOTAL: 3
- pass 2 (+-): 0 found - 1 modified | TOTAL: 3
- pass 1 (--): 3 found - 3 modified | TOTAL: 6
- pass 2 (--): 0 found - 3 modified | TOTAL: 6
- pass 1 (-+): 3 found - 3 modified | TOTAL: 9
- pass 2 (-+): 0 found - 3 modified | TOTAL: 9
- Iteration Number : 3
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz-): 1 found - 1 modified | TOTAL: 1
- pass 2 (yz-): 0 found - 1 modified | TOTAL: 1
- pass 1 (xz+): 1 found - 1 modified | TOTAL: 2
- pass 2 (xz+): 0 found - 1 modified | TOTAL: 2
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 2
- Iteration Number : 3
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 3
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 4
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 4
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 4
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Total Number of Modified Voxels = 1145 (out of 524771: 0.218190)
- binarizing input wm segmentation...
- Ambiguous edge configurations...
- mri_pretess done
- #--------------------------------------------
- #@# Fill Thu Aug 8 18:34:13 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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
- 1.100 -0.074 0.018 -8.391;
- 0.081 1.119 0.320 -34.301;
- -0.042 -0.279 0.989 27.435;
- 0.000 0.000 0.000 1.000;
- voxel to talairach voxel transform
- 1.100 -0.074 0.018 -8.391;
- 0.081 1.119 0.320 -34.301;
- -0.042 -0.279 0.989 27.435;
- 0.000 0.000 0.000 1.000;
- reading segmented volume aseg.auto_noCCseg.mgz...
- Looking for area (min, max) = (350, 1400)
- area[0] = 1467 (min = 350, max = 1400), aspect = 0.48 (min = 0.10, max = 0.75)
- need search nearby
- using seed (125, 116, 88), TAL = (3.0, -40.0, 12.0)
- talairach voxel to voxel transform
- 0.904 0.051 -0.033 10.252;
- -0.070 0.823 -0.265 34.898;
- 0.018 0.234 0.935 -17.461;
- 0.000 0.000 0.000 1.000;
- segmentation indicates cc at (125, 116, 88) --> (3.0, -40.0, 12.0)
- done.
- writing output to filled.mgz...
- filling took 1.0 minutes
- talairach cc position changed to (3.00, -40.00, 12.00)
- Erasing brainstem...done.
- seed_search_size = 9, min_neighbors = 5
- search rh wm seed point around talairach space:(21.00, -40.00, 12.00) SRC: (110.06, 99.47, 93.99)
- search lh wm seed point around talairach space (-15.00, -40.00, 12.00), SRC: (142.61, 96.94, 94.65)
- 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 18:35:12 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts
- mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz
- Iteration Number : 1
- pass 1 (xy+): 1 found - 1 modified | TOTAL: 1
- pass 2 (xy+): 0 found - 1 modified | TOTAL: 1
- pass 1 (xy-): 1 found - 1 modified | TOTAL: 2
- pass 2 (xy-): 0 found - 1 modified | TOTAL: 2
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 2
- pass 1 (yz-): 3 found - 3 modified | TOTAL: 5
- pass 2 (yz-): 0 found - 3 modified | TOTAL: 5
- pass 1 (xz+): 1 found - 1 modified | TOTAL: 6
- pass 2 (xz+): 0 found - 1 modified | TOTAL: 6
- pass 1 (xz-): 2 found - 2 modified | TOTAL: 8
- pass 2 (xz-): 0 found - 2 modified | TOTAL: 8
- Iteration Number : 1
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 2 found - 2 modified | TOTAL: 2
- pass 2 (+++): 0 found - 2 modified | TOTAL: 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 2
- Iteration Number : 1
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 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
- Iteration Number : 2
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Total Number of Modified Voxels = 11 (out of 252305: 0.004360)
- Ambiguous edge configurations...
- mri_pretess done
- mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix
- $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- slice 40: 369 vertices, 442 faces
- slice 50: 5096 vertices, 5342 faces
- slice 60: 14713 vertices, 15113 faces
- slice 70: 25609 vertices, 25991 faces
- slice 80: 36637 vertices, 37045 faces
- slice 90: 47909 vertices, 48274 faces
- slice 100: 59689 vertices, 60118 faces
- slice 110: 71655 vertices, 72016 faces
- slice 120: 82662 vertices, 83062 faces
- slice 130: 93039 vertices, 93456 faces
- slice 140: 103686 vertices, 104077 faces
- slice 150: 113884 vertices, 114206 faces
- slice 160: 122538 vertices, 122871 faces
- slice 170: 129522 vertices, 129746 faces
- slice 180: 135300 vertices, 135518 faces
- slice 190: 139566 vertices, 139717 faces
- slice 200: 140950 vertices, 140968 faces
- slice 210: 140950 vertices, 140968 faces
- slice 220: 140950 vertices, 140968 faces
- slice 230: 140950 vertices, 140968 faces
- slice 240: 140950 vertices, 140968 faces
- slice 250: 140950 vertices, 140968 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...
- 140950 voxel in cpt #1: X=-18 [v=140950,e=422904,f=281936] located at (-25.064953, -17.840284, 40.186329)
- For the whole surface: X=-18 [v=140950,e=422904,f=281936]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Smooth1 lh Thu Aug 8 18:35:21 CEST 2013
- mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 18:35:25 CEST 2013
- mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts
- avg radius = 46.9 mm, total surface area = 73518 mm^2
- writing inflated surface to ../surf/lh.inflated.nofix
- inflation took 0.6 minutes
- Not saving sulc
-
step 000: RMS=0.101 (target=0.015)
step 005: RMS=0.074 (target=0.015)
step 010: RMS=0.052 (target=0.015)
step 015: RMS=0.042 (target=0.015)
step 020: RMS=0.036 (target=0.015)
step 025: RMS=0.031 (target=0.015)
step 030: RMS=0.027 (target=0.015)
step 035: RMS=0.025 (target=0.015)
step 040: RMS=0.023 (target=0.015)
step 045: RMS=0.022 (target=0.015)
step 050: RMS=0.022 (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 18:36:01 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts
- mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix
- doing quick spherical unfolding.
- setting seed for random number genererator to 1234
- $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading original vertex positions...
- unfolding cortex into spherical form...
- surface projected - minimizing metric distortion...
- vertex spacing 0.97 +- 0.57 (0.00-->6.20) (max @ vno 57771 --> 57772)
- face area 0.03 +- 0.03 (-0.08-->0.61)
- scaling brain by 0.315...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=176.193, avgs=0
- 005/300: dt: 0.9000, rms radial error=175.934, avgs=0
- 010/300: dt: 0.9000, rms radial error=175.377, avgs=0
- 015/300: dt: 0.9000, rms radial error=174.646, avgs=0
- 020/300: dt: 0.9000, rms radial error=173.815, avgs=0
- 025/300: dt: 0.9000, rms radial error=172.927, avgs=0
- 030/300: dt: 0.9000, rms radial error=172.011, avgs=0
- 035/300: dt: 0.9000, rms radial error=171.078, avgs=0
- 040/300: dt: 0.9000, rms radial error=170.137, avgs=0
- 045/300: dt: 0.9000, rms radial error=169.193, avgs=0
- 050/300: dt: 0.9000, rms radial error=168.250, avgs=0
- 055/300: dt: 0.9000, rms radial error=167.310, avgs=0
- 060/300: dt: 0.9000, rms radial error=166.373, avgs=0
- 065/300: dt: 0.9000, rms radial error=165.440, avgs=0
- 070/300: dt: 0.9000, rms radial error=164.512, avgs=0
- 075/300: dt: 0.9000, rms radial error=163.588, avgs=0
- 080/300: dt: 0.9000, rms radial error=162.669, avgs=0
- 085/300: dt: 0.9000, rms radial error=161.755, avgs=0
- 090/300: dt: 0.9000, rms radial error=160.846, avgs=0
- 095/300: dt: 0.9000, rms radial error=159.942, avgs=0
- 100/300: dt: 0.9000, rms radial error=159.043, avgs=0
- 105/300: dt: 0.9000, rms radial error=158.148, avgs=0
- 110/300: dt: 0.9000, rms radial error=157.258, avgs=0
- 115/300: dt: 0.9000, rms radial error=156.373, avgs=0
- 120/300: dt: 0.9000, rms radial error=155.494, avgs=0
- 125/300: dt: 0.9000, rms radial error=154.618, avgs=0
- 130/300: dt: 0.9000, rms radial error=153.748, avgs=0
- 135/300: dt: 0.9000, rms radial error=152.882, avgs=0
- 140/300: dt: 0.9000, rms radial error=152.021, avgs=0
- 145/300: dt: 0.9000, rms radial error=151.165, avgs=0
- 150/300: dt: 0.9000, rms radial error=150.314, avgs=0
- 155/300: dt: 0.9000, rms radial error=149.467, avgs=0
- 160/300: dt: 0.9000, rms radial error=148.624, avgs=0
- 165/300: dt: 0.9000, rms radial error=147.787, avgs=0
- 170/300: dt: 0.9000, rms radial error=146.954, avgs=0
- 175/300: dt: 0.9000, rms radial error=146.126, avgs=0
- 180/300: dt: 0.9000, rms radial error=145.302, avgs=0
- 185/300: dt: 0.9000, rms radial error=144.484, avgs=0
- 190/300: dt: 0.9000, rms radial error=143.673, avgs=0
- 195/300: dt: 0.9000, rms radial error=142.865, avgs=0
- 200/300: dt: 0.9000, rms radial error=142.062, avgs=0
- 205/300: dt: 0.9000, rms radial error=141.264, avgs=0
- 210/300: dt: 0.9000, rms radial error=140.470, avgs=0
- 215/300: dt: 0.9000, rms radial error=139.680, avgs=0
- 220/300: dt: 0.9000, rms radial error=138.895, avgs=0
- 225/300: dt: 0.9000, rms radial error=138.114, avgs=0
- 230/300: dt: 0.9000, rms radial error=137.337, avgs=0
- 235/300: dt: 0.9000, rms radial error=136.565, avgs=0
- 240/300: dt: 0.9000, rms radial error=135.797, avgs=0
- 245/300: dt: 0.9000, rms radial error=135.033, avgs=0
- 250/300: dt: 0.9000, rms radial error=134.273, avgs=0
- 255/300: dt: 0.9000, rms radial error=133.518, avgs=0
- 260/300: dt: 0.9000, rms radial error=132.767, avgs=0
- 265/300: dt: 0.9000, rms radial error=132.019, avgs=0
- 270/300: dt: 0.9000, rms radial error=131.276, avgs=0
- 275/300: dt: 0.9000, rms radial error=130.538, avgs=0
- 280/300: dt: 0.9000, rms radial error=129.803, avgs=0
- 285/300: dt: 0.9000, rms radial error=129.072, avgs=0
- 290/300: dt: 0.9000, rms radial error=128.345, avgs=0
- 295/300: dt: 0.9000, rms radial error=127.623, avgs=0
- 300/300: dt: 0.9000, rms radial error=126.904, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 16464.00
- 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 = 2748.27
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00010
- epoch 3 (K=160.0), pass 1, starting sse = 270.71
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.11/12 = 0.00934
- epoch 4 (K=640.0), pass 1, starting sse = 12.09
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.12/13 = 0.00952
- final writing spherical brain to ../surf/lh.qsphere.nofix
- spherical transformation took 0.08 hours
- distance error %100000.00
- #--------------------------------------------
- #@# Fix Topology lh Thu Aug 8 18:41:03 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/sub018/scripts
- mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub018 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=-18 (nv=140950, nf=281936, ne=422904, g=10)
- using quasi-homeomorphic spherical map to tessellate cortical surface...
- Correction of the Topology
- Finding true center and radius of Spherical Surface...done
- Surface centered at (0,0,0) with radius 100.0 in 10 iterations
- marking ambiguous vertices...
- 1221 ambiguous faces found in tessellation
- segmenting defects...
- 18 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- 18 defects to be corrected
- 0 vertices coincident
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -9.7732 (-4.8866)
- -vertex loglikelihood: -6.6526 (-3.3263)
- -normal dot loglikelihood: -3.6298 (-3.6298)
- -quad curv loglikelihood: -6.5572 (-3.2786)
- Total Loglikelihood : -26.6128
- CORRECTING DEFECT 0 (vertices=69, convex hull=33)
- After retessellation of defect 0, euler #=-15 (140193,420265,280057) : difference with theory (-15) = 0
- CORRECTING DEFECT 1 (vertices=100, convex hull=112)
- After retessellation of defect 1, euler #=-14 (140237,420445,280194) : difference with theory (-14) = 0
- CORRECTING DEFECT 2 (vertices=66, convex hull=82)
- After retessellation of defect 2, euler #=-13 (140256,420539,280270) : difference with theory (-13) = 0
- CORRECTING DEFECT 3 (vertices=39, convex hull=58)
- After retessellation of defect 3, euler #=-12 (140281,420637,280344) : difference with theory (-12) = 0
- CORRECTING DEFECT 4 (vertices=82, convex hull=30)
- After retessellation of defect 4, euler #=-11 (140290,420675,280374) : difference with theory (-11) = 0
- CORRECTING DEFECT 5 (vertices=21, convex hull=49)
- After retessellation of defect 5, euler #=-10 (140303,420729,280416) : difference with theory (-10) = 0
- CORRECTING DEFECT 6 (vertices=25, convex hull=42)
- After retessellation of defect 6, euler #=-9 (140312,420774,280453) : difference with theory (-9) = 0
- CORRECTING DEFECT 7 (vertices=64, convex hull=38)
- After retessellation of defect 7, euler #=-8 (140317,420806,280481) : difference with theory (-8) = 0
- CORRECTING DEFECT 8 (vertices=18, convex hull=37)
- After retessellation of defect 8, euler #=-7 (140328,420850,280515) : difference with theory (-7) = 0
- CORRECTING DEFECT 9 (vertices=68, convex hull=53)
- After retessellation of defect 9, euler #=-6 (140335,420896,280555) : difference with theory (-6) = 0
- CORRECTING DEFECT 10 (vertices=28, convex hull=34)
- After retessellation of defect 10, euler #=-5 (140335,420907,280567) : difference with theory (-5) = 0
- CORRECTING DEFECT 11 (vertices=41, convex hull=58)
- After retessellation of defect 11, euler #=-4 (140356,420992,280632) : difference with theory (-4) = 0
- CORRECTING DEFECT 12 (vertices=47, convex hull=26)
- After retessellation of defect 12, euler #=-3 (140361,421013,280649) : difference with theory (-3) = 0
- CORRECTING DEFECT 13 (vertices=6, convex hull=24)
- After retessellation of defect 13, euler #=-2 (140362,421022,280658) : difference with theory (-2) = 0
- CORRECTING DEFECT 14 (vertices=24, convex hull=30)
- After retessellation of defect 14, euler #=-1 (140365,421039,280673) : difference with theory (-1) = 0
- CORRECTING DEFECT 15 (vertices=35, convex hull=57)
- After retessellation of defect 15, euler #=0 (140381,421107,280726) : difference with theory (0) = 0
- CORRECTING DEFECT 16 (vertices=8, convex hull=26)
- After retessellation of defect 16, euler #=1 (140382,421116,280735) : difference with theory (1) = 0
- CORRECTING DEFECT 17 (vertices=22, convex hull=61)
- After retessellation of defect 17, euler #=2 (140393,421173,280782) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.88 +- 0.21 (0.12-->5.92) (max @ vno 116747 --> 119326)
- face area 0.00 +- 0.00 (0.00-->0.00)
- performing soap bubble on retessellated vertices for 0 iterations...
- vertex spacing 0.88 +- 0.21 (0.12-->5.92) (max @ vno 116747 --> 119326)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 58 mutations (34.3%), 111 crossovers (65.7%), 15 vertices were eliminated
- building final representation...
- 557 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=140393, nf=280782, ne=421173, g=0)
- writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 11.0 minutes
- 0 defective edges
- removing intersecting faces
- 000: 72 intersecting
- 001: 6 intersecting
- mris_euler_number ../surf/lh.orig
- euler # = v-e+f = 2g-2: 140393 - 421173 + 280782 = 2 --> 0 holes
- F =2V-4: 280782 = 280786-4 (0)
- 2E=3F: 842346 = 842346 (0)
- total defect index = 0
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts
- mris_remove_intersection ../surf/lh.orig ../surf/lh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 6 intersecting
- writing corrected surface to ../surf/lh.orig
- rm ../surf/lh.inflated
- #--------------------------------------------
- #@# Make White Surf lh Thu Aug 8 18:52:08 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts
- mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub018 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/sub018/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/wm.mgz...
- 18104 bright wm thresholded.
- 357 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.orig...
- computing class statistics...
- border white: 252064 voxels (1.50%)
- border gray 291583 voxels (1.74%)
- WM (92.0): 92.8 +- 10.4 [70.0 --> 110.0]
- GM (74.0) : 73.1 +- 12.6 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 46.4 (was 70)
- setting MAX_BORDER_WHITE to 115.4 (was 105)
- setting MIN_BORDER_WHITE to 59.0 (was 85)
- setting MAX_CSF to 33.9 (was 40)
- setting MAX_GRAY to 94.6 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 52.7 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 21.3 (was 40)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.81 +- 0.22 (0.02-->2.38) (max @ vno 106072 --> 140333)
- face area 0.28 +- 0.12 (0.00-->1.59)
- mean absolute distance = 0.68 +- 0.81
- 3584 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=59
- mean inside = 92.7, mean outside = 68.4
- smoothing surface for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 2 vertex label from ripped group
- mean border=72.3, 46 (46) missing vertices, mean dist 0.4 [0.5 (%31.0)->0.8 (%69.0))]
- %71 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.92 +- 0.26 (0.09-->3.87) (max @ vno 106917 --> 107997)
- face area 0.28 +- 0.13 (0.00-->2.22)
- mean absolute distance = 0.31 +- 0.45
- 2784 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=7593535.0, rms=13.69
- 001: dt: 0.5000, sse=7623433.5, rms=9.925 (0.000%)
- 002: dt: 0.5000, sse=7783613.5, rms=7.737 (0.000%)
- 003: dt: 0.5000, sse=7928952.5, rms=6.320 (0.000%)
- 004: dt: 0.5000, sse=8101897.0, rms=5.481 (0.000%)
- 005: dt: 0.5000, sse=8220709.5, rms=4.985 (0.000%)
- 006: dt: 0.5000, sse=8272811.5, rms=4.733 (0.000%)
- 007: dt: 0.5000, sse=8306699.5, rms=4.565 (0.000%)
- 008: dt: 0.5000, sse=8310262.5, rms=4.482 (0.000%)
- 009: dt: 0.5000, sse=8284134.0, rms=4.398 (0.000%)
- rms = 4.36, time step reduction 1 of 3 to 0.250...
- 010: dt: 0.5000, sse=8276810.5, rms=4.365 (0.000%)
- 011: dt: 0.2500, sse=5265968.0, rms=3.045 (0.000%)
- 012: dt: 0.2500, sse=4850102.0, rms=2.615 (0.000%)
- 013: dt: 0.2500, sse=4584692.5, rms=2.513 (0.000%)
- 014: dt: 0.2500, sse=4506709.5, rms=2.420 (0.000%)
- rms = 2.38, time step reduction 2 of 3 to 0.125...
- 015: dt: 0.2500, sse=4401575.5, rms=2.383 (0.000%)
- 016: dt: 0.1250, sse=4179055.0, rms=2.151 (0.000%)
- rms = 2.12, time step reduction 3 of 3 to 0.062...
- 017: dt: 0.1250, sse=4133489.2, rms=2.118 (0.000%)
- positioning took 2.3 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
- removing 4 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 1 vertex label from ripped group
- removing 2 vertex label from ripped group
- mean border=77.1, 29 (1) missing vertices, mean dist -0.2 [0.3 (%79.3)->0.2 (%20.7))]
- %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 (0.12-->3.57) (max @ vno 104764 --> 104766)
- face area 0.35 +- 0.16 (0.00-->2.88)
- mean absolute distance = 0.21 +- 0.28
- 2447 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5193968.0, rms=6.31
- 018: dt: 0.5000, sse=5327800.5, rms=4.178 (0.000%)
- rms = 4.51, time step reduction 1 of 3 to 0.250...
- 019: dt: 0.2500, sse=4858880.0, rms=3.036 (0.000%)
- 020: dt: 0.2500, sse=4654450.5, rms=2.406 (0.000%)
- 021: dt: 0.2500, sse=4601864.0, rms=1.993 (0.000%)
- 022: dt: 0.2500, sse=4568304.5, rms=1.942 (0.000%)
- 023: dt: 0.2500, sse=4511403.0, rms=1.852 (0.000%)
- rms = 1.86, time step reduction 2 of 3 to 0.125...
- 024: dt: 0.1250, sse=4453722.5, rms=1.774 (0.000%)
- 025: dt: 0.1250, sse=4370604.0, rms=1.668 (0.000%)
- rms = 1.66, time step reduction 3 of 3 to 0.062...
- 026: dt: 0.1250, sse=4327520.5, rms=1.663 (0.000%)
- positioning took 1.3 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 1 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- mean border=80.4, 30 (0) missing vertices, mean dist -0.1 [0.2 (%76.6)->0.2 (%23.4))]
- %90 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.25 (0.10-->3.64) (max @ vno 140247 --> 57770)
- face area 0.34 +- 0.16 (0.00-->2.83)
- mean absolute distance = 0.16 +- 0.24
- 2791 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4728897.5, rms=4.32
- 027: dt: 0.5000, sse=5132050.0, rms=4.118 (0.000%)
- rms = 4.33, time step reduction 1 of 3 to 0.250...
- 028: dt: 0.2500, sse=4651926.5, rms=2.591 (0.000%)
- 029: dt: 0.2500, sse=4517009.5, rms=2.128 (0.000%)
- 030: dt: 0.2500, sse=4575766.5, rms=1.791 (0.000%)
- rms = 1.84, time step reduction 2 of 3 to 0.125...
- 031: dt: 0.1250, sse=4509472.5, rms=1.655 (0.000%)
- 032: dt: 0.1250, sse=4419950.0, rms=1.467 (0.000%)
- rms = 1.45, time step reduction 3 of 3 to 0.062...
- 033: dt: 0.1250, sse=4382431.0, rms=1.448 (0.000%)
- positioning took 1.1 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 1 vertex label from ripped group
- mean border=81.4, 27 (0) missing vertices, mean dist -0.0 [0.2 (%58.3)->0.2 (%41.7))]
- %92 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- writing white matter surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.white...
- writing smoothed curvature to lh.curv
- 000: dt: 0.0000, sse=4408231.0, rms=1.82
- rms = 2.75, time step reduction 1 of 3 to 0.250...
- 034: dt: 0.2500, sse=4506050.0, rms=1.205 (0.000%)
- 035: dt: 0.2500, sse=4678282.5, rms=1.078 (0.000%)
- rms = 1.08, time step reduction 2 of 3 to 0.125...
- rms = 1.07, time step reduction 3 of 3 to 0.062...
- 036: dt: 0.1250, sse=4681872.0, rms=1.067 (0.000%)
- positioning took 0.6 minutes
- inhibiting deformation at non-cortical midline structures...
- generating cortex label...
- 12 non-cortical segments detected
- only using segment with 1853 vertices
- erasing segment 1 (vno[0] = 80872)
- erasing segment 2 (vno[0] = 85194)
- erasing segment 3 (vno[0] = 85231)
- erasing segment 4 (vno[0] = 96348)
- erasing segment 5 (vno[0] = 98385)
- erasing segment 6 (vno[0] = 98405)
- erasing segment 7 (vno[0] = 99451)
- erasing segment 8 (vno[0] = 100513)
- erasing segment 9 (vno[0] = 107997)
- erasing segment 10 (vno[0] = 108015)
- erasing segment 11 (vno[0] = 108027)
- writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/label/lh.cortex.label...
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.curv
- writing smoothed area to lh.area
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.area
- vertex spacing 0.90 +- 0.25 (0.06-->3.87) (max @ vno 107997 --> 106917)
- face area 0.34 +- 0.16 (0.00-->2.82)
- refinement took 7.7 minutes
- #--------------------------------------------
- #@# Smooth2 lh Thu Aug 8 18:59:52 CEST 2013
- mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts
- smoothing for 3 iterations
- setting seed for random number generator to 1234
- smoothing surface tessellation for 3 iterations...
- smoothing complete - recomputing first and second fundamental forms...
- #--------------------------------------------
- #@# Inflation2 lh Thu Aug 8 18:59:57 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts
- mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated
- avg radius = 47.0 mm, total surface area = 85951 mm^2
- writing inflated surface to ../surf/lh.inflated
- writing sulcal depths to ../surf/lh.sulc
-
step 000: RMS=0.118 (target=0.015)
step 005: RMS=0.082 (target=0.015)
step 010: RMS=0.058 (target=0.015)
step 015: RMS=0.047 (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=0.022 (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=0.015 (target=0.015)
- inflation complete.
- inflation took 0.7 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
- 160 vertices thresholded to be in k1 ~ [-0.49 0.42], k2 ~ [-0.31 0.06]
- total integrated curvature = 0.616*4pi (7.743) --> 0 handles
- ICI = 1.6, FI = 10.8, variation=180.166
- 134 vertices thresholded to be in [-0.04 0.02]
- writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level
- curvature mean = 0.000, std = 0.001
- 120 vertices thresholded to be in [-0.17 0.19]
- done.
- writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.016, std = 0.024
- done.
- #-----------------------------------------
- #@# Curvature Stats lh Thu Aug 8 19:02:33 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub018 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 [ sub018/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 [ 284 ]
- Gb_filter = 0
- WARN: S lookup min: -0.503964
- WARN: S explicit min: 0.000000 vertex = 37
- #--------------------------------------------
- #@# Sphere lh Thu Aug 8 19:02:38 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 0.291...
- MRISunfold() max_passes = 1 -------
- tol=5.0e-01, sigma=0.0, host=snake, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
- using quadratic fit line minimization
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 1.000000
- desired_rms_height -1.000000
- momentum 0.900000
- nbhd_size 7
- max_nbrs 8
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 1234
- --------------------
- mrisRemoveNegativeArea()
- pass 1: epoch 1 of 3 starting distance error %20.26
- pass 1: epoch 2 of 3 starting distance error %20.22
- unfolding complete - removing small folds...
- starting distance error %20.12
- removing remaining folds...
- final distance error %20.14
- MRISunfold() return, current seed 1234
- writing spherical brain to ../surf/lh.sphere
- spherical transformation took 1.10 hours
- #--------------------------------------------
- #@# Surf Reg lh Thu Aug 8 20:08:53 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 = 0.575
- curvature mean = 0.028, std = 0.935
- curvature mean = 0.025, std = 0.848
- Starting MRISrigidBodyAlignGlobal()
- d=32.00 min @ (0.00, -8.00, 0.00) sse = 258895.9, tmin=2.6441
- d=16.00 min @ (4.00, 4.00, -4.00) sse = 223271.4, tmin=4.0141
- d=8.00 min @ (0.00, -2.00, 0.00) sse = 221178.8, tmin=5.4640
- d=4.00 min @ (0.00, 1.00, 1.00) sse = 218526.3, tmin=6.9095
- d=2.00 min @ (-0.50, 0.00, 0.00) sse = 218236.0, tmin=8.4010
- d=1.00 min @ (0.00, -0.25, 0.00) sse = 218099.9, tmin=9.8591
- tol=1.0e+00, sigma=0.5, host=snake, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
- using quadratic fit line minimization
- MRISrigidBodyAlignGlobal() done 11.29 min
- curvature mean = 0.017, std = 0.946
- curvature mean = 0.013, std = 0.934
- curvature mean = 0.017, std = 0.958
- curvature mean = 0.006, std = 0.970
- curvature mean = 0.016, std = 0.960
- curvature mean = 0.002, std = 0.987
- 2 Reading smoothwm
- curvature mean = -0.024, std = 0.311
- curvature mean = 0.004, std = 0.067
- curvature mean = 0.073, std = 0.312
- curvature mean = 0.004, std = 0.079
- curvature mean = 0.035, std = 0.506
- curvature mean = 0.004, std = 0.085
- curvature mean = 0.020, std = 0.646
- curvature mean = 0.005, std = 0.087
- curvature mean = 0.007, std = 0.757
- MRISregister() return, current seed 0
- writing registered surface to ../surf/lh.sphere.reg...
- expanding nbhd size to 1
- #--------------------------------------------
- #@# Jacobian white lh Thu Aug 8 20:40:56 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 20:40:59 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 20:41:01 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub018 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...
- 1406 labels changed using aseg
- relabeling using gibbs priors...
- 000: 3202 changed, 140393 examined...
- 001: 746 changed, 13633 examined...
- 002: 172 changed, 4130 examined...
- 003: 50 changed, 1030 examined...
- 004: 26 changed, 303 examined...
- 005: 14 changed, 142 examined...
- 006: 8 changed, 70 examined...
- 007: 5 changed, 50 examined...
- 008: 4 changed, 26 examined...
- 009: 2 changed, 25 examined...
- 010: 1 changed, 12 examined...
- 011: 0 changed, 8 examined...
- 214 labels changed using aseg
- 000: 141 total segments, 99 labels (244 vertices) changed
- 001: 44 total segments, 4 labels (19 vertices) changed
- 002: 40 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...
- 1613 vertices marked for relabeling...
- 1613 labels changed in reclassification.
- writing output to ../label/lh.aparc.annot...
- classification took 1 minutes and 5 seconds.
- #--------------------------------------------
- #@# Make Pial Surf lh Thu Aug 8 20:42:06 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts
- mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub018 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/sub018/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/wm.mgz...
- 18104 bright wm thresholded.
- 357 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.orig...
- computing class statistics...
- border white: 252064 voxels (1.50%)
- border gray 291583 voxels (1.74%)
- WM (92.0): 92.8 +- 10.4 [70.0 --> 110.0]
- GM (74.0) : 73.1 +- 12.6 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 46.4 (was 70)
- setting MAX_BORDER_WHITE to 115.4 (was 105)
- setting MIN_BORDER_WHITE to 59.0 (was 85)
- setting MAX_CSF to 33.9 (was 40)
- setting MAX_GRAY to 94.6 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 52.7 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 21.3 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=105, GM=59
- mean inside = 92.7, mean outside = 68.4
- 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/sub018/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.81 +- 0.22 (0.02-->2.38) (max @ vno 106072 --> 140333)
- face area 0.28 +- 0.12 (0.00-->1.59)
- mean absolute distance = 0.68 +- 0.81
- 3711 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 18 points - only 5.56% unknown
- deleting segment 1 with 6 points - only 0.00% unknown
- deleting segment 2 with 8 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 3 with 4 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 5 with 4 points - only 0.00% unknown
- deleting segment 7 with 9 points - only 0.00% unknown
- deleting segment 8 with 936 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 9 with 4 points - only 0.00% unknown
- deleting segment 10 with 6 points - only 0.00% unknown
- deleting segment 12 with 17 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 13 with 2 points - only 0.00% unknown
- mean border=72.3, 46 (46) missing vertices, mean dist 0.4 [0.5 (%31.0)->0.8 (%69.0))]
- %71 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.92 +- 0.26 (0.08-->3.87) (max @ vno 106917 --> 107997)
- face area 0.28 +- 0.13 (0.00-->2.22)
- mean absolute distance = 0.31 +- 0.46
- 2879 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=7621995.5, rms=13.66
- 001: dt: 0.5000, sse=7660257.0, rms=9.906 (0.000%)
- 002: dt: 0.5000, sse=7828697.5, rms=7.722 (0.000%)
- 003: dt: 0.5000, sse=7974345.0, rms=6.309 (0.000%)
- 004: dt: 0.5000, sse=8155546.5, rms=5.472 (0.000%)
- 005: dt: 0.5000, sse=8276563.0, rms=4.977 (0.000%)
- 006: dt: 0.5000, sse=8335153.0, rms=4.727 (0.000%)
- 007: dt: 0.5000, sse=8362605.0, rms=4.559 (0.000%)
- 008: dt: 0.5000, sse=8378905.5, rms=4.476 (0.000%)
- 009: dt: 0.5000, sse=8346949.0, rms=4.393 (0.000%)
- rms = 4.36, time step reduction 1 of 3 to 0.250...
- 010: dt: 0.5000, sse=8344572.5, rms=4.360 (0.000%)
- 011: dt: 0.2500, sse=5306193.5, rms=3.044 (0.000%)
- 012: dt: 0.2500, sse=4887464.0, rms=2.615 (0.000%)
- 013: dt: 0.2500, sse=4619242.5, rms=2.514 (0.000%)
- 014: dt: 0.2500, sse=4542062.0, rms=2.422 (0.000%)
- rms = 2.38, time step reduction 2 of 3 to 0.125...
- 015: dt: 0.2500, sse=4437022.5, rms=2.385 (0.000%)
- 016: dt: 0.1250, sse=4214991.5, rms=2.155 (0.000%)
- rms = 2.12, time step reduction 3 of 3 to 0.062...
- 017: dt: 0.1250, sse=4168743.5, rms=2.122 (0.000%)
- positioning took 2.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 27 points - only 3.70% unknown
- removing 4 vertex label from ripped group
- deleting segment 1 with 4 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 2 with 4 points - only 0.00% unknown
- deleting segment 3 with 8 points - only 0.00% unknown
- deleting segment 8 with 9 points - only 0.00% unknown
- deleting segment 9 with 760 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 11 with 4 points - only 0.00% unknown
- deleting segment 12 with 7 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 16 with 22 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 17 with 2 points - only 0.00% unknown
- mean border=77.0, 34 (0) missing vertices, mean dist -0.2 [0.3 (%79.3)->0.2 (%20.7))]
- %84 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 (0.07-->3.44) (max @ vno 140247 --> 57770)
- face area 0.35 +- 0.16 (0.00-->2.88)
- mean absolute distance = 0.21 +- 0.29
- 2578 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5235586.5, rms=6.30
- 018: dt: 0.5000, sse=5374121.5, rms=4.174 (0.000%)
- rms = 4.50, time step reduction 1 of 3 to 0.250...
- 019: dt: 0.2500, sse=4902543.0, rms=3.036 (0.000%)
- 020: dt: 0.2500, sse=4698838.5, rms=2.409 (0.000%)
- 021: dt: 0.2500, sse=4646128.5, rms=2.000 (0.000%)
- 022: dt: 0.2500, sse=4612254.0, rms=1.948 (0.000%)
- 023: dt: 0.2500, sse=4555632.5, rms=1.859 (0.000%)
- rms = 1.87, time step reduction 2 of 3 to 0.125...
- 024: dt: 0.1250, sse=4497848.0, rms=1.781 (0.000%)
- 025: dt: 0.1250, sse=4415576.0, rms=1.676 (0.000%)
- rms = 1.67, time step reduction 3 of 3 to 0.062...
- 026: dt: 0.1250, sse=4373170.0, rms=1.671 (0.000%)
- positioning took 1.4 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 25 points - only 4.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 1 with 1 points - only 0.00% unknown
- deleting segment 2 with 7 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 3 with 4 points - only 0.00% unknown
- deleting segment 4 with 8 points - only 0.00% unknown
- deleting segment 5 with 9 points - only 0.00% unknown
- deleting segment 6 with 844 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 7 with 4 points - only 0.00% unknown
- deleting segment 8 with 7 points - only 0.00% unknown
- deleting segment 10 with 24 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 11 with 2 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 12 with 2 points - only 0.00% unknown
- mean border=80.4, 26 (0) missing vertices, mean dist -0.1 [0.2 (%76.5)->0.2 (%23.5))]
- %91 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.25 (0.10-->3.64) (max @ vno 140247 --> 57770)
- face area 0.34 +- 0.16 (0.00-->2.83)
- mean absolute distance = 0.16 +- 0.24
- 2917 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4775664.0, rms=4.31
- 027: dt: 0.5000, sse=5184141.0, rms=4.113 (0.000%)
- rms = 4.32, time step reduction 1 of 3 to 0.250...
- 028: dt: 0.2500, sse=4703077.0, rms=2.593 (0.000%)
- 029: dt: 0.2500, sse=4569690.5, rms=2.130 (0.000%)
- 030: dt: 0.2500, sse=4627375.5, rms=1.796 (0.000%)
- rms = 1.85, time step reduction 2 of 3 to 0.125...
- 031: dt: 0.1250, sse=4561258.0, rms=1.662 (0.000%)
- 032: dt: 0.1250, sse=4472172.5, rms=1.475 (0.000%)
- rms = 1.46, time step reduction 3 of 3 to 0.062...
- 033: dt: 0.1250, sse=4434970.0, rms=1.457 (0.000%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 25 points - only 4.00% 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 4 vertex label from ripped group
- deleting segment 3 with 4 points - only 0.00% unknown
- deleting segment 4 with 8 points - only 0.00% unknown
- deleting segment 5 with 9 points - only 0.00% unknown
- deleting segment 6 with 832 points - only 0.00% unknown
- deleting segment 7 with 6 points - only 0.00% unknown
- deleting segment 8 with 7 points - only 0.00% unknown
- deleting segment 9 with 24 points - only 0.00% unknown
- deleting segment 10 with 9 points - only 0.00% unknown
- mean border=81.4, 23 (0) missing vertices, mean dist -0.0 [0.2 (%58.2)->0.2 (%41.8))]
- %92 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- repositioning cortical surface to gray/csf boundary.
- smoothing T1 volume with sigma = 2.000
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4460609.5, rms=1.82
- rms = 2.74, time step reduction 1 of 3 to 0.250...
- 034: dt: 0.2500, sse=4564330.0, rms=1.211 (0.000%)
- 035: dt: 0.2500, sse=4743142.5, rms=1.085 (0.000%)
- rms = 1.09, time step reduction 2 of 3 to 0.125...
- rms = 1.08, time step reduction 3 of 3 to 0.062...
- 036: dt: 0.1250, sse=4746944.0, rms=1.075 (0.000%)
- positioning took 0.5 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- deleting segment 0 with 2 points - only 0.00% unknown
- smoothing surface for 5 iterations...
- mean border=48.9, 43 (43) missing vertices, mean dist 1.7 [0.1 (%0.0)->2.4 (%100.0))]
- %16 local maxima, %53 large gradients and %26 min vals, 1454 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=30063754.0, rms=31.85
- 001: dt: 0.5000, sse=21528794.0, rms=26.341 (0.000%)
- 002: dt: 0.5000, sse=15669557.0, rms=21.799 (0.000%)
- 003: dt: 0.5000, sse=11786185.0, rms=18.150 (0.000%)
- 004: dt: 0.5000, sse=9423024.0, rms=15.280 (0.000%)
- 005: dt: 0.5000, sse=8114454.5, rms=13.092 (0.000%)
- 006: dt: 0.5000, sse=7403228.5, rms=11.445 (0.000%)
- 007: dt: 0.5000, sse=6982222.5, rms=10.046 (0.000%)
- 008: dt: 0.5000, sse=6682913.5, rms=8.755 (0.000%)
- 009: dt: 0.5000, sse=6516733.0, rms=7.576 (0.000%)
- 010: dt: 0.5000, sse=6528485.0, rms=6.573 (0.000%)
- 011: dt: 0.5000, sse=6626331.5, rms=5.815 (0.000%)
- 012: dt: 0.5000, sse=6805241.5, rms=5.283 (0.000%)
- 013: dt: 0.5000, sse=6982417.5, rms=4.950 (0.000%)
- 014: dt: 0.5000, sse=7075462.5, rms=4.699 (0.000%)
- 015: dt: 0.5000, sse=7209154.5, rms=4.537 (0.000%)
- 016: dt: 0.5000, sse=7271487.0, rms=4.371 (0.000%)
- 017: dt: 0.5000, sse=7277579.0, rms=4.296 (0.000%)
- 018: dt: 0.5000, sse=7301311.0, rms=4.199 (0.000%)
- rms = 4.17, time step reduction 1 of 3 to 0.250...
- 019: dt: 0.5000, sse=7313636.5, rms=4.174 (0.000%)
- 020: dt: 0.2500, sse=5187138.0, rms=3.420 (0.000%)
- 021: dt: 0.2500, sse=4989134.5, rms=3.199 (0.000%)
- rms = 3.17, time step reduction 2 of 3 to 0.125...
- 022: dt: 0.2500, sse=4851979.0, rms=3.174 (0.000%)
- 023: dt: 0.1250, sse=4606620.5, rms=3.027 (0.000%)
- rms = 3.01, time step reduction 3 of 3 to 0.062...
- 024: dt: 0.1250, sse=4567122.0, rms=3.008 (0.000%)
- positioning took 3.0 minutes
- mean border=46.5, 1028 (1) missing vertices, mean dist 0.2 [0.2 (%45.8)->0.5 (%54.2))]
- %33 local maxima, %41 large gradients and %21 min vals, 517 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=5220012.5, rms=4.93
- 025: dt: 0.5000, sse=5544372.5, rms=4.330 (0.000%)
- rms = 4.29, time step reduction 1 of 3 to 0.250...
- 026: dt: 0.5000, sse=7141533.5, rms=4.293 (0.000%)
- 027: dt: 0.2500, sse=5351392.5, rms=3.401 (0.000%)
- 028: dt: 0.2500, sse=5407391.5, rms=3.143 (0.000%)
- rms = 3.12, time step reduction 2 of 3 to 0.125...
- 029: dt: 0.2500, sse=5262638.5, rms=3.121 (0.000%)
- 030: dt: 0.1250, sse=5051425.5, rms=2.909 (0.000%)
- rms = 2.87, time step reduction 3 of 3 to 0.062...
- 031: dt: 0.1250, sse=5028570.5, rms=2.873 (0.000%)
- positioning took 0.9 minutes
- mean border=44.1, 1171 (1) missing vertices, mean dist 0.1 [0.2 (%36.6)->0.4 (%63.4))]
- %52 local maxima, %22 large gradients and %21 min vals, 595 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=5322592.5, rms=4.29
- rms = 4.25, time step reduction 1 of 3 to 0.250...
- 032: dt: 0.5000, sse=5611925.5, rms=4.246 (0.000%)
- 033: dt: 0.2500, sse=5443074.0, rms=3.199 (0.000%)
- 034: dt: 0.2500, sse=5500722.5, rms=2.993 (0.000%)
- rms = 3.00, time step reduction 2 of 3 to 0.125...
- 035: dt: 0.1250, sse=5383388.0, rms=2.896 (0.000%)
- 036: dt: 0.1250, sse=5211532.0, rms=2.756 (0.000%)
- rms = 2.73, time step reduction 3 of 3 to 0.062...
- 037: dt: 0.1250, sse=5181308.5, rms=2.726 (0.000%)
- positioning took 0.9 minutes
- mean border=43.0, 2334 (1) missing vertices, mean dist 0.0 [0.2 (%45.2)->0.3 (%54.8))]
- %54 local maxima, %19 large gradients and %21 min vals, 456 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/sub018/surf/lh.pial...
- writing smoothed curvature to lh.curv.pial
- 000: dt: 0.0000, sse=5233645.0, rms=3.08
- rms = 3.95, time step reduction 1 of 3 to 0.250...
- 038: dt: 0.2500, sse=5105996.5, rms=2.796 (0.000%)
- 039: dt: 0.2500, sse=5307478.5, rms=2.738 (0.000%)
- rms = 2.74, time step reduction 2 of 3 to 0.125...
- 040: dt: 0.2500, sse=5357674.5, rms=2.738 (0.000%)
- 041: dt: 0.1250, sse=5252671.5, rms=2.598 (0.000%)
- rms = 2.58, time step reduction 3 of 3 to 0.062...
- 042: dt: 0.1250, sse=5265458.5, rms=2.577 (0.000%)
- positioning took 0.8 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.curv.pial
- writing smoothed area to lh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.area.pial
- vertex spacing 1.02 +- 0.43 (0.08-->8.77) (max @ vno 105864 --> 105855)
- face area 0.41 +- 0.30 (0.00-->6.11)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 140393 vertices processed
- 25000 of 140393 vertices processed
- 50000 of 140393 vertices processed
- 75000 of 140393 vertices processed
- 100000 of 140393 vertices processed
- 125000 of 140393 vertices processed
- 0 of 140393 vertices processed
- 25000 of 140393 vertices processed
- 50000 of 140393 vertices processed
- 75000 of 140393 vertices processed
- 100000 of 140393 vertices processed
- 125000 of 140393 vertices processed
- thickness calculation complete, 531:971 truncations.
- 29027 vertices at 0 distance
- 91199 vertices at 1 distance
- 91889 vertices at 2 distance
- 38639 vertices at 3 distance
- 11593 vertices at 4 distance
- 3553 vertices at 5 distance
- 1201 vertices at 6 distance
- 426 vertices at 7 distance
- 168 vertices at 8 distance
- 81 vertices at 9 distance
- 58 vertices at 10 distance
- 32 vertices at 11 distance
- 24 vertices at 12 distance
- 21 vertices at 13 distance
- 22 vertices at 14 distance
- 22 vertices at 15 distance
- 15 vertices at 16 distance
- 6 vertices at 17 distance
- 7 vertices at 18 distance
- 3 vertices at 19 distance
- 12 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.thickness
- positioning took 14.7 minutes
- #--------------------------------------------
- #@# Surf Volume lh Thu Aug 8 20:56:47 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 20:56:48 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts
- pctsurfcon --s sub018 --lh-only
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts/pctsurfcon.log
- Thu Aug 8 20:56:48 CEST 2013
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/tmp.pctsurfcon.5580/lh.wm.mgh --regheader sub018 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/label/lh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 = 108892
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/label/lh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/tmp.pctsurfcon.5580/lh.wm.mgh
- Dim: 140393 1 1
- mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/tmp.pctsurfcon.5580/lh.gm.mgh --projfrac 0.3 --regheader sub018 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/label/lh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.white
- Done reading source surface
- Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 = 124928
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/label/lh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/tmp.pctsurfcon.5580/lh.gm.mgh
- Dim: 140393 1 1
- mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/tmp.pctsurfcon.5580/lh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/tmp.pctsurfcon.5580/lh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/surf/lh.w-g.pct.mgh
- mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.w-g.pct.mgh --annot sub018 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/surf/lh.w-g.pct.mgh --annot sub018 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/surf/lh.w-g.pct.mgh
- Vertex Area is 0.67026 mm^3
- Generating list of segmentation ids
- Found 36 segmentations
- Computing statistics for each segmentation
- 0 1000 unknown 0 0.000
- 1 1001 bankssts 1852 1259.917
- 2 1002 caudalanteriorcingulate 1196 780.580
- 3 1003 caudalmiddlefrontal 3440 2289.014
- 4 1004 corpuscallosum 0 0.000
- 5 1005 cuneus 1824 1238.933
- 6 1006 entorhinal 678 499.968
- 7 1007 fusiform 5745 3862.256
- 8 1008 inferiorparietal 7495 5033.733
- 9 1009 inferiortemporal 5631 3831.789
- 10 1010 isthmuscingulate 1580 1052.516
- 11 1011 lateraloccipital 7198 4698.103
- 12 1012 lateralorbitofrontal 3274 2189.129
- 13 1013 lingual 3909 2703.998
- 14 1014 medialorbitofrontal 2719 1797.822
- 15 1015 middletemporal 5284 3650.135
- 16 1016 parahippocampal 1033 713.050
- 17 1017 paracentral 2203 1451.589
- 18 1018 parsopercularis 2306 1618.291
- 19 1019 parsorbitalis 870 560.306
- 20 1020 parstriangularis 1903 1282.946
- 21 1021 pericalcarine 1774 1193.827
- 22 1022 postcentral 7175 4734.376
- 23 1023 posteriorcingulate 2231 1461.519
- 24 1024 precentral 7197 4745.302
- 25 1025 precuneus 5474 3707.295
- 26 1026 rostralanteriorcingulate 1415 926.042
- 27 1027 rostralmiddlefrontal 9507 6529.832
- 28 1028 superiorfrontal 11324 7799.412
- 29 1029 superiorparietal 8021 5314.134
- 30 1030 superiortemporal 6471 4277.174
- 31 1031 supramarginal 5690 3868.281
- 32 1032 frontalpole 436 279.005
- 33 1033 temporalpole 793 537.071
- 34 1034 transversetemporal 776 496.099
- 35 1035 insula 3379 2195.280
- Reporting on 34 segmentations
- mri_segstats done
- Cleaning up
- #-----------------------------------------
- #@# Parcellation Stats lh Thu Aug 8 20:57:02 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 sub018 lh white
- computing statistics for each annotation in ../label/lh.aparc.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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
- 1852 1260 3420 2.848 0.437 0.136 0.038 23 3.1 bankssts
- 1196 781 2418 2.825 0.763 0.158 0.049 26 2.5 caudalanteriorcingulate
- 3440 2289 6238 2.523 0.381 0.123 0.039 37 5.1 caudalmiddlefrontal
- 1824 1239 2715 2.012 0.407 0.179 0.076 40 5.8 cuneus
- 678 500 2301 3.466 0.777 0.155 0.057 14 1.6 entorhinal
- 5745 3862 12326 2.773 0.513 0.159 0.069 133 15.1 fusiform
- 7495 5034 13974 2.471 0.418 0.142 0.052 211 15.9 inferiorparietal
- 5631 3832 12344 2.830 0.627 0.159 0.078 143 15.3 inferiortemporal
- 1580 1053 2810 2.415 0.795 0.170 0.071 33 4.4 isthmuscingulate
- 7198 4698 11769 2.212 0.418 0.167 0.127 346 50.7 lateraloccipital
- 3274 2189 6927 2.742 0.731 0.163 0.080 83 10.3 lateralorbitofrontal
- 3909 2704 6263 2.106 0.506 0.176 0.084 95 12.5 lingual
- 2719 1798 5068 2.395 0.772 0.152 0.074 80 8.0 medialorbitofrontal
- 5284 3650 12540 2.838 0.555 0.166 0.062 124 13.2 middletemporal
- 1033 713 2681 3.126 0.837 0.172 0.075 35 3.2 parahippocampal
- 2203 1452 3996 2.372 0.471 0.126 0.038 26 3.3 paracentral
- 2306 1618 4788 2.567 0.407 0.146 0.048 43 4.3 parsopercularis
- 870 560 2060 2.883 0.604 0.169 0.067 21 2.6 parsorbitalis
- 1903 1283 3803 2.554 0.441 0.135 0.043 32 3.5 parstriangularis
- 1774 1194 1960 1.747 0.409 0.160 0.104 161 4.7 pericalcarine
- 7175 4734 11311 2.118 0.529 0.133 0.041 102 12.0 postcentral
- 2231 1462 3632 2.253 0.704 0.153 0.055 51 5.0 posteriorcingulate
- 7197 4745 13464 2.599 0.483 0.125 0.040 87 12.1 precentral
- 5474 3707 9773 2.441 0.495 0.143 0.053 107 12.1 precuneus
- 1415 926 3093 2.824 0.616 0.146 0.055 31 3.1 rostralanteriorcingulate
- 9507 6530 17771 2.383 0.477 0.161 0.069 225 26.4 rostralmiddlefrontal
- 11324 7799 22717 2.554 0.517 0.140 0.049 188 22.0 superiorfrontal
- 8021 5314 13208 2.241 0.392 0.141 0.051 148 14.8 superiorparietal
- 6471 4277 13766 2.779 0.607 0.129 0.041 89 11.1 superiortemporal
- 5690 3868 11055 2.582 0.480 0.141 0.047 92 10.6 supramarginal
- 436 279 930 2.393 0.527 0.190 0.112 17 2.1 frontalpole
- 793 537 2610 3.720 0.554 0.150 0.060 13 2.1 temporalpole
- 776 496 1233 2.333 0.328 0.152 0.056 13 1.7 transversetemporal
- 3379 2195 7645 3.220 0.850 0.131 0.134 291 15.2 insula
- #-----------------------------------------
- #@# Cortical Parc 2 lh Thu Aug 8 20:57:22 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub018 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...
- 42 labels changed using aseg
- relabeling using gibbs priors...
- 000: 9776 changed, 140393 examined...
- 001: 2378 changed, 37338 examined...
- 002: 744 changed, 12271 examined...
- 003: 329 changed, 4211 examined...
- 004: 161 changed, 1868 examined...
- 005: 92 changed, 919 examined...
- 006: 66 changed, 511 examined...
- 007: 28 changed, 358 examined...
- 008: 19 changed, 170 examined...
- 009: 5 changed, 96 examined...
- 010: 4 changed, 27 examined...
- 011: 2 changed, 26 examined...
- 012: 4 changed, 14 examined...
- 013: 1 changed, 20 examined...
- 014: 1 changed, 7 examined...
- 015: 2 changed, 6 examined...
- 016: 1 changed, 14 examined...
- 017: 3 changed, 7 examined...
- 018: 4 changed, 17 examined...
- 019: 0 changed, 14 examined...
- 1 labels changed using aseg
- 000: 299 total segments, 213 labels (2941 vertices) changed
- 001: 106 total segments, 20 labels (56 vertices) changed
- 002: 88 total segments, 2 labels (2 vertices) changed
- 003: 86 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 158 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 892 vertices marked for relabeling...
- 892 labels changed in reclassification.
- writing output to ../label/lh.aparc.a2009s.annot...
- classification took 1 minutes and 13 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 2 lh Thu Aug 8 20:58:34 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 sub018 lh white
- computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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
- 1425 996 2706 2.534 0.597 0.183 0.093 38 5.7 G_and_S_frontomargin
- 1770 1176 3109 2.329 0.385 0.169 0.289 161 36.2 G_and_S_occipital_inf
- 1774 1125 3438 2.430 0.513 0.131 0.044 25 2.9 G_and_S_paracentral
- 1451 961 2967 2.663 0.437 0.154 0.056 26 3.1 G_and_S_subcentral
- 770 539 1597 2.319 0.464 0.195 0.098 25 2.9 G_and_S_transv_frontopol
- 2761 1820 5144 2.493 0.577 0.134 0.048 48 5.7 G_and_S_cingul-Ant
- 1455 987 2814 2.677 0.626 0.140 0.047 22 2.8 G_and_S_cingul-Mid-Ant
- 1841 1251 3198 2.389 0.546 0.144 0.048 30 3.7 G_and_S_cingul-Mid-Post
- 509 340 1263 2.743 0.540 0.193 0.078 14 1.6 G_cingul-Post-dorsal
- 282 176 501 2.469 0.856 0.181 0.084 7 0.9 G_cingul-Post-ventral
- 1690 1133 2665 2.013 0.463 0.193 0.089 46 6.2 G_cuneus
- 1460 1016 3421 2.697 0.446 0.175 0.072 39 4.1 G_front_inf-Opercular
- 363 222 883 3.113 0.373 0.185 0.083 10 1.2 G_front_inf-Orbital
- 1122 736 2551 2.681 0.365 0.141 0.048 23 2.3 G_front_inf-Triangul
- 5123 3456 10918 2.484 0.405 0.165 0.074 140 15.2 G_front_middle
- 7360 5054 16642 2.681 0.494 0.152 0.058 154 16.7 G_front_sup
- 563 345 1419 3.373 0.851 0.134 0.133 39 1.9 G_Ins_lg_and_S_cent_ins
- 713 455 2445 3.726 0.729 0.133 0.136 36 4.3 G_insular_short
- 2459 1595 5190 2.495 0.388 0.180 0.089 183 8.8 G_occipital_middle
- 1589 1020 3074 2.381 0.463 0.164 0.067 35 3.9 G_occipital_sup
- 2121 1381 4936 2.787 0.481 0.176 0.082 70 6.5 G_oc-temp_lat-fusifor
- 2444 1675 4320 2.138 0.486 0.205 0.116 81 10.4 G_oc-temp_med-Lingual
- 1307 919 4239 3.413 0.713 0.174 0.079 42 4.3 G_oc-temp_med-Parahip
- 2342 1533 6393 2.998 0.706 0.191 0.102 81 9.9 G_orbital
- 2511 1695 5759 2.620 0.438 0.161 0.065 61 6.1 G_pariet_inf-Angular
- 3129 2093 6863 2.700 0.455 0.150 0.054 62 6.4 G_pariet_inf-Supramar
- 2981 1980 5370 2.242 0.373 0.144 0.048 57 5.7 G_parietal_sup
- 2944 1894 5335 2.278 0.477 0.142 0.045 53 5.5 G_postcentral
- 2434 1601 5626 2.677 0.400 0.135 0.049 45 5.1 G_precentral
- 2408 1614 5043 2.561 0.522 0.151 0.055 51 5.3 G_precuneus
- 1032 675 2352 2.449 0.672 0.197 0.107 53 4.6 G_rectus
- 290 196 758 3.623 0.694 0.141 0.060 7 0.6 G_subcallosal
- 575 352 1043 2.391 0.403 0.152 0.059 11 1.3 G_temp_sup-G_T_transv
- 2376 1567 6403 2.989 0.477 0.161 0.055 53 5.5 G_temp_sup-Lateral
- 901 598 2402 3.653 0.682 0.105 0.039 6 1.3 G_temp_sup-Plan_polar
- 1095 748 2218 2.609 0.469 0.122 0.035 12 1.4 G_temp_sup-Plan_tempo
- 3300 2243 8481 2.919 0.660 0.180 0.099 111 11.5 G_temporal_inf
- 3541 2457 9221 2.873 0.566 0.178 0.068 96 10.1 G_temporal_middle
- 301 211 523 2.410 0.349 0.114 0.025 3 0.3 Lat_Fis-ant-Horizont
- 202 147 387 2.545 0.331 0.104 0.025 1 0.2 Lat_Fis-ant-Vertical
- 1232 843 1643 2.409 0.569 0.134 0.042 12 2.1 Lat_Fis-post
- 1863 1198 2857 2.119 0.409 0.178 0.098 89 5.5 Pole_occipital
- 2068 1389 6178 3.329 0.639 0.170 0.080 48 6.5 Pole_temporal
- 2189 1508 2770 1.931 0.615 0.156 0.088 163 5.2 S_calcarine
- 3325 2243 4062 1.990 0.548 0.108 0.028 20 4.0 S_central
- 1153 777 1764 2.323 0.531 0.123 0.035 13 1.7 S_cingul-Marginalis
- 658 434 1159 3.105 0.660 0.120 0.051 11 1.7 S_circular_insula_ant
- 1323 882 2320 2.902 0.726 0.088 0.022 6 1.2 S_circular_insula_inf
- 1840 1210 2777 2.640 0.539 0.125 0.126 201 7.0 S_circular_insula_sup
- 1436 1023 2620 2.739 0.524 0.117 0.031 10 1.9 S_collat_transv_ant
- 416 272 500 2.332 0.363 0.157 0.058 6 0.9 S_collat_transv_post
- 2133 1487 3388 2.333 0.343 0.121 0.030 19 2.8 S_front_inf
- 2110 1411 2958 2.127 0.412 0.127 0.044 24 3.2 S_front_middle
- 3069 2145 5145 2.362 0.403 0.125 0.037 37 4.6 S_front_sup
- 85 58 105 2.214 0.411 0.128 0.035 1 0.2 S_interm_prim-Jensen
- 2900 1986 4194 2.167 0.335 0.119 0.039 40 3.8 S_intrapariet_and_P_trans
- 1447 965 1785 1.951 0.306 0.144 0.047 20 3.0 S_oc_middle_and_Lunatus
- 1262 844 1688 2.131 0.296 0.134 0.037 14 2.0 S_oc_sup_and_transversal
- 928 615 1327 2.267 0.399 0.120 0.033 7 1.4 S_occipital_ant
- 1313 868 2077 2.650 0.417 0.135 0.046 16 2.3 S_oc-temp_lat
- 2062 1449 3335 2.422 0.578 0.136 0.041 27 3.5 S_oc-temp_med_and_Lingual
- 491 324 634 2.277 0.452 0.120 0.031 3 0.7 S_orbital_lateral
- 805 531 1323 2.512 0.975 0.129 0.061 17 1.8 S_orbital_med-olfact
- 986 687 1624 2.315 0.479 0.145 0.059 18 1.8 S_orbital-H_Shaped
- 1888 1285 2633 2.231 0.446 0.131 0.037 19 3.0 S_parieto_occipital
- 1698 1067 1935 2.073 0.961 0.141 0.042 26 3.0 S_pericallosal
- 3474 2341 4903 2.206 0.445 0.132 0.044 43 5.7 S_postcentral
- 1573 1067 2455 2.478 0.404 0.117 0.030 14 2.0 S_precentral-inf-part
- 1122 730 1650 2.567 0.415 0.114 0.028 8 1.3 S_precentral-sup-part
- 518 354 761 2.049 0.447 0.154 0.081 12 1.5 S_suborbital
- 1430 959 2510 2.472 0.369 0.155 0.076 51 4.7 S_subparietal
- 1102 762 1869 2.718 0.614 0.138 0.066 22 2.2 S_temporal_inf
- 6687 4534 11334 2.585 0.463 0.128 0.038 81 10.5 S_temporal_sup
- 503 348 710 2.357 0.355 0.113 0.028 3 0.7 S_temporal_transverse
- #-----------------------------------------
- #@# Cortical Parc 3 lh Thu Aug 8 20:58:56 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub018 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...
- 1069 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2877 changed, 140393 examined...
- 001: 703 changed, 12283 examined...
- 002: 172 changed, 3678 examined...
- 003: 67 changed, 1030 examined...
- 004: 31 changed, 412 examined...
- 005: 13 changed, 196 examined...
- 006: 9 changed, 84 examined...
- 007: 6 changed, 53 examined...
- 008: 6 changed, 44 examined...
- 009: 2 changed, 33 examined...
- 010: 1 changed, 13 examined...
- 011: 1 changed, 7 examined...
- 012: 0 changed, 7 examined...
- 111 labels changed using aseg
- 000: 66 total segments, 33 labels (344 vertices) changed
- 001: 33 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 39 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 599 vertices marked for relabeling...
- 599 labels changed in reclassification.
- writing output to ../label/lh.aparc.DKTatlas40.annot...
- classification took 1 minutes and 5 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 3 lh Thu Aug 8 21:00:01 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 sub018 lh white
- computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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
- 2015 1320 3918 2.750 0.670 0.143 0.043 34 3.6 caudalanteriorcingulate
- 3524 2361 6444 2.525 0.381 0.124 0.039 38 5.3 caudalmiddlefrontal
- 2619 1770 3994 2.053 0.415 0.163 0.067 48 7.0 cuneus
- 645 485 2166 3.392 0.764 0.153 0.057 13 1.5 entorhinal
- 5088 3432 10500 2.736 0.494 0.156 0.063 112 12.5 fusiform
- 6971 4701 12889 2.454 0.423 0.141 0.052 201 14.7 inferiorparietal
- 5743 3883 13245 2.897 0.644 0.165 0.086 158 17.2 inferiortemporal
- 1583 1052 2828 2.418 0.799 0.169 0.070 33 4.4 isthmuscingulate
- 7551 4921 12394 2.222 0.424 0.167 0.124 353 51.5 lateraloccipital
- 3578 2414 7876 2.790 0.782 0.173 0.096 106 14.0 lateralorbitofrontal
- 3879 2678 6213 2.105 0.505 0.177 0.084 95 12.5 lingual
- 2285 1513 4414 2.379 0.767 0.163 0.083 78 7.8 medialorbitofrontal
- 7103 4872 15934 2.808 0.540 0.159 0.057 149 16.6 middletemporal
- 1051 727 2729 3.120 0.836 0.173 0.075 35 3.2 parahippocampal
- 2518 1649 4445 2.375 0.470 0.127 0.038 29 3.7 paracentral
- 2116 1492 4348 2.566 0.411 0.147 0.048 40 4.1 parsopercularis
- 1087 690 2379 2.956 0.540 0.153 0.059 21 2.7 parsorbitalis
- 2368 1579 4408 2.491 0.407 0.132 0.041 36 4.0 parstriangularis
- 1760 1188 1957 1.750 0.407 0.160 0.104 161 4.6 pericalcarine
- 7913 5220 12357 2.128 0.534 0.134 0.042 116 13.2 postcentral
- 2387 1573 3831 2.265 0.688 0.153 0.054 52 5.3 posteriorcingulate
- 7128 4696 13263 2.595 0.487 0.125 0.040 85 12.1 precentral
- 5444 3667 9847 2.454 0.484 0.145 0.054 110 12.2 precuneus
- 1810 1187 3850 2.760 0.650 0.143 0.052 35 3.8 rostralanteriorcingulate
- 6603 4540 12618 2.380 0.470 0.157 0.064 151 16.8 rostralmiddlefrontal
- 12690 8746 25302 2.503 0.514 0.148 0.056 248 28.2 superiorfrontal
- 6317 4215 10485 2.259 0.382 0.141 0.051 120 11.6 superiorparietal
- 8764 5845 19245 2.869 0.655 0.133 0.047 149 16.1 superiortemporal
- 5688 3849 10937 2.571 0.486 0.142 0.048 92 10.9 supramarginal
- 721 460 1143 2.323 0.330 0.151 0.057 12 1.6 transversetemporal
- 2854 1852 6651 3.246 0.794 0.120 0.125 246 12.6 insula
- #--------------------------------------------
- #@# Tessellate rh Thu Aug 8 21:00:24 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts
- mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz
- Iteration Number : 1
- pass 1 (xy+): 3 found - 3 modified | TOTAL: 3
- pass 2 (xy+): 0 found - 3 modified | TOTAL: 3
- pass 1 (xy-): 1 found - 1 modified | TOTAL: 4
- pass 2 (xy-): 0 found - 1 modified | TOTAL: 4
- pass 1 (yz+): 3 found - 3 modified | TOTAL: 7
- pass 2 (yz+): 0 found - 3 modified | TOTAL: 7
- pass 1 (yz-): 3 found - 3 modified | TOTAL: 10
- pass 2 (yz-): 0 found - 3 modified | TOTAL: 10
- pass 1 (xz+): 2 found - 2 modified | TOTAL: 12
- pass 2 (xz+): 0 found - 2 modified | TOTAL: 12
- pass 1 (xz-): 2 found - 2 modified | TOTAL: 14
- pass 2 (xz-): 0 found - 2 modified | TOTAL: 14
- Iteration Number : 1
- 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 (+++): 2 found - 2 modified | TOTAL: 4
- pass 2 (+++): 0 found - 2 modified | TOTAL: 4
- pass 1 (+++): 0 found - 0 modified | TOTAL: 4
- 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 (--): 3 found - 3 modified | TOTAL: 4
- pass 2 (--): 0 found - 3 modified | TOTAL: 4
- pass 1 (-+): 2 found - 2 modified | TOTAL: 6
- pass 2 (-+): 0 found - 2 modified | TOTAL: 6
- Iteration Number : 2
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz-): 1 found - 1 modified | TOTAL: 1
- pass 2 (yz-): 0 found - 1 modified | TOTAL: 1
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 1
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 1
- 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 (--): 1 found - 1 modified | TOTAL: 1
- pass 2 (--): 0 found - 1 modified | TOTAL: 1
- pass 1 (-+): 0 found - 0 modified | TOTAL: 1
- Iteration Number : 3
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 3
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 3
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Total Number of Modified Voxels = 26 (out of 253765: 0.010246)
- Ambiguous edge configurations...
- mri_pretess done
- mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix
- $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- slice 40: 331 vertices, 371 faces
- slice 50: 5078 vertices, 5341 faces
- slice 60: 14015 vertices, 14396 faces
- slice 70: 25467 vertices, 25875 faces
- slice 80: 36908 vertices, 37355 faces
- slice 90: 48626 vertices, 49004 faces
- slice 100: 60756 vertices, 61146 faces
- slice 110: 72130 vertices, 72516 faces
- slice 120: 83319 vertices, 83720 faces
- slice 130: 94132 vertices, 94519 faces
- slice 140: 104736 vertices, 105132 faces
- slice 150: 114706 vertices, 115067 faces
- slice 160: 123354 vertices, 123680 faces
- slice 170: 130307 vertices, 130553 faces
- slice 180: 135997 vertices, 136219 faces
- slice 190: 140127 vertices, 140268 faces
- slice 200: 141786 vertices, 141818 faces
- slice 210: 141786 vertices, 141818 faces
- slice 220: 141786 vertices, 141818 faces
- slice 230: 141786 vertices, 141818 faces
- slice 240: 141786 vertices, 141818 faces
- slice 250: 141786 vertices, 141818 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...
- 141786 voxel in cpt #1: X=-32 [v=141786,e=425454,f=283636] located at (28.757198, -17.942865, 38.571156)
- For the whole surface: X=-32 [v=141786,e=425454,f=283636]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Smooth1 rh Thu Aug 8 21:00:33 CEST 2013
- mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 21:00:38 CEST 2013
- mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts
- avg radius = 46.8 mm, total surface area = 73891 mm^2
- writing inflated surface to ../surf/rh.inflated.nofix
- inflation took 0.6 minutes
- Not saving sulc
-
step 000: RMS=0.103 (target=0.015)
step 005: RMS=0.075 (target=0.015)
step 010: RMS=0.054 (target=0.015)
step 015: RMS=0.045 (target=0.015)
step 020: RMS=0.040 (target=0.015)
step 025: RMS=0.034 (target=0.015)
step 030: RMS=0.030 (target=0.015)
step 035: RMS=0.028 (target=0.015)
step 040: RMS=0.026 (target=0.015)
step 045: RMS=0.025 (target=0.015)
step 050: RMS=0.023 (target=0.015)
step 055: RMS=0.024 (target=0.015)
step 060: RMS=0.023 (target=0.015)
- inflation complete.
- Not saving sulc
- #--------------------------------------------
- #@# QSphere rh Thu Aug 8 21:01:13 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts
- mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix
- doing quick spherical unfolding.
- setting seed for random number genererator to 1234
- $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading original vertex positions...
- unfolding cortex into spherical form...
- surface projected - minimizing metric distortion...
- vertex spacing 0.97 +- 0.56 (0.00-->6.33) (max @ vno 107641 --> 108659)
- face area 0.03 +- 0.03 (-0.07-->0.62)
- scaling brain by 0.315...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=176.101, avgs=0
- 005/300: dt: 0.9000, rms radial error=175.844, avgs=0
- 010/300: dt: 0.9000, rms radial error=175.293, avgs=0
- 015/300: dt: 0.9000, rms radial error=174.567, avgs=0
- 020/300: dt: 0.9000, rms radial error=173.741, avgs=0
- 025/300: dt: 0.9000, rms radial error=172.857, avgs=0
- 030/300: dt: 0.9000, rms radial error=171.941, avgs=0
- 035/300: dt: 0.9000, rms radial error=171.008, avgs=0
- 040/300: dt: 0.9000, rms radial error=170.068, avgs=0
- 045/300: dt: 0.9000, rms radial error=169.126, avgs=0
- 050/300: dt: 0.9000, rms radial error=168.185, avgs=0
- 055/300: dt: 0.9000, rms radial error=167.246, avgs=0
- 060/300: dt: 0.9000, rms radial error=166.311, avgs=0
- 065/300: dt: 0.9000, rms radial error=165.381, avgs=0
- 070/300: dt: 0.9000, rms radial error=164.455, avgs=0
- 075/300: dt: 0.9000, rms radial error=163.533, avgs=0
- 080/300: dt: 0.9000, rms radial error=162.617, avgs=0
- 085/300: dt: 0.9000, rms radial error=161.705, avgs=0
- 090/300: dt: 0.9000, rms radial error=160.799, avgs=0
- 095/300: dt: 0.9000, rms radial error=159.898, avgs=0
- 100/300: dt: 0.9000, rms radial error=159.001, avgs=0
- 105/300: dt: 0.9000, rms radial error=158.109, avgs=0
- 110/300: dt: 0.9000, rms radial error=157.222, avgs=0
- 115/300: dt: 0.9000, rms radial error=156.340, avgs=0
- 120/300: dt: 0.9000, rms radial error=155.463, avgs=0
- 125/300: dt: 0.9000, rms radial error=154.590, avgs=0
- 130/300: dt: 0.9000, rms radial error=153.722, avgs=0
- 135/300: dt: 0.9000, rms radial error=152.859, avgs=0
- 140/300: dt: 0.9000, rms radial error=152.001, avgs=0
- 145/300: dt: 0.9000, rms radial error=151.148, avgs=0
- 150/300: dt: 0.9000, rms radial error=150.299, avgs=0
- 155/300: dt: 0.9000, rms radial error=149.455, avgs=0
- 160/300: dt: 0.9000, rms radial error=148.615, avgs=0
- 165/300: dt: 0.9000, rms radial error=147.781, avgs=0
- 170/300: dt: 0.9000, rms radial error=146.951, avgs=0
- 175/300: dt: 0.9000, rms radial error=146.125, avgs=0
- 180/300: dt: 0.9000, rms radial error=145.304, avgs=0
- 185/300: dt: 0.9000, rms radial error=144.488, avgs=0
- 190/300: dt: 0.9000, rms radial error=143.676, avgs=0
- 195/300: dt: 0.9000, rms radial error=142.869, avgs=0
- 200/300: dt: 0.9000, rms radial error=142.066, avgs=0
- 205/300: dt: 0.9000, rms radial error=141.267, avgs=0
- 210/300: dt: 0.9000, rms radial error=140.473, avgs=0
- 215/300: dt: 0.9000, rms radial error=139.684, avgs=0
- 220/300: dt: 0.9000, rms radial error=138.898, avgs=0
- 225/300: dt: 0.9000, rms radial error=138.117, avgs=0
- 230/300: dt: 0.9000, rms radial error=137.340, avgs=0
- 235/300: dt: 0.9000, rms radial error=136.568, avgs=0
- 240/300: dt: 0.9000, rms radial error=135.799, avgs=0
- 245/300: dt: 0.9000, rms radial error=135.035, avgs=0
- 250/300: dt: 0.9000, rms radial error=134.276, avgs=0
- 255/300: dt: 0.9000, rms radial error=133.520, avgs=0
- 260/300: dt: 0.9000, rms radial error=132.769, avgs=0
- 265/300: dt: 0.9000, rms radial error=132.022, avgs=0
- 270/300: dt: 0.9000, rms radial error=131.279, avgs=0
- 275/300: dt: 0.9000, rms radial error=130.540, avgs=0
- 280/300: dt: 0.9000, rms radial error=129.805, avgs=0
- 285/300: dt: 0.9000, rms radial error=129.074, avgs=0
- 290/300: dt: 0.9000, rms radial error=128.348, avgs=0
- 295/300: dt: 0.9000, rms radial error=127.625, avgs=0
- 300/300: dt: 0.9000, rms radial error=126.906, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 16544.76
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00012
- epoch 2 (K=40.0), pass 1, starting sse = 2751.23
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00011
- epoch 3 (K=160.0), pass 1, starting sse = 277.17
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.11/12 = 0.00932
- epoch 4 (K=640.0), pass 1, starting sse = 14.00
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.08/13 = 0.00601
- final writing spherical brain to ../surf/rh.qsphere.nofix
- spherical transformation took 0.08 hours
- distance error %100000.00
- #--------------------------------------------
- #@# Fix Topology rh Thu Aug 8 21:06:10 CEST 2013
- cp ../surf/rh.orig.nofix ../surf/rh.orig
- cp ../surf/rh.inflated.nofix ../surf/rh.inflated
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts
- mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub018 rh
- reading spherical homeomorphism from 'qsphere.nofix'
- using genetic algorithm with optimized parameters
- setting seed for random number genererator to 1234
- *************************************************************
- Topology Correction Parameters
- retessellation mode: genetic search
- number of patches/generation : 10
- number of generations : 10
- surface mri loglikelihood coefficient : 1.0
- volume mri loglikelihood coefficient : 10.0
- normal dot loglikelihood coefficient : 1.0
- quadratic curvature loglikelihood coefficient : 1.0
- volume resolution : 2
- eliminate vertices during search : 1
- initial patch selection : 1
- select all defect vertices : 0
- ordering dependant retessellation: 0
- use precomputed edge table : 0
- smooth retessellated patch : 2
- match retessellated patch : 1
- verbose mode : 0
- *************************************************************
- INFO: assuming .mgz format
- $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- before topology correction, eno=-32 (nv=141786, nf=283636, ne=425454, g=17)
- using quasi-homeomorphic spherical map to tessellate cortical surface...
- Correction of the Topology
- Finding true center and radius of Spherical Surface...done
- Surface centered at (0,0,0) with radius 100.0 in 7 iterations
- marking ambiguous vertices...
- 2360 ambiguous faces found in tessellation
- segmenting defects...
- 29 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- 29 defects to be corrected
- 0 vertices coincident
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -9.8497 (-4.9249)
- -vertex loglikelihood: -6.7026 (-3.3513)
- -normal dot loglikelihood: -3.6949 (-3.6949)
- -quad curv loglikelihood: -6.4290 (-3.2145)
- Total Loglikelihood : -26.6762
- CORRECTING DEFECT 0 (vertices=46, convex hull=88)
- After retessellation of defect 0, euler #=-26 (140321,420356,280009) : difference with theory (-26) = 0
- CORRECTING DEFECT 1 (vertices=44, convex hull=81)
- After retessellation of defect 1, euler #=-25 (140339,420441,280077) : difference with theory (-25) = 0
- CORRECTING DEFECT 2 (vertices=18, convex hull=59)
- After retessellation of defect 2, euler #=-24 (140347,420484,280113) : difference with theory (-24) = 0
- CORRECTING DEFECT 3 (vertices=58, convex hull=47)
- After retessellation of defect 3, euler #=-23 (140360,420540,280157) : difference with theory (-23) = 0
- CORRECTING DEFECT 4 (vertices=39, convex hull=80)
- After retessellation of defect 4, euler #=-22 (140385,420648,280241) : difference with theory (-22) = 0
- CORRECTING DEFECT 5 (vertices=35, convex hull=66)
- After retessellation of defect 5, euler #=-21 (140407,420739,280311) : difference with theory (-21) = 0
- CORRECTING DEFECT 6 (vertices=37, convex hull=52)
- After retessellation of defect 6, euler #=-20 (140425,420813,280368) : difference with theory (-20) = 0
- CORRECTING DEFECT 7 (vertices=24, convex hull=56)
- After retessellation of defect 7, euler #=-19 (140437,420870,280414) : difference with theory (-19) = 0
- CORRECTING DEFECT 8 (vertices=29, convex hull=29)
- After retessellation of defect 8, euler #=-18 (140442,420898,280438) : difference with theory (-18) = 0
- CORRECTING DEFECT 9 (vertices=30, convex hull=24)
- After retessellation of defect 9, euler #=-17 (140447,420921,280457) : difference with theory (-17) = 0
- CORRECTING DEFECT 10 (vertices=7, convex hull=18)
- After retessellation of defect 10, euler #=-16 (140449,420933,280468) : difference with theory (-16) = 0
- CORRECTING DEFECT 11 (vertices=13, convex hull=27)
- After retessellation of defect 11, euler #=-15 (140450,420946,280481) : difference with theory (-15) = 0
- CORRECTING DEFECT 12 (vertices=17, convex hull=18)
- After retessellation of defect 12, euler #=-14 (140451,420957,280492) : difference with theory (-14) = 0
- CORRECTING DEFECT 13 (vertices=45, convex hull=81)
- After retessellation of defect 13, euler #=-13 (140471,421051,280567) : difference with theory (-13) = 0
- CORRECTING DEFECT 14 (vertices=98, convex hull=57)
- After retessellation of defect 14, euler #=-12 (140486,421117,280619) : difference with theory (-12) = 0
- CORRECTING DEFECT 15 (vertices=41, convex hull=25)
- After retessellation of defect 15, euler #=-11 (140492,421141,280638) : difference with theory (-11) = 0
- CORRECTING DEFECT 16 (vertices=64, convex hull=94)
- After retessellation of defect 16, euler #=-10 (140505,421217,280702) : difference with theory (-10) = 0
- CORRECTING DEFECT 17 (vertices=357, convex hull=73)
- After retessellation of defect 17, euler #=-9 (140519,421291,280763) : difference with theory (-9) = 0
- CORRECTING DEFECT 18 (vertices=6, convex hull=26)
- After retessellation of defect 18, euler #=-8 (140522,421307,280777) : difference with theory (-8) = 0
- CORRECTING DEFECT 19 (vertices=20, convex hull=49)
- After retessellation of defect 19, euler #=-7 (140532,421356,280817) : difference with theory (-7) = 0
- CORRECTING DEFECT 20 (vertices=103, convex hull=89)
- After retessellation of defect 20, euler #=-6 (140549,421453,280898) : difference with theory (-6) = 0
- CORRECTING DEFECT 21 (vertices=93, convex hull=51)
- After retessellation of defect 21, euler #=-5 (140566,421523,280952) : difference with theory (-5) = 0
- CORRECTING DEFECT 22 (vertices=25, convex hull=65)
- After retessellation of defect 22, euler #=-4 (140578,421581,280999) : difference with theory (-4) = 0
- CORRECTING DEFECT 23 (vertices=54, convex hull=61)
- After retessellation of defect 23, euler #=-3 (140605,421686,281078) : difference with theory (-3) = 0
- CORRECTING DEFECT 24 (vertices=42, convex hull=85)
- After retessellation of defect 24, euler #=-2 (140630,421799,281167) : difference with theory (-2) = 0
- CORRECTING DEFECT 25 (vertices=11, convex hull=25)
- After retessellation of defect 25, euler #=-1 (140634,421818,281183) : difference with theory (-1) = 0
- CORRECTING DEFECT 26 (vertices=56, convex hull=82)
- After retessellation of defect 26, euler #=0 (140655,421917,281262) : difference with theory (0) = 0
- CORRECTING DEFECT 27 (vertices=5, convex hull=16)
- After retessellation of defect 27, euler #=1 (140655,421923,281269) : difference with theory (1) = 0
- CORRECTING DEFECT 28 (vertices=58, convex hull=95)
- After retessellation of defect 28, euler #=2 (140674,422016,281344) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.88 +- 0.22 (0.04-->8.60) (max @ vno 104127 --> 112533)
- face area 0.00 +- 0.00 (0.00-->0.00)
- performing soap bubble on retessellated vertices for 0 iterations...
- vertex spacing 0.88 +- 0.22 (0.04-->8.60) (max @ vno 104127 --> 112533)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 91 mutations (32.5%), 189 crossovers (67.5%), 81 vertices were eliminated
- building final representation...
- 1112 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=140674, nf=281344, ne=422016, g=0)
- writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 16.9 minutes
- 0 defective edges
- removing intersecting faces
- 000: 118 intersecting
- mris_euler_number ../surf/rh.orig
- euler # = v-e+f = 2g-2: 140674 - 422016 + 281344 = 2 --> 0 holes
- F =2V-4: 281344 = 281348-4 (0)
- 2E=3F: 844032 = 844032 (0)
- total defect index = 0
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts
- mris_remove_intersection ../surf/rh.orig ../surf/rh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 4 intersecting
- writing corrected surface to ../surf/rh.orig
- rm ../surf/rh.inflated
- #--------------------------------------------
- #@# Make White Surf rh Thu Aug 8 21:23:13 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts
- mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub018 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/sub018/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/wm.mgz...
- 18329 bright wm thresholded.
- 358 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.orig...
- computing class statistics...
- border white: 252064 voxels (1.50%)
- border gray 291583 voxels (1.74%)
- WM (92.0): 92.8 +- 10.3 [70.0 --> 110.0]
- GM (75.0) : 73.1 +- 12.8 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 46.2 (was 70)
- setting MAX_BORDER_WHITE to 115.3 (was 105)
- setting MIN_BORDER_WHITE to 59.0 (was 85)
- setting MAX_CSF to 33.3 (was 40)
- setting MAX_GRAY to 94.7 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 52.6 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 20.5 (was 40)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.81 +- 0.22 (0.03-->3.39) (max @ vno 112533 --> 112541)
- face area 0.28 +- 0.12 (0.00-->1.58)
- mean absolute distance = 0.67 +- 0.80
- 3416 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=59
- mean inside = 92.3, mean outside = 68.0
- smoothing surface for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 3 vertex label from ripped group
- mean border=72.1, 17 (17) missing vertices, mean dist 0.4 [0.5 (%31.1)->0.8 (%68.9))]
- %69 local maxima, %26 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 (0.06-->3.76) (max @ vno 112533 --> 112541)
- face area 0.28 +- 0.13 (0.00-->2.08)
- mean absolute distance = 0.30 +- 0.45
- 2693 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=7638578.5, rms=13.66
- 001: dt: 0.5000, sse=7735224.0, rms=9.914 (0.000%)
- 002: dt: 0.5000, sse=7946793.0, rms=7.765 (0.000%)
- 003: dt: 0.5000, sse=8078725.0, rms=6.376 (0.000%)
- 004: dt: 0.5000, sse=8303485.0, rms=5.534 (0.000%)
- 005: dt: 0.5000, sse=8364559.5, rms=5.026 (0.000%)
- 006: dt: 0.5000, sse=8479828.0, rms=4.769 (0.000%)
- 007: dt: 0.5000, sse=8483572.0, rms=4.601 (0.000%)
- 008: dt: 0.5000, sse=8509081.0, rms=4.524 (0.000%)
- 009: dt: 0.5000, sse=8453526.0, rms=4.444 (0.000%)
- rms = 4.41, time step reduction 1 of 3 to 0.250...
- 010: dt: 0.5000, sse=8477690.0, rms=4.412 (0.000%)
- 011: dt: 0.2500, sse=5390386.5, rms=3.088 (0.000%)
- 012: dt: 0.2500, sse=4957025.5, rms=2.644 (0.000%)
- 013: dt: 0.2500, sse=4668622.5, rms=2.543 (0.000%)
- 014: dt: 0.2500, sse=4598623.5, rms=2.448 (0.000%)
- rms = 2.42, time step reduction 2 of 3 to 0.125...
- 015: dt: 0.2500, sse=4492008.5, rms=2.416 (0.000%)
- 016: dt: 0.1250, sse=4263743.5, rms=2.179 (0.000%)
- rms = 2.15, time step reduction 3 of 3 to 0.062...
- 017: dt: 0.1250, sse=4217011.5, rms=2.147 (0.000%)
- positioning took 2.2 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 1 vertex label from ripped group
- removing 2 vertex label from ripped group
- mean border=76.7, 42 (0) missing vertices, mean dist -0.2 [0.3 (%78.9)->0.2 (%21.1))]
- %83 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.90 +- 0.25 (0.09-->3.79) (max @ vno 109649 --> 108789)
- face area 0.35 +- 0.17 (0.00-->2.94)
- mean absolute distance = 0.21 +- 0.28
- 2483 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5232417.5, rms=6.11
- 018: dt: 0.5000, sse=5443994.5, rms=4.119 (0.000%)
- rms = 4.51, time step reduction 1 of 3 to 0.250...
- 019: dt: 0.2500, sse=4946836.5, rms=2.960 (0.000%)
- 020: dt: 0.2500, sse=4758923.0, rms=2.385 (0.000%)
- 021: dt: 0.2500, sse=4709420.0, rms=2.017 (0.000%)
- rms = 1.98, time step reduction 2 of 3 to 0.125...
- 022: dt: 0.2500, sse=4680545.0, rms=1.983 (0.000%)
- 023: dt: 0.1250, sse=4513012.0, rms=1.752 (0.000%)
- rms = 1.72, time step reduction 3 of 3 to 0.062...
- 024: dt: 0.1250, sse=4461856.0, rms=1.718 (0.000%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 4 vertex label from ripped group
- mean border=80.1, 38 (0) missing vertices, mean dist -0.1 [0.2 (%76.5)->0.2 (%23.5))]
- %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.25 (0.11-->3.97) (max @ vno 105781 --> 105775)
- face area 0.34 +- 0.16 (0.00-->2.97)
- mean absolute distance = 0.16 +- 0.23
- 2695 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4872873.5, rms=4.37
- 025: dt: 0.5000, sse=5245514.0, rms=4.128 (0.000%)
- rms = 4.38, time step reduction 1 of 3 to 0.250...
- 026: dt: 0.2500, sse=4759571.5, rms=2.605 (0.000%)
- 027: dt: 0.2500, sse=4629446.5, rms=2.143 (0.000%)
- 028: dt: 0.2500, sse=4698822.5, rms=1.812 (0.000%)
- rms = 1.87, time step reduction 2 of 3 to 0.125...
- 029: dt: 0.1250, sse=4629751.5, rms=1.678 (0.000%)
- 030: dt: 0.1250, sse=4536684.0, rms=1.494 (0.000%)
- rms = 1.48, time step reduction 3 of 3 to 0.062...
- 031: dt: 0.1250, sse=4498084.5, rms=1.477 (0.000%)
- positioning took 1.1 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 1 vertex label from ripped group
- removing 1 vertex label from ripped group
- mean border=81.1, 43 (0) missing vertices, mean dist -0.0 [0.2 (%58.0)->0.2 (%42.0))]
- %92 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- writing white matter surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.white...
- writing smoothed curvature to rh.curv
- 000: dt: 0.0000, sse=4525111.0, rms=1.87
- rms = 2.83, time step reduction 1 of 3 to 0.250...
- 032: dt: 0.2500, sse=4622103.5, rms=1.231 (0.000%)
- 033: dt: 0.2500, sse=4792168.0, rms=1.095 (0.000%)
- rms = 1.10, time step reduction 2 of 3 to 0.125...
- rms = 1.08, time step reduction 3 of 3 to 0.062...
- 034: dt: 0.1250, sse=4794696.5, rms=1.083 (0.000%)
- positioning took 0.6 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- generating cortex label...
- 21 non-cortical segments detected
- only using segment with 1862 vertices
- erasing segment 1 (vno[0] = 85895)
- erasing segment 2 (vno[0] = 90215)
- erasing segment 3 (vno[0] = 91287)
- erasing segment 4 (vno[0] = 92317)
- erasing segment 5 (vno[0] = 93344)
- erasing segment 6 (vno[0] = 98491)
- erasing segment 7 (vno[0] = 101512)
- erasing segment 8 (vno[0] = 102484)
- erasing segment 9 (vno[0] = 103653)
- erasing segment 10 (vno[0] = 103691)
- erasing segment 11 (vno[0] = 103760)
- erasing segment 12 (vno[0] = 104760)
- erasing segment 13 (vno[0] = 104772)
- erasing segment 14 (vno[0] = 104776)
- erasing segment 15 (vno[0] = 108752)
- erasing segment 16 (vno[0] = 110467)
- erasing segment 17 (vno[0] = 113223)
- erasing segment 18 (vno[0] = 114132)
- erasing segment 19 (vno[0] = 114135)
- erasing segment 20 (vno[0] = 114967)
- writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/label/rh.cortex.label...
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.curv
- writing smoothed area to rh.area
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.area
- vertex spacing 0.90 +- 0.25 (0.07-->3.94) (max @ vno 105775 --> 105781)
- face area 0.34 +- 0.16 (0.00-->2.90)
- refinement took 7.2 minutes
- #--------------------------------------------
- #@# Smooth2 rh Thu Aug 8 21:30:26 CEST 2013
- mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts
- smoothing for 3 iterations
- setting seed for random number generator to 1234
- smoothing surface tessellation for 3 iterations...
- smoothing complete - recomputing first and second fundamental forms...
- #--------------------------------------------
- #@# Inflation2 rh Thu Aug 8 21:30:31 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts
- mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated
- avg radius = 47.0 mm, total surface area = 86269 mm^2
- writing inflated surface to ../surf/rh.inflated
- writing sulcal depths to ../surf/rh.sulc
-
step 000: RMS=0.119 (target=0.015)
step 005: RMS=0.082 (target=0.015)
step 010: RMS=0.058 (target=0.015)
step 015: RMS=0.048 (target=0.015)
step 020: RMS=0.040 (target=0.015)
step 025: RMS=0.033 (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=0.017 (target=0.015)
step 050: RMS=0.015 (target=0.015)
- inflation complete.
- inflation took 0.6 minutes
- mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated
- normalizing curvature values.
- averaging curvature patterns 5 times.
- sampling 10 neighbors out to a distance of 10 mm
- 194 vertices thresholded to be in k1 ~ [-0.45 0.28], k2 ~ [-0.13 0.09]
- total integrated curvature = 0.497*4pi (6.245) --> 1 handles
- ICI = 1.6, FI = 12.1, variation=197.838
- 124 vertices thresholded to be in [-0.01 0.03]
- writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level
- curvature mean = 0.000, std = 0.001
- 148 vertices thresholded to be in [-0.20 0.15]
- done.
- writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.017, std = 0.025
- done.
- #-----------------------------------------
- #@# Curvature Stats rh Thu Aug 8 21:32:56 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub018 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 [ sub018/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 [ 290 ]
- Gb_filter = 0
- WARN: S lookup min: -0.858727
- WARN: S explicit min: 0.000000 vertex = 57
- #--------------------------------------------
- #@# Sphere rh Thu Aug 8 21:33:01 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 0.291...
- MRISunfold() max_passes = 1 -------
- tol=5.0e-01, sigma=0.0, host=snake, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
- using quadratic fit line minimization
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 1.000000
- desired_rms_height -1.000000
- momentum 0.900000
- nbhd_size 7
- max_nbrs 8
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 1234
- --------------------
- mrisRemoveNegativeArea()
- pass 1: epoch 1 of 3 starting distance error %19.39
- pass 1: epoch 2 of 3 starting distance error %19.36
- unfolding complete - removing small folds...
- starting distance error %19.25
- removing remaining folds...
- final distance error %19.28
- MRISunfold() return, current seed 1234
- writing spherical brain to ../surf/rh.sphere
- spherical transformation took 0.92 hours
- #--------------------------------------------
- #@# Surf Reg rh Thu Aug 8 22:28:10 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 = 0.571
- curvature mean = 0.025, std = 0.941
- curvature mean = 0.024, std = 0.846
- Starting MRISrigidBodyAlignGlobal()
- d=32.00 min @ (8.00, 0.00, 0.00) sse = 330420.8, tmin=2.3634
- d=16.00 min @ (-4.00, -4.00, -4.00) sse = 290384.7, tmin=3.5345
- d=8.00 min @ (2.00, 0.00, 2.00) sse = 283195.0, tmin=4.8137
- d=4.00 min @ (0.00, -1.00, 0.00) sse = 281545.2, tmin=6.1740
- d=1.00 min @ (0.00, 0.25, -0.25) sse = 281422.7, tmin=8.8672
- d=0.50 min @ (-0.12, -0.12, 0.00) sse = 281390.3, tmin=10.1250
- tol=1.0e+00, sigma=0.5, host=snake, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
- using quadratic fit line minimization
- MRISrigidBodyAlignGlobal() done 10.13 min
- curvature mean = 0.009, std = 0.945
- curvature mean = 0.012, std = 0.933
- curvature mean = 0.005, std = 0.953
- curvature mean = 0.006, std = 0.969
- curvature mean = 0.004, std = 0.952
- curvature mean = 0.002, std = 0.987
- 2 Reading smoothwm
- curvature mean = -0.026, std = 0.309
- curvature mean = 0.005, std = 0.070
- curvature mean = 0.074, std = 0.321
- curvature mean = 0.006, std = 0.083
- curvature mean = 0.037, std = 0.512
- curvature mean = 0.006, std = 0.089
- curvature mean = 0.020, std = 0.655
- curvature mean = 0.006, std = 0.092
- curvature mean = 0.007, std = 0.771
- MRISregister() return, current seed 0
- writing registered surface to ../surf/rh.sphere.reg...
- expanding nbhd size to 1
- #--------------------------------------------
- #@# Jacobian white rh Thu Aug 8 22:58:53 CEST 2013
- mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white
- reading surface from ../surf/rh.white...
- writing curvature file ../surf/rh.jacobian_white
- #--------------------------------------------
- #@# AvgCurv rh Thu Aug 8 22:58:56 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts
- mrisp_paint -a 5 /opt/freesurfer/5.3.0/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv
- averaging curvature patterns 5 times...
- reading surface from ../surf/rh.sphere.reg...
- reading template parameterization from /opt/freesurfer/5.3.0/average/rh.average.curvature.filled.buckner40.tif...
- writing curvature file to ../surf/rh.avg_curv...
- #-----------------------------------------
- #@# Cortical Parc rh Thu Aug 8 22:58:58 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub018 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...
- 1248 labels changed using aseg
- relabeling using gibbs priors...
- 000: 3001 changed, 140674 examined...
- 001: 700 changed, 12875 examined...
- 002: 154 changed, 3895 examined...
- 003: 54 changed, 949 examined...
- 004: 22 changed, 332 examined...
- 005: 11 changed, 142 examined...
- 006: 11 changed, 63 examined...
- 007: 4 changed, 52 examined...
- 008: 1 changed, 22 examined...
- 009: 0 changed, 7 examined...
- 204 labels changed using aseg
- 000: 115 total segments, 78 labels (379 vertices) changed
- 001: 42 total segments, 5 labels (21 vertices) changed
- 002: 37 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 56 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 1633 vertices marked for relabeling...
- 1633 labels changed in reclassification.
- writing output to ../label/rh.aparc.annot...
- classification took 1 minutes and 6 seconds.
- #--------------------------------------------
- #@# Make Pial Surf rh Thu Aug 8 23:00:04 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts
- mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub018 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/sub018/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/wm.mgz...
- 18329 bright wm thresholded.
- 358 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.orig...
- computing class statistics...
- border white: 252064 voxels (1.50%)
- border gray 291583 voxels (1.74%)
- WM (92.0): 92.8 +- 10.3 [70.0 --> 110.0]
- GM (75.0) : 73.1 +- 12.8 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 46.2 (was 70)
- setting MAX_BORDER_WHITE to 115.3 (was 105)
- setting MIN_BORDER_WHITE to 59.0 (was 85)
- setting MAX_CSF to 33.3 (was 40)
- setting MAX_GRAY to 94.7 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 52.6 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 20.5 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=105, GM=59
- mean inside = 92.3, mean outside = 68.0
- 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/sub018/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.81 +- 0.22 (0.03-->3.39) (max @ vno 112533 --> 112541)
- face area 0.28 +- 0.12 (0.00-->1.58)
- mean absolute distance = 0.68 +- 0.81
- 3552 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 14 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 1 with 4 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 3 with 4 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 5 with 554 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 6 with 3 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 7 with 4 points - only 0.00% unknown
- deleting segment 8 with 7 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 9 with 3 points - only 0.00% unknown
- deleting segment 10 with 11 points - only 0.00% unknown
- mean border=72.1, 27 (27) missing vertices, mean dist 0.4 [0.5 (%31.1)->0.8 (%68.9))]
- %70 local maxima, %26 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 (0.06-->3.76) (max @ vno 112533 --> 112541)
- face area 0.28 +- 0.13 (0.00-->1.65)
- mean absolute distance = 0.31 +- 0.46
- 2809 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=7659028.0, rms=13.64
- 001: dt: 0.5000, sse=7760990.0, rms=9.904 (0.000%)
- 002: dt: 0.5000, sse=7975447.5, rms=7.757 (0.000%)
- 003: dt: 0.5000, sse=8111912.0, rms=6.371 (0.000%)
- 004: dt: 0.5000, sse=8339576.0, rms=5.532 (0.000%)
- 005: dt: 0.5000, sse=8403690.0, rms=5.024 (0.000%)
- 006: dt: 0.5000, sse=8516842.0, rms=4.767 (0.000%)
- 007: dt: 0.5000, sse=8522448.0, rms=4.599 (0.000%)
- 008: dt: 0.5000, sse=8553356.0, rms=4.523 (0.000%)
- 009: dt: 0.5000, sse=8496498.0, rms=4.443 (0.000%)
- rms = 4.41, time step reduction 1 of 3 to 0.250...
- 010: dt: 0.5000, sse=8521070.0, rms=4.411 (0.000%)
- 011: dt: 0.2500, sse=5420795.0, rms=3.090 (0.000%)
- 012: dt: 0.2500, sse=4984787.5, rms=2.647 (0.000%)
- 013: dt: 0.2500, sse=4696399.0, rms=2.547 (0.000%)
- 014: dt: 0.2500, sse=4625884.0, rms=2.452 (0.000%)
- rms = 2.42, time step reduction 2 of 3 to 0.125...
- 015: dt: 0.2500, sse=4521661.0, rms=2.420 (0.000%)
- 016: dt: 0.1250, sse=4292207.0, rms=2.185 (0.000%)
- rms = 2.15, time step reduction 3 of 3 to 0.062...
- 017: dt: 0.1250, sse=4244613.5, rms=2.153 (0.000%)
- positioning took 2.2 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 19 points - only 0.00% unknown
- deleting segment 1 with 5 points - only 0.00% unknown
- deleting segment 3 with 9 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 6 with 380 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 7 with 2 points - only 0.00% unknown
- deleting segment 10 with 6 points - only 0.00% unknown
- deleting segment 11 with 6 points - only 0.00% unknown
- deleting segment 12 with 5 points - only 0.00% unknown
- deleting segment 13 with 13 points - only 0.00% unknown
- mean border=76.7, 47 (0) missing vertices, mean dist -0.2 [0.3 (%78.8)->0.2 (%21.2))]
- %83 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.90 +- 0.25 (0.09-->3.79) (max @ vno 109649 --> 108789)
- face area 0.35 +- 0.16 (0.00-->2.26)
- mean absolute distance = 0.21 +- 0.29
- 2620 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5262403.0, rms=6.11
- 018: dt: 0.5000, sse=5477437.5, rms=4.119 (0.000%)
- rms = 4.51, time step reduction 1 of 3 to 0.250...
- 019: dt: 0.2500, sse=4979068.5, rms=2.963 (0.000%)
- 020: dt: 0.2500, sse=4792263.5, rms=2.392 (0.000%)
- 021: dt: 0.2500, sse=4739906.5, rms=2.026 (0.000%)
- rms = 1.99, time step reduction 2 of 3 to 0.125...
- 022: dt: 0.2500, sse=4714875.0, rms=1.991 (0.000%)
- 023: dt: 0.1250, sse=4547834.5, rms=1.762 (0.000%)
- rms = 1.73, time step reduction 3 of 3 to 0.062...
- 024: dt: 0.1250, sse=4497464.5, rms=1.728 (0.000%)
- positioning took 0.9 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 23 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 1 with 4 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 3 with 406 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 4 with 2 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 6 with 5 points - only 0.00% unknown
- deleting segment 7 with 5 points - only 0.00% unknown
- deleting segment 8 with 6 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 9 with 4 points - only 0.00% unknown
- deleting segment 10 with 6 points - only 0.00% unknown
- deleting segment 11 with 14 points - only 0.00% unknown
- mean border=80.1, 50 (0) missing vertices, mean dist -0.1 [0.2 (%76.3)->0.2 (%23.7))]
- %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.25 (0.11-->3.90) (max @ vno 109649 --> 108789)
- face area 0.34 +- 0.16 (0.00-->2.21)
- mean absolute distance = 0.16 +- 0.24
- 2854 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4909105.0, rms=4.37
- 025: dt: 0.5000, sse=5282792.5, rms=4.123 (0.000%)
- rms = 4.38, time step reduction 1 of 3 to 0.250...
- 026: dt: 0.2500, sse=4797796.0, rms=2.606 (0.000%)
- 027: dt: 0.2500, sse=4671445.5, rms=2.146 (0.000%)
- 028: dt: 0.2500, sse=4740144.0, rms=1.818 (0.000%)
- rms = 1.87, time step reduction 2 of 3 to 0.125...
- 029: dt: 0.1250, sse=4671353.0, rms=1.685 (0.000%)
- 030: dt: 0.1250, sse=4579445.0, rms=1.503 (0.000%)
- rms = 1.49, time step reduction 3 of 3 to 0.062...
- 031: dt: 0.1250, sse=4541135.5, rms=1.486 (0.000%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 23 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 1 with 4 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 3 with 404 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 4 with 3 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 6 with 5 points - only 0.00% unknown
- deleting segment 7 with 5 points - only 0.00% unknown
- deleting segment 8 with 6 points - only 0.00% unknown
- deleting segment 9 with 18 points - only 0.00% unknown
- deleting segment 10 with 6 points - only 0.00% unknown
- deleting segment 11 with 15 points - only 0.00% unknown
- mean border=81.1, 62 (0) missing vertices, mean dist -0.0 [0.2 (%58.0)->0.2 (%42.0))]
- %92 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- repositioning cortical surface to gray/csf boundary.
- smoothing T1 volume with sigma = 2.000
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4569562.0, rms=1.88
- rms = 2.83, time step reduction 1 of 3 to 0.250...
- 032: dt: 0.2500, sse=4669610.5, rms=1.244 (0.000%)
- 033: dt: 0.2500, sse=4848851.5, rms=1.105 (0.000%)
- rms = 1.11, time step reduction 2 of 3 to 0.125...
- rms = 1.09, time step reduction 3 of 3 to 0.062...
- 034: dt: 0.1250, sse=4850852.5, rms=1.093 (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=48.7, 46 (46) missing vertices, mean dist 1.7 [1.8 (%0.0)->2.3 (%100.0))]
- %15 local maxima, %55 large gradients and %25 min vals, 1642 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=30324244.0, rms=31.89
- 001: dt: 0.5000, sse=21799216.0, rms=26.441 (0.000%)
- 002: dt: 0.5000, sse=15906418.0, rms=21.922 (0.000%)
- 003: dt: 0.5000, sse=11987753.0, rms=18.262 (0.000%)
- 004: dt: 0.5000, sse=9634395.0, rms=15.373 (0.000%)
- 005: dt: 0.5000, sse=8367373.0, rms=13.175 (0.000%)
- 006: dt: 0.5000, sse=7643142.5, rms=11.511 (0.000%)
- 007: dt: 0.5000, sse=7218855.0, rms=10.131 (0.000%)
- 008: dt: 0.5000, sse=6936126.5, rms=8.862 (0.000%)
- 009: dt: 0.5000, sse=6762184.0, rms=7.687 (0.000%)
- 010: dt: 0.5000, sse=6701401.0, rms=6.633 (0.000%)
- 011: dt: 0.5000, sse=6778396.5, rms=5.817 (0.000%)
- 012: dt: 0.5000, sse=6853216.0, rms=5.210 (0.000%)
- 013: dt: 0.5000, sse=7049942.0, rms=4.811 (0.000%)
- 014: dt: 0.5000, sse=7157293.0, rms=4.558 (0.000%)
- 015: dt: 0.5000, sse=7281402.0, rms=4.409 (0.000%)
- 016: dt: 0.5000, sse=7318152.5, rms=4.275 (0.000%)
- 017: dt: 0.5000, sse=7368391.0, rms=4.210 (0.000%)
- 018: dt: 0.5000, sse=7383507.0, rms=4.136 (0.000%)
- rms = 4.12, time step reduction 1 of 3 to 0.250...
- 019: dt: 0.5000, sse=7414520.5, rms=4.120 (0.000%)
- 020: dt: 0.2500, sse=5230792.5, rms=3.345 (0.000%)
- 021: dt: 0.2500, sse=5021916.5, rms=3.133 (0.000%)
- rms = 3.11, time step reduction 2 of 3 to 0.125...
- 022: dt: 0.2500, sse=4890396.0, rms=3.109 (0.000%)
- 023: dt: 0.1250, sse=4647630.0, rms=2.942 (0.000%)
- rms = 2.92, time step reduction 3 of 3 to 0.062...
- 024: dt: 0.1250, sse=4612350.0, rms=2.923 (0.000%)
- positioning took 3.0 minutes
- mean border=46.3, 908 (3) missing vertices, mean dist 0.1 [0.2 (%47.8)->0.5 (%52.2))]
- %33 local maxima, %42 large gradients and %21 min vals, 536 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=5263673.0, rms=4.84
- 025: dt: 0.5000, sse=5619839.5, rms=4.202 (0.000%)
- rms = 4.20, time step reduction 1 of 3 to 0.250...
- 026: dt: 0.5000, sse=7308819.5, rms=4.198 (0.000%)
- 027: dt: 0.2500, sse=5476913.5, rms=3.310 (0.000%)
- 028: dt: 0.2500, sse=5516556.5, rms=3.060 (0.000%)
- rms = 3.05, time step reduction 2 of 3 to 0.125...
- 029: dt: 0.2500, sse=5368743.0, rms=3.050 (0.000%)
- 030: dt: 0.1250, sse=5169254.5, rms=2.832 (0.000%)
- rms = 2.80, time step reduction 3 of 3 to 0.062...
- 031: dt: 0.1250, sse=5149804.0, rms=2.799 (0.000%)
- positioning took 0.9 minutes
- mean border=43.9, 1070 (2) missing vertices, mean dist 0.1 [0.2 (%37.8)->0.4 (%62.2))]
- %52 local maxima, %23 large gradients and %21 min vals, 668 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=5445441.0, rms=4.23
- rms = 4.24, time step reduction 1 of 3 to 0.250...
- 032: dt: 0.2500, sse=5194419.5, rms=3.559 (0.000%)
- 033: dt: 0.2500, sse=5128623.0, rms=3.096 (0.000%)
- 034: dt: 0.2500, sse=5406338.0, rms=2.976 (0.000%)
- rms = 2.96, time step reduction 2 of 3 to 0.125...
- 035: dt: 0.2500, sse=5458813.0, rms=2.963 (0.000%)
- 036: dt: 0.1250, sse=5262790.0, rms=2.783 (0.000%)
- rms = 2.75, time step reduction 3 of 3 to 0.062...
- 037: dt: 0.1250, sse=5265726.0, rms=2.750 (0.000%)
- positioning took 0.8 minutes
- mean border=42.8, 2160 (1) missing vertices, mean dist 0.0 [0.2 (%46.2)->0.3 (%53.8))]
- %54 local maxima, %19 large gradients and %21 min vals, 522 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/sub018/surf/rh.pial...
- writing smoothed curvature to rh.curv.pial
- 000: dt: 0.0000, sse=5320184.0, rms=3.11
- rms = 3.95, time step reduction 1 of 3 to 0.250...
- 038: dt: 0.2500, sse=5198895.0, rms=2.829 (0.000%)
- 039: dt: 0.2500, sse=5420553.5, rms=2.766 (0.000%)
- rms = 2.76, time step reduction 2 of 3 to 0.125...
- 040: dt: 0.2500, sse=5492392.5, rms=2.756 (0.000%)
- 041: dt: 0.1250, sse=5391824.0, rms=2.619 (0.000%)
- rms = 2.60, time step reduction 3 of 3 to 0.062...
- 042: dt: 0.1250, sse=5402777.0, rms=2.598 (0.000%)
- positioning took 0.7 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.curv.pial
- writing smoothed area to rh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.area.pial
- vertex spacing 1.02 +- 0.43 (0.07-->7.56) (max @ vno 95616 --> 94572)
- face area 0.41 +- 0.30 (0.00-->4.80)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 140674 vertices processed
- 25000 of 140674 vertices processed
- 50000 of 140674 vertices processed
- 75000 of 140674 vertices processed
- 100000 of 140674 vertices processed
- 125000 of 140674 vertices processed
- 0 of 140674 vertices processed
- 25000 of 140674 vertices processed
- 50000 of 140674 vertices processed
- 75000 of 140674 vertices processed
- 100000 of 140674 vertices processed
- 125000 of 140674 vertices processed
- thickness calculation complete, 430:749 truncations.
- 30437 vertices at 0 distance
- 92836 vertices at 1 distance
- 92683 vertices at 2 distance
- 38465 vertices at 3 distance
- 10644 vertices at 4 distance
- 2743 vertices at 5 distance
- 834 vertices at 6 distance
- 292 vertices at 7 distance
- 129 vertices at 8 distance
- 71 vertices at 9 distance
- 37 vertices at 10 distance
- 30 vertices at 11 distance
- 27 vertices at 12 distance
- 30 vertices at 13 distance
- 19 vertices at 14 distance
- 16 vertices at 15 distance
- 18 vertices at 16 distance
- 21 vertices at 17 distance
- 15 vertices at 18 distance
- 9 vertices at 19 distance
- 10 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.thickness
- positioning took 14.4 minutes
- #--------------------------------------------
- #@# Surf Volume rh Thu Aug 8 23:14:27 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf
- mris_calc -o rh.area.mid rh.area add rh.area.pial
- Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o rh.area.mid rh.area.mid div 2
- Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o rh.volume rh.area.mid mul rh.thickness
- Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ]
- #-----------------------------------------
- #@# WM/GM Contrast rh Thu Aug 8 23:14:33 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts
- pctsurfcon --s sub018 --rh-only
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts/pctsurfcon.log
- Thu Aug 8 23:14:35 CEST 2013
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/tmp.pctsurfcon.17811/rh.wm.mgh --regheader sub018 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/label/rh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 = 109099
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/label/rh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/tmp.pctsurfcon.17811/rh.wm.mgh
- Dim: 140674 1 1
- mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/tmp.pctsurfcon.17811/rh.gm.mgh --projfrac 0.3 --regheader sub018 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/label/rh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.white
- Done reading source surface
- Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 = 125400
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/label/rh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/tmp.pctsurfcon.17811/rh.gm.mgh
- Dim: 140674 1 1
- mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/tmp.pctsurfcon.17811/rh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/tmp.pctsurfcon.17811/rh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/surf/rh.w-g.pct.mgh
- mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.w-g.pct.mgh --annot sub018 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/surf/rh.w-g.pct.mgh --annot sub018 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/surf/rh.w-g.pct.mgh
- Vertex Area is 0.671661 mm^3
- Generating list of segmentation ids
- Found 36 segmentations
- Computing statistics for each segmentation
- 0 2000 unknown 0 0.000
- 1 2001 bankssts 1434 1010.913
- 2 2002 caudalanteriorcingulate 1126 779.239
- 3 2003 caudalmiddlefrontal 2468 1663.740
- 4 2004 corpuscallosum 0 0.000
- 5 2005 cuneus 2184 1480.223
- 6 2006 entorhinal 543 417.656
- 7 2007 fusiform 5301 3632.559
- 8 2008 inferiorparietal 8787 5906.465
- 9 2009 inferiortemporal 5251 3472.157
- 10 2010 isthmuscingulate 1300 849.411
- 11 2011 lateraloccipital 6951 4616.411
- 12 2012 lateralorbitofrontal 4082 2812.683
- 13 2013 lingual 3755 2601.209
- 14 2014 medialorbitofrontal 2900 1936.270
- 15 2015 middletemporal 5356 3735.882
- 16 2016 parahippocampal 1018 700.393
- 17 2017 paracentral 2628 1761.580
- 18 2018 parsopercularis 1907 1300.100
- 19 2019 parsorbitalis 1415 959.741
- 20 2020 parstriangularis 2410 1635.932
- 21 2021 pericalcarine 1888 1307.391
- 22 2022 postcentral 6371 4168.021
- 23 2023 posteriorcingulate 1993 1311.019
- 24 2024 precentral 7540 4920.251
- 25 2025 precuneus 5646 3797.060
- 26 2026 rostralanteriorcingulate 1100 729.041
- 27 2027 rostralmiddlefrontal 8852 6071.164
- 28 2028 superiorfrontal 11828 8067.851
- 29 2029 superiorparietal 8476 5627.131
- 30 2030 superiortemporal 6446 4263.047
- 31 2031 supramarginal 6581 4451.633
- 32 2032 frontalpole 499 338.852
- 33 2033 temporalpole 670 442.973
- 34 2034 transversetemporal 590 365.158
- 35 2035 insula 3241 2161.131
- Reporting on 34 segmentations
- mri_segstats done
- Cleaning up
- #-----------------------------------------
- #@# Parcellation Stats rh Thu Aug 8 23:14:54 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 sub018 rh white
- computing statistics for each annotation in ../label/rh.aparc.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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
- 1434 1011 2845 2.668 0.433 0.129 0.034 15 2.1 bankssts
- 1126 779 2237 2.516 0.836 0.158 0.044 21 2.0 caudalanteriorcingulate
- 2468 1664 4367 2.449 0.398 0.125 0.036 28 3.8 caudalmiddlefrontal
- 2184 1480 3241 1.953 0.389 0.178 0.077 56 6.4 cuneus
- 543 418 1858 3.013 0.881 0.172 0.065 10 1.5 entorhinal
- 5301 3633 11180 2.664 0.546 0.158 0.065 105 14.4 fusiform
- 8787 5906 16518 2.452 0.502 0.149 0.061 186 20.5 inferiorparietal
- 5251 3472 9976 2.377 0.720 0.163 0.105 175 19.8 inferiortemporal
- 1300 849 2238 2.409 0.792 0.165 0.066 29 3.3 isthmuscingulate
- 6951 4616 11391 2.190 0.444 0.169 0.079 165 20.4 lateraloccipital
- 4082 2813 8628 2.760 0.665 0.159 0.092 94 11.0 lateralorbitofrontal
- 3755 2601 6116 2.062 0.500 0.171 0.116 280 19.6 lingual
- 2900 1936 5426 2.458 0.630 0.152 0.080 75 6.8 medialorbitofrontal
- 5356 3736 12540 2.704 0.665 0.154 0.057 118 12.8 middletemporal
- 1018 700 2257 2.903 0.797 0.155 0.070 19 2.6 parahippocampal
- 2628 1762 4585 2.304 0.445 0.131 0.044 55 5.6 paracentral
- 1907 1300 3925 2.646 0.450 0.143 0.054 33 3.7 parsopercularis
- 1415 960 3519 2.886 0.553 0.186 0.097 45 4.8 parsorbitalis
- 2410 1636 4844 2.559 0.436 0.150 0.057 45 5.4 parstriangularis
- 1888 1307 2317 1.788 0.387 0.162 0.091 49 5.3 pericalcarine
- 6371 4168 9711 2.044 0.543 0.126 0.038 82 10.1 postcentral
- 1993 1311 3544 2.420 0.831 0.166 0.070 47 5.3 posteriorcingulate
- 7540 4920 13968 2.575 0.465 0.123 0.046 133 14.8 precentral
- 5646 3797 9941 2.451 0.506 0.141 0.048 92 11.0 precuneus
- 1100 729 2659 3.092 0.603 0.162 0.075 25 3.3 rostralanteriorcingulate
- 8852 6071 17140 2.445 0.501 0.169 0.082 237 25.0 rostralmiddlefrontal
- 11828 8068 23629 2.591 0.483 0.143 0.049 198 22.8 superiorfrontal
- 8476 5627 13056 2.125 0.395 0.144 0.049 152 17.3 superiorparietal
- 6446 4263 13607 2.763 0.568 0.139 0.051 102 12.4 superiortemporal
- 6581 4452 12030 2.352 0.477 0.138 0.044 96 11.1 supramarginal
- 499 339 1213 2.732 0.452 0.231 0.124 25 2.3 frontalpole
- 670 443 2046 3.472 0.763 0.172 0.108 22 2.9 temporalpole
- 590 365 1014 2.417 0.387 0.153 0.065 10 1.6 transversetemporal
- 3241 2161 7378 3.120 0.884 0.149 0.109 112 14.2 insula
- #-----------------------------------------
- #@# Cortical Parc 2 rh Thu Aug 8 23:15:17 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub018 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...
- 13 labels changed using aseg
- relabeling using gibbs priors...
- 000: 10136 changed, 140674 examined...
- 001: 2434 changed, 38479 examined...
- 002: 752 changed, 12552 examined...
- 003: 333 changed, 4263 examined...
- 004: 171 changed, 1808 examined...
- 005: 85 changed, 943 examined...
- 006: 52 changed, 510 examined...
- 007: 25 changed, 289 examined...
- 008: 14 changed, 147 examined...
- 009: 8 changed, 86 examined...
- 010: 6 changed, 45 examined...
- 011: 3 changed, 36 examined...
- 012: 0 changed, 10 examined...
- 12 labels changed using aseg
- 000: 307 total segments, 220 labels (2856 vertices) changed
- 001: 115 total segments, 29 labels (186 vertices) changed
- 002: 90 total segments, 4 labels (6 vertices) changed
- 003: 86 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 129 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 1024 vertices marked for relabeling...
- 1024 labels changed in reclassification.
- writing output to ../label/rh.aparc.a2009s.annot...
- classification took 1 minutes and 18 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 2 rh Thu Aug 8 23:16:36 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 sub018 rh white
- computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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
- 1041 764 2222 2.506 0.573 0.206 0.092 36 3.4 G_and_S_frontomargin
- 1312 897 2297 2.260 0.629 0.155 0.063 27 3.4 G_and_S_occipital_inf
- 1518 968 2882 2.390 0.499 0.125 0.050 45 3.6 G_and_S_paracentral
- 1262 849 2529 2.496 0.467 0.144 0.045 20 2.3 G_and_S_subcentral
- 1103 741 2359 2.466 0.397 0.189 0.102 38 3.7 G_and_S_transv_frontopol
- 2971 2003 6127 2.745 0.500 0.152 0.067 62 7.5 G_and_S_cingul-Ant
- 1658 1132 3451 2.805 0.503 0.140 0.045 24 3.0 G_and_S_cingul-Mid-Ant
- 1453 1007 2730 2.531 0.601 0.148 0.056 25 3.1 G_and_S_cingul-Mid-Post
- 559 349 1396 2.999 0.623 0.210 0.109 23 2.3 G_cingul-Post-dorsal
- 204 129 495 3.164 0.832 0.183 0.092 5 0.6 G_cingul-Post-ventral
- 2090 1412 3116 1.924 0.405 0.186 0.091 61 7.1 G_cuneus
- 1200 835 3079 2.838 0.416 0.159 0.071 28 2.8 G_front_inf-Opercular
- 369 238 952 2.894 0.362 0.170 0.069 9 1.0 G_front_inf-Orbital
- 1092 732 2736 2.740 0.390 0.174 0.074 30 3.2 G_front_inf-Triangul
- 4265 2910 9680 2.581 0.458 0.176 0.096 146 13.8 G_front_middle
- 7826 5283 17102 2.634 0.496 0.151 0.054 157 16.6 G_front_sup
- 547 360 1477 3.374 0.800 0.159 0.257 58 6.6 G_Ins_lg_and_S_cent_ins
- 727 480 2511 3.709 0.695 0.186 0.145 30 3.4 G_insular_short
- 2896 1929 5865 2.436 0.451 0.178 0.079 85 9.0 G_occipital_middle
- 1636 1074 2826 2.217 0.337 0.167 0.057 37 3.7 G_occipital_sup
- 2234 1486 5268 2.805 0.491 0.182 0.083 65 7.8 G_oc-temp_lat-fusifor
- 2277 1554 4210 2.189 0.493 0.199 0.159 262 16.1 G_oc-temp_med-Lingual
- 1682 1167 5005 3.229 0.874 0.178 0.150 47 5.8 G_oc-temp_med-Parahip
- 3212 2167 8377 2.984 0.615 0.186 0.094 104 11.4 G_orbital
- 2393 1609 5839 2.770 0.512 0.180 0.087 72 7.5 G_pariet_inf-Angular
- 3652 2471 7604 2.442 0.478 0.143 0.042 60 6.3 G_pariet_inf-Supramar
- 2961 1953 5272 2.234 0.439 0.156 0.053 61 6.4 G_parietal_sup
- 2413 1532 4290 2.172 0.457 0.139 0.045 39 4.7 G_postcentral
- 2819 1815 6443 2.732 0.438 0.139 0.059 78 6.3 G_precentral
- 2480 1689 5164 2.472 0.474 0.169 0.071 74 7.2 G_precuneus
- 687 484 1522 2.451 0.645 0.186 0.125 28 2.3 G_rectus
- 497 294 883 2.666 0.795 0.092 0.091 6 0.7 G_subcallosal
- 531 312 954 2.485 0.362 0.155 0.066 11 1.4 G_temp_sup-G_T_transv
- 2219 1449 5994 2.973 0.478 0.162 0.070 56 5.8 G_temp_sup-Lateral
- 854 556 2152 3.202 0.792 0.138 0.064 12 2.4 G_temp_sup-Plan_polar
- 897 619 1761 2.549 0.458 0.131 0.034 11 1.1 G_temp_sup-Plan_tempo
- 2894 1881 6090 2.394 0.810 0.189 0.157 147 15.8 G_temporal_inf
- 3138 2214 8748 2.891 0.624 0.174 0.072 93 9.5 G_temporal_middle
- 411 275 583 2.378 0.383 0.100 0.026 2 0.4 Lat_Fis-ant-Horizont
- 248 176 460 2.474 0.417 0.138 0.031 2 0.4 Lat_Fis-ant-Vertical
- 1420 938 1956 2.278 0.438 0.120 0.044 12 2.1 Lat_Fis-post
- 2963 1947 4540 2.066 0.414 0.179 0.104 83 10.6 Pole_occipital
- 1816 1217 5130 3.037 0.701 0.174 0.091 56 6.7 Pole_temporal
- 2135 1476 2697 1.911 0.637 0.152 0.075 47 4.9 S_calcarine
- 3254 2154 3911 2.004 0.612 0.110 0.041 43 6.6 S_central
- 1624 1105 2435 2.198 0.448 0.126 0.042 21 2.9 S_cingul-Marginalis
- 687 471 1162 2.665 0.535 0.133 0.043 5 1.2 S_circular_insula_ant
- 1251 853 2012 2.600 0.733 0.101 0.031 8 1.6 S_circular_insula_inf
- 1355 922 2080 2.599 0.445 0.119 0.034 9 2.1 S_circular_insula_sup
- 1220 871 2124 2.455 0.483 0.114 0.028 8 1.5 S_collat_transv_ant
- 443 318 570 1.902 0.370 0.128 0.039 3 0.7 S_collat_transv_post
- 2061 1376 2986 2.234 0.420 0.132 0.041 24 3.3 S_front_inf
- 1949 1330 3123 2.395 0.500 0.146 0.049 27 3.7 S_front_middle
- 2826 2003 4733 2.368 0.422 0.133 0.039 32 4.6 S_front_sup
- 829 564 1113 2.061 0.410 0.136 0.042 9 1.4 S_interm_prim-Jensen
- 3068 2059 4090 2.075 0.341 0.124 0.035 32 4.7 S_intrapariet_and_P_trans
- 1192 810 1627 2.047 0.354 0.130 0.045 16 2.0 S_oc_middle_and_Lunatus
- 1743 1151 2301 2.079 0.332 0.119 0.032 18 2.3 S_oc_sup_and_transversal
- 825 558 1533 2.461 0.339 0.158 0.071 15 2.9 S_occipital_ant
- 1279 832 1698 2.287 0.372 0.122 0.037 11 2.0 S_oc-temp_lat
- 1762 1258 2795 2.349 0.474 0.130 0.038 19 2.9 S_oc-temp_med_and_Lingual
- 576 405 989 2.452 0.463 0.171 0.081 13 1.7 S_orbital_lateral
- 777 562 1254 2.266 0.742 0.117 0.036 7 1.2 S_orbital_med-olfact
- 1372 972 2425 2.582 0.662 0.149 0.049 19 2.9 S_orbital-H_Shaped
- 2211 1481 3066 2.244 0.463 0.134 0.038 25 3.5 S_parieto_occipital
- 1784 1148 2017 2.027 0.877 0.143 0.039 26 2.8 S_pericallosal
- 2732 1818 3332 2.003 0.385 0.115 0.038 25 4.6 S_postcentral
- 1192 800 1809 2.448 0.425 0.097 0.022 6 1.1 S_precentral-inf-part
- 1695 1112 2426 2.366 0.369 0.112 0.032 16 2.2 S_precentral-sup-part
- 449 298 654 2.260 0.666 0.124 0.035 5 0.6 S_suborbital
- 977 668 1573 2.509 0.375 0.132 0.038 10 1.5 S_subparietal
- 1254 856 1558 2.143 0.571 0.128 0.033 10 1.8 S_temporal_inf
- 7172 4887 12111 2.503 0.470 0.130 0.042 98 11.5 S_temporal_sup
- 416 281 656 2.441 0.365 0.123 0.032 3 0.6 S_temporal_transverse
- #-----------------------------------------
- #@# Cortical Parc 3 rh Thu Aug 8 23:16:59 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub018 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...
- 1124 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2895 changed, 140674 examined...
- 001: 653 changed, 12295 examined...
- 002: 168 changed, 3484 examined...
- 003: 53 changed, 989 examined...
- 004: 21 changed, 332 examined...
- 005: 9 changed, 118 examined...
- 006: 6 changed, 57 examined...
- 007: 6 changed, 32 examined...
- 008: 6 changed, 37 examined...
- 009: 7 changed, 30 examined...
- 010: 6 changed, 35 examined...
- 011: 2 changed, 28 examined...
- 012: 1 changed, 12 examined...
- 013: 0 changed, 7 examined...
- 139 labels changed using aseg
- 000: 74 total segments, 41 labels (163 vertices) changed
- 001: 35 total segments, 2 labels (4 vertices) changed
- 002: 33 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 48 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 962 vertices marked for relabeling...
- 962 labels changed in reclassification.
- writing output to ../label/rh.aparc.DKTatlas40.annot...
- classification took 1 minutes and 3 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 3 rh Thu Aug 8 23:18:03 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 sub018 rh white
- computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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
- 1128 783 2268 2.540 0.832 0.159 0.045 21 2.0 caudalanteriorcingulate
- 2596 1755 4571 2.455 0.402 0.126 0.036 30 4.0 caudalmiddlefrontal
- 2775 1865 4100 1.974 0.394 0.173 0.070 67 7.6 cuneus
- 568 447 1975 3.045 0.869 0.170 0.062 10 1.5 entorhinal
- 4625 3178 9767 2.668 0.549 0.158 0.064 91 12.4 fusiform
- 8162 5472 15093 2.436 0.497 0.151 0.062 174 19.4 inferiorparietal
- 5883 3875 11234 2.400 0.701 0.163 0.103 190 21.8 inferiortemporal
- 1374 900 2322 2.393 0.791 0.162 0.064 29 3.3 isthmuscingulate
- 7341 4888 12159 2.202 0.445 0.170 0.077 174 21.3 lateraloccipital
- 4438 3077 9736 2.776 0.666 0.171 0.100 123 13.3 lateralorbitofrontal
- 3782 2614 6148 2.063 0.502 0.170 0.114 280 19.6 lingual
- 2331 1570 4435 2.405 0.695 0.150 0.088 59 5.5 medialorbitofrontal
- 6278 4394 14194 2.678 0.633 0.148 0.052 124 13.8 middletemporal
- 992 681 2205 2.911 0.804 0.155 0.072 19 2.6 parahippocampal
- 2745 1840 4727 2.296 0.440 0.131 0.045 58 5.8 paracentral
- 1952 1328 4000 2.638 0.451 0.144 0.053 35 3.8 parsopercularis
- 1394 946 3285 2.830 0.528 0.164 0.079 32 4.0 parsorbitalis
- 2539 1716 4855 2.526 0.443 0.153 0.059 47 5.8 parstriangularis
- 1880 1304 2319 1.785 0.384 0.163 0.096 51 5.3 pericalcarine
- 7018 4599 10623 2.060 0.538 0.128 0.040 98 11.9 postcentral
- 2150 1407 3902 2.457 0.806 0.165 0.068 51 5.7 posteriorcingulate
- 7137 4651 13353 2.581 0.473 0.122 0.047 128 14.0 precentral
- 5678 3833 10067 2.443 0.506 0.142 0.048 95 11.1 precuneus
- 1087 736 2616 3.089 0.575 0.167 0.071 25 3.3 rostralanteriorcingulate
- 6110 4151 12012 2.474 0.527 0.171 0.083 177 18.3 rostralmiddlefrontal
- 15075 10266 29872 2.567 0.472 0.148 0.055 281 31.3 superiorfrontal
- 7145 4728 11129 2.136 0.395 0.140 0.047 120 14.1 superiorparietal
- 8369 5556 18190 2.829 0.642 0.142 0.055 143 18.1 superiortemporal
- 6348 4314 11766 2.359 0.496 0.138 0.045 93 11.0 supramarginal
- 583 361 1009 2.423 0.389 0.153 0.066 10 1.6 transversetemporal
- 3054 2058 7007 3.066 0.849 0.143 0.105 103 12.9 insula
- #--------------------------------------------
- #@# Refine Pial Surfs w/ T2/FLAIR Thu Aug 8 23:18:22 CEST 2013
- bbregister --s sub018 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/T2raw.lta --init-fsl --T2
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/T2raw.dat.log
- Thu Aug 8 23:18:22 CEST 2013
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts
- /opt/freesurfer/5.3.0/bin/bbregister --s sub018 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/template.nii
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/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/sub018/mri/orig/T2raw.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.998519, 0.0146261, 0.052401)
- j_ras = (0.020019, 0.994384, 0.103917)
- k_ras = (0.0505869, -0.104812, 0.993205)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/template.nii...
- fslregister --s sub018 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/fslregister --dof 6 --fsvol brainmask.mgz
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/reg.init.dat.fslregister.log
- Thu Aug 8 23:18:28 CEST 2013
- --s sub018 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/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/sub018/scripts
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/fslregister/refvol.fslregister.nii
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/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/sub018/mri/brainmask.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, -1.86265e-09, 0)
- j_ras = (0, 2.23517e-08, -1)
- k_ras = (-9.31323e-10, 1, 7.45058e-09)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/fslregister/refvol.fslregister.nii...
- --------------------------------------
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/fslregister/movvol.fslregister.nii --frame 0
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/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/sub018/mri/transforms/tmp.bbregister.18743/template.nii...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.998519, 0.0146261, 0.052401)
- j_ras = (0.020019, 0.994384, 0.103917)
- k_ras = (0.0505869, -0.104812, 0.993205)
- keeping frame 0
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/fslregister/movvol.fslregister.nii...
- Mov determinant is -0.311083
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts
- tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/fslregister/movvol.fslregister.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/fslregister/reg0.18809.dat --regheader --fslregout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/reg.init.dat.fsl.mat0 --s sub018 --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/sub018/mri/transforms/tmp.bbregister.18743/fslregister/movvol.fslregister.nii
- reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/fslregister/reg0.18809.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/sub018/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/sub018/mri/transforms/tmp.bbregister.18743/fslregister/movvol.fslregister.nii
- Tmov: --------------------
- -0.700 0.000 0.000 95.891;
- 0.000 0.000 0.667 -128.000;
- 0.000 -0.667 0.000 128.000;
- 0.000 0.000 0.000 1.000;
- mkheaderreg = 1, float2int = 0
- Computing reg from header (and possibly input matrix)
- ---- Input registration matrix (computed) --------
- 0.999 -0.015 -0.052 0.000;
- 0.051 -0.105 0.993 -0.000;
- -0.020 -0.994 -0.104 -0.000;
- 0.000 0.000 0.000 1.000;
- ---------------------------------------
- ---- Input registration matrix --------
- 0.999 -0.015 -0.052 0.000;
- 0.051 -0.105 0.993 -0.000;
- -0.020 -0.994 -0.104 -0.000;
- 0.000 0.000 0.000 1.000;
- Determinant 1
- subject = sub018
- RegMat ---------------------------
- 0.999 -0.015 -0.052 0.000;
- 0.051 -0.105 0.993 -0.000;
- -0.020 -0.994 -0.104 -0.000;
- 0.000 0.000 0.000 1.000;
- FSLOUTPUTTYPE NIFTI
- tkreg2FSL: mov det = -0.311083, ref det = -1
- Thu Aug 8 23:18:36 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts
- flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/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/sub018/mri/transforms/tmp.bbregister.18743/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/reg.init.dat.fsl.mat0
- Thu Aug 8 23:23:10 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts
- flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/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/sub018/mri/transforms/tmp.bbregister.18743/reg.init.dat.fsl.mat -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/fslregister/fslmat0.trans.mat -schedule /opt/freesurfer/5.3.0/bin/flirt.newdefault.20080811.sch
- tkregister2_cmdl --s sub018 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/reg.init.dat --fslreg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/reg.init.dat.fsl.mat --noedit
- tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl
- ---- FSL registration matrix --------
- 0.999 -0.010 -0.036 38.367;
- -0.037 -0.079 -0.996 271.929;
- 0.007 0.997 -0.080 7.702;
- 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/sub018/mri/transforms/tmp.bbregister.18743/template.nii
- reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/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/sub018/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/sub018/mri/transforms/tmp.bbregister.18743/template.nii
- Tmov: --------------------
- -0.700 0.000 0.000 95.891;
- 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 = -0.311083, ref det = -1
- ---- Input registration matrix (computed) --------
- 0.999 -0.007 -0.037 0.114;
- 0.036 -0.080 0.996 2.546;
- -0.010 -0.997 -0.079 -2.406;
- 0.000 0.000 0.000 1.000;
- ---------------------------------------
- ---- Input registration matrix --------
- 0.999 -0.007 -0.037 0.114;
- 0.036 -0.080 0.996 2.546;
- -0.010 -0.997 -0.079 -2.406;
- 0.000 0.000 0.000 1.000;
- Determinant 0.999999
- subject = sub018
- RegMat ---------------------------
- 0.999 -0.007 -0.037 0.114;
- 0.036 -0.080 0.996 2.546;
- -0.010 -0.997 -0.079 -2.406;
- 0.000 0.000 0.000 1.000;
-
- Started at Thu Aug 8 23:18:28 CEST 2013
- Ended at Thu Aug 8 23:28:56 CEST 2013
-
- fslregister Done
-
- To check results, run:
- tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/reg.init.dat --surf orig
-
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/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/sub018/scripts
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/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/sub018/mri/transforms/tmp.bbregister.18743/template.nii
- regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/reg.init.dat
- subject sub018
- dof 6
- outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/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 1376242799
- TransRandMax 0.000000
- RotRandMax 0.000000
- Translations 0.000000 0.000000 0.000000
- Rotations 0.000000 0.000000 0.000000
- Input reg
- 0.999 -0.007 -0.037 0.114;
- 0.036 -0.080 0.996 2.546;
- -0.010 -0.997 -0.079 -2.406;
- 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 1.041746
- 1 -25.0 -25.0 25.0 0.984698
- 2 -25.0 25.0 -25.0 1.011810
- 3 -25.0 25.0 25.0 1.025865
- 4 25.0 -25.0 -25.0 1.055057
- 5 25.0 -25.0 25.0 1.039686
- 6 25.0 25.0 -25.0 1.030573
- 7 25.0 25.0 25.0 0.991700
- REL: 8 0.588958 8.181136 1.022642 rel = 0.575918
- Initial costs ----------------
- Number of surface hits 2640
- WM Intensity 67.8500 +/- 11.4675
- Ctx Intensity 77.5842 +/- 18.1108
- Pct Contrast 12.0347 +/- 24.6941
- Cost 0.5890
- RelCost 0.5759
- ------------------------------------
- Brute force preopt -4 4 4, n = 729
- 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9661 0.9661 0.0
- 4 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.0000 0.9622 0.9622 0.0
- 9 -4.0000 -4.0000 -4.0000 0.0000 -4.0000 -4.0000 0.9606 0.9606 0.0
- 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.9344 0.9344 0.0
- 18 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 -4.0000 0.9141 0.9141 0.0
- 21 -4.0000 -4.0000 -4.0000 4.0000 0.0000 -4.0000 0.8603 0.8603 0.0
- 39 -4.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.8092 0.8092 0.0
- 120 -4.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.7879 0.7879 0.0
- 265 0.0000 -4.0000 -4.0000 4.0000 0.0000 0.0000 0.7760 0.7760 0.0
- 283 0.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.6998 0.6998 0.0
- 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.5890 0.5890 0.0
- Brute Force --------------------------
- Min cost was 0.588958
- Number of iterations 729
- Search time 2.197000 sec
- Parameters at best (transmm, rotdeg)
- 0.000 0.000 0.000 0.000 0.000 0.000
- --------------------------------------------
- Starting Powell Minimization
- Init Powel Params dof = 6
- 0 0
- 1 0
- 2 0
- 3 0
- 4 0
- 5 0
- 6 0.382 0.000 0.000 0.000 0.000 0.000 0.5879920980
- 7 0.224 0.000 0.000 0.000 0.000 0.000 0.5867100454
- 10 0.247 0.000 0.000 0.000 0.000 0.000 0.5860232764
- 11 0.254 0.000 0.000 0.000 0.000 0.000 0.5858303350
- 12 0.266 0.000 0.000 0.000 0.000 0.000 0.5857333842
- 13 0.264 0.000 0.000 0.000 0.000 0.000 0.5857094534
- 14 0.262 0.000 0.000 0.000 0.000 0.000 0.5857073857
- 18 0.262 -1.618 0.000 0.000 0.000 0.000 0.4161117247
- 23 0.262 -1.686 0.000 0.000 0.000 0.000 0.4141458505
- 26 0.262 -1.692 0.000 0.000 0.000 0.000 0.4140394165
- 28 0.262 -1.702 0.000 0.000 0.000 0.000 0.4139065104
- 30 0.262 -1.704 0.000 0.000 0.000 0.000 0.4138997323
- 34 0.262 -1.704 1.000 0.000 0.000 0.000 0.2384291117
- 37 0.262 -1.704 1.618 0.000 0.000 0.000 0.2093884544
- 39 0.262 -1.704 1.669 0.000 0.000 0.000 0.2077620808
- 40 0.262 -1.704 1.749 0.000 0.000 0.000 0.2068155934
- 41 0.262 -1.704 1.748 0.000 0.000 0.000 0.2068002212
- 43 0.262 -1.704 1.739 0.000 0.000 0.000 0.2067601614
- 44 0.262 -1.704 1.741 0.000 0.000 0.000 0.2067571153
- 52 0.262 -1.704 1.741 -0.209 0.000 0.000 0.2048846490
- 53 0.262 -1.704 1.741 -0.144 0.000 0.000 0.2039094829
- 61 0.262 -1.704 1.741 -0.144 -0.618 0.000 0.1966389266
- 63 0.262 -1.704 1.741 -0.144 -0.375 0.000 0.1945087313
- 64 0.262 -1.704 1.741 -0.144 -0.416 0.000 0.1942394525
- 66 0.262 -1.704 1.741 -0.144 -0.406 0.000 0.1941748574
- 76 0.262 -1.704 1.741 -0.144 -0.406 0.382 0.1682036035
- 77 0.262 -1.704 1.741 -0.144 -0.406 0.455 0.1664617252
- 79 0.262 -1.704 1.741 -0.144 -0.406 0.486 0.1663602688
- 81 0.262 -1.704 1.741 -0.144 -0.406 0.499 0.1663421996
- 86 0.262 -1.704 1.741 -0.144 -0.406 0.498 0.1663410348
- 93 0.644 -1.704 1.741 -0.144 -0.406 0.498 0.1603594329
- 94 0.551 -1.704 1.741 -0.144 -0.406 0.498 0.1591008981
- 98 0.543 -1.704 1.741 -0.144 -0.406 0.498 0.1590989369
- 100 0.546 -1.704 1.741 -0.144 -0.406 0.498 0.1590925179
- 108 0.546 -1.322 1.741 -0.144 -0.406 0.498 0.1552985040
- 109 0.546 -1.450 1.741 -0.144 -0.406 0.498 0.1523504292
- 112 0.546 -1.439 1.741 -0.144 -0.406 0.498 0.1522467919
- 114 0.546 -1.440 1.741 -0.144 -0.406 0.498 0.1522467704
- 123 0.546 -1.440 1.754 -0.144 -0.406 0.498 0.1522174389
- 124 0.546 -1.440 1.757 -0.144 -0.406 0.498 0.1522148949
- 127 0.546 -1.440 1.758 -0.144 -0.406 0.498 0.1522134162
- 129 0.546 -1.440 1.759 -0.144 -0.406 0.498 0.1522132120
- 136 0.546 -1.440 1.759 -0.150 -0.406 0.498 0.1521746023
- 139 0.546 -1.440 1.759 -0.151 -0.406 0.498 0.1521742852
- 147 0.546 -1.440 1.759 -0.151 -0.382 0.498 0.1519943474
- 150 0.546 -1.440 1.759 -0.151 -0.379 0.498 0.1519908503
- 161 0.546 -1.440 1.759 -0.151 -0.379 0.474 0.1515666271
- 163 0.546 -1.440 1.759 -0.151 -0.379 0.467 0.1515640098
- 164 0.546 -1.440 1.759 -0.151 -0.379 0.470 0.1515627603
- 176 0.557 -1.440 1.759 -0.151 -0.379 0.470 0.1513918774
- 177 0.562 -1.440 1.759 -0.151 -0.379 0.470 0.1513736202
- 188 0.562 -1.451 1.759 -0.151 -0.379 0.470 0.1513468517
- 189 0.562 -1.448 1.759 -0.151 -0.379 0.470 0.1513354966
- 201 0.562 -1.448 1.753 -0.151 -0.379 0.470 0.1513139863
- 202 0.562 -1.448 1.754 -0.151 -0.379 0.470 0.1513122666
- 210 0.562 -1.448 1.754 -0.157 -0.379 0.470 0.1512945001
- 222 0.562 -1.448 1.754 -0.157 -0.382 0.470 0.1512942819
- 224 0.562 -1.448 1.754 -0.157 -0.381 0.470 0.1512929437
- 234 0.562 -1.448 1.754 -0.157 -0.381 0.476 0.1512685837
- 248 0.561 -1.448 1.754 -0.157 -0.381 0.476 0.1512684864
- 270 0.561 -1.448 1.755 -0.157 -0.381 0.476 0.1512676976
- 278 0.561 -1.448 1.755 -0.158 -0.381 0.476 0.1512659353
- 279 0.561 -1.448 1.755 -0.161 -0.381 0.476 0.1512644976
- 285 0.561 -1.448 1.755 -0.166 -0.381 0.476 0.1512520652
- 287 0.561 -1.448 1.755 -0.165 -0.381 0.476 0.1512518804
- 308 0.561 -1.448 1.755 -0.165 -0.381 0.477 0.1512509105
- 309 0.561 -1.448 1.755 -0.165 -0.381 0.478 0.1512503998
- 311 0.561 -1.448 1.755 -0.165 -0.381 0.479 0.1512495714
- 325 0.560 -1.448 1.755 -0.165 -0.381 0.479 0.1512493680
- 337 0.560 -1.449 1.755 -0.165 -0.381 0.479 0.1512482459
- 348 0.560 -1.449 1.754 -0.165 -0.381 0.479 0.1512479253
- 358 0.560 -1.449 1.754 -0.166 -0.381 0.479 0.1512471210
- Powell done niters = 4
- Computing relative cost
- 0 -25.0 -25.0 -25.0 1.042787
- 1 -25.0 -25.0 25.0 1.011592
- 2 -25.0 25.0 -25.0 0.995579
- 3 -25.0 25.0 25.0 0.996637
- 4 25.0 -25.0 -25.0 1.043201
- 5 25.0 -25.0 25.0 1.036614
- 6 25.0 25.0 -25.0 0.996732
- 7 25.0 25.0 25.0 1.010675
- REL: 8 0.151247 8.133818 1.016727 rel = 0.148759
- Number of iterations 4
- Min cost was 0.151247
- Number of FunctionCalls 382
- TolPowell 0.000100
- nMaxItersPowell 36
- OptimizationTime 1.311000 sec
- Parameters at optimum (transmm) 0.55998 -1.44907 1.75383
- Parameters at optimum (rotdeg) -0.16627 -0.38085 0.47888
- Final costs ----------------
- Number of surface hits 2640
- WM Intensity 64.0135 +/- 8.6665
- Ctx Intensity 77.1130 +/- 9.0735
- Pct Contrast 18.6154 +/- 13.4914
- Cost 0.1512
- RelCost 0.5759
- Reg at min cost was
- 0.999 -0.000 -0.045 0.669;
- 0.045 -0.083 0.996 1.091;
- -0.004 -0.997 -0.082 -0.659;
- 0.000 0.000 0.000 1.000;
- Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/bbr.pass1.dat, type = 14
- Original Reg
- 0.999 -0.007 -0.037 0.114;
- 0.036 -0.080 0.996 2.546;
- -0.010 -0.997 -0.079 -2.406;
- 0.000 0.000 0.000 1.000;
- Original Reg - Optimal Reg
- 0.000 -0.007 0.008 -0.555;
- -0.008 0.003 0.001 1.455;
- -0.007 -0.000 0.003 -1.747;
- 0.000 0.000 0.000 0.000;
- Computing change in lh position
- LH rmsDiffMean 2.219454
- Computing change in rh position
- Surface RMS Diff (mm) 2.208397 2.510514
- mri_segreg done
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/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/sub018/scripts
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/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/sub018/mri/transforms/tmp.bbregister.18743/template.nii
- regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/bbr.pass1.dat
- subject sub018
- dof 6
- outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 1376918144
- TransRandMax 0.000000
- RotRandMax 0.000000
- Translations 0.000000 0.000000 0.000000
- Rotations 0.000000 0.000000 0.000000
- Input reg
- 0.999 -0.000 -0.045 0.669;
- 0.045 -0.083 0.996 1.091;
- -0.004 -0.997 -0.082 -0.659;
- 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 1.024493
- 1 -25.0 -25.0 25.0 0.996708
- 2 -25.0 25.0 -25.0 1.002013
- 3 -25.0 25.0 25.0 1.014795
- 4 25.0 -25.0 -25.0 1.035938
- 5 25.0 -25.0 25.0 1.025038
- 6 25.0 25.0 -25.0 1.014441
- 7 25.0 25.0 25.0 1.030576
- REL: 8 0.152406 8.144001 1.018000 rel = 0.149711
- Initial costs ----------------
- Number of surface hits 264340
- WM Intensity 64.0253 +/- 8.8203
- Ctx Intensity 77.0513 +/- 8.9915
- Pct Contrast 18.5621 +/- 13.3074
- Cost 0.1524
- RelCost 0.1497
- ------------------------------------
- Brute force preopt -0.1 0.1 0.1, n = 729
- 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1700 0.1700 0.0
- 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1665 0.1665 0.0
- 2 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.1645 0.1645 0.0
- 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.1643 0.1643 0.0
- 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.1605 0.1605 0.0
- 5 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1000 0.1603 0.1603 0.0
- 7 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.0000 0.1591 0.1591 0.0
- 11 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.1000 0.1591 0.1591 0.0
- 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.1574 0.1574 0.0
- 14 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.1000 0.1566 0.1566 0.0
- 23 -0.1000 -0.1000 -0.1000 0.1000 0.0000 0.1000 0.1554 0.1554 0.0
- 41 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.1000 0.1545 0.1545 0.0
- 115 -0.1000 0.0000 0.0000 -0.1000 0.1000 0.0000 0.1540 0.1540 0.0
- 361 0.0000 0.0000 0.0000 0.0000 -0.1000 0.0000 0.1538 0.1538 0.0
- 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1512 0.1512 0.0
- Brute Force --------------------------
- Min cost was 0.151247
- Number of iterations 729
- Search time 2.508000 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 -0.103 0.000 0.000 0.000 0.000 0.000 0.1514410443
- 8 -0.098 0.000 0.000 0.000 0.000 0.000 0.1514376236
- 10 -0.099 0.000 0.000 0.000 0.000 0.000 0.1514375714
- 18 -0.099 -0.188 0.000 0.000 0.000 0.000 0.1474554874
- 20 -0.099 -0.204 0.000 0.000 0.000 0.000 0.1474188042
- 23 -0.099 -0.207 0.000 0.000 0.000 0.000 0.1474174539
- 32 -0.099 -0.207 0.085 0.000 0.000 0.000 0.1470072030
- 33 -0.099 -0.207 0.070 0.000 0.000 0.000 0.1469717651
- 34 -0.099 -0.207 0.066 0.000 0.000 0.000 0.1469699249
- 35 -0.099 -0.207 0.065 0.000 0.000 0.000 0.1469698799
- 44 -0.099 -0.207 0.065 0.004 0.000 0.000 0.1469677710
- 45 -0.099 -0.207 0.065 0.003 0.000 0.000 0.1469674959
- 53 -0.099 -0.207 0.065 0.003 -0.045 0.000 0.1466450423
- 55 -0.099 -0.207 0.065 0.003 -0.049 0.000 0.1466425446
- 64 -0.099 -0.207 0.065 0.003 -0.049 0.078 0.1464056346
- 65 -0.099 -0.207 0.065 0.003 -0.049 0.053 0.1463072446
- 76 -0.026 -0.207 0.065 0.003 -0.049 0.053 0.1457893481
- 77 -0.025 -0.207 0.065 0.003 -0.049 0.053 0.1457890903
- 87 -0.025 -0.211 0.065 0.003 -0.049 0.053 0.1457842654
- 88 -0.025 -0.212 0.065 0.003 -0.049 0.053 0.1457838702
- 97 -0.025 -0.212 0.067 0.003 -0.049 0.053 0.1457826645
- 98 -0.025 -0.212 0.069 0.003 -0.049 0.053 0.1457823566
- 107 -0.025 -0.212 0.069 0.001 -0.049 0.053 0.1457796311
- 108 -0.025 -0.212 0.069 -0.000 -0.049 0.053 0.1457794023
- 116 -0.025 -0.212 0.069 -0.000 -0.058 0.053 0.1457480750
- 117 -0.025 -0.212 0.069 -0.000 -0.069 0.053 0.1457342743
- 126 -0.025 -0.212 0.069 -0.000 -0.069 0.122 0.1456523038
- 127 -0.025 -0.212 0.069 -0.000 -0.069 0.093 0.1455206534
- 128 -0.025 -0.212 0.069 -0.000 -0.069 0.091 0.1455204359
- 130 0.048 -0.217 0.073 -0.003 -0.090 0.130 0.1452989735
- 137 0.043 -0.217 0.072 -0.003 -0.088 0.127 0.1452987752
- 138 0.045 -0.217 0.073 -0.003 -0.089 0.128 0.1452984860
- 140 0.045 -0.217 0.072 -0.003 -0.089 0.128 0.1452984346
- 154 0.045 -0.217 0.073 -0.003 -0.089 0.125 0.1452969859
- 155 0.045 -0.217 0.073 -0.003 -0.089 0.124 0.1452969832
- 165 0.045 -0.218 0.073 -0.003 -0.089 0.124 0.1452965334
- 166 0.045 -0.219 0.073 -0.003 -0.089 0.124 0.1452964729
- 175 0.045 -0.219 0.077 -0.003 -0.089 0.124 0.1452953222
- 185 0.045 -0.219 0.076 -0.005 -0.089 0.124 0.1452950500
- 187 0.045 -0.219 0.076 -0.004 -0.089 0.124 0.1452948291
- 195 0.045 -0.219 0.076 -0.004 -0.080 0.124 0.1452900846
- 197 0.045 -0.219 0.076 -0.004 -0.079 0.124 0.1452900215
- 210 0.046 -0.219 0.076 -0.004 -0.080 0.125 0.1452899887
- 211 0.046 -0.219 0.076 -0.004 -0.079 0.124 0.1452899581
- 213 0.045 -0.219 0.076 -0.004 -0.079 0.124 0.1452899287
- 216 0.045 -0.219 0.076 -0.004 -0.079 0.124 0.1452899224
- 226 0.045 -0.219 0.076 -0.004 -0.079 0.127 0.1452891807
- 246 0.045 -0.219 0.078 -0.004 -0.079 0.127 0.1452887423
- 255 0.045 -0.219 0.078 -0.007 -0.079 0.127 0.1452878948
- 257 0.045 -0.219 0.078 -0.008 -0.079 0.127 0.1452878558
- 266 0.045 -0.219 0.078 -0.008 -0.078 0.127 0.1452875652
- 274 0.043 -0.219 0.077 -0.008 -0.077 0.126 0.1452872541
- 308 0.043 -0.219 0.080 -0.008 -0.077 0.126 0.1452869217
- 318 0.043 -0.219 0.080 -0.009 -0.077 0.126 0.1452868518
- 327 0.043 -0.219 0.080 -0.009 -0.076 0.126 0.1452868253
- 338 0.043 -0.219 0.080 -0.009 -0.076 0.125 0.1452867932
- 369 0.043 -0.219 0.081 -0.009 -0.076 0.125 0.1452867836
- 397 0.042 -0.219 0.081 -0.009 -0.076 0.125 0.1452867634
- 401 0.042 -0.219 0.081 -0.009 -0.076 0.125 0.1452867545
- Powell done niters = 6
- Computing relative cost
- 0 -25.0 -25.0 -25.0 1.021529
- 1 -25.0 -25.0 25.0 0.997812
- 2 -25.0 25.0 -25.0 1.001644
- 3 -25.0 25.0 25.0 1.014670
- 4 25.0 -25.0 -25.0 1.037124
- 5 25.0 -25.0 25.0 1.023458
- 6 25.0 25.0 -25.0 1.013873
- 7 25.0 25.0 25.0 1.028459
- REL: 8 0.145287 8.138568 1.017321 rel = 0.142813
- Number of iterations 6
- Min cost was 0.145287
- Number of FunctionCalls 462
- TolPowell 0.000000
- nMaxItersPowell 36
- OptimizationTime 51.225000 sec
- Parameters at optimum (transmm) 0.04247 -0.21886 0.08104
- Parameters at optimum (rotdeg) -0.00864 -0.07592 0.12517
- Final costs ----------------
- Number of surface hits 264340
- WM Intensity 63.9905 +/- 8.6991
- Ctx Intensity 77.0184 +/- 8.9911
- Pct Contrast 18.5599 +/- 13.1458
- Cost 0.1453
- RelCost 0.1497
- Reg at min cost was
- 0.999 0.001 -0.047 0.710;
- 0.047 -0.083 0.995 0.874;
- -0.002 -0.997 -0.083 -0.577;
- 0.000 0.000 0.000 1.000;
- Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/T2raw.dat, type = 14
- Original Reg
- 0.999 -0.000 -0.045 0.669;
- 0.045 -0.083 0.996 1.091;
- -0.004 -0.997 -0.082 -0.659;
- 0.000 0.000 0.000 1.000;
- Original Reg - Optimal Reg
- 0.000 -0.002 0.002 -0.041;
- -0.002 0.000 0.000 0.218;
- -0.001 -0.000 0.000 -0.082;
- 0.000 0.000 0.000 0.000;
- Computing change in lh position
- LH rmsDiffMean 0.294693
- Computing change in rh position
- Surface RMS Diff (mm) 0.256290 0.360918
- mri_segreg done
- tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/T2raw.dat --noedit --ltaout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/mri/orig/T2raw.mgz
- reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 0.001 -0.047 0.710;
- 0.047 -0.083 0.995 0.874;
- -0.002 -0.997 -0.083 -0.577;
- 0.000 0.000 0.000 1.000;
- float2int = 0
- ---------------------------------------
- INFO: loading target /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/mri/orig/T2raw.mgz
- Tmov: --------------------
- -0.700 0.000 0.000 95.891;
- 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 0.001 -0.047 0.710;
- 0.047 -0.083 0.995 0.874;
- -0.002 -0.997 -0.083 -0.577;
- 0.000 0.000 0.000 1.000;
- Determinant 0.999999
- subject = sub018
- RegMat ---------------------------
- 0.999 0.001 -0.047 0.710;
- 0.047 -0.083 0.995 0.874;
- -0.002 -0.997 -0.083 -0.577;
- 0.000 0.000 0.000 1.000;
- transformed matrix:
- 1.000 -0.017 -0.006 -0.343;
- 0.017 1.000 0.021 0.018;
- 0.005 -0.021 1.000 -0.206;
- 0.000 0.000 0.000 1.000;
- transformed matrix:
- 0.699 -0.002 -0.031 39.264;
- -0.033 -0.055 -0.664 271.374;
- -0.001 0.664 -0.055 10.656;
- 0.000 0.000 0.000 1.000;
- Cleaning up
-
- Started at Thu Aug 8 23:18:22 CEST 2013
- Ended at Thu Aug 8 23:30:41 CEST 2013
- BBR-Run-Time-Sec 739
-
- bbregister Done
- To check results, run:
- tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/T2raw.dat --surf
-
- mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/T2.mgz
- mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/mri/orig/T2raw.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.998519, 0.0146261, 0.052401)
- j_ras = (0.020019, 0.994384, 0.103917)
- k_ras = (0.0505869, -0.104812, 0.993205)
- INFO: Reading transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/T2raw.lta...
- Reading transform with LTAreadEx()
- reading extra input line subject sub018
- reading extra input line fscale 0.150000
- reading template info from volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/orig.mgz...
- INFO: Applying transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/T2raw.lta...
- ---------------------------------
- INFO: Transform Matrix (linear_ras_to_ras)
- 1.000 -0.017 -0.006 -0.343;
- 0.017 1.000 0.021 0.018;
- 0.005 -0.021 1.000 -0.206;
- 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/sub018/mri/T2.mgz...
- mri_normalize -aseg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/aseg.mgz -sigma 4 -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.white identity.nofile -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.white identity.nofile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/T2.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/mri/T2.mgz...
- computing distance transform
- computing distance transform
- computing nonmaximum suppression
- 10518 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/sub018/mri/T2.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts
- cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.woT2.pial
- `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.woT2.pial'
- mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub018 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/sub018/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/wm.mgz...
- 18104 bright wm thresholded.
- 357 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.orig...
- computing class statistics...
- border white: 252064 voxels (1.50%)
- border gray 291583 voxels (1.74%)
- WM (92.0): 92.8 +- 10.4 [70.0 --> 110.0]
- GM (74.0) : 73.1 +- 12.6 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 46.4 (was 70)
- setting MAX_BORDER_WHITE to 115.4 (was 105)
- setting MIN_BORDER_WHITE to 59.0 (was 85)
- setting MAX_CSF to 33.9 (was 40)
- setting MAX_GRAY to 94.6 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 52.7 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 21.3 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=105, GM=59
- mean inside = 92.7, mean outside = 68.4
- 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/sub018/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.90 +- 0.26 (0.02-->3.87) (max @ vno 106917 --> 107997)
- face area 0.34 +- 0.16 (0.00-->2.81)
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- deleting segment 0 with 2 points - only 0.00% unknown
- deleting segment 1 with 18 points - only 5.56% unknown
- deleting segment 2 with 6 points - only 0.00% unknown
- deleting segment 3 with 7 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 4 with 4 points - only 0.00% unknown
- deleting segment 5 with 8 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- removing 1 vertex label from ripped group
- deleting segment 9 with 9 points - only 0.00% unknown
- deleting segment 10 with 941 points - only 0.00% unknown
- deleting segment 11 with 6 points - only 0.00% unknown
- deleting segment 12 with 6 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 13 with 3 points - only 0.00% unknown
- deleting segment 16 with 17 points - only 0.00% unknown
- deleting segment 17 with 16 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 18 with 1 points - only 0.00% unknown
- tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.90 +- 0.25 (0.06-->3.70) (max @ vno 140247 --> 57770)
- face area 0.34 +- 0.16 (0.00-->2.81)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4681382.0, rms=0.00
- rms = 1.19, time step reduction 1 of 3 to 0.250...
- rms = 0.29, time step reduction 2 of 3 to 0.125...
- rms = 0.04, time step reduction 3 of 3 to 0.062...
- 001: dt: 0.1250, sse=4681382.0, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- deleting segment 0 with 2 points - only 0.00% unknown
- deleting segment 1 with 18 points - only 5.56% unknown
- deleting segment 2 with 6 points - only 0.00% unknown
- deleting segment 3 with 7 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 4 with 4 points - only 0.00% unknown
- deleting segment 5 with 8 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- removing 1 vertex label from ripped group
- deleting segment 8 with 9 points - only 0.00% unknown
- deleting segment 9 with 941 points - only 0.00% unknown
- deleting segment 10 with 6 points - only 0.00% unknown
- deleting segment 11 with 6 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 12 with 3 points - only 0.00% unknown
- deleting segment 13 with 17 points - only 0.00% unknown
- deleting segment 14 with 16 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 15 with 1 points - only 0.00% unknown
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.90 +- 0.25 (0.06-->3.70) (max @ vno 140247 --> 57770)
- face area 0.34 +- 0.16 (0.00-->2.81)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4681382.0, rms=0.00
- rms = 1.19, time step reduction 1 of 3 to 0.250...
- rms = 0.29, time step reduction 2 of 3 to 0.125...
- rms = 0.04, time step reduction 3 of 3 to 0.062...
- 002: dt: 0.1250, sse=4681382.0, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- deleting segment 0 with 2 points - only 0.00% unknown
- deleting segment 1 with 18 points - only 5.56% unknown
- deleting segment 2 with 6 points - only 0.00% unknown
- deleting segment 3 with 7 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 4 with 4 points - only 0.00% unknown
- deleting segment 5 with 8 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- removing 1 vertex label from ripped group
- deleting segment 8 with 9 points - only 0.00% unknown
- deleting segment 9 with 941 points - only 0.00% unknown
- deleting segment 10 with 6 points - only 0.00% unknown
- deleting segment 11 with 6 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 12 with 3 points - only 0.00% unknown
- deleting segment 13 with 17 points - only 0.00% unknown
- deleting segment 14 with 16 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 15 with 1 points - only 0.00% unknown
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.25 (0.06-->3.70) (max @ vno 140247 --> 57770)
- face area 0.34 +- 0.16 (0.00-->2.81)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4681382.0, rms=0.00
- rms = 1.19, time step reduction 1 of 3 to 0.250...
- rms = 0.29, time step reduction 2 of 3 to 0.125...
- rms = 0.04, time step reduction 3 of 3 to 0.062...
- 003: dt: 0.1250, sse=4681382.0, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- deleting segment 0 with 2 points - only 0.00% unknown
- deleting segment 1 with 18 points - only 5.56% unknown
- deleting segment 2 with 6 points - only 0.00% unknown
- deleting segment 3 with 7 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 4 with 4 points - only 0.00% unknown
- deleting segment 5 with 8 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- removing 1 vertex label from ripped group
- deleting segment 8 with 9 points - only 0.00% unknown
- deleting segment 9 with 941 points - only 0.00% unknown
- deleting segment 10 with 6 points - only 0.00% unknown
- deleting segment 11 with 6 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 12 with 3 points - only 0.00% unknown
- deleting segment 13 with 17 points - only 0.00% unknown
- deleting segment 14 with 16 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 15 with 1 points - only 0.00% unknown
- tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- repositioning cortical surface to gray/csf boundary.
- smoothing T1 volume with sigma = 2.000
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4681382.0, rms=0.00
- rms = 1.19, time step reduction 1 of 3 to 0.250...
- rms = 0.29, time step reduction 2 of 3 to 0.125...
- rms = 0.04, time step reduction 3 of 3 to 0.062...
- 004: dt: 0.1250, sse=4681382.0, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 1 vertex label from ripped group
- smoothing surface for 5 iterations...
- reading initial pial vertex positions from woT2.pial...
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [98.20 197.80], gm=148.00+-16.60, and vertices in regions > 139.7
- 48371 surface locations found to contain inconsistent values (7249 in, 41122 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=518552.8, rms=0.25
- 001: dt: 0.5000, sse=484730.8, rms=0.237 (0.000%)
- 002: dt: 0.5000, sse=463887.4, rms=0.223 (0.000%)
- 003: dt: 0.5000, sse=450499.2, rms=0.212 (0.000%)
- 004: dt: 0.5000, sse=439782.9, rms=0.203 (0.000%)
- 005: dt: 0.5000, sse=431609.1, rms=0.195 (0.000%)
- 006: dt: 0.5000, sse=425387.3, rms=0.188 (0.000%)
- 007: dt: 0.5000, sse=420621.0, rms=0.182 (0.000%)
- 008: dt: 0.5000, sse=416597.2, rms=0.177 (0.000%)
- 009: dt: 0.5000, sse=413149.0, rms=0.172 (0.000%)
- 010: dt: 0.5000, sse=410282.3, rms=0.168 (0.000%)
- 011: dt: 0.5000, sse=407744.1, rms=0.165 (0.000%)
- 012: dt: 0.5000, sse=405407.5, rms=0.162 (0.000%)
- 013: dt: 0.5000, sse=403395.5, rms=0.160 (0.000%)
- 014: dt: 0.5000, sse=401590.5, rms=0.158 (0.000%)
- 015: dt: 0.5000, sse=399903.2, rms=0.156 (0.000%)
- 016: dt: 0.5000, sse=398341.5, rms=0.154 (0.000%)
- 017: dt: 0.5000, sse=397009.2, rms=0.153 (0.000%)
- 018: dt: 0.5000, sse=395486.3, rms=0.152 (0.000%)
- 019: dt: 0.5000, sse=394187.9, rms=0.151 (0.000%)
- 020: dt: 0.5000, sse=392849.1, rms=0.150 (0.000%)
- 021: dt: 0.5000, sse=391597.4, rms=0.149 (0.000%)
- 022: dt: 0.5000, sse=390378.1, rms=0.149 (0.000%)
- 023: dt: 0.5000, sse=389127.1, rms=0.148 (0.000%)
- 024: dt: 0.5000, sse=388217.4, rms=0.148 (0.000%)
- 025: dt: 0.5000, sse=387028.1, rms=0.148 (0.000%)
- 026: dt: 0.5000, sse=385734.9, rms=0.148 (0.000%)
- 027: dt: 0.5000, sse=384735.2, rms=0.148 (0.000%)
- 028: dt: 0.5000, sse=383646.8, rms=0.147 (0.000%)
- 029: dt: 0.5000, sse=382348.2, rms=0.148 (0.000%)
- 030: dt: 0.5000, sse=381476.7, rms=0.148 (0.000%)
- positioning took 3.8 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [91.90 204.10], gm=148.00+-18.70, and vertices in regions > 138.6
- 40560 surface locations found to contain inconsistent values (1380 in, 39180 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=40035.6, rms=0.13
- 031: dt: 0.5000, sse=39744.6, rms=0.129 (0.000%)
- 032: dt: 0.5000, sse=40575.2, rms=0.117 (0.000%)
- 033: dt: 0.5000, sse=41644.4, rms=0.108 (0.000%)
- 034: dt: 0.5000, sse=42539.4, rms=0.103 (0.000%)
- 035: dt: 0.5000, sse=43306.9, rms=0.098 (0.000%)
- 036: dt: 0.5000, sse=44077.8, rms=0.093 (0.000%)
- 037: dt: 0.5000, sse=44816.4, rms=0.089 (0.000%)
- 038: dt: 0.5000, sse=45517.9, rms=0.085 (0.000%)
- 039: dt: 0.5000, sse=46207.3, rms=0.081 (0.000%)
- 040: dt: 0.5000, sse=46861.9, rms=0.077 (0.000%)
- 041: dt: 0.5000, sse=47500.9, rms=0.074 (0.000%)
- 042: dt: 0.5000, sse=48092.5, rms=0.071 (0.000%)
- 043: dt: 0.5000, sse=48642.2, rms=0.068 (0.000%)
- 044: dt: 0.5000, sse=49177.7, rms=0.066 (0.000%)
- 045: dt: 0.5000, sse=49657.5, rms=0.064 (0.000%)
- 046: dt: 0.5000, sse=50124.4, rms=0.061 (0.000%)
- 047: dt: 0.5000, sse=50548.6, rms=0.059 (0.000%)
- 048: dt: 0.5000, sse=50948.0, rms=0.057 (0.000%)
- 049: dt: 0.5000, sse=51315.6, rms=0.056 (0.000%)
- 050: dt: 0.5000, sse=51667.8, rms=0.054 (0.000%)
- 051: dt: 0.5000, sse=52005.2, rms=0.053 (0.000%)
- 052: dt: 0.5000, sse=52307.1, rms=0.051 (0.000%)
- 053: dt: 0.5000, sse=52592.9, rms=0.050 (0.000%)
- 054: dt: 0.5000, sse=52862.3, rms=0.049 (0.000%)
- 055: dt: 0.5000, sse=53107.9, rms=0.047 (0.000%)
- 056: dt: 0.5000, sse=53321.7, rms=0.046 (0.000%)
- 057: dt: 0.5000, sse=53544.5, rms=0.045 (0.000%)
- 058: dt: 0.5000, sse=53733.9, rms=0.044 (0.000%)
- 059: dt: 0.5000, sse=53928.5, rms=0.044 (0.000%)
- 060: dt: 0.5000, sse=54086.1, rms=0.043 (0.000%)
- positioning took 3.8 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [88.00 208.00], gm=148.00+-20.00, and vertices in regions > 138.0
- 39904 surface locations found to contain inconsistent values (196 in, 39708 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=5962.3, rms=0.06
- 061: dt: 0.5000, sse=5914.0, rms=0.062 (0.000%)
- 062: dt: 0.5000, sse=5976.0, rms=0.053 (0.000%)
- 063: dt: 0.5000, sse=6066.8, rms=0.048 (0.000%)
- 064: dt: 0.5000, sse=6144.3, rms=0.045 (0.000%)
- 065: dt: 0.5000, sse=6199.1, rms=0.043 (0.000%)
- 066: dt: 0.5000, sse=6231.9, rms=0.041 (0.000%)
- 067: dt: 0.5000, sse=6250.7, rms=0.040 (0.000%)
- 068: dt: 0.5000, sse=6266.9, rms=0.038 (0.000%)
- 069: dt: 0.5000, sse=6283.2, rms=0.037 (0.000%)
- 070: dt: 0.5000, sse=6297.0, rms=0.036 (0.000%)
- 071: dt: 0.5000, sse=6311.6, rms=0.035 (0.000%)
- 072: dt: 0.5000, sse=6323.0, rms=0.034 (0.000%)
- 073: dt: 0.5000, sse=6333.2, rms=0.033 (0.000%)
- 074: dt: 0.5000, sse=6342.9, rms=0.032 (0.000%)
- 075: dt: 0.5000, sse=6350.4, rms=0.031 (0.000%)
- 076: dt: 0.5000, sse=6357.1, rms=0.031 (0.000%)
- 077: dt: 0.5000, sse=6364.1, rms=0.030 (0.000%)
- 078: dt: 0.5000, sse=6368.8, rms=0.029 (0.000%)
- 079: dt: 0.5000, sse=6373.8, rms=0.029 (0.000%)
- 080: dt: 0.5000, sse=6378.7, rms=0.028 (0.000%)
- 081: dt: 0.5000, sse=6382.8, rms=0.028 (0.000%)
- 082: dt: 0.5000, sse=6387.8, rms=0.028 (0.000%)
- 083: dt: 0.5000, sse=6392.5, rms=0.027 (0.000%)
- 084: dt: 0.5000, sse=6395.8, rms=0.027 (0.000%)
- 085: dt: 0.5000, sse=6398.5, rms=0.027 (0.000%)
- 086: dt: 0.5000, sse=6401.3, rms=0.027 (0.000%)
- 087: dt: 0.5000, sse=6403.1, rms=0.026 (0.000%)
- 088: dt: 0.5000, sse=6405.5, rms=0.026 (0.000%)
- 089: dt: 0.5000, sse=6406.4, rms=0.026 (0.000%)
- 090: dt: 0.5000, sse=6408.0, rms=0.026 (0.000%)
- positioning took 3.7 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [86.80 209.20], gm=148.00+-20.40, and vertices in regions > 137.8
- 39827 surface locations found to contain inconsistent values (57 in, 39770 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/sub018/surf/lh.pial...
- writing smoothed curvature to lh.curv.pial
- 000: dt: 0.0000, sse=817.3, rms=0.04
- 091: dt: 0.5000, sse=806.3, rms=0.036 (0.000%)
- 092: dt: 0.5000, sse=773.5, rms=0.031 (0.000%)
- 093: dt: 0.5000, sse=763.7, rms=0.030 (0.000%)
- 094: dt: 0.5000, sse=758.7, rms=0.029 (0.000%)
- 095: dt: 0.5000, sse=754.5, rms=0.028 (0.000%)
- 096: dt: 0.5000, sse=750.9, rms=0.027 (0.000%)
- 097: dt: 0.5000, sse=748.2, rms=0.027 (0.000%)
- 098: dt: 0.5000, sse=745.7, rms=0.026 (0.000%)
- 099: dt: 0.5000, sse=743.6, rms=0.026 (0.000%)
- 100: dt: 0.5000, sse=741.3, rms=0.026 (0.000%)
- 101: dt: 0.5000, sse=739.4, rms=0.025 (0.000%)
- 102: dt: 0.5000, sse=737.4, rms=0.025 (0.000%)
- 103: dt: 0.5000, sse=735.3, rms=0.025 (0.000%)
- 104: dt: 0.5000, sse=733.6, rms=0.024 (0.000%)
- 105: dt: 0.5000, sse=733.2, rms=0.024 (0.000%)
- 106: dt: 0.5000, sse=731.6, rms=0.024 (0.000%)
- 107: dt: 0.5000, sse=730.2, rms=0.024 (0.000%)
- 108: dt: 0.5000, sse=729.1, rms=0.024 (0.000%)
- 109: dt: 0.5000, sse=728.0, rms=0.023 (0.000%)
- 110: dt: 0.5000, sse=727.1, rms=0.023 (0.000%)
- 111: dt: 0.5000, sse=726.2, rms=0.023 (0.000%)
- 112: dt: 0.5000, sse=725.7, rms=0.023 (0.000%)
- 113: dt: 0.5000, sse=725.1, rms=0.023 (0.000%)
- 114: dt: 0.5000, sse=724.7, rms=0.023 (0.000%)
- 115: dt: 0.5000, sse=723.9, rms=0.023 (0.000%)
- 116: dt: 0.5000, sse=723.5, rms=0.022 (0.000%)
- 117: dt: 0.5000, sse=723.2, rms=0.022 (0.000%)
- 118: dt: 0.5000, sse=722.7, rms=0.022 (0.000%)
- 119: dt: 0.5000, sse=722.5, rms=0.022 (0.000%)
- 120: dt: 0.5000, sse=722.2, rms=0.022 (0.000%)
- positioning took 3.6 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.curv.pial
- writing smoothed area to lh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.area.pial
- vertex spacing 1.03 +- 0.44 (0.05-->8.78) (max @ vno 105864 --> 105855)
- face area 0.41 +- 0.32 (0.00-->6.08)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 140393 vertices processed
- 25000 of 140393 vertices processed
- 50000 of 140393 vertices processed
- 75000 of 140393 vertices processed
- 100000 of 140393 vertices processed
- 125000 of 140393 vertices processed
- 0 of 140393 vertices processed
- 25000 of 140393 vertices processed
- 50000 of 140393 vertices processed
- 75000 of 140393 vertices processed
- 100000 of 140393 vertices processed
- 125000 of 140393 vertices processed
- thickness calculation complete, 504:1123 truncations.
- 28473 vertices at 0 distance
- 90269 vertices at 1 distance
- 91832 vertices at 2 distance
- 39562 vertices at 3 distance
- 12001 vertices at 4 distance
- 3696 vertices at 5 distance
- 1308 vertices at 6 distance
- 460 vertices at 7 distance
- 159 vertices at 8 distance
- 80 vertices at 9 distance
- 51 vertices at 10 distance
- 41 vertices at 11 distance
- 21 vertices at 12 distance
- 25 vertices at 13 distance
- 22 vertices at 14 distance
- 24 vertices at 15 distance
- 13 vertices at 16 distance
- 10 vertices at 17 distance
- 8 vertices at 18 distance
- 8 vertices at 19 distance
- 11 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.thickness
- positioning took 18.6 minutes
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts
- cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.woT2.pial
- `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.woT2.pial'
- mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub018 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/sub018/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/wm.mgz...
- 18329 bright wm thresholded.
- 358 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.orig...
- computing class statistics...
- border white: 252064 voxels (1.50%)
- border gray 291583 voxels (1.74%)
- WM (92.0): 92.8 +- 10.3 [70.0 --> 110.0]
- GM (75.0) : 73.1 +- 12.8 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 46.2 (was 70)
- setting MAX_BORDER_WHITE to 115.3 (was 105)
- setting MIN_BORDER_WHITE to 59.0 (was 85)
- setting MAX_CSF to 33.3 (was 40)
- setting MAX_GRAY to 94.7 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 52.6 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 20.5 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=105, GM=59
- mean inside = 92.3, mean outside = 68.0
- 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/sub018/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.90 +- 0.25 (0.05-->3.94) (max @ vno 105775 --> 105781)
- face area 0.34 +- 0.16 (0.00-->2.89)
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 14 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 2 with 5 points - only 0.00% unknown
- deleting segment 4 with 9 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 6 with 517 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 7 with 3 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 8 with 1 points - only 0.00% unknown
- deleting segment 9 with 5 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 10 with 2 points - only 0.00% unknown
- deleting segment 11 with 5 points - only 0.00% unknown
- deleting segment 12 with 12 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 13 with 2 points - only 0.00% unknown
- tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.90 +- 0.25 (0.07-->3.94) (max @ vno 105775 --> 105781)
- face area 0.34 +- 0.16 (0.00-->2.89)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4786804.0, rms=0.00
- rms = 1.12, time step reduction 1 of 3 to 0.250...
- rms = 0.30, 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=4786804.0, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 14 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 2 with 5 points - only 0.00% unknown
- deleting segment 3 with 9 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 5 with 517 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 6 with 3 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 7 with 1 points - only 0.00% unknown
- deleting segment 8 with 5 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 9 with 2 points - only 0.00% unknown
- deleting segment 10 with 5 points - only 0.00% unknown
- deleting segment 11 with 12 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 12 with 2 points - only 0.00% unknown
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.90 +- 0.25 (0.07-->3.94) (max @ vno 105775 --> 105781)
- face area 0.34 +- 0.16 (0.00-->2.89)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4786804.0, rms=0.00
- rms = 1.12, time step reduction 1 of 3 to 0.250...
- rms = 0.30, 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=4786804.0, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 14 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 2 with 5 points - only 0.00% unknown
- deleting segment 3 with 9 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 5 with 517 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 6 with 3 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 7 with 1 points - only 0.00% unknown
- deleting segment 8 with 5 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 9 with 2 points - only 0.00% unknown
- deleting segment 10 with 5 points - only 0.00% unknown
- deleting segment 11 with 12 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 12 with 2 points - only 0.00% unknown
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.90 +- 0.25 (0.07-->3.94) (max @ vno 105775 --> 105781)
- face area 0.34 +- 0.16 (0.00-->2.89)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4786804.0, rms=0.00
- rms = 1.12, time step reduction 1 of 3 to 0.250...
- rms = 0.30, 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=4786804.0, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 14 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 2 with 5 points - only 0.00% unknown
- deleting segment 3 with 9 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 5 with 517 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 6 with 3 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 7 with 1 points - only 0.00% unknown
- deleting segment 8 with 5 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 9 with 2 points - only 0.00% unknown
- deleting segment 10 with 5 points - only 0.00% unknown
- deleting segment 11 with 12 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 12 with 2 points - only 0.00% unknown
- tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- repositioning cortical surface to gray/csf boundary.
- smoothing T1 volume with sigma = 2.000
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4786804.0, rms=0.00
- rms = 1.12, time step reduction 1 of 3 to 0.250...
- rms = 0.30, 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=4786804.0, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- 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 [95.50 206.50], gm=151.00+-18.50, and vertices in regions > 141.7
- 44232 surface locations found to contain inconsistent values (4850 in, 39382 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=530450.2, rms=0.24
- 001: dt: 0.5000, sse=496390.7, rms=0.228 (0.000%)
- 002: dt: 0.5000, sse=475648.5, rms=0.214 (0.000%)
- 003: dt: 0.5000, sse=462108.0, rms=0.203 (0.000%)
- 004: dt: 0.5000, sse=451678.9, rms=0.193 (0.000%)
- 005: dt: 0.5000, sse=444022.7, rms=0.185 (0.000%)
- 006: dt: 0.5000, sse=438176.1, rms=0.178 (0.000%)
- 007: dt: 0.5000, sse=433698.3, rms=0.172 (0.000%)
- 008: dt: 0.5000, sse=430027.5, rms=0.167 (0.000%)
- 009: dt: 0.5000, sse=426949.0, rms=0.162 (0.000%)
- 010: dt: 0.5000, sse=424324.4, rms=0.158 (0.000%)
- 011: dt: 0.5000, sse=422159.2, rms=0.155 (0.000%)
- 012: dt: 0.5000, sse=420066.1, rms=0.153 (0.000%)
- 013: dt: 0.5000, sse=418046.2, rms=0.150 (0.000%)
- 014: dt: 0.5000, sse=416339.5, rms=0.149 (0.000%)
- 015: dt: 0.5000, sse=414964.9, rms=0.147 (0.000%)
- 016: dt: 0.5000, sse=413199.2, rms=0.146 (0.000%)
- 017: dt: 0.5000, sse=411796.6, rms=0.145 (0.000%)
- 018: dt: 0.5000, sse=410236.3, rms=0.144 (0.000%)
- 019: dt: 0.5000, sse=408883.5, rms=0.143 (0.000%)
- 020: dt: 0.5000, sse=407251.7, rms=0.143 (0.000%)
- 021: dt: 0.5000, sse=405678.5, rms=0.143 (0.000%)
- 022: dt: 0.5000, sse=404358.2, rms=0.142 (0.000%)
- 023: dt: 0.5000, sse=403124.8, rms=0.142 (0.000%)
- 024: dt: 0.5000, sse=402216.7, rms=0.142 (0.000%)
- 025: dt: 0.5000, sse=401032.8, rms=0.142 (0.000%)
- 026: dt: 0.5000, sse=399742.6, rms=0.142 (0.000%)
- 027: dt: 0.5000, sse=399105.4, rms=0.142 (0.000%)
- 028: dt: 0.5000, sse=397467.0, rms=0.142 (0.000%)
- 029: dt: 0.5000, sse=396512.8, rms=0.143 (0.000%)
- 030: dt: 0.5000, sse=395344.1, rms=0.143 (0.000%)
- positioning took 3.8 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [95.00 209.00], gm=152.00+-19.00, and vertices in regions > 142.5
- 36893 surface locations found to contain inconsistent values (1674 in, 35219 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=41072.2, rms=0.12
- 031: dt: 0.5000, sse=40811.2, rms=0.119 (0.000%)
- 032: dt: 0.5000, sse=41752.4, rms=0.108 (0.000%)
- 033: dt: 0.5000, sse=42858.4, rms=0.100 (0.000%)
- 034: dt: 0.5000, sse=43748.3, rms=0.095 (0.000%)
- 035: dt: 0.5000, sse=44465.2, rms=0.090 (0.000%)
- 036: dt: 0.5000, sse=45185.7, rms=0.086 (0.000%)
- 037: dt: 0.5000, sse=45831.9, rms=0.082 (0.000%)
- 038: dt: 0.5000, sse=46480.4, rms=0.078 (0.000%)
- 039: dt: 0.5000, sse=47102.3, rms=0.074 (0.000%)
- 040: dt: 0.5000, sse=47684.6, rms=0.071 (0.000%)
- 041: dt: 0.5000, sse=48250.4, rms=0.068 (0.000%)
- 042: dt: 0.5000, sse=48767.7, rms=0.065 (0.000%)
- 043: dt: 0.5000, sse=49249.2, rms=0.063 (0.000%)
- 044: dt: 0.5000, sse=49677.4, rms=0.061 (0.000%)
- 045: dt: 0.5000, sse=50121.8, rms=0.058 (0.000%)
- 046: dt: 0.5000, sse=50552.3, rms=0.056 (0.000%)
- 047: dt: 0.5000, sse=50947.3, rms=0.055 (0.000%)
- 048: dt: 0.5000, sse=51327.3, rms=0.053 (0.000%)
- 049: dt: 0.5000, sse=51671.2, rms=0.051 (0.000%)
- 050: dt: 0.5000, sse=51978.6, rms=0.050 (0.000%)
- 051: dt: 0.5000, sse=52259.2, rms=0.049 (0.000%)
- 052: dt: 0.5000, sse=52553.6, rms=0.048 (0.000%)
- 053: dt: 0.5000, sse=52788.2, rms=0.046 (0.000%)
- 054: dt: 0.5000, sse=53029.3, rms=0.045 (0.000%)
- 055: dt: 0.5000, sse=53250.7, rms=0.044 (0.000%)
- 056: dt: 0.5000, sse=53457.5, rms=0.043 (0.000%)
- 057: dt: 0.5000, sse=53632.2, rms=0.043 (0.000%)
- 058: dt: 0.5000, sse=53805.5, rms=0.042 (0.000%)
- 059: dt: 0.5000, sse=53961.0, rms=0.041 (0.000%)
- 060: dt: 0.5000, sse=54098.8, rms=0.040 (0.000%)
- positioning took 3.8 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [92.80 209.20], gm=151.00+-19.40, and vertices in regions > 141.3
- 33949 surface locations found to contain inconsistent values (300 in, 33649 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=5741.9, rms=0.05
- 061: dt: 0.5000, sse=5735.1, rms=0.049 (0.000%)
- 062: dt: 0.5000, sse=5759.6, rms=0.046 (0.000%)
- 063: dt: 0.5000, sse=5779.8, rms=0.043 (0.000%)
- 064: dt: 0.5000, sse=5800.0, rms=0.041 (0.000%)
- 065: dt: 0.5000, sse=5811.0, rms=0.039 (0.000%)
- 066: dt: 0.5000, sse=5818.1, rms=0.038 (0.000%)
- 067: dt: 0.5000, sse=5822.6, rms=0.036 (0.000%)
- 068: dt: 0.5000, sse=5824.8, rms=0.035 (0.000%)
- 069: dt: 0.5000, sse=5828.1, rms=0.034 (0.000%)
- 070: dt: 0.5000, sse=5832.3, rms=0.033 (0.000%)
- 071: dt: 0.5000, sse=5835.2, rms=0.033 (0.000%)
- 072: dt: 0.5000, sse=5840.0, rms=0.032 (0.000%)
- 073: dt: 0.5000, sse=5843.6, rms=0.031 (0.000%)
- 074: dt: 0.5000, sse=5846.3, rms=0.030 (0.000%)
- 075: dt: 0.5000, sse=5849.5, rms=0.029 (0.000%)
- 076: dt: 0.5000, sse=5850.6, rms=0.029 (0.000%)
- 077: dt: 0.5000, sse=5853.0, rms=0.028 (0.000%)
- 078: dt: 0.5000, sse=5855.4, rms=0.028 (0.000%)
- 079: dt: 0.5000, sse=5857.1, rms=0.027 (0.000%)
- 080: dt: 0.5000, sse=5859.6, rms=0.027 (0.000%)
- 081: dt: 0.5000, sse=5861.7, rms=0.026 (0.000%)
- 082: dt: 0.5000, sse=5863.9, rms=0.026 (0.000%)
- 083: dt: 0.5000, sse=5865.9, rms=0.025 (0.000%)
- 084: dt: 0.5000, sse=5868.4, rms=0.025 (0.000%)
- 085: dt: 0.5000, sse=5869.6, rms=0.025 (0.000%)
- 086: dt: 0.5000, sse=5870.3, rms=0.024 (0.000%)
- 087: dt: 0.5000, sse=5872.2, rms=0.024 (0.000%)
- 088: dt: 0.5000, sse=5874.2, rms=0.024 (0.000%)
- 089: dt: 0.5000, sse=5876.5, rms=0.024 (0.000%)
- 090: dt: 0.5000, sse=5877.6, rms=0.024 (0.000%)
- positioning took 3.7 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [92.50 209.50], gm=151.00+-19.50, and vertices in regions > 141.2
- 34266 surface locations found to contain inconsistent values (62 in, 34204 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/sub018/surf/rh.pial...
- writing smoothed curvature to rh.curv.pial
- 000: dt: 0.0000, sse=699.2, rms=0.03
- 091: dt: 0.5000, sse=698.4, rms=0.030 (0.000%)
- 092: dt: 0.5000, sse=689.3, rms=0.028 (0.000%)
- 093: dt: 0.5000, sse=683.6, rms=0.027 (0.000%)
- 094: dt: 0.5000, sse=678.6, rms=0.026 (0.000%)
- 095: dt: 0.5000, sse=674.1, rms=0.026 (0.000%)
- 096: dt: 0.5000, sse=670.6, rms=0.025 (0.000%)
- 097: dt: 0.5000, sse=667.7, rms=0.025 (0.000%)
- 098: dt: 0.5000, sse=665.2, rms=0.024 (0.000%)
- 099: dt: 0.5000, sse=663.1, rms=0.024 (0.000%)
- 100: dt: 0.5000, sse=660.9, rms=0.024 (0.000%)
- 101: dt: 0.5000, sse=659.7, rms=0.023 (0.000%)
- 102: dt: 0.5000, sse=658.1, rms=0.023 (0.000%)
- 103: dt: 0.5000, sse=657.1, rms=0.023 (0.000%)
- 104: dt: 0.5000, sse=655.2, rms=0.023 (0.000%)
- 105: dt: 0.5000, sse=653.8, rms=0.022 (0.000%)
- 106: dt: 0.5000, sse=652.3, rms=0.022 (0.000%)
- 107: dt: 0.5000, sse=651.3, rms=0.022 (0.000%)
- 108: dt: 0.5000, sse=650.1, rms=0.022 (0.000%)
- 109: dt: 0.5000, sse=649.0, rms=0.021 (0.000%)
- 110: dt: 0.5000, sse=648.2, rms=0.021 (0.000%)
- 111: dt: 0.5000, sse=648.1, rms=0.021 (0.000%)
- 112: dt: 0.5000, sse=647.5, rms=0.021 (0.000%)
- 113: dt: 0.5000, sse=647.0, rms=0.021 (0.000%)
- 114: dt: 0.5000, sse=647.6, rms=0.021 (0.000%)
- 115: dt: 0.5000, sse=647.1, rms=0.021 (0.000%)
- 116: dt: 0.5000, sse=646.2, rms=0.021 (0.000%)
- 117: dt: 0.5000, sse=645.5, rms=0.021 (0.000%)
- 118: dt: 0.5000, sse=645.0, rms=0.021 (0.000%)
- 119: dt: 0.5000, sse=644.5, rms=0.021 (0.000%)
- 120: dt: 0.5000, sse=644.1, rms=0.021 (0.000%)
- positioning took 3.6 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.curv.pial
- writing smoothed area to rh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.area.pial
- vertex spacing 1.03 +- 0.44 (0.09-->7.51) (max @ vno 95616 --> 94572)
- face area 0.41 +- 0.31 (0.00-->4.80)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 140674 vertices processed
- 25000 of 140674 vertices processed
- 50000 of 140674 vertices processed
- 75000 of 140674 vertices processed
- 100000 of 140674 vertices processed
- 125000 of 140674 vertices processed
- 0 of 140674 vertices processed
- 25000 of 140674 vertices processed
- 50000 of 140674 vertices processed
- 75000 of 140674 vertices processed
- 100000 of 140674 vertices processed
- 125000 of 140674 vertices processed
- thickness calculation complete, 475:801 truncations.
- 29524 vertices at 0 distance
- 92204 vertices at 1 distance
- 92773 vertices at 2 distance
- 39374 vertices at 3 distance
- 11163 vertices at 4 distance
- 2833 vertices at 5 distance
- 823 vertices at 6 distance
- 324 vertices at 7 distance
- 118 vertices at 8 distance
- 70 vertices at 9 distance
- 38 vertices at 10 distance
- 34 vertices at 11 distance
- 26 vertices at 12 distance
- 19 vertices at 13 distance
- 25 vertices at 14 distance
- 11 vertices at 15 distance
- 14 vertices at 16 distance
- 16 vertices at 17 distance
- 11 vertices at 18 distance
- 13 vertices at 19 distance
- 11 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.thickness
- positioning took 18.5 minutes
- #--------------------------------------------
- #@# Surf Volume lh Fri Aug 9 00:09:30 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf
- mris_calc -o lh.area.mid lh.area add lh.area.pial
- Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o lh.area.mid lh.area.mid div 2
- Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o lh.volume lh.area.mid mul lh.thickness
- Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ]
- #--------------------------------------------
- #@# Surf Volume rh Fri Aug 9 00:09:30 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf
- mris_calc -o rh.area.mid rh.area add rh.area.pial
- Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o rh.area.mid rh.area.mid div 2
- Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ]
- mris_calc -o rh.volume rh.area.mid mul rh.thickness
- Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ]
- #--------------------------------------------
- #@# Cortical ribbon mask Fri Aug 9 00:09:31 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri
- mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon sub018
- 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 = 27
- writing volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/ribbon.mgz
- writing ribbon files
- #--------------------------------------------
- #@# ASeg Stats Fri Aug 9 00:27:32 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018
- 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 sub018
- $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 sub018
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- UseRobust 0
- atlas_icv (eTIV) = 1181492 mm^3 (det: 1.648852 )
- Computing euler number
- orig.nofix lheno = -18, rheno = -32
- orig.nofix lhholes = 10, rhholes = 17
- Loading mri/aseg.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 262772.781 262088.000 diff= 684.8 pctdiff= 0.261
- rhCtxGM: 259118.403 258515.000 diff= 603.4 pctdiff= 0.233
- lhCtxWM: 216828.496 216683.000 diff= 145.5 pctdiff= 0.067
- rhCtxWM: 218597.423 218508.000 diff= 89.4 pctdiff= 0.041
- SubCortGMVol 63231.000
- SupraTentVol 1038215.103 (1035985.000) diff=2230.103 pctdiff=0.215
- SupraTentVolNotVent 1021603.103 (1019373.000) diff=2230.103 pctdiff=0.218
- BrainSegVol 1156426.000 (1153227.000) diff=3199.000 pctdiff=0.277
- BrainSegVolNotVent 1135637.000 (1136886.103) diff=-1249.103 pctdiff=-0.110
- BrainSegVolNotVent 1135637.000
- CerebellumVol 115990.000
- VentChorVol 16612.000
- 3rd4th5thCSF 4177.000
- CSFVol 997.000, OptChiasmVol 255.000
- MaskVol 1567075.000
- 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 6794 6793.784
- 4 5 Left-Inf-Lat-Vent 648 647.810
- 5 7 Left-Cerebellum-White-Matter 13292 13292.321
- 6 8 Left-Cerebellum-Cortex 44830 44830.324
- 7 10 Left-Thalamus-Proper 8046 8045.522
- 8 11 Left-Caudate 3815 3814.885
- 9 12 Left-Putamen 6339 6339.314
- 10 13 Left-Pallidum 1831 1830.605
- 11 14 3rd-Ventricle 814 814.475
- 12 15 4th-Ventricle 2579 2579.153
- 13 16 Brain-Stem 21153 21152.502
- 14 17 Left-Hippocampus 3717 3717.286
- 15 18 Left-Amygdala 1772 1771.706
- 16 24 CSF 988 988.454
- 17 26 Left-Accumbens-area 680 680.352
- 18 28 Left-VentralDC 4406 4406.250
- 19 30 Left-vessel 137 137.068
- 20 31 Left-choroid-plexus 1239 1239.441
- 23 43 Right-Lateral-Ventricle 6025 6025.433
- 24 44 Right-Inf-Lat-Vent 317 317.407
- 25 46 Right-Cerebellum-White-Matter 13968 13967.782
- 26 47 Right-Cerebellum-Cortex 46835 46834.531
- 27 49 Right-Thalamus-Proper 7796 7795.538
- 28 50 Right-Caudate 3946 3946.068
- 29 51 Right-Putamen 5839 5838.778
- 30 52 Right-Pallidum 2229 2228.593
- 31 53 Right-Hippocampus 3824 3823.980
- 32 54 Right-Amygdala 1798 1797.534
- 33 58 Right-Accumbens-area 719 719.100
- 34 60 Right-VentralDC 4067 4067.275
- 35 62 Right-vessel 183 182.967
- 36 63 Right-choroid-plexus 1566 1565.628
- 37 72 5th-Ventricle 0 0.000
- 38 77 WM-hypointensities 1449 1449.195
- 39 78 Left-WM-hypointensities 0 0.000
- 40 79 Right-WM-hypointensities 0 0.000
- 41 80 non-WM-hypointensities 15 14.949
- 42 81 Left-non-WM-hypointensities 0 0.000
- 43 82 Right-non-WM-hypointensities 0 0.000
- 44 85 Optic-Chiasm 264 263.729
- 45 251 CC_Posterior 879 879.355
- 46 252 CC_Mid_Posterior 427 426.819
- 47 253 CC_Central 415 414.964
- 48 254 CC_Mid_Anterior 448 448.003
- 49 255 CC_Anterior 883 882.874
- Reporting on 45 segmentations
- mri_segstats done
- #-----------------------------------------
- #@# AParc-to-ASeg Fri Aug 9 00:31:05 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018
- mri_aparc2aseg --s sub018 --volmask
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- subject sub018
- outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/aparc+aseg.mgz
- useribbon 0
- baseoffset 0
- RipUnknown 0
- Reading lh white surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.white
- Reading lh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.pial
- Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/surf/rh.white
- Reading rh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.pial
- Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/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/sub018/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 = 518587
- Used brute-force search on 0 voxels
- Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/aparc+aseg.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018
- mri_aparc2aseg --s sub018 --volmask --a2009s
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- subject sub018
- outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/aparc.a2009s+aseg.mgz
- useribbon 0
- baseoffset 10100
- RipUnknown 0
- Reading lh white surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.white
- Reading lh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.pial
- Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/surf/rh.white
- Reading rh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.pial
- Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/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/sub018/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 = 518587
- Used brute-force search on 0 voxels
- Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/aparc.a2009s+aseg.mgz
- #-----------------------------------------
- #@# WMParc Fri Aug 9 00:36:01 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018
- mri_aparc2aseg --s sub018 --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 sub018
- 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/sub018/mri/aparc+aseg.mgz
- Reading lh white surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.white
- Reading lh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.pial
- Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/surf/rh.white
- Reading rh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.pial
- Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/mri/ribbon.mgz
- Loading filled from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/filled.mgz
- Ripping vertices labeled as unkown
- Ripped 8590 vertices from left hemi
- Ripped 8137 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/sub018/mri/aseg.mgz
- Loading Ctx Seg File /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 = 952645
- Used brute-force search on 13 voxels
- Fixing Parahip LH WM
- Found 6 clusters
- 0 k 1.000000
- 1 k 3.000000
- 2 k 1.000000
- 3 k 14.000000
- 4 k 1539.000000
- 5 k 1.000000
- Fixing Parahip RH WM
- Found 10 clusters
- 0 k 1.000000
- 1 k 6.000000
- 2 k 1.000000
- 3 k 2.000000
- 4 k 2.000000
- 5 k 1.000000
- 6 k 1538.000000
- 7 k 2.000000
- 8 k 2.000000
- 9 k 1.000000
- Writing output aseg to mri/wmparc.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018
- 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 sub018 --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 sub018 --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) = 1181492 mm^3 (det: 1.648852 )
- Loading mri/wmparc.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 262772.781 262088.000 diff= 684.8 pctdiff= 0.261
- rhCtxGM: 259118.403 258515.000 diff= 603.4 pctdiff= 0.233
- lhCtxWM: 216828.496 216683.000 diff= 145.5 pctdiff= 0.067
- rhCtxWM: 218597.423 218508.000 diff= 89.4 pctdiff= 0.041
- SubCortGMVol 63231.000
- SupraTentVol 1038215.103 (1035985.000) diff=2230.103 pctdiff=0.215
- SupraTentVolNotVent 1021603.103 (1019373.000) diff=2230.103 pctdiff=0.218
- BrainSegVol 1156426.000 (1153227.000) diff=3199.000 pctdiff=0.277
- BrainSegVolNotVent 1135637.000 (1136886.103) diff=-1249.103 pctdiff=-0.110
- BrainSegVolNotVent 1135637.000
- CerebellumVol 115990.000
- VentChorVol 16612.000
- 3rd4th5thCSF 4177.000
- CSFVol 997.000, OptChiasmVol 255.000
- MaskVol 1567075.000
- 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 3834 3834.180
- 2 3002 wm-lh-caudalanteriorcingulate 3150 3150.293
- 3 3003 wm-lh-caudalmiddlefrontal 6313 6313.133
- 4 3004 wm-lh-corpuscallosum 0 0.000
- 5 3005 wm-lh-cuneus 1769 1769.453
- 6 3006 wm-lh-entorhinal 908 908.430
- 7 3007 wm-lh-fusiform 6895 6894.660
- 8 3008 wm-lh-inferiorparietal 9785 9785.111
- 9 3009 wm-lh-inferiortemporal 7366 7365.650
- 10 3010 wm-lh-isthmuscingulate 3607 3606.861
- 11 3011 wm-lh-lateraloccipital 7569 7569.262
- 12 3012 wm-lh-lateralorbitofrontal 5739 5739.259
- 13 3013 wm-lh-lingual 4006 4006.169
- 14 3014 wm-lh-medialorbitofrontal 3596 3596.006
- 15 3015 wm-lh-middletemporal 5975 5974.587
- 16 3016 wm-lh-parahippocampal 1628 1627.826
- 17 3017 wm-lh-paracentral 3248 3248.455
- 18 3018 wm-lh-parsopercularis 3153 3153.196
- 19 3019 wm-lh-parsorbitalis 808 808.422
- 20 3020 wm-lh-parstriangularis 2984 2983.516
- 21 3021 wm-lh-pericalcarine 2502 2502.453
- 22 3022 wm-lh-postcentral 8140 8140.377
- 23 3023 wm-lh-posteriorcingulate 4864 4863.969
- 24 3024 wm-lh-precentral 12193 12192.650
- 25 3025 wm-lh-precuneus 8386 8386.383
- 26 3026 wm-lh-rostralanteriorcingulate 2341 2340.538
- 27 3027 wm-lh-rostralmiddlefrontal 13413 13413.009
- 28 3028 wm-lh-superiorfrontal 19154 19153.689
- 29 3029 wm-lh-superiorparietal 10914 10914.403
- 30 3030 wm-lh-superiortemporal 7361 7360.979
- 31 3031 wm-lh-supramarginal 8190 8190.038
- 32 3032 wm-lh-frontalpole 250 249.765
- 33 3033 wm-lh-temporalpole 648 647.571
- 34 3034 wm-lh-transversetemporal 703 703.380
- 35 3035 wm-lh-insula 8161 8161.229
- 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 2756 2755.612
- 120 4002 wm-rh-caudalanteriorcingulate 3185 3185.482
- 121 4003 wm-rh-caudalmiddlefrontal 5015 5015.476
- 122 4004 wm-rh-corpuscallosum 0 0.000
- 123 4005 wm-rh-cuneus 2053 2053.431
- 124 4006 wm-rh-entorhinal 721 720.908
- 125 4007 wm-rh-fusiform 6605 6604.547
- 126 4008 wm-rh-inferiorparietal 12158 12158.270
- 127 4009 wm-rh-inferiortemporal 6430 6429.956
- 128 4010 wm-rh-isthmuscingulate 3147 3147.056
- 129 4011 wm-rh-lateraloccipital 7412 7411.778
- 130 4012 wm-rh-lateralorbitofrontal 6967 6966.981
- 131 4013 wm-rh-lingual 4173 4173.202
- 132 4014 wm-rh-medialorbitofrontal 3871 3870.739
- 133 4015 wm-rh-middletemporal 5838 5837.609
- 134 4016 wm-rh-parahippocampal 1605 1604.617
- 135 4017 wm-rh-paracentral 4572 4572.180
- 136 4018 wm-rh-parsopercularis 2959 2958.815
- 137 4019 wm-rh-parsorbitalis 1131 1130.534
- 138 4020 wm-rh-parstriangularis 3535 3534.822
- 139 4021 wm-rh-pericalcarine 2413 2412.734
- 140 4022 wm-rh-postcentral 7238 7237.606
- 141 4023 wm-rh-posteriorcingulate 4396 4395.841
- 142 4024 wm-rh-precentral 13016 13015.992
- 143 4025 wm-rh-precuneus 8389 8389.447
- 144 4026 wm-rh-rostralanteriorcingulate 2165 2165.278
- 145 4027 wm-rh-rostralmiddlefrontal 12097 12097.344
- 146 4028 wm-rh-superiorfrontal 20235 20235.414
- 147 4029 wm-rh-superiorparietal 10732 10731.582
- 148 4030 wm-rh-superiortemporal 7022 7021.965
- 149 4031 wm-rh-supramarginal 9521 9520.531
- 150 4032 wm-rh-frontalpole 335 335.450
- 151 4033 wm-rh-temporalpole 663 662.949
- 152 4034 wm-rh-transversetemporal 619 619.070
- 153 4035 wm-rh-insula 8261 8261.174
- 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 27380 27380.078
- 237 5002 Right-UnsegmentedWhiteMatter 28233 28233.395
- 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/sub018/label
- #--------------------------------------------
- #@# BA Labels lh Fri Aug 9 00:47:03 CEST 2013
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
- Number of reverse mapping hits = 365
- Checking for and removing duplicates
- Writing label file ./lh.BA1.label 4494
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
- Number of reverse mapping hits = 839
- Checking for and removing duplicates
- Writing label file ./lh.BA2.label 8748
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
- Number of reverse mapping hits = 160
- Checking for and removing duplicates
- Writing label file ./lh.BA3a.label 4237
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
- Number of reverse mapping hits = 372
- Checking for and removing duplicates
- Writing label file ./lh.BA3b.label 6355
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
- Number of reverse mapping hits = 304
- Checking for and removing duplicates
- Writing label file ./lh.BA4a.label 6088
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
- Number of reverse mapping hits = 244
- Checking for and removing duplicates
- Writing label file ./lh.BA4p.label 4314
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
- Number of reverse mapping hits = 1162
- Checking for and removing duplicates
- Writing label file ./lh.BA6.label 14751
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
- Number of reverse mapping hits = 405
- Checking for and removing duplicates
- Writing label file ./lh.BA44.label 4586
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
- Number of reverse mapping hits = 800
- Checking for and removing duplicates
- Writing label file ./lh.BA45.label 4222
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
- Number of reverse mapping hits = 930
- Checking for and removing duplicates
- Writing label file ./lh.V1.label 5571
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
- Number of reverse mapping hits = 1979
- Checking for and removing duplicates
- Writing label file ./lh.V2.label 10093
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
- Number of reverse mapping hits = 576
- Checking for and removing duplicates
- Writing label file ./lh.MT.label 2594
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.perirhinal.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
- Number of reverse mapping hits = 176
- Checking for and removing duplicates
- Writing label file ./lh.perirhinal.label 1375
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.thresh.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
- Number of reverse mapping hits = 100
- Checking for and removing duplicates
- Writing label file ./lh.BA1.thresh.label 1114
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.thresh.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
- Number of reverse mapping hits = 419
- Checking for and removing duplicates
- Writing label file ./lh.BA2.thresh.label 2511
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.thresh.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
- 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 sub018 --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 = sub018
- 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/sub018/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
- Number of reverse mapping hits = 158
- Checking for and removing duplicates
- Writing label file ./lh.BA3b.thresh.label 2154
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.thresh.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
- Number of reverse mapping hits = 127
- Checking for and removing duplicates
- Writing label file ./lh.BA4a.thresh.label 2446
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.thresh.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
- Number of reverse mapping hits = 135
- Checking for and removing duplicates
- Writing label file ./lh.BA4p.thresh.label 1684
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.thresh.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
- Number of reverse mapping hits = 470
- Checking for and removing duplicates
- Writing label file ./lh.BA6.thresh.label 7505
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.thresh.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
- Number of reverse mapping hits = 185
- Checking for and removing duplicates
- Writing label file ./lh.BA44.thresh.label 2097
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.thresh.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
- Number of reverse mapping hits = 293
- Checking for and removing duplicates
- Writing label file ./lh.BA45.thresh.label 1444
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.thresh.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
- Number of reverse mapping hits = 676
- Checking for and removing duplicates
- Writing label file ./lh.V1.thresh.label 4081
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.thresh.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
- Number of reverse mapping hits = 882
- Checking for and removing duplicates
- Writing label file ./lh.V2.thresh.label 4216
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.thresh.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
- Number of reverse mapping hits = 149
- Checking for and removing duplicates
- Writing label file ./lh.MT.thresh.label 662
- mri_label2label: Done
- mris_label2annot --s sub018 --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/sub018/label
- cmdline mris_label2annot --s sub018 --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 sub018
- 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/sub018/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 99758 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/label/lh.BA.annot
- mris_label2annot --s sub018 --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/sub018/label
- cmdline mris_label2annot --s sub018 --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 sub018
- 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/sub018/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 117311 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/label/lh.BA.thresh.annot
- mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab sub018 lh white
- computing statistics for each annotation in ./lh.BA.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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
- 1117 652 2411 2.596 0.340 0.150 0.050 24 2.3 BA1
- 4705 3179 8224 2.393 0.462 0.141 0.048 73 8.5 BA2
- 1035 680 1095 2.050 0.468 0.126 0.034 8 1.5 BA3a
- 2486 1706 4034 2.048 0.516 0.121 0.033 28 3.4 BA3b
- 1588 1048 3784 2.874 0.483 0.110 0.027 12 1.9 BA4a
- 1400 928 2434 2.678 0.484 0.112 0.045 18 3.0 BA4p
- 9095 6141 21857 2.897 0.476 0.130 0.043 130 15.8 BA6
- 2321 1632 5130 2.669 0.425 0.146 0.051 41 4.7 BA44
- 3198 2184 6564 2.589 0.400 0.140 0.044 55 5.9 BA45
- 3034 2100 4226 1.901 0.436 0.174 0.118 244 9.9 V1
- 7288 4817 11472 2.180 0.432 0.181 0.078 174 22.2 V2
- 2263 1492 4134 2.407 0.416 0.145 0.230 159 36.4 MT
- 1105 796 3622 3.511 0.745 0.166 0.071 24 3.1 perirhinal
- mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab sub018 lh white
- computing statistics for each annotation in ./lh.BA.thresh.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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
- 796 422 1641 2.633 0.350 0.162 0.057 20 2.0 BA1
- 2086 1444 3762 2.308 0.463 0.135 0.040 30 3.5 BA2
- 849 557 863 2.020 0.445 0.131 0.036 7 1.3 BA3a
- 1624 1124 2248 1.816 0.346 0.102 0.024 11 1.5 BA3b
- 1522 1009 3694 2.941 0.458 0.102 0.025 9 1.7 BA4a
- 1162 767 1943 2.631 0.491 0.108 0.046 16 2.5 BA4p
- 4822 3276 11752 2.936 0.446 0.135 0.045 77 9.5 BA6
- 1515 1090 3362 2.624 0.388 0.156 0.057 33 3.4 BA44
- 1264 845 3095 2.744 0.368 0.158 0.055 31 2.9 BA45
- 3279 2247 4606 1.912 0.443 0.179 0.122 256 11.6 V1
- 3559 2380 5249 2.084 0.432 0.185 0.083 85 11.0 V2
- 604 402 1032 2.290 0.412 0.141 0.047 9 1.2 MT
- #--------------------------------------------
- #@# BA Labels rh Fri Aug 9 00:51:40 CEST 2013
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
- Number of reverse mapping hits = 314
- Checking for and removing duplicates
- Writing label file ./rh.BA1.label 4276
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
- Number of reverse mapping hits = 501
- Checking for and removing duplicates
- Writing label file ./rh.BA2.label 7188
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
- Number of reverse mapping hits = 262
- Checking for and removing duplicates
- Writing label file ./rh.BA3a.label 4242
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
- Number of reverse mapping hits = 370
- Checking for and removing duplicates
- Writing label file ./rh.BA3b.label 4892
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
- Number of reverse mapping hits = 545
- Checking for and removing duplicates
- Writing label file ./rh.BA4a.label 6292
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
- Number of reverse mapping hits = 302
- Checking for and removing duplicates
- Writing label file ./rh.BA4p.label 4775
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
- Number of reverse mapping hits = 1365
- Checking for and removing duplicates
- Writing label file ./rh.BA6.label 13621
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
- Number of reverse mapping hits = 741
- Checking for and removing duplicates
- Writing label file ./rh.BA44.label 7653
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
- Number of reverse mapping hits = 1304
- Checking for and removing duplicates
- Writing label file ./rh.BA45.label 6659
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
- Number of reverse mapping hits = 1009
- Checking for and removing duplicates
- Writing label file ./rh.V1.label 5736
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
- Number of reverse mapping hits = 2277
- Checking for and removing duplicates
- Writing label file ./rh.V2.label 10293
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
- Number of reverse mapping hits = 700
- Checking for and removing duplicates
- Writing label file ./rh.MT.label 2632
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.perirhinal.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
- Number of reverse mapping hits = 102
- Checking for and removing duplicates
- Writing label file ./rh.perirhinal.label 854
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.thresh.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
- Number of reverse mapping hits = 52
- Checking for and removing duplicates
- Writing label file ./rh.BA1.thresh.label 928
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.thresh.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
- Number of reverse mapping hits = 126
- Checking for and removing duplicates
- Writing label file ./rh.BA2.thresh.label 2814
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.thresh.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
- Number of reverse mapping hits = 48
- Checking for and removing duplicates
- Writing label file ./rh.BA3a.thresh.label 1746
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.thresh.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
- Number of reverse mapping hits = 257
- Checking for and removing duplicates
- Writing label file ./rh.BA3b.thresh.label 2440
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.thresh.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
- Number of reverse mapping hits = 140
- Checking for and removing duplicates
- Writing label file ./rh.BA4a.thresh.label 1528
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.thresh.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
- Number of reverse mapping hits = 150
- Checking for and removing duplicates
- Writing label file ./rh.BA4p.thresh.label 1639
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.thresh.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
- Number of reverse mapping hits = 770
- Checking for and removing duplicates
- Writing label file ./rh.BA6.thresh.label 7729
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.thresh.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
- Number of reverse mapping hits = 111
- Checking for and removing duplicates
- Writing label file ./rh.BA44.thresh.label 1123
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.thresh.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
- Number of reverse mapping hits = 300
- Checking for and removing duplicates
- Writing label file ./rh.BA45.thresh.label 1478
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.thresh.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
- Number of reverse mapping hits = 600
- Checking for and removing duplicates
- Writing label file ./rh.V1.thresh.label 3832
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.thresh.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
- Number of reverse mapping hits = 1069
- Checking for and removing duplicates
- Writing label file ./rh.V2.thresh.label 4506
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.thresh.label --trgsubject sub018 --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 = sub018
- 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/sub018/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
- Number of reverse mapping hits = 92
- Checking for and removing duplicates
- Writing label file ./rh.MT.thresh.label 360
- mri_label2label: Done
- mris_label2annot --s sub018 --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/sub018/label
- cmdline mris_label2annot --s sub018 --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 sub018
- 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/sub018/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 99034 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/label/rh.BA.annot
- mris_label2annot --s sub018 --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/sub018/label
- cmdline mris_label2annot --s sub018 --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 sub018
- 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/sub018/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 118121 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/label/rh.BA.thresh.annot
- mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab sub018 rh white
- computing statistics for each annotation in ./rh.BA.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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
- 928 531 1920 2.488 0.307 0.157 0.058 21 2.5 BA1
- 3550 2407 5755 2.239 0.438 0.115 0.039 33 5.8 BA2
- 1097 722 1100 1.949 0.441 0.130 0.038 11 1.9 BA3a
- 2235 1467 3499 2.024 0.486 0.122 0.035 27 3.2 BA3b
- 1493 968 3438 2.828 0.528 0.117 0.043 36 3.4 BA4a
- 1371 862 2318 2.673 0.427 0.105 0.065 32 4.4 BA4p
- 9038 6079 20115 2.770 0.508 0.131 0.042 144 15.2 BA6
- 3104 2109 6505 2.709 0.451 0.134 0.048 46 5.7 BA44
- 4822 3257 10301 2.661 0.495 0.159 0.066 108 12.8 BA45
- 3267 2258 4841 1.937 0.425 0.174 0.117 88 12.3 V1
- 7626 5079 11946 2.119 0.445 0.176 0.093 389 29.3 V2
- 2446 1668 4354 2.416 0.404 0.151 0.069 48 7.2 MT
- 663 489 1850 2.969 0.754 0.173 0.069 14 2.0 perirhinal
- mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab sub018 rh white
- computing statistics for each annotation in ./rh.BA.thresh.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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
- 591 327 1198 2.461 0.285 0.175 0.069 16 1.9 BA1
- 1814 1237 3024 2.241 0.427 0.109 0.029 14 2.1 BA2
- 921 609 860 1.942 0.410 0.135 0.040 8 1.6 BA3a
- 1885 1281 2678 1.882 0.424 0.110 0.029 16 2.3 BA3b
- 1054 641 2371 2.830 0.576 0.118 0.055 35 2.9 BA4a
- 1143 732 1919 2.683 0.411 0.109 0.071 29 4.2 BA4p
- 5698 3807 12616 2.737 0.485 0.133 0.044 108 10.0 BA6
- 788 545 1847 2.768 0.465 0.149 0.071 18 1.7 BA44
- 1275 866 3257 2.811 0.408 0.169 0.072 32 3.5 BA45
- 3083 2141 4478 1.922 0.439 0.170 0.116 79 11.2 V1
- 3962 2660 5991 2.044 0.453 0.195 0.099 130 14.5 V2
- 339 241 700 2.666 0.335 0.196 0.076 9 1.0 MT
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/label
- #--------------------------------------------
- #@# Ex-vivo Entorhinal Cortex Label lh Fri Aug 9 00:56:17 CEST 2013
- mris_spherical_average -erode 1 -orig white -t 0.4 -o sub018 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label
- painting output onto subject sub018.
- processing subject lh.EC_average...
- reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 1051 points to lh.entorhinal_exvivo.label...
- mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label sub018 lh white
- limiting computations to label ./lh.entorhinal_exvivo.label.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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
- 393 258 1336 3.300 0.587 0.155 0.080 12 1.5 ./lh.entorhinal_exvivo.label
- #--------------------------------------------
- #@# Ex-vivo Entorhinal Cortex Label rh Fri Aug 9 00:56:32 CEST 2013
- mris_spherical_average -erode 1 -orig white -t 0.4 -o sub018 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label
- painting output onto subject sub018.
- processing subject rh.EC_average...
- reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 814 points to rh.entorhinal_exvivo.label...
- mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label sub018 rh white
- limiting computations to label ./rh.entorhinal_exvivo.label.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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
- 283 199 1034 3.216 0.614 0.154 0.059 4 0.8 ./rh.entorhinal_exvivo.label
- #------------------------------------------
- Started at Thu Aug 8 10:53:55 CEST 2013
- Ended at Fri Aug 9 00:56:47 CEST 2013
- #@#%# recon-all-run-time-hours 14.048
- recon-all -s sub018 finished without error at Fri Aug 9 00:56:47 CEST 2013
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