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- Thu Aug 8 10:53:42 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007
- /opt/freesurfer/5.3.0/bin/recon-all
- -i /home/data/exppsy/forrest_gump/openfmri.org/sub007/anatomy/highres001.nii.gz -cw256 -all -T2 /home/data/exppsy/forrest_gump/openfmri.org/sub007/anatomy/other/t2w001.nii.gz -T2pial -subjid sub007 -sd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- subjid sub007
- 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 snake4 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 96396048 2805644 0 188520 94505440
- -/+ buffers/cache: 1702088 97499604
- Swap: 25165780 532 25165248
- ########################################
- program versions used
- $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
- $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
- mri_convert -all-info
- ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:42-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- FLIRT version 5.5
- $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
- mri_convert --version
- stable5
- ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- Program nu_correct, built from:
- Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
- ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:44-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:44-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:44-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ======= NUMBER OF OPENMP THREADS = 1 =======
- ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:44-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:44-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:45-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:45-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:45-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:45-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:45-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:45-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:45-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:45-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:45-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:46-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:46-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:46-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:46-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:46-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:46-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:46-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:46-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: fkaule Machine: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:47-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:47-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:47-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: snake4 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: 2013/08/08-08:53:47-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: snake4 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: 2013/08/08-08:53:47-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:48-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:48-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:48-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: snake4 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 40400
- ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/08/08-08:53:49-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: snake4 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/sub007
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub007/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/orig/001.mgz
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub007/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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/sub007/anatomy/highres001.nii.gz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.998766, -0.0418513, -0.0267421)
- j_ras = (-0.0444513, 0.99343, 0.105455)
- k_ras = (-0.022153, -0.106514, 0.994064)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/orig/001.mgz...
- #--------------------------------------------
- #@# T2/FLAIR Input Thu Aug 8 10:54:04 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub007/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/orig/T2raw.mgz
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub007/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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/sub007/anatomy/other/t2w001.nii.gz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.998766, -0.0418513, -0.0267421)
- j_ras = (-0.0444513, 0.99343, 0.105455)
- k_ras = (-0.022153, -0.106514, 0.994064)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/orig/T2raw.mgz...
- #--------------------------------------------
- #@# MotionCor Thu Aug 8 10:54:19 CEST 2013
- Found 1 runs
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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/sub007/mri/orig/001.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/rawavg.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/orig.mgz --conform --cw256
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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/sub007/mri/rawavg.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.998766, -0.0418513, -0.0267421)
- j_ras = (-0.0444513, 0.99343, 0.105455)
- k_ras = (-0.022153, -0.106514, 0.994064)
- Original Data has (0.699921, 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/sub007/mri/orig.mgz...
- mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/talairach.xfm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/orig.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Talairach Thu Aug 8 10:54:56 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri
- mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
- talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
- cp transforms/talairach.auto.xfm transforms/talairach.xfm
- #--------------------------------------------
- #@# Talairach Failure Detection Thu Aug 8 10:57:30 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri
- talairach_afd -T 0.005 -xfm transforms/talairach.xfm
- talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6339, pval=0.3663 >= threshold=0.0050)
- awk -f /opt/freesurfer/5.3.0/bin/extract_talairach_avi_QA.awk /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/talairach_avi.log
- tal_QC_AZS /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/talairach_avi.log
- TalAviQA: 0.95944
- z-score: -4
- #--------------------------------------------
- #@# Nu Intensity Correction Thu Aug 8 10:57:30 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/sub007/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 snake4 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
- Thu Aug 8 10:57:30 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.19125
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.19125/nu0.mnc -odt float
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.19125/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, 4.65661e-09, 3.72529e-09)
- j_ras = (5.58794e-09, -1.49012e-08, -1)
- k_ras = (-8.61473e-09, 1, 1.49012e-08)
- changing data type from uchar to float (noscale = 0)...
- writing to ./tmp.mri_nu_correct.mni.19125/nu0.mnc...
-
- --------------------------------------------------------
- Iteration 1 Thu Aug 8 10:57:33 CEST 2013
- nu_correct -clobber ./tmp.mri_nu_correct.mni.19125/nu0.mnc ./tmp.mri_nu_correct.mni.19125/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.19125/0/
- [fkaule@snake4:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/] [2013-08-08 10:57:33] 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.19125/0/ ./tmp.mri_nu_correct.mni.19125/nu0.mnc ./tmp.mri_nu_correct.mni.19125/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: 0.00108356
- [fkaule@snake4:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/] [2013-08-08 10:58:34] running:
- /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.19125/nu0.mnc ./tmp.mri_nu_correct.mni.19125/0//template.mnc
- Transforming slices:......................................................................................Done
- Transforming slices:................................................................................................................................................................................................................................................................Done
-
-
- --------------------------------------------------------
- Iteration 2 Thu Aug 8 10:58:40 CEST 2013
- nu_correct -clobber ./tmp.mri_nu_correct.mni.19125/nu1.mnc ./tmp.mri_nu_correct.mni.19125/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.19125/1/
- [fkaule@snake4:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/] [2013-08-08 10:58:40] 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.19125/1/ ./tmp.mri_nu_correct.mni.19125/nu1.mnc ./tmp.mri_nu_correct.mni.19125/nu2.imp
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Number of iterations: 30
- CV of field change: 0.000993593
- [fkaule@snake4:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/] [2013-08-08 10:59:20] running:
- /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.19125/nu1.mnc ./tmp.mri_nu_correct.mni.19125/1//template.mnc
- Transforming slices:......................................................................................Done
- Transforming slices:................................................................................................................................................................................................................................................................Done
-
-
-
- mri_binarize --i ./tmp.mri_nu_correct.mni.19125/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.19125/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/sub007/mri
- cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.19125/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.19125/ones.mgz
- sysname Linux
- hostname snake4
- machine x86_64
- user fkaule
- input ./tmp.mri_nu_correct.mni.19125/nu2.mnc
- frame 0
- nErode3d 0
- nErode2d 0
- output ./tmp.mri_nu_correct.mni.19125/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.19125/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.19125/sum.junk --avgwf ./tmp.mri_nu_correct.mni.19125/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.19125/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.19125/sum.junk --avgwf ./tmp.mri_nu_correct.mni.19125/input.mean.dat
- sysname Linux
- hostname snake4
- machine x86_64
- user fkaule
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.19125/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.19125/input.mean.dat
- mri_segstats done
- mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.19125/ones.mgz --i ./tmp.mri_nu_correct.mni.19125/nu2.mnc --sum ./tmp.mri_nu_correct.mni.19125/sum.junk --avgwf ./tmp.mri_nu_correct.mni.19125/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.19125/ones.mgz --i ./tmp.mri_nu_correct.mni.19125/nu2.mnc --sum ./tmp.mri_nu_correct.mni.19125/sum.junk --avgwf ./tmp.mri_nu_correct.mni.19125/output.mean.dat
- sysname Linux
- hostname snake4
- machine x86_64
- user fkaule
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.19125/ones.mgz
- Loading ./tmp.mri_nu_correct.mni.19125/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.19125/output.mean.dat
- mri_segstats done
- mris_calc -o ./tmp.mri_nu_correct.mni.19125/nu2.mnc ./tmp.mri_nu_correct.mni.19125/nu2.mnc mul .91764183674996134785
- Saving result to './tmp.mri_nu_correct.mni.19125/nu2.mnc' (type = MINC ) [ ok ]
- mri_convert ./tmp.mri_nu_correct.mni.19125/nu2.mnc nu.mgz --like orig.mgz
- mri_convert ./tmp.mri_nu_correct.mni.19125/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.19125/nu2.mnc...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, 4.65661e-09, 3.72529e-09)
- j_ras = (5.58794e-09, -1.49012e-08, -1)
- k_ras = (-8.61473e-09, 1, 1.49012e-08)
- INFO: transform src into the like-volume: orig.mgz
- writing to nu.mgz...
- mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz
- type change took 0 minutes and 8 seconds.
- mapping ( 5, 150) to ( 3, 110)
-
-
- Thu Aug 8 11:00:05 CEST 2013
- mri_nu_correct.mni done
- mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/talairach.xfm nu.mgz nu.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Intensity Normalization Thu Aug 8 11:00:06 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri
- mri_normalize -g 1 nu.mgz T1.mgz
- using max gradient = 1.000
- reading from nu.mgz...
- normalizing image...
- talairach transform
- 1.083 0.051 0.061 4.127;
- -0.112 1.040 0.323 -34.242;
- -0.000 -0.364 1.048 4.649;
- 0.000 0.000 0.000 1.000;
- processing without aseg, no1d=0
- MRInormInit():
- INFO: Modifying talairach volume c_(r,a,s) based on average_305
- MRInormalize():
- MRIsplineNormalize(): npeaks = 18
- Starting OpenSpline(): npoints = 18
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Iterating 2 times
- ---------------------------------
- 3d normalization pass 1 of 2
- white matter peak found at 111
- white matter peak found at 107
- gm peak at 56 (56), valley at 33 (33)
- csf peak at 28, setting threshold to 46
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- ---------------------------------
- 3d normalization pass 2 of 2
- white matter peak found at 111
- white matter peak found at 110
- gm peak at 58 (58), valley at 33 (33)
- csf peak at 29, setting threshold to 48
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Done iterating ---------------------------------
- writing output to T1.mgz
- 3D bias adjustment took 2 minutes and 57 seconds.
- #--------------------------------------------
- #@# Skull Stripping Thu Aug 8 11:03:03 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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=13.0
- skull bounding box = (52, 16, 22) --> (203, 255, 201)
- using (102, 96, 112) as brain centroid...
- mean wm in atlas = 126, using box (83,66,90) --> (120, 125,134) to find MRI wm
- before smoothing, mri peak at 110
- after smoothing, mri peak at 109, scaling input intensities by 1.156
- scaling channel 0 by 1.15596
- initial log_p = -4.8
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -4.430507 @ (-9.091, 27.273, -9.091)
- max log p = -4.269811 @ (4.545, -4.545, -4.545)
- max log p = -4.269811 @ (0.000, 0.000, 0.000)
- max log p = -4.237854 @ (1.136, 1.136, 1.136)
- max log p = -4.237854 @ (0.000, 0.000, 0.000)
- max log p = -4.237854 @ (0.000, 0.000, 0.000)
- Found translation: (-3.4, 23.9, -12.5): log p = -4.238
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.2 (thresh=-4.2)
- 0.991 0.052 -0.120 6.814;
- 0.000 1.068 0.421 -25.128;
- 0.140 -0.428 0.979 20.956;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 0.991 0.052 -0.120 6.814;
- 0.000 1.068 0.421 -25.128;
- 0.140 -0.428 0.979 20.956;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.2500
- ****************************************
- Nine parameter search. iteration 2 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-4.0 (thresh=-4.0)
- 0.976 0.077 -0.074 1.470;
- -0.048 1.060 0.315 -8.726;
- 0.107 -0.321 1.020 9.060;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 3 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 0.976 0.077 -0.074 1.470;
- -0.048 1.060 0.315 -8.726;
- 0.107 -0.321 1.020 9.060;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.0625
- ****************************************
- Nine parameter search. iteration 4 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 0.973 0.071 -0.085 4.100;
- -0.039 1.061 0.324 -11.766;
- 0.115 -0.329 1.015 9.213;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 5 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 0.973 0.077 -0.074 1.758;
- -0.048 1.064 0.316 -10.117;
- 0.107 -0.321 1.020 8.546;
- 0.000 0.000 0.000 1.000;
- min search scale 0.025000 reached
- ***********************************************
- Computing MAP estimate using 3481 samples...
- ***********************************************
- dt = 5.00e-06, momentum=0.80, tol=1.00e-05
- l_intensity = 1.0000
- Aligning input volume to GCA...
- Transform matrix
- 0.97348 0.07738 -0.07416 1.75816;
- -0.04799 1.06420 0.31625 -10.11703;
- 0.10721 -0.32135 1.01961 8.54551;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 3481
- Quasinewton: input matrix
- 0.97348 0.07738 -0.07416 1.75816;
- -0.04799 1.06420 0.31625 -10.11703;
- 0.10721 -0.32135 1.01961 8.54551;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 0.973 0.077 -0.074 1.758;
- -0.048 1.064 0.316 -10.117;
- 0.107 -0.321 1.020 8.546;
- 0.000 0.000 0.000 1.000;
- pass 1, spacing 8: log(p) = -3.9 (old=-4.8)
- transform before final EM align:
- 0.973 0.077 -0.074 1.758;
- -0.048 1.064 0.316 -10.117;
- 0.107 -0.321 1.020 8.546;
- 0.000 0.000 0.000 1.000;
- **************************************************
- EM alignment process ...
- Computing final MAP estimate using 382743 samples.
- **************************************************
- dt = 5.00e-06, momentum=0.80, tol=1.00e-07
- l_intensity = 1.0000
- Aligning input volume to GCA...
- Transform matrix
- 0.97348 0.07738 -0.07416 1.75816;
- -0.04799 1.06420 0.31625 -10.11703;
- 0.10721 -0.32135 1.01961 8.54551;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 382743
- Quasinewton: input matrix
- 0.97348 0.07738 -0.07416 1.75816;
- -0.04799 1.06420 0.31625 -10.11703;
- 0.10721 -0.32135 1.01961 8.54551;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = 4.3 tol 0.000000
- final transform:
- 0.973 0.077 -0.074 1.758;
- -0.048 1.064 0.316 -10.117;
- 0.107 -0.321 1.020 8.546;
- 0.000 0.000 0.000 1.000;
- writing output transformation to transforms/talairach_with_skull.lta...
- registration took 29 minutes and 26 seconds.
- mri_watershed -T1 -brain_atlas /opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz
- Mode: T1 normalized volume
- Mode: Use the information of atlas (default parms, --help for details)
- *********************************************************
- The input file is T1.mgz
- The output file is brainmask.auto.mgz
- Weighting the input with atlas information before watershed
- *************************WATERSHED**************************
- Sorting...
- first estimation of the COG coord: x=129 y=82 z=114 r=95
- first estimation of the main basin volume: 3643088 voxels
- Looking for seedpoints
- 2 found in the cerebellum
- 16 found in the rest of the brain
- global maximum in x=148, y=84, z=73, 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=20056565544 voxels, voxel volume =1.000
- = 20056565544 mmm3 = 20056565.760 cm3
- done.
- PostAnalyze...Basin Prior
- 121 basins merged thanks to atlas
- ***** 0 basin(s) merged in 1 iteration(s)
- ***** 0 voxel(s) added to the main basin
- done.
- Weighting the input with prior template
- ****************TEMPLATE DEFORMATION****************
- second estimation of the COG coord: x=128,y=93, z=111, r=10354 iterations
- ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^
- GLOBAL CSF_MIN=0, CSF_intensity=3, CSF_MAX=11 , nb = 45568
- RIGHT_CER CSF_MIN=0, CSF_intensity=4, CSF_MAX=23 , nb = -1030619603
- LEFT_CER CSF_MIN=0, CSF_intensity=5, CSF_MAX=20 , nb = 1095589073
- RIGHT_BRAIN CSF_MIN=0, CSF_intensity=3, CSF_MAX=10 , nb = -1062755037
- LEFT_BRAIN CSF_MIN=0, CSF_intensity=3, CSF_MAX=10 , nb = 1081859768
- OTHER CSF_MIN=0, CSF_intensity=9, CSF_MAX=23 , nb = 1073551676
-
- CSF_MAX TRANSITION GM_MIN GM
- GLOBAL
- before analyzing : 11, 14, 28, 57
- after analyzing : 11, 23, 28, 31
- RIGHT_CER
- before analyzing : 23, 23, 25, 59
- after analyzing : 23, 24, 25, 32
- LEFT_CER
- before analyzing : 20, 25, 35, 60
- after analyzing : 20, 31, 35, 38
- RIGHT_BRAIN
- before analyzing : 10, 12, 26, 57
- after analyzing : 10, 21, 26, 30
- LEFT_BRAIN
- before analyzing : 10, 12, 26, 57
- after analyzing : 10, 21, 26, 30
- OTHER
- before analyzing : 23, 52, 81, 95
- after analyzing : 23, 71, 81, 77
- mri_strip_skull: done peeling brain
- highly tesselated surface with 10242 vertices
- matching...71 iterations
- *********************VALIDATION*********************
- curvature mean = -0.012, std = 0.011
- curvature mean = 73.083, std = 7.549
- No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
- before rotation: sse = 2.12, sigma = 3.31
- after rotation: sse = 2.12, sigma = 3.31
- Localization of inacurate regions: Erosion-Dilation steps
- the sse mean is 2.23, its var is 3.24
- before Erosion-Dilatation 0.28% 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...38 iterations
- mri_strip_skull: done peeling brain
- Brain Size = 1938502 voxels, voxel volume = 1.000 mm3
- = 1938502 mmm3 = 1938.502 cm3
- ******************************
- Saving brainmask.auto.mgz
- done
- cp brainmask.auto.mgz brainmask.mgz
- #-------------------------------------
- #@# EM Registration Thu Aug 8 11:32:57 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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=24.0
- skull bounding box = (58, 33, 37) --> (197, 178, 204)
- using (104, 81, 121) as brain centroid...
- mean wm in atlas = 107, using box (87,63,100) --> (121, 98,141) to find MRI wm
- before smoothing, mri peak at 108
- after smoothing, mri peak at 108, scaling input intensities by 0.991
- scaling channel 0 by 0.990741
- initial log_p = -4.6
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -3.889388 @ (-9.091, 27.273, -9.091)
- max log p = -3.727010 @ (4.545, -4.545, -4.545)
- max log p = -3.727010 @ (0.000, 0.000, 0.000)
- max log p = -3.708223 @ (1.136, 3.409, 1.136)
- max log p = -3.708223 @ (0.000, 0.000, 0.000)
- max log p = -3.706241 @ (0.284, -1.420, -1.989)
- Found translation: (-3.1, 24.7, -14.5): log p = -3.706
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p =-3.7 (thresh=-3.7)
- 1.000 0.000 0.000 -3.125;
- 0.000 1.038 0.278 -12.233;
- 0.000 -0.259 0.966 21.461;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p =-3.5 (thresh=-3.5)
- 0.991 0.034 -0.126 8.933;
- 0.000 1.038 0.278 -12.233;
- 0.131 -0.257 0.958 5.219;
- 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 =-3.5 (thresh=-3.4)
- 0.991 0.034 -0.126 8.933;
- 0.000 1.038 0.278 -12.233;
- 0.131 -0.257 0.958 5.219;
- 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=-3.3, old_max_log_p =-3.5 (thresh=-3.4)
- 1.035 0.052 -0.056 -6.239;
- -0.034 1.037 0.280 -6.072;
- 0.067 -0.263 0.982 11.414;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 4 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3)
- 1.035 0.052 -0.056 -6.239;
- -0.034 1.037 0.280 -6.072;
- 0.067 -0.263 0.982 11.414;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.0625
- ****************************************
- Nine parameter search. iteration 5 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.3 (thresh=-3.3)
- 1.036 0.058 -0.046 -8.170;
- -0.042 1.036 0.289 -6.348;
- 0.058 -0.271 0.977 14.330;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 6 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2)
- 1.034 0.058 -0.046 -7.853;
- -0.042 1.036 0.289 -6.348;
- 0.058 -0.271 0.977 14.330;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 7 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2)
- 1.034 0.058 -0.046 -7.853;
- -0.042 1.036 0.289 -6.348;
- 0.058 -0.271 0.977 14.330;
- 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
- 1.03371 0.05769 -0.04602 -7.85319;
- -0.04187 1.03583 0.28896 -6.34804;
- 0.05819 -0.27106 0.97659 14.32976;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 2772
- Quasinewton: input matrix
- 1.03371 0.05769 -0.04602 -7.85319;
- -0.04187 1.03583 0.28896 -6.34804;
- 0.05819 -0.27106 0.97659 14.32976;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 1.034 0.058 -0.046 -7.853;
- -0.042 1.036 0.289 -6.348;
- 0.058 -0.271 0.977 14.330;
- 0.000 0.000 0.000 1.000;
- pass 1, spacing 8: log(p) = -3.2 (old=-4.6)
- transform before final EM align:
- 1.034 0.058 -0.046 -7.853;
- -0.042 1.036 0.289 -6.348;
- 0.058 -0.271 0.977 14.330;
- 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
- 1.03371 0.05769 -0.04602 -7.85319;
- -0.04187 1.03583 0.28896 -6.34804;
- 0.05819 -0.27106 0.97659 14.32976;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 312841
- Quasinewton: input matrix
- 1.03371 0.05769 -0.04602 -7.85319;
- -0.04187 1.03583 0.28896 -6.34804;
- 0.05819 -0.27106 0.97659 14.32976;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 012: -log(p) = 3.8 tol 0.000000
- final transform:
- 1.034 0.058 -0.046 -7.853;
- -0.042 1.036 0.289 -6.348;
- 0.058 -0.271 0.977 14.330;
- 0.000 0.000 0.000 1.000;
- writing output transformation to transforms/talairach.lta...
- registration took 29 minutes and 36 seconds.
- #--------------------------------------
- #@# CA Normalize Thu Aug 8 12:02:33 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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=24.0
- skull bounding box = (58, 33, 37) --> (197, 178, 204)
- using (104, 81, 121) as brain centroid...
- mean wm in atlas = 107, using box (87,63,100) --> (121, 98,141) to find MRI wm
- before smoothing, mri peak at 108
- after smoothing, mri peak at 108, scaling input intensities by 0.991
- scaling channel 0 by 0.990741
- using 244171 sample points...
- INFO: compute sample coordinates transform
- 1.034 0.058 -0.046 -7.853;
- -0.042 1.036 0.289 -6.348;
- 0.058 -0.271 0.977 14.330;
- 0.000 0.000 0.000 1.000;
- INFO: transform used
- finding control points in Left_Cerebral_White_Matter....
- found 41584 control points for structure...
- bounding box (122, 34, 38) --> (192, 144, 198)
- Left_Cerebral_White_Matter: limiting intensities to 99.0 --> 176.0
- 0 of 12 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 40735 control points for structure...
- bounding box (66, 32, 38) --> (132, 135, 200)
- Right_Cerebral_White_Matter: limiting intensities to 105.0 --> 176.0
- 0 of 9 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3012 control points for structure...
- bounding box (127, 117, 67) --> (174, 160, 119)
- Left_Cerebellum_White_Matter: limiting intensities to 85.0 --> 176.0
- 0 of 11 (0.0%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2764 control points for structure...
- bounding box (81, 117, 66) --> (127, 156, 121)
- Right_Cerebellum_White_Matter: limiting intensities to 90.0 --> 176.0
- 0 of 13 (0.0%) samples deleted
- finding control points in Brain_Stem....
- found 3520 control points for structure...
- bounding box (112, 105, 100) --> (144, 171, 130)
- Brain_Stem: limiting intensities to 79.0 --> 176.0
- 3 of 16 (18.8%) samples deleted
- using 61 total control points for intensity normalization...
- bias field = 0.935 +- 0.073
- 0 of 58 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 41584 control points for structure...
- bounding box (122, 34, 38) --> (192, 144, 198)
- Left_Cerebral_White_Matter: limiting intensities to 93.0 --> 167.0
- 1 of 72 (1.4%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 40735 control points for structure...
- bounding box (66, 32, 38) --> (132, 135, 200)
- Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 167.0
- 0 of 96 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3012 control points for structure...
- bounding box (127, 117, 67) --> (174, 160, 119)
- Left_Cerebellum_White_Matter: limiting intensities to 78.0 --> 167.0
- 0 of 17 (0.0%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2764 control points for structure...
- bounding box (81, 117, 66) --> (127, 156, 121)
- Right_Cerebellum_White_Matter: limiting intensities to 90.0 --> 167.0
- 12 of 38 (31.6%) samples deleted
- finding control points in Brain_Stem....
- found 3520 control points for structure...
- bounding box (112, 105, 100) --> (144, 171, 130)
- Brain_Stem: limiting intensities to 92.0 --> 167.0
- 26 of 33 (78.8%) samples deleted
- using 256 total control points for intensity normalization...
- bias field = 1.000 +- 0.049
- 0 of 217 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 41584 control points for structure...
- bounding box (122, 34, 38) --> (192, 144, 198)
- Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 164.0
- 0 of 185 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 40735 control points for structure...
- bounding box (66, 32, 38) --> (132, 135, 200)
- Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 164.0
- 0 of 191 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3012 control points for structure...
- bounding box (127, 117, 67) --> (174, 160, 119)
- Left_Cerebellum_White_Matter: limiting intensities to 77.0 --> 164.0
- 0 of 26 (0.0%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2764 control points for structure...
- bounding box (81, 117, 66) --> (127, 156, 121)
- Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 164.0
- 5 of 30 (16.7%) samples deleted
- finding control points in Brain_Stem....
- found 3520 control points for structure...
- bounding box (112, 105, 100) --> (144, 171, 130)
- Brain_Stem: limiting intensities to 77.0 --> 164.0
- 9 of 56 (16.1%) samples deleted
- using 488 total control points for intensity normalization...
- bias field = 1.004 +- 0.048
- 2 of 474 control points discarded
- writing normalized volume to norm.mgz...
- writing control points to ctrl_pts.mgz
- freeing GCA...done.
- normalization took 2 minutes and 5 seconds.
- #--------------------------------------
- #@# CA Reg Thu Aug 8 12:04:38 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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) = 1.13 (predicted orig area = 7.1)
- 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=0.899, neg=0, invalid=96777
- 0001: dt=129.472000, rms=0.855 (4.913%), neg=0, invalid=96777
- 0002: dt=221.952000, rms=0.842 (1.535%), neg=0, invalid=96777
- 0003: dt=221.952000, rms=0.827 (1.775%), neg=0, invalid=96777
- 0004: dt=92.480000, rms=0.824 (0.335%), neg=0, invalid=96777
- 0005: dt=1479.680000, rms=0.803 (2.570%), neg=0, invalid=96777
- 0006: dt=73.984000, rms=0.798 (0.588%), neg=0, invalid=96777
- 0007: dt=443.904000, rms=0.792 (0.780%), neg=0, invalid=96777
- 0008: dt=129.472000, rms=0.790 (0.245%), neg=0, invalid=96777
- 0009: dt=129.472000, rms=0.789 (0.152%), neg=0, invalid=96777
- 0010: dt=129.472000, rms=0.787 (0.246%), neg=0, invalid=96777
- 0011: dt=129.472000, rms=0.784 (0.360%), neg=0, invalid=96777
- 0012: dt=129.472000, rms=0.781 (0.408%), neg=0, invalid=96777
- 0013: dt=129.472000, rms=0.778 (0.442%), neg=0, invalid=96777
- 0014: dt=129.472000, rms=0.774 (0.520%), neg=0, invalid=96777
- 0015: dt=129.472000, rms=0.770 (0.500%), neg=0, invalid=96777
- 0016: dt=129.472000, rms=0.766 (0.488%), neg=0, invalid=96777
- 0017: dt=129.472000, rms=0.762 (0.511%), neg=0, invalid=96777
- 0018: dt=129.472000, rms=0.758 (0.486%), neg=0, invalid=96777
- 0019: dt=129.472000, rms=0.755 (0.482%), neg=0, invalid=96777
- 0020: dt=129.472000, rms=0.751 (0.457%), neg=0, invalid=96777
- 0021: dt=129.472000, rms=0.748 (0.404%), neg=0, invalid=96777
- 0022: dt=129.472000, rms=0.745 (0.372%), neg=0, invalid=96777
- 0023: dt=129.472000, rms=0.743 (0.377%), neg=0, invalid=96777
- 0024: dt=129.472000, rms=0.740 (0.290%), neg=0, invalid=96777
- 0025: dt=129.472000, rms=0.739 (0.225%), neg=0, invalid=96777
- 0026: dt=129.472000, rms=0.737 (0.259%), neg=0, invalid=96777
- 0027: dt=129.472000, rms=0.735 (0.264%), neg=0, invalid=96777
- 0028: dt=129.472000, rms=0.733 (0.221%), neg=0, invalid=96777
- 0029: dt=129.472000, rms=0.732 (0.189%), neg=0, invalid=96777
- 0030: dt=129.472000, rms=0.730 (0.230%), neg=0, invalid=96777
- 0031: dt=129.472000, rms=0.729 (0.223%), neg=0, invalid=96777
- 0032: dt=129.472000, rms=0.727 (0.195%), neg=0, invalid=96777
- 0033: dt=129.472000, rms=0.726 (0.173%), neg=0, invalid=96777
- 0034: dt=129.472000, rms=0.725 (0.132%), neg=0, invalid=96777
- 0035: dt=129.472000, rms=0.723 (0.212%), neg=0, invalid=96777
- 0036: dt=129.472000, rms=0.722 (0.148%), neg=0, invalid=96777
- 0037: dt=129.472000, rms=0.722 (0.087%), neg=0, invalid=96777
- 0038: dt=129.472000, rms=0.721 (0.104%), neg=0, invalid=96777
- 0039: dt=129.472000, rms=0.720 (0.120%), neg=0, invalid=96777
- 0040: dt=129.472000, rms=0.720 (0.073%), neg=0, invalid=96777
- 0041: dt=517.888000, rms=0.719 (0.039%), neg=0, invalid=96777
- 0042: dt=517.888000, rms=0.719 (-1.479%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.719, neg=0, invalid=96777
- 0043: dt=73.984000, rms=0.719 (0.034%), neg=0, invalid=96777
- 0044: dt=369.920000, rms=0.718 (0.159%), neg=0, invalid=96777
- 0045: dt=129.472000, rms=0.717 (0.059%), neg=0, invalid=96777
- 0046: dt=129.472000, rms=0.717 (-0.048%), neg=0, invalid=96777
- setting smoothness coefficient to 0.154
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.727, neg=0, invalid=96777
- 0047: dt=145.152000, rms=0.716 (1.483%), neg=0, invalid=96777
- 0048: dt=145.152000, rms=0.705 (1.521%), neg=0, invalid=96777
- 0049: dt=62.208000, rms=0.701 (0.632%), neg=0, invalid=96777
- 0050: dt=497.664000, rms=0.684 (2.438%), neg=0, invalid=96777
- 0051: dt=36.288000, rms=0.679 (0.707%), neg=0, invalid=96777
- 0052: dt=82.944000, rms=0.676 (0.413%), neg=0, invalid=96777
- 0053: dt=103.680000, rms=0.674 (0.355%), neg=0, invalid=96777
- 0054: dt=15.552000, rms=0.673 (0.094%), neg=0, invalid=96777
- 0055: dt=15.552000, rms=0.673 (0.069%), neg=0, invalid=96777
- 0056: dt=15.552000, rms=0.672 (0.061%), neg=0, invalid=96777
- 0057: dt=15.552000, rms=0.671 (0.129%), neg=0, invalid=96777
- 0058: dt=15.552000, rms=0.670 (0.159%), neg=0, invalid=96777
- 0059: dt=15.552000, rms=0.669 (0.190%), neg=0, invalid=96777
- 0060: dt=15.552000, rms=0.668 (0.210%), neg=0, invalid=96777
- 0061: dt=15.552000, rms=0.666 (0.221%), neg=0, invalid=96777
- 0062: dt=15.552000, rms=0.664 (0.237%), neg=0, invalid=96777
- 0063: dt=15.552000, rms=0.663 (0.260%), neg=0, invalid=96777
- 0064: dt=15.552000, rms=0.661 (0.246%), neg=0, invalid=96777
- 0065: dt=15.552000, rms=0.660 (0.242%), neg=0, invalid=96777
- 0066: dt=15.552000, rms=0.658 (0.238%), neg=0, invalid=96777
- 0067: dt=15.552000, rms=0.657 (0.203%), neg=0, invalid=96777
- 0068: dt=15.552000, rms=0.656 (0.149%), neg=0, invalid=96777
- 0069: dt=15.552000, rms=0.655 (0.155%), neg=0, invalid=96777
- 0070: dt=15.552000, rms=0.653 (0.183%), neg=0, invalid=96777
- 0071: dt=15.552000, rms=0.652 (0.194%), neg=0, invalid=96777
- 0072: dt=15.552000, rms=0.651 (0.196%), neg=0, invalid=96777
- 0073: dt=15.552000, rms=0.650 (0.176%), neg=0, invalid=96777
- 0074: dt=15.552000, rms=0.648 (0.186%), neg=0, invalid=96777
- 0075: dt=15.552000, rms=0.647 (0.188%), neg=0, invalid=96777
- 0076: dt=15.552000, rms=0.646 (0.165%), neg=0, invalid=96777
- 0077: dt=15.552000, rms=0.645 (0.135%), neg=0, invalid=96777
- 0078: dt=15.552000, rms=0.645 (0.119%), neg=0, invalid=96777
- 0079: dt=15.552000, rms=0.644 (0.134%), neg=0, invalid=96777
- 0080: dt=15.552000, rms=0.643 (0.146%), neg=0, invalid=96777
- 0081: dt=15.552000, rms=0.642 (0.124%), neg=0, invalid=96777
- 0082: dt=15.552000, rms=0.641 (0.094%), neg=0, invalid=96777
- 0083: dt=20.736000, rms=0.641 (0.009%), neg=0, invalid=96777
- 0084: dt=20.736000, rms=0.641 (0.005%), neg=0, invalid=96777
- 0085: dt=20.736000, rms=0.641 (0.000%), neg=0, invalid=96777
- 0086: dt=20.736000, rms=0.641 (0.019%), neg=0, invalid=96777
- 0087: dt=20.736000, rms=0.641 (0.029%), neg=0, invalid=96777
- 0088: dt=20.736000, rms=0.641 (0.041%), neg=0, invalid=96777
- 0089: dt=20.736000, rms=0.640 (0.036%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.640, neg=0, invalid=96777
- 0090: dt=31.104000, rms=0.640 (0.033%), neg=0, invalid=96777
- 0091: dt=36.288000, rms=0.640 (0.033%), neg=0, invalid=96777
- 0092: dt=36.288000, rms=0.640 (-0.020%), neg=0, invalid=96777
- setting smoothness coefficient to 0.588
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.668, neg=0, invalid=96777
- 0093: dt=0.000000, rms=0.668 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.668, neg=0, invalid=96777
- 0094: dt=0.000000, rms=0.668 (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=0.752, neg=0, invalid=96777
- 0095: dt=4.314233, rms=0.733 (2.563%), neg=0, invalid=96777
- 0096: dt=2.304000, rms=0.732 (0.153%), neg=0, invalid=96777
- 0097: dt=2.304000, rms=0.732 (-0.037%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.732, neg=0, invalid=96777
- 0098: dt=0.000000, rms=0.732 (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=0.818, neg=0, invalid=96777
- 0099: dt=1.326316, rms=0.810 (0.956%), neg=0, invalid=96777
- 0100: dt=1.900000, rms=0.803 (0.891%), neg=0, invalid=96777
- 0101: dt=0.464286, rms=0.802 (0.080%), neg=0, invalid=96777
- 0102: dt=0.464286, rms=0.802 (0.031%), neg=0, invalid=96777
- 0103: dt=0.464286, rms=0.802 (0.006%), neg=0, invalid=96777
- 0104: dt=0.464286, rms=0.802 (-0.055%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.802, neg=0, invalid=96777
- 0105: dt=1.280000, rms=0.800 (0.198%), neg=0, invalid=96777
- 0106: dt=0.000000, rms=0.800 (-0.003%), 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=0.748, neg=0, invalid=96777
- 0107: dt=0.160811, rms=0.738 (1.268%), neg=0, invalid=96777
- 0108: dt=0.000016, rms=0.738 (0.006%), neg=0, invalid=96777
- 0109: dt=0.000016, rms=0.738 (-0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.738, neg=0, invalid=96777
- 0110: dt=0.293974, rms=0.735 (0.429%), neg=0, invalid=96777
- 0111: dt=0.096000, rms=0.734 (0.194%), neg=0, invalid=96777
- 0112: dt=0.096000, rms=0.733 (0.049%), neg=0, invalid=96777
- 0113: dt=0.096000, rms=0.733 (0.088%), neg=0, invalid=96777
- 0114: dt=0.096000, rms=0.732 (0.143%), neg=0, invalid=96777
- 0115: dt=0.096000, rms=0.730 (0.172%), neg=0, invalid=96777
- 0116: dt=0.096000, rms=0.729 (0.174%), neg=0, invalid=96777
- 0117: dt=0.096000, rms=0.728 (0.156%), neg=0, invalid=96777
- 0118: dt=0.096000, rms=0.727 (0.129%), neg=0, invalid=96777
- 0119: dt=0.096000, rms=0.726 (0.110%), neg=0, invalid=96777
- 0120: dt=0.096000, rms=0.725 (0.086%), neg=0, invalid=96777
- 0121: dt=0.000000, rms=0.725 (0.000%), neg=0, invalid=96777
- 0122: dt=0.050000, rms=0.725 (-0.008%), neg=0, invalid=96777
- renormalizing by structure alignment....
- renormalizing input #0
- gca peak = 0.11725 (24)
- mri peak = 0.14528 ( 9)
- Left_Lateral_Ventricle (4): linear fit = 0.31 x + 0.0 (2696 voxels, overlap=0.006)
- Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (2696 voxels, peak = 8), gca=9.6
- gca peak = 0.14022 (22)
- mri peak = 0.14212 ( 9)
- Right_Lateral_Ventricle (43): linear fit = 0.37 x + 0.0 (2324 voxels, overlap=0.007)
- Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (2324 voxels, peak = 8), gca=8.8
- gca peak = 0.24234 (100)
- mri peak = 0.07781 (85)
- Right_Pallidum (52): linear fit = 0.89 x + 0.0 (458 voxels, overlap=0.046)
- Right_Pallidum (52): linear fit = 0.89 x + 0.0 (458 voxels, peak = 90), gca=89.5
- gca peak = 0.19192 (97)
- mri peak = 0.07281 (89)
- Left_Pallidum (13): linear fit = 0.88 x + 0.0 (279 voxels, overlap=0.219)
- Left_Pallidum (13): linear fit = 0.88 x + 0.0 (279 voxels, peak = 85), gca=84.9
- gca peak = 0.24007 (63)
- mri peak = 0.07954 (56)
- Right_Hippocampus (53): linear fit = 0.86 x + 0.0 (654 voxels, overlap=0.304)
- Right_Hippocampus (53): linear fit = 0.86 x + 0.0 (654 voxels, peak = 54), gca=53.9
- gca peak = 0.29892 (64)
- mri peak = 0.06582 (57)
- Left_Hippocampus (17): linear fit = 0.85 x + 0.0 (452 voxels, overlap=0.016)
- Left_Hippocampus (17): linear fit = 0.85 x + 0.0 (452 voxels, peak = 54), gca=54.1
- gca peak = 0.12541 (104)
- mri peak = 0.08147 (105)
- Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (67035 voxels, overlap=0.812)
- Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (67035 voxels, peak = 106), gca=105.6
- gca peak = 0.13686 (104)
- mri peak = 0.08126 (106)
- Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (69420 voxels, overlap=0.713)
- Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (69420 voxels, peak = 109), gca=108.7
- gca peak = 0.11691 (63)
- mri peak = 0.04954 (53)
- Left_Cerebral_Cortex (3): linear fit = 0.85 x + 0.0 (19339 voxels, overlap=0.274)
- Left_Cerebral_Cortex (3): linear fit = 0.85 x + 0.0 (19339 voxels, peak = 53), gca=53.2
- gca peak = 0.13270 (63)
- mri peak = 0.05351 (51)
- Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (20489 voxels, overlap=0.110)
- Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (20489 voxels, peak = 52), gca=52.0
- gca peak = 0.15182 (70)
- mri peak = 0.09398 (62)
- Right_Caudate (50): linear fit = 0.86 x + 0.0 (466 voxels, overlap=0.074)
- Right_Caudate (50): linear fit = 0.86 x + 0.0 (466 voxels, peak = 60), gca=59.9
- gca peak = 0.14251 (76)
- mri peak = 0.09039 (65)
- Left_Caudate (11): linear fit = 0.81 x + 0.0 (942 voxels, overlap=0.017)
- Left_Caudate (11): linear fit = 0.81 x + 0.0 (942 voxels, peak = 61), gca=61.2
- gca peak = 0.12116 (60)
- mri peak = 0.04320 (56)
- Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (10810 voxels, overlap=0.732)
- Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (10810 voxels, peak = 56), gca=56.1
- gca peak = 0.12723 (61)
- mri peak = 0.04288 (56)
- Right_Cerebellum_Cortex (47): linear fit = 0.92 x + 0.0 (11432 voxels, overlap=0.717)
- Right_Cerebellum_Cortex (47): linear fit = 0.92 x + 0.0 (11432 voxels, peak = 56), gca=55.8
- gca peak = 0.22684 (88)
- mri peak = 0.05734 (92)
- Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (6426 voxels, overlap=0.771)
- Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (6426 voxels, peak = 95), gca=95.5
- gca peak = 0.21067 (87)
- mri peak = 0.06701 (93)
- Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (6101 voxels, overlap=0.924)
- Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (6101 voxels, peak = 94), gca=93.5
- gca peak = 0.25455 (62)
- mri peak = 0.07099 (60)
- Left_Amygdala (18): linear fit = 0.94 x + 0.0 (330 voxels, overlap=0.858)
- Left_Amygdala (18): linear fit = 0.94 x + 0.0 (330 voxels, peak = 59), gca=58.6
- gca peak = 0.39668 (62)
- mri peak = 0.10213 (59)
- Right_Amygdala (54): linear fit = 0.94 x + 0.0 (360 voxels, overlap=0.809)
- Right_Amygdala (54): linear fit = 0.94 x + 0.0 (360 voxels, peak = 58), gca=58.0
- gca peak = 0.10129 (93)
- mri peak = 0.05189 (89)
- Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (5423 voxels, overlap=0.919)
- Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (5423 voxels, peak = 89), gca=88.8
- gca peak = 0.12071 (89)
- mri peak = 0.05671 (87)
- Right_Thalamus_Proper (49): linear fit = 0.95 x + 0.0 (3659 voxels, overlap=0.887)
- Right_Thalamus_Proper (49): linear fit = 0.95 x + 0.0 (3659 voxels, peak = 85), gca=85.0
- gca peak = 0.13716 (82)
- mri peak = 0.05989 (74)
- Left_Putamen (12): linear fit = 0.92 x + 0.0 (1893 voxels, overlap=0.630)
- Left_Putamen (12): linear fit = 0.92 x + 0.0 (1893 voxels, peak = 75), gca=75.0
- gca peak = 0.15214 (84)
- mri peak = 0.05235 (74)
- Right_Putamen (51): linear fit = 0.87 x + 0.0 (2006 voxels, overlap=0.094)
- Right_Putamen (51): linear fit = 0.87 x + 0.0 (2006 voxels, peak = 73), gca=72.7
- gca peak = 0.08983 (85)
- mri peak = 0.06605 (84)
- Brain_Stem (16): linear fit = 1.07 x + 0.0 (9966 voxels, overlap=0.778)
- Brain_Stem (16): linear fit = 1.07 x + 0.0 (9966 voxels, peak = 91), gca=90.5
- gca peak = 0.11809 (92)
- mri peak = 0.06667 (87)
- Right_VentralDC (60): linear fit = 0.98 x + 0.0 (753 voxels, overlap=0.807)
- Right_VentralDC (60): linear fit = 0.98 x + 0.0 (753 voxels, peak = 90), gca=89.7
- gca peak = 0.12914 (94)
- mri peak = 0.05912 (94)
- Left_VentralDC (28): linear fit = 0.96 x + 0.0 (865 voxels, overlap=0.965)
- Left_VentralDC (28): linear fit = 0.96 x + 0.0 (865 voxels, peak = 91), gca=90.7
- gca peak = 0.21100 (36)
- mri peak = 0.02978 ( 6)
- gca peak = 0.13542 (27)
- mri peak = 0.20168 ( 8)
- Fourth_Ventricle (15): linear fit = 0.28 x + 0.0 (476 voxels, overlap=0.024)
- Fourth_Ventricle (15): linear fit = 0.28 x + 0.0 (476 voxels, peak = 7), gca=7.4
- gca peak Unknown = 0.94427 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.21802 (40)
- gca peak Third_Ventricle = 0.21100 (36)
- gca peak Fourth_Ventricle = 0.13542 (27)
- gca peak CSF = 0.17123 (45)
- gca peak Left_Accumbens_area = 0.25875 (69)
- gca peak Left_undetermined = 0.96240 (36)
- gca peak Left_vessel = 0.33262 (65)
- gca peak Left_choroid_plexus = 0.09846 (46)
- gca peak Right_Inf_Lat_Vent = 0.28113 (34)
- gca peak Right_Accumbens_area = 0.27120 (72)
- gca peak Right_vessel = 0.61915 (60)
- gca peak Right_choroid_plexus = 0.12775 (51)
- gca peak Fifth_Ventricle = 0.45329 (44)
- gca peak WM_hypointensities = 0.11729 (81)
- gca peak non_WM_hypointensities = 0.10912 (56)
- gca peak Optic_Chiasm = 0.33287 (75)
- label assignment complete, 0 changed (0.00%)
- not using caudate to estimate GM means
- estimating mean gm scale to be 0.88 x + 0.0
- estimating mean wm scale to be 1.03 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=0.754, neg=0, invalid=96777
- 0123: dt=129.472000, rms=0.747 (0.979%), neg=0, invalid=96777
- 0124: dt=295.936000, rms=0.743 (0.490%), neg=0, invalid=96777
- 0125: dt=32.368000, rms=0.742 (0.136%), neg=0, invalid=96777
- 0126: dt=73.984000, rms=0.741 (0.097%), neg=0, invalid=96777
- 0127: dt=517.888000, rms=0.737 (0.578%), neg=0, invalid=96777
- 0128: dt=32.368000, rms=0.736 (0.063%), neg=0, invalid=96777
- 0129: dt=32.368000, rms=0.736 (0.015%), neg=0, invalid=96777
- 0130: dt=32.368000, rms=0.736 (0.013%), neg=0, invalid=96777
- 0131: dt=32.368000, rms=0.736 (0.018%), neg=0, invalid=96777
- 0132: dt=32.368000, rms=0.736 (0.028%), neg=0, invalid=96777
- 0133: dt=32.368000, rms=0.735 (0.060%), neg=0, invalid=96777
- 0134: dt=32.368000, rms=0.735 (0.099%), neg=0, invalid=96777
- 0135: dt=32.368000, rms=0.734 (0.125%), neg=0, invalid=96777
- 0136: dt=32.368000, rms=0.733 (0.133%), neg=0, invalid=96777
- 0137: dt=32.368000, rms=0.732 (0.128%), neg=0, invalid=96777
- 0138: dt=32.368000, rms=0.731 (0.122%), neg=0, invalid=96777
- 0139: dt=32.368000, rms=0.730 (0.110%), neg=0, invalid=96777
- 0140: dt=32.368000, rms=0.729 (0.100%), neg=0, invalid=96777
- 0141: dt=32.368000, rms=0.729 (0.101%), neg=0, invalid=96777
- 0142: dt=32.368000, rms=0.728 (0.112%), neg=0, invalid=96777
- 0143: dt=32.368000, rms=0.727 (0.119%), neg=0, invalid=96777
- 0144: dt=32.368000, rms=0.726 (0.112%), neg=0, invalid=96777
- 0145: dt=32.368000, rms=0.725 (0.108%), neg=0, invalid=96777
- 0146: dt=32.368000, rms=0.725 (0.100%), neg=0, invalid=96777
- 0147: dt=32.368000, rms=0.724 (0.091%), neg=0, invalid=96777
- 0148: dt=32.368000, rms=0.723 (0.088%), neg=0, invalid=96777
- 0149: dt=32.368000, rms=0.723 (0.089%), neg=0, invalid=96777
- 0150: dt=32.368000, rms=0.722 (0.095%), neg=0, invalid=96777
- 0151: dt=32.368000, rms=0.721 (0.097%), neg=0, invalid=96777
- 0152: dt=32.368000, rms=0.721 (0.092%), neg=0, invalid=96777
- 0153: dt=32.368000, rms=0.720 (0.084%), neg=0, invalid=96777
- 0154: dt=32.368000, rms=0.720 (0.081%), neg=0, invalid=96777
- 0155: dt=32.368000, rms=0.719 (0.081%), neg=0, invalid=96777
- 0156: dt=32.368000, rms=0.718 (0.079%), neg=0, invalid=96777
- 0157: dt=32.368000, rms=0.718 (0.081%), neg=0, invalid=96777
- 0158: dt=32.368000, rms=0.717 (0.077%), neg=0, invalid=96777
- 0159: dt=32.368000, rms=0.717 (0.076%), neg=0, invalid=96777
- 0160: dt=32.368000, rms=0.716 (0.071%), neg=0, invalid=96777
- 0161: dt=32.368000, rms=0.716 (0.068%), neg=0, invalid=96777
- 0162: dt=32.368000, rms=0.715 (0.066%), neg=0, invalid=96777
- 0163: dt=32.368000, rms=0.715 (0.062%), neg=0, invalid=96777
- 0164: dt=32.368000, rms=0.714 (0.060%), neg=0, invalid=96777
- 0165: dt=32.368000, rms=0.714 (0.055%), neg=0, invalid=96777
- 0166: dt=32.368000, rms=0.714 (0.057%), neg=0, invalid=96777
- 0167: dt=32.368000, rms=0.713 (0.055%), neg=0, invalid=96777
- 0168: dt=32.368000, rms=0.713 (0.050%), neg=0, invalid=96777
- 0169: dt=32.368000, rms=0.712 (0.047%), neg=0, invalid=96777
- 0170: dt=32.368000, rms=0.712 (0.045%), neg=0, invalid=96777
- 0171: dt=32.368000, rms=0.712 (0.044%), neg=0, invalid=96777
- 0172: dt=32.368000, rms=0.712 (0.048%), neg=0, invalid=96777
- 0173: dt=32.368000, rms=0.711 (0.047%), neg=0, invalid=96777
- 0174: dt=32.368000, rms=0.711 (0.046%), neg=0, invalid=96777
- 0175: dt=32.368000, rms=0.711 (0.042%), neg=0, invalid=96777
- 0176: dt=32.368000, rms=0.710 (0.038%), neg=0, invalid=96777
- 0177: dt=32.368000, rms=0.710 (0.035%), neg=0, invalid=96777
- 0178: dt=32.368000, rms=0.710 (0.032%), neg=0, invalid=96777
- 0179: dt=32.368000, rms=0.710 (0.032%), neg=0, invalid=96777
- 0180: dt=32.368000, rms=0.709 (0.035%), neg=0, invalid=96777
- 0181: dt=32.368000, rms=0.709 (0.037%), neg=0, invalid=96777
- 0182: dt=32.368000, rms=0.709 (0.037%), neg=0, invalid=96777
- 0183: dt=32.368000, rms=0.709 (0.033%), neg=0, invalid=96777
- 0184: dt=32.368000, rms=0.708 (0.031%), neg=0, invalid=96777
- 0185: dt=32.368000, rms=0.708 (0.031%), neg=0, invalid=96777
- 0186: dt=32.368000, rms=0.708 (0.028%), neg=0, invalid=96777
- 0187: dt=32.368000, rms=0.708 (0.032%), neg=0, invalid=96777
- 0188: dt=32.368000, rms=0.707 (0.035%), neg=0, invalid=96777
- 0189: dt=32.368000, rms=0.707 (0.034%), neg=0, invalid=96777
- 0190: dt=32.368000, rms=0.707 (0.032%), neg=0, invalid=96777
- 0191: dt=32.368000, rms=0.707 (0.025%), neg=0, invalid=96777
- 0192: dt=32.368000, rms=0.707 (0.022%), neg=0, invalid=96777
- 0193: dt=32.368000, rms=0.707 (0.018%), neg=0, invalid=96777
- 0194: dt=1183.744000, rms=0.706 (0.062%), neg=0, invalid=96777
- 0195: dt=32.368000, rms=0.706 (0.014%), neg=0, invalid=96777
- 0196: dt=32.368000, rms=0.706 (0.004%), neg=0, invalid=96777
- 0197: dt=32.368000, rms=0.706 (0.005%), neg=0, invalid=96777
- 0198: dt=32.368000, rms=0.706 (-0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.706, neg=0, invalid=96777
- 0199: dt=295.936000, rms=0.705 (0.143%), neg=0, invalid=96777
- 0200: dt=129.472000, rms=0.705 (0.059%), neg=0, invalid=96777
- 0201: dt=0.000000, rms=0.705 (0.000%), neg=0, invalid=96777
- 0202: dt=0.850000, rms=0.705 (-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=0.705, neg=0, invalid=96777
- 0203: dt=248.832000, rms=0.690 (2.195%), neg=0, invalid=96777
- 0204: dt=36.288000, rms=0.683 (0.940%), neg=0, invalid=96777
- 0205: dt=36.288000, rms=0.680 (0.494%), neg=0, invalid=96777
- 0206: dt=82.944000, rms=0.676 (0.534%), neg=0, invalid=96777
- 0207: dt=25.920000, rms=0.674 (0.373%), neg=0, invalid=96777
- 0208: dt=103.680000, rms=0.671 (0.440%), neg=0, invalid=96777
- 0209: dt=20.736000, rms=0.669 (0.313%), neg=0, invalid=96777
- 0210: dt=580.608000, rms=0.655 (2.070%), neg=0, invalid=96777
- 0211: dt=31.104000, rms=0.653 (0.235%), neg=0, invalid=96777
- 0212: dt=62.208000, rms=0.651 (0.281%), neg=0, invalid=96777
- 0213: dt=25.920000, rms=0.651 (0.085%), neg=0, invalid=96777
- 0214: dt=145.152000, rms=0.648 (0.370%), neg=0, invalid=96777
- 0215: dt=145.152000, rms=0.647 (0.263%), neg=0, invalid=96777
- 0216: dt=36.288000, rms=0.646 (0.154%), neg=0, invalid=96777
- 0217: dt=36.288000, rms=0.645 (0.081%), neg=0, invalid=96777
- 0218: dt=103.680000, rms=0.644 (0.171%), neg=0, invalid=96777
- 0219: dt=36.288000, rms=0.643 (0.218%), neg=0, invalid=96777
- 0220: dt=7.776000, rms=0.643 (0.012%), neg=0, invalid=96777
- 0221: dt=1.944000, rms=0.642 (0.012%), neg=0, invalid=96777
- 0222: dt=0.972000, rms=0.642 (0.001%), neg=0, invalid=96777
- 0223: dt=0.243000, rms=0.642 (0.000%), neg=0, invalid=96777
- 0224: dt=0.141750, rms=0.642 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.642, neg=0, invalid=96777
- 0225: dt=0.004860, rms=0.642 (-0.000%), neg=0, invalid=96777
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.647, neg=0, invalid=96777
- 0226: dt=0.000488, rms=0.647 (0.000%), neg=0, invalid=96777
- 0227: dt=0.000000, rms=0.647 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.647, neg=0, invalid=96777
- 0228: dt=0.000000, rms=0.647 (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=0.662, neg=0, invalid=96777
- 0229: dt=0.864000, rms=0.658 (0.632%), neg=0, invalid=96777
- 0230: dt=4.032000, rms=0.640 (2.741%), neg=0, invalid=96777
- 0231: dt=1.008000, rms=0.636 (0.529%), neg=0, invalid=96777
- 0232: dt=0.252000, rms=0.635 (0.123%), neg=0, invalid=96777
- 0233: dt=0.252000, rms=0.635 (0.122%), neg=0, invalid=96777
- 0234: dt=0.011250, rms=0.635 (0.005%), neg=0, invalid=96777
- 0235: dt=0.001406, rms=0.635 (0.001%), neg=0, invalid=96777
- 0236: dt=0.000703, rms=0.635 (0.000%), neg=0, invalid=96777
- 0237: dt=0.000044, rms=0.635 (0.000%), neg=0, invalid=96777
- 0238: dt=0.000000, rms=0.635 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.635, neg=0, invalid=96777
- 0239: dt=0.000000, rms=0.635 (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=0.665, neg=0, invalid=96777
- 0240: dt=0.448000, rms=0.661 (0.624%), neg=0, invalid=96777
- 0241: dt=0.448000, rms=0.657 (0.545%), neg=0, invalid=96777
- 0242: dt=1.536000, rms=0.647 (1.590%), neg=0, invalid=96777
- 0243: dt=0.448000, rms=0.645 (0.272%), neg=0, invalid=96777
- 0244: dt=0.448000, rms=0.643 (0.237%), neg=0, invalid=96777
- 0245: dt=1.792000, rms=0.638 (0.828%), neg=0, invalid=96777
- 0246: dt=0.448000, rms=0.637 (0.125%), neg=0, invalid=96777
- 0247: dt=0.448000, rms=0.636 (0.109%), neg=0, invalid=96777
- 0248: dt=0.448000, rms=0.636 (0.101%), neg=0, invalid=96777
- 0249: dt=1.792000, rms=0.634 (0.341%), neg=0, invalid=96777
- 0250: dt=0.900000, rms=0.633 (0.107%), neg=0, invalid=96777
- 0251: dt=0.607143, rms=0.633 (0.061%), neg=0, invalid=96777
- 0252: dt=0.593750, rms=0.632 (0.054%), neg=0, invalid=96777
- 0253: dt=1.280000, rms=0.632 (0.106%), neg=0, invalid=96777
- 0254: dt=0.448000, rms=0.631 (0.025%), neg=0, invalid=96777
- 0255: dt=0.448000, rms=0.631 (0.030%), neg=0, invalid=96777
- 0256: dt=0.448000, rms=0.631 (0.054%), neg=0, invalid=96777
- 0257: dt=0.448000, rms=0.631 (0.021%), neg=0, invalid=96777
- 0258: dt=0.448000, rms=0.630 (0.036%), neg=0, invalid=96777
- 0259: dt=0.448000, rms=0.630 (0.045%), neg=0, invalid=96777
- 0260: dt=0.448000, rms=0.630 (0.049%), neg=0, invalid=96777
- 0261: dt=0.448000, rms=0.630 (0.048%), neg=0, invalid=96777
- 0262: dt=0.448000, rms=0.629 (0.037%), neg=0, invalid=96777
- 0263: dt=0.448000, rms=0.629 (0.033%), neg=0, invalid=96777
- 0264: dt=0.448000, rms=0.629 (0.013%), neg=0, invalid=96777
- 0265: dt=0.448000, rms=0.629 (-0.018%), neg=0, invalid=96777
- 0266: dt=0.000000, rms=0.629 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.629, neg=0, invalid=96777
- 0267: dt=0.448000, rms=0.629 (0.064%), neg=0, invalid=96777
- 0268: dt=0.750000, rms=0.628 (0.105%), neg=0, invalid=96777
- 0269: dt=0.448000, rms=0.628 (0.044%), neg=0, invalid=96777
- 0270: dt=0.448000, rms=0.628 (0.044%), neg=0, invalid=96777
- 0271: dt=0.448000, rms=0.627 (0.041%), neg=0, invalid=96777
- 0272: dt=0.448000, rms=0.627 (0.075%), neg=0, invalid=96777
- 0273: dt=0.448000, rms=0.626 (0.094%), neg=0, invalid=96777
- 0274: dt=0.448000, rms=0.626 (0.106%), neg=0, invalid=96777
- 0275: dt=0.448000, rms=0.625 (0.096%), neg=0, invalid=96777
- 0276: dt=0.448000, rms=0.624 (0.081%), neg=0, invalid=96777
- 0277: dt=0.448000, rms=0.624 (0.012%), neg=0, invalid=96777
- 0278: dt=0.448000, rms=0.624 (0.014%), neg=0, invalid=96777
- 0279: dt=0.448000, rms=0.624 (0.011%), neg=0, invalid=96777
- 0280: dt=0.448000, rms=0.624 (-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=0.602, neg=0, invalid=96777
- 0281: dt=0.001750, rms=0.602 (0.017%), neg=0, invalid=96777
- 0282: dt=0.001750, rms=0.602 (0.017%), neg=0, invalid=96777
- 0283: dt=0.001750, rms=0.602 (0.017%), neg=0, invalid=96777
- 0284: dt=0.001750, rms=0.602 (0.032%), neg=0, invalid=96777
- 0285: dt=0.001750, rms=0.602 (0.045%), neg=0, invalid=96777
- 0286: dt=0.001750, rms=0.601 (0.057%), neg=0, invalid=96777
- 0287: dt=0.001750, rms=0.601 (0.068%), neg=0, invalid=96777
- 0288: dt=0.001750, rms=0.600 (0.077%), neg=0, invalid=96777
- 0289: dt=0.001750, rms=0.600 (0.085%), neg=0, invalid=96777
- 0290: dt=0.001750, rms=0.599 (0.093%), neg=0, invalid=96777
- 0291: dt=0.001750, rms=0.599 (0.097%), neg=0, invalid=96777
- 0292: dt=0.001750, rms=0.598 (0.103%), neg=0, invalid=96777
- 0293: dt=0.001750, rms=0.598 (0.108%), neg=0, invalid=96777
- 0294: dt=0.001750, rms=0.597 (0.112%), neg=0, invalid=96777
- 0295: dt=0.001750, rms=0.596 (0.114%), neg=0, invalid=96777
- 0296: dt=0.001750, rms=0.596 (0.117%), neg=0, invalid=96777
- 0297: dt=0.001750, rms=0.595 (0.118%), neg=0, invalid=96777
- 0298: dt=0.001750, rms=0.594 (0.119%), neg=0, invalid=96777
- 0299: dt=0.001750, rms=0.593 (0.120%), neg=0, invalid=96777
- 0300: dt=0.001750, rms=0.593 (0.120%), neg=0, invalid=96777
- 0301: dt=0.001750, rms=0.592 (0.120%), neg=0, invalid=96777
- 0302: dt=0.001750, rms=0.591 (0.118%), neg=0, invalid=96777
- 0303: dt=0.001750, rms=0.591 (0.119%), neg=0, invalid=96777
- 0304: dt=0.000875, rms=0.591 (0.005%), neg=0, invalid=96777
- 0305: dt=0.000875, rms=0.591 (0.005%), neg=0, invalid=96777
- 0306: dt=0.000875, rms=0.590 (0.010%), neg=0, invalid=96777
- 0307: dt=0.000875, rms=0.590 (0.015%), neg=0, invalid=96777
- 0308: dt=0.000875, rms=0.590 (0.019%), neg=0, invalid=96777
- 0309: dt=0.000875, rms=0.590 (0.023%), neg=0, invalid=96777
- 0310: dt=0.000875, rms=0.590 (0.025%), neg=0, invalid=96777
- 0311: dt=0.000875, rms=0.590 (0.028%), neg=0, invalid=96777
- 0312: dt=0.000875, rms=0.590 (0.031%), neg=0, invalid=96777
- 0313: dt=0.000875, rms=0.589 (0.032%), neg=0, invalid=96777
- 0314: dt=0.000875, rms=0.589 (0.033%), neg=0, invalid=96777
- 0315: dt=0.000219, rms=0.589 (0.001%), neg=0, invalid=96777
- 0316: dt=0.000219, rms=0.589 (0.001%), neg=0, invalid=96777
- 0317: dt=0.028000, rms=0.588 (0.163%), neg=0, invalid=96777
- 0318: dt=0.001750, rms=0.588 (0.009%), neg=0, invalid=96777
- 0319: dt=0.001750, rms=0.588 (0.009%), neg=0, invalid=96777
- 0320: dt=0.001750, rms=0.588 (0.009%), neg=0, invalid=96777
- 0321: dt=0.001750, rms=0.588 (0.019%), neg=0, invalid=96777
- 0322: dt=0.001750, rms=0.588 (0.026%), neg=0, invalid=96777
- 0323: dt=0.001750, rms=0.588 (0.033%), neg=0, invalid=96777
- 0324: dt=0.001750, rms=0.587 (0.039%), neg=0, invalid=96777
- 0325: dt=0.001750, rms=0.587 (0.046%), neg=0, invalid=96777
- 0326: dt=0.001750, rms=0.587 (0.049%), neg=0, invalid=96777
- 0327: dt=0.001750, rms=0.587 (0.054%), neg=0, invalid=96777
- 0328: dt=0.001750, rms=0.586 (0.057%), neg=0, invalid=96777
- 0329: dt=0.001750, rms=0.586 (0.061%), neg=0, invalid=96777
- 0330: dt=0.001750, rms=0.585 (0.062%), neg=0, invalid=96777
- 0331: dt=0.001750, rms=0.585 (0.065%), neg=0, invalid=96777
- 0332: dt=0.001750, rms=0.585 (0.009%), neg=0, invalid=96777
- 0333: dt=0.001750, rms=0.585 (0.016%), neg=0, invalid=96777
- 0334: dt=0.001750, rms=0.585 (0.022%), neg=0, invalid=96777
- 0335: dt=0.001750, rms=0.585 (0.029%), neg=0, invalid=96777
- 0336: dt=0.001750, rms=0.584 (0.034%), neg=0, invalid=96777
- 0337: dt=0.001750, rms=0.584 (0.039%), neg=0, invalid=96777
- 0338: dt=0.001750, rms=0.584 (0.041%), neg=0, invalid=96777
- 0339: dt=0.001750, rms=0.584 (0.046%), neg=0, invalid=96777
- 0340: dt=0.001750, rms=0.583 (0.049%), neg=0, invalid=96777
- 0341: dt=0.001750, rms=0.583 (0.053%), neg=0, invalid=96777
- 0342: dt=0.001750, rms=0.583 (0.054%), neg=0, invalid=96777
- 0343: dt=0.001750, rms=0.582 (0.057%), neg=0, invalid=96777
- 0344: dt=0.001750, rms=0.582 (0.057%), neg=0, invalid=96777
- 0345: dt=0.001750, rms=0.582 (0.007%), neg=0, invalid=96777
- 0346: dt=0.001750, rms=0.582 (0.014%), neg=0, invalid=96777
- 0347: dt=0.001750, rms=0.582 (0.005%), neg=0, invalid=96777
- 0348: dt=0.001750, rms=0.582 (0.008%), neg=0, invalid=96777
- 0349: dt=0.028000, rms=0.581 (0.111%), neg=0, invalid=96777
- 0350: dt=0.007000, rms=0.581 (0.028%), neg=0, invalid=96777
- 0351: dt=0.007000, rms=0.581 (0.025%), neg=0, invalid=96777
- 0352: dt=0.007000, rms=0.581 (0.051%), neg=0, invalid=96777
- 0353: dt=0.007000, rms=0.580 (0.071%), neg=0, invalid=96777
- 0354: dt=0.007000, rms=0.580 (0.087%), neg=0, invalid=96777
- 0355: dt=0.007000, rms=0.579 (0.103%), neg=0, invalid=96777
- 0356: dt=0.007000, rms=0.579 (0.116%), neg=0, invalid=96777
- 0357: dt=0.007000, rms=0.578 (0.129%), neg=0, invalid=96777
- 0358: dt=0.007000, rms=0.577 (0.134%), neg=0, invalid=96777
- 0359: dt=0.003500, rms=0.577 (0.010%), neg=0, invalid=96777
- 0360: dt=0.003500, rms=0.577 (0.011%), neg=0, invalid=96777
- 0361: dt=0.001750, rms=0.577 (0.004%), neg=0, invalid=96777
- 0362: dt=0.007000, rms=0.577 (0.019%), neg=0, invalid=96777
- 0363: dt=0.028000, rms=0.576 (0.078%), neg=0, invalid=96777
- 0364: dt=0.001750, rms=0.576 (0.004%), neg=0, invalid=96777
- 0365: dt=0.001750, rms=0.576 (0.004%), neg=0, invalid=96777
- 0366: dt=0.001750, rms=0.576 (0.005%), neg=0, invalid=96777
- 0367: dt=0.001750, rms=0.576 (0.010%), neg=0, invalid=96777
- 0368: dt=0.001750, rms=0.576 (0.011%), neg=0, invalid=96777
- 0369: dt=0.001750, rms=0.576 (0.016%), neg=0, invalid=96777
- 0370: dt=0.001750, rms=0.576 (0.019%), neg=0, invalid=96777
- 0371: dt=0.001750, rms=0.576 (0.022%), neg=0, invalid=96777
- 0372: dt=0.001750, rms=0.576 (0.024%), neg=0, invalid=96777
- 0373: dt=0.001750, rms=0.576 (0.006%), neg=0, invalid=96777
- 0374: dt=0.001750, rms=0.576 (0.008%), neg=0, invalid=96777
- 0375: dt=0.001750, rms=0.575 (0.011%), neg=0, invalid=96777
- 0376: dt=0.001750, rms=0.575 (0.014%), neg=0, invalid=96777
- 0377: dt=0.001750, rms=0.575 (0.019%), neg=0, invalid=96777
- 0378: dt=0.001750, rms=0.575 (0.020%), neg=0, invalid=96777
- 0379: dt=0.001750, rms=0.575 (0.022%), neg=0, invalid=96777
- 0380: dt=0.001750, rms=0.575 (0.026%), neg=0, invalid=96777
- 0381: dt=0.001750, rms=0.575 (0.028%), neg=0, invalid=96777
- 0382: dt=0.001750, rms=0.575 (0.027%), neg=0, invalid=96777
- 0383: dt=0.001750, rms=0.574 (0.030%), neg=0, invalid=96777
- 0384: dt=0.001750, rms=0.574 (-0.000%), neg=0, invalid=96777
- 0385: dt=0.005000, rms=0.574 (0.011%), neg=0, invalid=96777
- 0386: dt=0.000040, 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
- 0387: dt=0.000078, rms=0.574 (0.000%), neg=0, invalid=96777
- 0388: dt=0.007000, rms=0.574 (0.035%), neg=0, invalid=96777
- 0389: dt=0.020000, rms=0.574 (0.097%), neg=0, invalid=96777
- 0390: dt=0.001250, rms=0.574 (0.006%), neg=0, invalid=96777
- 0391: dt=0.000625, rms=0.574 (0.003%), neg=0, invalid=96777
- 0392: dt=0.000625, rms=0.574 (0.005%), neg=0, invalid=96777
- 0393: dt=0.000625, rms=0.573 (0.008%), neg=0, invalid=96777
- 0394: dt=0.000625, rms=0.573 (0.010%), neg=0, invalid=96777
- 0395: dt=0.000625, rms=0.573 (0.012%), neg=0, invalid=96777
- 0396: dt=0.000625, rms=0.573 (0.008%), neg=0, invalid=96777
- 0397: dt=0.000625, rms=0.573 (0.017%), neg=0, invalid=96777
- 0398: dt=0.000625, rms=0.573 (0.016%), neg=0, invalid=96777
- 0399: dt=0.028000, rms=0.572 (0.127%), neg=0, invalid=96777
- 0400: dt=0.007000, rms=0.572 (0.032%), neg=0, invalid=96777
- 0401: dt=0.003500, rms=0.572 (0.014%), neg=0, invalid=96777
- 0402: dt=0.001750, rms=0.572 (0.007%), neg=0, invalid=96777
- 0403: dt=0.001750, rms=0.572 (0.014%), neg=0, invalid=96777
- 0404: dt=0.001750, rms=0.572 (0.020%), neg=0, invalid=96777
- 0405: dt=0.001750, rms=0.572 (0.025%), neg=0, invalid=96777
- 0406: dt=0.001750, rms=0.572 (0.030%), neg=0, invalid=96777
- 0407: dt=0.001750, rms=0.571 (0.035%), neg=0, invalid=96777
- 0408: dt=0.001750, rms=0.571 (0.037%), neg=0, invalid=96777
- 0409: dt=0.001750, rms=0.571 (0.041%), neg=0, invalid=96777
- 0410: dt=0.001750, rms=0.571 (0.042%), neg=0, invalid=96777
- 0411: dt=0.001750, rms=0.570 (0.046%), neg=0, invalid=96777
- 0412: dt=0.001750, rms=0.570 (0.048%), neg=0, invalid=96777
- 0413: dt=0.001750, rms=0.570 (0.052%), neg=0, invalid=96777
- 0414: dt=0.001750, rms=0.570 (0.048%), neg=0, invalid=96777
- 0415: dt=0.001750, rms=0.569 (0.052%), neg=0, invalid=96777
- 0416: dt=0.001750, rms=0.569 (0.054%), neg=0, invalid=96777
- 0417: dt=0.001750, rms=0.569 (0.003%), neg=0, invalid=96777
- 0418: dt=0.001750, rms=0.569 (0.011%), neg=0, invalid=96777
- 0419: dt=0.001750, rms=0.569 (0.018%), neg=0, invalid=96777
- 0420: dt=0.001750, rms=0.569 (0.004%), neg=0, invalid=96777
- 0421: dt=0.001750, rms=0.569 (0.004%), neg=0, invalid=96777
- 0422: dt=0.001750, rms=0.569 (0.009%), neg=0, invalid=96777
- 0423: dt=0.001750, rms=0.569 (0.008%), neg=0, invalid=96777
- 0424: dt=0.001750, rms=0.569 (0.015%), neg=0, invalid=96777
- 0425: dt=0.001750, rms=0.568 (0.019%), neg=0, invalid=96777
- 0426: dt=0.001750, rms=0.568 (0.025%), neg=0, invalid=96777
- 0427: dt=0.001750, rms=0.568 (0.025%), neg=0, invalid=96777
- 0428: dt=0.001750, rms=0.568 (0.026%), neg=0, invalid=96777
- 0429: dt=0.001750, rms=0.568 (0.029%), neg=0, invalid=96777
- 0430: dt=0.001750, rms=0.568 (0.033%), neg=0, invalid=96777
- 0431: dt=0.001750, rms=0.568 (0.004%), neg=0, invalid=96777
- 0432: dt=0.001750, rms=0.568 (0.010%), neg=0, invalid=96777
- 0433: dt=0.001750, rms=0.568 (0.016%), neg=0, invalid=96777
- 0434: dt=0.001750, rms=0.567 (0.019%), neg=0, invalid=96777
- 0435: dt=0.001750, rms=0.567 (0.016%), neg=0, invalid=96777
- 0436: dt=0.007000, rms=0.567 (0.023%), neg=0, invalid=96777
- 0437: dt=0.000109, rms=0.567 (-0.000%), 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=0.566, neg=0, invalid=96777
- 0438: dt=110.976000, rms=0.565 (0.096%), neg=0, invalid=96777
- 0439: dt=92.480000, rms=0.565 (0.026%), neg=0, invalid=96777
- 0440: dt=92.480000, rms=0.565 (0.005%), neg=0, invalid=96777
- 0441: dt=92.480000, rms=0.565 (0.040%), neg=0, invalid=96777
- 0442: dt=92.480000, rms=0.565 (-0.004%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.565, neg=0, invalid=96777
- 0443: dt=110.976000, rms=0.564 (0.107%), neg=0, invalid=96777
- 0444: dt=32.368000, rms=0.564 (0.033%), neg=0, invalid=96777
- 0445: dt=32.368000, rms=0.564 (0.008%), neg=0, invalid=96777
- 0446: dt=32.368000, rms=0.564 (0.018%), neg=0, invalid=96777
- 0447: dt=32.368000, rms=0.564 (0.017%), neg=0, invalid=96777
- 0448: dt=32.368000, rms=0.564 (0.024%), neg=0, invalid=96777
- 0449: dt=32.368000, rms=0.563 (0.026%), neg=0, invalid=96777
- 0450: dt=32.368000, rms=0.563 (0.025%), neg=0, invalid=96777
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.563, neg=0, invalid=96777
- 0451: dt=82.944000, rms=0.559 (0.853%), neg=0, invalid=96777
- iter 0, gcam->neg = 15
- after 200 iterations, nbhd size=2, neg = 2
- starting rms=0.008, neg=2, removing folds in lattice....
- iter 1, dt=0.000030: new neg 0, old_neg 2, delta 2, rms=0.001 (86.080%)
- 0452: dt=124.416000, rms=0.555 (0.658%), neg=0, invalid=96777
- 0453: dt=36.288000, rms=0.553 (0.255%), neg=0, invalid=96777
- 0454: dt=25.920000, rms=0.553 (0.069%), neg=0, invalid=96777
- 0455: dt=25.920000, rms=0.553 (0.093%), neg=0, invalid=96777
- 0456: dt=25.920000, rms=0.552 (0.108%), neg=0, invalid=96777
- 0457: dt=25.920000, rms=0.551 (0.125%), neg=0, invalid=96777
- iter 0, gcam->neg = 2
- after 200 iterations, nbhd size=4, neg = 2
- starting rms=0.007, neg=2, removing folds in lattice....
- iter 1, dt=0.000031: new neg 0, old_neg 2, delta 2, rms=0.001 (80.018%)
- 0458: dt=25.920000, rms=0.551 (0.137%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0459: dt=25.920000, rms=0.550 (0.056%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 5 iterations, nbhd size=1, neg = 0
- 0460: dt=25.920000, rms=0.550 (0.058%), neg=0, invalid=96777
- iter 0, gcam->neg = 2
- after 6 iterations, nbhd size=1, neg = 0
- 0461: dt=25.920000, rms=0.549 (0.086%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 5 iterations, nbhd size=1, neg = 0
- 0462: dt=25.920000, rms=0.549 (0.085%), neg=0, invalid=96777
- 0463: dt=36.288000, rms=0.549 (0.041%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 5 iterations, nbhd size=1, neg = 0
- 0464: dt=36.288000, rms=0.549 (0.015%), neg=0, invalid=96777
- 0465: dt=36.288000, rms=0.548 (0.080%), neg=0, invalid=96777
- 0466: dt=36.288000, rms=0.548 (0.086%), neg=0, invalid=96777
- iter 0, gcam->neg = 3
- after 200 iterations, nbhd size=1, neg = 3
- starting rms=0.010, neg=3, removing folds in lattice....
- iter 1, dt=0.000023: new neg 0, old_neg 3, delta 3, rms=0.002 (83.656%)
- 0467: dt=36.288000, rms=0.547 (0.072%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0468: dt=36.288000, rms=0.547 (0.015%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.547, neg=0, invalid=96777
- 0469: dt=103.680000, rms=0.544 (0.580%), neg=0, invalid=96777
- 0470: dt=15.552000, rms=0.544 (0.100%), neg=0, invalid=96777
- 0471: dt=15.552000, rms=0.543 (0.070%), neg=0, invalid=96777
- 0472: dt=15.552000, rms=0.543 (0.094%), neg=0, invalid=96777
- 0473: dt=15.552000, rms=0.542 (0.095%), neg=0, invalid=96777
- 0474: dt=15.552000, rms=0.542 (0.102%), neg=0, invalid=96777
- 0475: dt=15.552000, rms=0.541 (0.103%), neg=0, invalid=96777
- 0476: dt=15.552000, rms=0.540 (0.107%), neg=0, invalid=96777
- 0477: dt=15.552000, rms=0.540 (0.105%), neg=0, invalid=96777
- 0478: dt=15.552000, rms=0.539 (0.076%), neg=0, invalid=96777
- 0479: dt=103.680000, rms=0.539 (0.059%), neg=0, invalid=96777
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.540, neg=0, invalid=96777
- iter 0, gcam->neg = 178
- after 200 iterations, nbhd size=1, neg = 6
- starting rms=0.014, neg=6, removing folds in lattice....
- iter 1, dt=0.000023: new neg 5, old_neg 6, delta 1, rms=0.004 (70.836%)
- iter 2, dt=0.000246: new neg 2, old_neg 5, delta 3, rms=0.002 (48.689%)
- iter 3, dt=0.000143: new neg 0, old_neg 2, delta 2, rms=0.002 (19.161%)
- 0480: dt=44.800000, rms=0.532 (1.399%), neg=0, invalid=96777
- iter 0, gcam->neg = 15
- after 42 iterations, nbhd size=4, neg = 0
- 0481: dt=11.200000, rms=0.530 (0.420%), neg=0, invalid=96777
- iter 0, gcam->neg = 6
- after 200 iterations, nbhd size=3, neg = 4
- starting rms=0.013, neg=4, removing folds in lattice....
- iter 1, dt=0.000023: new neg 2, old_neg 4, delta 2, rms=0.003 (76.052%)
- iter 2, dt=0.000328: new neg 0, old_neg 2, delta 2, rms=0.001 (53.161%)
- 0482: dt=11.200000, rms=0.528 (0.372%), neg=0, invalid=96777
- iter 0, gcam->neg = 5
- after 48 iterations, nbhd size=3, neg = 0
- 0483: dt=11.200000, rms=0.527 (0.170%), neg=0, invalid=96777
- iter 0, gcam->neg = 2
- after 200 iterations, nbhd size=1, neg = 4
- starting rms=0.013, neg=4, removing folds in lattice....
- iter 1, dt=0.000023: new neg 2, old_neg 4, delta 2, rms=0.003 (79.236%)
- iter 2, dt=0.000328: new neg 0, old_neg 2, delta 2, rms=0.002 (41.256%)
- 0484: dt=11.200000, rms=0.525 (0.345%), neg=0, invalid=96777
- iter 0, gcam->neg = 7
- after 200 iterations, nbhd size=4, neg = 5
- starting rms=0.012, neg=5, removing folds in lattice....
- iter 1, dt=0.000031: new neg 4, old_neg 5, delta 1, rms=0.003 (79.496%)
- iter 2, dt=0.000410: new neg 0, old_neg 4, delta 4, rms=0.002 (36.813%)
- 0485: dt=11.200000, rms=0.525 (0.114%), neg=0, invalid=96777
- iter 0, gcam->neg = 6
- after 200 iterations, nbhd size=4, neg = 4
- starting rms=0.013, neg=4, removing folds in lattice....
- iter 1, dt=0.000031: new neg 3, old_neg 4, delta 1, rms=0.003 (77.037%)
- iter 2, dt=0.000328: new neg 0, old_neg 3, delta 3, rms=0.002 (44.008%)
- 0486: dt=11.200000, rms=0.523 (0.295%), neg=0, invalid=96777
- iter 0, gcam->neg = 13
- after 200 iterations, nbhd size=2, neg = 1
- starting rms=0.002, neg=1, removing folds in lattice....
- iter 1, dt=0.000875: new neg 0, old_neg 1, delta 1, rms=0.002 (20.282%)
- 0487: dt=11.200000, rms=0.523 (0.090%), neg=0, invalid=96777
- 0488: dt=11.200000, rms=0.521 (0.261%), neg=0, invalid=96777
- 0489: dt=11.200000, rms=0.520 (0.269%), neg=0, invalid=96777
- iter 0, gcam->neg = 11
- after 45 iterations, nbhd size=1, neg = 0
- 0490: dt=11.200000, rms=0.518 (0.347%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 5 iterations, nbhd size=1, neg = 0
- 0491: dt=11.200000, rms=0.516 (0.435%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 1 iterations, nbhd size=0, neg = 0
- 0492: dt=11.200000, rms=0.513 (0.469%), neg=0, invalid=96777
- 0493: dt=11.200000, rms=0.511 (0.436%), neg=0, invalid=96777
- iter 0, gcam->neg = 23
- after 200 iterations, nbhd size=1, neg = 3
- starting rms=0.013, neg=3, removing folds in lattice....
- iter 1, dt=0.000031: new neg 1, old_neg 3, delta 2, rms=0.004 (72.235%)
- iter 2, dt=0.000428: new neg 0, old_neg 1, delta 1, rms=0.003 (11.380%)
- 0494: dt=11.200000, rms=0.509 (0.355%), neg=0, invalid=96777
- iter 0, gcam->neg = 5
- after 200 iterations, nbhd size=2, neg = 3
- starting rms=0.013, neg=3, removing folds in lattice....
- iter 1, dt=0.000031: new neg 2, old_neg 3, delta 1, rms=0.004 (72.960%)
- iter 2, dt=0.000328: new neg 0, old_neg 2, delta 2, rms=0.003 (18.273%)
- 0495: dt=11.200000, rms=0.509 (0.078%), neg=0, invalid=96777
- iter 0, gcam->neg = 8
- after 200 iterations, nbhd size=4, neg = 4
- starting rms=0.013, neg=4, removing folds in lattice....
- iter 1, dt=0.000031: new neg 3, old_neg 4, delta 1, rms=0.004 (70.863%)
- iter 2, dt=0.000328: new neg 0, old_neg 3, delta 3, rms=0.003 (25.684%)
- 0496: dt=11.200000, rms=0.509 (0.024%), neg=0, invalid=96777
- iter 0, gcam->neg = 31
- after 200 iterations, nbhd size=4, neg = 4
- starting rms=0.013, neg=4, removing folds in lattice....
- iter 1, dt=0.000031: new neg 3, old_neg 4, delta 1, rms=0.004 (72.208%)
- iter 2, dt=0.000328: new neg 0, old_neg 3, delta 3, rms=0.003 (24.502%)
- 0497: dt=25.600000, rms=0.508 (0.158%), neg=0, invalid=96777
- 0498: dt=0.175000, rms=0.508 (-0.017%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.508, neg=0, invalid=96777
- iter 0, gcam->neg = 15
- after 200 iterations, nbhd size=2, neg = 4
- starting rms=0.013, neg=4, removing folds in lattice....
- iter 1, dt=0.000023: new neg 2, old_neg 4, delta 2, rms=0.004 (72.352%)
- iter 2, dt=0.000328: new neg 0, old_neg 2, delta 2, rms=0.002 (32.870%)
- 0499: dt=8.000000, rms=0.507 (0.146%), neg=0, invalid=96777
- iter 0, gcam->neg = 8
- after 200 iterations, nbhd size=3, neg = 4
- starting rms=0.013, neg=4, removing folds in lattice....
- iter 1, dt=0.000031: new neg 3, old_neg 4, delta 1, rms=0.003 (75.685%)
- iter 2, dt=0.000328: new neg 0, old_neg 3, delta 3, rms=0.002 (38.013%)
- 0500: dt=25.600000, rms=0.505 (0.445%), neg=0, invalid=96777
- 0501: dt=3.913043, rms=0.505 (0.119%), neg=0, invalid=96777
- 0502: dt=3.913043, rms=0.504 (0.046%), neg=0, invalid=96777
- iter 0, gcam->neg = 5
- after 24 iterations, nbhd size=3, neg = 0
- 0503: dt=3.913043, rms=0.504 (0.058%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 46 iterations, nbhd size=3, neg = 0
- 0504: dt=3.913043, rms=0.504 (0.093%), neg=0, invalid=96777
- 0505: dt=3.913043, rms=0.503 (0.130%), neg=0, invalid=96777
- 0506: dt=3.913043, rms=0.502 (0.152%), neg=0, invalid=96777
- 0507: dt=3.913043, rms=0.502 (0.113%), neg=0, invalid=96777
- 0508: dt=3.913043, rms=0.501 (0.079%), neg=0, invalid=96777
- 0509: dt=8.000000, rms=0.501 (0.019%), neg=0, invalid=96777
- 0510: dt=8.000000, rms=0.501 (0.059%), neg=0, invalid=96777
- 0511: dt=8.000000, rms=0.500 (0.079%), neg=0, invalid=96777
- 0512: dt=8.000000, rms=0.500 (0.069%), neg=0, invalid=96777
- iter 0, gcam->neg = 7
- after 200 iterations, nbhd size=1, neg = 4
- starting rms=0.012, neg=4, removing folds in lattice....
- iter 1, dt=0.000031: new neg 1, old_neg 4, delta 3, rms=0.002 (82.726%)
- iter 2, dt=0.000328: new neg 0, old_neg 1, delta 1, rms=0.001 (39.833%)
- 0513: dt=8.000000, rms=0.500 (0.052%), neg=0, invalid=96777
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.506, neg=0, invalid=96777
- iter 0, gcam->neg = 45
- after 200 iterations, nbhd size=2, neg = 3
- starting rms=0.012, neg=3, removing folds in lattice....
- iter 1, dt=0.000031: new neg 1, old_neg 3, delta 2, rms=0.002 (83.660%)
- iter 2, dt=0.000410: new neg 0, old_neg 1, delta 1, rms=0.001 (40.934%)
- 0514: dt=2.880000, rms=0.506 (0.135%), neg=0, invalid=96777
- iter 0, gcam->neg = 26
- after 200 iterations, nbhd size=2, neg = 3
- starting rms=0.012, neg=3, removing folds in lattice....
- iter 1, dt=0.000031: new neg 1, old_neg 3, delta 2, rms=0.002 (85.017%)
- iter 2, dt=0.000410: new neg 0, old_neg 1, delta 1, rms=0.001 (34.903%)
- 0515: dt=2.304000, rms=0.505 (0.088%), neg=0, invalid=96777
- iter 0, gcam->neg = 27
- after 200 iterations, nbhd size=2, neg = 3
- starting rms=0.011, neg=3, removing folds in lattice....
- iter 1, dt=0.000031: new neg 1, old_neg 3, delta 2, rms=0.002 (86.555%)
- iter 2, dt=0.000410: new neg 0, old_neg 1, delta 1, rms=0.001 (34.901%)
- 0516: dt=2.304000, rms=0.505 (0.084%), neg=0, invalid=96777
- iter 0, gcam->neg = 33
- after 200 iterations, nbhd size=2, neg = 3
- starting rms=0.011, neg=3, removing folds in lattice....
- iter 1, dt=0.000031: new neg 1, old_neg 3, delta 2, rms=0.002 (85.651%)
- iter 2, dt=0.000573: new neg 0, old_neg 1, delta 1, rms=0.001 (32.474%)
- 0517: dt=2.304000, rms=0.505 (0.064%), neg=0, invalid=96777
- iter 0, gcam->neg = 28
- after 200 iterations, nbhd size=3, neg = 3
- starting rms=0.011, neg=3, removing folds in lattice....
- iter 1, dt=0.000031: new neg 1, old_neg 3, delta 2, rms=0.002 (86.034%)
- iter 2, dt=0.000573: new neg 0, old_neg 1, delta 1, rms=0.001 (27.348%)
- 0518: dt=2.304000, rms=0.504 (0.047%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.504, neg=0, invalid=96777
- iter 0, gcam->neg = 8
- after 200 iterations, nbhd size=4, neg = 3
- starting rms=0.011, neg=3, removing folds in lattice....
- iter 1, dt=0.000031: new neg 1, old_neg 3, delta 2, rms=0.001 (88.768%)
- iter 2, dt=0.000573: new neg 0, old_neg 1, delta 1, rms=0.001 (25.377%)
- 0519: dt=1.008000, rms=0.504 (0.036%), neg=0, invalid=96777
- iter 0, gcam->neg = 19
- after 200 iterations, nbhd size=3, neg = 3
- starting rms=0.011, neg=3, removing folds in lattice....
- iter 1, dt=0.000031: new neg 0, old_neg 3, delta 3, rms=0.001 (88.844%)
- 0520: dt=1.500000, rms=0.504 (0.035%), neg=0, invalid=96777
- 0521: dt=1.500000, rms=0.504 (0.004%), neg=0, invalid=96777
- iter 0, gcam->neg = 4
- after 1 iterations, nbhd size=0, neg = 0
- 0522: dt=1.500000, rms=0.504 (0.023%), neg=0, invalid=96777
- iter 0, gcam->neg = 8
- after 8 iterations, nbhd size=1, neg = 0
- 0523: dt=1.500000, rms=0.504 (0.035%), neg=0, invalid=96777
- iter 0, gcam->neg = 9
- after 14 iterations, nbhd size=2, neg = 0
- 0524: dt=1.500000, rms=0.504 (0.002%), neg=0, invalid=96777
- iter 0, gcam->neg = 6
- after 15 iterations, nbhd size=2, neg = 0
- 0525: dt=1.500000, rms=0.504 (-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=0.512, neg=0, invalid=96777
- 0526: dt=0.000000, rms=0.512 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.512, neg=0, invalid=96777
- 0527: dt=0.000000, rms=0.512 (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=0.498, neg=0, invalid=96777
- iter 0, gcam->neg = 1004
- after 34 iterations, nbhd size=3, neg = 0
- 0528: dt=2.106399, rms=0.446 (10.442%), neg=0, invalid=96777
- 0529: dt=0.000078, rms=0.446 (-0.012%), neg=0, invalid=96777
- 0530: dt=0.000078, rms=0.446 (0.000%), neg=0, invalid=96777
- 0531: dt=0.000078, rms=0.446 (-0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.446, neg=0, invalid=96777
- 0532: dt=0.000438, rms=0.446 (0.001%), neg=0, invalid=96777
- 0533: dt=0.000109, rms=0.446 (0.000%), neg=0, invalid=96777
- 0534: dt=0.000109, rms=0.446 (-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=0.424, neg=0, invalid=96777
- 0535: dt=0.000000, rms=0.426 (-0.596%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.426, neg=0, invalid=96777
- 0536: dt=8.092000, rms=0.426 (0.000%), neg=0, invalid=96777
- 0537: dt=1.156000, rms=0.426 (0.000%), neg=0, invalid=96777
- 0538: dt=1.156000, rms=0.426 (-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=0.426, neg=0, invalid=96777
- 0539: dt=0.450000, rms=0.426 (0.000%), neg=0, invalid=96777
- 0540: dt=0.001582, rms=0.426 (0.000%), neg=0, invalid=96777
- 0541: dt=0.001582, rms=0.426 (-0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.426, neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 12 iterations, nbhd size=2, neg = 0
- 0542: dt=31.104000, rms=0.426 (0.030%), neg=0, invalid=96777
- 0543: dt=1.944000, rms=0.426 (0.000%), neg=0, invalid=96777
- 0544: dt=1.944000, rms=0.426 (0.001%), neg=0, invalid=96777
- 0545: dt=1.944000, rms=0.426 (0.002%), neg=0, invalid=96777
- 0546: dt=1.944000, rms=0.426 (0.003%), neg=0, invalid=96777
- 0547: dt=1.944000, rms=0.426 (0.004%), neg=0, invalid=96777
- 0548: dt=1.944000, rms=0.426 (0.004%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 13 iterations, nbhd size=2, neg = 0
- 0549: dt=1.944000, rms=0.426 (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=0.427, neg=0, invalid=96777
- 0550: dt=1.600000, rms=0.427 (0.010%), neg=0, invalid=96777
- iter 0, gcam->neg = 9
- after 30 iterations, nbhd size=4, neg = 0
- 0551: dt=19.200000, rms=0.426 (0.180%), neg=0, invalid=96777
- 0552: dt=2.000000, rms=0.426 (0.002%), neg=0, invalid=96777
- 0553: dt=2.000000, rms=0.426 (0.015%), neg=0, invalid=96777
- 0554: dt=2.000000, rms=0.426 (0.026%), neg=0, invalid=96777
- 0555: dt=2.000000, rms=0.426 (0.028%), neg=0, invalid=96777
- 0556: dt=2.000000, rms=0.426 (0.023%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 5 iterations, nbhd size=1, neg = 0
- 0557: dt=2.000000, rms=0.426 (0.009%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.426, neg=0, invalid=96777
- iter 0, gcam->neg = 4
- 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 1, old_neg 4, delta 3, rms=0.004 (53.278%)
- iter 2, dt=0.002294: new neg 0, old_neg 1, delta 1, rms=0.003 (21.022%)
- 0558: dt=38.400000, rms=0.424 (0.530%), neg=0, invalid=96777
- iter 0, gcam->neg = 21
- 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 1, old_neg 3, delta 2, rms=0.004 (47.772%)
- iter 2, dt=0.000983: new neg 0, old_neg 1, delta 1, rms=0.004 (15.992%)
- 0559: dt=44.800000, rms=0.422 (0.388%), neg=0, invalid=96777
- iter 0, gcam->neg = 2
- after 200 iterations, nbhd size=4, neg = 5
- starting rms=0.009, neg=5, removing folds in lattice....
- iter 1, dt=0.000023: new neg 1, old_neg 5, delta 4, rms=0.004 (52.632%)
- iter 2, dt=0.002294: new neg 0, old_neg 1, delta 1, rms=0.003 (22.330%)
- 0560: dt=25.600000, rms=0.422 (0.075%), neg=0, invalid=96777
- iter 0, gcam->neg = 2
- after 200 iterations, nbhd size=1, neg = 5
- starting rms=0.009, neg=5, removing folds in lattice....
- iter 1, dt=0.000023: new neg 1, old_neg 5, delta 4, rms=0.004 (57.270%)
- iter 2, dt=0.002294: new neg 0, old_neg 1, delta 1, rms=0.003 (19.210%)
- 0561: dt=25.600000, rms=0.421 (0.158%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 200 iterations, nbhd size=4, neg = 1
- starting rms=0.003, neg=1, removing folds in lattice....
- iter 1, dt=0.000219: new neg 0, old_neg 1, delta 1, rms=0.003 (3.971%)
- 0562: dt=25.600000, rms=0.421 (0.119%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0563: dt=25.600000, rms=0.420 (0.123%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 1 iterations, nbhd size=0, neg = 0
- 0564: dt=25.600000, rms=0.420 (0.081%), neg=0, invalid=96777
- 0565: dt=44.800000, rms=0.419 (0.178%), neg=0, invalid=96777
- 0566: dt=44.800000, rms=0.418 (0.111%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0567: dt=44.800000, rms=0.418 (0.070%), neg=0, invalid=96777
- iter 0, gcam->neg = 15
- after 50 iterations, nbhd size=4, neg = 0
- 0568: dt=44.800000, rms=0.418 (0.065%), neg=0, invalid=96777
- iter 0, gcam->neg = 22
- after 118 iterations, nbhd size=3, neg = 0
- 0569: dt=44.800000, rms=0.418 (-0.270%), neg=0, invalid=96777
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.422, neg=0, invalid=96777
- 0570: dt=0.003375, rms=0.422 (0.000%), neg=0, invalid=96777
- 0571: dt=0.252000, rms=0.422 (0.001%), neg=0, invalid=96777
- iter 0, gcam->neg = 4
- after 7 iterations, nbhd size=1, neg = 0
- 0572: dt=3.481481, rms=0.422 (0.069%), neg=0, invalid=96777
- 0573: dt=0.000211, rms=0.422 (0.000%), neg=0, invalid=96777
- 0574: dt=0.000211, rms=0.422 (-0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.422, neg=0, invalid=96777
- 0575: dt=0.002250, rms=0.422 (0.000%), neg=0, invalid=96777
- 0576: dt=0.009000, rms=0.422 (0.000%), neg=0, invalid=96777
- 0577: dt=1.008000, rms=0.422 (0.005%), neg=0, invalid=96777
- iter 0, gcam->neg = 9
- after 18 iterations, nbhd size=2, neg = 0
- 0578: dt=4.148148, rms=0.422 (0.106%), neg=0, invalid=96777
- 0579: dt=0.000984, rms=0.422 (0.000%), neg=0, invalid=96777
- 0580: dt=0.000984, rms=0.422 (0.000%), neg=0, invalid=96777
- 0581: dt=0.000984, rms=0.422 (-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=0.431, neg=0, invalid=96777
- 0582: dt=0.000000, rms=0.431 (0.000%), neg=0, invalid=96777
- iter 0, gcam->neg = 2
- after 0 iterations, nbhd size=0, neg = 0
- 0583: dt=0.100000, rms=0.431 (-0.091%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.431, neg=0, invalid=96777
- 0584: dt=0.000000, rms=0.431 (-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=0.416, neg=0, invalid=96777
- iter 0, gcam->neg = 785
- after 23 iterations, nbhd size=2, neg = 0
- 0585: dt=1.024000, rms=0.397 (4.346%), neg=0, invalid=96777
- 0586: dt=0.000109, rms=0.397 (0.003%), neg=0, invalid=96777
- 0587: dt=0.000109, rms=0.397 (0.000%), neg=0, invalid=96777
- 0588: dt=0.000109, rms=0.397 (-0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.397, neg=0, invalid=96777
- 0589: dt=0.000375, rms=0.397 (0.000%), neg=0, invalid=96777
- 0590: dt=0.000000, rms=0.397 (0.000%), neg=0, invalid=96777
- writing output transformation to transforms/talairach.m3z...
- GCAMwrite
- registration took 5 hours, 12 minutes and 17 seconds.
- #--------------------------------------
- #@# CA Reg Inv Thu Aug 8 17:16:55 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 17:18:13 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...
- 10707204 nonbrain voxels erased
- writing output to nu_noneck.mgz...
- nonbrain removal took 1 minutes and 21 seconds.
- #--------------------------------------
- #@# SkullLTA Thu Aug 8 17:19:35 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=15.0
- skull bounding box = (54, 15, 20) --> (208, 207, 195)
- using (105, 79, 108) as brain centroid...
- mean wm in atlas = 126, using box (86,55,86) --> (123, 102,129) to find MRI wm
- before smoothing, mri peak at 110
- after smoothing, mri peak at 109, scaling input intensities by 1.156
- scaling channel 0 by 1.15596
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.9, old_max_log_p =-4.0 (thresh=-4.0)
- 1.034 0.058 -0.046 -7.853;
- -0.042 1.036 0.289 -6.348;
- 0.058 -0.271 0.977 14.330;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 1.034 0.058 -0.046 -7.853;
- -0.042 1.036 0.289 -6.348;
- 0.058 -0.271 0.977 14.330;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.2500
- ****************************************
- Nine parameter search. iteration 2 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 1.013 0.034 -0.088 1.900;
- -0.006 1.047 0.325 -16.121;
- 0.096 -0.313 1.001 10.789;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 3 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 1.013 0.034 -0.088 1.900;
- -0.006 1.047 0.325 -16.121;
- 0.096 -0.313 1.001 10.789;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.0625
- ****************************************
- Nine parameter search. iteration 4 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 1.010 0.034 -0.087 2.190;
- -0.008 1.050 0.308 -13.757;
- 0.095 -0.295 1.004 9.254;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 5 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 1.010 0.034 -0.087 2.190;
- -0.008 1.050 0.308 -13.757;
- 0.095 -0.295 1.004 9.254;
- 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
- 1.01017 0.03364 -0.08743 2.19026;
- -0.00777 1.04953 0.30804 -13.75732;
- 0.09516 -0.29505 1.00400 9.25363;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 3481
- Quasinewton: input matrix
- 1.01017 0.03364 -0.08743 2.19026;
- -0.00777 1.04953 0.30804 -13.75732;
- 0.09516 -0.29505 1.00400 9.25363;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 007: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 1.010 0.034 -0.087 2.190;
- -0.008 1.050 0.308 -13.757;
- 0.095 -0.295 1.004 9.254;
- 0.000 0.000 0.000 1.000;
- pass 1, spacing 8: log(p) = -3.9 (old=-4.0)
- transform before final EM align:
- 1.010 0.034 -0.087 2.190;
- -0.008 1.050 0.308 -13.757;
- 0.095 -0.295 1.004 9.254;
- 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
- 1.01017 0.03364 -0.08743 2.19026;
- -0.00777 1.04953 0.30804 -13.75732;
- 0.09516 -0.29505 1.00400 9.25363;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 382743
- Quasinewton: input matrix
- 1.01017 0.03364 -0.08743 2.19026;
- -0.00777 1.04953 0.30804 -13.75732;
- 0.09516 -0.29505 1.00400 9.25363;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = 4.3 tol 0.000000
- final transform:
- 1.010 0.034 -0.087 2.190;
- -0.008 1.050 0.308 -13.757;
- 0.095 -0.295 1.004 9.254;
- 0.000 0.000 0.000 1.000;
- writing output transformation to transforms/talairach_with_skull_2.lta...
- registration took 31 minutes and 27 seconds.
- #--------------------------------------
- #@# SubCort Seg Thu Aug 8 17:51:01 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 snake4
- machine x86_64
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 = 0.13985 ( 9)
- Left_Lateral_Ventricle (4): linear fit = 0.29 x + 0.0 (8969 voxels, overlap=0.006)
- Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (8969 voxels, peak = 8), gca=10.8
- gca peak = 0.14982 (20)
- mri peak = 0.12920 ( 9)
- Right_Lateral_Ventricle (43): linear fit = 0.31 x + 0.0 (7782 voxels, overlap=0.007)
- Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (7782 voxels, peak = 6), gca=8.0
- gca peak = 0.28003 (97)
- mri peak = 0.11364 (90)
- Right_Pallidum (52): linear fit = 0.89 x + 0.0 (396 voxels, overlap=0.045)
- Right_Pallidum (52): linear fit = 0.89 x + 0.0 (396 voxels, peak = 87), gca=86.8
- gca peak = 0.18160 (96)
- mri peak = 0.09357 (89)
- Left_Pallidum (13): linear fit = 0.92 x + 0.0 (342 voxels, overlap=0.637)
- Left_Pallidum (13): linear fit = 0.92 x + 0.0 (342 voxels, peak = 88), gca=87.8
- gca peak = 0.27536 (62)
- mri peak = 0.08262 (56)
- Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (576 voxels, overlap=0.478)
- Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (576 voxels, peak = 55), gca=54.9
- gca peak = 0.32745 (63)
- mri peak = 0.07391 (57)
- Left_Hippocampus (17): linear fit = 0.88 x + 0.0 (530 voxels, overlap=0.349)
- Left_Hippocampus (17): linear fit = 0.88 x + 0.0 (530 voxels, peak = 55), gca=55.1
- gca peak = 0.08597 (105)
- mri peak = 0.07429 (105)
- Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (38618 voxels, overlap=0.744)
- Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (38618 voxels, peak = 107), gca=106.6
- gca peak = 0.09209 (106)
- mri peak = 0.07886 (108)
- Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (35572 voxels, overlap=0.613)
- Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (35572 voxels, peak = 111), gca=110.8
- gca peak = 0.07826 (63)
- mri peak = 0.04857 (55)
- Left_Cerebral_Cortex (3): linear fit = 0.85 x + 0.0 (15695 voxels, overlap=0.445)
- Left_Cerebral_Cortex (3): linear fit = 0.85 x + 0.0 (15695 voxels, peak = 53), gca=53.2
- gca peak = 0.08598 (64)
- mri peak = 0.05492 (51)
- Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (15904 voxels, overlap=0.266)
- Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (15904 voxels, peak = 53), gca=52.8
- gca peak = 0.24164 (71)
- mri peak = 0.10772 (62)
- Right_Caudate (50): linear fit = 0.88 x + 0.0 (961 voxels, overlap=0.027)
- Right_Caudate (50): linear fit = 0.88 x + 0.0 (961 voxels, peak = 62), gca=62.1
- gca peak = 0.18227 (75)
- mri peak = 0.10000 (63)
- Left_Caudate (11): linear fit = 0.81 x + 0.0 (1090 voxels, overlap=0.024)
- Left_Caudate (11): linear fit = 0.81 x + 0.0 (1090 voxels, peak = 61), gca=61.1
- gca peak = 0.10629 (62)
- mri peak = 0.06011 (56)
- Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (8667 voxels, overlap=0.971)
- Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (8667 voxels, peak = 58), gca=58.0
- gca peak = 0.11668 (59)
- mri peak = 0.05395 (56)
- Right_Cerebellum_Cortex (47): linear fit = 0.92 x + 0.0 (8010 voxels, overlap=0.850)
- Right_Cerebellum_Cortex (47): linear fit = 0.92 x + 0.0 (8010 voxels, peak = 54), gca=54.0
- gca peak = 0.17849 (88)
- mri peak = 0.06365 (92)
- Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (4179 voxels, overlap=0.875)
- Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (4179 voxels, peak = 95), gca=94.6
- gca peak = 0.16819 (86)
- mri peak = 0.07806 (93)
- Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (4396 voxels, overlap=0.945)
- Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (4396 voxels, peak = 92), gca=91.6
- gca peak = 0.41688 (64)
- mri peak = 0.08738 (60)
- Left_Amygdala (18): linear fit = 0.93 x + 0.0 (317 voxels, overlap=1.050)
- Left_Amygdala (18): linear fit = 0.93 x + 0.0 (317 voxels, peak = 59), gca=59.2
- gca peak = 0.42394 (62)
- mri peak = 0.08357 (59)
- Right_Amygdala (54): linear fit = 0.94 x + 0.0 (364 voxels, overlap=1.036)
- Right_Amygdala (54): linear fit = 0.94 x + 0.0 (364 voxels, peak = 58), gca=58.0
- gca peak = 0.10041 (96)
- mri peak = 0.06785 (89)
- Left_Thalamus_Proper (10): linear fit = 0.94 x + 0.0 (3624 voxels, overlap=0.714)
- Left_Thalamus_Proper (10): linear fit = 0.94 x + 0.0 (3624 voxels, peak = 91), gca=90.7
- gca peak = 0.13978 (88)
- mri peak = 0.07257 (87)
- Right_Thalamus_Proper (49): linear fit = 0.94 x + 0.0 (3173 voxels, overlap=0.887)
- Right_Thalamus_Proper (49): linear fit = 0.94 x + 0.0 (3173 voxels, peak = 83), gca=83.2
- gca peak = 0.08514 (81)
- mri peak = 0.06110 (75)
- Left_Putamen (12): linear fit = 0.87 x + 0.0 (1936 voxels, overlap=0.464)
- Left_Putamen (12): linear fit = 0.87 x + 0.0 (1936 voxels, peak = 70), gca=70.1
- gca peak = 0.09624 (82)
- mri peak = 0.07461 (70)
- Right_Putamen (51): linear fit = 0.85 x + 0.0 (1921 voxels, overlap=0.325)
- Right_Putamen (51): linear fit = 0.85 x + 0.0 (1921 voxels, peak = 69), gca=69.3
- gca peak = 0.07543 (88)
- mri peak = 0.06958 (84)
- Brain_Stem (16): linear fit = 1.03 x + 0.0 (10028 voxels, overlap=0.765)
- Brain_Stem (16): linear fit = 1.03 x + 0.0 (10028 voxels, peak = 91), gca=91.1
- gca peak = 0.12757 (95)
- mri peak = 0.06829 (92)
- Right_VentralDC (60): linear fit = 0.94 x + 0.0 (775 voxels, overlap=0.883)
- Right_VentralDC (60): linear fit = 0.94 x + 0.0 (775 voxels, peak = 90), gca=89.8
- gca peak = 0.17004 (92)
- mri peak = 0.06695 (91)
- Left_VentralDC (28): linear fit = 0.98 x + 0.0 (804 voxels, overlap=0.916)
- Left_VentralDC (28): linear fit = 0.98 x + 0.0 (804 voxels, peak = 90), gca=89.7
- gca peak = 0.21361 (36)
- mri peak = 0.17248 (10)
- gca peak = 0.26069 (23)
- mri peak = 0.18536 ( 8)
- Fourth_Ventricle (15): linear fit = 0.31 x + 0.0 (186 voxels, overlap=0.024)
- Fourth_Ventricle (15): linear fit = 0.31 x + 0.0 (186 voxels, peak = 7), gca=7.0
- gca peak Unknown = 0.94427 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.31795 (35)
- gca peak Third_Ventricle = 0.21361 (36)
- gca peak Fourth_Ventricle = 0.26069 (23)
- gca peak CSF = 0.14367 (38)
- gca peak Left_Accumbens_area = 0.57033 (70)
- gca peak Left_undetermined = 1.00000 (35)
- gca peak Left_vessel = 0.65201 (62)
- gca peak Left_choroid_plexus = 0.09084 (48)
- gca peak Right_Inf_Lat_Vent = 0.31129 (32)
- gca peak Right_Accumbens_area = 0.30219 (72)
- gca peak Right_vessel = 0.83418 (60)
- gca peak Right_choroid_plexus = 0.10189 (48)
- gca peak Fifth_Ventricle = 0.72939 (42)
- gca peak WM_hypointensities = 0.14821 (82)
- gca peak non_WM_hypointensities = 0.10354 (53)
- gca peak Optic_Chiasm = 0.34849 (76)
- not using caudate to estimate GM means
- estimating mean gm scale to be 0.88 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 = 0.13985 ( 9)
- Left_Lateral_Ventricle (4): linear fit = 0.70 x + 0.0 (8969 voxels, overlap=0.941)
- Left_Lateral_Ventricle (4): linear fit = 0.70 x + 0.0 (8969 voxels, peak = 8), gca=7.8
- gca peak = 0.29325 ( 9)
- mri peak = 0.12920 ( 9)
- Right_Lateral_Ventricle (43): linear fit = 0.76 x + 0.0 (7782 voxels, overlap=0.968)
- Right_Lateral_Ventricle (43): linear fit = 0.76 x + 0.0 (7782 voxels, peak = 7), gca=6.9
- gca peak = 0.29084 (87)
- mri peak = 0.11364 (90)
- Right_Pallidum (52): linear fit = 1.00 x + 0.0 (396 voxels, overlap=1.016)
- Right_Pallidum (52): linear fit = 1.00 x + 0.0 (396 voxels, peak = 87), gca=87.4
- gca peak = 0.18461 (88)
- mri peak = 0.09357 (89)
- Left_Pallidum (13): linear fit = 1.00 x + 0.0 (342 voxels, overlap=1.024)
- Left_Pallidum (13): linear fit = 1.00 x + 0.0 (342 voxels, peak = 88), gca=87.6
- gca peak = 0.31426 (55)
- mri peak = 0.08262 (56)
- Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (576 voxels, overlap=1.010)
- Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (576 voxels, peak = 55), gca=55.0
- gca peak = 0.32572 (55)
- mri peak = 0.07391 (57)
- Left_Hippocampus (17): linear fit = 1.01 x + 0.0 (530 voxels, overlap=1.007)
- Left_Hippocampus (17): linear fit = 1.01 x + 0.0 (530 voxels, peak = 56), gca=55.8
- gca peak = 0.08544 (107)
- mri peak = 0.07429 (105)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (38618 voxels, overlap=0.799)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (38618 voxels, peak = 107), gca=107.0
- gca peak = 0.08575 (111)
- mri peak = 0.07886 (108)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (35572 voxels, overlap=0.778)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (35572 voxels, peak = 111), gca=111.0
- gca peak = 0.09148 (53)
- mri peak = 0.04857 (55)
- Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (15695 voxels, overlap=0.993)
- Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (15695 voxels, peak = 53), gca=53.0
- gca peak = 0.10548 (53)
- mri peak = 0.05492 (51)
- Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (15904 voxels, overlap=0.986)
- Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (15904 voxels, peak = 52), gca=52.2
- gca peak = 0.24214 (64)
- mri peak = 0.10772 (62)
- Right_Caudate (50): linear fit = 1.00 x + 0.0 (961 voxels, overlap=1.004)
- Right_Caudate (50): linear fit = 1.00 x + 0.0 (961 voxels, peak = 64), gca=64.0
- gca peak = 0.18407 (61)
- mri peak = 0.10000 (63)
- Left_Caudate (11): linear fit = 0.99 x + 0.0 (1090 voxels, overlap=0.985)
- Left_Caudate (11): linear fit = 0.99 x + 0.0 (1090 voxels, peak = 60), gca=60.1
- gca peak = 0.11329 (57)
- mri peak = 0.06011 (56)
- Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (8667 voxels, overlap=0.998)
- Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (8667 voxels, peak = 58), gca=58.4
- gca peak = 0.13073 (55)
- mri peak = 0.05395 (56)
- Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (8010 voxels, overlap=1.000)
- Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (8010 voxels, peak = 55), gca=55.0
- gca peak = 0.17137 (94)
- mri peak = 0.06365 (92)
- Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (4179 voxels, overlap=0.999)
- Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (4179 voxels, peak = 93), gca=92.6
- gca peak = 0.16068 (92)
- mri peak = 0.07806 (93)
- Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4396 voxels, overlap=1.000)
- Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4396 voxels, peak = 92), gca=91.5
- gca peak = 0.41590 (59)
- mri peak = 0.08738 (60)
- Left_Amygdala (18): linear fit = 1.00 x + 0.0 (317 voxels, overlap=1.037)
- Left_Amygdala (18): linear fit = 1.00 x + 0.0 (317 voxels, peak = 59), gca=59.0
- gca peak = 0.43413 (58)
- mri peak = 0.08357 (59)
- Right_Amygdala (54): linear fit = 1.00 x + 0.0 (364 voxels, overlap=1.023)
- Right_Amygdala (54): linear fit = 1.00 x + 0.0 (364 voxels, peak = 58), gca=58.0
- gca peak = 0.10977 (89)
- mri peak = 0.06785 (89)
- Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (3624 voxels, overlap=0.999)
- Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (3624 voxels, peak = 88), gca=87.7
- gca peak = 0.13244 (83)
- mri peak = 0.07257 (87)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3173 voxels, overlap=1.000)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3173 voxels, peak = 83), gca=82.6
- gca peak = 0.09481 (74)
- mri peak = 0.06110 (75)
- Left_Putamen (12): linear fit = 1.03 x + 0.0 (1936 voxels, overlap=1.000)
- Left_Putamen (12): linear fit = 1.03 x + 0.0 (1936 voxels, peak = 77), gca=76.6
- gca peak = 0.12360 (64)
- mri peak = 0.07461 (70)
- Right_Putamen (51): linear fit = 1.03 x + 0.0 (1921 voxels, overlap=1.001)
- Right_Putamen (51): linear fit = 1.03 x + 0.0 (1921 voxels, peak = 66), gca=66.2
- gca peak = 0.07145 (91)
- mri peak = 0.06958 (84)
- Brain_Stem (16): linear fit = 0.99 x + 0.0 (10028 voxels, overlap=0.819)
- Brain_Stem (16): linear fit = 0.99 x + 0.0 (10028 voxels, peak = 90), gca=89.6
- gca peak = 0.12798 (86)
- mri peak = 0.06829 (92)
- Right_VentralDC (60): linear fit = 1.00 x + 0.0 (775 voxels, overlap=0.821)
- Right_VentralDC (60): linear fit = 1.00 x + 0.0 (775 voxels, peak = 86), gca=85.6
- gca peak = 0.14946 (90)
- mri peak = 0.06695 (91)
- Left_VentralDC (28): linear fit = 1.00 x + 0.0 (804 voxels, overlap=0.934)
- Left_VentralDC (28): linear fit = 1.00 x + 0.0 (804 voxels, peak = 90), gca=89.6
- gca peak = 0.35640 (14)
- mri peak = 0.17248 (10)
- gca peak = 0.33827 ( 9)
- mri peak = 0.18536 ( 8)
- Fourth_Ventricle (15): linear fit = 0.76 x + 0.0 (186 voxels, overlap=0.932)
- Fourth_Ventricle (15): linear fit = 0.76 x + 0.0 (186 voxels, peak = 7), gca=6.9
- gca peak Unknown = 0.94427 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.27467 (31)
- gca peak Third_Ventricle = 0.35640 (14)
- gca peak CSF = 0.30128 (18)
- gca peak Left_Accumbens_area = 0.68081 (57)
- gca peak Left_undetermined = 1.00000 (35)
- gca peak Left_vessel = 0.38311 (62)
- gca peak Left_choroid_plexus = 0.09087 (48)
- gca peak Right_Inf_Lat_Vent = 0.33369 (28)
- gca peak Right_Accumbens_area = 0.31148 (63)
- gca peak Right_vessel = 0.58297 (60)
- gca peak Right_choroid_plexus = 0.10278 (48)
- gca peak Fifth_Ventricle = 0.45329 (19)
- gca peak WM_hypointensities = 0.17437 (84)
- gca peak non_WM_hypointensities = 0.08722 (54)
- gca peak Optic_Chiasm = 0.34849 (76)
- not using caudate to estimate GM means
- estimating mean gm scale to be 1.00 x + 0.0
- estimating mean wm scale to be 1.00 x + 0.0
- estimating mean csf scale to be 0.75 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
- 13609 gm and wm labels changed (%12 to gray, %88 to white out of all changed labels)
- 534 hippocampal voxels changed.
- 5 amygdala voxels changed.
- pass 1: 102789 changed. image ll: -2.265, PF=1.000
- pass 2: 19030 changed. image ll: -2.262, PF=1.000
- pass 3: 7451 changed.
- pass 4: 3515 changed.
- writing labeled volume to aseg.auto_noCCseg.mgz...
- auto-labeling took 18 minutes and 54 seconds.
- mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/cc_up.lta sub007
- 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/sub007/mri/transforms/cc_up.lta
- reading aseg from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/aseg.auto_noCCseg.mgz
- reading norm from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/norm.mgz
- 36276 voxels in left wm, 68759 in right wm, xrange [122, 135]
- searching rotation angles z=[-10 4], y=[-10 4]
-
searching scale 1 Z rot -10.3
searching scale 1 Z rot -10.0
searching scale 1 Z rot -9.8
searching scale 1 Z rot -9.5
searching scale 1 Z rot -9.3
searching scale 1 Z rot -9.0
searching scale 1 Z rot -8.8
searching scale 1 Z rot -8.5
searching scale 1 Z rot -8.3
searching scale 1 Z rot -8.0
searching scale 1 Z rot -7.8
searching scale 1 Z rot -7.5
searching scale 1 Z rot -7.3
searching scale 1 Z rot -7.0
searching scale 1 Z rot -6.8
searching scale 1 Z rot -6.5
searching scale 1 Z rot -6.3
searching scale 1 Z rot -6.0
searching scale 1 Z rot -5.8
searching scale 1 Z rot -5.5
searching scale 1 Z rot -5.3
searching scale 1 Z rot -5.0
searching scale 1 Z rot -4.8
searching scale 1 Z rot -4.5
searching scale 1 Z rot -4.3
searching scale 1 Z rot -4.0
searching scale 1 Z rot -3.8
searching scale 1 Z rot -3.5
searching scale 1 Z rot -3.3
searching scale 1 Z rot -3.0
searching scale 1 Z rot -2.8
searching scale 1 Z rot -2.5
searching scale 1 Z rot -2.3
searching scale 1 Z rot -2.0
searching scale 1 Z rot -1.8
searching scale 1 Z rot -1.5
searching scale 1 Z rot -1.3
searching scale 1 Z rot -1.0
searching scale 1 Z rot -0.8
searching scale 1 Z rot -0.5
searching scale 1 Z rot -0.3
searching scale 1 Z rot -0.0
searching scale 1 Z rot 0.2
searching scale 1 Z rot 0.5
searching scale 1 Z rot 0.7
searching scale 1 Z rot 1.0
searching scale 1 Z rot 1.2
searching scale 1 Z rot 1.5
searching scale 1 Z rot 1.7
searching scale 1 Z rot 2.0
searching scale 1 Z rot 2.2
searching scale 1 Z rot 2.5
searching scale 1 Z rot 2.7
searching scale 1 Z rot 3.0
searching scale 1 Z rot 3.2
searching scale 1 Z rot 3.5 global minimum found at slice 129.5, rotations (-2.85, -3.28)
- final transformation (x=129.5, yr=-2.848, zr=-3.284):
- 0.997 0.057 -0.050 -0.096;
- -0.057 0.998 0.003 61.228;
- 0.050 0.000 0.999 15.697;
- 0.000 0.000 0.000 1.000;
- updating x range to be [126, 132] in xformed coordinates
- best xformed slice 129
- cc center is found at 129 157 114
- eigenvectors:
- -0.001 0.004 1.000;
- -0.174 -0.985 0.003;
- 0.985 -0.174 0.002;
- error in mid anterior detected - correcting...
- error in mid anterior detected - correcting...
- error in mid anterior detected - correcting...
- writing aseg with callosum to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/aseg.auto.mgz...
- corpus callosum matter segmentation took 1.2 minutes
- #--------------------------------------
- #@# Merge ASeg Thu Aug 8 18:11:10 CEST 2013
- cp aseg.auto.mgz aseg.mgz
- #--------------------------------------------
- #@# Intensity Normalization2 Thu Aug 8 18:11:10 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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...
- 3509 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 22 (22)
- csf peak at 28, setting threshold to 46
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- ---------------------------------
- 3d normalization pass 2 of 2
- white matter peak found at 111
- white matter peak found at 110
- gm peak at 58 (58), valley at 24 (24)
- csf peak at 29, setting threshold to 48
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Done iterating ---------------------------------
- writing output to brain.mgz
- 3D bias adjustment took 4 minutes and 19 seconds.
- #--------------------------------------------
- #@# Mask BFS Thu Aug 8 18:15:31 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri
- mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
- threshold mask volume at 5
- DoAbs = 0
- Found 1803371 voxels in mask (pct= 10.75)
- Writing masked volume to brain.finalsurfs.mgz...done.
- #--------------------------------------------
- #@# WM Segmentation Thu Aug 8 18:15:33 CEST 2013
- mri_segment brain.mgz wm.seg.mgz
- doing initial intensity segmentation...
- using local statistics to label ambiguous voxels...
- computing class statistics for intensity windows...
- WM (107.0): 107.5 +- 4.9 [80.0 --> 125.0]
- GM (67.0) : 66.2 +- 9.7 [30.0 --> 96.0]
- setting bottom of white matter range to 75.9
- setting top of gray matter range to 85.6
- 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...
- 7559 sparsely connected voxels removed...
- thickening thin strands....
- 20 segments, 7068 filled
- 842 bright non-wm voxels segmented.
- 4243 diagonally connected voxels added...
- white matter segmentation took 1.9 minutes
- writing output to wm.seg.mgz...
- mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz
- preserving editing changes in input volume...
- auto filling took 0.74 minutes
- reading wm segmentation from wm.seg.mgz...
- 652 voxels added to wm to prevent paths from MTL structures to cortex
- 1896 additional wm voxels added
- 0 additional wm voxels added
- SEG EDIT: 107136 voxels turned on, 39490 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+): 28 found - 28 modified | TOTAL: 28
- pass 2 (xy+): 0 found - 28 modified | TOTAL: 28
- pass 1 (xy-): 24 found - 24 modified | TOTAL: 52
- pass 2 (xy-): 0 found - 24 modified | TOTAL: 52
- pass 1 (yz+): 38 found - 38 modified | TOTAL: 90
- pass 2 (yz+): 0 found - 38 modified | TOTAL: 90
- pass 1 (yz-): 37 found - 37 modified | TOTAL: 127
- pass 2 (yz-): 0 found - 37 modified | TOTAL: 127
- pass 1 (xz+): 51 found - 51 modified | TOTAL: 178
- pass 2 (xz+): 0 found - 51 modified | TOTAL: 178
- pass 1 (xz-): 28 found - 28 modified | TOTAL: 206
- pass 2 (xz-): 0 found - 28 modified | TOTAL: 206
- Iteration Number : 1
- pass 1 (+++): 11 found - 11 modified | TOTAL: 11
- pass 2 (+++): 0 found - 11 modified | TOTAL: 11
- pass 1 (+++): 16 found - 16 modified | TOTAL: 27
- pass 2 (+++): 0 found - 16 modified | TOTAL: 27
- pass 1 (+++): 14 found - 14 modified | TOTAL: 41
- pass 2 (+++): 0 found - 14 modified | TOTAL: 41
- pass 1 (+++): 21 found - 21 modified | TOTAL: 62
- pass 2 (+++): 0 found - 21 modified | TOTAL: 62
- Iteration Number : 1
- pass 1 (++): 224 found - 224 modified | TOTAL: 224
- pass 2 (++): 0 found - 224 modified | TOTAL: 224
- pass 1 (+-): 200 found - 200 modified | TOTAL: 424
- pass 2 (+-): 0 found - 200 modified | TOTAL: 424
- pass 1 (--): 232 found - 232 modified | TOTAL: 656
- pass 2 (--): 0 found - 232 modified | TOTAL: 656
- pass 1 (-+): 186 found - 186 modified | TOTAL: 842
- pass 2 (-+): 0 found - 186 modified | TOTAL: 842
- Iteration Number : 2
- pass 1 (xy+): 4 found - 4 modified | TOTAL: 4
- pass 2 (xy+): 0 found - 4 modified | TOTAL: 4
- pass 1 (xy-): 6 found - 6 modified | TOTAL: 10
- pass 2 (xy-): 0 found - 6 modified | TOTAL: 10
- pass 1 (yz+): 13 found - 13 modified | TOTAL: 23
- pass 2 (yz+): 0 found - 13 modified | TOTAL: 23
- pass 1 (yz-): 10 found - 10 modified | TOTAL: 33
- pass 2 (yz-): 0 found - 10 modified | TOTAL: 33
- pass 1 (xz+): 7 found - 7 modified | TOTAL: 40
- pass 2 (xz+): 0 found - 7 modified | TOTAL: 40
- pass 1 (xz-): 9 found - 9 modified | TOTAL: 49
- pass 2 (xz-): 0 found - 9 modified | TOTAL: 49
- 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 (++): 7 found - 7 modified | TOTAL: 7
- pass 2 (++): 0 found - 7 modified | TOTAL: 7
- pass 1 (+-): 1 found - 1 modified | TOTAL: 8
- pass 2 (+-): 0 found - 1 modified | TOTAL: 8
- pass 1 (--): 3 found - 3 modified | TOTAL: 11
- pass 2 (--): 0 found - 3 modified | TOTAL: 11
- pass 1 (-+): 0 found - 0 modified | TOTAL: 11
- Iteration Number : 3
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 2 found - 2 modified | TOTAL: 2
- pass 2 (yz+): 0 found - 2 modified | TOTAL: 2
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 2
- pass 1 (xz+): 1 found - 1 modified | TOTAL: 3
- pass 2 (xz+): 0 found - 1 modified | TOTAL: 3
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 3
- Iteration Number : 3
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 3
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 1 found - 1 modified | TOTAL: 1
- pass 2 (-+): 0 found - 1 modified | TOTAL: 1
- Iteration Number : 4
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 4
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 4
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Total Number of Modified Voxels = 1176 (out of 635003: 0.185196)
- binarizing input wm segmentation...
- Ambiguous edge configurations...
- mri_pretess done
- #--------------------------------------------
- #@# Fill Thu Aug 8 18:18:16 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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
- 1.034 0.058 -0.046 -7.853;
- -0.042 1.036 0.289 -6.348;
- 0.058 -0.271 0.977 14.330;
- 0.000 0.000 0.000 1.000;
- voxel to talairach voxel transform
- 1.034 0.058 -0.046 -7.853;
- -0.042 1.036 0.289 -6.348;
- 0.058 -0.271 0.977 14.330;
- 0.000 0.000 0.000 1.000;
- reading segmented volume aseg.auto_noCCseg.mgz...
- Looking for area (min, max) = (350, 1400)
- area[0] = 1592 (min = 350, max = 1400), aspect = 0.41 (min = 0.10, max = 0.75)
- need search nearby
- using seed (126, 110, 88), TAL = (2.0, -40.0, 18.0)
- talairach voxel to voxel transform
- 0.963 -0.039 0.057 6.499;
- 0.051 0.894 -0.262 9.831;
- -0.043 0.250 0.948 -12.332;
- 0.000 0.000 0.000 1.000;
- segmentation indicates cc at (126, 110, 88) --> (2.0, -40.0, 18.0)
- done.
- writing output to filled.mgz...
- filling took 0.9 minutes
- talairach cc position changed to (2.00, -40.00, 18.00)
- Erasing brainstem...done.
- seed_search_size = 9, min_neighbors = 5
- search rh wm seed point around talairach space:(20.00, -40.00, 18.00) SRC: (111.20, 90.61, 93.96)
- search lh wm seed point around talairach space (-16.00, -40.00, 18.00), SRC: (145.86, 92.44, 92.40)
- 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 18:19:12 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/scripts
- mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz
- Iteration Number : 1
- pass 1 (xy+): 4 found - 4 modified | TOTAL: 4
- pass 2 (xy+): 0 found - 4 modified | TOTAL: 4
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 4
- pass 1 (yz+): 2 found - 2 modified | TOTAL: 6
- pass 2 (yz+): 0 found - 2 modified | TOTAL: 6
- pass 1 (yz-): 3 found - 3 modified | TOTAL: 9
- pass 2 (yz-): 0 found - 3 modified | TOTAL: 9
- pass 1 (xz+): 2 found - 2 modified | TOTAL: 11
- pass 2 (xz+): 0 found - 2 modified | TOTAL: 11
- pass 1 (xz-): 5 found - 5 modified | TOTAL: 16
- pass 2 (xz-): 0 found - 5 modified | TOTAL: 16
- Iteration Number : 1
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 1
- pass 1 (++): 3 found - 3 modified | TOTAL: 3
- pass 2 (++): 0 found - 3 modified | TOTAL: 3
- pass 1 (+-): 0 found - 0 modified | TOTAL: 3
- pass 1 (--): 3 found - 3 modified | TOTAL: 6
- pass 2 (--): 0 found - 3 modified | TOTAL: 6
- pass 1 (-+): 1 found - 1 modified | TOTAL: 7
- pass 2 (-+): 0 found - 1 modified | TOTAL: 7
- 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 = 23 (out of 306864: 0.007495)
- 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: 790 vertices, 901 faces
- slice 50: 8036 vertices, 8329 faces
- slice 60: 19496 vertices, 19954 faces
- slice 70: 33555 vertices, 34002 faces
- slice 80: 47332 vertices, 47773 faces
- slice 90: 60197 vertices, 60587 faces
- slice 100: 73250 vertices, 73688 faces
- slice 110: 85807 vertices, 86267 faces
- slice 120: 98249 vertices, 98720 faces
- slice 130: 110492 vertices, 110920 faces
- slice 140: 122264 vertices, 122668 faces
- slice 150: 132187 vertices, 132570 faces
- slice 160: 141149 vertices, 141452 faces
- slice 170: 148111 vertices, 148372 faces
- slice 180: 154514 vertices, 154756 faces
- slice 190: 159710 vertices, 159885 faces
- slice 200: 162641 vertices, 162687 faces
- slice 210: 162700 vertices, 162728 faces
- slice 220: 162700 vertices, 162728 faces
- slice 230: 162700 vertices, 162728 faces
- slice 240: 162700 vertices, 162728 faces
- slice 250: 162700 vertices, 162728 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...
- 162700 voxel in cpt #1: X=-28 [v=162700,e=488184,f=325456] located at (-29.760523, -19.762274, 38.981236)
- For the whole surface: X=-28 [v=162700,e=488184,f=325456]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Smooth1 lh Thu Aug 8 18:19:20 CEST 2013
- mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 18:19:26 CEST 2013
- mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/scripts
- avg radius = 49.5 mm, total surface area = 85469 mm^2
- writing inflated surface to ../surf/lh.inflated.nofix
- inflation took 0.6 minutes
- Not saving sulc
-
step 000: RMS=0.100 (target=0.015)
step 005: RMS=0.073 (target=0.015)
step 010: RMS=0.054 (target=0.015)
step 015: RMS=0.045 (target=0.015)
step 020: RMS=0.039 (target=0.015)
step 025: RMS=0.034 (target=0.015)
step 030: RMS=0.030 (target=0.015)
step 035: RMS=0.027 (target=0.015)
step 040: RMS=0.026 (target=0.015)
step 045: RMS=0.024 (target=0.015)
step 050: RMS=0.024 (target=0.015)
step 055: RMS=0.024 (target=0.015)
step 060: RMS=0.023 (target=0.015)
- inflation complete.
- Not saving sulc
- #--------------------------------------------
- #@# QSphere lh Thu Aug 8 18:20:04 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/scripts
- mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix
- doing quick spherical unfolding.
- setting seed for random number genererator to 1234
- $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading original vertex positions...
- unfolding cortex into spherical form...
- surface projected - minimizing metric distortion...
- vertex spacing 0.91 +- 0.53 (0.00-->7.49) (max @ vno 121896 --> 121908)
- face area 0.02 +- 0.03 (-0.08-->0.85)
- scaling brain by 0.298...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=175.723, avgs=0
- 005/300: dt: 0.9000, rms radial error=175.470, avgs=0
- 010/300: dt: 0.9000, rms radial error=174.920, avgs=0
- 015/300: dt: 0.9000, rms radial error=174.192, avgs=0
- 020/300: dt: 0.9000, rms radial error=173.364, avgs=0
- 025/300: dt: 0.9000, rms radial error=172.479, avgs=0
- 030/300: dt: 0.9000, rms radial error=171.562, avgs=0
- 035/300: dt: 0.9000, rms radial error=170.628, avgs=0
- 040/300: dt: 0.9000, rms radial error=169.687, avgs=0
- 045/300: dt: 0.9000, rms radial error=168.744, avgs=0
- 050/300: dt: 0.9000, rms radial error=167.802, avgs=0
- 055/300: dt: 0.9000, rms radial error=166.862, avgs=0
- 060/300: dt: 0.9000, rms radial error=165.926, avgs=0
- 065/300: dt: 0.9000, rms radial error=164.995, avgs=0
- 070/300: dt: 0.9000, rms radial error=164.068, avgs=0
- 075/300: dt: 0.9000, rms radial error=163.146, avgs=0
- 080/300: dt: 0.9000, rms radial error=162.229, avgs=0
- 085/300: dt: 0.9000, rms radial error=161.317, avgs=0
- 090/300: dt: 0.9000, rms radial error=160.410, avgs=0
- 095/300: dt: 0.9000, rms radial error=159.508, avgs=0
- 100/300: dt: 0.9000, rms radial error=158.612, avgs=0
- 105/300: dt: 0.9000, rms radial error=157.720, avgs=0
- 110/300: dt: 0.9000, rms radial error=156.833, avgs=0
- 115/300: dt: 0.9000, rms radial error=155.951, avgs=0
- 120/300: dt: 0.9000, rms radial error=155.075, avgs=0
- 125/300: dt: 0.9000, rms radial error=154.203, avgs=0
- 130/300: dt: 0.9000, rms radial error=153.336, avgs=0
- 135/300: dt: 0.9000, rms radial error=152.473, avgs=0
- 140/300: dt: 0.9000, rms radial error=151.616, avgs=0
- 145/300: dt: 0.9000, rms radial error=150.763, avgs=0
- 150/300: dt: 0.9000, rms radial error=149.914, avgs=0
- 155/300: dt: 0.9000, rms radial error=149.071, avgs=0
- 160/300: dt: 0.9000, rms radial error=148.232, avgs=0
- 165/300: dt: 0.9000, rms radial error=147.398, avgs=0
- 170/300: dt: 0.9000, rms radial error=146.568, avgs=0
- 175/300: dt: 0.9000, rms radial error=145.743, avgs=0
- 180/300: dt: 0.9000, rms radial error=144.922, avgs=0
- 185/300: dt: 0.9000, rms radial error=144.106, avgs=0
- 190/300: dt: 0.9000, rms radial error=143.295, avgs=0
- 195/300: dt: 0.9000, rms radial error=142.487, avgs=0
- 200/300: dt: 0.9000, rms radial error=141.685, avgs=0
- 205/300: dt: 0.9000, rms radial error=140.886, avgs=0
- 210/300: dt: 0.9000, rms radial error=140.093, avgs=0
- 215/300: dt: 0.9000, rms radial error=139.303, avgs=0
- 220/300: dt: 0.9000, rms radial error=138.518, avgs=0
- 225/300: dt: 0.9000, rms radial error=137.737, avgs=0
- 230/300: dt: 0.9000, rms radial error=136.961, avgs=0
- 235/300: dt: 0.9000, rms radial error=136.189, avgs=0
- 240/300: dt: 0.9000, rms radial error=135.422, avgs=0
- 245/300: dt: 0.9000, rms radial error=134.659, avgs=0
- 250/300: dt: 0.9000, rms radial error=133.901, avgs=0
- 255/300: dt: 0.9000, rms radial error=133.146, avgs=0
- 260/300: dt: 0.9000, rms radial error=132.396, avgs=0
- 265/300: dt: 0.9000, rms radial error=131.650, avgs=0
- 270/300: dt: 0.9000, rms radial error=130.908, avgs=0
- 275/300: dt: 0.9000, rms radial error=130.170, avgs=0
- 280/300: dt: 0.9000, rms radial error=129.436, avgs=0
- 285/300: dt: 0.9000, rms radial error=128.707, avgs=0
- 290/300: dt: 0.9000, rms radial error=127.981, avgs=0
- 295/300: dt: 0.9000, rms radial error=127.260, avgs=0
- 300/300: dt: 0.9000, rms radial error=126.543, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 19329.25
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00011
- epoch 2 (K=40.0), pass 1, starting sse = 3340.51
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00004
- epoch 3 (K=160.0), pass 1, starting sse = 345.30
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.08/11 = 0.00742
- epoch 4 (K=640.0), pass 1, starting sse = 17.58
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.18/15 = 0.01179
- final writing spherical brain to ../surf/lh.qsphere.nofix
- spherical transformation took 0.11 hours
- distance error %100000.00
- #--------------------------------------------
- #@# Fix Topology lh Thu Aug 8 18:26:29 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/sub007/scripts
- mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub007 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=-28 (nv=162700, nf=325456, ne=488184, g=15)
- using quasi-homeomorphic spherical map to tessellate cortical surface...
- Correction of the Topology
- Finding true center and radius of Spherical Surface...done
- Surface centered at (0,0,0) with radius 100.0 in 9 iterations
- marking ambiguous vertices...
- 2352 ambiguous faces found in tessellation
- segmenting defects...
- 24 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- -merging segment 4 into 3
- -merging segment 7 into 3
- 22 defects to be corrected
- 0 vertices coincident
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/lh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -9.8538 (-4.9269)
- -vertex loglikelihood: -6.7167 (-3.3583)
- -normal dot loglikelihood: -3.6324 (-3.6324)
- -quad curv loglikelihood: -6.0687 (-3.0344)
- Total Loglikelihood : -26.2715
- CORRECTING DEFECT 0 (vertices=44, convex hull=80)
- After retessellation of defect 0, euler #=-20 (161305,483439,322114) : difference with theory (-19) = 1
- CORRECTING DEFECT 1 (vertices=10, convex hull=20)
- After retessellation of defect 1, euler #=-19 (161307,483450,322124) : difference with theory (-18) = 1
- CORRECTING DEFECT 2 (vertices=68, convex hull=35)
- After retessellation of defect 2, euler #=-19 (161316,483492,322157) : difference with theory (-17) = 2
- CORRECTING DEFECT 3 (vertices=468, convex hull=203)
- After retessellation of defect 3, euler #=-16 (161373,483769,322380) : difference with theory (-16) = 0
- CORRECTING DEFECT 4 (vertices=120, convex hull=111)
- After retessellation of defect 4, euler #=-15 (161414,483943,322514) : difference with theory (-15) = 0
- CORRECTING DEFECT 5 (vertices=230, convex hull=102)
- After retessellation of defect 5, euler #=-14 (161458,484123,322651) : difference with theory (-14) = 0
- CORRECTING DEFECT 6 (vertices=14, convex hull=14)
- After retessellation of defect 6, euler #=-13 (161460,484131,322658) : difference with theory (-13) = 0
- CORRECTING DEFECT 7 (vertices=15, convex hull=31)
- After retessellation of defect 7, euler #=-12 (161461,484143,322670) : difference with theory (-12) = 0
- CORRECTING DEFECT 8 (vertices=8, convex hull=23)
- After retessellation of defect 8, euler #=-11 (161461,484151,322679) : difference with theory (-11) = 0
- CORRECTING DEFECT 9 (vertices=35, convex hull=70)
- After retessellation of defect 9, euler #=-10 (161472,484213,322731) : difference with theory (-10) = 0
- CORRECTING DEFECT 10 (vertices=9, convex hull=29)
- After retessellation of defect 10, euler #=-9 (161473,484227,322745) : difference with theory (-9) = 0
- CORRECTING DEFECT 11 (vertices=6, convex hull=14)
- After retessellation of defect 11, euler #=-8 (161474,484232,322750) : difference with theory (-8) = 0
- CORRECTING DEFECT 12 (vertices=5, convex hull=21)
- After retessellation of defect 12, euler #=-7 (161475,484239,322757) : difference with theory (-7) = 0
- CORRECTING DEFECT 13 (vertices=67, convex hull=46)
- After retessellation of defect 13, euler #=-6 (161484,484283,322793) : difference with theory (-6) = 0
- CORRECTING DEFECT 14 (vertices=58, convex hull=104)
- After retessellation of defect 14, euler #=-5 (161511,484407,322891) : difference with theory (-5) = 0
- CORRECTING DEFECT 15 (vertices=12, convex hull=15)
- After retessellation of defect 15, euler #=-4 (161511,484412,322897) : difference with theory (-4) = 0
- CORRECTING DEFECT 16 (vertices=44, convex hull=71)
- After retessellation of defect 16, euler #=-3 (161529,484493,322961) : difference with theory (-3) = 0
- CORRECTING DEFECT 17 (vertices=57, convex hull=25)
- After retessellation of defect 17, euler #=-2 (161530,484508,322976) : difference with theory (-2) = 0
- CORRECTING DEFECT 18 (vertices=5, convex hull=29)
- After retessellation of defect 18, euler #=-1 (161531,484522,322990) : difference with theory (-1) = 0
- CORRECTING DEFECT 19 (vertices=27, convex hull=52)
- After retessellation of defect 19, euler #=0 (161542,484572,323030) : difference with theory (0) = 0
- CORRECTING DEFECT 20 (vertices=87, convex hull=66)
- After retessellation of defect 20, euler #=1 (161568,484679,323112) : difference with theory (1) = 0
- CORRECTING DEFECT 21 (vertices=34, convex hull=54)
- After retessellation of defect 21, euler #=2 (161579,484731,323154) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.88 +- 0.22 (0.14-->12.06) (max @ vno 80468 --> 94667)
- 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 (0.14-->12.06) (max @ vno 80468 --> 94667)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 72 mutations (37.7%), 119 crossovers (62.3%), 82 vertices were eliminated
- building final representation...
- 1121 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=161579, nf=323154, ne=484731, g=0)
- writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/lh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 16.0 minutes
- 0 defective edges
- removing intersecting faces
- 000: 178 intersecting
- 001: 2 intersecting
- mris_euler_number ../surf/lh.orig
- euler # = v-e+f = 2g-2: 161579 - 484731 + 323154 = 2 --> 0 holes
- F =2V-4: 323154 = 323158-4 (0)
- 2E=3F: 969462 = 969462 (0)
- total defect index = 0
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/scripts
- mris_remove_intersection ../surf/lh.orig ../surf/lh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 68 intersecting
- 001: 10 intersecting
- writing corrected surface to ../surf/lh.orig
- rm ../surf/lh.inflated
- #--------------------------------------------
- #@# Make White Surf lh Thu Aug 8 18:42:34 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/scripts
- mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub007 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/sub007/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/wm.mgz...
- 23464 bright wm thresholded.
- 975 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/lh.orig...
- computing class statistics...
- border white: 296565 voxels (1.77%)
- border gray 332938 voxels (1.98%)
- WM (92.0): 93.6 +- 10.1 [70.0 --> 110.0]
- GM (76.0) : 73.7 +- 13.2 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 46.8 (was 70)
- setting MAX_BORDER_WHITE to 116.1 (was 105)
- setting MIN_BORDER_WHITE to 60.0 (was 85)
- setting MAX_CSF to 33.7 (was 40)
- setting MAX_GRAY to 95.9 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 53.4 (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/sub007/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.82 +- 0.22 (0.02-->5.31) (max @ vno 80468 --> 161340)
- face area 0.28 +- 0.12 (0.00-->2.17)
- mean absolute distance = 0.65 +- 0.77
- 4038 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=106, GM=60
- mean inside = 93.1, mean outside = 68.6
- smoothing surface for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- mean border=73.0, 173 (173) missing vertices, mean dist 0.4 [0.5 (%30.4)->0.7 (%69.6))]
- %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 0.91 +- 0.26 (0.08-->6.43) (max @ vno 80468 --> 161340)
- face area 0.28 +- 0.13 (0.00-->3.95)
- mean absolute distance = 0.32 +- 0.46
- 4377 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=8548052.0, rms=13.57
- 001: dt: 0.5000, sse=8466790.0, rms=9.694 (0.000%)
- 002: dt: 0.5000, sse=8702490.0, rms=7.483 (0.000%)
- 003: dt: 0.5000, sse=8821822.0, rms=6.082 (0.000%)
- 004: dt: 0.5000, sse=9152202.0, rms=5.304 (0.000%)
- 005: dt: 0.5000, sse=9208737.0, rms=4.838 (0.000%)
- 006: dt: 0.5000, sse=9371784.0, rms=4.627 (0.000%)
- 007: dt: 0.5000, sse=9325665.0, rms=4.473 (0.000%)
- rms = 4.42, time step reduction 1 of 3 to 0.250...
- 008: dt: 0.5000, sse=9381554.0, rms=4.425 (0.000%)
- 009: dt: 0.2500, sse=5802390.5, rms=3.073 (0.000%)
- 010: dt: 0.2500, sse=5342905.5, rms=2.625 (0.000%)
- 011: dt: 0.2500, sse=5034984.0, rms=2.533 (0.000%)
- 012: dt: 0.2500, sse=4957096.0, rms=2.445 (0.000%)
- rms = 2.41, time step reduction 2 of 3 to 0.125...
- 013: dt: 0.2500, sse=4846810.5, rms=2.412 (0.000%)
- 014: dt: 0.1250, sse=4532434.0, rms=2.105 (0.000%)
- rms = 2.06, time step reduction 3 of 3 to 0.062...
- 015: dt: 0.1250, sse=4479049.0, rms=2.062 (0.000%)
- positioning took 2.1 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 1 vertex label from ripped group
- mean border=78.0, 175 (73) missing vertices, mean dist -0.2 [0.3 (%80.5)->0.2 (%19.5))]
- %81 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.90 +- 0.25 (0.10-->6.47) (max @ vno 80468 --> 161340)
- face area 0.35 +- 0.16 (0.00-->4.95)
- mean absolute distance = 0.21 +- 0.28
- 3849 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5742308.0, rms=6.37
- 016: dt: 0.5000, sse=5839220.0, rms=4.357 (0.000%)
- rms = 4.63, time step reduction 1 of 3 to 0.250...
- 017: dt: 0.2500, sse=5295096.0, rms=3.209 (0.000%)
- 018: dt: 0.2500, sse=5096912.0, rms=2.595 (0.000%)
- 019: dt: 0.2500, sse=5011879.5, rms=2.137 (0.000%)
- 020: dt: 0.2500, sse=5000992.5, rms=2.049 (0.000%)
- 021: dt: 0.2500, sse=4914822.0, rms=1.916 (0.000%)
- rms = 1.90, time step reduction 2 of 3 to 0.125...
- 022: dt: 0.2500, sse=4941023.0, rms=1.900 (0.000%)
- 023: dt: 0.1250, sse=4727820.0, rms=1.639 (0.000%)
- rms = 1.61, time step reduction 3 of 3 to 0.062...
- 024: dt: 0.1250, sse=4682711.0, rms=1.606 (0.000%)
- positioning took 1.3 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 3 vertex label from ripped group
- mean border=81.7, 162 (63) missing vertices, mean dist -0.1 [0.2 (%79.5)->0.2 (%20.5))]
- %89 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.89 +- 0.24 (0.11-->6.50) (max @ vno 80468 --> 161340)
- face area 0.33 +- 0.16 (0.00-->4.91)
- mean absolute distance = 0.15 +- 0.23
- 3390 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5226443.0, rms=4.61
- 025: dt: 0.5000, sse=5537337.5, rms=4.297 (0.000%)
- rms = 4.33, time step reduction 1 of 3 to 0.250...
- 026: dt: 0.2500, sse=4982111.0, rms=2.714 (0.000%)
- 027: dt: 0.2500, sse=4834725.0, rms=2.187 (0.000%)
- 028: dt: 0.2500, sse=4918559.0, rms=1.801 (0.000%)
- rms = 1.86, time step reduction 2 of 3 to 0.125...
- 029: dt: 0.1250, sse=4838009.0, rms=1.641 (0.000%)
- 030: dt: 0.1250, sse=4737490.5, rms=1.411 (0.000%)
- rms = 1.38, time step reduction 3 of 3 to 0.062...
- 031: dt: 0.1250, sse=4693270.5, rms=1.379 (0.000%)
- positioning took 1.1 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 3 vertex label from ripped group
- mean border=82.8, 149 (57) missing vertices, mean dist -0.0 [0.2 (%59.9)->0.1 (%40.1))]
- %91 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- writing white matter surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/lh.white...
- writing smoothed curvature to lh.curv
- 000: dt: 0.0000, sse=4736355.0, rms=1.90
- rms = 2.86, time step reduction 1 of 3 to 0.250...
- 032: dt: 0.2500, sse=4816702.0, rms=1.225 (0.000%)
- 033: dt: 0.2500, sse=4968005.0, rms=1.048 (0.000%)
- rms = 1.04, time step reduction 2 of 3 to 0.125...
- 034: dt: 0.2500, sse=5046743.5, rms=1.041 (0.000%)
- rms = 1.02, time step reduction 3 of 3 to 0.062...
- 035: dt: 0.1250, sse=5080059.0, rms=1.020 (0.000%)
- positioning took 0.6 minutes
- inhibiting deformation at non-cortical midline structures...
- generating cortex label...
- 22 non-cortical segments detected
- only using segment with 1764 vertices
- erasing segment 1 (vno[0] = 71716)
- erasing segment 2 (vno[0] = 72829)
- erasing segment 3 (vno[0] = 84014)
- erasing segment 4 (vno[0] = 94447)
- erasing segment 5 (vno[0] = 95632)
- erasing segment 6 (vno[0] = 98225)
- erasing segment 7 (vno[0] = 101930)
- erasing segment 8 (vno[0] = 105530)
- erasing segment 9 (vno[0] = 108016)
- erasing segment 10 (vno[0] = 111295)
- erasing segment 11 (vno[0] = 116088)
- erasing segment 12 (vno[0] = 117104)
- erasing segment 13 (vno[0] = 120563)
- erasing segment 14 (vno[0] = 120616)
- erasing segment 15 (vno[0] = 121671)
- erasing segment 16 (vno[0] = 123782)
- erasing segment 17 (vno[0] = 125662)
- erasing segment 18 (vno[0] = 126636)
- erasing segment 19 (vno[0] = 127528)
- erasing segment 20 (vno[0] = 128405)
- erasing segment 21 (vno[0] = 130535)
- writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/label/lh.cortex.label...
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/lh.curv
- writing smoothed area to lh.area
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/lh.area
- vertex spacing 0.89 +- 0.24 (0.03-->6.54) (max @ vno 80468 --> 161340)
- face area 0.33 +- 0.15 (0.00-->4.87)
- refinement took 7.6 minutes
- #--------------------------------------------
- #@# Smooth2 lh Thu Aug 8 18:50:12 CEST 2013
- mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 18:50:17 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/scripts
- mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated
- avg radius = 49.8 mm, total surface area = 97457 mm^2
- writing inflated surface to ../surf/lh.inflated
- writing sulcal depths to ../surf/lh.sulc
-
step 000: RMS=0.114 (target=0.015)
step 005: RMS=0.079 (target=0.015)
step 010: RMS=0.057 (target=0.015)
step 015: RMS=0.046 (target=0.015)
step 020: RMS=0.039 (target=0.015)
step 025: RMS=0.033 (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=0.018 (target=0.015)
step 050: RMS=0.017 (target=0.015)
step 055: RMS=0.015 (target=0.015)
- inflation complete.
- inflation took 0.6 minutes
- mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated
- normalizing curvature values.
- averaging curvature patterns 5 times.
- sampling 10 neighbors out to a distance of 10 mm
- 212 vertices thresholded to be in k1 ~ [-0.27 0.62], k2 ~ [-0.15 0.12]
- total integrated curvature = 0.536*4pi (6.733) --> 0 handles
- ICI = 1.6, FI = 11.9, variation=194.604
- 188 vertices thresholded to be in [-0.05 0.01]
- writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level
- curvature mean = 0.000, std = 0.001
- 143 vertices thresholded to be in [-0.14 0.20]
- done.
- writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.015, std = 0.023
- done.
- #-----------------------------------------
- #@# Curvature Stats lh Thu Aug 8 18:52:58 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub007 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 [ sub007/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 [ 312 ]
- Gb_filter = 0
- WARN: S lookup min: -0.134706
- WARN: S explicit min: 0.000000 vertex = 921
- #--------------------------------------------
- #@# Sphere lh Thu Aug 8 18:53:03 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 0.278...
- MRISunfold() max_passes = 1 -------
- tol=5.0e-01, sigma=0.0, host=snake, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
- using quadratic fit line minimization
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 1.000000
- desired_rms_height -1.000000
- momentum 0.900000
- nbhd_size 7
- max_nbrs 8
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 1234
- --------------------
- mrisRemoveNegativeArea()
- pass 1: epoch 1 of 3 starting distance error %19.85
- pass 1: epoch 2 of 3 starting distance error %19.74
- unfolding complete - removing small folds...
- starting distance error %19.67
- removing remaining folds...
- final distance error %19.68
- MRISunfold() return, current seed 1234
- writing spherical brain to ../surf/lh.sphere
- spherical transformation took 1.09 hours
- #--------------------------------------------
- #@# Surf Reg lh Thu Aug 8 19:58:35 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 = 0.586
- curvature mean = 0.050, std = 0.940
- curvature mean = 0.026, std = 0.837
- Starting MRISrigidBodyAlignGlobal()
- d=64.00 min @ (0.00, -16.00, 0.00) sse = 356020.9, tmin=1.2702
- d=32.00 min @ (8.00, 0.00, -8.00) sse = 335558.5, tmin=2.5593
- d=16.00 min @ (0.00, 4.00, 4.00) sse = 286202.5, tmin=3.8714
- d=4.00 min @ (-1.00, 0.00, 0.00) sse = 284750.7, tmin=6.5624
- d=2.00 min @ (0.50, 0.50, -0.50) sse = 284076.0, tmin=7.9108
- d=0.50 min @ (-0.12, 0.00, 0.12) sse = 284050.8, tmin=10.5732
- 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 10.57 min
- curvature mean = 0.028, std = 0.936
- curvature mean = 0.012, std = 0.927
- curvature mean = 0.027, std = 0.947
- curvature mean = 0.006, std = 0.965
- curvature mean = 0.024, std = 0.945
- curvature mean = 0.002, std = 0.983
- 2 Reading smoothwm
- curvature mean = -0.024, std = 0.300
- curvature mean = 0.004, std = 0.066
- curvature mean = 0.069, std = 0.313
- curvature mean = 0.004, std = 0.077
- curvature mean = 0.032, std = 0.503
- curvature mean = 0.005, std = 0.082
- curvature mean = 0.016, std = 0.650
- curvature mean = 0.005, std = 0.084
- curvature mean = 0.006, std = 0.762
- MRISregister() return, current seed 0
- writing registered surface to ../surf/lh.sphere.reg...
- #--------------------------------------------
- #@# Jacobian white lh Thu Aug 8 20:30:12 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 20:30:15 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 20:30:17 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub007 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...
- 1450 labels changed using aseg
- relabeling using gibbs priors...
- 000: 3630 changed, 161579 examined...
- 001: 827 changed, 15252 examined...
- 002: 211 changed, 4559 examined...
- 003: 90 changed, 1286 examined...
- 004: 44 changed, 536 examined...
- 005: 16 changed, 250 examined...
- 006: 7 changed, 90 examined...
- 007: 3 changed, 38 examined...
- 008: 2 changed, 18 examined...
- 009: 1 changed, 10 examined...
- 010: 2 changed, 9 examined...
- 011: 0 changed, 6 examined...
- 314 labels changed using aseg
- 000: 154 total segments, 109 labels (407 vertices) changed
- 001: 45 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 54 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 1738 vertices marked for relabeling...
- 1738 labels changed in reclassification.
- writing output to ../label/lh.aparc.annot...
- classification took 1 minutes and 11 seconds.
- #--------------------------------------------
- #@# Make Pial Surf lh Thu Aug 8 20:31:29 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/scripts
- mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub007 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/sub007/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/wm.mgz...
- 23464 bright wm thresholded.
- 975 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/lh.orig...
- computing class statistics...
- border white: 296565 voxels (1.77%)
- border gray 332938 voxels (1.98%)
- WM (92.0): 93.6 +- 10.1 [70.0 --> 110.0]
- GM (76.0) : 73.7 +- 13.2 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 46.8 (was 70)
- setting MAX_BORDER_WHITE to 116.1 (was 105)
- setting MIN_BORDER_WHITE to 60.0 (was 85)
- setting MAX_CSF to 33.7 (was 40)
- setting MAX_GRAY to 95.9 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 53.4 (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=106, GM=60
- mean inside = 93.1, mean outside = 68.6
- 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/sub007/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.82 +- 0.22 (0.02-->5.31) (max @ vno 80468 --> 161340)
- face area 0.28 +- 0.12 (0.00-->2.17)
- mean absolute distance = 0.65 +- 0.77
- 4076 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- deleting segment 0 with 4 points - only 0.00% unknown
- deleting segment 1 with 7 points - only 0.00% unknown
- deleting segment 2 with 6 points - only 0.00% unknown
- deleting segment 4 with 8 points - only 0.00% unknown
- deleting segment 5 with 752 points - only 0.00% unknown
- deleting segment 7 with 6 points - only 0.00% unknown
- deleting segment 8 with 126 points - only 0.00% unknown
- mean border=73.0, 173 (173) missing vertices, mean dist 0.4 [0.5 (%30.5)->0.7 (%69.5))]
- %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 0.91 +- 0.25 (0.08-->6.43) (max @ vno 80468 --> 161340)
- face area 0.28 +- 0.13 (0.00-->3.95)
- mean absolute distance = 0.32 +- 0.46
- 4415 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=8573591.0, rms=13.55
- 001: dt: 0.5000, sse=8504003.0, rms=9.678 (0.000%)
- 002: dt: 0.5000, sse=8740979.0, rms=7.471 (0.000%)
- 003: dt: 0.5000, sse=8870188.0, rms=6.073 (0.000%)
- 004: dt: 0.5000, sse=9197858.0, rms=5.297 (0.000%)
- 005: dt: 0.5000, sse=9264524.0, rms=4.834 (0.000%)
- 006: dt: 0.5000, sse=9423559.0, rms=4.623 (0.000%)
- 007: dt: 0.5000, sse=9381653.0, rms=4.470 (0.000%)
- rms = 4.42, time step reduction 1 of 3 to 0.250...
- 008: dt: 0.5000, sse=9435614.0, rms=4.421 (0.000%)
- 009: dt: 0.2500, sse=5832946.5, rms=3.072 (0.000%)
- 010: dt: 0.2500, sse=5370118.0, rms=2.623 (0.000%)
- 011: dt: 0.2500, sse=5061375.5, rms=2.531 (0.000%)
- 012: dt: 0.2500, sse=4983857.5, rms=2.444 (0.000%)
- rms = 2.41, time step reduction 2 of 3 to 0.125...
- 013: dt: 0.2500, sse=4873814.0, rms=2.411 (0.000%)
- 014: dt: 0.1250, sse=4558153.5, rms=2.105 (0.000%)
- rms = 2.06, time step reduction 3 of 3 to 0.062...
- 015: dt: 0.1250, sse=4504696.5, rms=2.061 (0.000%)
- positioning took 2.2 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- deleting segment 0 with 4 points - only 0.00% unknown
- deleting segment 1 with 10 points - only 0.00% unknown
- deleting segment 2 with 6 points - only 0.00% unknown
- deleting segment 4 with 9 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 5 with 2 points - only 0.00% unknown
- deleting segment 6 with 613 points - only 0.00% unknown
- deleting segment 11 with 16 points - only 0.00% unknown
- deleting segment 13 with 146 points - only 0.00% unknown
- mean border=77.9, 175 (73) missing vertices, mean dist -0.2 [0.3 (%80.4)->0.2 (%19.6))]
- %82 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.90 +- 0.24 (0.10-->6.47) (max @ vno 80468 --> 161340)
- face area 0.35 +- 0.16 (0.00-->4.94)
- mean absolute distance = 0.21 +- 0.28
- 3895 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5771240.5, rms=6.36
- 016: dt: 0.5000, sse=5872988.5, rms=4.352 (0.000%)
- rms = 4.63, time step reduction 1 of 3 to 0.250...
- 017: dt: 0.2500, sse=5325562.5, rms=3.205 (0.000%)
- 018: dt: 0.2500, sse=5128056.0, rms=2.593 (0.000%)
- 019: dt: 0.2500, sse=5042291.0, rms=2.136 (0.000%)
- 020: dt: 0.2500, sse=5032399.5, rms=2.049 (0.000%)
- 021: dt: 0.2500, sse=4945473.0, rms=1.916 (0.000%)
- rms = 1.90, time step reduction 2 of 3 to 0.125...
- 022: dt: 0.2500, sse=4972291.5, rms=1.901 (0.000%)
- 023: dt: 0.1250, sse=4758094.5, rms=1.640 (0.000%)
- rms = 1.61, time step reduction 3 of 3 to 0.062...
- 024: dt: 0.1250, sse=4712928.5, rms=1.608 (0.000%)
- positioning took 1.3 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- deleting segment 0 with 4 points - only 0.00% unknown
- deleting segment 1 with 10 points - only 0.00% unknown
- deleting segment 2 with 6 points - only 0.00% unknown
- deleting segment 3 with 10 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 4 with 2 points - only 0.00% unknown
- deleting segment 5 with 684 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 6 with 2 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 8 with 19 points - only 0.00% unknown
- deleting segment 10 with 143 points - only 0.00% unknown
- mean border=81.6, 162 (63) missing vertices, mean dist -0.1 [0.2 (%79.4)->0.2 (%20.6))]
- %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.89 +- 0.24 (0.11-->6.50) (max @ vno 80468 --> 161340)
- face area 0.33 +- 0.15 (0.00-->4.91)
- mean absolute distance = 0.15 +- 0.23
- 3446 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5258597.5, rms=4.61
- 025: dt: 0.5000, sse=5570952.5, rms=4.292 (0.000%)
- rms = 4.33, time step reduction 1 of 3 to 0.250...
- 026: dt: 0.2500, sse=5014007.0, rms=2.713 (0.000%)
- 027: dt: 0.2500, sse=4870226.0, rms=2.188 (0.000%)
- 028: dt: 0.2500, sse=4951772.0, rms=1.802 (0.000%)
- rms = 1.86, time step reduction 2 of 3 to 0.125...
- 029: dt: 0.1250, sse=4870819.0, rms=1.643 (0.000%)
- 030: dt: 0.1250, sse=4770470.0, rms=1.414 (0.000%)
- rms = 1.38, time step reduction 3 of 3 to 0.062...
- 031: dt: 0.1250, sse=4725103.5, rms=1.381 (0.000%)
- positioning took 1.1 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- deleting segment 0 with 4 points - only 0.00% unknown
- deleting segment 1 with 13 points - only 0.00% unknown
- deleting segment 2 with 8 points - only 0.00% unknown
- deleting segment 3 with 10 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 4 with 2 points - only 0.00% unknown
- deleting segment 5 with 691 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 6 with 2 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 8 with 19 points - only 0.00% unknown
- deleting segment 9 with 140 points - only 0.00% unknown
- mean border=82.7, 149 (57) missing vertices, mean dist -0.0 [0.2 (%59.8)->0.1 (%40.2))]
- %92 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- repositioning cortical surface to gray/csf boundary.
- smoothing T1 volume with sigma = 2.000
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4768244.0, rms=1.90
- rms = 2.86, time step reduction 1 of 3 to 0.250...
- 032: dt: 0.2500, sse=4851066.0, rms=1.227 (0.000%)
- 033: dt: 0.2500, sse=5006119.5, rms=1.050 (0.000%)
- rms = 1.04, time step reduction 2 of 3 to 0.125...
- 034: dt: 0.2500, sse=5085631.5, rms=1.043 (0.000%)
- rms = 1.02, time step reduction 3 of 3 to 0.062...
- 035: dt: 0.1250, sse=5118818.5, rms=1.022 (0.000%)
- positioning took 0.7 minutes
- inhibiting deformation at non-cortical midline structures...
- smoothing surface for 5 iterations...
- mean border=49.9, 209 (209) missing vertices, mean dist 1.7 [2.7 (%0.0)->2.2 (%100.0))]
- %15 local maxima, %60 large gradients and %20 min vals, 1803 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=35348924.0, rms=32.29
- 001: dt: 0.5000, sse=25212236.0, rms=26.707 (0.000%)
- 002: dt: 0.5000, sse=18274862.0, rms=22.107 (0.000%)
- 003: dt: 0.5000, sse=13737696.0, rms=18.411 (0.000%)
- 004: dt: 0.5000, sse=11020499.0, rms=15.489 (0.000%)
- 005: dt: 0.5000, sse=9504050.0, rms=13.235 (0.000%)
- 006: dt: 0.5000, sse=8640207.0, rms=11.515 (0.000%)
- 007: dt: 0.5000, sse=8110846.5, rms=10.030 (0.000%)
- 008: dt: 0.5000, sse=7702535.0, rms=8.660 (0.000%)
- 009: dt: 0.5000, sse=7470163.0, rms=7.390 (0.000%)
- 010: dt: 0.5000, sse=7413151.0, rms=6.285 (0.000%)
- 011: dt: 0.5000, sse=7450255.0, rms=5.434 (0.000%)
- 012: dt: 0.5000, sse=7609593.0, rms=4.852 (0.000%)
- 013: dt: 0.5000, sse=7768464.0, rms=4.511 (0.000%)
- 014: dt: 0.5000, sse=7925724.5, rms=4.304 (0.000%)
- 015: dt: 0.5000, sse=8010142.0, rms=4.183 (0.000%)
- 016: dt: 0.5000, sse=8081719.5, rms=4.088 (0.000%)
- rms = 4.05, time step reduction 1 of 3 to 0.250...
- 017: dt: 0.5000, sse=8090288.5, rms=4.047 (0.000%)
- 018: dt: 0.2500, sse=5583389.5, rms=3.277 (0.000%)
- 019: dt: 0.2500, sse=5348225.5, rms=3.067 (0.000%)
- rms = 3.05, time step reduction 2 of 3 to 0.125...
- 020: dt: 0.2500, sse=5183861.0, rms=3.047 (0.000%)
- 021: dt: 0.1250, sse=4945416.5, rms=2.911 (0.000%)
- rms = 2.89, time step reduction 3 of 3 to 0.062...
- 022: dt: 0.1250, sse=4911860.0, rms=2.893 (0.000%)
- positioning took 3.0 minutes
- mean border=47.6, 857 (44) missing vertices, mean dist 0.2 [0.2 (%50.0)->0.6 (%50.0))]
- %35 local maxima, %43 large gradients and %17 min vals, 501 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=5662279.5, rms=4.90
- 023: dt: 0.5000, sse=5979811.0, rms=4.138 (0.000%)
- rms = 4.16, time step reduction 1 of 3 to 0.250...
- 024: dt: 0.2500, sse=5549092.0, rms=3.554 (0.000%)
- 025: dt: 0.2500, sse=5633847.0, rms=3.265 (0.000%)
- 026: dt: 0.2500, sse=5561359.0, rms=3.136 (0.000%)
- 027: dt: 0.2500, sse=5641604.5, rms=3.067 (0.000%)
- rms = 3.03, time step reduction 2 of 3 to 0.125...
- 028: dt: 0.2500, sse=5638181.0, rms=3.029 (0.000%)
- 029: dt: 0.1250, sse=5450173.5, rms=2.893 (0.000%)
- rms = 2.86, time step reduction 3 of 3 to 0.062...
- 030: dt: 0.1250, sse=5444373.5, rms=2.864 (0.000%)
- positioning took 1.2 minutes
- mean border=44.9, 1030 (35) missing vertices, mean dist 0.2 [0.2 (%35.0)->0.4 (%65.0))]
- %60 local maxima, %19 large gradients and %17 min vals, 694 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=5865349.5, rms=4.55
- 031: dt: 0.5000, sse=6045513.5, rms=4.095 (0.000%)
- rms = 4.17, time step reduction 1 of 3 to 0.250...
- 032: dt: 0.2500, sse=5659236.5, rms=3.321 (0.000%)
- 033: dt: 0.2500, sse=5908564.5, rms=2.991 (0.000%)
- 034: dt: 0.2500, sse=5855477.0, rms=2.906 (0.000%)
- rms = 2.87, time step reduction 2 of 3 to 0.125...
- 035: dt: 0.2500, sse=5916220.5, rms=2.868 (0.000%)
- 036: dt: 0.1250, sse=5682437.0, rms=2.712 (0.000%)
- rms = 2.68, time step reduction 3 of 3 to 0.062...
- 037: dt: 0.1250, sse=5670058.0, rms=2.681 (0.000%)
- positioning took 1.1 minutes
- mean border=43.6, 1971 (29) missing vertices, mean dist 0.1 [0.2 (%42.2)->0.3 (%57.8))]
- %65 local maxima, %13 large gradients and %16 min vals, 500 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/sub007/surf/lh.pial...
- writing smoothed curvature to lh.curv.pial
- 000: dt: 0.0000, sse=5753021.0, rms=3.13
- rms = 3.85, time step reduction 1 of 3 to 0.250...
- 038: dt: 0.2500, sse=5565778.0, rms=2.796 (0.000%)
- 039: dt: 0.2500, sse=5776912.5, rms=2.683 (0.000%)
- rms = 2.64, time step reduction 2 of 3 to 0.125...
- 040: dt: 0.2500, sse=5857200.0, rms=2.642 (0.000%)
- 041: dt: 0.1250, sse=5764430.5, rms=2.527 (0.000%)
- rms = 2.50, time step reduction 3 of 3 to 0.062...
- 042: dt: 0.1250, sse=5754699.0, rms=2.503 (0.000%)
- positioning took 0.8 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/lh.curv.pial
- writing smoothed area to lh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/lh.area.pial
- vertex spacing 1.01 +- 0.41 (0.07-->7.36) (max @ vno 123782 --> 123779)
- face area 0.40 +- 0.29 (0.00-->5.97)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 161579 vertices processed
- 25000 of 161579 vertices processed
- 50000 of 161579 vertices processed
- 75000 of 161579 vertices processed
- 100000 of 161579 vertices processed
- 125000 of 161579 vertices processed
- 150000 of 161579 vertices processed
- 0 of 161579 vertices processed
- 25000 of 161579 vertices processed
- 50000 of 161579 vertices processed
- 75000 of 161579 vertices processed
- 100000 of 161579 vertices processed
- 125000 of 161579 vertices processed
- 150000 of 161579 vertices processed
- thickness calculation complete, 198:415 truncations.
- 41543 vertices at 0 distance
- 116316 vertices at 1 distance
- 101697 vertices at 2 distance
- 37336 vertices at 3 distance
- 9339 vertices at 4 distance
- 2282 vertices at 5 distance
- 646 vertices at 6 distance
- 197 vertices at 7 distance
- 83 vertices at 8 distance
- 38 vertices at 9 distance
- 48 vertices at 10 distance
- 35 vertices at 11 distance
- 12 vertices at 12 distance
- 12 vertices at 13 distance
- 11 vertices at 14 distance
- 11 vertices at 15 distance
- 8 vertices at 16 distance
- 6 vertices at 17 distance
- 3 vertices at 18 distance
- 3 vertices at 19 distance
- 4 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/lh.thickness
- positioning took 15.5 minutes
- #--------------------------------------------
- #@# Surf Volume lh Thu Aug 8 20:46:57 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 20:46:57 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/scripts
- pctsurfcon --s sub007 --lh-only
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/scripts/pctsurfcon.log
- Thu Aug 8 20:46:57 CEST 2013
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/scripts
- /opt/freesurfer/5.3.0/bin/pctsurfcon
- $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $
- Linux snake4 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/sub007/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/tmp.pctsurfcon.646/lh.wm.mgh --regheader sub007 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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/sub007/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/label/lh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 = 124409
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/label/lh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/tmp.pctsurfcon.646/lh.wm.mgh
- Dim: 161579 1 1
- mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/tmp.pctsurfcon.646/lh.gm.mgh --projfrac 0.3 --regheader sub007 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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/sub007/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/label/lh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/lh.white
- Done reading source surface
- Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 = 144186
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/label/lh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/tmp.pctsurfcon.646/lh.gm.mgh
- Dim: 161579 1 1
- mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/tmp.pctsurfcon.646/lh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/tmp.pctsurfcon.646/lh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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/sub007/surf/lh.w-g.pct.mgh
- mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/lh.w-g.pct.mgh --annot sub007 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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/sub007/surf/lh.w-g.pct.mgh --annot sub007 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/stats/lh.w-g.pct.stats --snr
- sysname Linux
- hostname snake4
- 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/sub007/surf/lh.w-g.pct.mgh
- Vertex Area is 0.657425 mm^3
- Generating list of segmentation ids
- Found 36 segmentations
- Computing statistics for each segmentation
- 0 1000 unknown 0 0.000
- 1 1001 bankssts 1589 1109.570
- 2 1002 caudalanteriorcingulate 1027 689.731
- 3 1003 caudalmiddlefrontal 4454 2944.495
- 4 1004 corpuscallosum 0 0.000
- 5 1005 cuneus 2566 1654.858
- 6 1006 entorhinal 567 404.056
- 7 1007 fusiform 5867 3934.144
- 8 1008 inferiorparietal 7603 4976.940
- 9 1009 inferiortemporal 5765 3832.635
- 10 1010 isthmuscingulate 1935 1240.849
- 11 1011 lateraloccipital 9208 5869.738
- 12 1012 lateralorbitofrontal 4710 3121.407
- 13 1013 lingual 5912 3884.931
- 14 1014 medialorbitofrontal 2841 1903.955
- 15 1015 middletemporal 4711 3291.798
- 16 1016 parahippocampal 1455 963.902
- 17 1017 paracentral 2523 1683.982
- 18 1018 parsopercularis 3479 2330.639
- 19 1019 parsorbitalis 1163 768.679
- 20 1020 parstriangularis 2376 1573.813
- 21 1021 pericalcarine 2130 1429.023
- 22 1022 postcentral 7091 4485.042
- 23 1023 posteriorcingulate 1991 1328.917
- 24 1024 precentral 8812 5360.462
- 25 1025 precuneus 7315 4822.405
- 26 1026 rostralanteriorcingulate 1840 1177.214
- 27 1027 rostralmiddlefrontal 10556 7143.751
- 28 1028 superiorfrontal 12455 8412.521
- 29 1029 superiorparietal 9850 6468.527
- 30 1030 superiortemporal 7351 4818.728
- 31 1031 supramarginal 7596 5088.936
- 32 1032 frontalpole 324 219.171
- 33 1033 temporalpole 747 513.222
- 34 1034 transversetemporal 973 584.475
- 35 1035 insula 3883 2565.659
- Reporting on 34 segmentations
- mri_segstats done
- Cleaning up
- #-----------------------------------------
- #@# Parcellation Stats lh Thu Aug 8 20:47:11 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 sub007 lh white
- computing statistics for each annotation in ../label/lh.aparc.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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
- 1589 1110 2702 2.456 0.431 0.130 0.035 16 2.3 bankssts
- 1027 690 1492 2.120 0.524 0.147 0.038 18 1.6 caudalanteriorcingulate
- 4454 2944 8688 2.591 0.512 0.128 0.036 53 6.6 caudalmiddlefrontal
- 2566 1655 3638 2.091 0.437 0.156 0.060 42 6.3 cuneus
- 567 404 1908 3.677 0.636 0.154 0.063 8 1.5 entorhinal
- 5867 3934 12270 2.701 0.555 0.147 0.053 97 12.6 fusiform
- 7603 4977 13124 2.336 0.455 0.138 0.050 118 13.7 inferiorparietal
- 5765 3833 11772 2.553 0.646 0.146 0.058 109 14.0 inferiortemporal
- 1935 1241 3115 2.280 0.731 0.178 0.130 69 11.3 isthmuscingulate
- 9208 5870 14598 2.177 0.444 0.146 0.052 148 19.2 lateraloccipital
- 4710 3121 8483 2.382 0.685 0.158 0.076 114 15.4 lateralorbitofrontal
- 5912 3885 9413 2.182 0.512 0.168 0.104 125 17.2 lingual
- 2841 1904 4738 2.186 0.696 0.171 0.178 151 18.2 medialorbitofrontal
- 4711 3292 10292 2.532 0.589 0.150 0.052 93 9.7 middletemporal
- 1455 964 2667 2.422 0.598 0.131 0.054 22 3.1 parahippocampal
- 2523 1684 4737 2.544 0.575 0.122 0.049 29 3.8 paracentral
- 3479 2331 6677 2.496 0.440 0.130 0.039 48 5.7 parsopercularis
- 1163 769 2386 2.524 0.602 0.156 0.059 26 2.8 parsorbitalis
- 2376 1574 4226 2.342 0.510 0.142 0.047 37 4.6 parstriangularis
- 2130 1429 2442 1.771 0.459 0.145 0.056 28 5.1 pericalcarine
- 7091 4485 11129 2.149 0.584 0.123 0.041 109 12.3 postcentral
- 1991 1329 3641 2.398 0.715 0.159 0.058 41 4.6 posteriorcingulate
- 8812 5360 15944 2.651 0.579 0.112 0.034 98 12.5 precentral
- 7315 4822 12494 2.360 0.520 0.137 0.048 117 14.0 precuneus
- 1840 1177 3260 2.276 0.581 0.143 0.051 36 3.9 rostralanteriorcingulate
- 10556 7144 19813 2.355 0.548 0.161 0.063 262 25.2 rostralmiddlefrontal
- 12455 8413 26990 2.684 0.606 0.142 0.051 207 25.6 superiorfrontal
- 9850 6469 16174 2.183 0.466 0.136 0.044 179 17.7 superiorparietal
- 7351 4819 14999 2.705 0.634 0.128 0.041 93 12.6 superiortemporal
- 7596 5089 14495 2.515 0.509 0.143 0.050 137 14.1 supramarginal
- 324 219 848 2.709 0.488 0.208 0.105 12 1.4 frontalpole
- 747 513 2403 3.468 0.867 0.165 0.117 20 2.2 temporalpole
- 973 584 1607 2.338 0.353 0.116 0.049 12 1.4 transversetemporal
- 3883 2566 7815 2.945 0.717 0.128 0.054 51 8.2 insula
- #-----------------------------------------
- #@# Cortical Parc 2 lh Thu Aug 8 20:47:34 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub007 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...
- 45 labels changed using aseg
- relabeling using gibbs priors...
- 000: 11004 changed, 161579 examined...
- 001: 2710 changed, 42298 examined...
- 002: 807 changed, 13841 examined...
- 003: 361 changed, 4535 examined...
- 004: 174 changed, 2034 examined...
- 005: 98 changed, 963 examined...
- 006: 49 changed, 519 examined...
- 007: 32 changed, 300 examined...
- 008: 17 changed, 185 examined...
- 009: 5 changed, 89 examined...
- 010: 4 changed, 31 examined...
- 011: 2 changed, 18 examined...
- 012: 1 changed, 9 examined...
- 013: 0 changed, 5 examined...
- 28 labels changed using aseg
- 000: 329 total segments, 246 labels (2779 vertices) changed
- 001: 97 total segments, 15 labels (35 vertices) changed
- 002: 82 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 164 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 766 vertices marked for relabeling...
- 766 labels changed in reclassification.
- writing output to ../label/lh.aparc.a2009s.annot...
- classification took 1 minutes and 21 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 2 lh Thu Aug 8 20:48:55 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 sub007 lh white
- computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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
- 1663 1126 2792 2.168 0.561 0.165 0.068 40 4.7 G_and_S_frontomargin
- 2065 1329 3425 2.251 0.458 0.137 0.055 30 4.3 G_and_S_occipital_inf
- 1927 1211 3705 2.514 0.572 0.133 0.045 30 3.6 G_and_S_paracentral
- 1819 1181 3914 2.706 0.532 0.149 0.050 32 3.6 G_and_S_subcentral
- 908 632 2008 2.370 0.523 0.213 0.128 39 4.2 G_and_S_transv_frontopol
- 3028 2006 5222 2.345 0.549 0.135 0.045 46 5.5 G_and_S_cingul-Ant
- 1663 1124 3006 2.449 0.519 0.134 0.038 22 2.8 G_and_S_cingul-Mid-Ant
- 1435 981 2853 2.622 0.466 0.147 0.049 22 2.9 G_and_S_cingul-Mid-Post
- 670 438 1512 2.628 0.558 0.185 0.084 17 2.4 G_cingul-Post-dorsal
- 462 283 707 2.027 0.801 0.172 0.125 13 1.8 G_cingul-Post-ventral
- 2557 1627 3647 1.981 0.457 0.166 0.071 51 7.6 G_cuneus
- 2233 1466 4577 2.567 0.462 0.129 0.042 33 4.0 G_front_inf-Opercular
- 359 238 884 2.589 0.395 0.191 0.075 12 1.1 G_front_inf-Orbital
- 1495 971 3140 2.572 0.431 0.162 0.060 31 3.6 G_front_inf-Triangul
- 6017 4030 14362 2.666 0.531 0.166 0.060 169 14.5 G_front_middle
- 8163 5478 19772 2.828 0.627 0.150 0.059 156 18.8 G_front_sup
- 615 384 1533 3.326 0.557 0.134 0.072 11 1.5 G_Ins_lg_and_S_cent_ins
- 842 532 2359 3.355 0.720 0.138 0.070 17 2.4 G_insular_short
- 2679 1689 5461 2.460 0.408 0.157 0.071 63 6.3 G_occipital_middle
- 1963 1237 3666 2.333 0.448 0.145 0.048 35 3.8 G_occipital_sup
- 2237 1470 5435 2.868 0.464 0.169 0.066 55 6.1 G_oc-temp_lat-fusifor
- 3951 2567 6611 2.167 0.481 0.176 0.125 92 12.7 G_oc-temp_med-Lingual
- 1523 990 3601 2.863 0.758 0.139 0.061 26 3.7 G_oc-temp_med-Parahip
- 3010 1947 6698 2.580 0.745 0.182 0.098 99 12.4 G_orbital
- 2371 1534 4570 2.414 0.485 0.152 0.055 47 5.0 G_pariet_inf-Angular
- 3889 2569 8745 2.676 0.523 0.152 0.061 93 8.0 G_pariet_inf-Supramar
- 3536 2276 6987 2.383 0.485 0.156 0.061 107 8.7 G_parietal_sup
- 2780 1645 4755 2.256 0.483 0.131 0.050 63 6.2 G_postcentral
- 3173 1721 6940 3.013 0.490 0.111 0.037 45 4.9 G_precentral
- 3393 2214 6981 2.484 0.505 0.149 0.057 71 7.5 G_precuneus
- 882 581 1763 2.299 0.583 0.203 0.138 43 4.4 G_rectus
- 674 440 1267 2.666 0.813 0.188 0.346 96 3.8 G_subcallosal
- 737 432 1391 2.432 0.303 0.116 0.053 12 1.2 G_temp_sup-G_T_transv
- 2511 1643 6898 3.012 0.590 0.161 0.058 51 6.1 G_temp_sup-Lateral
- 703 478 2024 3.657 0.764 0.128 0.099 10 1.6 G_temp_sup-Plan_polar
- 1756 1166 3240 2.480 0.447 0.125 0.038 22 2.8 G_temp_sup-Plan_tempo
- 2999 1974 6965 2.597 0.705 0.164 0.078 77 9.7 G_temporal_inf
- 2740 1918 7035 2.686 0.565 0.174 0.066 72 7.1 G_temporal_middle
- 390 255 498 2.018 0.393 0.129 0.046 5 0.7 Lat_Fis-ant-Horizont
- 144 114 230 2.040 0.286 0.129 0.029 1 0.2 Lat_Fis-ant-Vertical
- 1632 1080 2188 2.450 0.483 0.128 0.040 16 2.7 Lat_Fis-post
- 2851 1810 4202 2.044 0.461 0.168 0.062 56 7.3 Pole_occipital
- 2094 1400 6291 3.230 0.710 0.159 0.068 46 5.7 Pole_temporal
- 2649 1772 3189 1.975 0.633 0.143 0.058 36 6.0 S_calcarine
- 3354 2191 3989 2.000 0.648 0.105 0.028 25 4.0 S_central
- 1487 999 2157 2.287 0.478 0.101 0.048 14 1.6 S_cingul-Marginalis
- 781 508 1229 2.693 0.726 0.125 0.037 7 1.3 S_circular_insula_ant
- 1695 1126 2661 2.603 0.555 0.097 0.030 9 2.3 S_circular_insula_inf
- 2039 1406 2908 2.367 0.479 0.114 0.029 13 2.6 S_circular_insula_sup
- 1122 786 1988 2.585 0.491 0.128 0.035 13 1.7 S_collat_transv_ant
- 471 293 458 1.837 0.290 0.139 0.044 6 0.9 S_collat_transv_post
- 3383 2277 5211 2.309 0.425 0.124 0.033 35 4.6 S_front_inf
- 1509 1040 2287 2.203 0.488 0.147 0.059 25 2.8 S_front_middle
- 3524 2403 5845 2.436 0.471 0.117 0.031 33 4.6 S_front_sup
- 305 203 612 2.515 0.387 0.142 0.040 6 0.5 S_interm_prim-Jensen
- 4226 2805 5645 2.058 0.368 0.118 0.032 37 5.6 S_intrapariet_and_P_trans
- 1555 1030 2149 2.140 0.373 0.123 0.036 14 2.1 S_oc_middle_and_Lunatus
- 1576 1053 2048 2.057 0.321 0.119 0.031 13 2.1 S_oc_sup_and_transversal
- 937 615 1348 2.117 0.469 0.116 0.034 7 1.3 S_occipital_ant
- 1142 764 1813 2.402 0.497 0.127 0.039 12 1.7 S_oc-temp_lat
- 3136 2183 5011 2.402 0.465 0.138 0.045 37 5.5 S_oc-temp_med_and_Lingual
- 578 386 788 1.897 0.531 0.141 0.042 10 1.0 S_orbital_lateral
- 804 566 1341 2.258 0.790 0.131 0.182 11 9.7 S_orbital_med-olfact
- 1704 1151 2449 2.158 0.458 0.132 0.043 22 3.1 S_orbital-H_Shaped
- 2507 1650 3628 2.312 0.536 0.132 0.042 35 4.3 S_parieto_occipital
- 1605 1014 1474 1.681 0.563 0.166 0.111 56 8.9 S_pericallosal
- 3363 2298 4565 2.108 0.386 0.120 0.031 32 4.2 S_postcentral
- 1745 1150 2705 2.391 0.371 0.102 0.024 12 1.7 S_precentral-inf-part
- 1817 1209 2636 2.303 0.410 0.106 0.026 12 2.1 S_precentral-sup-part
- 689 474 945 1.897 0.454 0.147 0.041 10 1.3 S_suborbital
- 1553 1055 2402 2.266 0.427 0.145 0.049 24 3.2 S_subparietal
- 1798 1214 2551 2.338 0.453 0.116 0.029 14 2.4 S_temporal_inf
- 6595 4460 10508 2.334 0.484 0.121 0.036 72 9.4 S_temporal_sup
- 477 332 583 2.067 0.347 0.113 0.026 3 0.6 S_temporal_transverse
- #-----------------------------------------
- #@# Cortical Parc 3 lh Thu Aug 8 20:49:19 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub007 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...
- 1014 labels changed using aseg
- relabeling using gibbs priors...
- 000: 3224 changed, 161579 examined...
- 001: 748 changed, 13655 examined...
- 002: 210 changed, 4145 examined...
- 003: 89 changed, 1169 examined...
- 004: 32 changed, 544 examined...
- 005: 19 changed, 182 examined...
- 006: 11 changed, 105 examined...
- 007: 5 changed, 59 examined...
- 008: 1 changed, 31 examined...
- 009: 0 changed, 5 examined...
- 195 labels changed using aseg
- 000: 82 total segments, 49 labels (386 vertices) changed
- 001: 33 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 44 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 669 vertices marked for relabeling...
- 669 labels changed in reclassification.
- writing output to ../label/lh.aparc.DKTatlas40.annot...
- classification took 1 minutes and 12 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 3 lh Thu Aug 8 20:50:31 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 sub007 lh white
- computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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
- 1844 1233 3225 2.350 0.563 0.142 0.039 30 3.0 caudalanteriorcingulate
- 4563 3008 8954 2.600 0.509 0.128 0.036 54 6.8 caudalmiddlefrontal
- 3650 2345 5183 2.095 0.452 0.147 0.053 58 7.8 cuneus
- 547 390 1764 3.611 0.614 0.152 0.064 8 1.4 entorhinal
- 5287 3550 10343 2.621 0.510 0.146 0.050 87 11.0 fusiform
- 7227 4740 12178 2.316 0.454 0.135 0.049 105 12.4 inferiorparietal
- 5989 3971 13030 2.636 0.699 0.149 0.060 115 15.1 inferiortemporal
- 1939 1239 3126 2.286 0.732 0.178 0.131 70 11.4 isthmuscingulate
- 9566 6104 15153 2.174 0.450 0.146 0.053 154 20.1 lateraloccipital
- 5118 3407 9573 2.403 0.692 0.165 0.083 175 18.3 lateralorbitofrontal
- 5872 3864 9348 2.181 0.511 0.168 0.105 124 17.1 lingual
- 2279 1526 3896 2.169 0.711 0.171 0.135 65 15.3 medialorbitofrontal
- 6139 4255 12698 2.519 0.566 0.147 0.050 111 12.2 middletemporal
- 1462 969 2689 2.425 0.598 0.131 0.054 22 3.1 parahippocampal
- 2867 1920 5497 2.561 0.573 0.123 0.048 32 4.3 paracentral
- 3085 2054 5933 2.523 0.428 0.132 0.039 44 5.0 parsopercularis
- 1243 821 2271 2.286 0.514 0.146 0.056 24 3.0 parsorbitalis
- 3015 2021 5313 2.306 0.519 0.136 0.042 45 5.3 parstriangularis
- 2145 1440 2472 1.776 0.463 0.145 0.056 28 5.1 pericalcarine
- 7711 4906 12040 2.155 0.583 0.125 0.041 118 13.3 postcentral
- 2124 1420 3832 2.383 0.712 0.160 0.058 44 5.0 posteriorcingulate
- 8778 5342 15778 2.646 0.577 0.112 0.034 97 12.6 precentral
- 7079 4684 12466 2.382 0.510 0.139 0.050 118 14.1 precuneus
- 2284 1485 4004 2.290 0.573 0.151 0.122 83 6.0 rostralanteriorcingulate
- 7410 5000 13870 2.380 0.563 0.159 0.057 179 16.4 rostralmiddlefrontal
- 13996 9467 29875 2.631 0.615 0.147 0.057 259 31.0 superiorfrontal
- 7951 5221 13167 2.192 0.459 0.134 0.044 148 14.3 superiorparietal
- 9605 6384 20445 2.747 0.679 0.132 0.049 137 17.9 superiortemporal
- 7449 4966 14173 2.511 0.508 0.145 0.051 139 14.2 supramarginal
- 948 567 1566 2.329 0.359 0.116 0.049 12 1.4 transversetemporal
- 3493 2298 7119 2.973 0.683 0.120 0.047 41 6.5 insula
- #--------------------------------------------
- #@# Tessellate rh Thu Aug 8 20:50:54 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/scripts
- mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz
- Iteration Number : 1
- pass 1 (xy+): 7 found - 7 modified | TOTAL: 7
- pass 2 (xy+): 0 found - 7 modified | TOTAL: 7
- pass 1 (xy-): 1 found - 1 modified | TOTAL: 8
- pass 2 (xy-): 0 found - 1 modified | TOTAL: 8
- pass 1 (yz+): 3 found - 3 modified | TOTAL: 11
- pass 2 (yz+): 0 found - 3 modified | TOTAL: 11
- pass 1 (yz-): 3 found - 3 modified | TOTAL: 14
- pass 2 (yz-): 0 found - 3 modified | TOTAL: 14
- pass 1 (xz+): 3 found - 3 modified | TOTAL: 17
- pass 2 (xz+): 0 found - 3 modified | TOTAL: 17
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 17
- 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 (+++): 0 found - 0 modified | TOTAL: 2
- pass 1 (+++): 3 found - 3 modified | TOTAL: 5
- pass 2 (+++): 0 found - 3 modified | TOTAL: 5
- 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 (--): 1 found - 1 modified | TOTAL: 3
- pass 2 (--): 0 found - 1 modified | TOTAL: 3
- pass 1 (-+): 2 found - 2 modified | TOTAL: 5
- pass 2 (-+): 0 found - 2 modified | TOTAL: 5
- 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-): 1 found - 1 modified | TOTAL: 2
- pass 2 (xz-): 0 found - 1 modified | TOTAL: 2
- Iteration Number : 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 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 = 30 (out of 304977: 0.009837)
- 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: 207 vertices, 245 faces
- slice 50: 4765 vertices, 5012 faces
- slice 60: 13916 vertices, 14280 faces
- slice 70: 26072 vertices, 26511 faces
- slice 80: 38676 vertices, 39062 faces
- slice 90: 50789 vertices, 51195 faces
- slice 100: 63306 vertices, 63714 faces
- slice 110: 76185 vertices, 76636 faces
- slice 120: 88895 vertices, 89329 faces
- slice 130: 101576 vertices, 102018 faces
- slice 140: 113606 vertices, 114035 faces
- slice 150: 125255 vertices, 125646 faces
- slice 160: 134550 vertices, 134874 faces
- slice 170: 143303 vertices, 143590 faces
- slice 180: 150331 vertices, 150589 faces
- slice 190: 156219 vertices, 156432 faces
- slice 200: 160858 vertices, 160992 faces
- slice 210: 161290 vertices, 161320 faces
- slice 220: 161290 vertices, 161320 faces
- slice 230: 161290 vertices, 161320 faces
- slice 240: 161290 vertices, 161320 faces
- slice 250: 161290 vertices, 161320 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...
- 161290 voxel in cpt #1: X=-30 [v=161290,e=483960,f=322640] located at (27.835302, -13.806318, 42.948242)
- For the whole surface: X=-30 [v=161290,e=483960,f=322640]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Smooth1 rh Thu Aug 8 20:51:03 CEST 2013
- mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/scripts
- setting seed for random number generator to 1234
- smoothing surface tessellation for 10 iterations...
- smoothing complete - recomputing first and second fundamental forms...
- #--------------------------------------------
- #@# Inflation1 rh Thu Aug 8 20:51:08 CEST 2013
- mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/scripts
- avg radius = 48.8 mm, total surface area = 85008 mm^2
- writing inflated surface to ../surf/rh.inflated.nofix
- inflation took 0.6 minutes
- Not saving sulc
-
step 000: RMS=0.100 (target=0.015)
step 005: RMS=0.073 (target=0.015)
step 010: RMS=0.054 (target=0.015)
step 015: RMS=0.046 (target=0.015)
step 020: RMS=0.040 (target=0.015)
step 025: RMS=0.035 (target=0.015)
step 030: RMS=0.031 (target=0.015)
step 035: RMS=0.029 (target=0.015)
step 040: RMS=0.027 (target=0.015)
step 045: RMS=0.026 (target=0.015)
step 050: RMS=0.025 (target=0.015)
step 055: RMS=0.025 (target=0.015)
step 060: RMS=0.025 (target=0.015)
- inflation complete.
- Not saving sulc
- #--------------------------------------------
- #@# QSphere rh Thu Aug 8 20:51:47 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 0.92 +- 0.53 (0.00-->5.86) (max @ vno 121583 --> 121610)
- face area 0.02 +- 0.03 (-0.14-->0.60)
- scaling brain by 0.295...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=176.176, avgs=0
- 005/300: dt: 0.9000, rms radial error=175.916, avgs=0
- 010/300: dt: 0.9000, rms radial error=175.359, avgs=0
- 015/300: dt: 0.9000, rms radial error=174.628, avgs=0
- 020/300: dt: 0.9000, rms radial error=173.796, avgs=0
- 025/300: dt: 0.9000, rms radial error=172.908, avgs=0
- 030/300: dt: 0.9000, rms radial error=171.989, avgs=0
- 035/300: dt: 0.9000, rms radial error=171.053, avgs=0
- 040/300: dt: 0.9000, rms radial error=170.109, avgs=0
- 045/300: dt: 0.9000, rms radial error=169.163, avgs=0
- 050/300: dt: 0.9000, rms radial error=168.218, avgs=0
- 055/300: dt: 0.9000, rms radial error=167.275, avgs=0
- 060/300: dt: 0.9000, rms radial error=166.337, avgs=0
- 065/300: dt: 0.9000, rms radial error=165.403, avgs=0
- 070/300: dt: 0.9000, rms radial error=164.473, avgs=0
- 075/300: dt: 0.9000, rms radial error=163.549, avgs=0
- 080/300: dt: 0.9000, rms radial error=162.629, avgs=0
- 085/300: dt: 0.9000, rms radial error=161.714, avgs=0
- 090/300: dt: 0.9000, rms radial error=160.805, avgs=0
- 095/300: dt: 0.9000, rms radial error=159.900, avgs=0
- 100/300: dt: 0.9000, rms radial error=159.000, avgs=0
- 105/300: dt: 0.9000, rms radial error=158.105, avgs=0
- 110/300: dt: 0.9000, rms radial error=157.215, avgs=0
- 115/300: dt: 0.9000, rms radial error=156.330, avgs=0
- 120/300: dt: 0.9000, rms radial error=155.449, avgs=0
- 125/300: dt: 0.9000, rms radial error=154.574, avgs=0
- 130/300: dt: 0.9000, rms radial error=153.703, avgs=0
- 135/300: dt: 0.9000, rms radial error=152.837, avgs=0
- 140/300: dt: 0.9000, rms radial error=151.976, avgs=0
- 145/300: dt: 0.9000, rms radial error=151.120, avgs=0
- 150/300: dt: 0.9000, rms radial error=150.268, avgs=0
- 155/300: dt: 0.9000, rms radial error=149.421, avgs=0
- 160/300: dt: 0.9000, rms radial error=148.580, avgs=0
- 165/300: dt: 0.9000, rms radial error=147.742, avgs=0
- 170/300: dt: 0.9000, rms radial error=146.910, avgs=0
- 175/300: dt: 0.9000, rms radial error=146.082, avgs=0
- 180/300: dt: 0.9000, rms radial error=145.259, avgs=0
- 185/300: dt: 0.9000, rms radial error=144.441, avgs=0
- 190/300: dt: 0.9000, rms radial error=143.627, avgs=0
- 195/300: dt: 0.9000, rms radial error=142.818, avgs=0
- 200/300: dt: 0.9000, rms radial error=142.014, avgs=0
- 205/300: dt: 0.9000, rms radial error=141.214, avgs=0
- 210/300: dt: 0.9000, rms radial error=140.418, avgs=0
- 215/300: dt: 0.9000, rms radial error=139.627, avgs=0
- 220/300: dt: 0.9000, rms radial error=138.840, avgs=0
- 225/300: dt: 0.9000, rms radial error=138.058, avgs=0
- 230/300: dt: 0.9000, rms radial error=137.280, avgs=0
- 235/300: dt: 0.9000, rms radial error=136.507, avgs=0
- 240/300: dt: 0.9000, rms radial error=135.738, avgs=0
- 245/300: dt: 0.9000, rms radial error=134.973, avgs=0
- 250/300: dt: 0.9000, rms radial error=134.213, avgs=0
- 255/300: dt: 0.9000, rms radial error=133.457, avgs=0
- 260/300: dt: 0.9000, rms radial error=132.705, avgs=0
- 265/300: dt: 0.9000, rms radial error=131.958, avgs=0
- 270/300: dt: 0.9000, rms radial error=131.214, avgs=0
- 275/300: dt: 0.9000, rms radial error=130.475, avgs=0
- 280/300: dt: 0.9000, rms radial error=129.740, avgs=0
- 285/300: dt: 0.9000, rms radial error=129.009, avgs=0
- 290/300: dt: 0.9000, rms radial error=128.282, avgs=0
- 295/300: dt: 0.9000, rms radial error=127.560, avgs=0
- 300/300: dt: 0.9000, rms radial error=126.841, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 19172.30
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00017
- epoch 2 (K=40.0), pass 1, starting sse = 3296.11
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00006
- epoch 3 (K=160.0), pass 1, starting sse = 347.47
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.11/12 = 0.00891
- epoch 4 (K=640.0), pass 1, starting sse = 18.74
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.25/26 = 0.00962
- final writing spherical brain to ../surf/rh.qsphere.nofix
- spherical transformation took 0.11 hours
- distance error %100000.00
- #--------------------------------------------
- #@# Fix Topology rh Thu Aug 8 20:58:22 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/sub007/scripts
- mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub007 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=-30 (nv=161290, nf=322640, ne=483960, g=16)
- 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...
- 2611 ambiguous faces found in tessellation
- segmenting defects...
- 23 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- -merging segment 7 into 5
- 22 defects to be corrected
- 0 vertices coincident
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/rh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -9.9380 (-4.9690)
- -vertex loglikelihood: -6.6984 (-3.3492)
- -normal dot loglikelihood: -3.6457 (-3.6457)
- -quad curv loglikelihood: -6.4396 (-3.2198)
- Total Loglikelihood : -26.7216
- CORRECTING DEFECT 0 (vertices=13, convex hull=23)
- After retessellation of defect 0, euler #=-20 (159713,478629,318896) : difference with theory (-19) = 1
- CORRECTING DEFECT 1 (vertices=8, convex hull=30)
- After retessellation of defect 1, euler #=-19 (159715,478644,318910) : difference with theory (-18) = 1
- CORRECTING DEFECT 2 (vertices=23, convex hull=50)
- After retessellation of defect 2, euler #=-18 (159728,478703,318957) : difference with theory (-17) = 1
- CORRECTING DEFECT 3 (vertices=159, convex hull=107)
- After retessellation of defect 3, euler #=-17 (159755,478837,319065) : difference with theory (-16) = 1
- CORRECTING DEFECT 4 (vertices=341, convex hull=153)
- Warning - incorrect dp selected!!!!(-119.563638 >= -119.563640 )
- After retessellation of defect 4, euler #=-16 (159764,478938,319158) : difference with theory (-15) = 1
- CORRECTING DEFECT 5 (vertices=414, convex hull=172)
- After retessellation of defect 5, euler #=-14 (159785,479080,319281) : difference with theory (-14) = 0
- CORRECTING DEFECT 6 (vertices=21, convex hull=35)
- After retessellation of defect 6, euler #=-13 (159789,479101,319299) : difference with theory (-13) = 0
- CORRECTING DEFECT 7 (vertices=54, convex hull=31)
- After retessellation of defect 7, euler #=-12 (159793,479126,319321) : difference with theory (-12) = 0
- CORRECTING DEFECT 8 (vertices=12, convex hull=26)
- After retessellation of defect 8, euler #=-11 (159797,479145,319337) : difference with theory (-11) = 0
- CORRECTING DEFECT 9 (vertices=22, convex hull=20)
- After retessellation of defect 9, euler #=-10 (159800,479161,319351) : difference with theory (-10) = 0
- CORRECTING DEFECT 10 (vertices=19, convex hull=30)
- After retessellation of defect 10, euler #=-9 (159803,479180,319368) : difference with theory (-9) = 0
- CORRECTING DEFECT 11 (vertices=154, convex hull=52)
- After retessellation of defect 11, euler #=-8 (159812,479230,319410) : difference with theory (-8) = 0
- CORRECTING DEFECT 12 (vertices=20, convex hull=39)
- After retessellation of defect 12, euler #=-7 (159815,479251,319429) : difference with theory (-7) = 0
- CORRECTING DEFECT 13 (vertices=12, convex hull=24)
- After retessellation of defect 13, euler #=-6 (159817,479265,319442) : difference with theory (-6) = 0
- CORRECTING DEFECT 14 (vertices=69, convex hull=60)
- After retessellation of defect 14, euler #=-5 (159841,479361,319515) : difference with theory (-5) = 0
- CORRECTING DEFECT 15 (vertices=23, convex hull=62)
- After retessellation of defect 15, euler #=-4 (159850,479410,319556) : difference with theory (-4) = 0
- CORRECTING DEFECT 16 (vertices=46, convex hull=57)
- After retessellation of defect 16, euler #=-3 (159855,479450,319592) : difference with theory (-3) = 0
- CORRECTING DEFECT 17 (vertices=14, convex hull=30)
- After retessellation of defect 17, euler #=-2 (159855,479461,319604) : difference with theory (-2) = 0
- CORRECTING DEFECT 18 (vertices=96, convex hull=98)
- After retessellation of defect 18, euler #=-1 (159892,479616,319723) : difference with theory (-1) = 0
- CORRECTING DEFECT 19 (vertices=19, convex hull=49)
- After retessellation of defect 19, euler #=0 (159901,479660,319759) : difference with theory (0) = 0
- CORRECTING DEFECT 20 (vertices=19, convex hull=55)
- After retessellation of defect 20, euler #=1 (159910,479706,319797) : difference with theory (1) = 0
- CORRECTING DEFECT 21 (vertices=21, convex hull=55)
- After retessellation of defect 21, euler #=2 (159917,479745,319830) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.88 +- 0.22 (0.15-->11.79) (max @ vno 137445 --> 146623)
- 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 (0.15-->11.79) (max @ vno 137445 --> 146623)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 90 mutations (34.4%), 172 crossovers (65.6%), 228 vertices were eliminated
- building final representation...
- 1373 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=159917, nf=319830, ne=479745, g=0)
- writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/rh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 24.2 minutes
- 0 defective edges
- removing intersecting faces
- 000: 159 intersecting
- mris_euler_number ../surf/rh.orig
- euler # = v-e+f = 2g-2: 159917 - 479745 + 319830 = 2 --> 0 holes
- F =2V-4: 319830 = 319834-4 (0)
- 2E=3F: 959490 = 959490 (0)
- total defect index = 0
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/scripts
- mris_remove_intersection ../surf/rh.orig ../surf/rh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 20 intersecting
- writing corrected surface to ../surf/rh.orig
- rm ../surf/rh.inflated
- #--------------------------------------------
- #@# Make White Surf rh Thu Aug 8 21:22:42 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/scripts
- mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub007 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/sub007/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/wm.mgz...
- 23624 bright wm thresholded.
- 971 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/rh.orig...
- computing class statistics...
- border white: 296565 voxels (1.77%)
- border gray 332938 voxels (1.98%)
- WM (92.0): 93.6 +- 10.2 [70.0 --> 110.0]
- GM (75.0) : 73.8 +- 12.9 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 46.1 (was 70)
- setting MAX_BORDER_WHITE to 116.2 (was 105)
- setting MIN_BORDER_WHITE to 59.0 (was 85)
- setting MAX_CSF to 33.1 (was 40)
- setting MAX_GRAY to 95.8 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 52.5 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 20.2 (was 40)
- repositioning cortical surface to gray/white boundary
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.82 +- 0.22 (0.03-->5.18) (max @ vno 137445 --> 146623)
- face area 0.28 +- 0.12 (0.00-->2.10)
- mean absolute distance = 0.65 +- 0.74
- 5329 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=106, GM=59
- mean inside = 93.2, mean outside = 68.4
- smoothing surface for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 3 vertex label from ripped group
- mean border=72.6, 148 (148) missing vertices, mean dist 0.4 [0.4 (%29.3)->0.7 (%70.7))]
- %73 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.92 +- 0.26 (0.11-->4.48) (max @ vno 137445 --> 146623)
- face area 0.28 +- 0.13 (0.00-->2.99)
- mean absolute distance = 0.32 +- 0.47
- 3607 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=8623208.0, rms=13.76
- 001: dt: 0.5000, sse=8370681.0, rms=9.864 (0.000%)
- 002: dt: 0.5000, sse=8576162.0, rms=7.599 (0.000%)
- 003: dt: 0.5000, sse=8700918.0, rms=6.159 (0.000%)
- 004: dt: 0.5000, sse=8967526.0, rms=5.300 (0.000%)
- 005: dt: 0.5000, sse=9059357.0, rms=4.841 (0.000%)
- 006: dt: 0.5000, sse=9217536.0, rms=4.591 (0.000%)
- 007: dt: 0.5000, sse=9189250.0, rms=4.466 (0.000%)
- 008: dt: 0.5000, sse=9249014.0, rms=4.380 (0.000%)
- rms = 4.34, time step reduction 1 of 3 to 0.250...
- 009: dt: 0.5000, sse=9177273.0, rms=4.344 (0.000%)
- 010: dt: 0.2500, sse=5705868.5, rms=2.972 (0.000%)
- 011: dt: 0.2500, sse=5209792.0, rms=2.512 (0.000%)
- 012: dt: 0.2500, sse=4919736.0, rms=2.405 (0.000%)
- 013: dt: 0.2500, sse=4831841.0, rms=2.316 (0.000%)
- rms = 2.28, time step reduction 2 of 3 to 0.125...
- 014: dt: 0.2500, sse=4731313.0, rms=2.283 (0.000%)
- 015: dt: 0.1250, sse=4445347.5, rms=1.987 (0.000%)
- rms = 1.95, time step reduction 3 of 3 to 0.062...
- 016: dt: 0.1250, sse=4397422.5, rms=1.945 (0.000%)
- positioning took 2.2 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- mean border=77.7, 64 (20) missing vertices, mean dist -0.2 [0.3 (%81.1)->0.2 (%18.9))]
- %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 (0.12-->4.29) (max @ vno 137445 --> 146623)
- face area 0.35 +- 0.16 (0.00-->3.71)
- mean absolute distance = 0.21 +- 0.27
- 4212 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5754404.5, rms=6.56
- 017: dt: 0.5000, sse=5784848.0, rms=4.391 (0.000%)
- rms = 4.66, time step reduction 1 of 3 to 0.250...
- 018: dt: 0.2500, sse=5247327.0, rms=3.251 (0.000%)
- 019: dt: 0.2500, sse=5036295.0, rms=2.580 (0.000%)
- 020: dt: 0.2500, sse=4948373.5, rms=2.118 (0.000%)
- 021: dt: 0.2500, sse=4940272.5, rms=2.021 (0.000%)
- 022: dt: 0.2500, sse=4841749.5, rms=1.887 (0.000%)
- rms = 1.87, time step reduction 2 of 3 to 0.125...
- 023: dt: 0.2500, sse=4871625.0, rms=1.867 (0.000%)
- 024: dt: 0.1250, sse=4664704.5, rms=1.610 (0.000%)
- rms = 1.58, time step reduction 3 of 3 to 0.062...
- 025: dt: 0.1250, sse=4615541.5, rms=1.576 (0.000%)
- positioning took 1.3 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- mean border=81.4, 66 (11) missing vertices, mean dist -0.1 [0.2 (%79.5)->0.2 (%20.5))]
- %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 0.89 +- 0.25 (0.05-->4.20) (max @ vno 137445 --> 146623)
- face area 0.34 +- 0.16 (0.00-->3.40)
- mean absolute distance = 0.15 +- 0.21
- 2713 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5160973.5, rms=4.64
- 026: dt: 0.5000, sse=5467722.0, rms=4.272 (0.000%)
- rms = 4.38, time step reduction 1 of 3 to 0.250...
- 027: dt: 0.2500, sse=4914323.0, rms=2.675 (0.000%)
- 028: dt: 0.2500, sse=4769598.5, rms=2.177 (0.000%)
- 029: dt: 0.2500, sse=4848682.5, rms=1.788 (0.000%)
- rms = 1.84, time step reduction 2 of 3 to 0.125...
- 030: dt: 0.1250, sse=4768976.5, rms=1.627 (0.000%)
- 031: dt: 0.1250, sse=4668875.0, rms=1.394 (0.000%)
- rms = 1.36, time step reduction 3 of 3 to 0.062...
- 032: dt: 0.1250, sse=4628942.5, rms=1.364 (0.000%)
- positioning took 1.1 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 1 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 4 vertex label from ripped group
- mean border=82.5, 75 (10) missing vertices, mean dist -0.0 [0.1 (%59.9)->0.1 (%40.1))]
- %93 local maxima, % 2 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- writing white matter surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/rh.white...
- writing smoothed curvature to rh.curv
- 000: dt: 0.0000, sse=4667223.5, rms=1.86
- rms = 2.86, time step reduction 1 of 3 to 0.250...
- 033: dt: 0.2500, sse=4746091.5, rms=1.180 (0.000%)
- 034: dt: 0.2500, sse=4879803.0, rms=1.025 (0.000%)
- rms = 1.04, time step reduction 2 of 3 to 0.125...
- rms = 1.01, time step reduction 3 of 3 to 0.062...
- 035: dt: 0.1250, sse=4881234.0, rms=1.013 (0.000%)
- positioning took 0.6 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- generating cortex label...
- 23 non-cortical segments detected
- only using segment with 1372 vertices
- erasing segment 0 (vno[0] = 59581)
- erasing segment 1 (vno[0] = 67906)
- erasing segment 2 (vno[0] = 75388)
- erasing segment 3 (vno[0] = 80317)
- erasing segment 5 (vno[0] = 86387)
- erasing segment 6 (vno[0] = 97588)
- erasing segment 7 (vno[0] = 100293)
- erasing segment 8 (vno[0] = 102522)
- erasing segment 9 (vno[0] = 107383)
- erasing segment 10 (vno[0] = 111861)
- erasing segment 11 (vno[0] = 112037)
- erasing segment 12 (vno[0] = 113188)
- erasing segment 13 (vno[0] = 114343)
- erasing segment 14 (vno[0] = 116812)
- erasing segment 15 (vno[0] = 119144)
- erasing segment 16 (vno[0] = 120207)
- erasing segment 17 (vno[0] = 121260)
- erasing segment 18 (vno[0] = 122375)
- erasing segment 19 (vno[0] = 123443)
- erasing segment 20 (vno[0] = 124453)
- erasing segment 21 (vno[0] = 124481)
- erasing segment 22 (vno[0] = 124497)
- writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/label/rh.cortex.label...
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/rh.curv
- writing smoothed area to rh.area
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/rh.area
- vertex spacing 0.89 +- 0.25 (0.06-->4.19) (max @ vno 137445 --> 146623)
- face area 0.33 +- 0.15 (0.00-->3.40)
- refinement took 7.6 minutes
- #--------------------------------------------
- #@# Smooth2 rh Thu Aug 8 21:30:20 CEST 2013
- mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 21:30:25 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/scripts
- mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated
- avg radius = 49.1 mm, total surface area = 97220 mm^2
- writing inflated surface to ../surf/rh.inflated
- writing sulcal depths to ../surf/rh.sulc
-
step 000: RMS=0.114 (target=0.015)
step 005: RMS=0.079 (target=0.015)
step 010: RMS=0.057 (target=0.015)
step 015: RMS=0.048 (target=0.015)
step 020: RMS=0.040 (target=0.015)
step 025: RMS=0.032 (target=0.015)
step 030: RMS=0.026 (target=0.015)
step 035: RMS=0.023 (target=0.015)
step 040: RMS=0.020 (target=0.015)
step 045: RMS=0.018 (target=0.015)
step 050: RMS=0.017 (target=0.015)
step 055: RMS=0.015 (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
- 211 vertices thresholded to be in k1 ~ [-0.44 0.49], k2 ~ [-0.21 0.09]
- total integrated curvature = 0.545*4pi (6.850) --> 0 handles
- ICI = 1.6, FI = 11.6, variation=193.007
- 170 vertices thresholded to be in [-0.04 0.01]
- writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level
- curvature mean = 0.000, std = 0.001
- 137 vertices thresholded to be in [-0.15 0.18]
- done.
- writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.015, std = 0.023
- done.
- #-----------------------------------------
- #@# Curvature Stats rh Thu Aug 8 21:33:03 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub007 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 [ sub007/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 [ 323 ]
- Gb_filter = 0
- WARN: S lookup min: -0.439492
- WARN: S explicit min: 0.000000 vertex = 86
- #--------------------------------------------
- #@# Sphere rh Thu Aug 8 21:33:08 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 0.276...
- MRISunfold() max_passes = 1 -------
- tol=5.0e-01, sigma=0.0, host=snake, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
- using quadratic fit line minimization
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 1.000000
- desired_rms_height -1.000000
- momentum 0.900000
- nbhd_size 7
- max_nbrs 8
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 1234
- --------------------
- mrisRemoveNegativeArea()
- pass 1: epoch 1 of 3 starting distance error %20.10
- pass 1: epoch 2 of 3 starting distance error %20.01
- unfolding complete - removing small folds...
- starting distance error %19.85
- removing remaining folds...
- final distance error %19.87
- MRISunfold() return, current seed 1234
- writing spherical brain to ../surf/rh.sphere
- spherical transformation took 1.26 hours
- #--------------------------------------------
- #@# Surf Reg rh Thu Aug 8 22:48:51 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 = 0.603
- curvature mean = 0.036, std = 0.938
- curvature mean = 0.023, std = 0.845
- Starting MRISrigidBodyAlignGlobal()
- d=64.00 min @ (16.00, -16.00, 0.00) sse = 428877.3, tmin=1.2678
- d=32.00 min @ (0.00, 8.00, 0.00) sse = 346212.4, tmin=2.5437
- d=16.00 min @ (-4.00, -4.00, 0.00) sse = 329571.7, tmin=3.8265
- d=8.00 min @ (0.00, 2.00, 2.00) sse = 321188.2, tmin=5.1614
- d=4.00 min @ (0.00, -1.00, 0.00) sse = 319511.8, tmin=6.5358
- d=2.00 min @ (0.50, 0.50, -0.50) sse = 319366.2, tmin=7.9195
- d=1.00 min @ (-0.25, -0.25, 0.25) sse = 319174.2, tmin=9.2686
- d=0.50 min @ (0.00, 0.12, -0.12) sse = 319158.3, tmin=10.6278
- 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 10.63 min
- curvature mean = 0.020, std = 0.935
- curvature mean = 0.012, std = 0.932
- curvature mean = 0.014, std = 0.940
- curvature mean = 0.006, std = 0.969
- curvature mean = 0.011, std = 0.938
- curvature mean = 0.002, std = 0.986
- 2 Reading smoothwm
- curvature mean = -0.022, std = 0.304
- curvature mean = 0.006, std = 0.069
- curvature mean = 0.067, std = 0.311
- curvature mean = 0.006, std = 0.081
- curvature mean = 0.031, std = 0.495
- curvature mean = 0.007, std = 0.087
- curvature mean = 0.015, std = 0.635
- curvature mean = 0.007, std = 0.089
- curvature mean = 0.005, std = 0.743
- MRISregister() return, current seed 0
- writing registered surface to ../surf/rh.sphere.reg...
- #--------------------------------------------
- #@# Jacobian white rh Thu Aug 8 23:21:57 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 23:22:01 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 23:22:04 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub007 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...
- 1426 labels changed using aseg
- relabeling using gibbs priors...
- 000: 3389 changed, 159917 examined...
- 001: 751 changed, 14324 examined...
- 002: 174 changed, 4185 examined...
- 003: 51 changed, 1042 examined...
- 004: 15 changed, 313 examined...
- 005: 5 changed, 79 examined...
- 006: 6 changed, 37 examined...
- 007: 4 changed, 36 examined...
- 008: 3 changed, 20 examined...
- 009: 2 changed, 13 examined...
- 010: 0 changed, 14 examined...
- 245 labels changed using aseg
- 000: 117 total segments, 80 labels (565 vertices) changed
- 001: 37 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 33 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 2127 vertices marked for relabeling...
- 2127 labels changed in reclassification.
- writing output to ../label/rh.aparc.annot...
- classification took 1 minutes and 10 seconds.
- #--------------------------------------------
- #@# Make Pial Surf rh Thu Aug 8 23:23:14 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/scripts
- mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub007 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/sub007/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/wm.mgz...
- 23624 bright wm thresholded.
- 971 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/rh.orig...
- computing class statistics...
- border white: 296565 voxels (1.77%)
- border gray 332938 voxels (1.98%)
- WM (92.0): 93.6 +- 10.2 [70.0 --> 110.0]
- GM (75.0) : 73.8 +- 12.9 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 46.1 (was 70)
- setting MAX_BORDER_WHITE to 116.2 (was 105)
- setting MIN_BORDER_WHITE to 59.0 (was 85)
- setting MAX_CSF to 33.1 (was 40)
- setting MAX_GRAY to 95.8 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 52.5 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 20.2 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=106, GM=59
- mean inside = 93.2, 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/sub007/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.82 +- 0.22 (0.03-->5.18) (max @ vno 137445 --> 146623)
- face area 0.28 +- 0.12 (0.00-->2.10)
- mean absolute distance = 0.65 +- 0.75
- 5381 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 11 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 1 with 4 points - only 0.00% unknown
- deleting segment 3 with 412 points - only 0.00% unknown
- deleting segment 5 with 33 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 6 with 3 points - only 0.00% unknown
- mean border=72.6, 148 (148) missing vertices, mean dist 0.4 [0.4 (%29.3)->0.7 (%70.7))]
- %74 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.92 +- 0.26 (0.11-->4.48) (max @ vno 137445 --> 146623)
- face area 0.28 +- 0.13 (0.00-->2.99)
- mean absolute distance = 0.32 +- 0.47
- 3621 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=8642088.0, rms=13.75
- 001: dt: 0.5000, sse=8390758.0, rms=9.861 (0.000%)
- 002: dt: 0.5000, sse=8596269.0, rms=7.597 (0.000%)
- 003: dt: 0.5000, sse=8726595.0, rms=6.156 (0.000%)
- 004: dt: 0.5000, sse=8993203.0, rms=5.297 (0.000%)
- 005: dt: 0.5000, sse=9090630.0, rms=4.839 (0.000%)
- 006: dt: 0.5000, sse=9246731.0, rms=4.589 (0.000%)
- 007: dt: 0.5000, sse=9221209.0, rms=4.464 (0.000%)
- 008: dt: 0.5000, sse=9278438.0, rms=4.378 (0.000%)
- rms = 4.34, time step reduction 1 of 3 to 0.250...
- 009: dt: 0.5000, sse=9211683.0, rms=4.342 (0.000%)
- 010: dt: 0.2500, sse=5723580.5, rms=2.972 (0.000%)
- 011: dt: 0.2500, sse=5225776.5, rms=2.513 (0.000%)
- 012: dt: 0.2500, sse=4934200.5, rms=2.406 (0.000%)
- 013: dt: 0.2500, sse=4846626.0, rms=2.317 (0.000%)
- rms = 2.28, time step reduction 2 of 3 to 0.125...
- 014: dt: 0.2500, sse=4747718.5, rms=2.285 (0.000%)
- 015: dt: 0.1250, sse=4461502.0, rms=1.989 (0.000%)
- rms = 1.95, time step reduction 3 of 3 to 0.062...
- 016: dt: 0.1250, sse=4413342.0, rms=1.948 (0.000%)
- positioning took 2.2 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 11 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 1 with 4 points - only 0.00% unknown
- deleting segment 3 with 261 points - only 0.00% unknown
- deleting segment 6 with 13 points - only 0.00% unknown
- deleting segment 7 with 6 points - only 0.00% unknown
- mean border=77.7, 64 (20) missing vertices, mean dist -0.2 [0.3 (%81.0)->0.2 (%19.0))]
- %84 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.90 +- 0.25 (0.06-->4.29) (max @ vno 137445 --> 146623)
- face area 0.35 +- 0.16 (0.00-->3.71)
- mean absolute distance = 0.21 +- 0.27
- 4227 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5772139.5, rms=6.56
- 017: dt: 0.5000, sse=5805011.5, rms=4.386 (0.000%)
- rms = 4.65, time step reduction 1 of 3 to 0.250...
- 018: dt: 0.2500, sse=5265872.5, rms=3.247 (0.000%)
- 019: dt: 0.2500, sse=5055267.5, rms=2.579 (0.000%)
- 020: dt: 0.2500, sse=4965998.5, rms=2.119 (0.000%)
- 021: dt: 0.2500, sse=4957039.5, rms=2.022 (0.000%)
- 022: dt: 0.2500, sse=4860358.0, rms=1.889 (0.000%)
- rms = 1.87, time step reduction 2 of 3 to 0.125...
- 023: dt: 0.2500, sse=4891125.5, rms=1.868 (0.000%)
- 024: dt: 0.1250, sse=4683219.0, rms=1.612 (0.000%)
- rms = 1.58, time step reduction 3 of 3 to 0.062...
- 025: dt: 0.1250, sse=4633938.0, rms=1.578 (0.000%)
- positioning took 1.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 11 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 1 with 4 points - only 0.00% unknown
- deleting segment 2 with 365 points - only 0.00% unknown
- deleting segment 3 with 19 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 4 with 2 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 6 with 4 points - only 0.00% unknown
- deleting segment 7 with 11 points - only 0.00% unknown
- deleting segment 8 with 5 points - only 0.00% unknown
- mean border=81.4, 67 (11) missing vertices, mean dist -0.1 [0.2 (%79.5)->0.2 (%20.5))]
- %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 0.89 +- 0.24 (0.05-->4.20) (max @ vno 137445 --> 146623)
- face area 0.34 +- 0.15 (0.00-->3.40)
- mean absolute distance = 0.15 +- 0.21
- 2739 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5180353.5, rms=4.63
- 026: dt: 0.5000, sse=5485788.5, rms=4.268 (0.000%)
- rms = 4.38, time step reduction 1 of 3 to 0.250...
- 027: dt: 0.2500, sse=4932349.5, rms=2.673 (0.000%)
- 028: dt: 0.2500, sse=4790560.0, rms=2.176 (0.000%)
- 029: dt: 0.2500, sse=4868275.5, rms=1.788 (0.000%)
- rms = 1.84, time step reduction 2 of 3 to 0.125...
- 030: dt: 0.1250, sse=4788323.0, rms=1.628 (0.000%)
- 031: dt: 0.1250, sse=4687535.0, rms=1.396 (0.000%)
- rms = 1.37, time step reduction 3 of 3 to 0.062...
- 032: dt: 0.1250, sse=4647592.5, rms=1.366 (0.000%)
- positioning took 1.1 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 11 points - only 0.00% unknown
- deleting segment 1 with 5 points - only 0.00% unknown
- deleting segment 3 with 372 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 4 with 1 points - only 0.00% unknown
- deleting segment 5 with 22 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 6 with 2 points - only 0.00% unknown
- deleting segment 7 with 8 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 8 with 4 points - only 0.00% unknown
- deleting segment 9 with 11 points - only 0.00% unknown
- deleting segment 10 with 5 points - only 0.00% unknown
- mean border=82.4, 75 (10) missing vertices, mean dist -0.0 [0.1 (%59.9)->0.1 (%40.1))]
- %93 local maxima, % 2 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- 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=4686341.5, rms=1.86
- rms = 2.86, time step reduction 1 of 3 to 0.250...
- 033: dt: 0.2500, sse=4766499.5, rms=1.183 (0.000%)
- 034: dt: 0.2500, sse=4902740.5, rms=1.026 (0.000%)
- rms = 1.04, time step reduction 2 of 3 to 0.125...
- rms = 1.01, time step reduction 3 of 3 to 0.062...
- 035: dt: 0.1250, sse=4904233.0, rms=1.014 (0.000%)
- positioning took 0.6 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- deleting segment 1 with 3 points - only 0.00% unknown
- smoothing surface for 5 iterations...
- mean border=49.1, 74 (74) missing vertices, mean dist 1.8 [0.1 (%0.0)->2.3 (%100.0))]
- %14 local maxima, %60 large gradients and %22 min vals, 1670 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=36072696.0, rms=32.83
- 001: dt: 0.5000, sse=25664840.0, rms=27.151 (0.000%)
- 002: dt: 0.5000, sse=18519372.0, rms=22.459 (0.000%)
- 003: dt: 0.5000, sse=13804149.0, rms=18.688 (0.000%)
- 004: dt: 0.5000, sse=10970160.0, rms=15.737 (0.000%)
- 005: dt: 0.5000, sse=9419252.0, rms=13.481 (0.000%)
- 006: dt: 0.5000, sse=8585935.0, rms=11.747 (0.000%)
- 007: dt: 0.5000, sse=8110419.0, rms=10.268 (0.000%)
- 008: dt: 0.5000, sse=7769100.5, rms=8.906 (0.000%)
- 009: dt: 0.5000, sse=7483225.0, rms=7.624 (0.000%)
- 010: dt: 0.5000, sse=7405152.5, rms=6.485 (0.000%)
- 011: dt: 0.5000, sse=7465171.5, rms=5.574 (0.000%)
- 012: dt: 0.5000, sse=7564392.5, rms=4.931 (0.000%)
- 013: dt: 0.5000, sse=7740784.0, rms=4.531 (0.000%)
- 014: dt: 0.5000, sse=7901746.0, rms=4.286 (0.000%)
- 015: dt: 0.5000, sse=8009468.5, rms=4.149 (0.000%)
- 016: dt: 0.5000, sse=8076473.0, rms=4.052 (0.000%)
- rms = 4.01, time step reduction 1 of 3 to 0.250...
- 017: dt: 0.5000, sse=8134698.0, rms=4.014 (0.000%)
- 018: dt: 0.2500, sse=5559762.5, rms=3.192 (0.000%)
- 019: dt: 0.2500, sse=5310335.0, rms=2.970 (0.000%)
- rms = 2.94, time step reduction 2 of 3 to 0.125...
- 020: dt: 0.2500, sse=5133077.5, rms=2.942 (0.000%)
- 021: dt: 0.1250, sse=4892418.0, rms=2.784 (0.000%)
- rms = 2.77, time step reduction 3 of 3 to 0.062...
- 022: dt: 0.1250, sse=4856715.5, rms=2.766 (0.000%)
- positioning took 2.9 minutes
- mean border=46.9, 758 (7) missing vertices, mean dist 0.1 [0.2 (%49.9)->0.5 (%50.1))]
- %35 local maxima, %42 large gradients and %18 min vals, 479 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=5558230.0, rms=4.67
- 023: dt: 0.5000, sse=5873405.5, rms=3.978 (0.000%)
- rms = 4.07, time step reduction 1 of 3 to 0.250...
- 024: dt: 0.2500, sse=5448535.5, rms=3.338 (0.000%)
- 025: dt: 0.2500, sse=5567487.5, rms=3.060 (0.000%)
- 026: dt: 0.2500, sse=5510675.5, rms=2.947 (0.000%)
- rms = 2.90, time step reduction 2 of 3 to 0.125...
- 027: dt: 0.2500, sse=5593578.5, rms=2.901 (0.000%)
- 028: dt: 0.1250, sse=5351963.0, rms=2.727 (0.000%)
- rms = 2.69, time step reduction 3 of 3 to 0.062...
- 029: dt: 0.1250, sse=5339891.5, rms=2.693 (0.000%)
- positioning took 1.1 minutes
- mean border=44.3, 932 (5) missing vertices, mean dist 0.1 [0.2 (%35.4)->0.4 (%64.6))]
- %59 local maxima, %18 large gradients and %18 min vals, 694 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=5727991.0, rms=4.36
- 030: dt: 0.5000, sse=5999872.0, rms=4.034 (0.000%)
- rms = 4.11, time step reduction 1 of 3 to 0.250...
- 031: dt: 0.2500, sse=5601447.0, rms=3.185 (0.000%)
- 032: dt: 0.2500, sse=5821003.0, rms=2.846 (0.000%)
- rms = 2.80, time step reduction 2 of 3 to 0.125...
- 033: dt: 0.2500, sse=5799965.5, rms=2.802 (0.000%)
- 034: dt: 0.1250, sse=5590315.5, rms=2.612 (0.000%)
- rms = 2.59, time step reduction 3 of 3 to 0.062...
- 035: dt: 0.1250, sse=5578606.5, rms=2.586 (0.000%)
- positioning took 0.9 minutes
- mean border=42.9, 2069 (5) missing vertices, mean dist 0.1 [0.2 (%42.6)->0.3 (%57.4))]
- %63 local maxima, %14 large gradients and %18 min vals, 517 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/sub007/surf/rh.pial...
- writing smoothed curvature to rh.curv.pial
- 000: dt: 0.0000, sse=5658481.0, rms=3.04
- rms = 3.91, time step reduction 1 of 3 to 0.250...
- 036: dt: 0.2500, sse=5487022.0, rms=2.702 (0.000%)
- 037: dt: 0.2500, sse=5698804.0, rms=2.594 (0.000%)
- rms = 2.56, time step reduction 2 of 3 to 0.125...
- 038: dt: 0.2500, sse=5774040.5, rms=2.560 (0.000%)
- 039: dt: 0.1250, sse=5680046.5, rms=2.429 (0.000%)
- rms = 2.40, time step reduction 3 of 3 to 0.062...
- 040: dt: 0.1250, sse=5685728.5, rms=2.403 (0.000%)
- positioning took 0.8 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/rh.curv.pial
- writing smoothed area to rh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/rh.area.pial
- vertex spacing 1.01 +- 0.42 (0.03-->6.82) (max @ vno 111978 --> 113239)
- face area 0.41 +- 0.29 (0.00-->8.43)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 159917 vertices processed
- 25000 of 159917 vertices processed
- 50000 of 159917 vertices processed
- 75000 of 159917 vertices processed
- 100000 of 159917 vertices processed
- 125000 of 159917 vertices processed
- 150000 of 159917 vertices processed
- 0 of 159917 vertices processed
- 25000 of 159917 vertices processed
- 50000 of 159917 vertices processed
- 75000 of 159917 vertices processed
- 100000 of 159917 vertices processed
- 125000 of 159917 vertices processed
- 150000 of 159917 vertices processed
- thickness calculation complete, 157:494 truncations.
- 42102 vertices at 0 distance
- 115353 vertices at 1 distance
- 98487 vertices at 2 distance
- 36994 vertices at 3 distance
- 9943 vertices at 4 distance
- 2360 vertices at 5 distance
- 665 vertices at 6 distance
- 185 vertices at 7 distance
- 101 vertices at 8 distance
- 63 vertices at 9 distance
- 50 vertices at 10 distance
- 41 vertices at 11 distance
- 37 vertices at 12 distance
- 20 vertices at 13 distance
- 14 vertices at 14 distance
- 3 vertices at 15 distance
- 8 vertices at 16 distance
- 7 vertices at 17 distance
- 4 vertices at 18 distance
- 4 vertices at 19 distance
- 9 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/rh.thickness
- positioning took 14.8 minutes
- #--------------------------------------------
- #@# Surf Volume rh Thu Aug 8 23:38:02 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 23:38:03 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/scripts
- pctsurfcon --s sub007 --rh-only
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/scripts/pctsurfcon.log
- Thu Aug 8 23:38:03 CEST 2013
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/scripts
- /opt/freesurfer/5.3.0/bin/pctsurfcon
- $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $
- Linux snake4 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/sub007/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/tmp.pctsurfcon.4507/rh.wm.mgh --regheader sub007 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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/sub007/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/label/rh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 = 123925
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/label/rh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/tmp.pctsurfcon.4507/rh.wm.mgh
- Dim: 159917 1 1
- mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/tmp.pctsurfcon.4507/rh.gm.mgh --projfrac 0.3 --regheader sub007 --cortex
- srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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/sub007/mri/orig.mgz as target reference.
- Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/label/rh.cortex.label
- Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/rh.white
- Done reading source surface
- Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 = 142743
- Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/label/rh.cortex.label
- Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/tmp.pctsurfcon.4507/rh.gm.mgh
- Dim: 159917 1 1
- mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/tmp.pctsurfcon.4507/rh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/tmp.pctsurfcon.4507/rh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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/sub007/surf/rh.w-g.pct.mgh
- mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/rh.w-g.pct.mgh --annot sub007 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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/sub007/surf/rh.w-g.pct.mgh --annot sub007 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/stats/rh.w-g.pct.stats --snr
- sysname Linux
- hostname snake4
- 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/sub007/surf/rh.w-g.pct.mgh
- Vertex Area is 0.661771 mm^3
- Generating list of segmentation ids
- Found 36 segmentations
- Computing statistics for each segmentation
- 0 2000 unknown 0 0.000
- 1 2001 bankssts 1644 1100.932
- 2 2002 caudalanteriorcingulate 1133 785.027
- 3 2003 caudalmiddlefrontal 3930 2637.184
- 4 2004 corpuscallosum 0 0.000
- 5 2005 cuneus 2799 1807.399
- 6 2006 entorhinal 339 243.539
- 7 2007 fusiform 6251 4216.410
- 8 2008 inferiorparietal 10671 7148.029
- 9 2009 inferiortemporal 5031 3462.153
- 10 2010 isthmuscingulate 1925 1272.390
- 11 2011 lateraloccipital 8218 5295.799
- 12 2012 lateralorbitofrontal 4784 3219.397
- 13 2013 lingual 5664 3734.762
- 14 2014 medialorbitofrontal 2748 1894.958
- 15 2015 middletemporal 5819 3885.760
- 16 2016 parahippocampal 1623 1061.070
- 17 2017 paracentral 2661 1758.828
- 18 2018 parsopercularis 3066 2015.037
- 19 2019 parsorbitalis 1467 1002.620
- 20 2020 parstriangularis 2584 1793.995
- 21 2021 pericalcarine 2492 1712.665
- 22 2022 postcentral 8167 5255.545
- 23 2023 posteriorcingulate 1786 1209.155
- 24 2024 precentral 8303 5156.102
- 25 2025 precuneus 7512 5045.326
- 26 2026 rostralanteriorcingulate 1359 911.653
- 27 2027 rostralmiddlefrontal 10678 7141.040
- 28 2028 superiorfrontal 12170 8200.266
- 29 2029 superiorparietal 9200 5939.784
- 30 2030 superiortemporal 6490 4295.062
- 31 2031 supramarginal 5704 3834.979
- 32 2032 frontalpole 420 288.094
- 33 2033 temporalpole 653 449.495
- 34 2034 transversetemporal 660 406.059
- 35 2035 insula 3691 2409.411
- Reporting on 34 segmentations
- mri_segstats done
- Cleaning up
- #-----------------------------------------
- #@# Parcellation Stats rh Thu Aug 8 23:38:17 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 sub007 rh white
- computing statistics for each annotation in ../label/rh.aparc.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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
- 1644 1101 2944 2.468 0.560 0.129 0.044 24 3.1 bankssts
- 1133 785 2174 2.387 0.718 0.142 0.035 19 1.7 caudalanteriorcingulate
- 3930 2637 8078 2.660 0.501 0.129 0.039 47 6.3 caudalmiddlefrontal
- 2799 1807 4128 2.033 0.437 0.152 0.051 49 6.1 cuneus
- 339 244 1297 3.756 0.580 0.128 0.048 3 0.7 entorhinal
- 6251 4216 12434 2.511 0.546 0.143 0.060 147 16.3 fusiform
- 10671 7148 18979 2.322 0.527 0.141 0.049 200 22.5 inferiorparietal
- 5031 3462 10981 2.576 0.698 0.153 0.116 190 14.9 inferiortemporal
- 1925 1272 3504 2.611 0.841 0.199 0.317 2134 37.5 isthmuscingulate
- 8218 5296 13499 2.225 0.460 0.145 0.057 135 17.3 lateraloccipital
- 4784 3219 8909 2.530 0.629 0.156 0.073 103 12.2 lateralorbitofrontal
- 5664 3735 8868 2.138 0.546 0.162 0.066 106 14.0 lingual
- 2748 1895 4738 2.226 0.541 0.171 0.076 82 9.1 medialorbitofrontal
- 5819 3886 13593 2.823 0.689 0.134 0.047 87 10.8 middletemporal
- 1623 1061 2864 2.428 0.626 0.119 0.041 18 2.9 parahippocampal
- 2661 1759 4863 2.498 0.527 0.118 0.037 25 4.7 paracentral
- 3066 2015 5700 2.481 0.464 0.126 0.034 37 4.3 parsopercularis
- 1467 1003 3302 2.645 0.601 0.175 0.069 33 3.9 parsorbitalis
- 2584 1794 4982 2.351 0.496 0.144 0.049 44 5.3 parstriangularis
- 2492 1713 3119 1.827 0.384 0.155 0.067 39 6.4 pericalcarine
- 8167 5256 12982 2.146 0.572 0.130 0.058 193 17.9 postcentral
- 1786 1209 3338 2.427 0.783 0.165 0.064 104 4.3 posteriorcingulate
- 8303 5156 15651 2.706 0.567 0.116 0.048 100 20.7 precentral
- 7512 5045 13408 2.426 0.491 0.138 0.048 127 14.6 precuneus
- 1359 912 2801 2.747 0.560 0.165 0.063 35 3.3 rostralanteriorcingulate
- 10678 7141 19916 2.419 0.518 0.158 0.061 231 24.7 rostralmiddlefrontal
- 12170 8200 26492 2.805 0.555 0.139 0.044 172 21.9 superiorfrontal
- 9200 5940 14362 2.161 0.419 0.124 0.040 125 14.7 superiorparietal
- 6490 4295 13699 2.774 0.622 0.119 0.039 92 10.6 superiortemporal
- 5704 3835 10843 2.542 0.476 0.139 0.044 83 10.5 supramarginal
- 420 288 1004 2.494 0.536 0.220 0.110 20 1.7 frontalpole
- 653 449 2159 3.743 0.824 0.175 0.114 22 2.6 temporalpole
- 660 406 1164 2.349 0.364 0.131 0.052 7 1.3 transversetemporal
- 3691 2409 7296 2.880 0.633 0.138 0.074 59 12.3 insula
- #-----------------------------------------
- #@# Cortical Parc 2 rh Thu Aug 8 23:38:40 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub007 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...
- 44 labels changed using aseg
- relabeling using gibbs priors...
- 000: 11136 changed, 159917 examined...
- 001: 2801 changed, 42401 examined...
- 002: 936 changed, 14023 examined...
- 003: 401 changed, 5138 examined...
- 004: 205 changed, 2217 examined...
- 005: 100 changed, 1092 examined...
- 006: 60 changed, 583 examined...
- 007: 39 changed, 326 examined...
- 008: 30 changed, 218 examined...
- 009: 16 changed, 147 examined...
- 010: 9 changed, 81 examined...
- 011: 12 changed, 60 examined...
- 012: 7 changed, 49 examined...
- 013: 3 changed, 39 examined...
- 014: 0 changed, 14 examined...
- 36 labels changed using aseg
- 000: 304 total segments, 218 labels (2748 vertices) changed
- 001: 99 total segments, 13 labels (27 vertices) changed
- 002: 86 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 156 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 1467 vertices marked for relabeling...
- 1467 labels changed in reclassification.
- writing output to ../label/rh.aparc.a2009s.annot...
- classification took 1 minutes and 21 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 2 rh Thu Aug 8 23:40:01 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 sub007 rh white
- computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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
- 1410 972 2608 2.319 0.559 0.193 0.088 46 4.5 G_and_S_frontomargin
- 2112 1393 3966 2.454 0.516 0.150 0.049 35 4.3 G_and_S_occipital_inf
- 1564 926 2728 2.537 0.551 0.119 0.065 27 5.1 G_and_S_paracentral
- 1838 1239 3651 2.485 0.527 0.141 0.049 27 3.8 G_and_S_subcentral
- 917 664 2292 2.675 0.615 0.190 0.073 29 2.4 G_and_S_transv_frontopol
- 3109 2164 6041 2.574 0.558 0.142 0.047 50 5.8 G_and_S_cingul-Ant
- 1325 947 2746 2.690 0.492 0.125 0.031 13 1.6 G_and_S_cingul-Mid-Ant
- 1260 873 2561 2.656 0.586 0.152 0.053 22 2.6 G_and_S_cingul-Mid-Post
- 611 414 1532 2.869 0.569 0.206 0.082 85 2.0 G_cingul-Post-dorsal
- 313 197 737 2.765 0.906 0.290 1.053 2011 25.0 G_cingul-Post-ventral
- 2657 1699 3968 2.014 0.464 0.161 0.061 53 6.7 G_cuneus
- 1747 1156 4086 2.670 0.416 0.139 0.044 30 3.3 G_front_inf-Opercular
- 355 256 963 2.751 0.405 0.196 0.087 11 1.2 G_front_inf-Orbital
- 1409 960 3146 2.572 0.389 0.154 0.057 31 3.2 G_front_inf-Triangul
- 4999 3273 12234 2.795 0.448 0.165 0.065 123 12.5 G_front_middle
- 8855 5846 21428 2.900 0.562 0.152 0.053 165 19.4 G_front_sup
- 771 489 1555 2.775 0.567 0.136 0.069 14 2.0 G_Ins_lg_and_S_cent_ins
- 746 514 2326 3.464 0.569 0.181 0.095 22 2.6 G_insular_short
- 2820 1816 5627 2.399 0.465 0.161 0.066 65 6.9 G_occipital_middle
- 2045 1268 3453 2.208 0.423 0.135 0.050 37 4.3 G_occipital_sup
- 2712 1805 6026 2.628 0.518 0.156 0.074 102 9.2 G_oc-temp_lat-fusifor
- 3996 2562 6428 2.175 0.570 0.170 0.077 85 11.1 G_oc-temp_med-Lingual
- 1582 1036 3829 2.952 0.831 0.158 0.120 58 10.8 G_oc-temp_med-Parahip
- 3292 2203 7981 2.728 0.643 0.176 0.088 95 10.3 G_orbital
- 3728 2455 8259 2.537 0.535 0.154 0.068 109 11.0 G_pariet_inf-Angular
- 2903 1938 6792 2.721 0.457 0.148 0.050 71 6.3 G_pariet_inf-Supramar
- 2624 1675 4866 2.305 0.457 0.141 0.053 56 5.0 G_parietal_sup
- 2927 1796 5479 2.341 0.574 0.139 0.087 129 8.3 G_postcentral
- 3177 1848 7562 3.067 0.431 0.120 0.071 55 13.2 G_precentral
- 3532 2322 7642 2.569 0.508 0.151 0.057 79 8.9 G_precuneus
- 653 438 1208 2.193 0.586 0.217 0.129 34 4.0 G_rectus
- 491 320 981 2.842 0.591 0.103 0.046 6 0.8 G_subcallosal
- 516 311 995 2.450 0.356 0.139 0.059 8 1.2 G_temp_sup-G_T_transv
- 2177 1398 6082 3.103 0.500 0.148 0.061 44 5.3 G_temp_sup-Lateral
- 869 586 2350 3.601 0.754 0.106 0.037 6 1.2 G_temp_sup-Plan_polar
- 1019 711 1938 2.479 0.366 0.105 0.025 7 1.1 G_temp_sup-Plan_tempo
- 2732 1895 7082 2.698 0.657 0.170 0.179 161 10.9 G_temporal_inf
- 3290 2197 9131 3.028 0.702 0.150 0.059 65 7.4 G_temporal_middle
- 378 263 559 2.290 0.379 0.125 0.035 3 0.5 Lat_Fis-ant-Horizont
- 191 135 258 2.216 0.271 0.120 0.028 1 0.2 Lat_Fis-ant-Vertical
- 1523 1014 2056 2.468 0.354 0.126 0.042 13 2.6 Lat_Fis-post
- 3371 2161 5025 2.025 0.410 0.151 0.063 58 7.5 Pole_occipital
- 1891 1306 5731 3.211 0.741 0.165 0.087 46 6.4 Pole_temporal
- 2716 1890 3502 2.025 0.527 0.154 0.063 39 7.0 S_calcarine
- 3457 2286 4121 1.982 0.595 0.112 0.031 23 4.6 S_central
- 1391 953 2179 2.342 0.436 0.102 0.026 7 1.5 S_cingul-Marginalis
- 807 530 1273 2.696 0.516 0.131 0.040 7 1.4 S_circular_insula_ant
- 1379 897 2110 2.652 0.518 0.095 0.057 8 4.9 S_circular_insula_inf
- 1586 1046 2332 2.529 0.412 0.118 0.033 12 2.3 S_circular_insula_sup
- 976 665 1733 2.602 0.506 0.137 0.048 12 1.8 S_collat_transv_ant
- 840 554 1056 2.015 0.335 0.111 0.030 5 1.0 S_collat_transv_post
- 3103 2046 4591 2.249 0.418 0.126 0.035 34 4.4 S_front_inf
- 2622 1769 3994 2.232 0.453 0.147 0.057 45 5.7 S_front_middle
- 2927 2052 4766 2.424 0.403 0.111 0.028 21 3.4 S_front_sup
- 355 239 411 2.209 0.357 0.136 0.031 3 0.5 S_interm_prim-Jensen
- 3633 2429 4835 2.041 0.336 0.105 0.026 25 4.0 S_intrapariet_and_P_trans
- 798 529 1221 2.143 0.472 0.151 0.055 13 1.7 S_oc_middle_and_Lunatus
- 1981 1320 2627 2.067 0.349 0.120 0.031 18 2.6 S_oc_sup_and_transversal
- 905 611 1321 2.259 0.321 0.122 0.035 11 1.3 S_occipital_ant
- 1240 841 1583 2.003 0.562 0.120 0.038 15 2.1 S_oc-temp_lat
- 2658 1870 4187 2.266 0.433 0.119 0.033 22 3.5 S_oc-temp_med_and_Lingual
- 740 498 1056 2.070 0.535 0.148 0.046 11 1.5 S_orbital_lateral
- 842 606 1241 2.237 0.698 0.131 0.061 14 1.2 S_orbital_med-olfact
- 1967 1329 3081 2.361 0.554 0.150 0.053 30 4.2 S_orbital-H_Shaped
- 2640 1763 3727 2.261 0.438 0.126 0.034 26 3.9 S_parieto_occipital
- 2054 1299 2103 1.992 0.686 0.155 0.096 102 6.0 S_pericallosal
- 3587 2365 4685 2.087 0.378 0.121 0.036 37 5.5 S_postcentral
- 2068 1398 3062 2.299 0.462 0.104 0.025 12 2.3 S_precentral-inf-part
- 1567 1040 2373 2.512 0.492 0.110 0.026 11 1.7 S_precentral-sup-part
- 319 215 406 1.995 0.484 0.184 0.057 5 0.9 S_suborbital
- 1837 1253 2912 2.331 0.443 0.132 0.046 29 2.9 S_subparietal
- 1456 981 2238 2.245 0.529 0.120 0.032 13 2.1 S_temporal_inf
- 8356 5603 12951 2.347 0.542 0.122 0.035 92 12.0 S_temporal_sup
- 398 274 486 2.105 0.255 0.128 0.036 3 0.7 S_temporal_transverse
- #-----------------------------------------
- #@# Cortical Parc 3 rh Thu Aug 8 23:40:28 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub007 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...
- 912 labels changed using aseg
- relabeling using gibbs priors...
- 000: 3015 changed, 159917 examined...
- 001: 738 changed, 12955 examined...
- 002: 193 changed, 3950 examined...
- 003: 70 changed, 1127 examined...
- 004: 35 changed, 399 examined...
- 005: 23 changed, 204 examined...
- 006: 15 changed, 132 examined...
- 007: 10 changed, 90 examined...
- 008: 5 changed, 50 examined...
- 009: 5 changed, 30 examined...
- 010: 1 changed, 28 examined...
- 011: 1 changed, 7 examined...
- 012: 3 changed, 9 examined...
- 013: 2 changed, 11 examined...
- 014: 1 changed, 11 examined...
- 015: 1 changed, 8 examined...
- 016: 2 changed, 5 examined...
- 017: 0 changed, 11 examined...
- 169 labels changed using aseg
- 000: 67 total segments, 34 labels (160 vertices) changed
- 001: 33 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 37 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 1481 vertices marked for relabeling...
- 1481 labels changed in reclassification.
- writing output to ../label/rh.aparc.DKTatlas40.annot...
- classification took 1 minutes and 11 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 3 rh Thu Aug 8 23:41:39 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 sub007 rh white
- computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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
- 1132 789 2165 2.368 0.719 0.145 0.036 19 1.7 caudalanteriorcingulate
- 4001 2682 8130 2.654 0.501 0.130 0.039 49 6.3 caudalmiddlefrontal
- 3415 2224 4985 2.024 0.425 0.151 0.049 57 6.8 cuneus
- 331 238 1276 3.744 0.586 0.125 0.048 3 0.6 entorhinal
- 5594 3789 10949 2.494 0.529 0.141 0.058 134 14.3 fusiform
- 10285 6867 17852 2.294 0.503 0.140 0.050 191 21.4 inferiorparietal
- 5671 3878 12385 2.576 0.697 0.152 0.110 201 16.7 inferiortemporal
- 1838 1186 3312 2.546 0.829 0.183 0.280 2101 30.9 isthmuscingulate
- 8593 5536 14118 2.220 0.466 0.145 0.057 145 18.3 lateraloccipital
- 5214 3550 10166 2.526 0.619 0.164 0.076 122 14.2 lateralorbitofrontal
- 5692 3750 8912 2.137 0.544 0.162 0.066 106 14.1 lingual
- 2280 1541 4009 2.260 0.603 0.172 0.086 75 8.4 medialorbitofrontal
- 7104 4750 16034 2.775 0.690 0.134 0.046 107 13.3 middletemporal
- 1776 1186 3154 2.502 0.667 0.141 0.093 52 9.6 parahippocampal
- 2800 1854 5094 2.501 0.530 0.119 0.037 27 4.9 paracentral
- 3128 2065 5827 2.487 0.462 0.127 0.035 39 4.5 parsopercularis
- 1669 1125 3547 2.644 0.590 0.163 0.064 33 4.1 parsorbitalis
- 2838 1958 5212 2.289 0.495 0.143 0.047 48 5.5 parstriangularis
- 2470 1701 3086 1.822 0.385 0.153 0.067 37 6.4 pericalcarine
- 8853 5701 13858 2.145 0.556 0.130 0.057 204 19.2 postcentral
- 1764 1194 3295 2.439 0.777 0.164 0.065 103 4.2 posteriorcingulate
- 8170 5057 15589 2.715 0.567 0.116 0.048 99 20.4 precentral
- 7552 5057 13663 2.434 0.486 0.138 0.048 130 14.9 precuneus
- 1468 989 2955 2.693 0.547 0.169 0.064 38 3.6 rostralanteriorcingulate
- 7132 4719 13428 2.452 0.497 0.159 0.063 156 17.2 rostralmiddlefrontal
- 15578 10539 32799 2.708 0.586 0.143 0.047 248 29.5 superiorfrontal
- 7625 4926 12016 2.178 0.416 0.123 0.039 102 12.0 superiorparietal
- 8187 5455 17974 2.840 0.699 0.125 0.047 128 15.2 superiortemporal
- 5263 3546 10175 2.561 0.473 0.138 0.044 76 9.6 supramarginal
- 670 411 1168 2.342 0.364 0.132 0.053 7 1.4 transversetemporal
- 3549 2323 6938 2.849 0.611 0.137 0.070 54 11.5 insula
- #--------------------------------------------
- #@# Refine Pial Surfs w/ T2/FLAIR Thu Aug 8 23:42:01 CEST 2013
- bbregister --s sub007 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/T2raw.lta --init-fsl --T2
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/T2raw.dat.log
- Thu Aug 8 23:42:01 CEST 2013
- setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/scripts
- /opt/freesurfer/5.3.0/bin/bbregister --s sub007 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/T2raw.lta --init-fsl --T2
- $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $
- Linux snake4 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/sub007/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/template.nii
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/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/sub007/mri/orig/T2raw.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.998766, -0.0418513, -0.0267421)
- j_ras = (-0.0444513, 0.99343, 0.105455)
- k_ras = (-0.022153, -0.106514, 0.994064)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/template.nii...
- fslregister --s sub007 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/fslregister --dof 6 --fsvol brainmask.mgz
- Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/reg.init.dat.fslregister.log
- Thu Aug 8 23:42:05 CEST 2013
- --s sub007 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/fslregister --dof 6 --fsvol brainmask.mgz
- $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $
- snake4
- Linux snake4 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/sub007/scripts
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/fslregister/refvol.fslregister.nii
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/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/sub007/mri/brainmask.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, 4.65661e-09, 3.72529e-09)
- j_ras = (5.58794e-09, -1.49012e-08, -1)
- k_ras = (-8.61473e-09, 1, 1.49012e-08)
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/fslregister/refvol.fslregister.nii...
- --------------------------------------
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/scripts
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/fslregister/movvol.fslregister.nii --frame 0
- mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/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/sub007/mri/transforms/tmp.bbregister.4692/template.nii...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.998766, -0.0418513, -0.0267421)
- j_ras = (-0.0444513, 0.99343, 0.105455)
- k_ras = (-0.022153, -0.106514, 0.994064)
- keeping frame 0
- writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/fslregister/movvol.fslregister.nii...
- Mov determinant is -0.311076
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/scripts
- tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/fslregister/movvol.fslregister.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/fslregister/reg0.4731.dat --regheader --fslregout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/reg.init.dat.fsl.mat0 --s sub007 --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/sub007/mri/transforms/tmp.bbregister.4692/fslregister/movvol.fslregister.nii
- reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/fslregister/reg0.4731.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/sub007/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/sub007/mri/transforms/tmp.bbregister.4692/fslregister/movvol.fslregister.nii
- Tmov: --------------------
- -0.700 0.000 0.000 95.889;
- 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 0.042 0.027 0.000;
- -0.022 -0.107 0.994 0.000;
- 0.044 -0.993 -0.105 -0.000;
- 0.000 0.000 0.000 1.000;
- ---------------------------------------
- ---- Input registration matrix --------
- 0.999 0.042 0.027 0.000;
- -0.022 -0.107 0.994 0.000;
- 0.044 -0.993 -0.105 -0.000;
- 0.000 0.000 0.000 1.000;
- Determinant 1
- subject = sub007
- RegMat ---------------------------
- 0.999 0.042 0.027 0.000;
- -0.022 -0.107 0.994 0.000;
- 0.044 -0.993 -0.105 -0.000;
- 0.000 0.000 0.000 1.000;
- FSLOUTPUTTYPE NIFTI
- tkreg2FSL: mov det = -0.311076, ref det = -1
- Thu Aug 8 23:42:12 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/scripts
- flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/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/sub007/mri/transforms/tmp.bbregister.4692/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/reg.init.dat.fsl.mat0
- Thu Aug 8 23:46:31 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/scripts
- flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/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/sub007/mri/transforms/tmp.bbregister.4692/reg.init.dat.fsl.mat -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/fslregister/fslmat0.trans.mat -schedule /opt/freesurfer/5.3.0/bin/flirt.newdefault.20080811.sch
- tkregister2_cmdl --s sub007 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/reg.init.dat --fslreg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/reg.init.dat.fsl.mat --noedit
- tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl
- ---- FSL registration matrix --------
- 0.998 0.049 0.030 22.056;
- 0.035 -0.095 -0.995 264.844;
- -0.046 0.994 -0.097 16.715;
- 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/sub007/mri/transforms/tmp.bbregister.4692/template.nii
- reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/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/sub007/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/sub007/mri/transforms/tmp.bbregister.4692/template.nii
- Tmov: --------------------
- -0.700 0.000 0.000 95.889;
- 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 = -0.311076, ref det = -1
- ---- Input registration matrix (computed) --------
- 0.998 0.046 0.035 0.046;
- -0.030 -0.097 0.995 0.583;
- 0.049 -0.994 -0.095 -0.900;
- 0.000 0.000 0.000 1.000;
- ---------------------------------------
- ---- Input registration matrix --------
- 0.998 0.046 0.035 0.046;
- -0.030 -0.097 0.995 0.583;
- 0.049 -0.994 -0.095 -0.900;
- 0.000 0.000 0.000 1.000;
- Determinant 1
- subject = sub007
- RegMat ---------------------------
- 0.998 0.046 0.035 0.046;
- -0.030 -0.097 0.995 0.583;
- 0.049 -0.994 -0.095 -0.900;
- 0.000 0.000 0.000 1.000;
-
- Started at Thu Aug 8 23:42:05 CEST 2013
- Ended at Thu Aug 8 23:52:25 CEST 2013
-
- fslregister Done
-
- To check results, run:
- tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/reg.init.dat --surf orig
-
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/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/sub007/scripts
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/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 snake4
- machine x86_64
- user fkaule
- movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/template.nii
- regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/reg.init.dat
- subject sub007
- dof 6
- outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/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 1376518834
- TransRandMax 0.000000
- RotRandMax 0.000000
- Translations 0.000000 0.000000 0.000000
- Rotations 0.000000 0.000000 0.000000
- Input reg
- 0.998 0.046 0.035 0.046;
- -0.030 -0.097 0.995 0.583;
- 0.049 -0.994 -0.095 -0.900;
- 0.000 0.000 0.000 1.000;
- Loading mov
- Projecting LH Surfs
- Loading lh.white surf
- Loading lh.thickness for GM
- GM Proj: 1 0.500000 2.000000
- WM Proj: 0 0.500000 2.000000
- Projecting RH Surfs
- Loading rh.white surf
- Loading rh.thickness
- Projecting RH Surfs
- Computing relative cost
- 0 -25.0 -25.0 -25.0 0.991249
- 1 -25.0 -25.0 25.0 0.991829
- 2 -25.0 25.0 -25.0 0.986389
- 3 -25.0 25.0 25.0 1.010019
- 4 25.0 -25.0 -25.0 1.016478
- 5 25.0 -25.0 25.0 1.018360
- 6 25.0 25.0 -25.0 1.026574
- 7 25.0 25.0 25.0 1.014561
- REL: 8 0.193677 8.055460 1.006932 rel = 0.192343
- Initial costs ----------------
- Number of surface hits 3043
- WM Intensity 55.5078 +/- 9.6160
- Ctx Intensity 67.6400 +/- 9.7926
- Pct Contrast 19.8581 +/- 15.4931
- Cost 0.1937
- RelCost 0.1923
- ------------------------------------
- Brute force preopt -4 4 4, n = 729
- 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9721 0.9721 0.0
- 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.8971 0.8971 0.0
- 21 -4.0000 -4.0000 -4.0000 4.0000 0.0000 -4.0000 0.8774 0.8774 0.0
- 102 -4.0000 0.0000 -4.0000 4.0000 0.0000 -4.0000 0.8240 0.8240 0.0
- 120 -4.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.7098 0.7098 0.0
- 346 0.0000 0.0000 -4.0000 4.0000 0.0000 0.0000 0.6742 0.6742 0.0
- 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1937 0.1937 0.0
- Brute Force --------------------------
- Min cost was 0.193677
- Number of iterations 729
- Search time 2.256000 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 -0.019 0.000 0.000 0.000 0.000 0.000 0.1934061585
- 8 -0.104 0.000 0.000 0.000 0.000 0.000 0.1929380224
- 12 -0.114 0.000 0.000 0.000 0.000 0.000 0.1929257262
- 14 -0.111 0.000 0.000 0.000 0.000 0.000 0.1929253878
- 16 -0.112 0.000 0.000 0.000 0.000 0.000 0.1929247277
- 17 -0.113 0.000 0.000 0.000 0.000 0.000 0.1929246708
- 24 -0.113 -0.093 0.000 0.000 0.000 0.000 0.1927190348
- 25 -0.113 -0.055 0.000 0.000 0.000 0.000 0.1923274726
- 26 -0.113 -0.051 0.000 0.000 0.000 0.000 0.1922827635
- 27 -0.113 -0.032 0.000 0.000 0.000 0.000 0.1921745445
- 30 -0.113 -0.033 0.000 0.000 0.000 0.000 0.1921719557
- 33 -0.113 -0.033 1.000 0.000 0.000 0.000 0.1739615505
- 37 -0.113 -0.033 0.618 0.000 0.000 0.000 0.1546181828
- 38 -0.113 -0.033 0.570 0.000 0.000 0.000 0.1536184433
- 40 -0.113 -0.033 0.553 0.000 0.000 0.000 0.1534524363
- 41 -0.113 -0.033 0.534 0.000 0.000 0.000 0.1534009548
- 42 -0.113 -0.033 0.536 0.000 0.000 0.000 0.1533939252
- 44 -0.113 -0.033 0.538 0.000 0.000 0.000 0.1533923823
- 52 -0.113 -0.033 0.538 0.174 0.000 0.000 0.1468022854
- 53 -0.113 -0.033 0.538 0.176 0.000 0.000 0.1467637315
- 55 -0.113 -0.033 0.538 0.198 0.000 0.000 0.1465500295
- 56 -0.113 -0.033 0.538 0.199 0.000 0.000 0.1465495950
- 57 -0.113 -0.033 0.538 0.200 0.000 0.000 0.1465482938
- 60 -0.113 -0.033 0.538 0.203 0.000 0.000 0.1465402647
- 70 -0.113 -0.033 0.538 0.203 0.024 0.000 0.1462816922
- 80 -0.113 -0.033 0.538 0.203 0.024 -0.119 0.1454949850
- 81 -0.113 -0.033 0.538 0.203 0.024 -0.097 0.1454077122
- 82 -0.113 -0.033 0.538 0.203 0.024 -0.090 0.1453918823
- 94 -0.107 -0.033 0.538 0.203 0.024 -0.090 0.1453520159
- 95 -0.081 -0.033 0.538 0.203 0.024 -0.090 0.1452226094
- 97 -0.058 -0.033 0.538 0.203 0.024 -0.090 0.1450797534
- 98 -0.016 -0.033 0.538 0.203 0.024 -0.090 0.1448732974
- 104 -0.017 -0.033 0.538 0.203 0.024 -0.090 0.1448730636
- 112 -0.017 0.099 0.538 0.203 0.024 -0.090 0.1421495608
- 114 -0.017 0.066 0.538 0.203 0.024 -0.090 0.1420170294
- 116 -0.017 0.078 0.538 0.203 0.024 -0.090 0.1419504451
- 118 -0.017 0.077 0.538 0.203 0.024 -0.090 0.1419496850
- 120 -0.017 0.076 0.538 0.203 0.024 -0.090 0.1419482133
- 128 -0.017 0.076 0.429 0.203 0.024 -0.090 0.1408250796
- 129 -0.017 0.076 0.444 0.203 0.024 -0.090 0.1406757515
- 130 -0.017 0.076 0.459 0.203 0.024 -0.090 0.1406291206
- 133 -0.017 0.076 0.462 0.203 0.024 -0.090 0.1406277824
- 134 -0.017 0.076 0.461 0.203 0.024 -0.090 0.1406275492
- 141 -0.017 0.076 0.461 0.244 0.024 -0.090 0.1402854869
- 142 -0.017 0.076 0.461 0.243 0.024 -0.090 0.1402772088
- 143 -0.017 0.076 0.461 0.233 0.024 -0.090 0.1401954529
- 145 -0.017 0.076 0.461 0.229 0.024 -0.090 0.1401783905
- 146 -0.017 0.076 0.461 0.228 0.024 -0.090 0.1401776098
- 155 -0.017 0.076 0.461 0.228 -0.008 -0.090 0.1400072837
- 156 -0.017 0.076 0.461 0.228 -0.007 -0.090 0.1400067285
- 157 -0.017 0.076 0.461 0.228 -0.006 -0.090 0.1400058131
- 159 -0.017 0.076 0.461 0.228 -0.001 -0.090 0.1400034554
- 161 -0.017 0.076 0.461 0.228 -0.003 -0.090 0.1400032237
- 169 -0.017 0.076 0.461 0.228 -0.003 -0.040 0.1395222284
- 170 -0.017 0.076 0.461 0.228 -0.003 -0.025 0.1394631486
- 182 -0.042 0.076 0.461 0.228 -0.003 -0.025 0.1392295453
- 183 -0.045 0.076 0.461 0.228 -0.003 -0.025 0.1392125962
- 185 -0.051 0.076 0.461 0.228 -0.003 -0.025 0.1391954150
- 186 -0.052 0.076 0.461 0.228 -0.003 -0.025 0.1391952674
- 207 -0.052 0.076 0.437 0.228 -0.003 -0.025 0.1389939393
- 208 -0.052 0.076 0.436 0.228 -0.003 -0.025 0.1389916174
- 210 -0.052 0.076 0.434 0.228 -0.003 -0.025 0.1389900252
- 219 -0.052 0.076 0.434 0.237 -0.003 -0.025 0.1389426087
- 220 -0.052 0.076 0.434 0.240 -0.003 -0.025 0.1389309996
- 222 -0.052 0.076 0.434 0.244 -0.003 -0.025 0.1389262283
- 223 -0.052 0.076 0.434 0.243 -0.003 -0.025 0.1389260747
- 235 -0.052 0.076 0.434 0.243 -0.007 -0.025 0.1389214808
- 238 -0.052 0.076 0.434 0.243 -0.008 -0.025 0.1389211114
- 245 -0.052 0.076 0.434 0.243 -0.008 -0.075 0.1387751442
- 246 -0.052 0.076 0.434 0.243 -0.008 -0.063 0.1386801727
- 247 -0.052 0.076 0.434 0.243 -0.008 -0.055 0.1386741770
- 248 -0.052 0.076 0.434 0.243 -0.008 -0.058 0.1386707715
- 251 -0.088 0.076 0.406 0.259 -0.013 -0.091 0.1383439096
- 254 -0.145 0.076 0.362 0.284 -0.021 -0.145 0.1378308224
- 259 -0.222 0.076 0.303 0.318 -0.032 -0.216 0.1376057260
- 260 -0.201 0.076 0.319 0.308 -0.029 -0.197 0.1375520973
- 277 -0.201 0.076 0.319 0.308 -0.029 -0.219 0.1374804300
- 279 -0.201 0.076 0.319 0.308 -0.029 -0.234 0.1374613638
- 280 -0.201 0.076 0.319 0.308 -0.029 -0.229 0.1374552182
- 281 -0.201 0.076 0.319 0.308 -0.029 -0.230 0.1374542155
- 291 -0.201 0.019 0.319 0.308 -0.029 -0.230 0.1362655158
- 293 -0.201 0.026 0.319 0.308 -0.029 -0.230 0.1362157040
- 295 -0.201 0.027 0.319 0.308 -0.029 -0.230 0.1362146064
- 302 -0.201 0.027 0.288 0.308 -0.029 -0.230 0.1360537655
- 304 -0.201 0.027 0.294 0.308 -0.029 -0.230 0.1360521244
- 306 -0.201 0.027 0.292 0.308 -0.029 -0.230 0.1360508154
- 315 -0.201 0.027 0.292 0.327 -0.029 -0.230 0.1359026204
- 317 -0.201 0.027 0.292 0.326 -0.029 -0.230 0.1359003914
- 328 -0.201 0.027 0.292 0.326 0.003 -0.230 0.1351833728
- 330 -0.201 0.027 0.292 0.326 0.002 -0.230 0.1351805432
- 332 -0.201 0.027 0.292 0.326 0.001 -0.230 0.1351789449
- 335 -0.236 0.027 0.264 0.342 -0.004 -0.263 0.1351470756
- 339 -0.223 0.027 0.275 0.336 -0.002 -0.250 0.1351446910
- 344 -0.224 0.027 0.274 0.337 -0.002 -0.251 0.1351438076
- 358 -0.224 0.027 0.274 0.337 -0.002 -0.245 0.1350866132
- 359 -0.224 0.027 0.274 0.337 -0.002 -0.234 0.1350508134
- 360 -0.224 0.027 0.274 0.337 -0.002 -0.235 0.1350502326
- 370 -0.224 0.038 0.274 0.337 -0.002 -0.235 0.1350105739
- 381 -0.224 0.038 0.267 0.337 -0.002 -0.235 0.1350010105
- 383 -0.224 0.038 0.268 0.337 -0.002 -0.235 0.1349998244
- 384 -0.224 0.038 0.269 0.337 -0.002 -0.235 0.1349988486
- 396 -0.224 0.038 0.269 0.338 -0.002 -0.235 0.1349985664
- 405 -0.224 0.038 0.269 0.338 0.016 -0.235 0.1348326439
- 406 -0.224 0.038 0.269 0.338 0.015 -0.235 0.1348291783
- 407 -0.224 0.038 0.269 0.338 0.013 -0.235 0.1348270992
- 418 -0.222 0.038 0.271 0.337 0.013 -0.233 0.1348259642
- 423 -0.222 0.038 0.271 0.337 0.013 -0.233 0.1348259627
- 425 -0.222 0.038 0.271 0.337 0.013 -0.233 0.1348257670
- 427 -0.220 0.049 0.268 0.337 0.029 -0.215 0.1347504837
- 433 -0.221 0.045 0.269 0.337 0.023 -0.222 0.1347441598
- 434 -0.221 0.047 0.269 0.337 0.026 -0.219 0.1347358587
- 435 -0.221 0.047 0.269 0.337 0.026 -0.219 0.1347357220
- 438 -0.221 0.047 0.269 0.337 0.026 -0.219 0.1347354803
- 442 -0.221 0.047 0.269 0.337 0.026 -0.219 0.1347354483
- 451 -0.221 0.047 0.269 0.337 0.026 -0.211 0.1347039705
- 452 -0.221 0.047 0.269 0.337 0.026 -0.209 0.1347034921
- 471 -0.221 0.047 0.254 0.337 0.026 -0.209 0.1346931341
- 472 -0.221 0.047 0.260 0.337 0.026 -0.209 0.1346611662
- 473 -0.221 0.047 0.261 0.337 0.026 -0.209 0.1346598212
- 483 -0.221 0.047 0.261 0.335 0.026 -0.209 0.1346555090
- 484 -0.221 0.047 0.261 0.334 0.026 -0.209 0.1346516761
- 487 -0.221 0.047 0.261 0.333 0.026 -0.209 0.1346507496
- 495 -0.220 0.047 0.262 0.333 0.026 -0.209 0.1346496957
- 497 -0.219 0.047 0.262 0.332 0.026 -0.208 0.1346489549
- 501 -0.219 0.047 0.262 0.332 0.026 -0.208 0.1346486518
- 509 -0.220 0.044 0.263 0.332 0.022 -0.213 0.1346368280
- 511 -0.220 0.044 0.263 0.332 0.022 -0.213 0.1346366468
- 529 -0.220 0.044 0.263 0.332 0.022 -0.212 0.1346322885
- 530 -0.220 0.044 0.263 0.332 0.022 -0.209 0.1346271251
- 532 -0.220 0.044 0.263 0.332 0.022 -0.207 0.1346270570
- 534 -0.220 0.044 0.263 0.332 0.022 -0.208 0.1346263451
- 546 -0.220 0.045 0.263 0.332 0.022 -0.208 0.1346254968
- 573 -0.221 0.045 0.262 0.333 0.022 -0.209 0.1346235626
- 574 -0.222 0.045 0.261 0.333 0.022 -0.210 0.1346228639
- 575 -0.222 0.045 0.261 0.333 0.022 -0.210 0.1346227487
- 579 -0.222 0.045 0.261 0.333 0.022 -0.210 0.1346226163
- 591 -0.222 0.044 0.261 0.333 0.021 -0.211 0.1346225497
- 592 -0.222 0.044 0.261 0.333 0.021 -0.210 0.1346223234
- 593 -0.222 0.045 0.261 0.333 0.021 -0.210 0.1346220382
- 607 -0.222 0.045 0.261 0.333 0.021 -0.209 0.1346214237
- 628 -0.222 0.045 0.264 0.333 0.021 -0.209 0.1346204271
- 630 -0.222 0.045 0.263 0.333 0.021 -0.209 0.1346197724
- 640 -0.222 0.045 0.263 0.332 0.021 -0.209 0.1346193403
- 650 -0.224 0.045 0.262 0.332 0.021 -0.211 0.1346189424
- 652 -0.223 0.045 0.262 0.332 0.021 -0.210 0.1346188666
- 654 -0.223 0.045 0.263 0.332 0.021 -0.210 0.1346187808
- 656 -0.223 0.045 0.263 0.332 0.021 -0.210 0.1346186327
- 658 -0.223 0.045 0.263 0.332 0.021 -0.210 0.1346185472
- 669 -0.223 0.044 0.263 0.332 0.021 -0.210 0.1346184823
- 671 -0.223 0.044 0.263 0.332 0.021 -0.210 0.1346184437
- Powell done niters = 7
- Computing relative cost
- 0 -25.0 -25.0 -25.0 0.978193
- 1 -25.0 -25.0 25.0 1.003211
- 2 -25.0 25.0 -25.0 0.997539
- 3 -25.0 25.0 25.0 1.003521
- 4 25.0 -25.0 -25.0 1.013809
- 5 25.0 -25.0 25.0 1.028591
- 6 25.0 25.0 -25.0 0.995395
- 7 25.0 25.0 25.0 1.008285
- REL: 8 0.134618 8.028544 1.003568 rel = 0.13414
- Number of iterations 7
- Min cost was 0.134618
- Number of FunctionCalls 675
- TolPowell 0.000100
- nMaxItersPowell 36
- OptimizationTime 1.992000 sec
- Parameters at optimum (transmm) -0.22291 0.04437 0.26269
- Parameters at optimum (rotdeg) 0.33207 0.02092 -0.21016
- Final costs ----------------
- Number of surface hits 3043
- WM Intensity 55.4287 +/- 9.2173
- Ctx Intensity 67.2313 +/- 9.3579
- Pct Contrast 19.4196 +/- 13.8146
- Cost 0.1346
- RelCost 0.1923
- Reg at min cost was
- 0.998 0.046 0.038 -0.175;
- -0.034 -0.091 0.995 0.633;
- 0.049 -0.995 -0.089 -0.634;
- 0.000 0.000 0.000 1.000;
- Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/bbr.pass1.dat, type = 14
- Original Reg
- 0.998 0.046 0.035 0.046;
- -0.030 -0.097 0.995 0.583;
- 0.049 -0.994 -0.095 -0.900;
- 0.000 0.000 0.000 1.000;
- Original Reg - Optimal Reg
- 0.000 0.001 -0.004 0.221;
- 0.004 -0.006 -0.000 -0.049;
- 0.001 0.001 -0.006 -0.266;
- 0.000 0.000 0.000 0.000;
- Computing change in lh position
- LH rmsDiffMean 0.592709
- Computing change in rh position
- Surface RMS Diff (mm) 0.591639 0.872507
- mri_segreg done
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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/sub007/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/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/sub007/scripts
- mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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/sub007/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5
- sysname Linux
- hostname snake4
- machine x86_64
- user fkaule
- movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/template.nii
- regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/tmp.bbregister.4692/bbr.pass1.dat
- subject sub007
- dof 6
- outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 1376598094
- TransRandMax 0.000000
- RotRandMax 0.000000
- Translations 0.000000 0.000000 0.000000
- Rotations 0.000000 0.000000 0.000000
- Input reg
- 0.998 0.046 0.038 -0.175;
- -0.034 -0.091 0.995 0.633;
- 0.049 -0.995 -0.089 -0.634;
- 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 1.003720
- 1 -25.0 -25.0 25.0 1.014011
- 2 -25.0 25.0 -25.0 1.011400
- 3 -25.0 25.0 25.0 1.010058
- 4 25.0 -25.0 -25.0 1.022451
- 5 25.0 -25.0 25.0 1.032368
- 6 25.0 25.0 -25.0 1.016719
- 7 25.0 25.0 25.0 1.016638
- REL: 8 0.146195 8.127364 1.015920 rel = 0.143904
- Initial costs ----------------
- Number of surface hits 304307
- WM Intensity 55.4986 +/- 9.4676
- Ctx Intensity 67.2995 +/- 9.4924
- Pct Contrast 19.4061 +/- 14.3630
- Cost 0.1462
- RelCost 0.1439
- ------------------------------------
- Brute force preopt -0.1 0.1 0.1, n = 729
- 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1466 0.1466 0.0
- 9 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 -0.1000 0.1430 0.1430 0.0
- 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.1421 0.1421 0.0
- 18 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 -0.1000 0.1413 0.1413 0.0
- 21 -0.1000 -0.1000 -0.1000 0.1000 0.0000 -0.1000 0.1381 0.1381 0.0
- 102 -0.1000 0.0000 -0.1000 0.1000 0.0000 -0.1000 0.1364 0.1364 0.0
- 120 -0.1000 0.0000 0.0000 0.0000 0.0000 -0.1000 0.1358 0.1358 0.0
- 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1346 0.1346 0.0
- Brute Force --------------------------
- Min cost was 0.134618
- Number of iterations 729
- Search time 2.143000 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 0.113 0.000 0.000 0.000 0.000 0.000 0.1450895347
- 8 0.110 0.000 0.000 0.000 0.000 0.000 0.1450858312
- 9 0.104 0.000 0.000 0.000 0.000 0.000 0.1450844897
- 11 0.106 0.000 0.000 0.000 0.000 0.000 0.1450841591
- 20 0.106 0.071 0.000 0.000 0.000 0.000 0.1446850063
- 21 0.106 0.061 0.000 0.000 0.000 0.000 0.1446593522
- 22 0.106 0.057 0.000 0.000 0.000 0.000 0.1446579395
- 31 0.106 0.057 0.106 0.000 0.000 0.000 0.1439143376
- 32 0.106 0.057 0.091 0.000 0.000 0.000 0.1438930402
- 34 0.106 0.057 0.093 0.000 0.000 0.000 0.1438928807
- 43 0.106 0.057 0.093 0.036 0.000 0.000 0.1438125946
- 44 0.106 0.057 0.093 0.024 0.000 0.000 0.1437849073
- 53 0.106 0.057 0.093 0.024 -0.084 0.000 0.1427550857
- 54 0.106 0.057 0.093 0.024 -0.103 0.000 0.1426795413
- 55 0.106 0.057 0.093 0.024 -0.117 0.000 0.1426586904
- 56 0.106 0.057 0.093 0.024 -0.121 0.000 0.1426579855
- 57 0.106 0.057 0.093 0.024 -0.120 0.000 0.1426577427
- 65 0.106 0.057 0.093 0.024 -0.120 0.055 0.1422166418
- 67 0.106 0.057 0.093 0.024 -0.120 0.057 0.1422163921
- 76 0.169 0.057 0.093 0.024 -0.120 0.057 0.1420836601
- 77 0.151 0.057 0.093 0.024 -0.120 0.057 0.1420548893
- 78 0.150 0.057 0.093 0.024 -0.120 0.057 0.1420547346
- 87 0.150 0.071 0.093 0.024 -0.120 0.057 0.1420279277
- 89 0.150 0.069 0.093 0.024 -0.120 0.057 0.1420276970
- 98 0.150 0.069 0.089 0.024 -0.120 0.057 0.1420185163
- 99 0.150 0.069 0.079 0.024 -0.120 0.057 0.1420076535
- 100 0.150 0.069 0.078 0.024 -0.120 0.057 0.1420072887
- 101 0.150 0.069 0.075 0.024 -0.120 0.057 0.1420072635
- 104 0.150 0.069 0.076 0.024 -0.120 0.057 0.1420072037
- 112 0.150 0.069 0.076 0.028 -0.120 0.057 0.1420046225
- 122 0.150 0.069 0.076 0.028 -0.126 0.057 0.1419991231
- 123 0.150 0.069 0.076 0.028 -0.130 0.057 0.1419963952
- 126 0.150 0.069 0.076 0.028 -0.133 0.057 0.1419958969
- 135 0.150 0.069 0.076 0.028 -0.133 0.079 0.1419321091
- 138 0.193 0.082 0.060 0.031 -0.145 0.102 0.1418299848
- 146 0.196 0.083 0.059 0.032 -0.146 0.103 0.1418299444
- 148 0.194 0.083 0.060 0.031 -0.146 0.103 0.1418298225
- 150 0.195 0.083 0.060 0.032 -0.146 0.103 0.1418298160
- 151 0.195 0.083 0.059 0.032 -0.146 0.103 0.1418297682
- 163 0.195 0.083 0.059 0.032 -0.146 0.102 0.1418293486
- 172 0.195 0.073 0.059 0.032 -0.146 0.102 0.1418252952
- 173 0.195 0.077 0.059 0.032 -0.146 0.102 0.1418238530
- 183 0.195 0.077 0.070 0.032 -0.146 0.102 0.1418164144
- 203 0.195 0.077 0.070 0.032 -0.140 0.102 0.1418147057
- 204 0.195 0.077 0.070 0.032 -0.141 0.102 0.1418146831
- 205 0.195 0.077 0.070 0.032 -0.142 0.102 0.1418146691
- 213 0.201 0.078 0.068 0.032 -0.144 0.105 0.1418121060
- 214 0.201 0.078 0.068 0.032 -0.144 0.105 0.1418121038
- 215 0.201 0.078 0.068 0.032 -0.144 0.105 0.1418120734
- 216 0.201 0.078 0.068 0.032 -0.144 0.105 0.1418120708
- 225 0.201 0.078 0.068 0.032 -0.144 0.104 0.1418120083
- 235 0.201 0.077 0.068 0.032 -0.144 0.104 0.1418116040
- 244 0.201 0.077 0.070 0.032 -0.144 0.104 0.1418115243
- 246 0.201 0.077 0.069 0.032 -0.144 0.104 0.1418114284
- 264 0.201 0.077 0.069 0.032 -0.141 0.104 0.1418105057
- 273 0.203 0.077 0.069 0.032 -0.142 0.105 0.1418098875
- 274 0.204 0.077 0.068 0.032 -0.142 0.106 0.1418094200
- 277 0.205 0.078 0.068 0.032 -0.142 0.106 0.1418093614
- 278 0.205 0.078 0.068 0.032 -0.142 0.106 0.1418093170
- 300 0.205 0.077 0.068 0.032 -0.142 0.106 0.1418092649
- 311 0.205 0.077 0.069 0.032 -0.142 0.106 0.1418092468
- 330 0.205 0.077 0.069 0.032 -0.141 0.106 0.1418091360
- 339 0.205 0.077 0.069 0.032 -0.141 0.106 0.1418090722
- 343 0.205 0.077 0.069 0.032 -0.141 0.106 0.1418090189
- 405 0.205 0.077 0.069 0.032 -0.141 0.106 0.1418089950
- 409 0.205 0.077 0.069 0.032 -0.141 0.106 0.1418089946
- Powell done niters = 6
- Computing relative cost
- 0 -25.0 -25.0 -25.0 1.004926
- 1 -25.0 -25.0 25.0 1.013640
- 2 -25.0 25.0 -25.0 1.012322
- 3 -25.0 25.0 25.0 1.009514
- 4 25.0 -25.0 -25.0 1.021360
- 5 25.0 -25.0 25.0 1.032719
- 6 25.0 25.0 -25.0 1.018272
- 7 25.0 25.0 25.0 1.018092
- REL: 8 0.141809 8.130844 1.016356 rel = 0.139527
- Number of iterations 6
- Min cost was 0.141809
- Number of FunctionCalls 472
- TolPowell 0.000000
- nMaxItersPowell 36
- OptimizationTime 57.287000 sec
- Parameters at optimum (transmm) 0.20508 0.07676 0.06874
- Parameters at optimum (rotdeg) 0.03240 -0.14135 0.10713
- Final costs ----------------
- Number of surface hits 304307
- WM Intensity 55.5048 +/- 9.5055
- Ctx Intensity 67.3034 +/- 9.4884
- Pct Contrast 19.4056 +/- 14.3131
- Cost 0.1418
- RelCost 0.1439
- Reg at min cost was
- 0.998 0.048 0.037 0.030;
- -0.032 -0.090 0.995 0.710;
- 0.051 -0.995 -0.089 -0.565;
- 0.000 0.000 0.000 1.000;
- Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/T2raw.dat, type = 14
- Original Reg
- 0.998 0.046 0.038 -0.175;
- -0.034 -0.091 0.995 0.633;
- 0.049 -0.995 -0.089 -0.634;
- 0.000 0.000 0.000 1.000;
- Original Reg - Optimal Reg
- 0.000 -0.003 0.002 -0.205;
- -0.002 -0.001 -0.000 -0.077;
- -0.002 -0.000 -0.001 -0.069;
- 0.000 0.000 0.000 0.000;
- Computing change in lh position
- LH rmsDiffMean 0.133062
- Computing change in rh position
- Surface RMS Diff (mm) 0.190373 0.408394
- mri_segreg done
- tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/T2raw.dat --noedit --ltaout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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/sub007/mri/orig/T2raw.mgz
- reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/T2raw.dat
- LoadVol 0
- ZeroCRAS 0
- $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
- Diagnostic Level -1
- ---- Input registration matrix --------
- 0.998 0.048 0.037 0.030;
- -0.032 -0.090 0.995 0.710;
- 0.051 -0.995 -0.089 -0.565;
- 0.000 0.000 0.000 1.000;
- float2int = 0
- ---------------------------------------
- INFO: loading target /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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/sub007/mri/orig/T2raw.mgz
- Tmov: --------------------
- -0.700 0.000 0.000 95.889;
- 0.000 0.000 0.667 -128.000;
- 0.000 -0.667 0.000 128.000;
- 0.000 0.000 0.000 1.000;
- mkheaderreg = 0, float2int = 0
- ---- Input registration matrix --------
- 0.998 0.048 0.037 0.030;
- -0.032 -0.090 0.995 0.710;
- 0.051 -0.995 -0.089 -0.565;
- 0.000 0.000 0.000 1.000;
- Determinant 1
- subject = sub007
- RegMat ---------------------------
- 0.998 0.048 0.037 0.030;
- -0.032 -0.090 0.995 0.710;
- 0.051 -0.995 -0.089 -0.565;
- 0.000 0.000 0.000 1.000;
- transformed matrix:
- 1.000 -0.006 -0.011 -0.131;
- 0.006 1.000 0.016 -0.013;
- 0.011 -0.016 1.000 -0.292;
- 0.000 0.000 0.000 1.000;
- transformed matrix:
- 0.699 0.034 0.022 21.553;
- 0.026 -0.059 -0.664 263.990;
- -0.034 0.663 -0.060 16.377;
- 0.000 0.000 0.000 1.000;
- Cleaning up
-
- Started at Thu Aug 8 23:42:01 CEST 2013
- Ended at Thu Aug 8 23:54:16 CEST 2013
- BBR-Run-Time-Sec 735
-
- bbregister Done
- To check results, run:
- tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/T2raw.dat --surf
-
- mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/T2.mgz
- mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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/sub007/mri/orig/T2raw.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-0.998766, -0.0418513, -0.0267421)
- j_ras = (-0.0444513, 0.99343, 0.105455)
- k_ras = (-0.022153, -0.106514, 0.994064)
- INFO: Reading transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/T2raw.lta...
- Reading transform with LTAreadEx()
- reading extra input line subject sub007
- reading extra input line fscale 0.150000
- reading template info from volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/orig.mgz...
- INFO: Applying transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/transforms/T2raw.lta...
- ---------------------------------
- INFO: Transform Matrix (linear_ras_to_ras)
- 1.000 -0.006 -0.011 -0.131;
- 0.006 1.000 0.016 -0.013;
- 0.011 -0.016 1.000 -0.292;
- 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/sub007/mri/T2.mgz...
- mri_normalize -aseg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/aseg.mgz -sigma 4 -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/rh.white identity.nofile -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/lh.white identity.nofile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/T2.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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/sub007/mri/T2.mgz...
- computing distance transform
- computing distance transform
- computing nonmaximum suppression
- 31334 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/sub007/mri/T2.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/scripts
- cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/lh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/lh.woT2.pial
- `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/lh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/lh.woT2.pial'
- mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub007 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/sub007/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/wm.mgz...
- 23464 bright wm thresholded.
- 975 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/lh.orig...
- computing class statistics...
- border white: 296565 voxels (1.77%)
- border gray 332938 voxels (1.98%)
- WM (92.0): 93.6 +- 10.1 [70.0 --> 110.0]
- GM (76.0) : 73.7 +- 13.2 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 46.8 (was 70)
- setting MAX_BORDER_WHITE to 116.1 (was 105)
- setting MIN_BORDER_WHITE to 60.0 (was 85)
- setting MAX_CSF to 33.7 (was 40)
- setting MAX_GRAY to 95.9 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 53.4 (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=106, GM=60
- mean inside = 93.1, mean outside = 68.6
- 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/sub007/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.89 +- 0.25 (0.02-->6.54) (max @ vno 80468 --> 161340)
- face area 0.33 +- 0.15 (0.00-->4.84)
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- deleting segment 0 with 4 points - only 0.00% unknown
- deleting segment 1 with 7 points - only 0.00% unknown
- deleting segment 2 with 6 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 4 with 2 points - only 0.00% unknown
- deleting segment 5 with 8 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 6 with 2 points - only 0.00% unknown
- deleting segment 7 with 764 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 8 with 2 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 13 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 12 with 1 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 13 with 1 points - only 0.00% unknown
- deleting segment 14 with 126 points - only 0.00% unknown
- tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.89 +- 0.24 (0.04-->6.54) (max @ vno 80468 --> 161340)
- face area 0.33 +- 0.15 (0.00-->4.84)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5061611.5, rms=0.00
- rms = 1.05, time step reduction 1 of 3 to 0.250...
- rms = 0.27, time step reduction 2 of 3 to 0.125...
- rms = 0.03, time step reduction 3 of 3 to 0.062...
- 001: dt: 0.1250, sse=5061611.5, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- deleting segment 0 with 4 points - only 0.00% unknown
- deleting segment 1 with 7 points - only 0.00% unknown
- deleting segment 2 with 6 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 3 with 2 points - only 0.00% unknown
- deleting segment 4 with 8 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 5 with 2 points - only 0.00% unknown
- deleting segment 6 with 764 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 7 with 2 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 8 with 2 points - only 0.00% unknown
- deleting segment 9 with 13 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 10 with 1 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 11 with 1 points - only 0.00% unknown
- deleting segment 12 with 126 points - only 0.00% unknown
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.89 +- 0.24 (0.04-->6.54) (max @ vno 80468 --> 161340)
- face area 0.33 +- 0.15 (0.00-->4.84)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5061611.5, rms=0.00
- rms = 1.04, time step reduction 1 of 3 to 0.250...
- rms = 0.27, time step reduction 2 of 3 to 0.125...
- rms = 0.03, time step reduction 3 of 3 to 0.062...
- 002: dt: 0.1250, sse=5061611.5, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- deleting segment 0 with 4 points - only 0.00% unknown
- deleting segment 1 with 7 points - only 0.00% unknown
- deleting segment 2 with 6 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 3 with 2 points - only 0.00% unknown
- deleting segment 4 with 8 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 5 with 2 points - only 0.00% unknown
- deleting segment 6 with 764 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 7 with 2 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 8 with 2 points - only 0.00% unknown
- deleting segment 9 with 13 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 10 with 1 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 11 with 1 points - only 0.00% unknown
- deleting segment 12 with 126 points - only 0.00% unknown
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.89 +- 0.24 (0.04-->6.54) (max @ vno 80468 --> 161340)
- face area 0.33 +- 0.15 (0.00-->4.84)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5061611.5, rms=0.00
- rms = 1.05, time step reduction 1 of 3 to 0.250...
- rms = 0.27, time step reduction 2 of 3 to 0.125...
- rms = 0.03, time step reduction 3 of 3 to 0.062...
- 003: dt: 0.1250, sse=5061611.5, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- deleting segment 0 with 4 points - only 0.00% unknown
- deleting segment 1 with 7 points - only 0.00% unknown
- deleting segment 2 with 6 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 3 with 2 points - only 0.00% unknown
- deleting segment 4 with 8 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 5 with 2 points - only 0.00% unknown
- deleting segment 6 with 764 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 7 with 2 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 8 with 2 points - only 0.00% unknown
- deleting segment 9 with 13 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 10 with 1 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 11 with 1 points - only 0.00% unknown
- deleting segment 12 with 126 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=5061611.5, rms=0.00
- rms = 1.04, time step reduction 1 of 3 to 0.250...
- rms = 0.27, time step reduction 2 of 3 to 0.125...
- rms = 0.03, time step reduction 3 of 3 to 0.062...
- 004: dt: 0.1250, sse=5061611.5, rms=0.000 (1.000%)
- positioning took 0.4 minutes
- inhibiting deformation at non-cortical midline structures...
- smoothing surface for 5 iterations...
- reading initial pial vertex positions from woT2.pial...
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [108.50 195.50], gm=152.00+-14.50, and vertices in regions > 144.7
- 49533 surface locations found to contain inconsistent values (11260 in, 38273 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=568705.3, rms=0.28
- 001: dt: 0.5000, sse=534043.2, rms=0.267 (0.000%)
- 002: dt: 0.5000, sse=512383.6, rms=0.254 (0.000%)
- 003: dt: 0.5000, sse=499383.3, rms=0.243 (0.000%)
- 004: dt: 0.5000, sse=489329.4, rms=0.234 (0.000%)
- 005: dt: 0.5000, sse=482459.6, rms=0.225 (0.000%)
- 006: dt: 0.5000, sse=478166.1, rms=0.218 (0.000%)
- 007: dt: 0.5000, sse=474675.9, rms=0.211 (0.000%)
- 008: dt: 0.5000, sse=472228.5, rms=0.205 (0.000%)
- 009: dt: 0.5000, sse=470456.7, rms=0.200 (0.000%)
- 010: dt: 0.5000, sse=469267.1, rms=0.196 (0.000%)
- 011: dt: 0.5000, sse=467717.8, rms=0.191 (0.000%)
- 012: dt: 0.5000, sse=467139.5, rms=0.188 (0.000%)
- 013: dt: 0.5000, sse=466447.3, rms=0.185 (0.000%)
- 014: dt: 0.5000, sse=465379.9, rms=0.182 (0.000%)
- 015: dt: 0.5000, sse=463933.9, rms=0.179 (0.000%)
- 016: dt: 0.5000, sse=463179.6, rms=0.177 (0.000%)
- 017: dt: 0.5000, sse=462249.3, rms=0.174 (0.000%)
- 018: dt: 0.5000, sse=461376.4, rms=0.173 (0.000%)
- 019: dt: 0.5000, sse=460244.3, rms=0.171 (0.000%)
- 020: dt: 0.5000, sse=459529.7, rms=0.169 (0.000%)
- 021: dt: 0.5000, sse=458383.7, rms=0.168 (0.000%)
- 022: dt: 0.5000, sse=457488.5, rms=0.167 (0.000%)
- 023: dt: 0.5000, sse=456274.5, rms=0.166 (0.000%)
- 024: dt: 0.5000, sse=455583.1, rms=0.165 (0.000%)
- 025: dt: 0.5000, sse=454673.0, rms=0.164 (0.000%)
- 026: dt: 0.5000, sse=453910.6, rms=0.163 (0.000%)
- 027: dt: 0.5000, sse=452866.3, rms=0.162 (0.000%)
- 028: dt: 0.5000, sse=451859.2, rms=0.162 (0.000%)
- 029: dt: 0.5000, sse=451261.2, rms=0.161 (0.000%)
- 030: dt: 0.5000, sse=450377.9, rms=0.161 (0.000%)
- positioning took 4.3 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [104.30 199.70], gm=152.00+-15.90, and vertices in regions > 144.0
- 37550 surface locations found to contain inconsistent values (2348 in, 35202 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=47022.6, rms=0.13
- 031: dt: 0.5000, sse=46753.5, rms=0.127 (0.000%)
- 032: dt: 0.5000, sse=47899.6, rms=0.117 (0.000%)
- 033: dt: 0.5000, sse=49225.2, rms=0.109 (0.000%)
- 034: dt: 0.5000, sse=50338.7, rms=0.104 (0.000%)
- 035: dt: 0.5000, sse=51323.0, rms=0.100 (0.000%)
- 036: dt: 0.5000, sse=52249.1, rms=0.095 (0.000%)
- 037: dt: 0.5000, sse=53112.0, rms=0.091 (0.000%)
- 038: dt: 0.5000, sse=53918.0, rms=0.087 (0.000%)
- 039: dt: 0.5000, sse=54736.7, rms=0.084 (0.000%)
- 040: dt: 0.5000, sse=55520.1, rms=0.080 (0.000%)
- 041: dt: 0.5000, sse=56189.4, rms=0.077 (0.000%)
- 042: dt: 0.5000, sse=56933.4, rms=0.074 (0.000%)
- 043: dt: 0.5000, sse=57576.4, rms=0.072 (0.000%)
- 044: dt: 0.5000, sse=58243.2, rms=0.070 (0.000%)
- 045: dt: 0.5000, sse=58804.9, rms=0.067 (0.000%)
- 046: dt: 0.5000, sse=59373.2, rms=0.065 (0.000%)
- 047: dt: 0.5000, sse=59844.9, rms=0.063 (0.000%)
- 048: dt: 0.5000, sse=60351.4, rms=0.062 (0.000%)
- 049: dt: 0.5000, sse=60753.2, rms=0.060 (0.000%)
- 050: dt: 0.5000, sse=61201.4, rms=0.058 (0.000%)
- 051: dt: 0.5000, sse=61588.1, rms=0.057 (0.000%)
- 052: dt: 0.5000, sse=61944.2, rms=0.056 (0.000%)
- 053: dt: 0.5000, sse=62250.4, rms=0.055 (0.000%)
- 054: dt: 0.5000, sse=62542.7, rms=0.054 (0.000%)
- 055: dt: 0.5000, sse=62801.6, rms=0.053 (0.000%)
- 056: dt: 0.5000, sse=63045.6, rms=0.052 (0.000%)
- 057: dt: 0.5000, sse=63308.7, rms=0.051 (0.000%)
- 058: dt: 0.5000, sse=63550.8, rms=0.050 (0.000%)
- 059: dt: 0.5000, sse=63713.8, rms=0.049 (0.000%)
- 060: dt: 0.5000, sse=63924.5, rms=0.049 (0.000%)
- positioning took 4.3 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [90.80 213.20], gm=152.00+-20.40, and vertices in regions > 141.8
- 34825 surface locations found to contain inconsistent values (90 in, 34735 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=7995.7, rms=0.10
- 061: dt: 0.5000, sse=7781.8, rms=0.095 (0.000%)
- 062: dt: 0.5000, sse=7573.3, rms=0.082 (0.000%)
- 063: dt: 0.5000, sse=7517.9, rms=0.073 (0.000%)
- 064: dt: 0.5000, sse=7541.0, rms=0.066 (0.000%)
- 065: dt: 0.5000, sse=7590.5, rms=0.060 (0.000%)
- 066: dt: 0.5000, sse=7635.6, rms=0.057 (0.000%)
- 067: dt: 0.5000, sse=7672.7, rms=0.054 (0.000%)
- 068: dt: 0.5000, sse=7712.0, rms=0.051 (0.000%)
- 069: dt: 0.5000, sse=7759.4, rms=0.048 (0.000%)
- 070: dt: 0.5000, sse=7807.2, rms=0.046 (0.000%)
- 071: dt: 0.5000, sse=7848.7, rms=0.044 (0.000%)
- 072: dt: 0.5000, sse=7897.2, rms=0.042 (0.000%)
- 073: dt: 0.5000, sse=7936.1, rms=0.041 (0.000%)
- 074: dt: 0.5000, sse=7971.3, rms=0.039 (0.000%)
- 075: dt: 0.5000, sse=8004.0, rms=0.038 (0.000%)
- 076: dt: 0.5000, sse=8036.0, rms=0.037 (0.000%)
- 077: dt: 0.5000, sse=8059.3, rms=0.036 (0.000%)
- 078: dt: 0.5000, sse=8085.8, rms=0.035 (0.000%)
- 079: dt: 0.5000, sse=8103.7, rms=0.034 (0.000%)
- 080: dt: 0.5000, sse=8124.9, rms=0.033 (0.000%)
- 081: dt: 0.5000, sse=8142.6, rms=0.033 (0.000%)
- 082: dt: 0.5000, sse=8154.5, rms=0.032 (0.000%)
- 083: dt: 0.5000, sse=8167.8, rms=0.032 (0.000%)
- 084: dt: 0.5000, sse=8180.2, rms=0.031 (0.000%)
- 085: dt: 0.5000, sse=8185.9, rms=0.031 (0.000%)
- 086: dt: 0.5000, sse=8201.3, rms=0.031 (0.000%)
- 087: dt: 0.5000, sse=8203.9, rms=0.031 (0.000%)
- 088: dt: 0.5000, sse=8215.3, rms=0.031 (0.000%)
- 089: dt: 0.5000, sse=8220.6, rms=0.030 (0.000%)
- 090: dt: 0.5000, sse=8225.7, rms=0.030 (0.000%)
- positioning took 4.1 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [89.60 214.40], gm=152.00+-20.80, and vertices in regions > 141.6
- 34124 surface locations found to contain inconsistent values (54 in, 34070 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/sub007/surf/lh.pial...
- writing smoothed curvature to lh.curv.pial
- 000: dt: 0.0000, sse=1043.2, rms=0.04
- 091: dt: 0.5000, sse=1031.6, rms=0.038 (0.000%)
- 092: dt: 0.5000, sse=996.8, rms=0.034 (0.000%)
- 093: dt: 0.5000, sse=984.4, rms=0.032 (0.000%)
- 094: dt: 0.5000, sse=977.2, rms=0.031 (0.000%)
- 095: dt: 0.5000, sse=971.4, rms=0.030 (0.000%)
- 096: dt: 0.5000, sse=967.1, rms=0.029 (0.000%)
- 097: dt: 0.5000, sse=964.5, rms=0.029 (0.000%)
- 098: dt: 0.5000, sse=961.0, rms=0.028 (0.000%)
- 099: dt: 0.5000, sse=958.6, rms=0.028 (0.000%)
- 100: dt: 0.5000, sse=955.2, rms=0.028 (0.000%)
- 101: dt: 0.5000, sse=952.2, rms=0.027 (0.000%)
- 102: dt: 0.5000, sse=949.9, rms=0.027 (0.000%)
- 103: dt: 0.5000, sse=947.9, rms=0.027 (0.000%)
- 104: dt: 0.5000, sse=945.5, rms=0.026 (0.000%)
- 105: dt: 0.5000, sse=943.8, rms=0.026 (0.000%)
- 106: dt: 0.5000, sse=943.0, rms=0.026 (0.000%)
- 107: dt: 0.5000, sse=941.8, rms=0.026 (0.000%)
- 108: dt: 0.5000, sse=940.8, rms=0.026 (0.000%)
- 109: dt: 0.5000, sse=939.3, rms=0.025 (0.000%)
- 110: dt: 0.5000, sse=937.7, rms=0.025 (0.000%)
- 111: dt: 0.5000, sse=936.8, rms=0.025 (0.000%)
- 112: dt: 0.5000, sse=936.2, rms=0.025 (0.000%)
- 113: dt: 0.5000, sse=935.8, rms=0.025 (0.000%)
- 114: dt: 0.5000, sse=935.4, rms=0.025 (0.000%)
- 115: dt: 0.5000, sse=935.6, rms=0.025 (0.000%)
- 116: dt: 0.5000, sse=934.3, rms=0.025 (0.000%)
- 117: dt: 0.5000, sse=933.4, rms=0.024 (0.000%)
- 118: dt: 0.5000, sse=932.9, rms=0.024 (0.000%)
- 119: dt: 0.5000, sse=932.1, rms=0.024 (0.000%)
- 120: dt: 0.5000, sse=931.6, rms=0.024 (0.000%)
- positioning took 4.1 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/lh.curv.pial
- writing smoothed area to lh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/lh.area.pial
- vertex spacing 1.03 +- 0.43 (0.03-->7.42) (max @ vno 123782 --> 123779)
- face area 0.41 +- 0.30 (0.00-->5.88)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 161579 vertices processed
- 25000 of 161579 vertices processed
- 50000 of 161579 vertices processed
- 75000 of 161579 vertices processed
- 100000 of 161579 vertices processed
- 125000 of 161579 vertices processed
- 150000 of 161579 vertices processed
- 0 of 161579 vertices processed
- 25000 of 161579 vertices processed
- 50000 of 161579 vertices processed
- 75000 of 161579 vertices processed
- 100000 of 161579 vertices processed
- 125000 of 161579 vertices processed
- 150000 of 161579 vertices processed
- thickness calculation complete, 175:465 truncations.
- 40477 vertices at 0 distance
- 116109 vertices at 1 distance
- 102013 vertices at 2 distance
- 37706 vertices at 3 distance
- 9582 vertices at 4 distance
- 2438 vertices at 5 distance
- 767 vertices at 6 distance
- 244 vertices at 7 distance
- 105 vertices at 8 distance
- 49 vertices at 9 distance
- 53 vertices at 10 distance
- 45 vertices at 11 distance
- 18 vertices at 12 distance
- 11 vertices at 13 distance
- 10 vertices at 14 distance
- 12 vertices at 15 distance
- 16 vertices at 16 distance
- 8 vertices at 17 distance
- 5 vertices at 18 distance
- 4 vertices at 19 distance
- 4 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/lh.thickness
- positioning took 20.6 minutes
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/scripts
- cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/rh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/rh.woT2.pial
- `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/rh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/rh.woT2.pial'
- mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub007 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/sub007/mri/filled.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/brain.finalsurfs.mgz...
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/wm.mgz...
- 23624 bright wm thresholded.
- 971 bright non-wm voxels segmented.
- reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/rh.orig...
- computing class statistics...
- border white: 296565 voxels (1.77%)
- border gray 332938 voxels (1.98%)
- WM (92.0): 93.6 +- 10.2 [70.0 --> 110.0]
- GM (75.0) : 73.8 +- 12.9 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 46.1 (was 70)
- setting MAX_BORDER_WHITE to 116.2 (was 105)
- setting MIN_BORDER_WHITE to 59.0 (was 85)
- setting MAX_CSF to 33.1 (was 40)
- setting MAX_GRAY to 95.8 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 52.5 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 20.2 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=106, GM=59
- mean inside = 93.2, 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/sub007/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.89 +- 0.25 (0.03-->4.19) (max @ vno 137445 --> 146623)
- face area 0.33 +- 0.15 (0.00-->3.39)
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 11 points - only 0.00% unknown
- deleting segment 1 with 5 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 3 with 1 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 4 with 2 points - only 0.00% unknown
- deleting segment 5 with 422 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- removing 1 vertex label from ripped group
- deleting segment 7 with 1 points - only 0.00% unknown
- deleting segment 10 with 7 points - only 0.00% unknown
- deleting segment 11 with 34 points - only 0.00% unknown
- deleting segment 12 with 8 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 13 with 1 points - only 0.00% unknown
- deleting segment 14 with 6 points - only 0.00% unknown
- tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.89 +- 0.25 (0.06-->4.19) (max @ vno 137445 --> 146623)
- face area 0.33 +- 0.15 (0.00-->3.39)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4870654.5, rms=0.00
- rms = 1.55, time step reduction 1 of 3 to 0.250...
- rms = 0.39, time step reduction 2 of 3 to 0.125...
- rms = 0.05, time step reduction 3 of 3 to 0.062...
- 001: dt: 0.1250, sse=4870654.5, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 11 points - only 0.00% unknown
- deleting segment 1 with 5 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 2 with 1 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 3 with 2 points - only 0.00% unknown
- deleting segment 4 with 422 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- removing 1 vertex label from ripped group
- deleting segment 6 with 1 points - only 0.00% unknown
- deleting segment 7 with 7 points - only 0.00% unknown
- deleting segment 8 with 34 points - only 0.00% unknown
- deleting segment 9 with 8 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 10 with 1 points - only 0.00% unknown
- deleting segment 11 with 6 points - only 0.00% unknown
- tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.500
- vertex spacing 0.89 +- 0.25 (0.06-->4.19) (max @ vno 137445 --> 146623)
- face area 0.33 +- 0.15 (0.00-->3.39)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4870654.5, rms=0.00
- rms = 1.55, time step reduction 1 of 3 to 0.250...
- rms = 0.39, time step reduction 2 of 3 to 0.125...
- rms = 0.05, time step reduction 3 of 3 to 0.062...
- 002: dt: 0.1250, sse=4870654.5, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 11 points - only 0.00% unknown
- deleting segment 1 with 5 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 2 with 1 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 3 with 2 points - only 0.00% unknown
- deleting segment 4 with 422 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- removing 1 vertex label from ripped group
- deleting segment 6 with 1 points - only 0.00% unknown
- deleting segment 7 with 7 points - only 0.00% unknown
- deleting segment 8 with 34 points - only 0.00% unknown
- deleting segment 9 with 8 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 10 with 1 points - only 0.00% unknown
- deleting segment 11 with 6 points - only 0.00% unknown
- tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- smoothing T1 volume with sigma = 0.250
- vertex spacing 0.89 +- 0.25 (0.06-->4.19) (max @ vno 137445 --> 146623)
- face area 0.33 +- 0.15 (0.00-->3.39)
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4870654.5, rms=0.00
- rms = 1.55, time step reduction 1 of 3 to 0.250...
- rms = 0.39, time step reduction 2 of 3 to 0.125...
- rms = 0.05, time step reduction 3 of 3 to 0.062...
- 003: dt: 0.1250, sse=4870654.5, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 11 points - only 0.00% unknown
- deleting segment 1 with 5 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 2 with 1 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 3 with 2 points - only 0.00% unknown
- deleting segment 4 with 422 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- removing 1 vertex label from ripped group
- deleting segment 6 with 1 points - only 0.00% unknown
- deleting segment 7 with 7 points - only 0.00% unknown
- deleting segment 8 with 34 points - only 0.00% unknown
- deleting segment 9 with 8 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 10 with 1 points - only 0.00% unknown
- deleting segment 11 with 6 points - only 0.00% unknown
- tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- repositioning cortical surface to gray/csf boundary.
- smoothing T1 volume with sigma = 2.000
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=4870654.5, rms=0.00
- rms = 1.55, time step reduction 1 of 3 to 0.250...
- rms = 0.39, time step reduction 2 of 3 to 0.125...
- rms = 0.05, time step reduction 3 of 3 to 0.062...
- 004: dt: 0.1250, sse=4870654.5, rms=0.000 (1.000%)
- positioning took 0.3 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- deleting segment 1 with 2 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- smoothing surface for 5 iterations...
- reading initial pial vertex positions from woT2.pial...
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [99.20 204.80], gm=152.00+-17.60, and vertices in regions > 143.2
- 43571 surface locations found to contain inconsistent values (7523 in, 36048 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=561291.8, rms=0.22
- 001: dt: 0.5000, sse=525515.5, rms=0.217 (0.000%)
- 002: dt: 0.5000, sse=503782.8, rms=0.203 (0.000%)
- 003: dt: 0.5000, sse=489929.3, rms=0.193 (0.000%)
- 004: dt: 0.5000, sse=481257.3, rms=0.183 (0.000%)
- 005: dt: 0.5000, sse=473216.2, rms=0.175 (0.000%)
- 006: dt: 0.5000, sse=467942.3, rms=0.168 (0.000%)
- 007: dt: 0.5000, sse=464370.0, rms=0.162 (0.000%)
- 008: dt: 0.5000, sse=461449.3, rms=0.157 (0.000%)
- 009: dt: 0.5000, sse=458998.8, rms=0.153 (0.000%)
- 010: dt: 0.5000, sse=457493.0, rms=0.149 (0.000%)
- 011: dt: 0.5000, sse=455539.5, rms=0.146 (0.000%)
- 012: dt: 0.5000, sse=454033.4, rms=0.144 (0.000%)
- 013: dt: 0.5000, sse=452708.1, rms=0.142 (0.000%)
- 014: dt: 0.5000, sse=451406.0, rms=0.140 (0.000%)
- 015: dt: 0.5000, sse=449959.9, rms=0.139 (0.000%)
- 016: dt: 0.5000, sse=448545.6, rms=0.138 (0.000%)
- 017: dt: 0.5000, sse=447365.4, rms=0.137 (0.000%)
- 018: dt: 0.5000, sse=445905.2, rms=0.136 (0.000%)
- 019: dt: 0.5000, sse=444714.2, rms=0.135 (0.000%)
- 020: dt: 0.5000, sse=443422.2, rms=0.135 (0.000%)
- 021: dt: 0.5000, sse=441995.2, rms=0.135 (0.000%)
- 022: dt: 0.5000, sse=440727.2, rms=0.134 (0.000%)
- 023: dt: 0.5000, sse=439837.1, rms=0.134 (0.000%)
- 024: dt: 0.5000, sse=438774.5, rms=0.134 (0.000%)
- 025: dt: 0.5000, sse=437480.4, rms=0.134 (0.000%)
- 026: dt: 0.5000, sse=436623.9, rms=0.134 (0.000%)
- 027: dt: 0.5000, sse=435222.4, rms=0.134 (0.000%)
- 028: dt: 0.5000, sse=434369.2, rms=0.134 (0.000%)
- 029: dt: 0.5000, sse=433068.6, rms=0.135 (0.000%)
- 030: dt: 0.5000, sse=432148.7, rms=0.135 (0.000%)
- positioning took 4.1 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [91.60 216.40], gm=154.00+-20.80, and vertices in regions > 143.6
- 31496 surface locations found to contain inconsistent values (689 in, 30807 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=45130.8, rms=0.13
- 031: dt: 0.5000, sse=44731.6, rms=0.121 (0.000%)
- 032: dt: 0.5000, sse=45131.1, rms=0.109 (0.000%)
- 033: dt: 0.5000, sse=45936.9, rms=0.100 (0.000%)
- 034: dt: 0.5000, sse=46781.8, rms=0.094 (0.000%)
- 035: dt: 0.5000, sse=47700.0, rms=0.088 (0.000%)
- 036: dt: 0.5000, sse=48569.6, rms=0.084 (0.000%)
- 037: dt: 0.5000, sse=49361.1, rms=0.079 (0.000%)
- 038: dt: 0.5000, sse=50143.4, rms=0.075 (0.000%)
- 039: dt: 0.5000, sse=50923.7, rms=0.072 (0.000%)
- 040: dt: 0.5000, sse=51678.0, rms=0.068 (0.000%)
- 041: dt: 0.5000, sse=52406.0, rms=0.065 (0.000%)
- 042: dt: 0.5000, sse=53084.0, rms=0.062 (0.000%)
- 043: dt: 0.5000, sse=53736.4, rms=0.060 (0.000%)
- 044: dt: 0.5000, sse=54349.0, rms=0.057 (0.000%)
- 045: dt: 0.5000, sse=54940.0, rms=0.055 (0.000%)
- 046: dt: 0.5000, sse=55468.8, rms=0.053 (0.000%)
- 047: dt: 0.5000, sse=55974.7, rms=0.051 (0.000%)
- 048: dt: 0.5000, sse=56453.8, rms=0.049 (0.000%)
- 049: dt: 0.5000, sse=56898.8, rms=0.048 (0.000%)
- 050: dt: 0.5000, sse=57302.8, rms=0.046 (0.000%)
- 051: dt: 0.5000, sse=57674.1, rms=0.045 (0.000%)
- 052: dt: 0.5000, sse=58007.3, rms=0.044 (0.000%)
- 053: dt: 0.5000, sse=58345.5, rms=0.042 (0.000%)
- 054: dt: 0.5000, sse=58648.4, rms=0.041 (0.000%)
- 055: dt: 0.5000, sse=58916.2, rms=0.040 (0.000%)
- 056: dt: 0.5000, sse=59181.7, rms=0.039 (0.000%)
- 057: dt: 0.5000, sse=59430.7, rms=0.038 (0.000%)
- 058: dt: 0.5000, sse=59670.4, rms=0.037 (0.000%)
- 059: dt: 0.5000, sse=59884.7, rms=0.037 (0.000%)
- 060: dt: 0.5000, sse=60083.7, rms=0.036 (0.000%)
- positioning took 4.1 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [89.30 214.70], gm=152.00+-20.90, and vertices in regions > 141.5
- 21765 surface locations found to contain inconsistent values (237 in, 21528 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=6428.6, rms=0.05
- 061: dt: 0.5000, sse=6416.4, rms=0.052 (0.000%)
- 062: dt: 0.5000, sse=6398.5, rms=0.047 (0.000%)
- 063: dt: 0.5000, sse=6394.6, rms=0.044 (0.000%)
- 064: dt: 0.5000, sse=6401.4, rms=0.041 (0.000%)
- 065: dt: 0.5000, sse=6412.9, rms=0.038 (0.000%)
- 066: dt: 0.5000, sse=6422.8, rms=0.036 (0.000%)
- 067: dt: 0.5000, sse=6430.0, rms=0.035 (0.000%)
- 068: dt: 0.5000, sse=6433.7, rms=0.034 (0.000%)
- 069: dt: 0.5000, sse=6437.3, rms=0.033 (0.000%)
- 070: dt: 0.5000, sse=6441.5, rms=0.031 (0.000%)
- 071: dt: 0.5000, sse=6447.4, rms=0.031 (0.000%)
- 072: dt: 0.5000, sse=6454.2, rms=0.029 (0.000%)
- 073: dt: 0.5000, sse=6460.4, rms=0.029 (0.000%)
- 074: dt: 0.5000, sse=6466.6, rms=0.028 (0.000%)
- 075: dt: 0.5000, sse=6472.3, rms=0.027 (0.000%)
- 076: dt: 0.5000, sse=6478.8, rms=0.026 (0.000%)
- 077: dt: 0.5000, sse=6483.6, rms=0.026 (0.000%)
- 078: dt: 0.5000, sse=6487.7, rms=0.025 (0.000%)
- 079: dt: 0.5000, sse=6493.3, rms=0.025 (0.000%)
- 080: dt: 0.5000, sse=6499.0, rms=0.024 (0.000%)
- 081: dt: 0.5000, sse=6503.8, rms=0.024 (0.000%)
- 082: dt: 0.5000, sse=6507.9, rms=0.023 (0.000%)
- 083: dt: 0.5000, sse=6513.1, rms=0.023 (0.000%)
- 084: dt: 0.5000, sse=6517.5, rms=0.023 (0.000%)
- 085: dt: 0.5000, sse=6521.4, rms=0.022 (0.000%)
- 086: dt: 0.5000, sse=6525.1, rms=0.022 (0.000%)
- 087: dt: 0.5000, sse=6528.5, rms=0.022 (0.000%)
- 088: dt: 0.5000, sse=6531.7, rms=0.022 (0.000%)
- 089: dt: 0.5000, sse=6534.4, rms=0.022 (0.000%)
- 090: dt: 0.5000, sse=6536.4, rms=0.021 (0.000%)
- positioning took 4.1 minutes
- repositioning pial surface locations using ../mri/T2.mgz
- locating cortical regions not in the range [89.00 215.00], gm=152.00+-21.00, and vertices in regions > 141.5
- 22677 surface locations found to contain inconsistent values (54 in, 22623 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/sub007/surf/rh.pial...
- writing smoothed curvature to rh.curv.pial
- 000: dt: 0.0000, sse=752.2, rms=0.03
- 091: dt: 0.5000, sse=750.1, rms=0.026 (0.000%)
- 092: dt: 0.5000, sse=743.1, rms=0.025 (0.000%)
- 093: dt: 0.5000, sse=738.6, rms=0.024 (0.000%)
- 094: dt: 0.5000, sse=734.5, rms=0.023 (0.000%)
- 095: dt: 0.5000, sse=730.9, rms=0.023 (0.000%)
- 096: dt: 0.5000, sse=728.3, rms=0.022 (0.000%)
- 097: dt: 0.5000, sse=726.6, rms=0.022 (0.000%)
- 098: dt: 0.5000, sse=725.1, rms=0.022 (0.000%)
- 099: dt: 0.5000, sse=723.4, rms=0.022 (0.000%)
- 100: dt: 0.5000, sse=721.9, rms=0.021 (0.000%)
- 101: dt: 0.5000, sse=720.4, rms=0.021 (0.000%)
- 102: dt: 0.5000, sse=719.2, rms=0.021 (0.000%)
- 103: dt: 0.5000, sse=718.0, rms=0.021 (0.000%)
- 104: dt: 0.5000, sse=716.8, rms=0.021 (0.000%)
- 105: dt: 0.5000, sse=715.7, rms=0.020 (0.000%)
- 106: dt: 0.5000, sse=715.2, rms=0.020 (0.000%)
- 107: dt: 0.5000, sse=714.7, rms=0.020 (0.000%)
- 108: dt: 0.5000, sse=714.1, rms=0.020 (0.000%)
- 109: dt: 0.5000, sse=713.5, rms=0.020 (0.000%)
- 110: dt: 0.5000, sse=713.1, rms=0.020 (0.000%)
- 111: dt: 0.5000, sse=712.7, rms=0.020 (0.000%)
- 112: dt: 0.5000, sse=712.2, rms=0.020 (0.000%)
- 113: dt: 0.5000, sse=711.7, rms=0.020 (0.000%)
- 114: dt: 0.5000, sse=711.5, rms=0.020 (0.000%)
- 115: dt: 0.5000, sse=711.0, rms=0.019 (0.000%)
- 116: dt: 0.5000, sse=710.6, rms=0.019 (0.000%)
- 117: dt: 0.5000, sse=710.4, rms=0.019 (0.000%)
- 118: dt: 0.5000, sse=710.7, rms=0.019 (0.000%)
- 119: dt: 0.5000, sse=710.4, rms=0.019 (0.000%)
- 120: dt: 0.5000, sse=710.1, rms=0.019 (0.000%)
- positioning took 4.1 minutes
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/rh.curv.pial
- writing smoothed area to rh.area.pial
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/rh.area.pial
- vertex spacing 1.02 +- 0.43 (0.04-->6.79) (max @ vno 111978 --> 113239)
- face area 0.41 +- 0.30 (0.00-->7.21)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 159917 vertices processed
- 25000 of 159917 vertices processed
- 50000 of 159917 vertices processed
- 75000 of 159917 vertices processed
- 100000 of 159917 vertices processed
- 125000 of 159917 vertices processed
- 150000 of 159917 vertices processed
- 0 of 159917 vertices processed
- 25000 of 159917 vertices processed
- 50000 of 159917 vertices processed
- 75000 of 159917 vertices processed
- 100000 of 159917 vertices processed
- 125000 of 159917 vertices processed
- 150000 of 159917 vertices processed
- thickness calculation complete, 172:491 truncations.
- 40890 vertices at 0 distance
- 115402 vertices at 1 distance
- 98770 vertices at 2 distance
- 37399 vertices at 3 distance
- 10290 vertices at 4 distance
- 2546 vertices at 5 distance
- 688 vertices at 6 distance
- 204 vertices at 7 distance
- 93 vertices at 8 distance
- 48 vertices at 9 distance
- 41 vertices at 10 distance
- 35 vertices at 11 distance
- 25 vertices at 12 distance
- 22 vertices at 13 distance
- 8 vertices at 14 distance
- 7 vertices at 15 distance
- 2 vertices at 16 distance
- 2 vertices at 17 distance
- 5 vertices at 18 distance
- 2 vertices at 19 distance
- 11 vertices at 20 distance
- writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/rh.thickness
- positioning took 20.0 minutes
- #--------------------------------------------
- #@# Surf Volume lh Fri Aug 9 00:36:23 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 00:36:23 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 00:36:24 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri
- mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon sub007
- 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 = 29
- writing volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/ribbon.mgz
- writing ribbon files
- #--------------------------------------------
- #@# ASeg Stats Fri Aug 9 00:54:40 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007
- 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 sub007
- $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 sub007
- sysname Linux
- hostname snake4
- machine x86_64
- user fkaule
- UseRobust 0
- atlas_icv (eTIV) = 1479761 mm^3 (det: 1.316500 )
- Computing euler number
- orig.nofix lheno = -28, rheno = -30
- orig.nofix lhholes = 15, rhholes = 16
- Loading mri/aseg.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 287624.204 286090.000 diff= 1534.2 pctdiff= 0.533
- rhCtxGM: 289516.212 288282.000 diff= 1234.2 pctdiff= 0.426
- lhCtxWM: 242615.980 241783.500 diff= 832.5 pctdiff= 0.343
- rhCtxWM: 245385.917 246161.500 diff= -775.6 pctdiff=-0.316
- SubCortGMVol 68475.000
- SupraTentVol 1192288.313 (1188182.000) diff=4106.313 pctdiff=0.344
- SupraTentVolNotVent 1135302.313 (1131196.000) diff=4106.313 pctdiff=0.362
- BrainSegVol 1330176.000 (1327020.000) diff=3156.000 pctdiff=0.237
- BrainSegVolNotVent 1268535.000 (1271063.313) diff=-2528.313 pctdiff=-0.199
- BrainSegVolNotVent 1268535.000
- CerebellumVol 137042.000
- VentChorVol 56986.000
- 3rd4th5thCSF 4655.000
- CSFVol 1510.000, OptChiasmVol 286.000
- MaskVol 1935152.000
- 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 27099 27098.996
- 4 5 Left-Inf-Lat-Vent 746 746.218
- 5 7 Left-Cerebellum-White-Matter 14869 14868.646
- 6 8 Left-Cerebellum-Cortex 53749 53748.801
- 7 10 Left-Thalamus-Proper 9438 9437.657
- 8 11 Left-Caudate 4632 4632.144
- 9 12 Left-Putamen 7053 7053.497
- 10 13 Left-Pallidum 2175 2175.092
- 11 14 3rd-Ventricle 1331 1330.604
- 12 15 4th-Ventricle 2027 2026.925
- 13 16 Brain-Stem 24802 24801.572
- 14 17 Left-Hippocampus 3706 3706.218
- 15 18 Left-Amygdala 1815 1814.616
- 16 24 CSF 1445 1445.200
- 17 26 Left-Accumbens-area 688 688.108
- 18 28 Left-VentralDC 4129 4129.331
- 19 30 Left-vessel 160 160.434
- 20 31 Left-choroid-plexus 1418 1418.140
- 23 43 Right-Lateral-Ventricle 24942 24941.529
- 24 44 Right-Inf-Lat-Vent 859 859.379
- 25 46 Right-Cerebellum-White-Matter 15385 15384.791
- 26 47 Right-Cerebellum-Cortex 55350 55349.562
- 27 49 Right-Thalamus-Proper 8230 8229.534
- 28 50 Right-Caudate 4882 4882.218
- 29 51 Right-Putamen 6576 6575.822
- 30 52 Right-Pallidum 2431 2430.987
- 31 53 Right-Hippocampus 3288 3288.456
- 32 54 Right-Amygdala 2248 2248.185
- 33 58 Right-Accumbens-area 801 801.264
- 34 60 Right-VentralDC 3958 3958.295
- 35 62 Right-vessel 209 208.831
- 36 63 Right-choroid-plexus 1740 1740.183
- 37 72 5th-Ventricle 0 0.000
- 38 77 WM-hypointensities 2252 2252.069
- 39 78 Left-WM-hypointensities 0 0.000
- 40 79 Right-WM-hypointensities 0 0.000
- 41 80 non-WM-hypointensities 11 10.525
- 42 81 Left-non-WM-hypointensities 0 0.000
- 43 82 Right-non-WM-hypointensities 0 0.000
- 44 85 Optic-Chiasm 281 281.063
- 45 251 CC_Posterior 931 930.826
- 46 252 CC_Mid_Posterior 312 312.040
- 47 253 CC_Central 308 307.739
- 48 254 CC_Mid_Anterior 321 320.949
- 49 255 CC_Anterior 775 774.954
- Reporting on 45 segmentations
- mri_segstats done
- #-----------------------------------------
- #@# AParc-to-ASeg Fri Aug 9 00:57:20 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007
- mri_aparc2aseg --s sub007 --volmask
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- subject sub007
- outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/aparc+aseg.mgz
- useribbon 0
- baseoffset 0
- RipUnknown 0
- Reading lh white surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/lh.white
- Reading lh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/lh.pial
- Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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/sub007/surf/rh.white
- Reading rh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/rh.pial
- Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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/sub007/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/sub007/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 = 572710
- Used brute-force search on 0 voxels
- Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/aparc+aseg.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007
- mri_aparc2aseg --s sub007 --volmask --a2009s
- SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
- subject sub007
- outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/aparc.a2009s+aseg.mgz
- useribbon 0
- baseoffset 10100
- RipUnknown 0
- Reading lh white surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/lh.white
- Reading lh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/lh.pial
- Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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/sub007/surf/rh.white
- Reading rh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/rh.pial
- Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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/sub007/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/sub007/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 = 572710
- Used brute-force search on 0 voxels
- Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/aparc.a2009s+aseg.mgz
- #-----------------------------------------
- #@# WMParc Fri Aug 9 01:02:35 CEST 2013
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007
- mri_aparc2aseg --s sub007 --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 sub007
- 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/sub007/mri/aparc+aseg.mgz
- Reading lh white surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/lh.white
- Reading lh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/lh.pial
- Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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/sub007/surf/rh.white
- Reading rh pial surface
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/rh.pial
- Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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/sub007/mri/ribbon.mgz
- Loading filled from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/filled.mgz
- Ripping vertices labeled as unkown
- Ripped 8914 vertices from left hemi
- Ripped 8275 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/sub007/mri/aseg.mgz
- Loading Ctx Seg File /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 = 1059540
- Used brute-force search on 376 voxels
- Fixing Parahip LH WM
- Found 8 clusters
- 0 k 2.000000
- 1 k 1.000000
- 2 k 2.000000
- 3 k 43.000000
- 4 k 3.000000
- 5 k 2.000000
- 6 k 9.000000
- 7 k 1575.000000
- Fixing Parahip RH WM
- Found 22 clusters
- 0 k 1.000000
- 1 k 3.000000
- 2 k 1.000000
- 3 k 2.000000
- 4 k 1.000000
- 5 k 1.000000
- 6 k 5.000000
- 7 k 1.000000
- 8 k 1.000000
- 9 k 1.000000
- 10 k 2.000000
- 11 k 1.000000
- 12 k 4.000000
- 13 k 1.000000
- 14 k 7.000000
- 15 k 2154.000000
- 16 k 1.000000
- 17 k 5.000000
- 18 k 5.000000
- 19 k 18.000000
- 20 k 1.000000
- 21 k 1.000000
- Writing output aseg to mri/wmparc.mgz
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007
- 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 sub007 --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 sub007 --surf-wm-vol --ctab /opt/freesurfer/5.3.0/WMParcStatsLUT.txt --etiv
- sysname Linux
- hostname snake4
- machine x86_64
- user fkaule
- UseRobust 0
- atlas_icv (eTIV) = 1479761 mm^3 (det: 1.316500 )
- Loading mri/wmparc.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 287624.204 286090.000 diff= 1534.2 pctdiff= 0.533
- rhCtxGM: 289516.212 288282.000 diff= 1234.2 pctdiff= 0.426
- lhCtxWM: 242615.980 241783.500 diff= 832.5 pctdiff= 0.343
- rhCtxWM: 245385.917 246161.500 diff= -775.6 pctdiff=-0.316
- SubCortGMVol 68475.000
- SupraTentVol 1192288.313 (1188182.000) diff=4106.313 pctdiff=0.344
- SupraTentVolNotVent 1135302.313 (1131196.000) diff=4106.313 pctdiff=0.362
- BrainSegVol 1330176.000 (1327020.000) diff=3156.000 pctdiff=0.237
- BrainSegVolNotVent 1268535.000 (1271063.313) diff=-2528.313 pctdiff=-0.199
- BrainSegVolNotVent 1268535.000
- CerebellumVol 137042.000
- VentChorVol 56986.000
- 3rd4th5thCSF 4655.000
- CSFVol 1510.000, OptChiasmVol 286.000
- MaskVol 1935152.000
- 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 3154 3153.913
- 2 3002 wm-lh-caudalanteriorcingulate 2972 2972.113
- 3 3003 wm-lh-caudalmiddlefrontal 8275 8275.277
- 4 3004 wm-lh-corpuscallosum 0 0.000
- 5 3005 wm-lh-cuneus 2540 2539.679
- 6 3006 wm-lh-entorhinal 772 772.495
- 7 3007 wm-lh-fusiform 7401 7401.436
- 8 3008 wm-lh-inferiorparietal 10740 10739.660
- 9 3009 wm-lh-inferiortemporal 7216 7216.179
- 10 3010 wm-lh-isthmuscingulate 4430 4430.004
- 11 3011 wm-lh-lateraloccipital 10720 10719.810
- 12 3012 wm-lh-lateralorbitofrontal 7066 7066.030
- 13 3013 wm-lh-lingual 6645 6645.365
- 14 3014 wm-lh-medialorbitofrontal 3183 3183.087
- 15 3015 wm-lh-middletemporal 5196 5195.744
- 16 3016 wm-lh-parahippocampal 1716 1716.442
- 17 3017 wm-lh-paracentral 4864 4864.201
- 18 3018 wm-lh-parsopercularis 4845 4845.142
- 19 3019 wm-lh-parsorbitalis 1038 1037.999
- 20 3020 wm-lh-parstriangularis 3039 3039.450
- 21 3021 wm-lh-pericalcarine 2506 2506.010
- 22 3022 wm-lh-postcentral 7691 7691.204
- 23 3023 wm-lh-posteriorcingulate 4440 4440.179
- 24 3024 wm-lh-precentral 13699 13698.847
- 25 3025 wm-lh-precuneus 10766 10766.237
- 26 3026 wm-lh-rostralanteriorcingulate 2922 2921.959
- 27 3027 wm-lh-rostralmiddlefrontal 14665 14664.667
- 28 3028 wm-lh-superiorfrontal 18741 18741.410
- 29 3029 wm-lh-superiorparietal 13243 13242.832
- 30 3030 wm-lh-superiortemporal 9551 9550.660
- 31 3031 wm-lh-supramarginal 10107 10106.726
- 32 3032 wm-lh-frontalpole 203 202.638
- 33 3033 wm-lh-temporalpole 701 701.405
- 34 3034 wm-lh-transversetemporal 866 865.663
- 35 3035 wm-lh-insula 9780 9779.663
- 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 2321 2321.251
- 120 4002 wm-rh-caudalanteriorcingulate 2566 2566.323
- 121 4003 wm-rh-caudalmiddlefrontal 6507 6506.814
- 122 4004 wm-rh-corpuscallosum 0 0.000
- 123 4005 wm-rh-cuneus 2609 2608.796
- 124 4006 wm-rh-entorhinal 510 509.688
- 125 4007 wm-rh-fusiform 8285 8285.397
- 126 4008 wm-rh-inferiorparietal 14334 14333.663
- 127 4009 wm-rh-inferiortemporal 6136 6135.659
- 128 4010 wm-rh-isthmuscingulate 4036 4035.550
- 129 4011 wm-rh-lateraloccipital 9858 9858.188
- 130 4012 wm-rh-lateralorbitofrontal 7746 7745.896
- 131 4013 wm-rh-lingual 6173 6173.385
- 132 4014 wm-rh-medialorbitofrontal 3592 3592.180
- 133 4015 wm-rh-middletemporal 7303 7303.131
- 134 4016 wm-rh-parahippocampal 2158 2157.891
- 135 4017 wm-rh-paracentral 5318 5317.781
- 136 4018 wm-rh-parsopercularis 4364 4363.938
- 137 4019 wm-rh-parsorbitalis 1293 1292.720
- 138 4020 wm-rh-parstriangularis 3372 3371.584
- 139 4021 wm-rh-pericalcarine 2885 2885.262
- 140 4022 wm-rh-postcentral 9349 9348.502
- 141 4023 wm-rh-posteriorcingulate 4022 4022.124
- 142 4024 wm-rh-precentral 14456 14455.990
- 143 4025 wm-rh-precuneus 11736 11736.276
- 144 4026 wm-rh-rostralanteriorcingulate 2451 2451.267
- 145 4027 wm-rh-rostralmiddlefrontal 14509 14509.368
- 146 4028 wm-rh-superiorfrontal 19270 19269.854
- 147 4029 wm-rh-superiorparietal 12693 12692.627
- 148 4030 wm-rh-superiortemporal 8158 8157.717
- 149 4031 wm-rh-supramarginal 9084 9083.567
- 150 4032 wm-rh-frontalpole 253 252.539
- 151 4033 wm-rh-temporalpole 852 852.331
- 152 4034 wm-rh-transversetemporal 524 523.583
- 153 4035 wm-rh-insula 9220 9220.396
- 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 28070 28069.562
- 237 5002 Right-UnsegmentedWhiteMatter 29842 29842.420
- 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/sub007/label
- #--------------------------------------------
- #@# BA Labels lh Fri Aug 9 01:15:03 CEST 2013
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 161579
- Number of reverse mapping hits = 506
- Checking for and removing duplicates
- Writing label file ./lh.BA1.label 4635
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 161579
- Number of reverse mapping hits = 860
- Checking for and removing duplicates
- Writing label file ./lh.BA2.label 8769
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 161579
- Number of reverse mapping hits = 299
- Checking for and removing duplicates
- Writing label file ./lh.BA3a.label 4376
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 161579
- Number of reverse mapping hits = 622
- Checking for and removing duplicates
- Writing label file ./lh.BA3b.label 6605
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 161579
- Number of reverse mapping hits = 812
- Checking for and removing duplicates
- Writing label file ./lh.BA4a.label 6596
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 161579
- Number of reverse mapping hits = 536
- Checking for and removing duplicates
- Writing label file ./lh.BA4p.label 4606
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 161579
- Number of reverse mapping hits = 2420
- Checking for and removing duplicates
- Writing label file ./lh.BA6.label 16009
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 161579
- Number of reverse mapping hits = 1240
- Checking for and removing duplicates
- Writing label file ./lh.BA44.label 5421
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 161579
- Number of reverse mapping hits = 1838
- Checking for and removing duplicates
- Writing label file ./lh.BA45.label 5260
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 161579
- Number of reverse mapping hits = 1743
- Checking for and removing duplicates
- Writing label file ./lh.V1.label 6384
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 161579
- Number of reverse mapping hits = 4489
- Checking for and removing duplicates
- Writing label file ./lh.V2.label 12603
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 161579
- Number of reverse mapping hits = 767
- Checking for and removing duplicates
- Writing label file ./lh.MT.label 2785
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.perirhinal.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 161579
- Number of reverse mapping hits = 164
- Checking for and removing duplicates
- Writing label file ./lh.perirhinal.label 1363
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.thresh.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 161579
- Number of reverse mapping hits = 183
- Checking for and removing duplicates
- Writing label file ./lh.BA1.thresh.label 1197
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.thresh.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 161579
- Number of reverse mapping hits = 235
- Checking for and removing duplicates
- Writing label file ./lh.BA2.thresh.label 2327
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.thresh.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 161579
- Number of reverse mapping hits = 71
- Checking for and removing duplicates
- Writing label file ./lh.BA3a.thresh.label 1575
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.thresh.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 161579
- Number of reverse mapping hits = 211
- Checking for and removing duplicates
- Writing label file ./lh.BA3b.thresh.label 2207
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.thresh.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 161579
- Number of reverse mapping hits = 312
- Checking for and removing duplicates
- Writing label file ./lh.BA4a.thresh.label 2631
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.thresh.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 161579
- Number of reverse mapping hits = 167
- Checking for and removing duplicates
- Writing label file ./lh.BA4p.thresh.label 1716
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.thresh.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 161579
- Number of reverse mapping hits = 1293
- Checking for and removing duplicates
- Writing label file ./lh.BA6.thresh.label 8328
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.thresh.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 161579
- Number of reverse mapping hits = 677
- Checking for and removing duplicates
- Writing label file ./lh.BA44.thresh.label 2589
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.thresh.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 161579
- Number of reverse mapping hits = 764
- Checking for and removing duplicates
- Writing label file ./lh.BA45.thresh.label 1915
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.thresh.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 161579
- Number of reverse mapping hits = 1195
- Checking for and removing duplicates
- Writing label file ./lh.V1.thresh.label 4600
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.thresh.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 161579
- Number of reverse mapping hits = 1982
- Checking for and removing duplicates
- Writing label file ./lh.V2.thresh.label 5316
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.thresh.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/lh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 161579
- Number of reverse mapping hits = 169
- Checking for and removing duplicates
- Writing label file ./lh.MT.thresh.label 682
- mri_label2label: Done
- mris_label2annot --s sub007 --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/sub007/label
- cmdline mris_label2annot --s sub007 --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 snake4
- machine x86_64
- user fkaule
- subject sub007
- 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/sub007/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 111671 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/label/lh.BA.annot
- mris_label2annot --s sub007 --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/sub007/label
- cmdline mris_label2annot --s sub007 --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 snake4
- machine x86_64
- user fkaule
- subject sub007
- 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/sub007/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 132761 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/label/lh.BA.thresh.annot
- mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab sub007 lh white
- computing statistics for each annotation in ./lh.BA.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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
- 1246 655 2405 2.425 0.494 0.151 0.071 48 3.9 BA1
- 4418 2948 7871 2.420 0.464 0.126 0.036 50 6.6 BA2
- 1078 736 1109 1.924 0.413 0.138 0.040 9 1.8 BA3a
- 2743 1777 4032 1.984 0.606 0.116 0.035 31 3.9 BA3b
- 1878 1095 4385 3.119 0.546 0.109 0.035 20 3.0 BA4a
- 1503 906 2617 2.844 0.552 0.102 0.031 18 2.1 BA4p
- 11511 7414 26931 2.861 0.622 0.128 0.044 163 20.1 BA6
- 3648 2408 7443 2.666 0.466 0.123 0.037 46 5.7 BA44
- 4321 2887 8482 2.455 0.487 0.140 0.045 71 8.0 BA45
- 3766 2483 4817 1.819 0.459 0.164 0.120 74 10.8 V1
- 10241 6597 15397 2.139 0.453 0.162 0.062 189 26.1 V2
- 2467 1585 4414 2.404 0.404 0.135 0.045 35 4.5 MT
- 1088 750 2898 3.041 0.905 0.144 0.058 15 2.6 perirhinal
- mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab sub007 lh white
- computing statistics for each annotation in ./lh.BA.thresh.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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
- 876 427 1493 2.288 0.504 0.149 0.078 40 3.3 BA1
- 1760 1154 3400 2.486 0.459 0.112 0.031 16 2.3 BA2
- 892 605 865 1.909 0.413 0.143 0.041 8 1.6 BA3a
- 1703 1123 2174 1.751 0.483 0.098 0.025 13 1.6 BA3b
- 1869 1081 4335 3.178 0.532 0.102 0.033 19 2.7 BA4a
- 1133 696 1893 2.767 0.491 0.102 0.033 14 1.5 BA4p
- 6645 4185 15564 2.890 0.615 0.124 0.047 98 12.5 BA6
- 2396 1592 4777 2.582 0.444 0.117 0.032 27 3.2 BA44
- 1846 1221 4110 2.632 0.447 0.153 0.051 36 3.9 BA45
- 4108 2711 5308 1.822 0.461 0.165 0.116 81 12.2 V1
- 4977 3234 7347 2.103 0.433 0.167 0.065 95 13.1 V2
- 613 406 1095 2.438 0.470 0.132 0.043 7 1.0 MT
- #--------------------------------------------
- #@# BA Labels rh Fri Aug 9 01:20:06 CEST 2013
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 159917
- Number of reverse mapping hits = 797
- Checking for and removing duplicates
- Writing label file ./rh.BA1.label 4759
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 159917
- Number of reverse mapping hits = 1153
- Checking for and removing duplicates
- Writing label file ./rh.BA2.label 7840
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 159917
- Number of reverse mapping hits = 393
- Checking for and removing duplicates
- Writing label file ./rh.BA3a.label 4373
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 159917
- Number of reverse mapping hits = 754
- Checking for and removing duplicates
- Writing label file ./rh.BA3b.label 5276
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 159917
- Number of reverse mapping hits = 713
- Checking for and removing duplicates
- Writing label file ./rh.BA4a.label 6460
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 159917
- Number of reverse mapping hits = 493
- Checking for and removing duplicates
- Writing label file ./rh.BA4p.label 4966
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 159917
- Number of reverse mapping hits = 1649
- Checking for and removing duplicates
- Writing label file ./rh.BA6.label 13905
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 159917
- Number of reverse mapping hits = 1870
- Checking for and removing duplicates
- Writing label file ./rh.BA44.label 8782
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 159917
- Number of reverse mapping hits = 2162
- Checking for and removing duplicates
- Writing label file ./rh.BA45.label 7517
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 159917
- Number of reverse mapping hits = 2015
- Checking for and removing duplicates
- Writing label file ./rh.V1.label 6742
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 159917
- Number of reverse mapping hits = 4189
- Checking for and removing duplicates
- Writing label file ./rh.V2.label 12205
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 159917
- Number of reverse mapping hits = 833
- Checking for and removing duplicates
- Writing label file ./rh.MT.label 2765
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.perirhinal.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 159917
- Number of reverse mapping hits = 63
- Checking for and removing duplicates
- Writing label file ./rh.perirhinal.label 815
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.thresh.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 159917
- Number of reverse mapping hits = 155
- Checking for and removing duplicates
- Writing label file ./rh.BA1.thresh.label 1031
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.thresh.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 159917
- Number of reverse mapping hits = 483
- Checking for and removing duplicates
- Writing label file ./rh.BA2.thresh.label 3171
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.thresh.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 159917
- Number of reverse mapping hits = 58
- Checking for and removing duplicates
- Writing label file ./rh.BA3a.thresh.label 1756
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.thresh.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 159917
- Number of reverse mapping hits = 454
- Checking for and removing duplicates
- Writing label file ./rh.BA3b.thresh.label 2637
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.thresh.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 159917
- Number of reverse mapping hits = 296
- Checking for and removing duplicates
- Writing label file ./rh.BA4a.thresh.label 1684
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.thresh.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 159917
- Number of reverse mapping hits = 159
- Checking for and removing duplicates
- Writing label file ./rh.BA4p.thresh.label 1648
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.thresh.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 159917
- Number of reverse mapping hits = 801
- Checking for and removing duplicates
- Writing label file ./rh.BA6.thresh.label 7760
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.thresh.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 159917
- Number of reverse mapping hits = 505
- Checking for and removing duplicates
- Writing label file ./rh.BA44.thresh.label 1517
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.thresh.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 159917
- Number of reverse mapping hits = 476
- Checking for and removing duplicates
- Writing label file ./rh.BA45.thresh.label 1654
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.thresh.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 159917
- Number of reverse mapping hits = 1275
- Checking for and removing duplicates
- Writing label file ./rh.V1.thresh.label 4507
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.thresh.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 159917
- Number of reverse mapping hits = 2035
- Checking for and removing duplicates
- Writing label file ./rh.V2.thresh.label 5472
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.thresh.label --trgsubject sub007 --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 = sub007
- 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/sub007/surf/rh.white
- Reading target registration
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 159917
- Number of reverse mapping hits = 115
- Checking for and removing duplicates
- Writing label file ./rh.MT.thresh.label 383
- mri_label2label: Done
- mris_label2annot --s sub007 --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/sub007/label
- cmdline mris_label2annot --s sub007 --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 snake4
- machine x86_64
- user fkaule
- subject sub007
- 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/sub007/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 110439 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/label/rh.BA.annot
- mris_label2annot --s sub007 --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/sub007/label
- cmdline mris_label2annot --s sub007 --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 snake4
- machine x86_64
- user fkaule
- subject sub007
- 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/sub007/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 132631 unhit vertices
- Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/label/rh.BA.thresh.annot
- mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab sub007 rh white
- computing statistics for each annotation in ./rh.BA.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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
- 1153 688 2495 2.630 0.476 0.155 0.118 96 4.4 BA1
- 4294 2850 7089 2.339 0.471 0.116 0.035 43 6.4 BA2
- 1131 756 1189 1.969 0.430 0.139 0.039 11 1.9 BA3a
- 2556 1636 3935 2.014 0.561 0.122 0.060 39 5.9 BA3b
- 2037 1161 4285 2.987 0.583 0.110 0.089 34 11.4 BA4a
- 1386 853 2286 2.728 0.494 0.109 0.040 12 2.5 BA4p
- 9162 5995 22603 3.025 0.564 0.127 0.038 109 14.6 BA6
- 4792 3213 9116 2.536 0.472 0.123 0.036 54 7.1 BA44
- 5582 3794 11401 2.538 0.509 0.152 0.053 101 11.6 BA45
- 4348 2899 5837 1.875 0.413 0.161 0.072 77 11.5 V1
- 9860 6386 15065 2.158 0.483 0.155 0.060 175 22.6 V2
- 2583 1759 4337 2.303 0.422 0.139 0.044 39 4.9 MT
- 594 401 1739 3.135 0.908 0.129 0.046 6 1.2 perirhinal
- mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab sub007 rh white
- computing statistics for each annotation in ./rh.BA.thresh.annot.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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
- 747 416 1539 2.611 0.550 0.151 0.092 24 3.1 BA1
- 2660 1715 4750 2.403 0.524 0.121 0.040 32 4.5 BA2
- 965 651 914 1.889 0.381 0.137 0.038 8 1.6 BA3a
- 2124 1388 3010 1.906 0.501 0.118 0.051 26 3.3 BA3b
- 1320 716 2877 3.004 0.603 0.113 0.040 15 2.5 BA4a
- 1158 706 1930 2.786 0.487 0.107 0.037 10 1.6 BA4p
- 5710 3705 13709 2.982 0.587 0.127 0.039 70 9.4 BA6
- 1444 968 3094 2.532 0.541 0.133 0.035 22 2.3 BA44
- 1543 1041 3673 2.691 0.382 0.153 0.055 30 3.4 BA45
- 4101 2751 5522 1.881 0.405 0.159 0.073 71 10.6 V1
- 5154 3343 7480 2.067 0.461 0.164 0.067 96 13.2 V2
- 360 258 798 2.457 0.346 0.157 0.058 9 1.1 MT
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/label
- #--------------------------------------------
- #@# Ex-vivo Entorhinal Cortex Label lh Fri Aug 9 01:25:06 CEST 2013
- mris_spherical_average -erode 1 -orig white -t 0.4 -o sub007 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label
- painting output onto subject sub007.
- processing subject lh.EC_average...
- reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 1107 points to lh.entorhinal_exvivo.label...
- mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label sub007 lh white
- limiting computations to label ./lh.entorhinal_exvivo.label.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/lh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/lh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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
- 381 257 1073 2.848 0.836 0.140 0.050 7 0.9 ./lh.entorhinal_exvivo.label
- #--------------------------------------------
- #@# Ex-vivo Entorhinal Cortex Label rh Fri Aug 9 01:25:23 CEST 2013
- mris_spherical_average -erode 1 -orig white -t 0.4 -o sub007 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label
- painting output onto subject sub007.
- processing subject rh.EC_average...
- reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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 719 points to rh.entorhinal_exvivo.label...
- mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label sub007 rh white
- limiting computations to label ./rh.entorhinal_exvivo.label.
- reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/mri/wm.mgz...
- reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/rh.white...
- reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/surf/rh.pial...
- reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub007/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
- 244 164 808 3.318 0.883 0.106 0.031 1 0.4 ./rh.entorhinal_exvivo.label
- #------------------------------------------
- Started at Thu Aug 8 10:53:42 CEST 2013
- Ended at Fri Aug 9 01:25:40 CEST 2013
- #@#%# recon-all-run-time-hours 14.533
- recon-all -s sub007 finished without error at Fri Aug 9 01:25:40 CEST 2013
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