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- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri
- /opt/freesurfer/5.3.0/bin/mri_nu_correct.mni
- --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
- nIters 2
- $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $
- Linux snake5 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
- Thu Aug 8 10:58:20 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.13482
- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.13482/nu0.mnc -odt float
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.13482/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, 4.19095e-09, 0)
- j_ras = (0, 1.49012e-08, -1)
- k_ras = (0, 1, 0)
- changing data type from uchar to float (noscale = 0)...
- writing to ./tmp.mri_nu_correct.mni.13482/nu0.mnc...
-
- --------------------------------------------------------
- Iteration 1 Thu Aug 8 10:58:24 CEST 2013
- nu_correct -clobber ./tmp.mri_nu_correct.mni.13482/nu0.mnc ./tmp.mri_nu_correct.mni.13482/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.13482/0/
- [fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/] [2013-08-08 10:58:24] 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.13482/0/ ./tmp.mri_nu_correct.mni.13482/nu0.mnc ./tmp.mri_nu_correct.mni.13482/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
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- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Number of iterations: 24
- CV of field change: 0.000983369
- [fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/] [2013-08-08 10:59:04] running:
- /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.13482/nu0.mnc ./tmp.mri_nu_correct.mni.13482/0//template.mnc
- Transforming slices:......................................................................................Done
- Transforming slices:................................................................................................................................................................................................................................................................Done
-
-
- --------------------------------------------------------
- Iteration 2 Thu Aug 8 10:59:10 CEST 2013
- nu_correct -clobber ./tmp.mri_nu_correct.mni.13482/nu1.mnc ./tmp.mri_nu_correct.mni.13482/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.13482/1/
- [fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/] [2013-08-08 10:59:11] 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.13482/1/ ./tmp.mri_nu_correct.mni.13482/nu1.mnc ./tmp.mri_nu_correct.mni.13482/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
- Number of iterations: 19
- CV of field change: 0.000998983
- [fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/] [2013-08-08 10:59:43] running:
- /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.13482/nu1.mnc ./tmp.mri_nu_correct.mni.13482/1//template.mnc
- Transforming slices:......................................................................................Done
- Transforming slices:................................................................................................................................................................................................................................................................Done
-
-
-
- mri_binarize --i ./tmp.mri_nu_correct.mni.13482/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.13482/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/sub002/mri
- cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.13482/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.13482/ones.mgz
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- input ./tmp.mri_nu_correct.mni.13482/nu2.mnc
- frame 0
- nErode3d 0
- nErode2d 0
- output ./tmp.mri_nu_correct.mni.13482/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.13482/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.13482/sum.junk --avgwf ./tmp.mri_nu_correct.mni.13482/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.13482/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.13482/sum.junk --avgwf ./tmp.mri_nu_correct.mni.13482/input.mean.dat
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.13482/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.13482/input.mean.dat
- mri_segstats done
- mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.13482/ones.mgz --i ./tmp.mri_nu_correct.mni.13482/nu2.mnc --sum ./tmp.mri_nu_correct.mni.13482/sum.junk --avgwf ./tmp.mri_nu_correct.mni.13482/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.13482/ones.mgz --i ./tmp.mri_nu_correct.mni.13482/nu2.mnc --sum ./tmp.mri_nu_correct.mni.13482/sum.junk --avgwf ./tmp.mri_nu_correct.mni.13482/output.mean.dat
- sysname Linux
- hostname snake5
- machine x86_64
- user fkaule
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.13482/ones.mgz
- Loading ./tmp.mri_nu_correct.mni.13482/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.13482/output.mean.dat
- mri_segstats done
- mris_calc -o ./tmp.mri_nu_correct.mni.13482/nu2.mnc ./tmp.mri_nu_correct.mni.13482/nu2.mnc mul .95897357684828611735
- mri_convert ./tmp.mri_nu_correct.mni.13482/nu2.mnc nu.mgz --like orig.mgz
- mri_convert ./tmp.mri_nu_correct.mni.13482/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.13482/nu2.mnc...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, 4.19095e-09, 0)
- j_ras = (0, 1.49012e-08, -1)
- k_ras = (0, 1, 0)
- 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 (12, 186) to ( 3, 110)
-
-
- Thu Aug 8 11:00:37 CEST 2013
- mri_nu_correct.mni done
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