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- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051179/mri
- /pasteur/homes/ntraut/bin/freesurfer-6.0.0/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 1.27 2016/02/26 16:19:49 mreuter Exp $
- Linux tars-567 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
- Sat Oct 7 19:17:07 CEST 2017
- Program nu_correct, built from:
- Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
- tmpdir is ./tmp.mri_nu_correct.mni.29294
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051179/mri
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.29294/nu0.mnc -odt float
- mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.29294/nu0.mnc -odt float
- $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
- reading from orig.mgz...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, 0, 0)
- j_ras = (0, 0, -1)
- k_ras = (0, 1, 0)
- changing data type from uchar to float (noscale = 0)...
- writing to ./tmp.mri_nu_correct.mni.29294/nu0.mnc...
-
- --------------------------------------------------------
- Iteration 1 Sat Oct 7 19:17:10 CEST 2017
- nu_correct -clobber ./tmp.mri_nu_correct.mni.29294/nu0.mnc ./tmp.mri_nu_correct.mni.29294/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.29294/0/
- [ntraut@tars-567:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051179/mri/] [2017-10-07 19:17:10] running:
- /pasteur/homes/ntraut/bin/freesurfer-6.0.0/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 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.29294/0/ ./tmp.mri_nu_correct.mni.29294/nu0.mnc ./tmp.mri_nu_correct.mni.29294/nu1.imp
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Number of iterations: 9
- CV of field change: 0.000991317
-
-
- --------------------------------------------------------
- Iteration 2 Sat Oct 7 19:17:48 CEST 2017
- nu_correct -clobber ./tmp.mri_nu_correct.mni.29294/nu1.mnc ./tmp.mri_nu_correct.mni.29294/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.29294/1/
- [ntraut@tars-567:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051179/mri/] [2017-10-07 19:17:48] running:
- /pasteur/homes/ntraut/bin/freesurfer-6.0.0/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 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.29294/1/ ./tmp.mri_nu_correct.mni.29294/nu1.mnc ./tmp.mri_nu_correct.mni.29294/nu2.imp
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Number of iterations: 9
- CV of field change: 0.000978003
-
-
-
- mri_binarize --i ./tmp.mri_nu_correct.mni.29294/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.29294/ones.mgz
- $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
- cwd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051179/mri
- cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.29294/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.29294/ones.mgz
- sysname Linux
- hostname tars-567
- machine x86_64
- user ntraut
- input ./tmp.mri_nu_correct.mni.29294/nu2.mnc
- frame 0
- nErode3d 0
- nErode2d 0
- output ./tmp.mri_nu_correct.mni.29294/ones.mgz
- Binarizing based on threshold
- min -1
- max +infinity
- binval 1
- binvalnot 0
- fstart = 0, fend = 0, nframes = 1
- Found 16777216 values in range
- Counting number of voxels in first frame
- Found 16777216 voxels in final mask
- Count: 16777216 16777216.000000 16777216 100.000000
- mri_binarize done
- mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.29294/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.29294/sum.junk --avgwf ./tmp.mri_nu_correct.mni.29294/input.mean.dat
- $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
- cwd
- cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.29294/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.29294/sum.junk --avgwf ./tmp.mri_nu_correct.mni.29294/input.mean.dat
- sysname Linux
- hostname tars-567
- machine x86_64
- user ntraut
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.29294/ones.mgz
- Loading orig.mgz
- Voxel Volume is 1 mm^3
- Generating list of segmentation ids
- Found 1 segmentations
- Computing statistics for each segmentation
- Reporting on 1 segmentations
- Using PrintSegStat
- Computing spatial average of each frame
- 0
- Writing to ./tmp.mri_nu_correct.mni.29294/input.mean.dat
- mri_segstats done
- mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.29294/ones.mgz --i ./tmp.mri_nu_correct.mni.29294/nu2.mnc --sum ./tmp.mri_nu_correct.mni.29294/sum.junk --avgwf ./tmp.mri_nu_correct.mni.29294/output.mean.dat
- $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
- cwd
- cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.29294/ones.mgz --i ./tmp.mri_nu_correct.mni.29294/nu2.mnc --sum ./tmp.mri_nu_correct.mni.29294/sum.junk --avgwf ./tmp.mri_nu_correct.mni.29294/output.mean.dat
- sysname Linux
- hostname tars-567
- machine x86_64
- user ntraut
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.29294/ones.mgz
- Loading ./tmp.mri_nu_correct.mni.29294/nu2.mnc
- Voxel Volume is 1 mm^3
- Generating list of segmentation ids
- Found 1 segmentations
- Computing statistics for each segmentation
- Reporting on 1 segmentations
- Using PrintSegStat
- Computing spatial average of each frame
- 0
- Writing to ./tmp.mri_nu_correct.mni.29294/output.mean.dat
- mri_segstats done
- mris_calc -o ./tmp.mri_nu_correct.mni.29294/nu2.mnc ./tmp.mri_nu_correct.mni.29294/nu2.mnc mul 1.04195414073268254302
- mri_convert ./tmp.mri_nu_correct.mni.29294/nu2.mnc nu.mgz --like orig.mgz
- mri_convert.bin ./tmp.mri_nu_correct.mni.29294/nu2.mnc nu.mgz --like orig.mgz
- $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
- reading from ./tmp.mri_nu_correct.mni.29294/nu2.mnc...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, 0, 0)
- j_ras = (0, 0, -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 (10, 112) to ( 3, 110)
-
-
- Sat Oct 7 19:19:00 CEST 2017
- mri_nu_correct.mni done
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