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re-tuning N4BiasFieldCorrection parameters once more

...to avoid issues for dwi2mask subsequently.
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thijsdhollander committed Sep 27, 2017
1 parent b1ff2c3 commit df0ecd528cba733e225807c40b3a78d22416ba72
Showing with 1 addition and 1 deletion.
  1. +1 −1 bin/dwibiascorrect
@@ -108,7 +108,7 @@ elif app.args.ants:
run.command('mrconvert mean_bzero.mif mean_bzero.nii -stride +1,+2,+3')
run.command('mrconvert mask.mif mask.nii -stride +1,+2,+3')
bias_path = 'bias.nii'
run.command('N4BiasFieldCorrection -d 3 -i mean_bzero.nii -w mask.nii -o [corrected.nii,' + bias_path + '] -b [150,3] -c [1000x1000,0.0]')
run.command('N4BiasFieldCorrection -d 3 -i mean_bzero.nii -w mask.nii -o [corrected.nii,' + bias_path + '] -s 4 -b [100,3] -c [1000,0.0]')

run.command('mrcalc in.mif ' + bias_path + ' -div result.mif')
run.command('mrconvert result.mif ' + path.fromUser(app.args.output, True) + (' -force' if app.forceOverwrite else ''))

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