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[ENH] added additional processing for fieldmap #3

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[ENH] added additional processing for fieldmap #3

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10 changes: 10 additions & 0 deletions GE_dcm_to_nii.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -930,6 +930,16 @@ if [[ "${dcmSubSeries}" == "ia_stable_B0map" ]]; then
rm $outDir/${outBase}_master${imageExt}
# fieldmap should be a float32 not an int16
fslmaths $outDir/${outBase}${imageExt} $outDir/${outBase}${imageExt} -odt float

#Adjust the fieldMap_Hz to rad/s by multiplying by 6.28 (2*pi=6.28)
fslmaths $outDir/${outBase}${imageExt} -mul 6.28 $outDir/${outBase}_prepped${imageExt}

# https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FUGUE/Guide#Step_5_-_Regularising_the_fieldmap
# smooth (1mm), despike, median filter
fugue --loadfmap=$outDir/${outBase}_prepped${imageExt} -s 1 --savefmap=$outDir/${outBase}_prepped${imageExt}
fugue --loadfmap=$outDir/${outBase}_prepped${imageExt} --despike --savefmap=$outDir/${outBase}_prepped${imageExt}
fugue --loadfmap=$outDir/${outBase}_prepped${imageExt} -m --savefmap=$outDir/${outBase}_prepped${imageExt}

fi

#####################################################################################
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