diff --git a/GE_dcm_to_nii.sh b/GE_dcm_to_nii.sh index f84b793..7ae347f 100755 --- a/GE_dcm_to_nii.sh +++ b/GE_dcm_to_nii.sh @@ -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 #####################################################################################