Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Correction to Philips fieldmap preprocessing #271

Merged
merged 4 commits into from
Jul 24, 2023
Merged

Correction to Philips fieldmap preprocessing #271

Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
7bea1e4
implemented the proper Philips fieldmap preprocessing and distort. co…
May 4, 2023
c34e9e0
Merge remote-tracking branch 'upstream/master' into philips_fieldmap_fix
axkralj990 Jul 19, 2023
0afe56d
remove debug/support statements from fieldmap scripts
axkralj990 Jul 19, 2023
cc24fd2
fix the indentation incosistencies with tabs-spaces throughout FieldM…
axkralj990 Jul 20, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
101 changes: 56 additions & 45 deletions global/scripts/FieldMapPreprocessingAll.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -17,24 +17,24 @@ PHILIPS_METHOD_OPT="PhilipsFieldMap"
# ------------------------------------------------------------------------------

if [ -z "${HCPPIPEDIR}" ]; then
echo "$(basename ${0}): ABORTING: HCPPIPEDIR environment variable must be set"
exit 1
echo "$(basename ${0}): ABORTING: HCPPIPEDIR environment variable must be set"
exit 1
else
echo "$(basename ${0}): HCPPIPEDIR: ${HCPPIPEDIR}"
echo "$(basename ${0}): HCPPIPEDIR: ${HCPPIPEDIR}"
fi

if [ -z "${FSLDIR}" ]; then
echo "$(basename ${0}): ABORTING: FSLDIR environment variable must be set"
exit 1
echo "$(basename ${0}): ABORTING: FSLDIR environment variable must be set"
exit 1
else
echo "$(basename ${0}): FSLDIR: ${FSLDIR}"
echo "$(basename ${0}): FSLDIR: ${FSLDIR}"
fi

if [ -z "${HCPPIPEDIR_Global}" ]; then
echo "$(basename ${0}): ABORTING: HCPPIPEDIR_Global environment variable must be set"
exit 1
echo "$(basename ${0}): ABORTING: HCPPIPEDIR_Global environment variable must be set"
exit 1
else
echo "$(basename ${0}): HCPPIPEDIR_Global: ${HCPPIPEDIR_Global}"
echo "$(basename ${0}): HCPPIPEDIR_Global: ${HCPPIPEDIR_Global}"
fi

################################################ SUPPORT FUNCTIONS ##################################################
Expand Down Expand Up @@ -62,10 +62,10 @@ getopt1() {
sopt="$1"
shift 1
for fn in $@ ; do
if [ `echo $fn | grep -- "^${sopt}=" | wc -w` -gt 0 ] ; then
echo $fn | sed "s/^${sopt}=//"
return 0
fi
if [ `echo $fn | grep -- "^${sopt}=" | wc -w` -gt 0 ] ; then
echo $fn | sed "s/^${sopt}=//"
return 0
fi
done
}

Expand Down Expand Up @@ -101,8 +101,8 @@ case $DistortionCorrection in
# --------------------------------------

MagnitudeInputName=`getopt1 "--fmapmag" $@`
PhaseInputName=`getopt1 "--fmapphase" $@`
DeltaTE=`getopt1 "--echodiff" $@`
PhaseInputName=`getopt1 "--fmapphase" $@`
DeltaTE=`getopt1 "--echodiff" $@`

;;

Expand All @@ -123,7 +123,7 @@ case $DistortionCorrection in
# --------------------------------------

MagnitudeInputName=`getopt1 "--fmapmag" $@`
PhaseInputName=`getopt1 "--fmapphase" $@`
PhaseInputName=`getopt1 "--fmapphase" $@`
DeltaTE=`getopt1 "--echodiff" $@`

;;
Expand Down Expand Up @@ -164,10 +164,10 @@ case $DistortionCorrection in
# -- Siemens Gradient Echo Field Maps --
# --------------------------------------

${FSLDIR}/bin/fslmaths ${MagnitudeInputName} -Tmean ${WD}/Magnitude
${FSLDIR}/bin/bet ${WD}/Magnitude ${WD}/Magnitude_brain -f 0.35 -m #Brain extract the magnitude image
${FSLDIR}/bin/imcp ${PhaseInputName} ${WD}/Phase
${FSLDIR}/bin/fsl_prepare_fieldmap SIEMENS ${WD}/Phase ${WD}/Magnitude_brain ${WD}/FieldMap ${DeltaTE}
${FSLDIR}/bin/fslmaths ${MagnitudeInputName} -Tmean ${WD}/Magnitude
${FSLDIR}/bin/bet ${WD}/Magnitude ${WD}/Magnitude_brain -f 0.35 -m #Brain extract the magnitude image
${FSLDIR}/bin/imcp ${PhaseInputName} ${WD}/Phase
${FSLDIR}/bin/fsl_prepare_fieldmap SIEMENS ${WD}/Phase ${WD}/Magnitude_brain ${WD}/FieldMap ${DeltaTE}

;;

Expand All @@ -177,11 +177,11 @@ case $DistortionCorrection in
# -- General Electric Gradient Echo Field Maps --
# -----------------------------------------------

${FSLDIR}/bin/fslsplit ${GEB0InputName} # split image into vol0000=fieldmap and vol0001=magnitude
mv vol0000.nii.gz ${WD}/FieldMap_deg.nii.gz
mv vol0001.nii.gz ${WD}/Magnitude.nii.gz
${FSLDIR}/bin/bet ${WD}/Magnitude ${WD}/Magnitude_brain -f 0.35 -m #Brain extract the magnitude image
${FSLDIR}/bin/fslmaths ${WD}/FieldMap_deg.nii.gz -mul 6.28 ${WD}/FieldMap.nii.gz
${FSLDIR}/bin/fslsplit ${GEB0InputName} # split image into vol0000=fieldmap and vol0001=magnitude
mv vol0000.nii.gz ${WD}/FieldMap_deg.nii.gz
mv vol0001.nii.gz ${WD}/Magnitude.nii.gz
${FSLDIR}/bin/bet ${WD}/Magnitude ${WD}/Magnitude_brain -f 0.35 -m #Brain extract the magnitude image
${FSLDIR}/bin/fslmaths ${WD}/FieldMap_deg.nii.gz -mul 6.28 ${WD}/FieldMap.nii.gz

;;

Expand All @@ -191,26 +191,37 @@ case $DistortionCorrection in
# -- Philips Gradient Echo Field Maps --
# --------------------------------------

${FSLDIR}/bin/fslmaths ${MagnitudeInputName} -Tmean ${WD}/Magnitude
# Brain extract the magnitude image
${FSLDIR}/bin/bet ${WD}/Magnitude ${WD}/Magnitude_brain -f 0.35 -m
${FSLDIR}/bin/fslmaths ${WD}/Magnitude_brain -ero ${WD}/Magnitude_brain_ero
rm ${WD}/Magnitude_brain.nii.gz
mv ${WD}/Magnitude_brain_ero.nii.gz ${WD}/Magnitude_brain.nii.gz

# Create a binary brain mask
${FSLDIR}/bin/fslmaths ${WD}/Magnitude_brain.nii.gz -thr 0.00000001 -bin ${WD}/Mask_brain.nii.gz
# Convert fieldmap to radians
$FSLDIR/bin/fslmaths ${PhaseInputName} -mul 3.14159 -div 180 -mas ${WD}/Mask_brain.nii.gz ${WD}/FieldMap_rad -odt float
# Unwrap fieldmap
$FSLDIR/bin/prelude -p ${WD}/FieldMap_rad -a ${WD}/Magnitude_brain.nii.gz -m ${WD}/Mask_brain.nii.gz -o ${WD}/FieldMap_rad_unwrapped -v
# Convert to rads/sec (DeltaTE is echo time difference)
asym=`echo ${DeltaTE} / 1000 | bc -l`
$FSLDIR/bin/fslmaths ${WD}/FieldMap_rad_unwrapped -div $asym ${WD}/FieldMap_rps -odt float
# Call FUGUE to extrapolate from mask (fill holes, etc)
$FSLDIR/bin/fugue --loadfmap=${WD}/FieldMap_rps --mask=${WD}/Mask_brain.nii.gz --savefmap=${WD}/FieldMap.nii.gz
# Demean the image (avoid voxel translation)
$FSLDIR/bin/fslmaths ${WD}/FieldMap.nii.gz -sub `${FSLDIR}/bin/fslstats ${WD}/FieldMap.nii.gz -k ${WD}/Mask_brain.nii.gz -P 50` -mas ${WD}/Mask_brain.nii.gz ${WD}/FieldMap.nii.gz -odt float
${FSLDIR}/bin/fslmaths ${MagnitudeInputName} -Tmean ${WD}/Magnitude
# Brain extract the magnitude image
${FSLDIR}/bin/bet ${WD}/Magnitude ${WD}/Magnitude_brain -f 0.35 -m
${FSLDIR}/bin/fslmaths ${WD}/Magnitude_brain -ero ${WD}/Magnitude_brain_ero
rm ${WD}/Magnitude_brain.nii.gz
mv ${WD}/Magnitude_brain_ero.nii.gz ${WD}/Magnitude_brain.nii.gz

# Take the absolute value of the magnitude data (some images used negative values for the coding)
${FSLDIR}/bin/fslmaths ${WD}/Magnitude_brain.nii.gz -abs ${WD}/Magnitude_brain.nii.gz
# Create a binary brain mask
${FSLDIR}/bin/fslmaths ${WD}/Magnitude_brain.nii.gz -thr 0.00000001 -bin ${WD}/Mask_brain.nii.gz
# Convert fieldmap in Hz to rad/s
$FSLDIR/bin/fslmaths ${PhaseInputName} -mul 6.28318 -mas ${WD}/Mask_brain.nii.gz ${WD}/FieldMap_rad_per_s -odt float

# If echodiff was passed unwrap the fieldmap
if [ ! -z $DeltaTE ] && [ $DeltaTE != "NONE" ]
then
# DeltaTE is echo time difference in ms
asym=`echo ${DeltaTE} / 1000 | bc -l`
# Convert fieldmap in rad/s back to phasediff image in rad for unwrapping
$FSLDIR/bin/fslmaths ${WD}/FieldMap_rad_per_s -mul $asym -mas ${WD}/Mask_brain.nii.gz ${WD}/Phasediff_rad -odt float
# Unwrap fieldmap
$FSLDIR/bin/prelude -p ${WD}/Phasediff_rad -a ${WD}/Magnitude_brain.nii.gz -m ${WD}/Mask_brain.nii.gz -o ${WD}/Phasediff_rad_unwrapped -v
# Convert to fiedlmap in rads/sec
$FSLDIR/bin/fslmaths ${WD}/Phasediff_rad_unwrapped -div $asym ${WD}/FieldMap_rad_per_s -odt float
fi

# Call FUGUE to extrapolate from mask (fill holes, etc)
$FSLDIR/bin/fugue --loadfmap=${WD}/FieldMap_rad_per_s --mask=${WD}/Mask_brain.nii.gz --savefmap=${WD}/FieldMap.nii.gz
# Demean the image (avoid voxel translation)
$FSLDIR/bin/fslmaths ${WD}/FieldMap.nii.gz -sub `${FSLDIR}/bin/fslstats ${WD}/FieldMap.nii.gz -k ${WD}/Mask_brain.nii.gz -P 50` -mas ${WD}/Mask_brain.nii.gz ${WD}/FieldMap.nii.gz -odt float

;;

Expand Down