def __freesurferToDWITransformation(self, source, reference, extraArgs):
dwiToFreesurferMatrix = "dwiToFreesurfer_transformation.mat"
freesurferToDWIMatrix = "freesurferToDWI_transformation.mat"
cmd = "flirt -in {} -ref {} -omat {} {}".format(source, reference, dwiToFreesurferMatrix, extraArgs)
self.launchCommand(cmd)
mriutil.invertMatrix(dwiToFreesurferMatrix, freesurferToDWIMatrix)
return freesurferToDWIMatrix
def __freesurferToDWITransformation(self, source, reference, extraArgs):
dwiToFreesurferMatrix = "dwiToFreesurfer_transformation.mat"
freesurferToDWIMatrix = "freesurferToDWI_transformation.mat"
cmd = "flirt -in {} -ref {} -omat {} {}".format(
source, reference, dwiToFreesurferMatrix, extraArgs)
self.launchCommand(cmd)
mriutil.invertMatrix(dwiToFreesurferMatrix, freesurferToDWIMatrix)
return freesurferToDWIMatrix
def __computeFieldmap(self, dwi, bVals, mag, phase, norm, parcellationMask, freesurferAnat):
# extract a b0 from the dwi image
b0 = os.path.join(self.workingDir, os.path.basename(dwi).replace(self.get("prefix", 'dwi'), "b0_fieldmap_tmp"))
self.info(mriutil.extractFirstB0FromDwi(dwi, b0, bVals))
self.info("rescaling the phase image")
phaseRescale = self.__rescaleFieldMap(phase)
self.info('Coregistring magnitude image with the anatomical image produce by freesurfer')
fieldmapToAnat = self.__coregisterFieldmapToAnat(mag, freesurferAnat)
extraArgs = " -dof 6 "
if self.get("methodology", "intrasession"):
extraArgs += " -usesqform -dof 6"
interpolateMask, fm2anat, anat2fm = mriutil.computeDwiMaskFromFreesurfer(
mag,
norm,
parcellationMask,
self.buildName(parcellationMask, 'interpolate'),
extraArgs)
self.info('Resampling the anatomical mask into the phase image space')
# interpolateMask = self.__interpolateAnatMaskToFieldmap(anat, phaseRescale, invertFielmapToAnat, mask)
fieldmap = self.__computePhaseFieldmap(phaseRescale, interpolateMask)
self.info('Generate a lossy magnitude file with signal loss and distortion')
lossy = self.__simulateLossyMap(fieldmap, interpolateMask)
magnitudeMask = self.__computeMap(mag, interpolateMask, 'brain')
lossyMagnitude = self.__computeMap(magnitudeMask, lossy, 'lossy')
warped = self.__computeForwardDistorsion(fieldmap, lossyMagnitude, interpolateMask)
self.info('Coregister the simulated lossy fieldmap with the EPI')
matrixName = self.get("epiTo_b0fm")
self.__coregisterEpiLossyMap(b0, warped, matrixName, lossy)
self.info('Reslice magnitude and fieldmap in the EPI space')
invertMatrixName = self.buildName(matrixName, 'inverse', 'mat')
self.info(mriutil.invertMatrix(matrixName, invertMatrixName))
magnitudeIntoDwiSpace = self.__interpolateFieldmapInEpiSpace(warped, b0, invertMatrixName)
magnitudeIntoDwiSpaceMask = self.__mask(parcellationMask, b0, anat2fm, invertMatrixName)
interpolateFieldmap = self.__interpolateFieldmapInEpiSpace(fieldmap, b0, invertMatrixName)
self.info('Create the shift map')
saveshift = self.__performDistortionCorrection(b0, interpolateFieldmap, magnitudeIntoDwiSpaceMask)
self.info('Perform distortion correction of EPI data')
dwiUnwarp = self.__performDistortionCorrectionToDWI(dwi, magnitudeIntoDwiSpaceMask, saveshift)
return dwiUnwarp
def __computeFieldmap(self, dwi, bVals, mag, phase, norm, parcellationMask,
freesurferAnat):
# extract a b0 from the dwi image
b0 = os.path.join(
self.workingDir,
os.path.basename(dwi).replace(self.get("prefix", 'dwi'),
"b0_fieldmap_tmp"))
self.info(mriutil.extractFirstB0FromDwi(dwi, b0, bVals))
self.info("rescaling the phase image")
phaseRescale = self.__rescaleFieldMap(phase)
self.info(
'Coregistring magnitude image with the anatomical image produce by freesurfer'
)
fieldmapToAnat = self.__coregisterFieldmapToAnat(mag, freesurferAnat)
extraArgs = " -dof 6 "
if self.get("methodology", "intrasession"):
extraArgs += " -usesqform -dof 6"
interpolateMask = mriutil.computeDwiMaskFromFreesurfer(
mag, norm, parcellationMask,
self.buildName(parcellationMask, 'interpolate'), extraArgs)
self.info('Resampling the anatomical mask into the phase image space')
# interpolateMask = self.__interpolateAnatMaskToFieldmap(anat, phaseRescale, invertFielmapToAnat, mask)
fieldmap = self.__computePhaseFieldmap(phaseRescale, interpolateMask)
self.info(
'Generate a lossy magnitude file with signal loss and distortion')
lossy = self.__simulateLossyMap(fieldmap, interpolateMask)
magnitudeMask = self.__computeMap(mag, interpolateMask, 'brain')
lossyMagnitude = self.__computeMap(magnitudeMask, lossy, 'lossy')
warped = self.__computeForwardDistorsion(fieldmap, lossyMagnitude,
interpolateMask)
self.info('Coregister the simulated lossy fieldmap with the EPI')
matrixName = self.get("epiTo_b0fm")
self.__coregisterEpiLossyMap(b0, warped, matrixName, lossy)
self.info('Reslice magnitude and fieldmap in the EPI space')
invertMatrixName = self.buildName(matrixName, 'inverse', 'mat')
self.info(mriutil.invertMatrix(matrixName, invertMatrixName))
magnitudeIntoDwiSpace = self.__interpolateFieldmapInEpiSpace(
warped, b0, invertMatrixName)
magnitudeIntoDwiSpaceMask = self.__mask(magnitudeIntoDwiSpace)
interpolateFieldmap = self.__interpolateFieldmapInEpiSpace(
fieldmap, b0, invertMatrixName)
self.info('Create the shift map')
saveshift = self.__performDistortionCorrection(
b0, interpolateFieldmap, magnitudeIntoDwiSpaceMask)
self.info('Perform distortion correction of EPI data')
dwiUnwarp = self.__performDistortionCorrectionToDWI(
dwi, magnitudeIntoDwiSpaceMask, saveshift)
return dwiUnwarp
