def __produceEncodingFiles(self, bEncs, bVecs, bVals, dwi):
self.info("Produce .b .bvals and .bvecs gradient file if not existing")
if not bEncs:
bEncs = self.buildName(dwi, None, "b")
self.info(mriutil.fslToMrtrixEncoding(dwi, bVecs, bVals, bEncs))
else:
self.info("Linking {} to {}".format(
bEncs, util.symlink(bEncs, self.workingDir)))
if not bVecs or not bVals:
self.info(
mriutil.mrtrixToFslEncoding(dwi, bEncs,
self.buildName(dwi, None, "bvecs"),
self.buildName(dwi, None,
"bvals")))
else:
self.info("Linking {} to {}".format(
bVecs, util.symlink(bVecs, self.workingDir)))
self.info("Linking {} to {}".format(
bVals, util.symlink(bVals, self.workingDir)))
return (self.getImage('grad', None,
'b'), self.getImage('grad', None, 'bvecs'),
self.getImage('grad', None, 'bvals'))
def __produceEncodingFiles(self, bEncs, bVecs, bVals, dwi):
self.info("Produce .b .bvals and .bvecs gradient file if not existing")
if not bEncs:
bEncs = self.buildName(dwi, None, "b")
self.info(mriutil.fslToMrtrixEncoding(dwi, bVecs, bVals, bEncs))
else:
self.info("Linking {} to {}".format(bEncs, util.symlink(bEncs, self.workingDir)))
if not bVecs or not bVals:
self.info(mriutil.mrtrixToFslEncoding(dwi,
bEncs,
self.buildName(dwi, None, "bvecs"),
self.buildName(dwi, None, "bvals")))
else:
self.info("Linking {} to {}".format(bVecs, util.symlink(bVecs, self.workingDir)))
self.info("Linking {} to {}".format(bVals, util.symlink(bVals, self.workingDir)))
return (self.getImage('grad', None, 'b'),
self.getImage('grad', None, 'bvecs'),
self.getImage('grad', None, 'bvals'))
def implement(self):
dwi = self.getDenoisingImage('dwi', 'denoise')
if not dwi:
dwi = self.getPreparationImage('dwi')
b0AP = self.getPreparationImage('b0_ap')
b0PA = self.getPreparationImage('b0_pa')
bEnc = self.getPreparationImage('grad', None, 'b')
bVals = self.getPreparationImage('grad', None, 'bvals')
bVecs = self.getPreparationImage('grad', None, 'bvecs')
norm = self.getParcellationImage('norm')
parcellationMask = self.getParcellationImage('mask')
# Fieldmap only
mag = self.getPreparationImage("mag")
phase = self.getPreparationImage("phase")
freesurferAnat = self.getParcellationImage('anat', 'freesurfer')
self.info("extract b0 image from the dwi")
b0 = os.path.join(
self.workingDir,
os.path.basename(dwi).replace(self.get("prefix", 'dwi'),
self.get("prefix", 'b0')))
self.info(mriutil.extractFirstB0FromDwi(dwi, b0, bVals))
self.info(
"look if all images have the same voxel size and dimension scale")
self.__validateSizeAndDimension(dwi, b0, b0AP, b0PA)
# Generate a missing b0 image if we could. --> 0 = P>>A, 1 = A>>P
if self.get("phase_enc_dir") == "0" and b0AP and b0PA is False:
b0PA = b0
if self.get("phase_enc_dir") == "1" and b0PA and b0AP is False:
b0AP = b0
[dwi, b0, b0AP,
b0PA] = self.__oddEvenNumberOfSlices(dwi, b0, b0AP, b0PA)
self.set('method', None)
if b0AP is False or b0PA is False:
topupBaseName = None
b0Image = b0
self.set('method', 'fieldmap')
else:
# Concatenate B0 image together
if self.get("phase_enc_dir") == "0":
concatenateB0Image = self.__concatenateB0(
b0PA, b0AP, self.buildName("b0pa_b0ap", None, "nii.gz"))
elif self.get("phase_enc_dir") == "1":
concatenateB0Image = self.__concatenateB0(
b0AP, b0PA, self.buildName("b0ap_b0pa", None, "nii.gz"))
# Create the acquisition parameter file
acqpTopup = self.__createAcquisitionParameterFile('topup')
# Run topup on concatenate B0 image
[topupBaseName,
topupImage] = self.__topup(concatenateB0Image, acqpTopup,
self.get('b02b0_filename'))
b0Image = self.__fslmathsTmean(
os.path.join(self.workingDir, topupImage))
self.set('method', 'topup')
self.info("create a suitable mask for the dwi")
extraArgs = " -dof 6 " # same subject
if self.get("methodology", "intrasession"):
extraArgs += " -usesqform "
mask = mriutil.computeDwiMaskFromFreesurfer(
b0Image, norm, parcellationMask,
self.buildName(parcellationMask, 'temporary'), extraArgs)
# Create the acquisition parameter file for eddy
acqpEddy = self.__createAcquisitionParameterFile('eddy')
# Create an index file
indexFile = self.__createIndexFile(mriutil.getNbDirectionsFromDWI(dwi))
outputImage = self.__correctionEddy(dwi, mask, topupBaseName,
indexFile, acqpEddy, bVecs, bVals)
eddyParameterFiles = self.getImage('dwi', None, 'eddy_parameters')
if eddyParameterFiles:
self.info(
"Apply eddy movement correction to gradient encodings directions"
)
bEnc = mriutil.applyGradientCorrection(
bEnc, eddyParameterFiles,
self.buildName(outputImage, None, 'b'))
self.info(
mriutil.mrtrixToFslEncoding(
outputImage, bEnc,
self.buildName(outputImage, None, 'bvecs'),
self.buildName(outputImage, None, 'bvals')))
# Proceed with fieldmap if provided
if mag and phase and not self.__topupCorrection:
# OutputImage is now used for fieldmap correction
outputImage = self.__computeFieldmap(outputImage, bVals, mag,
phase, norm, parcellationMask,
freesurferAnat)
self.set('method', 'fieldmap')
# Produce a valid b0 and mask for QA
b0Corrected = self.buildName(b0, 'corrected')
self.info(
mriutil.extractFirstB0FromDwi(outputImage, b0Corrected, bVals))
maskCorrected = mriutil.computeDwiMaskFromFreesurfer(
b0Corrected, norm, parcellationMask,
self.buildName(parcellationMask, 'corrected'), extraArgs)
self.rename(outputImage, self.buildName(outputImage, 'corrected'))
def implement(self):
dwi = self.getDenoisingImage('dwi', 'denoise')
if not dwi:
dwi = self.getPreparationImage('dwi')
b0AP = self.getPreparationImage('b0_ap')
b0PA = self.getPreparationImage('b0_pa')
bEnc = self.getPreparationImage('grad', None, 'b')
bVals = self.getPreparationImage('grad', None, 'bvals')
bVecs = self.getPreparationImage('grad', None, 'bvecs')
norm = self.getParcellationImage('norm')
parcellationMask = self.getParcellationImage('mask')
# Fieldmap only
mag = self.getPreparationImage("mag")
phase = self.getPreparationImage("phase")
freesurferAnat = self.getParcellationImage('anat', 'freesurfer')
self.info("extract b0 image from the dwi")
b0 = os.path.join(self.workingDir,
os.path.basename(dwi).replace(self.get("prefix", 'dwi'), self.get("prefix", 'b0')))
self.info(mriutil.extractFirstB0FromDwi(dwi, b0, bVals))
self.info("look if all images have the same voxel size and dimension scale")
self.__validateSizeAndDimension(dwi, b0, b0AP, b0PA)
# Generate a missing b0 image if we could. --> 0 = P>>A, 1 = A>>P
if self.get("phase_enc_dir") == "0" and b0AP and b0PA is False:
b0PA = b0
if self.get("phase_enc_dir") == "1" and b0PA and b0AP is False:
b0AP = b0
[dwi, b0, b0AP, b0PA] = self.__oddEvenNumberOfSlices(dwi, b0, b0AP, b0PA)
self.set('method', None)
if b0AP is False or b0PA is False:
topupBaseName = None
b0Image = b0
self.set('method', 'fieldmap')
else:
# Concatenate B0 image together
if self.get("phase_enc_dir") == "0":
concatenateB0Image = self.__concatenateB0(b0PA, b0AP, self.buildName("b0pa_b0ap", None, "nii.gz"))
elif self.get("phase_enc_dir") == "1":
concatenateB0Image = self.__concatenateB0(b0AP, b0PA, self.buildName("b0ap_b0pa", None, "nii.gz"))
# Create the acquisition parameter file
acqpTopup = self.__createAcquisitionParameterFile('topup')
# Run topup on concatenate B0 image
[topupBaseName, topupImage] = self.__topup(concatenateB0Image, acqpTopup, self.get('b02b0_filename'))
b0Image = self.__fslmathsTmean(os.path.join(self.workingDir, topupImage))
self.set('method', 'topup')
self.info("create a suitable mask for the dwi")
extraArgs = " -dof 6 " # same subject
if self.get("methodology", "intrasession"):
extraArgs += " -usesqform "
mask = mriutil.computeDwiMaskFromFreesurfer(b0Image,
norm,
parcellationMask,
self.buildName(parcellationMask, 'temporary'),
extraArgs)
# Create the acquisition parameter file for eddy
acqpEddy = self.__createAcquisitionParameterFile('eddy')
# Create an index file
indexFile = self.__createIndexFile(mriutil.getNbDirectionsFromDWI(dwi))
outputImage = self.__correctionEddy(dwi, mask, topupBaseName, indexFile, acqpEddy, bVecs, bVals)
eddyParameterFiles = self.getImage('dwi', None, 'eddy_parameters')
if eddyParameterFiles:
self.info("Apply eddy movement correction to gradient encodings directions")
bEnc = mriutil.applyGradientCorrection(bEnc, eddyParameterFiles, self.buildName(outputImage, None, 'b'))
self.info(mriutil.mrtrixToFslEncoding(outputImage,
bEnc,
self.buildName(outputImage, None, 'bvecs'),
self.buildName(outputImage, None, 'bvals')))
# Proceed with fieldmap if provided
if mag and phase and not self.__topupCorrection:
# OutputImage is now used for fieldmap correction
outputImage = self.__computeFieldmap(outputImage, bVals, mag, phase, norm, parcellationMask, freesurferAnat)
self.set('method', 'fieldmap')
# Produce a valid b0 and mask for QA
b0Corrected = self.buildName(b0, 'corrected')
self.info(mriutil.extractFirstB0FromDwi(outputImage, b0Corrected, bVals))
maskCorrected = mriutil.computeDwiMaskFromFreesurfer(b0Corrected,
norm,
parcellationMask,
self.buildName(parcellationMask, 'corrected'),
extraArgs)
self.rename(outputImage, self.buildName(outputImage, 'corrected'))
