def __oddEvenNumberOfSlices(self, *args):
"""return a list of images that will count a odd number of slices in z direction
If an even number of slices is found, the upper volume will be remove
Args:
*args: a list of images
Returns:
a list of images stripped
"""
output = []
for image in args:
if image:
try:
zDims = int(mriutil.getMriDimensions(image)[2])
if zDims % 2 == 1:
target = self.buildName(image, "subset")
mriutil.extractSubVolume(image, target, '+2',
"0:{}".format(zDims - 2),
self.getNTreadsMrtrix())
output.append(target)
else:
output.append(image)
except ValueError:
output.append(image)
else:
output.append(False)
return output
def __oddEvenNumberOfSlices(self, *args):
"""return a list of images that will count a odd number of slices in z direction
If an even number of slices is found, the upper volume will be remove
Args:
*args: a list of images
Returns:
a list of images stripped
"""
output = []
for image in args:
if image:
try:
zDims = int(mriutil.getMriDimensions(image)[2])
if zDims%2 == 1:
target = self.buildName(image, "subset")
mriutil.extractSubVolume(image, target, '+2',"0:{}".format(zDims-2), self.getNTreadsMrtrix())
output.append(target)
else:
output.append(image)
except ValueError:
output.append(image)
else:
output.append(False)
return output
def __extractB0SubVolumeFromDWI(self, source):
"""Perform an extraction of a subset of the source image
Args:
source: The input DWI image
Returns:
The resulting file name
"""
self.info("Launch sub volume extraction from mrtrix")
target = os.path.join(self.workingDir, os.path.basename(source).replace(self.config.get("prefix",'dwi'),self.config.get("prefix",'b0')))
extractAtAxis = self.get('extract_at_axis')
if extractAtAxis not in ["1", "2", "3"]:
self.error('extract_at_axis must be value of 1 or 2 or 3, found {}'.format(extractAtAxis))
#make sure that we do not extract a volumes outside of the dimension
self.info(mriutil.extractSubVolume(source,
target,
extractAtAxis,
self.get("extract_at_coordinate"),
self.getNTreadsMrtrix()))
self.info("End extraction from mrtrix")
return target
def __extractB0SubVolumeFromDWI(self, source):
"""Perform an extraction of a subset of the source image
Args:
source: The input DWI image
Returns:
The resulting file name
"""
self.info("Launch sub volume extraction from mrtrix")
target = os.path.join(
self.workingDir,
os.path.basename(source).replace(self.config.get("prefix", 'dwi'),
self.config.get("prefix", 'b0')))
extractAtAxis = self.get('extract_at_axis')
if extractAtAxis not in ["1", "2", "3"]:
self.error(
'extract_at_axis must be value of 1 or 2 or 3, found {}'.
format(extractAtAxis))
#make sure that we do not extract a volumes outside of the dimension
self.info(
mriutil.extractSubVolume(source, target, extractAtAxis,
self.get("extract_at_coordinate"),
self.getNTreadsMrtrix()))
self.info("End extraction from mrtrix")
return target
def __extractWhiteMatterFrom5tt(self, source):
"""Extract the white matter part from the act
Args:
An 5tt image
Returns:
the resulting file filename
"""
target = self.buildName(source, ["wm", "mask"])
self.info(
mriutil.extractSubVolume(source, target,
self.get('act_extract_at_axis'),
self.get("act_extract_at_coordinate"),
self.getNTreadsMrtrix()))
return target
def __extractWhiteMatterFrom5tt(self, source):
"""Extract the white matter part from the act
Args:
An 5tt image
Returns:
the resulting file filename
"""
target = self.buildName(source, ["wm", "mask"])
self.info(mriutil.extractSubVolume(source,
target,
self.get('act_extract_at_axis'),
self.get("act_extract_at_coordinate"),
self.getNTreadsMrtrix()))
return target
def __extractB0APSubVolumeFromDWI(self, source):
self.info("Launch sub volume extraction from mrtrix")
#rename the file B0
target = os.path.join(
self.workingDir,
os.path.basename(source).replace(self.config.get("prefix", 'dwi'),
self.config.get("prefix",
'b0AP')))
extractAtAxis = self.get('b0AP_extract_at_axis')
if extractAtAxis not in ["1", "2", "3"]:
self.error(
'extract_at_axis must be value of 1 or 2 or 3, found {}'.
format(extractAtAxis))
#make sure that we do not extract a volumes outside of the dimension
self.info(
mriutil.extractSubVolume(source, target, extractAtAxis,
self.get("b0AP_extract_at_coordinate"),
self.getNTreadsMrtrix()))
self.info("End extraction from mrtrix")
return target
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')))
# Extract first n b0s from DWI
self.info(mriutil.extractFirstB0sFromDWI(dwi, b0, bVals, self.getNTreadsMrtrix()))
# Get number of b0s extracted from DWI
tDims = int(mriutil.getMriDimensions(b0)[3])
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
# Extract same number of volumes b0PA
try:
b0APDim = int(mriutil.getMriDimensions(b0AP)[3])
target = os.path.join(self.workingDir,
os.path.basename(dwi).replace(self.get("prefix", 'dwi'), self.get("prefix", 'b0_ap')))
self.info(mriutil.extractSubVolume(b0AP, target, '+3', "{}:{}".format(b0APDim-tDims, b0APDim-1 ), self.getNTreadsMrtrix()))
b0AP = target
except:
b0APDim = 1
if self.get("phase_enc_dir") == "1" and b0PA and b0AP is False:
b0AP = b0
# Extract same number of volumes b0PA
try:
b0PADim = int(mriutil.getMriDimensions(b0PA)[3])
target = os.path.join(self.workingDir,
os.path.basename(dwi).replace(self.get("prefix", 'dwi'), self.get("prefix", 'b0_pa')))
self.info(mriutil.extractSubVolume(b0PA, target, '+3', "{}:{}".format(b0PADim-tDims, b0PADim-1), self.getNTreadsMrtrix()))
b0PA = target
except:
b0PADim = 1
topupConfigFile = self.__checkOddEvenNumberOfSlices(dwi)
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"))
self.dimB0s = [mriutil.getNbDirectionsFromDWI(b0PA), mriutil.getNbDirectionsFromDWI(b0AP)]
elif self.get("phase_enc_dir") == "1":
concatenateB0Image = self.__concatenateB0(b0AP, b0PA, self.buildName("b0ap_b0pa", None, "nii.gz"))
self.dimB0s = [mriutil.getNbDirectionsFromDWI(b0AP), mriutil.getNbDirectionsFromDWI(b0PA)]
if int(mriutil.getMriDimensions(dwi)[2]) % 2 == 1: # Number of slice in z axis
if 'force' not in self.get('crop'): # Use odd number
[dwi, b0, b0AP, b0PA, concatenateB0Image] = self.__cropNumberOfSlices(dwi, b0, b0AP, b0PA, concatenateB0Image)
# Select config File for topup
topupConfigFile = self.__checkOddEvenNumberOfSlices(dwi)
# Create the acquisition parameter file
acqpTopup = self.__createAcquisitionParameterFile('topup')
# Run topup on concatenate B0 image
[topupBaseName, topupImage] = self.__topup(concatenateB0Image, acqpTopup, topupConfigFile)
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, _notUsed_a, _notUsed_b = 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, bEnc)
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'))
