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 __validateSizeAndDimension(self, *args):
names = []
dims = []
sizes = []
for source in args:
if source:
names.append(source)
dimensions = mriutil.getMriDimensions(source)
if len(dimensions) == 4:
dims.append([dimensions[0], dimensions[1], dimensions[2]])
else:
dims.append(dimensions)
# sourceSize sanitization
sourceSize = mriutil.getMriVoxelSize(source)
try:
sourceSize = [
"{:.1f}".format(float(val)) for val in sourceSize
]
except ValueError:
self.error("Error during sourceSize sanitization")
sizes.append(sourceSize)
if not dims[1:] == dims[:-1]:
self.error(
"Dimension for each scale mismatch found between images: {}".
format(", ".join(names)))
if not sizes[1:] == sizes[:-1]:
self.error("Voxel size mismatch found between images: {}".format(
", ".join(names)))
def __validateSizeAndDimension(self, *args):
names = []
dims = []
sizes = []
for source in args:
if source:
names.append(source)
dimensions = mriutil.getMriDimensions(source)
if len(dimensions) == 4:
dims.append([dimensions[0], dimensions[1], dimensions[2]])
else:
dims.append(dimensions)
# sourceSize sanitization
sourceSize = mriutil.getMriVoxelSize(source)
try:
sourceSize = ["{:.1f}".format(float(val)) for val in sourceSize]
except ValueError:
self.error("Error during sourceSize sanitization")
sizes.append(sourceSize)
if not dims[1:] == dims[:-1]:
self.error("Dimension for each scale mismatch found between images: {}".format(", ".join(names)))
if not sizes[1:] == sizes[:-1]:
self.error("Voxel size mismatch found between images: {}".format(", ".join(names)))
def implement(self):
dwi = self.getImage(self.dependDir, 'dwi')
b0PA = self.getImage(self.dependDir, 'b0PA')
b0AP = self.getImage(self.dependDir, 'b0AP')
bFile = self.getImage(self.dependDir, 'grad', None, 'b')
bVals = self.getImage(self.dependDir, 'grad', None, 'bval')
bVecs = self.getImage(self.dependDir, 'grad', None, 'bvec')
#make sure the 3 images have the same voxel size and dimension scale
self.__validateSizeAndDimension(dwi, b0PA, b0AP)
#make sure that the z dimension contain an odd number of slices
dwiZDims = int(mriutil.getMriDimensions(dwi)[2])
if dwiZDims%2 == 1:
dwi = self.__extractZVolumes(dwi, "0:{}".format(dwiZDims-2))
b0PA = self.__extractZVolumes(b0PA, "0:{}".format(dwiZDims-2))
b0AP = self.__extractZVolumes(b0AP, "0:{}".format(dwiZDims-2))
#concatenate B0 image together
b0Image = self.__concatenateB0(b0PA, b0AP,
os.path.join(self.workingDir, self.get('b0s_filename')))
#create an empty b02b0.cnf file
#b02b0File = os.path.join(self.workingDir, self.get('b02b0_filename'))
#open(b02b0File, 'a').close()
#create the acquisition parameter file
acqpTopup = self.__createAcquisitionParameterFile('topup')
acqpEddy = self.__createAcquisitionParameterFile('eddy')
#create an index file
indexFile = self.__createIndexFile(mriutil.getNbDirectionsFromDWI(dwi))
#Lauch topup on concatenate B0 image
[topupBaseName, topupImage] = self.__topup(b0Image, acqpTopup, self.get('b02b0_filename'))
outputFieldMask = self.__fslmaths_tmean(os.path.join(self.workingDir, topupImage))
outputFieldMaskExtracted = self.__bet(outputFieldMask)
outputEddyImage = self.__correction_eddy2(dwi,
outputFieldMaskExtracted, topupBaseName, indexFile, acqpEddy, bVecs, bVals)
self.info("Uncompressing eddy output image: {}".format(outputEddyImage))
util.gunzip(outputEddyImage)
#@TODO remove the glob and use getimage
eddyParameterFiles = glob.glob("{}/*.eddy_parameters".format(self.workingDir))
if len(eddyParameterFiles)>0:
bCorrected = mriutil.applyGradientCorrection(bFile, eddyParameterFiles.pop(0), self.workingDir)
#produce the bVal and bVec file accordingly
mriutil.bEnc2BVec(bCorrected, self.workingDir)
mriutil.bEnc2BVal(bCorrected, self.workingDir)
def __validateSizeAndDimension(self, dwi, b0PA, b0AP):
dwiDim = mriutil.getMriDimensions(dwi)
dwiVoxel = mriutil.getMriVoxelSize(dwi)
b0PADim = mriutil.getMriDimensions(b0PA)
b0PAVoxel = mriutil.getMriVoxelSize(b0PA)
b0APDim = mriutil.getMriDimensions(b0AP)
b0APVoxel = mriutil.getMriVoxelSize(b0AP)
self.info("Look if {} and {} and {} have the same voxel size".format(dwi, b0PA, b0AP))
if len(dwiVoxel) == len(b0PAVoxel) == len(b0APVoxel) == 3:
for i in range(0,len(dwiVoxel)):
if not (dwiVoxel[i] == b0PAVoxel[i] == b0APVoxel[i]):
self.error("Voxel size mismatch found at index {} for image {} {} {}".format(i, dwi, b0PA, b0AP))
else:
self.error("Found Voxel size inconsistency for image {} or {} or {}".format(dwi, b0PA, b0AP))
self.info("Look if {} and {} and {} have the same dimension for each scale".format(dwi, b0PA, b0AP))
for i in range(0,3):
if not (dwiDim[i]==b0PADim[i]==b0APDim[i]):
self.error("Dimensions mismatch found at index {} for image {} {} {}".format(i, dwi, b0PA, b0AP))
def qaSupplier(self):
"""Create and supply images for the report generated by qa task
"""
qaImages = Images()
tags = (
('anat', self.plot3dVolume, 'High resolution anatomical image'),
('dwi', self.plot4dVolume, 'Diffusion weighted image'))
tags = list(tags)
if self.getImage('b0_pa'):
if len(mriutil.getMriDimensions(self.getImage('b0_pa')))==4:
tags.append(('b0_pa', self.plot4dVolume, 'B0 PA images'))
else:
tags.append(('b0_pa', self.plot3dVolume, 'B0 PA image'))
if self.getImage('b0_ap'):
if len(mriutil.getMriDimensions(self.getImage('b0_ap')))==4:
tags.append(('b0_ap', self.plot4dVolume, 'B0 AP images'))
else:
tags.append(('b0_ap', self.plot3dVolume, 'B0 AP image'))
tags.append(('mag', self.plot3dVolume, 'Magnitude image'))
tags.append(('phase', self.plot3dVolume, 'Phase image'))
tags = tuple(tags)
for prefix, plotMethod, description in tags:
source = self.getImage(prefix)
if source:
qaImage = plotMethod(source)
qaImages.append((qaImage, description))
return qaImages
def __checkOddEvenNumberOfSlices(self, source):
"""return the config file b02b0
If an even number of slices is found, b02b0_even will be used otherwise we'll b02b0_odd
Args:
*args: a list of images
Returns:
config file b02b0
"""
zDims = int(mriutil.getMriDimensions(source)[2])
if zDims % 2 == 1:
return self.get('b02b0_odd')
else:
return self.get('b02b0_even')
def __validateSizeAndDimension(self, *args):
names = []
dims = []
sizes = []
for source in args:
if source:
names.append(source)
dimensions = mriutil.getMriDimensions(source)
if len(dimensions) == 4:
dims.append([dimensions[0], dimensions[1], dimensions[2]])
else:
dims.append(dimensions)
sizes.append(mriutil.getMriVoxelSize(source))
if not dims[1:] == dims[:-1]:
self.error("Dimension for each scale mismatch found between images: {}".format(", ".join(names)))
if not sizes[1:] == sizes[:-1]:
self.error("Voxel size mismatch found between images: {}".format(", ".join(names)))
def __correctionEddy(self, source, mask, topup, index, acqp, bVecs, bVals, bEnc):
"""Performs eddy correction on a dwi file.
Args:
source: File containing all the images to estimate distortions for
mask: Mask to indicate brain
topup: Base name for output files from topup
index: File containing indices for all volumes in --imain into --acqp and --topup
acqp: File containing acquisition parameters
bvecs: File containing the b-vectors for all volumes in --imain
bvals: File containing the b-values for all volumes in --imain
Returns:
The resulting file name
"""
self.info("Launch eddy correction from fsl")
tmp = self.buildName(source, "tmp")
target = self.buildName(source, "eddy")
cmd = "eddy_openmp_patch --imain={} --mask={} --index={} --acqp={} --bvecs={} --bvals={} --out={} " \
.format(source, mask, index, acqp, bVecs, bVals, tmp)
if len(mriutil.getBValues(source, bEnc))>2:
#cmd += " --data_is_shelled --mb={} " \
cmd += " --data_is_shelled"
zDims = int(mriutil.getMriDimensions(source)[2])
if zDims % int(self.get('multiband')) == 0:
cmd += " --mb={}".format(self.get('multiband'))
# .format(self.get('multiband'))
if topup is not None:
cmd += " --topup={}".format(topup)
self.getNTreadsEddy()
self.launchCommand(cmd, nice=5*60*60)
return self.rename(tmp, 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'))