def implement(self):
tt5 = self.getRegistrationImage("tt5", "register")
seed_gmwmi = self.getMaskingImage("tt5", ["register", "5tt2gmwmi"])
brodmann = self.getRegistrationImage("brodmann", "resample")
norm = self.getRegistrationImage("norm", "resample")
mask253 = self.getMaskingImage('aparc_aseg', ['253', 'mask'])
mask1024= self.getMaskingImage('aparc_aseg', ['1024', 'mask'])
dwi = self.getUpsamplingImage('dwi', 'upsample')
bFile = self.getUpsamplingImage('grad', None, 'b')
mask = self.getRegistrationImage('mask', 'resample')
#tensor part
tckDet = self.__tckgenTensor(dwi, self.buildName(dwi, 'tensor_det', 'tck'), mask, tt5, seed_gmwmi, bFile, 'Tensor_Det')
tckDetConnectome = self.__tck2connectome(tckDet, brodmann, self.buildName(tckDet, 'connectome', 'csv'))
tckDetConnectomeNormalize = self.__normalizeConnectome(tckDetConnectome, self.buildName(tckDetConnectome, 'normalize', 'csv'))
mriutil.plotConnectome(tckDetConnectomeNormalize, self.buildName(tckDetConnectomeNormalize, None, "png"))
tckDetRoi = self.__tckedit(tckDet, mask253, self.buildName(tckDet, 'roi','tck'))
tckDetRoiTrk = mriutil.tck2trk(tckDetRoi, norm , self.buildName(tckDetRoi, None, 'trk'))
tckProb = self.__tckgenTensor(dwi, self.buildName(dwi, 'tensor_prob', 'tck'), mask, tt5, seed_gmwmi, bFile, 'Tensor_Prob')
tckProbConnectome = self.__tck2connectome(tckProb, brodmann, self.buildName(tckProb, 'connectome', 'csv'))
tckProbConnectomeNormalize = self.__normalizeConnectome(tckProbConnectome, self.buildName(tckProbConnectome, 'normalize', 'csv'))
mriutil.plotConnectome(tckProbConnectomeNormalize, self.buildName(tckProbConnectomeNormalize, None, "png"))
tckProbRoi = self.__tckedit(tckProb, mask253, self.buildName(tckProb, 'roi','tck'))
tckProbRoiTrk = mriutil.tck2trk(tckProbRoi, norm , self.buildName(tckProbRoi, None, 'trk'))
#HARDI part
csd = self.getHardimrtrixImage('dwi','csd')
hardiTck = self.__tckgenHardi(csd, self.buildName(csd, 'hardi_prob', 'tck'), tt5)
hardiTckConnectome = self.__tck2connectome(hardiTck, brodmann, self.buildName(hardiTck, 'connectome', 'csv'))
hardiTckConnectomeNormalize = self.__normalizeConnectome(hardiTckConnectome, self.buildName(hardiTckConnectome, 'normalize', 'csv'))
mriutil.plotConnectome(hardiTckConnectomeNormalize, self.buildName(hardiTckConnectomeNormalize, None, "png"))
hardiTckRoi = self.__tckedit(hardiTck, mask253, self.buildName(hardiTck, 'roi','tck'))
tckgenRoiTrk = mriutil.tck2trk(hardiTckRoi, norm , self.buildName(hardiTckRoi, None, 'trk'))
tcksift = self.__tcksift(hardiTck, csd)
tcksiftConnectome = self.__tck2connectome(tcksift, brodmann, self.buildName(tcksift, 'connectome', 'csv'))
tcksiftConnectomeNormalize = self.__normalizeConnectome(tcksiftConnectome, self.buildName(tcksiftConnectome, 'normalize', 'csv'))
mriutil.plotConnectome(tcksiftConnectomeNormalize, self.buildName(tcksiftConnectomeNormalize, None, "png"))
tcksiftRoi = self.__tckedit(tcksift, mask253, self.buildName(tcksift, 'roi', 'tck'))
tcksiftRoiTrk = mriutil.tck2trk(tcksiftRoi, norm , self.buildName(tcksiftRoi, None, 'trk'))
#create PNG
if self.get('general', 'vtk_available'):
mriutil.createVtkPng(tckDetRoiTrk, norm, mask253)
mriutil.createVtkPng(tckProbRoiTrk, norm, mask253)
mriutil.createVtkPng(tckgenRoiTrk, norm, mask253)
mriutil.createVtkPng(tcksiftRoiTrk, norm, mask253)
def __plotConnectome(self, source, atlas, lut, prefix):
""" perform connectomme steps.
Args:
source: the input track file
atlas: the atlas
lut: an compatible itksnap lut file
Returns:
a connectome png image
"""
if lut is not None:
lutFile= os.path.join(self.toadDir, "templates", "lookup_tables", self.get("template", lut))
else:
lutFile= None
if self.get('arguments', 'debug'):
self.info('Source file: {}'.format(source))
self.info('Atlas file: {}'.format(atlas))
self.info('Lut file location: {}'.format(lutFile))
connectome = self.__tck2connectome(source, atlas, self.buildName(source, [ prefix , 'connectome'], 'csv'))
connectomeNormalize = self.__normalizeConnectome(connectome, self.buildName(connectome, 'normalize', 'csv'))
pngImage = mriutil.plotConnectome(connectomeNormalize, self.buildName(connectomeNormalize, None, "png"), lutFile)
return pngImage
def __plotConnectome(self, source, atlas, lut, prefix):
""" perform connectomme steps.
Args:
source: the input track file
atlas: the atlas
lut: an compatible itksnap lut file
Returns:
a connectome png image
"""
if lut is not None:
lutFile = os.path.join(self.toadDir, "templates", "lookup_tables",
self.get("template", lut))
else:
lutFile = None
if self.get('arguments', 'debug'):
self.info('Source file: {}'.format(source))
self.info('Atlas file: {}'.format(atlas))
self.info('Lut file location: {}'.format(lutFile))
connectome = self.__tck2connectome(
source, atlas, self.buildName(source, [prefix, 'connectome'],
'csv'))
connectomeNormalize = self.__normalizeConnectome(
connectome, self.buildName(connectome, 'normalize', 'csv'))
pngImage = mriutil.plotConnectome(
connectomeNormalize,
self.buildName(connectomeNormalize, None, "png"), lutFile)
return pngImage