Пример #1
0
    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)
Пример #2
0
    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
Пример #3
0
    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