Esempio n. 1
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    def implement(self):

        b0 = self.getUpsamplingImage('b0', 'upsample')
        mrtrixMatrix = self.getRegistrationImage("freesurfer_dwi",
                                                 ["transformation", "mrtrix"],
                                                 "mat")
        freesurferToDWI = self.getRegistrationImage("freesurfer_dwi",
                                                    "transformation", "mat")

        brodmann = self.getAtlasImage("brodmann")
        aal2 = self.getAtlasImage("aal2")
        networks7 = self.getAtlasImage("networks7")

        brodmannRegister = mriutil.applyRegistrationMrtrix(
            brodmann, mrtrixMatrix, self.buildName(brodmann, "register"))
        mriutil.applyResampleFsl(brodmann, b0, freesurferToDWI,
                                 self.buildName(brodmann, "resample"), True)

        aal2Register = mriutil.applyRegistrationMrtrix(
            aal2, mrtrixMatrix, self.buildName(aal2, "register"))
        mriutil.applyResampleFsl(aal2, b0, freesurferToDWI,
                                 self.buildName(aal2, "resample"), True)

        networks7Register = mriutil.applyRegistrationMrtrix(
            networks7, mrtrixMatrix, self.buildName(networks7, "register"))
        mriutil.applyResampleFsl(networks7, b0, freesurferToDWI,
                                 self.buildName(networks7, "resample"), True)
Esempio n. 2
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    def implement(self):

        b0 = self.getUpsamplingImage('b0','upsample')
        mrtrixMatrix =  self.getRegistrationImage("freesurfer_dwi", ["transformation", "mrtrix"], "mat")
        freesurferToDWI = self.getRegistrationImage("freesurfer_dwi", "transformation", "mat")

        brodmann = self.getAtlasImage("brodmann")
        aal2 = self.getAtlasImage("aal2")
        networks7 = self.getAtlasImage("networks7")

        brodmannRegister = mriutil.applyRegistrationMrtrix(brodmann, mrtrixMatrix, self.buildName(brodmann, "register"))
        mriutil.applyResampleFsl(brodmann, b0, freesurferToDWI, self.buildName(brodmann, "resample"), True)

        aal2Register = mriutil.applyRegistrationMrtrix(aal2, mrtrixMatrix, self.buildName(aal2, "register"))
        mriutil.applyResampleFsl(aal2, b0, freesurferToDWI, self.buildName(aal2, "resample"), True)

        networks7Register = mriutil.applyRegistrationMrtrix(networks7, mrtrixMatrix, self.buildName(networks7, "register"))
        mriutil.applyResampleFsl(networks7, b0, freesurferToDWI, self.buildName(networks7, "resample"), True)
Esempio n. 3
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    def implement(self):

        b0 = self.getUpsamplingImage('b0','upsample')
        norm= self.getParcellationImage('norm')
        anat = self.getParcellationImage('anat', 'freesurfer')
        aparcAsegFile =  self.getParcellationImage("aparc_aseg")
        wmparcFile = self.getParcellationImage("wmparc")
        rhRibbon = self.getParcellationImage("rh_ribbon")
        lhRibbon = self.getParcellationImage("lh_ribbon")
        tt5 = self.getParcellationImage("tt5")
        mask = self.getParcellationImage("mask")

        extraArgs = " -dof 6 " # Because same subject
        if self.get("methodology", "intrasession"):
            extraArgs += " -usesqform "

        freesurferToDWIMatrix = self.__freesurferToDWITransformation(b0, norm, extraArgs)
        mriutil.applyResampleFsl(anat, b0, freesurferToDWIMatrix, self.buildName(anat, "resample"))
        mrtrixMatrix = self.__transformFslToMrtrixMatrix(anat, b0, freesurferToDWIMatrix)

        """ Grey matter parcellation """
        mriutil.applyRegistrationMrtrix(aparcAsegFile, mrtrixMatrix, self.buildName(aparcAsegFile, "register"))
        mriutil.applyResampleFsl(aparcAsegFile, b0, freesurferToDWIMatrix, self.buildName(aparcAsegFile, "resample"), True)

        """ White matter parcellation """
        mriutil.applyRegistrationMrtrix(wmparcFile, mrtrixMatrix, self.buildName(wmparcFile, "register"))
        mriutil.applyResampleFsl(wmparcFile, b0, freesurferToDWIMatrix, self.buildName(wmparcFile, "resample"), True)

        lhRibbonRegister = mriutil.applyRegistrationMrtrix(lhRibbon, mrtrixMatrix, self.buildName(lhRibbon, "register"))
        rhRibbonRegister = mriutil.applyRegistrationMrtrix(rhRibbon, mrtrixMatrix, self.buildName(rhRibbon, "register"))
        tt5Register = mriutil.applyRegistrationMrtrix(tt5, mrtrixMatrix, self.buildName(tt5, "register"))
        maskRegister = mriutil.applyRegistrationMrtrix(mask, mrtrixMatrix, self.buildName(mask, "register"))
        normRegister = mriutil.applyRegistrationMrtrix(norm, mrtrixMatrix, self.buildName(norm, "register"))

        mriutil.applyResampleFsl(lhRibbon, b0, freesurferToDWIMatrix, self.buildName(lhRibbon, "resample"),True)
        mriutil.applyResampleFsl(rhRibbon, b0, freesurferToDWIMatrix, self.buildName(rhRibbon, "resample"),True)
        mriutil.applyResampleFsl(tt5, b0, freesurferToDWIMatrix, self.buildName(tt5, "resample"),True)
        mriutil.applyResampleFsl(mask, b0, freesurferToDWIMatrix, self.buildName(mask, "resample"),True)
        mriutil.applyResampleFsl(norm, b0, freesurferToDWIMatrix, self.buildName(norm, "resample"),True)
Esempio n. 4
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    def implement(self):

        b0 = self.getUpsamplingImage('b0', 'upsample')
        norm = self.getParcellationImage('norm')
        anat = self.getParcellationImage('anat', 'freesurfer')
        aparcAsegFile = self.getParcellationImage("aparc_aseg")
        wmparcFile = self.getParcellationImage("wmparc")
        rhRibbon = self.getParcellationImage("rh_ribbon")
        lhRibbon = self.getParcellationImage("lh_ribbon")
        tt5 = self.getParcellationImage("tt5")
        mask = self.getParcellationImage("mask")

        extraArgs = " -dof 6 "  # Because same subject
        if self.get("methodology", "intrasession"):
            extraArgs += " -usesqform "

        freesurferToDWIMatrix = self.__freesurferToDWITransformation(
            b0, norm, extraArgs)
        mriutil.applyResampleFsl(anat, b0, freesurferToDWIMatrix,
                                 self.buildName(anat, "resample"))
        mrtrixMatrix = self.__transformFslToMrtrixMatrix(
            anat, b0, freesurferToDWIMatrix)
        """ Grey matter parcellation """
        mriutil.applyRegistrationMrtrix(
            aparcAsegFile, mrtrixMatrix,
            self.buildName(aparcAsegFile, "register"))
        mriutil.applyResampleFsl(aparcAsegFile, b0, freesurferToDWIMatrix,
                                 self.buildName(aparcAsegFile, "resample"),
                                 True)
        """ White matter parcellation """
        mriutil.applyRegistrationMrtrix(wmparcFile, mrtrixMatrix,
                                        self.buildName(wmparcFile, "register"))
        mriutil.applyResampleFsl(wmparcFile, b0, freesurferToDWIMatrix,
                                 self.buildName(wmparcFile, "resample"), True)

        lhRibbonRegister = mriutil.applyRegistrationMrtrix(
            lhRibbon, mrtrixMatrix, self.buildName(lhRibbon, "register"))
        rhRibbonRegister = mriutil.applyRegistrationMrtrix(
            rhRibbon, mrtrixMatrix, self.buildName(rhRibbon, "register"))
        tt5Register = mriutil.applyRegistrationMrtrix(
            tt5, mrtrixMatrix, self.buildName(tt5, "register"))
        maskRegister = mriutil.applyRegistrationMrtrix(
            mask, mrtrixMatrix, self.buildName(mask, "register"))
        normRegister = mriutil.applyRegistrationMrtrix(
            norm, mrtrixMatrix, self.buildName(norm, "register"))

        mriutil.applyResampleFsl(lhRibbon, b0, freesurferToDWIMatrix,
                                 self.buildName(lhRibbon, "resample"), True)
        mriutil.applyResampleFsl(rhRibbon, b0, freesurferToDWIMatrix,
                                 self.buildName(rhRibbon, "resample"), True)
        mriutil.applyResampleFsl(tt5, b0, freesurferToDWIMatrix,
                                 self.buildName(tt5, "resample"), True)
        mriutil.applyResampleFsl(mask, b0, freesurferToDWIMatrix,
                                 self.buildName(mask, "resample"), True)
        mriutil.applyResampleFsl(norm, b0, freesurferToDWIMatrix,
                                 self.buildName(norm, "resample"), True)