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)
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)
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)
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)