def implement(self):
aparcAseg = self.getImage(self.dependDir, "aparc_aseg", "resample")
anatBrainResample = self.getImage(self.dependDir, 'anat',
['brain', 'resample'])
anatBrainWMResample = self.getImage(self.dependDir, 'anat',
['brain', 'wm', 'resample'])
self.__createMask(anatBrainWMResample)
extended = self.buildName('anat', 'extended', 'nii')
self.info(
"Add {} and {} images together in order to create the ultimate image"
.format(anatBrainResample, aparcAseg))
mriutil.fslmaths(anatBrainResample, extended, 'add', aparcAseg)
self.__createMask(extended)
self.__createMask(aparcAseg)
#produce optionnal mask
if self.get("start_seeds").strip():
self.__createRegionMaskFromAparcAseg(aparcAseg, 'start')
if self.get("stop_seeds").strip():
self.__createRegionMaskFromAparcAseg(aparcAseg, 'stop')
if self.get("exclude_seeds").strip():
self.__createRegionMaskFromAparcAseg(aparcAseg, 'exclude')
#Launch act_anat_prepare_freesurfer
act = self.__actAnatPrepareFreesurfer(aparcAseg)
#extract the white matter mask from the act
whiteMatterAct = self.__extractWhiteMatterFromAct(act)
#Produces a mask image suitable for seeding streamlines from the grey matter - white matter interface
seed_gmwmi = self.__launch5tt2gmwmi(act)
colorLut = "{}/templates/lookup_tables/FreeSurferColorLUT_ItkSnap.txt".format(
self.toadDir)
self.info("Copying {} file into {}".format(colorLut, self.workingDir))
shutil.copy(colorLut, self.workingDir)
def implement(self):
aparcAseg = self.getImage(self.dependDir,"aparc_aseg", "resample")
anatBrainResample = self.getImage(self.dependDir,'anat', ['brain','resample'] )
anatBrainWMResample = self.getImage(self.dependDir, 'anat', ['brain','wm','resample'])
self.__createMask(anatBrainWMResample)
extended = self.buildName('anat', 'extended','nii')
self.info("Add {} and {} images together in order to create the ultimate image"
.format(anatBrainResample, aparcAseg))
mriutil.fslmaths(anatBrainResample, extended, 'add', aparcAseg)
self.__createMask(extended)
self.__createMask(aparcAseg)
#produce optionnal mask
if self.get("start_seeds").strip():
self.__createRegionMaskFromAparcAseg(aparcAseg, 'start')
if self.get("stop_seeds").strip():
self.__createRegionMaskFromAparcAseg(aparcAseg, 'stop')
if self.get("exclude_seeds").strip():
self.__createRegionMaskFromAparcAseg(aparcAseg, 'exclude')
#Launch act_anat_prepare_freesurfer
act = self.__actAnatPrepareFreesurfer(aparcAseg)
#extract the white matter mask from the act
whiteMatterAct = self.__extractWhiteMatterFromAct(act)
#Produces a mask image suitable for seeding streamlines from the grey matter - white matter interface
seed_gmwmi = self.__launch5tt2gmwmi(act)
colorLut = "{}/templates/lookup_tables/FreeSurferColorLUT_ItkSnap.txt".format(self.toadDir)
self.info("Copying {} file into {}".format(colorLut, self.workingDir))
shutil.copy(colorLut, self.workingDir)
def __fslmathsTmean(self, source):
target = source.replace(".nii", "_tmean.nii")
self.info(mriutil.fslmaths(source, target, 'Tmean'))
return target
def __createMask(self, source):
self.info("Create mask from {} images".format(source))
self.info(
mriutil.fslmaths(source, self.buildName(source, 'mask'), 'bin'))
def __fslmathsTmean(self, source):
target = source.replace(".nii", "_tmean.nii")
self.info(mriutil.fslmaths(source, target, 'Tmean'))
return target
def __createMask(self, source):
self.info("Create mask from {} images".format(source))
self.info(mriutil.fslmaths(source, self.buildName(source, 'mask'), 'bin'))
