def implement(self):
anat = self.getPreparationImage('anat')
# Look if a freesurfer tree is already available
if not self.__findAndLinkFreesurferStructure():
self.__submitReconAll(anat)
# @TODO backup the recon-all to backup dir
if not self.__findImageInDirectory(
"brainstemSsLabels.v10.FSvoxelSpace.mgz",
os.path.join(self.workingDir, self.id)):
self.__submitSubSegmentation(anat, 'brainstem')
if not self.__findImageInDirectory(
"rh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz",
os.path.join(self.workingDir, self.id)):
self.__submitSubSegmentation(anat, 'hippocampus')
self.__convertFreesurferImageIntoNifti(anat)
self.__createSegmentationMask(self.get('aparc_aseg'), self.get('mask'))
self.__mergeParcellation(self.get('wmparc'), self.get('aparc_aseg'),
self.get('brainstem'), self.get('lhHipp'),
self.get('rhHipp'))
tt5Mgz = self.__create5ttImage()
mriutil.convertAndRestride(
tt5Mgz, self.get('tt5'),
self.get('preparation', 'stride_orientation'))
anatFreesurfer = self.getImage('anat', 'freesurfer')
if self.get('cleanup'):
self.__cleanup()
def __createImageFromAtlas(self, source, target):
"""
Create a area map base on a source name
Args:
source: template name as specify into config.cfg
target: output file name
Returns:
A brodmann area images
"""
tmpImage = 'tmp_{0:.6g}.mgz'.format(random.randint(0,999999))
template = os.path.join(self.toadDir, "templates", "mri", self.get(source))
self.info("Set SUBJECTS_DIR to {}".format(self.parcellationDir))
os.environ["SUBJECTS_DIR"] = self.parcellationDir
cmd = "mri_vol2vol --mov {} --targ $FREESURFER_HOME/subjects/fsaverage/mri/T1.mgz" \
" --o {} --regheader --interp nearest".format(template, tmpImage)
self.launchCommand(cmd)
cmd = "mri_vol2vol --mov $SUBJECTS_DIR/{0}/mri/norm.mgz --targ {1} --s {0} " \
" --m3z talairach.m3z --o {2} --interp nearest --inv-morph".format(self.get('parcellation', 'id'), tmpImage, target)
self.launchCommand(cmd)
return mriutil.convertAndRestride(target, target, self.get('preparation', 'stride_orientation'))
def __createImageFromAtlas(self, source, target):
"""
Create a area map base on a source name
Args:
source: template name as specify into config.cfg
target: output file name
Returns:
A brodmann area images
"""
tmpImage = 'tmp_{0:.6g}.mgz'.format(random.randint(0,999999))
template = os.path.join(self.toadDir, "templates", "mri", self.get(source))
self.info("Set SUBJECTS_DIR to {}".format(self.parcellationDir))
os.environ["SUBJECTS_DIR"] = self.parcellationDir
cmd = "mri_vol2vol --mov {} --targ $FREESURFER_HOME/subjects/fsaverage/mri/T1.mgz" \
" --o {} --regheader --interp nearest".format(template, tmpImage)
self.launchCommand(cmd)
cmd = "mri_vol2vol --mov $SUBJECTS_DIR/{0}/mri/norm.mgz --targ {1} --s {0} " \
" --m3z talairach.m3z --o {2} --interp nearest --inv-morph".format(self.get('parcellation', 'id'), tmpImage, target)
self.launchCommand(cmd)
return mriutil.convertAndRestride(target, target, self.get('preparation', 'stride_orientation'))
def implement(self):
anat = self.getPreparationImage('anat')
# Look if a freesurfer tree is already available
if not self.__findAndLinkFreesurferStructure():
self.__submitReconAll(anat)
# @TODO backup the recon-all to backup dir
self.__convertFeesurferImageIntoNifti(anat)
self.__createSegmentationMask(self.get('aparc_aseg'), self.get('mask'))
tt5Mgz = self.__create5ttImage()
mriutil.convertAndRestride(tt5Mgz, self.get('tt5'), self.get('preparation', 'stride_orientation'))
anatFreesurfer = self.getImage('anat', 'freesurfer')
if self.get('cleanup'):
self.__cleanup()
def __convertFeesurferImageIntoNifti(self, anatomicalName):
"""
Convert a List of mgz fresurfer into nifti compress format
Args:
anatomicalName: The subject anatomical image is need to identify the proper T1
"""
for (target, source) in [(self.buildName(anatomicalName, 'freesurfer'), "T1.mgz"),
(self.get('aparc_aseg'), "aparc+aseg.mgz"),
(self.get('wmparc'), "wmparc.mgz"),
(self.get('rh_ribbon'), "rh.ribbon.mgz"),
(self.get('lh_ribbon'), "lh.ribbon.mgz"),
(self.get('norm'), "norm.mgz")]:
mriutil.convertAndRestride(self.__findImageInDirectory(source, os.path.join(self.workingDir, self.id)),
target,
self.get('preparation', 'stride_orientation'))
def implement(self):
anat = self.getPreparationImage('anat')
# Look if a freesurfer tree is already available
if not self.__findAndLinkFreesurferStructure():
self.__submitReconAll(anat)
# @TODO backup the recon-all to backup dir
if not self.__findImageInDirectory("brainstemSsLabels.v10.FSvoxelSpace.mgz", os.path.join(self.workingDir, self.id)):
self.__submitSubSegmentation(anat, 'brainstem')
if not self.__findImageInDirectory("rh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz", os.path.join(self.workingDir, self.id)):
self.__submitSubSegmentation(anat, 'hippocampus')
self.__convertFreesurferImageIntoNifti(anat)
self.__createSegmentationMask(self.get('aparc_aseg'), self.get('mask'))
self.__mergeParcellation(self.get('wmparc'),self.get('aparc_aseg'),self.get('brainstem'),self.get('lhHipp'),self.get('rhHipp'))
tt5Mgz = self.__create5ttImage()
mriutil.convertAndRestride(tt5Mgz, self.get('tt5'), self.get('preparation', 'stride_orientation'))
anatFreesurfer = self.getImage('anat', 'freesurfer')
if self.get('cleanup'):
self.__cleanup()
def __convertFreesurferImageIntoNifti(self, anatomicalName):
"""
Convert a List of mgz fresurfer into nifti compress format
Args:
anatomicalName: The subject anatomical image is need to identify the proper T1
"""
for (target, source) in [
(self.buildName(anatomicalName, 'freesurfer'), "T1.mgz"),
(self.get('aparc_aseg'), "aparc+aseg.mgz"),
(self.get('wmparc'), "wmparc.mgz"),
(self.get('rh_ribbon'), "rh.ribbon.mgz"),
(self.get('lh_ribbon'), "lh.ribbon.mgz"),
(self.get('brainstem'), "brainstemSsLabels.v10.FSvoxelSpace.mgz"),
(self.get("rhHipp"), "rh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz"),
(self.get("lhHipp"), "lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz"),
(self.get('norm'), "norm.mgz")
]:
mriutil.convertAndRestride(
self.__findImageInDirectory(
source, os.path.join(self.workingDir, self.id)), target,
self.get('preparation', 'stride_orientation'))