EMBRACE/slicerScripts/segment.py

import slicer
import Elastix
import CTRegistration
import slicerNetwork

configFile = os.path.join(os.path.expanduser('~'), '.EMBRACE','onko-nix.json')

dataManager = CTRegistration.CTRegistrationLogic(configFile)
network = slicerNetwork.labkeyURIHandler()

dataManager.importer.setURIHandler(network)

elastix = Elastix.ElastixLogic()

registrationIndex = 17
"""
    id="par0023"
    modality="3D CT, 3D MR, multimodal"
    content="head and neck"
    description="intrapatient; rigid + B-spline transformation; localized mutual information combined with bending energy penalty"
    publications="Leibfarth (2013),  A strategy for multimodal deformable image registration to integrate PET/MR into radiotherapy treatment planning"
"""

RegistrationPresets_ParameterFilenames = 5
"""
['Rigid.txt', 'Deformable.txt']
"""

parameterFilenames = elastix.getRegistrationPresets()[registrationIndex][RegistrationPresets_ParameterFilenames]

transformNode=slicer.vtkMRMLGridTransformNode()
transformNode.SetName(transformNodeName)
slicer.mrmlScene.AddNode(transformNode)

for i in range(0,86):

    patientID = 'LJU'+'{:03d}'.format(i)

    dataManager.loadData(network,patientID)

    fixedVolumeNode = slicer.util.getFirstNodeByName(patientID+'_DMR')
    movingVolumeNode = slicer.util.getFirstNodeByName(patientID+'_CT')

    transformNodeName = patientID+'_T2_DF'

    elastix.registerVolumes(fixedVolumeNode, movingVolumeNode, parameterFilenames = parameterFilenames, outputVolumeNode = None, outputTransformNode = transformNode, fixedVolumeMaskNode = None, movingVolumeMaskNode = None, forceDisplacementFieldOutputTransform = True)

    dataManager.export(network, 'EMBRACE/Studija', patientID)