Adding automated script.

slicerScripts/segment.py

@@ -0,0 +1,48 @@
+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)