ENH: Add node references from output transform to inputs

This is related to the recent changes in Slicer, SlicerExecutionModel, and BRAINSTools, the goal of which is to update registration modules to have the output transforms reference the inputs (images/fiducial lists/models, fixed and moving separately).

Elastix/Elastix.py

@@ -471,7 +471,7 @@ def getStartupInfo(self):
     info.dwFlags = 1
     info.wShowWindow = 0
     return info
-    
+
   def startElastix(self, cmdLineArguments):
     self.addLog("Register volumes...")
     import subprocess
@@ -488,7 +488,7 @@ def startTransformix(self, cmdLineArguments):
     self.addLog("Generate output...")
     import subprocess
     executableFilePath = os.path.join(self.getElastixBinDir(), self.transformixFilename)
-    logging.info("Generate output using: " + executableFilePath + ": " + repr(cmdLineArguments))    
+    logging.info("Generate output using: " + executableFilePath + ": " + repr(cmdLineArguments))
     if subprocess.mswindows:
       return subprocess.Popen([os.path.join(self.getElastixBinDir(),self.transformixFilename)] + cmdLineArguments, env=self.getElastixEnv(),
                             stdout=subprocess.PIPE, universal_newlines = True, startupinfo=self.getStartupInfo())
@@ -617,6 +617,8 @@ def registerVolumes(self, fixedVolumeNode, movingVolumeNode, parameterFilenames
           slicer.mrmlScene.RemoveNode(loadedOutputTransformNode)
         else:
           self.addLog("Failed to load output transform from "+outputTransformPath)
+        outputTransformNode.AddNodeReferenceID(slicer.vtkMRMLTransformNode.GetMovingNodeReferenceRole(), movingVolumeNode.GetID())
+        outputTransformNode.AddNodeReferenceID(slicer.vtkMRMLTransformNode.GetFixedNodeReferenceRole(), fixedVolumeNode.GetID())
 
     # Clean up
     if self.deleteTemporaryFiles: