Need to convert vtkMRMLScalarVolumeNode and vtkMRMLCommandLineVolumeNode to Numpy Array

Support
1

I am using slicer module in my own module to get bias corrected volume. The following function is working correctly.

def biascorrection(volumeNode1):
  parameters = {}
  parameters["inputImageName"] = volumeNode1.GetID()
  outModel = slicer.vtkMRMLScalarVolumeNode()
  slicer.mrmlScene.AddNode(outModel)
  parameters["outputImageName"] = outModel.GetID()
  biascorrect = slicer.modules.n4itkbiasfieldcorrection
  return (slicer.cli.run(biascorrect, None, parameters))

Vol1_biasCorrect = biascorrection(nodet1)

Output node is (vtkCommonCorePython.vtkMRMLCommandLineModuleNode)0x7fc11452a808. To get numpy array of this vtk node, I have been used the following code:

Vol1_biasCorrectNode = slicer.util.getNode('Volume')
Vol1_biasCorrect_array = slicer.util.array(Vol1_biasCorrectNode.GetID())

The following error appears:

File "/home/siddique/Slicer-4.6.2-linux-amd64/bin/Python/slicer/util.py", line 583, in array
    shape = list(n.GetImageData().GetDimensions())
AttributeError: 'NoneType' object has no attribute 'GetDimensions'

As output volume is created as vtkMRMLScalarVolumeNode(), I think this volume should be converted to numpy array. Please help me to get the numpy array of bias corrected volume.

2

Specify wait_for_completion=True to block execution until the CLI execution is complete. See details here: https://www.slicer.org/wiki/Documentation/Nightly/Developers/Python_scripting#Running_a_CLI_from_Python