Attempting CT skull stripping in python

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I’m following the recipe for CT skull stripping (Overview | 3D Slicer segmentation recipes) which works perfectly in the GUI. I am attempting to automate this with python as I have many samples. I am new to this so sorry if any of this is trivial

Pseudocode/code steps as far as I can understand are the following:

  • Import ct image into masterVolume node
masterVolumeNode = slicer.util.loadVolume(pathct)
  • I have previously already thresholded out the skull (HU >300) and removed all small islands and need to load this array it into a Segmentation node.
#Create Labelmap Node
labelmapVolumeNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLLabelMapVolumeNode")
#set its voxels from a numpy array using slicer.util.updateVolumeFromArray
**Labelmap_Skull = slicer.util.updateVolumeFromArray(skull_seg_arr, labelmapVolumeNode)**
#Create segmentation node
segmentationNode = slicer.vtkMRMLSegmentationNode()
slicer.mrmlScene.AddNode(segmentationNode)
segmentationNode.CreateDefaultDisplayNodes() # only needed for display
segmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(masterVolumeNode)

#Convert to segmentation node
slicer.vtkSlicerSegmentationsModuleLogic.ImportLabelmapToSegmentationNode(Labelmap_Skull, segmentationNode, selectedSegmentIds)

Next, I need to implement the WrapSolidify effect with the following parameters:
#set region to Largest cavity
#Enable Split cavities and set cavity size slider to approximately 30mm

# import module
import SegmentEditorWrapSolidify

However, I’ve been looking around at the source code Slicer-SurfaceWrapSolidify/SegmentEditorWrapSolidify.py at master · sebastianandress/Slicer-SurfaceWrapSolidify · GitHub and am a little lost concerning how to actually implement this in Python. I don’t understand the difference between the 2 classes, SegmentEditorWrapSolidifyTest and SegmentEditorWrapSolidify. Nor how to invoke an instance of these classes seeing as Wrapsolidify = SegmentEditorWrapSolidify() shows the error “TypeError: ‘module’ object is not callable”

Are there any examples I could follow or anything similar?

Thanks in advance.

2

Dear all, I’m interested in achieving the same as described in this post. Could anyone provide an answer? Additionally, if there are any recent recommendations from the past two years on applying WrapSolidify in a Python script outside Slicer interface, please let me know.