Crop segment using shapeNode

Support
1

Hi all,

I’m working with a segment representing a tubular geometry, and I have a vtkMRMLMarkupsShapeNode representing a cylinder placed at the end of this structure.

I’d like to crop or cut the segment using the plane defined by the cylinder’s base (the red line).

Is there a recommended way to use the shape node’s geometry — particularly the cylinder’s plane — to perform this kind of clipping on the segment?

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Thanks :slight_smile:

2

A GUI method:

  • convert the segment to a model in the Data module (A)
  • convert the shape to a model using this module (B)
  • perform (A - B) difference in the Combine models module
  • convert the result to a segmentation in the Data module.

Alternatively, scripting in python would be faster. You would need to apply vtkPlane and vtkCutter on the segment’s closed surface representation.

3

Many thanks, I’ll try it. Is there any possibility of doing this directly using segmentation nodes instead of models?

4

Yes, you can create a segment from the shape and then use the Logical operators effect.

5

Erratum : vtkCutter won’t be useful actually, but vtkClipPolyData and/or vtkClipClosedSurface would be more appropriate.

1 Like
6

Thanks, how can I do that?

7

VTK classes are very well documented with example code available. For instance, the vtkClipClosedSurface online page points to sample use cases.

8

I am trying but I cannot figure out how to convert the ‘vtkMRMLMarkupsShapeNode’ (cylinder) to model. Lastly I tryied with markups to model, but it only creates a triangle with the 3 points that define the cylinder

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9

You can get the polydata of the Shape node like here.

And create a model from the polydata as there.

10

It works :smile:

This is the code, just in case is useful for anybody else:

shapeNode = getNode('MyMarkupsCylinder')
nodePolyData = shapeNode.GetShapeWorld()
modelNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLModelNode", "MyModel")
modelNode.SetAndObservePolyData(nodePolyData)
modelNode.CreateDefaultDisplayNodes()
modelNode.GetDisplayNode().SetColor(1, 0, 0)

Then I imported modelNode as segment using Segmentations module.