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@lassoan
Last active May 6, 2023 15:08
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This example demonstrates how to run Grow from seeds effect in batch mode (without GUI, using qMRMLSegmentEditorWidget) using 3D Slicer
# Generate input data
################################################
import SampleData
# Load master volume
sampleDataLogic = SampleData.SampleDataLogic()
masterVolumeNode = sampleDataLogic.downloadMRBrainTumor1()
# Create segmentation
segmentationNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSegmentationNode")
segmentationNode.CreateDefaultDisplayNodes() # only needed for display
segmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(masterVolumeNode)
# Create seed segment inside tumor
tumorSeed = vtk.vtkSphereSource()
tumorSeed.SetCenter(-6, 30, 28)
tumorSeed.SetRadius(10)
tumorSeed.Update()
segmentationNode.AddSegmentFromClosedSurfaceRepresentation(tumorSeed.GetOutput(), "Tumor", [1.0,0.0,0.0])
# Create seed segment outside tumor
backgroundSeedPositions = [[0,65,32], [1, -14, 30], [0, 28, -7], [0,30,64], [31, 33, 27], [-42, 30, 27]]
append = vtk.vtkAppendPolyData()
for backgroundSeedPosition in backgroundSeedPositions:
backgroundSeed = vtk.vtkSphereSource()
backgroundSeed.SetCenter(backgroundSeedPosition)
backgroundSeed.SetRadius(10)
backgroundSeed.Update()
append.AddInputData(backgroundSeed.GetOutput())
append.Update()
backgroundSegmentId = segmentationNode.AddSegmentFromClosedSurfaceRepresentation(append.GetOutput(), "Background", [0.0,1.0,0.0])
# Run filter
################################################
# Create segment editor to get access to effects
segmentEditorWidget = slicer.qMRMLSegmentEditorWidget()
# To show segment editor widget (useful for debugging): segmentEditorWidget.show()
segmentEditorWidget.setMRMLScene(slicer.mrmlScene)
segmentEditorNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSegmentEditorNode")
segmentEditorWidget.setMRMLSegmentEditorNode(segmentEditorNode)
segmentEditorWidget.setSegmentationNode(segmentationNode)
segmentEditorWidget.setMasterVolumeNode(masterVolumeNode)
# Run segmentation
segmentEditorWidget.setActiveEffectByName("Grow from seeds")
effect = segmentEditorWidget.activeEffect()
# You can change parameters by calling: effect.setParameter("MyParameterName", someValue)
# Most effect don't have onPreview, you can just call onApply
effect.self().onPreview()
effect.self().onApply()
# Clean up and show results
################################################
# Clean up
slicer.mrmlScene.RemoveNode(segmentEditorNode)
# Make segmentation results nicely visible in 3D
segmentationDisplayNode = segmentationNode.GetDisplayNode()
segmentationDisplayNode.SetSegmentVisibility(backgroundSegmentId, False)
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lassoan commented Mar 28, 2022

@DrMohamedAssadawy please post this question on the Slicer Forum.

@AApingp
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AApingp commented Apr 26, 2023

When I run this code using my own CT data, there is an error as follows. How can I solve it?
File "qt-scripted-modules\SegmentEditorEffects\AbstractScriptedSegmentEditorAutoCompleteEffect.py", line 301, in onApply
previewContainsClosedSurfaceRepresentation = previewNode.GetSegmentation().ContainsRepresentation(
AttributeError: 'NoneType' object has no attribute 'GetSegmentation'

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