Hi everyone
I would like to extract the cavity of brain space using “Wrap solidify” and Python script.
This is my code to implement what I thought
Before performing the “Wrap solidify”, the segmentation using "Threshold " works well. However, “Wrap solidify” gives the error “ValueError: Region segment cannot be the same segment as the current segment”
Could I get a solution to this error?
Compute
masterVolumeNode = getNode(“InputVolume”)
Create segmentation
segmentationNode = slicer.mrmlScene.AddNewNodeByClass(“vtkMRMLSegmentationNode”)
#segmentationNode = slicer.mrmlScene.GetFirstNodeByClass(“vtkMRMLSegmentationNode”)
#segmentationNode = slicer.util.getNode(‘Segmentation_1’)
segmentationNode.CreateDefaultDisplayNodes() # only needed for display
segmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(masterVolumeNode)Create temporary segment editor to get access to effects
segmentEditorWidget = slicer.qMRMLSegmentEditorWidget()
segmentEditorWidget.setMRMLScene(slicer.mrmlScene)
segmentEditorNode = slicer.mrmlScene.AddNewNodeByClass(“vtkMRMLSegmentEditorNode”)Do masking
addedSegmentID = segmentationNode.GetSegmentation().AddEmptySegment(“skull”)
segmentEditorNode.SetMaskSegmentID(addedSegmentID)
segmentEditorNode.SetOverwriteMode(slicer.vtkMRMLSegmentEditorNode.OverwriteAllSegments)
segmentEditorNode.SetMaskMode(slicer.vtkMRMLSegmentEditorNode.PaintAllowedInsideSingleSegment)segmentEditorWidget.setMRMLSegmentEditorNode(segmentEditorNode)
segmentEditorWidget.setSegmentationNode(segmentationNode)
segmentEditorWidget.setMasterVolumeNode(masterVolumeNode)
segmentationDisplayNode=segmentationNode.GetDisplayNode()
segmentation=segmentationNode.GetSegmentation()segmentEditorWidget.setActiveEffectByName(“Threshold”)
effect = segmentEditorWidget.activeEffect()
effect.setParameter(“MinimumThreshold”, 250)
effect.setParameter(“MaximumThreshold”, 3000)
effect.self().onApply()segmentEditorWidget.setActiveEffectByName(“Wrap Solidify”)
effect2 = segmentEditorWidget.activeEffect()
effect2.setParameter(“Largest cavity”, True)
effect2.setParameter(“Carve holes”, True)
effect2.setParameter(“Carve holes”, 25)effect2.self().onApply()