Problem setting output node for the mask volume effect in python

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Hi all,

I am trying to set the output volume node from the Mask Volume effect in Python. However, I am not having much luck trying to do this. I am just using the default parameters for the Mask Volume effect as they were described in the documentation. However, the Mask volume.OutputVolume parameter fails to put the results into the provided volume node and instead, a new volume node {inputvolname} masked is created with the results. I have tried passing the volume node ID and the volume node itself but both failed to populate the passed node.

I am not sure what I need to be doing differently to get this to work, so any guidance would be extremely appreciated.

Below is an example showing off the issue I am running into:

import slicer
import SampleData

# Load in some sample data
sampleDataLogic = SampleData.SampleDataLogic()
mrHead = sampleDataLogic.downloadMRHead()

# Create the segmentation node
segmentationNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSegmentationNode")
segmentationNode.CreateDefaultDisplayNodes() # only needed for display
segmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(mrHead)
segmentationNode.GetSegmentation().AddEmptySegment("Segment_1")

# Create temporary segment editor to get access to effects
segmentEditorWidget = slicer.qMRMLSegmentEditorWidget()
segmentEditorWidget.setMRMLScene(slicer.mrmlScene)
segmentEditorNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSegmentEditorNode")
segmentEditorWidget.setMRMLSegmentEditorNode(segmentEditorNode)
segmentEditorWidget.setSegmentationNode(segmentationNode)
segmentEditorWidget.setSourceVolumeNode(mrHead)

# Apply a threshold to get the mask
segmentEditorWidget.setActiveEffectByName("Threshold")
effect = segmentEditorWidget.activeEffect()
effect.setParameter("MinimumThreshold","70")
effect.setParameter("MaximumThreshold","280")
effect.self().onApply()

# Create a new volume to hold the mask
nodeName = "MyNewVolume"
imageSize = [512, 512, 512]
voxelType=vtk.VTK_UNSIGNED_CHAR
imageOrigin = [0.0, 0.0, 0.0]
imageSpacing = [1.0, 1.0, 1.0]
imageDirections = [[1,0,0], [0,1,0], [0,0,1]]
fillVoxelValue = 0
# Create an empty image volume, filled with fillVoxelValue
imageData = vtk.vtkImageData()
imageData.SetDimensions(imageSize)
imageData.AllocateScalars(voxelType, 1)
imageData.GetPointData().GetScalars().Fill(fillVoxelValue)
# Create volume node
volumeNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLScalarVolumeNode", nodeName)
volumeNode.SetOrigin(imageOrigin)
volumeNode.SetSpacing(imageSpacing)
volumeNode.SetIJKToRASDirections(imageDirections)
volumeNode.SetAndObserveImageData(imageData)
volumeNode.CreateDefaultDisplayNodes()
volumeNode.CreateDefaultStorageNode()

# Apply the mask effect
segmentEditorWidget.setActiveEffectByName("Mask volume")
effect = segmentEditorWidget.activeEffect()
effect.setParameter("Mask volume.InputVolume",mrHead.GetID()) # Input volume
effect.setParameter("Mask volume.OutputVolume",volumeNode.GetID()) # Expected result to be stored here, but it is not
effect.self().onApply()
2

Setting of noderef parameter types was not described in the documentation. I’ve added it now: Segment editor — 3D Slicer documentation

Something like this should work:

inputVolume = effect.parameterSetNode().SetNodeReferenceID("Mask volume.InputVolume", mrHead.GetID)
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3

Awesome, thank you so much this worked!

For those interested the working snippet for the mask effect is as follows:

# Apply the mask effect
segmentEditorWidget.setActiveEffectByName("Mask volume")
effect = segmentEditorWidget.activeEffect()
inputVolume = effect.parameterSetNode().SetNodeReferenceID("Mask volume.InputVolume", mrHead.GetID())
effect.self().onApply()
outputVolumeID = effect.parameterSetNode().GetNodeReferenceID("Mask volume.OutputVolume")
outputVolume = slicer.mrmlScene.GetNodeByID(outputVolumeID)
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