# Problem setting output node for the mask volume effect in python

**URL:** <https://discourse.slicer.org/t/problem-setting-output-node-for-the-mask-volume-effect-in-python/30858>\
**Category:** Development\
**Tags:** segmentation, python\
**Created:** [July 28, 2023, 3:03pm UTC](https://discourse.slicer.org/t/problem-setting-output-node-for-the-mask-volume-effect-in-python/30858 "2023-07-28T15:03:30Z")\
**Posts on this page:** 3\
**Page:** 1

<div class="post-metadata">

**Author:** ![Anthony.Lombardi](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/anthony.lombardi/32/77099_2.png) [@Anthony.Lombardi](https://discourse.slicer.org/u/Anthony.Lombardi)\
**Post date:** [July 28, 2023, 3:03pm UTC](https://discourse.slicer.org/t/problem-setting-output-node-for-the-mask-volume-effect-in-python/30858/1 "2023-07-28T15:03:30Z")

</div>

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](https://slicer.readthedocs.io/en/latest/developer_guide/modules/segmenteditor.html#mask-volume). 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:

```python
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()

```

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<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [July 28, 2023, 9:31pm UTC](https://discourse.slicer.org/t/problem-setting-output-node-for-the-mask-volume-effect-in-python/30858/2 "2023-07-28T21:31:11Z")

</div>

Setting of `noderef` parameter types was not described in the documentation. I’ve added it now: [Segment editor — 3D Slicer documentation](https://slicer.readthedocs.io/en/latest/developer_guide/modules/segmenteditor.html#effect-parameters)

Something like this should work:

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

```

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<div class="post-metadata">

**Author:** ![Anthony.Lombardi](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/anthony.lombardi/32/77099_2.png) [@Anthony.Lombardi](https://discourse.slicer.org/u/Anthony.Lombardi)\
**Post date:** [July 28, 2023, 10:53pm UTC](https://discourse.slicer.org/t/problem-setting-output-node-for-the-mask-volume-effect-in-python/30858/3 "2023-07-28T22:53:09Z")

</div>

Awesome, thank you so much this worked!

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

```python
# 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)

```