Slicer study notes (54) 3D display of slicer segmentation results

1、Create a segmentation from a labelmap volume and display in 3D

labelmapVolumeNode = getNode("label")
seg = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSegmentationNode")
slicer.modules.segmentations.logic().ImportLabelmapToSegmentationNode(labelmapVolumeNode, seg)
seg.CreateClosedSurfaceRepresentation()
slicer.mrmlScene.RemoveNode(labelmapVolumeNode)

The last line is optional. It removes the original labelmap volume so that the same information is not shown twice.

2、Export labelmap node from segmentation node

Export labelmap matching reference geometry of the segmentation:

segmentationNode = getNode("Segmentation")
labelmapVolumeNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLLabelMapVolumeNode")
slicer.modules.segmentations.logic().ExportAllSegmentsToLabelmapNode(segmentationNode, labelmapVolumeNode, slicer.vtkSegmentation.EXTENT_REFERENCE_GEOMETRY)

Export smallest possible labelmap:

segmentationNode = getNode("Segmentation")
labelmapVolumeNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLLabelMapVolumeNode")
slicer.modules.segmentations.logic().ExportAllSegmentsToLabelmapNode(segmentationNode, labelmapVolumeNode)

Export labelmap that matches geometry of a chosen reference volume:

segmentationNode = getNode("Segmentation")
labelmapVolumeNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLLabelMapVolumeNode")
slicer.modules.segmentations.logic().ExportVisibleSegmentsToLabelmapNode(segmentationNode, labelmapVolumeNode, referenceVolumeNode)

Export a selection of segments (identified by their names):

segmentNames = ["Prostate", "Urethra"]
segmentIds = vtk.vtkStringArray()
for segmentName in segmentNames:
  segmentId = segmentationNode.GetSegmentation().GetSegmentIdBySegmentName(segmentName)
  segmentIds.InsertNextValue(segmentId)
slicer.vtkSlicerSegmentationsModuleLogic.ExportSegmentsToLabelmapNode(segmentationNode, segmentIds, labelmapVolumeNode, referenceVolumeNode)

Export to file by pressing Ctrl+Shift+S key:

outputPath = "c:/tmp"

def exportLabelmap():
  segmentationNode = slicer.mrmlScene.GetFirstNodeByClass("vtkMRMLSegmentationNode")
  referenceVolumeNode = slicer.mrmlScene.GetFirstNodeByClass("vtkMRMLScalarVolumeNode")
  labelmapVolumeNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLLabelMapVolumeNode")
  slicer.modules.segmentations.logic().ExportVisibleSegmentsToLabelmapNode(segmentationNode, labelmapVolumeNode, referenceVolumeNode)
  filepath = outputPath + "/" + referenceVolumeNode.GetName() + "-label.nrrd"
  slicer.util.saveNode(labelmapVolumeNode, filepath)
  slicer.mrmlScene.RemoveNode(labelmapVolumeNode.GetDisplayNode().GetColorNode())
  slicer.mrmlScene.RemoveNode(labelmapVolumeNode)
  slicer.util.delayDisplay("Segmentation saved to " + filepath)

shortcut = qt.QShortcut(slicer.util.mainWindow())
shortcut.setKey(qt.QKeySequence("Ctrl+Shift+s"))
shortcut.connect( "activated()", exportLabelmap)

3、Export model nodes from segmentation node

segmentationNode = getNode("Segmentation")
shNode = slicer.mrmlScene.GetSubjectHierarchyNode()
exportFolderItemId = shNode.CreateFolderItem(shNode.GetSceneItemID(), "Segments")
slicer.modules.segmentations.logic().ExportAllSegmentsToModels(segmentationNode, exportFolderItemId)

4、Create a hollow model from boundary of solid segment

In most cases, the most robust and flexible tool for creating empty shell models (e.g., vessel wall model from contrast agent segmentation) is the “Hollow” effect in Segment Editor module. However, for very thin shells, extrusion of the exported surface mesh representation may be just as robust and require less memory and computation time. In this case it may be a better approach to to export the segment to a mesh and extrude it along surface normal direction:

Example using Dynamic Modeler module (allows real-time update of parameters, using GUI in Dynamic Modeler module):

segmentationNode = getNode("Segmentation")

# Export segments to models
shNode = slicer.mrmlScene.GetSubjectHierarchyNode()
exportFolderItemId = shNode.CreateFolderItem(shNode.GetSceneItemID(), "Segments")
slicer.modules.segmentations.logic().ExportAllSegmentsToModels(segmentationNode, exportFolderItemId)
segmentModels = vtk.vtkCollection()
shNode.GetDataNodesInBranch(exportFolderItemId, segmentModels)
# Get exported model of first segment
modelNode = segmentModels.GetItemAsObject(0)

# Set up Hollow tool
hollowModeler = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLDynamicModelerNode")
hollowModeler.SetToolName("Hollow")
hollowModeler.SetNodeReferenceID("Hollow.InputModel", modelNode.GetID())
hollowedModelNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLModelNode")  # this node will store the hollow model
hollowModeler.SetNodeReferenceID("Hollow.OutputModel", hollowedModelNode.GetID())
hollowModeler.SetAttribute("ShellThickness", "2.5")  # grow outside
hollowModeler.SetContinuousUpdate(True)  # auto-update output model if input parameters are changed

# Hide inputs, show output
segmentation.GetDisplayNode().SetVisibility(False)
modelNode.GetDisplayNode().SetVisibility(False)
hollowedModelNode.GetDisplayNode().SetOpacity(0.5)

Example using VTK filters:

# Get closed surface representation of the segment
shellThickness = 3.0  # mm
segmentationNode = getNode("Segmentation")
segmentationNode.CreateClosedSurfaceRepresentation()
polyData = segmentationNode.GetClosedSurfaceInternalRepresentation("Segment_1")

# Create shell
extrude = vtk.vtkLinearExtrusionFilter()
extrude.SetInputData(polyData)
extrude.SetExtrusionTypeToNormalExtrusion()
extrude.SetScaleFactor(shellThickness)

# Compute consistent surface normals
triangle_filter = vtk.vtkTriangleFilter()
triangle_filter.SetInputConnection(extrude.GetOutputPort())
normals = vtk.vtkPolyDataNormals()
normals.SetInputConnection(triangle_filter.GetOutputPort())
normals.FlipNormalsOn()

# Save result into new model node
slicer.modules.models.logic().AddModel(normals.GetOutputPort())

5、Show a segmentation in 3D

Segmentation can only be shown in 3D if closed surface representation (or other 3D-displayable representation) is available. To create closed surface representation:

segmentation.CreateClosedSurfaceRepresentation()

6、Modify segmentation display options

segmentation = getNode('Segmentation')
segmentID = 'Segment_1'

displayNode = segmentation.GetDisplayNode()
displayNode.SetOpacity3D(0.4)  # Set overall opacity of the segmentation
displayNode.SetSegmentOpacity3D(segmentID, 0.2)  # Set opacity of a single segment

# Segment color is not just a display property, but it is stored in the segment itself (and stored in the segmentation file)
segment = segmentation.GetSegmentation().GetSegment(segmentID)
segment.SetColor(1, 0, 0)  # red

# In very special cases (for example, when a segment's color only need to be changed in a specific view)
# the segment color can be overridden in the display node.
# This is not recommended for general use.
displayNode.SetSegmentOverrideColor(segmentID, 0, 0, 1)  # blue

参考:Create a segmentation from a labelmap volume and display in 3D